Genetic Analysis of the Major Capsid Protein of the Archaeal Fusellovirus SSV1: Mutational Flexibility and Conformational Change
Eric A. Iverson, David A. Goodman, Madeline E. Gorchels, Kenneth M. Stedman
Subject: Biology, Other Keywords: proteolysis; site-directed mutagenesis; complementation; mutants; morphology
Viruses with spindle or lemon-shaped virions are rare in the world of viruses, but are common in viruses of archaeal extremophiles, possibly due to the extreme conditions in which they thrive. However, the structural and genetic basis for the unique spindle shape is unknown. The best-studied spindle-shaped virus, SSV1, is composed mostly of the major capsid protein VP1. Similar to many other viruses, proteolytic cleavage of VP1 is thought to be critical for virion formation. Unlike half of the genes in SSV1, including the minor capsid protein gene vp3, the vp1 gene does not tolerate deletion or transposon insertion. In order determine the role of the vp1 gene and its proteolysis for virus function, we developed techniques for site-directed mutagenesis of the SSV1 genome and complemented deletion mutants with vp1 genes from other SSVs. By analyzing these mutants we demonstrate that the N-terminus of the VP1 protein is required, but the N-terminus, or entire SSV1 VP1 protein, can be exchanged with VP1s from other SSVs. However, the conserved glutamate at the cleavage site is not essential for infectivity. Interestingly, viruses containing point mutations at this position generate mostly abnormal virions.
Zika Virus Non-Structural Protein 1 Antigen-Capture Immunoassay
Brandon J. Beddingfield, Jessica N. Hartnett, Russell B. Wilson, Peter C. Kulakosky, Kristian G. Andersen, Argelia Aybar, Refugio Robles-Sikisaka, Nathan D. Grubaugh, Maria-Zunilla Nunez, Cesar D. Fermin, Robert F. Garry
Subject: Life Sciences, Biochemistry Keywords: Zika virus; non-structural protein 1; site-directed mutagenesis; polyclonal antibodies; antigen-capture ELISA
Infection with Zika virus (ZIKV), a member of the Flavivirus genus of the Flaviviridae family, typically results in mild self-limited illness, but severe neurological disease occurs in a limited subset of patients. In contrast, serious outcomes commonly occur in pregnancy that affect the developing fetus, including microcephaly and other major birth defects. The genetic similarity of ZIKV to other widespread flaviviruses, such as dengue virus (DENV), presents a challenge to the development of specific ZIKV diagnostic assays. Nonstructural protein 1 (NS1) is established for use in immunodiagnostic assays for flaviviruses. To address the cross-reactivity of ZIKV NS1 with proteins from other flaviviruses we used site-directed mutagenesis to modified putative epitopes. Goat polyclonal antibodies to variant ZIKV NS1 were affinity-purified to remove antibodies binding to the closely related NS1 protein of DENV. An antigen-capture ELISA configured with the affinity-purified polyclonal antibody showed a linear dynamic range between approximately 500 to 30 ng/mL, with a limit of detection of between 1.95 and 7.8 ng/mL. NS1 proteins from DENV, yellow fever virus, St. Louis encephalitis virus and West Nile virus showed significantly reduced reactivity in the ZIKV antigen-capture ELISA. Refinement of approaches similar to those employed here could lead to development of ZIKV-specific immunoassays suitable for use in areas where infections with related flaviviruses are common.
Veratridine Can Bind to a Site at the Mouth of the Channel Pore at Human Cardiac Sodium Channel NaV1.5
Alican Gulsevin, Andrew M Glazer, Tiffany Shields, Brett M Kroncke, Dan M Roden, Jens Meiler
Subject: Life Sciences, Biophysics Keywords: voltage-gated sodium channels; cardiac sodium channels; SCN5A; veratridine; toxins; molecular docking; Rosetta; electrophysiology; site-directed mutagenesis
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The cardiac sodium ion channel (NaV1.5) is a protein with four domains (DI-DIV), each with six transmembrane segments. Its opening and subsequent inactivation results in the brief rapid influx of Na+ ions resulting in the depolarization of cardiomyocytes. The neurotoxin veratridine (VTD) inhibits NaV1.5 inactivation resulting in longer channel opening times, and potentially fatal action potential prolongation. VTD is predicted to bind at the channel pore, but alternative binding sites have not been ruled out. To determine the binding site of VTD on NaV1.5, we performed docking calculations and high-throughput electrophysiology experiments. The docking calculations identified two distinct binding regions. The first site was in the pore, close to the binding site of NaV1.4 and NaV1.5 blocking drugs in experimental structures. The second site was at the "mouth" of the pore at the cytosolic side, partly solvent-exposed. Mutations at this site (L409, E417, and I1466) had large effects on VTD binding, while residues deeper in the pore had no effect, consistent with VTD binding at the mouth site. Overall, our results suggest a VTD binding site close to the cytoplasmic mouth of the channel pore. Binding at this alternative site might indicate an allosteric inactivation mechanism for VTD at NaV1.5.
Beyond the Toolpath: Site-Specific Melt Pool Size Control Enables Printing of Extra-Toolpath Geometry in Laser-Wire Directed Energy Deposition
Brian T. Gibson, Brad S. Richardson, Taylor W. Sundermann, Lonnie J. Love
Subject: Engineering, Control & Systems Engineering Keywords: site-specific; melt pool size; control; closed-loop; additive manufacturing; Directed Energy Deposition; 3D printing; metal; Titanium; lasers
A variety of techniques have been utilized in metal additive manufacturing (AM) for melt pool size management, including modeling and feed-forward approaches. In a few cases, closed-loop control has been demonstrated. In this research, closed-loop melt pool size control for large-scale, laser-wire based Directed Energy Deposition is demonstrated with a novel modification: site-specific changes to the controller set-point were commanded at trigger points, the locations of which were generated by the projection of a secondary geometry onto the primary 3D-printed component geometry. The present work shows that, through this technique, it is possible to print a specific geometry that occurs beyond the actual toolpath of the print head. This is denoted as an extra-toolpath geometry and is fundamentally different from other methods of generating component features in metal AM. A proof-of-principle experiment is presented in which a complex oak leaf geometry was embossed on an otherwise ordinary double-bead wall made from Ti-6Al-4V. The process is introduced and characterized primarily from a controls perspective with reports on the performance of the control system, the melt pool size response, and the resulting geometry. The implications of this capability, which extend beyond localized control of bead geometry to the potential mitigations of defects and functional grading of component properties, are discussed.
Integration of Nanometer-range Label-to-label Distances and their Distributions into Modelling Approaches
Gunnar Jeschke
Subject: Biology, Other Keywords: EPR spectroscopy; double electron electron resonance; FRET; ensemble model; intrinsic disorder; structural biology; site-directed spin labelling; molecular force fields
Labelling techniques such as electron paramagnetic resonance spectroscopy and single-molecule fluorescence resonance energy transfer, allow access to distances in the range of tens of angstroms, corresponding to the size of proteins and small to medium-sized protein complexes. Such measurements do not require long-range ordering and are therefore applicable to systems with partial disorder. Data from spin-label-based measurements can be processed into distance distributions that provide information about the extent of such disorder. Using such information in modelling presents several challenges, including a small number of restraints, the influence of the label itself on the measured distance and distribution width, and balancing the fitting quality of the long-range restraints with the fitting quality of other restraint subsets. Starting with general considerations about integrative and hybrid structural modelling, this review provides an overview of recent approaches to these problems and identifies where further progress is needed.
Frequency Domain Repercussions of Instantaneous Granger Causality
Luiz Antonio Baccalá, Koichi Sameshima
Subject: Mathematics & Computer Science, Probability And Statistics Keywords: instantaneous Granger causality; total partial directed coherence; information partial directed coherence; total directed transfer function; information directed transfer function; Granger connectivity; Granger influentiability.
Online: 9 July 2021 (09:34:38 CEST)
Using Directed Transfer Function (DTF) and Partial Directed Coherence (PDC) in their information version, this paper extends their theoretical framework to incorporate instantaneous Granger Causality (iGC)'s frequency domain description into a single unified perspective. We show that standard vector autoregressive models allow portraying iGC's repercussions associated with Granger Connectivity where interactions mediated without delay between time series can be easily detected.
Computing Persistent Homology of Directed Flag Complexes
Daniel Luetgehetmann, Dejan Govc, Jason P. Smith, Ran Levi
Subject: Mathematics & Computer Science, Computational Mathematics Keywords: neural networks; topology; directed graphs; directed flag complexes; persistent homology; computaional software
We present a new computing package Flagser, designed to construct the directed flag complex of a finite directed graph, and compute persistent homology for flexibly defined filtrations on the graph and the resulting complex. The persistent homology computation part of Flagser is based on the program Ripser [2], but is optimised specifically for large computations. The construction of the directed flag complex is done in a way that allows easy parallelisation by arbitrarily many cores. Flagser also has the option of working with undirected graphs. For homology computations Flagser has an Approximate option, which shortens compute time with remarkable accuracy. We demonstrate the power of Flagser by applying it to the construction of the directed flag complex of digital reconstructions of brain microcircuitry by the Blue Brain Project and several other examples. In some instances we perform computation of homology. For a more complete performance analysis, we also apply Flagser to some other data collections. In all cases the hardware used in the computation, the use of memory and the compute time are recorded.
Convert a Strongly Connected Directed Graph to a Black-and-White 3-SAT Problem by the Balatonboglár Model
Gábor Kusper, Csaba Biró
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: SAT problem; Directed Graph; Strongly Connectedness
Online: 5 November 2020 (14:16:43 CET)
In a previous paper we defined the Black-and-White SAT problem which has exactly two solutions, where each variable is either true or false. We showed that Black-and-White $2$-SAT problems represent strongly connected directed graphs. We presented also the strong model of communication graphs. In this work we introduce two new models, the weak model, and the Balatonbogl\'{a}r model of communication graphs. A communication graph is a directed graph, where no self loops are allowed. In this work we show that the weak model of a strongly connected communication graph is a Black-and-White SAT problem. We prove a powerful theorem, the so called Transitions Theorem. This theorem states that for any model which is between the strong and the weak model, we have that this model represents strongly connected communication graphs as Blask-and-White SAT problems. We show that the Balatonbogl\'{a}r model is between the strong and the weak model, and it generates $3$-SAT problems, so the Balatonbogl\'{a}r model represents strongly connected communication graphs as Black-and-White $3$-SAT problems. Our motivation to study these models is the following: The strong model generates a $2$-SAT problem from the input directed graph, so it does not give us a deep insight how to convert a general SAT problem into a directed graph. The weak model generates huge models, because it represents all cycles, even non-simple cycles, of the input directed graph. We need something between them to gain more experience. From the Balatonbogl\'{a}r model we learned that it is enough to have a subset of a clause, which represents a cycle in the weak model, to make the Balatonbogl\'{a}r model more compact. We still do not know how to represent a SAT problem as a directed graph, but this work gives a strong link between two prominent fields of formal methods: SAT problem and directed graphs.
Scaling Law for Liquid Splashing inside a Container Drop Impact on a Solid Surface
Bohua Sun
Subject: Physical Sciences, Applied Physics Keywords: liquid splashing; dimensional analysis; directed dimensional analysis
This letter attempts to find splashing height of liquid-filled container drop impact to a solid surface by dimensional analysis (DA). Two solutions were obtained by both traditional DA and directed DA without solving any governing equations. It is found that the directed DA can provide much more useful information than the traditional one. This study shows that the central controlling parameter is called splash number $\mathrm{Sp}=\mathrm{Ga} \mathrm{La}^\beta=(\frac{gR^3}{\nu^2})(\frac{\sigma R}{\rho \nu^2})^\beta$, which is the collective performance of each quantity. The splash height is given by $ \frac{h}{H}=(\frac{\rho\nu^2}{\sigma R})^\alpha f[\frac{gR^3}{\nu^2}(\frac{R\sigma}{\rho\nu^2})^\beta]=\frac{1}{\mathrm{La}^\alpha}f(\mathrm{Ga}\cdot \mathrm{La}^\beta)$. From the physics of the splashing number, we can have a fair good picture on the physics of the liquid splashing as follows: the jets propagation will generate vortex streets from the container bottom due to sudden pressure increasing from drop impact (water-hammer effect), which will travel along the container sidewall to the centre of the container and subsequently excite a gravity wave on the liquid surface. The interaction between the gravitational force, surface force and viscous force is responsible for creating droplet splash at the liquid surface.
Host-Directed Antivirals: a Realistic Alternative to Fight Zika Virus
Juan-Carlos Saiz, Nereida Jiménez de Oya, Ana-Belén Blázquez, Estela Escribano-Romero, Miguel A. Martín-Acebes
Subject: Life Sciences, Virology Keywords: flavivirus; Zika virus; therapy; host-directed antivirals
Zika virus (ZIKV), a mosquito-borne flavivirus, was an almost neglected pathogen until its introduction in the Americas in 2015, where it has been responsible for a threat to global health, causing a great social and sanitary alarm due to its increased virulence, rapid spread, and an association with severe neurological and ophthalmological complications. Currently, no specific antiviral therapy against ZIKV is available, and treatments are palliative and mainly directed to symptoms relief, such as fever and rash, by administering antipyretics, anti-histamines, and fluids for dehydration. Nevertheless, lately, a great effort has been made to search for antiviral candidates using different approaches and methodologies, ranging from repurposing of specific compounds with known antiviral activity to the screening of libraries and of natural compounds. The identified antiviral candidates include drugs targeting viral components (structural proteins and enzymes), as well as cellular ones. Here, we present an updated review of current knowledge about anti-ZIKV strategies, focusing on host-directed antivirals as a realistic alternative to combat ZIKV infection.
Reducing the Uncertainty of Radiata Pine Site Index Maps Using an Spatial Ensemble of Machine Learning Models
Gonzalo Gavilán-Acuña, Guillermo Federico Olmedo, Pablo Mena-Quijada, Mario Guevara, Beatriz Barria-Knopf, Michael S. Watt
Subject: Earth Sciences, Atmospheric Science Keywords: site productivity; precision silviculture; stand yield
Site Index has been widely used as an age normalised metric to account for variation in forest height at a range of spatial scales. Although previous research has used a range of modelling methods to describe regional variation in Site Index little research has examined gains that can be achieved through use of regression kriging or spatial ensemble methods. In this study an extensive set of environmental surfaces were used as covariates to predict Site Index measurements covering the environmental range of \textit{Pinus radiata} D. Don plantations in Chile. Using this dataset, the objectives of this research were to (i) compare predictive precision of a range of geostatistical, parametric and non-parametric models, (ii) determine if significant gains in precision can be attained through use of regression kriging, (iii) evaluate the precision of a spatial ensemble model that utilises predictions from the five most precise models, through using the model prediction with lowest error for a given pixel and (iv) produce a map of Site Index across the study area. The five most precise models were all geostatistical and included ordinary kriging and four regression kriging models that were based on partial least squares or random forests. A spatial ensemble model constructed from these five models was the most precise of those developed (RMSE = 1.851 m, RMSE% = 6.38%) and had relatively little bias. Climatic and edaphic variables were the strongest determinants of Site Index and in particular, variables related to soil water balance were well represented within the most precise predictive models. These results highlight the utility of predicting Site Index using a range of approaches, as these can be used to construct a spatial ensemble that may be more precise than predictions from the constituent models.
A Tutorial on Cross Site Scripting Attack - Defense
Vassilis Papaspirou, Leandros Maglaras, Mohamed Amine Ferrag
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: XSS; Cross site scripting; Sql injection
The danger is still very large from cross site scripting attacks. When designing web applications We must follow as much as we can prevention rules and don't leave any loophole to our programs. Experience is a great factor for programmers to know these attacks and for a trainee programmer is a difficult task to spot all the weak points. In this article we present a tutorial on launching an XSS attack and also we propose simple solutions.
Common Structural Pattern for Flecainide Binding in Atrial-Selective Kv1.5 and Nav1.5 Channels: A Computational Approach
Yuliet Mazola, José C.E. Márquez-Montesinos, David Ramírez, Leandro Zúñiga, Niels Decher, Ursula Ravens, Vladimir Yarov-Yarovoy, Wendy González
Subject: Life Sciences, Biophysics Keywords: atrial-fibrillation; multi-target; drug promiscuity; druggable binding site; flecainide; Nav1.5; Kv1.5; binding site comparison; polypharmacology
Atrial fibrillation (AF) is the most common cardiac arrhythmia. Its treatment includes antiarrhythmic drugs (AADs) to modulate the function of cardiac ion channels. However, AADs have been limited by proarrhythmic effects, non-cardiovascular toxicities as well as often modest antiarrhythmic efficacy. Theoretical models showed that combined blockade of Nav1.5 (and its current INa) and Kv1.5 (and its current, IKur) ion channels yield a synergistic anti-arrhythmic effect without effect on ventricles. We focused on Kv1.5 and Nav1.5 to search for structural similarities in their binding site (BS) for flecainide (a common blocker and widely prescribed AAD), as a first step for prospective rational multi-target directed ligand (MTDL) design strategies. We presented a computational workflow for flecainide BS comparison in a flecainide-Kv1.5 docking model and a solved structure of flecainide-Nav1.5 complex. The workflow includes docking, molecular dynamics, BS characterization and pattern matching. We identified a common structural pattern in flecainide BS for these channels. The latter belongs to the inner cavity and consist of a hydrophobic patch and a polar region, involving residues from S6 helix and P-loop. Since the rational MTDL design for AF is still incipient, our findings could advance multi-target atrial-selective strategies for AF treatment.
Characterization of PM2.5 at a Traffic Site Using Several Integrated Analytical Techniques
Naser Hamdan, Hussain Alawadhi, Mohamed Shameer
Subject: Earth Sciences, Environmental Sciences Keywords: PM2.5; chemical composition; analytical techniques; traffic site
We have conducted a comprehensive year-long sampling campaign for particulate matter (PM) pollutants at a site near a major highway, following standard protocols. Total mass, and elemental and chemical composition of the fine fractions (PM2.5) of traffic-related pollutants are determined utilizing several complementary techniques. These complementary techniques included gravimetric analysis, X-ray fluorescence (XRF), scanning electron microscopy and energy dispersive spectroscopy, X-ray diffraction (XRD) and black carbon multi-wavelength absorption. The results show that the PM2.5 mass concentrations are within or slightly above international standards and include natural dust and anthropogenic pollutants such as black carbon, sulfates and other traffic-related elements. Anthropogenic sources include the secondary pollutants Mascagnite and Koktaite, traffic emissions such as exhaust emissions and tires, brakes and road erosions. It was found that the sulfates are the highest contributors to PM2.5 (~40%), as evident from XRD results and the S content in the XRF analysis.
Ramsey Theory and Thermodynamics
Edward Bormashenko, Nir Shvalb, Mark Frenkel, Shraga Shoval
Subject: Physical Sciences, General & Theoretical Physics Keywords: thermodynamics; Ramsey theory; graph theory; directed graph; irreversible process.
Re-shaping of thermodynamics with the graph theory and Ramsey theory is suggested. Maps built of thermodynamic states are addressed. Thermodynamic states may be attainable and non-attainable by the thermodynamic process in the system of constant mass. We address the following question how large should be a graph describing connections between discrete thermodynamic states to guarantee the appearance of thermodynamic cycles? The Ramsey theory supplies the answer to this question. Direct graphs emerging from the chains of irreversible thermodynamic processes are considered. In any complete directed graph, representing the thermodynamic states of the system the Hamiltonian path is found. Transitive thermodynamic tournaments are addressed. The entire transitive thermodynamic tournament built of irreversible processes does not contain a cycle of length 3, or in other words, the transitive thermodynamic tournament is acyclic and contains no directed thermodynamic cycles.
A Complex Networks Approach to Analysing the Erdős-Straus Conjecture and Related Problems
Vikhyath Mondreti
Subject: Mathematics & Computer Science, Computational Mathematics Keywords: Erdős-Straus Conjecture; Directed Networks; Egyptian Fractions; Diophantine Equations.
For any positive integer n ≥ 2, the Erdős-Straus Conjecture claims that the Diophantine equation 4/n = 1/x + 1/y + 1/z has a solution where x, y, z are also positive integers. In this paper, a directed network based on this equation is generated, with properties such as its average clustering coefficient, average path length, degree distributions, and largest strongly connected component analysed to reveal some underlying trends about the nature of the conjecture. Potential connections between different numbers, that result from satisfying a source-solution relationship for this equation, are described using the appropriate number-theoretic interpretations wherever possible, while conjectures backed by these trends are made in other instances. Additionally, a directed configuration model is used to show that the origin of several results is the degree sequence of the network. Metrics relating to the prime number nodes, specifically their in and out degrees, are also explored to yield some intriguing observations. On the whole, the aim is to highlight the viability of complex networks as a computational tool to study this general class of problems pertaining to fixed-length unit fraction splits.
A Parsimonious Granger Causality Formulation for Capturing Arbitrarily Long Multivariate Associations
Andrea Duggento, Gaetano Valenza, Luca Passamonti, Salvatore Nigro, Maria Giovanna Bianco, Maria Guerrisi, Riccardo Barbieri, Nicola Toschi
Subject: Physical Sciences, Applied Physics Keywords: Granger causality; directed brain connectivity; MEG connectivity; Laguerre polynomials
High-frequency neuroelectric signals like electroencephalography (EEG) or magnetoencephalography (MEG) provide a unique opportunity to infer causal relationships between local activity of brain areas. While causal inference is commonly performed through Classical Granger causality (GC) based on multivariate autoregressive models, this method may encounter important limitations (e.g. data paucity) in the case of high dimensional data from densely connected systems like the brain. Additionally, physiological signals often present long-range dependencies which commonly require high autoregressive model orders / number of parameters. We present a generalization of autoregressive models for GC estimation based on Wiener-Volterra decompositions with Laguerre polynomials as basis functions. In this basis, the introduction of only one additional global parameter allows to capture arbitrary long dependencies without increasing model order, hence retaining model simplicity, linearity and ease of parameters estimation. We validate our method in synthetic data generated from families of complex, densely connected networks and demonstrate superior performance as compared to classical GC. Additionally, we apply our framework to studying the directed human brain connectome through MEG data from 89 subjects drawn from the Human Connectome Project (HCP) database, showing that it is able to reproduce current knowledge as well as to uncover previously unknown directed influences between cortical and limbic brain regions.
Preprint COMMUNICATION | doi:10.20944/preprints201912.0203.v1
Learning from Patient and Site Perspectives to Develop Better Mobile Clinical Trials: Recommendations from the Clinical Trials Transformation Initiative
Cindy Geoghegan, Virginia Nido, Angie Botto-Ven Bemden, Zachary Hallinan, Les Jordan, Lindsay Kehoe, Steve Morin, Amanda Niskar, Petros Okubagzi, William Wood
Subject: Keywords: mobile technology; patient engagement; mobile clinical trials; virtual trials; digital trials; hybrid trials; site engagement; site support; mobile devices
In order to harness the potential of mobile technologies to enhance the quality of clinical research, it is critical to first understand how to engage patients and research sites when planning and conducting mobile clinical trials. The Clinical Trials Transformation Initiative has developed the first comprehensive, evidence-based set of recommendations for incorporating patient and site perspectives in mobile clinical trials, which can aid in engaging stakeholders, addressing site challenges, and maximizing value for participants.
Surgical Site Infection after Breast Surgery: Retrospective Analysis of 5-year Postoperative Data from a Single Center in Poland
Anna Palubicka, Radoslaw Jaworski, Marcin Wekwejt, Beata Swieczko-Zurek, Michal Pikula, Janusz Jaskiewicz, Jacek Zielinski
Subject: Medicine & Pharmacology, Other Keywords: surgical site infection; breast surgery; breast implants; complications
Purpose: Surgical site infection (SSI) is a significant complication of non-reconstructive and reconstructive breast. This study aimed to assess SSI after breast surgery over 5 years in a single center in Poland. The microorganisms responsible for SSI and their antibiotic susceptibility were determined. Materials/methods: Data of 2129 patients acquired over 5 years postoperatively by the [center] were analyzed. Results: SSI was diagnosed in 132 patients (6.2%) and was an early infection in most cases (65.2%). The incidence of SSI was highest in patients who underwent subcutaneous amputation with simultaneous reconstruction using an artificial prosthesis (14.6%) and breast reconstruction via the TRAM flap method (14.3%). Gram-positive bacteria were responsible for SSI in most cases (72.1%), and these were mainly Staphylococcus strains (53.6%). These strains were 100% susceptible to all beta-lactam antibiotics (except penicillin), but were less susceptible to macrolides and lincosamides. Conclusions: SSI is a serious problem, and attention should be focused on its prevention. Reconstruction using an artificial prosthesis or via the TRAM flap method is connected to increased SSI incidence. Further studies are required to prevent SSI following breast surgery.
Preprint ESSAY | doi:10.20944/preprints202210.0085.v1
Using Directed Acyclic Graphs (Dags) to Represent the Data Generating Mechanisms of Disease and Healthcare Pathways: A Guide for Educators, Students, Practitioners and Researchers
George Ellison
Subject: Mathematics & Computer Science, Probability And Statistics Keywords: Directed Acyclic Graph; DAG; confounding; collider bias; epistemology; inferential statistics
Directed acyclic graphs (DAGs) are nonparametric causal path diagrams that have substantial utility as principled representations of disease and healthcare pathways, and of the underlying 'data generating mechanisms' these pathways involve. As such, DAGs provide a valuable bridge between: the aetiological knowledge, operational insight and professional experience on which clinical training and practice depend; and the more abstract epistemological and analytical considerations required to extract robust statistical insight from health and healthcare data. DAGs are nonetheless vulnerable to imperfect biomedical paradigms, partial clinical knowledge and limited empirical data. DAGs drawn under such circumstances offer limited scope for statistical insight free from cognitive, analytical or inferential bias if: they misrepresent the data generating mechanisms involved; or ignore the important role that omitted variables (whether measured, unmeasured or unacknowledged) might play therein. To address these weaknesses and broaden the appeal and application of DAGs, this chapter provides ten simple steps that educators can use to improve the analytical competence and statistical confidence of the healthcare students, qualified practitioners and experienced researchers they support. These steps use temporal logic to draw DAGs so as to: reduce reliance on uncertain knowledge, incomplete information, flawed assumptions or guesswork; and avoid, mitigate or acknowledge the errors and biases that each of these incur. The chapter comprises an accessible, non-technical overview of the perspective and thoughtfulness required to generate temporally coherent DAGs as objective representations of the probabilistic causal paths involved in context-specific data generating mechanisms. It encourages a focus on those variables operating as potential sources of analytical or inferential bias when estimating the plausible, probabilistic causal relationship between two pre-specified variables; and specifically addresses the challenges posed by: omitted; time-variant; non-asynchronous; and temporally obscure variables. The chapter includes a worked example based on a published clinical study to demonstrate how each of the steps required to generate temporally-informed DAGs can be applied to: critically appraise the analytical decisions made during applied healthcare research; and inform the decisions required when designing, undertaking and analysing primary and secondary, prospective and retrospective research. The appendices include a summary of ten recommendations for improving the reporting and interrogability of DAGs and DAG-informed analyses.
The Strengths and Weaknesses of Directed Acyclic Graphs (Dags) as Cognitive, Analytical and Educational Tools for Medical Statistics
Subject: Medicine & Pharmacology, Other Keywords: directed acyclic graph; DAG; causal inference; bias; inferential statistics; reproducibility
The origins of directed acyclic graphs (DAGs) date back to the emergence of 'graph theory' in the early 1700s (Biggs et al. 1986). DAGs are conceptual or literal, diagrammatic representations of causal paths between variables which are constructed – as their name suggests – on the basis of two over-riding principles: first, that all causal paths are 'directed' (i.e. for each pair of variables, only one can represent the cause, while the other must be its consequence); and second, that no direct cyclical paths, or indirect cyclical pathways (comprising sequences of consecutive paths) are allowed, such that no consequence can be considered its own direct or indirect cause (hence 'acyclic'; Law et al., 2012). As such DAGs reflect the knowledge, presumptions, assumptions and/or speculation of the analyst(s) concerned regarding the causal relationships between each of the variables included therein. Current convention dictates that variables are represented as nodes/vertices, and that any causal paths between variables are represented as directed arcs/edges/lines, often in the form of arrows (see Figure 1). Although each arc indicates the presence and direction of a known/presumed/assumed/speculative causal relationship between the two variables concerned, drawing an arc does not require the sign, magnitude, precision or shape of the relationship to be known or declared (Tennant et al., 2021). In this respect, DAGs provide a simple, uncomplicated, accessible and entirely nonparametric approach for postulating causal relationships amongst any variables of interest even when these are uncertain, unknown or entirely speculative (Ellison, 2020). Nonetheless, as a result of the parametric constraints imposed by the presence/absence of possible arcs within any given DAG, these also reflect and support a number of more sophisticated statistical applications which make it possible to use DAGs to inform the design of multivariable statistical models that reflect the causal structure(s) involved – albeit without the need to know or understand the mathematical technicalities on which these are based (Lewis and Kuerbis, 2016). These features make DAGs attractive cognitive, educational and analytical tools for strengthening the epistemological, theoretical and empirical basis of causal inference, and there has been a recent proliferation in the use of DAGs across a range of applied scientific disciplines (e.g. Knight and Winship, 2013), and an associated upsurge in analytical methods training (e.g. Elwert, 2011; Gilthorpe, 2017; Hernán 2018; Roy, 2021; Hünermund, 2021). This Chapter reflects on a decade of delivering medical statistics training to undergraduate medical students at the University of Leeds between 2012-2021 in which the third year research, evaluation and special studies module ('RESS3') has used DAGs to support the development of applied statistical skills relevant to the extended student-selected research and evaluation projects (ESREP) students undertake in their fourth and final years (Ellison, 2021; Ellison et al., 2014a,b). Based on successive iterations of the structure and content of the RESS3 module, together with notes made during formal and informal planning and review meetings with module leads, lecturers, tutors and students, we draw on the claims and criticisms made of DAGs in the epidemiological literature to identify a number of explicit strengths (and associated, often implicit. weaknesses) that are central to their use in prediction and causal inference modelling. While using DAGs requires (and benefits from) a clear understanding of their non-parametric nature and parametric implications, the weaknesses of DAGs seem likely to reflect both: the challenges inherent in the modelling of data generating processes when these are imperfectly understood; and troublesome cognitive and heuristic tendencies common to all analytical tools – in which the tool facilitates the task in hand by reducing the necessity (and benefits of) exploring uncertainties and identifying assumptions. These, more epistemological considerations appear particularly challenging for medical undergraduates to grasp (Ellison, 2021), but also appear poorly understood by many established analysts and clinical epidemiologists (Ellison, 2020).
Functionally Graded Material Fabricated by Powder-based Laser Directed Energy Deposition: From Conventional to Complex Concentrated Alloys
Kun Li, Xin Wang, Wei Xiong
Subject: Materials Science, Metallurgy Keywords: Directed energy deposition; functionally graded materials; precipitation; high-throughput design
Directed energy deposition (DED) is an efficient method to fabricate functionally graded materials (FGMs) with gradient composition and complex structures, allowing for local tailoring of properties instead of the costly need for extraneous welds and joints. In this study, a FGM from stainless steel to Inconel alloy was successfully fabricated using the powder-based laser DED. A very refined grain structure has been observed in at the composition with 75 wt.% Inconel alloy content, which also exhibits the highest (entropy). For the first time, the post heat treatments, microstructure and aging precipitation behaviors of FGMs were systematically studied via experimental characterization and computation, to elucidate their effects on the gradient smoothing and mechanical properties. The diffusion and segregation of Ni, Nb and Ti elements underly the transformation mechanism between Laves, δ, γ' and γ'' phases during precipitation. Homogenization on FGMs not only eliminates the heterogeneity inherited from the AM process, but also provides a practical way to smoothen the gradient on composition and microstructure for the eventual good gradient properties. It has a direct influence on the following precipitation behaviors in the FGM, which highly relies on the diffusion degree of the elements in the matrix and grain boundaries. The high-throughput thermodynamic modeling and kinetic modeling were exploited to evaluate the experimental microstructure and address computational uncertainty using different thermodynamic conditions and databases, which enables an accelerated design through local tailoring of process-structure-property relationships to develop new functional materials.
Safety and Efficacy of Adjunctive Catheter-Directed Thrombolysis During Primary PCI for ST-segment Elevation Myocardial Infarction With High Thrombus Burden
Satsuki Noma, Hideki Miyachi, Isamu Fukuizumi, Junya Matsuda, Hideto Sangen, Yoshiaki Kubota, Yoichi Imori, Yoshiyuki Saiki, Yusuke Hosokawa, Shuhei Tara, Yukichi Tokita, Koichi Akutsu, Wataru Shimizu, Takeshi Yamamoto, Hitoshi Takano
Subject: Medicine & Pharmacology, Cardiology Keywords: high coronary thrombus burden; tissue plasminogen activator; catheter-directed thrombolysis
Background: High coronary thrombus burden has been associated with unfavorable outcomes in patients with ST-segment elevation myocardial infarction (STEMI), the optimal management of which has not yet to be established. Methods: We evaluated the safety and efficacy of adjunctive catheter-directed thrombolysis (CDT) during primary percutaneous coronary intervention (PCI) in patients with STEMI and high thrombus burden. Results: Among the 1,849 consecutive patients with STEMI, 263 had high thrombus burden. Moreover, 41 patients received intracoronary infusion of tissue plasminogen activator during primary PCI (CDT group), whereas 222 did not receive (non-CDT group). No significant differences in bleeding complications and in-hospital and long-term mortalities were observed (9.8% vs. 7.2%, p=0.53; 7.3% vs. 2.3%, p=0.11; and 12.6% vs. 17.5%, p=0.84, CDT vs. non-CDT). In patients who underwent antecedent aspiration thrombectomy during PCI (75.6%; CDT group and 87.4%; non-CDT group), thrombolysis in myocardial infarction grade 2 or 3 flow rate after thrombectomy was significantly lower in the CDT group than in the non-CDT group (32.2% vs. 61.0%, p<0.01). However, the final rates improved considerably without significant difference (90.3% vs. 97.4%, p=0.14). Conclusions: For STEMI patients with high thrombus burden, adjunctive CDT is safe and effective for improving coronary flow. CDT resulted in favorable coronary flow even after unsatisfactory aspiration thrombectomy.
Engineering of Synthetic Transcriptional Switches in Yeast
Masahiro Tominaga, Akihiko Kondo, Jun Ishii
Subject: Life Sciences, Biotechnology Keywords: genetic switch; yeast; synthetic transcription factor; synthetic promoter; directed evolution
Genetic switches can be utilized for many purposes in synthetic biology including the assembly of complex genetic circuits to achieve sophisticated cellular systems and the construction of biosensors for real-time monitoring of intracellular metabolite concentrations. Although genetic switches have mainly been developed in prokaryotes to date, eukaryotic genetic switches are increasingly being reported as both rational and irrational engineering technologies mature. In this review, we describe genetic switches in yeast based on synthetic transcription factors and/or synthetic promoters. We also discuss directed evolution technologies for the rapid and robust construction of yeast genetic switches.
Structural Entropy Constrains Dynamics in Directed Networks
Blai Vidiella, Salva Duran-Nebreda, Sergi Valverde
Subject: Life Sciences, Biochemistry Keywords: structural entropy; dimensionality; flow dynamics; spin; directed network; scale-free
Online: 27 January 2021 (15:35:38 CET)
Complex systems can be described as the network of interactions between their components. In directed networks, information, energy and matter flow in dominant directions. Undirected networks, on the other hand, cannot easily capture these asymmetries. The local flow of information depends on the node spin, which is a function of the number of incoming and outgoing links attached to it. And yet, how the heterogeneous association between in-degree and out-degree constraints global dynamics remains poorly understood. Here, we develop a new theoretical model to study the relationship between node directionality and global flow dynamics. Our computational analysis of random and scale-free directed networks indicates that structural diversity constrains the dimensionality of reachable dynamical space. These results suggest how local directionality might be an universal driver of global dynamics in many systems, from social networks, to technological systems to the connectome.
The PACAP/PAC1 Receptor System and Feeding
Keerthana Sureshkumar, Andrea Saenz, Syed Muzzammil Ahmad, Kabirullah Lutfy
Subject: Life Sciences, Other Keywords: PACAP; PAC1; Homeostatic; Hedonic; Food Intake; Signaling; Neuroanatomical Site
Pituitary adenylyl cyclase activating polypeptide (PACAP) belongs to the vasoactive intestinal polypeptide (VIP)/secretin/glucagon superfamily. PACAP is present in two forms, PACAP-38 and PACAP-27, and binds to three guanine-regulatory (G) protein-coupled receptors (PAC1, VPAC1, and VPAC2). PACAP is expressed in the central and peripheral nervous systems with high PACAP levels found in the hypothalamus, a brain region involved in feeding and energy homeostasis. PAC1 receptors are high-affinity and PACAP-selective receptors, while VPAC1 and VPAC2 receptors show a comparable affinity to PACAP and VIP. PACAP and its receptors are expressed in the central and peripheral nervous systems, with moderate to high expression in the hypothalamus, amygdala, and other limbic structures. Consistent with their expression, PACAP is involved in several physiological responses and pathological states. A growing body of literature suggests that PACAP regulates food intake in laboratory animals. However, there is no comprehensive review of the literature on this topic. Thus, the purpose of this article is to review the literature regarding the role of PACAP and its receptors in food intake regulation and to synthesize how PACAP exerts its anorexic effects in different brain regions. To achieve this goal, we searched PubMed and reviewed 68 articles regarding the regulatory action of PACAP on food intake. Here, we present the literature regarding the effect of exogenous PACAP on feeding and the role of endogenous PACAP in this process. We also provide evidence regarding the effect of PACAP on the homeostatic and hedonic aspects of food intake, the neuroanatomical sites where PACAP exerts its regulatory action, which PACAP receptors may be involved, and the role of various signaling pathways and neurotransmitters in hypophagic effects of PACAP.
Incision and Prediction of Risk Factors Related to Surgical Site Infection Following Cesarean Section in Chinese Women
Qiuxiang Huang
Subject: Keywords: Cesarean Section; surgical site infection; premature rupture of membrane
Cesarean Section (CS) is one of the most frequently executed surgical procedures in gynecology and obstetrics. After a cesarean section, surgical site infection (SSI) increases hospital stay, lengthens maternal morbidity, and upsurges treatment costs. The current study determines the prevalence and risk factors for surgical site infection following cesarean section in China. A retrospective study was conducted on 23 cases of pregnant women who underwent cesarean section and incision severe infection and detection from March 2017 to January 2020 at Wuhan Maternal and Child Healthcare Hospital in China as the study group, and 20 cases of uninfected cesarean section during the same period were selected as the control group. Data were compared with the controls based on study variables and the presence of SSI. The mean age was 31±2.6. High fever and blood loss were observed in serous SSI-infected patients. The incidence rate of severe surgical site infection was 0.15 %. SSI was observed to be expected in pregnant women who had premature rupture of membrane before surgery (p < 0.001), who underwent postoperative antibiotic therapy (p < 0.001), and the patients who had gestational diabetes mellitus (p <0.001) and hematoma (p < 0.001) during surgery. Hence, following a cesarean section, surgical site infection is common. This research discovered several modifiable risk factors. SSI is associated with multifactorial rather than a single one. The development and strict implementation of a procedure by all health care practitioners can successfully reduce and prevent infection rates following cesarean section.
SARS-CoV-2 and the Secret of the Furin Site
Antonio R. Romeu, Enric Ollé
Subject: Keywords: SARS-CoV-2, RaTG13, Furin Site, Molecular Evolution, Bioinformatics.
Online: 10 February 2021 (15:46:12 CET)
The SARS-CoV-2 high infectivity is due to the functional polybasic furin cleavage site in the S protein. How it was acquired is unknown. There are two challenges to face: (i) an evolutionary model, to fit the origin of the coronavirus; and (ii) a molecular mechanism for the site acquisition. Here we show genomic fingerprints which are specific of Pangolin-CoVs, Bat-SARS-like (CoVZC45, CoVZXC21), bat RatG13 and human SARS-CoV-2 coronaviruses. This, along with phylogenetic analysis, we found that these species have the same evolutionary origin in the bat, including a genetic recombination of S gene between Pangolin-CoV (2017) and RatG13 ancestors. However, this does not explain why SARS-CoV-2 is the only of them with the furin site, which consists in four amino acid (PRRA) motif. The Arginine doublet is encoded by CGGCGG codons. Surprisingly, none of the Arginine doublet of other furin site of viral proteins from several type of viruses, are encoded by the CGGCGG codons. This makes it difficult to consider a virus recombination as mechanism for the PRRA acquisition. The origin of SARS-CoV-2, is the origin of the recognition cleavage site. The bat coronavirus RaTG13 appears to be the closest relative of the SARS-CoV-2, but was isolated in 2013. So, new RatG13 samples would provide insights into the acquisition of the polybasic motif.
Highly Sensitive Magnetic-SERS Dual-Function Silica Nanoprobes for Effective On-Site Organic Chemical Detection
Cheolhwan Jeong, Hyung-Mo Kim, So Yeon Park, Myeong Geun Cha, San Kyeong, Xuan-Hung Pham, Eunil Hahm, Yuna Ha, Dae Hong Jeong, Bong-Hyun Jun, Yoon-Sik Lee
Subject: Materials Science, Nanotechnology Keywords: surface-enhanced Raman scattering; magnetic aggregation; on-site detection
We report magnetic silver nanoshells (M AgNSs) that have both magnetic and SERS properties for SERS-based detection. The M AgNSs are composed of hundreds of Fe3O4 nanoparticles for rapid accumulation and bumpy silver shell for sensitive SERS detection by near-infrared laser excitation. The intensity of the SERS signal from the M AgNSs was strong enough to provide single particle-level detection. We obtained much stronger SERS signal intensity from the aggregated M AgNSs than from the non-aggregated AgNSs. 4-Fluorothiophenol was detected at concentrations as low as 1 nM, which corresponds to 0.16 ppb. The limit of detection for tetramethylthiuram disulfide was 10 μM, which corresponds to 3 ppm. The M AgNSs can be used to detect trace amounts of organic molecules using a portable Raman system.
Intangible Cultural Heritage and Sustainable Tourism in Córdoba, Spain
Francisco González Santa Cruz, Tomás López-Guzmán
Subject: Social Sciences, Business And Administrative Sciences Keywords: cultural tourism; world heritage site; sustainability; satisfaction; cordoba; Spain
The recognition of a place as a World Heritage Site (WHS) by UNESCO is fundamental to preserve its historical and artistic inheritance and, at the same time, to encourage visits to that area. The purpose of this article is to contribute to the study of the relationship between WHS and cultural tourism, with a marked sustainable character, through the presentation of the results of research conducted in the city of Cordoba (Spain) and which analyses the sociodemographic profile of the tourists, the variables that influence their level of satisfaction and of their loyalty and the classification of the travelers through different variables. The principal results of the research show the significant educational level of the surveyed tourists, as well as the high level of satisfaction with the visit, the high number of countries of origin and the outstanding motivation for knowing the city's heritage roots.
Measuring Organizational Skills in the General Population: Development and Preliminary Validation of the DOSQ
Guillaume Durand
Subject: Behavioral Sciences, General Psychology Keywords: Organizational skills, test development, general population, goal-directed behaviors, psychometric validation
Organizational skills are a set of cognitive abilities responsible for goal-directed behaviors. While they are moderately studied in clinical settings, the assessment of organizational skills in the general population remains under-studied. This paper presents the new Durand Organizational Skills Questionnaire (DOSQ), which was developed to examine the factors associated with organizational abilities in the general population. Exploratory factor analysis, validated by a confirmatory factor analysis, suggests eight factors: Work Organization, Communication Clarity, Punctuality, Goal-Oriented Behavior, Assiduity, Workspace Organization, Strategies, and Attentiveness. Three studies using samples from the general population provided evidence for the reliability and validity of the DOSQ's scores. Overall, the results suggest that the DOSQ offers a valid approach to measuring organizational skills in the general population.
New Formula for the Identification of Liquefaction Based on the Investigation of the Songyuan Site
Ping Li, Yuan Zhang, Yudong Zhang
Subject: Engineering, General Engineering Keywords: Songyuan earthquake; Songyuan site; sand liquefaction; hyperbolic model; discriminant formula
Based on the 5.7-magnitude earthquake that stroke Songyuan (China) and 172 groups of liquefaction data collected in mainland China, the hyperbolic liquefaction discriminant formula originally proposed by Sun Rui was revised, and a new formula for the liquefaction of sand was put forward. Groups of data derived from the Bachu earthquake in Xinjiang and an earthquake that occurred in New Zealand (47 and 195 groups, respectively) were used to carry out a back-judgment test, then, the results were compared with those of the existing standard method. Overall, the results showed that the new formula for hyperbolic liquefaction discrimination compensates for the conservative liquefaction discrimination of the older formula; moreover, it has a good applicability to different intensities, groundwater levels, and the deep sand layer of the Songyuan site, reflected by a more balanced success rate. Therefore, combining the existing liquefaction discrimination methods and the research results of discrimination, it is necessary to establish a suitable regional identification method through the continuous accumulation of liquefaction data and expanding database.
Working Paper SHORT NOTE
The Tripping Point – Minimum Planting Widths for Small-Stature Trees in Dense Urban Developments
Andrew K. Koeser, Richard J. Hauer, Deborah R. Hilbert, Robert J. Northrop, Hunter Thorn, Drew C. McLean, Allyson B. Salisbury
Subject: Biology, Forestry Keywords: ecosystem disservices; green infrastructure; site design; tree selection; urban forestry
As urban development increases in density, the space to grow urban trees becomes more constrained. In heavily developed areas, small stature trees can be planted to reduce both above- and below-ground conflicts with infrastructure elements. However, even these species have their limits when placed in extremely confining conditions. In this study, we build on past work to determine the minimum planting widths of small stature urban trees. We found that species, stem diameter, and the height at which stem diameter measurements occurred were all strong predictors of trunk flare diameter (adjusted R2 of 0.843). Additionally, we modelled the relationship between planting space and the presence or absence of hardscape conflicts – using the predictions derived from this effort to project the potential cost savings in two United States cities. Study results provide a guideline to create sufficient space for urban trees and minimize infrastructure damage and associated cost savings.
Alternative Exhibition Spaces. Multi-criteria Method of Comparative Analysis
Joanna Stefańska, Paulina Kowalczyk, Agata Gawlak
Subject: Arts & Humanities, Anthropology & Ethnography Keywords: white cube; exhibition space; space; work; architecture; site specific; interaction
The aim of this article is to make a multi-criteria analysis of various exhibition spaces of an originally non-exhibition character and to determine how these spaces affect the selection of works and the exhibition concept. The analysis is based on the exhibitions of art objects at collective exhibitions in unconventional architectural spaces: commercial, i.e. the modern office building of PBG Gallery Skalar Office Centre in Poznań, post-industrial i.e. in the former Zakłady Przemysłu Ziemniaczanego Lubanta S.A. and in the historic interior of the "U Jezuitów" Gallery of the Cultural Integration Centre in Poznań. The multi-criteria comparative analysis shows a variety of features of the studied spaces as well as the relationship between architecture and art and their mutual interaction. The participatory role of the non-exhibition space in the process of creating an exhibition and selecting works has been proven. It has also been confirmed that the presentation of works of art in originally non-exhibition spaces creates a new quality of the artwork. Unconventional architectural space, when used for the exhibition of works of art, expands and strengthens the area of ​​their influence through the interaction between the work and the architectural space. The specificity of the space adapted for exhibition needs, the presence and type of architectural details in the interior, the quantity and quality of light and its distribution in space, the volume and colour of the interior determine the exhibition space and influence the shape of the exhibitions organised and the reception of the artworks. The only condition for the change of the original function of an architectural space into that of an exhibition space is a coherent artistic vision of the creator. This should take into account the appropriate selection of the exhibited objects, where the process of searching for the relationship between architecture and art determines the features of the architectural space as integral components influencing the realisation of the exhibition .
Surgical Site Infection after Gastrointestinal and Hepatobiliary Surgeries- A Retrospective Evaluation from a Single Center of Western India
Bhavin B. Vasavada, Hardik Patel
Subject: Medicine & Pharmacology, Gastroenterology Keywords: laproscopic cholecystectomy; acute cholecystitis; gall stone; sepsis; surgical site infection
Aim: Aim of our study to evaluate various factors responsible for surgical site infection after gastrointestinal and hepatobiliary surgeries. Material and Methods: Patient who underwent gastrointestinal and hepatobiliary surgery in our department were evaluated retrospectively. Various factors associated with surgical site infection were evaluated using univariate and multivariate analysis. Surgical site infection was defined as any culture positive discharge from the wound within 30 days of surgery.Statistical analysis was done using SPSS version 23. Results: We evaluated total 331 patients operated between April 2018 to March 2020. 14 patients were lost to follow up after discharge and before completing post operative day 30. 18 patients expired before 30 days without developing SSI and were excluded from the study as per exclusion criteria. 299 patient included in the study. Total 20 patients developed surgical site infection. It showed SSI rate in our study population was 6.68%. On univariate analysis prolonged hospital stay, more blood product used, higher cdc grade of surgery, higher ASA grade, more operative time, open surgeries,colorectal and HPB surgeries were associated with surgical site infections. On multivariate analysis only prolonged hospital stay independently predicted Surgical Site Infectins. (p=0.014,0dds ratio 1.223, 95% confidence interal 1.042-1.435). Conclusion: Prolonged hospital stay independently predicts surgical site infections after gastrointestinal and hepatobiliary surgery.
Community Knowledge, Attitudes and Practices Regarding Onchocerciasis in Rural Villages With a High Epilepsy Prevalence in Mahenge, Tanzania: A Qualitative Study
Dan K. Bhwana, Isolde S. Massawe, Adiel K. Mushi, Pendo Mashili, Luis-Jorge Amaral, Williams Makunde, Bruno P. Mmbando, Robert Colebunders
Subject: Life Sciences, Other Keywords: onchocerciasis; community directed treatment with ivermectin; elimination; epilepsy; focus group discussions; misconceptions
Despite of over 20 years of community directed treatment with ivermectin (CDTI), a high prevalence of onchocerciasis and onchocerciasis-associated epilepsy were observed in rural villages in Mahenge, Tanzania. Therefore, we assessed the knowledge, attitude and practice about onchocerciasis in four rural villages in the Mahenge area. This was a qualitative study conducted between June and July 2019. Eleven focus group discussions were organized with persons with epilepsy and their caretakers, community resource persons, and community drug distributors (CDDs), and two in-depth interviews with district programme coordinators of neglected tropical diseases (NTD). Most participants were aware about symptoms of onchocerciasis using local terminologies such as "ukurutu/rough dry skin" and "kuwashwa/itching". A small proportion of people did not take ivermectin during CDTI for fear of adverse reactions such as itching and swelling. Some men believed that ivermectin may decrease libido. Challenges for high CDTI coverage included, long walking distance by CDDs to deliver drugs to households, persons being away for farming, low awareness of the disease and limited supervision by the NTD coordinators. In conclusion, ivermectin uptake in Mahenge should be optimised by continuous advocacy about the importance of taking ivermectin to prevent onchocerciasis-associated morbidity and by improving supervision during CDTI.
The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)
Vasundra Touré, Steven Vercruysse, Marcio Luis Acencio, Ruth Lovering, Sandra Orchard, Glyn Bradley, Cristina Casals-Casas, Claudine Chaouiya, Noemi del-Toro, Åsmund Flobak, Pascale Gaudet, Henning Hermjakob, Luana Licata, Astrid Lægreid, Christopher Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Denis Thieffry, Paul Thomas, Dénes Türei, Julio Saez-Rodriguez, Martin Kuiper
Subject: Biology, Other Keywords: causal statement; causal interaction; directed molecular interaction; minimum information; standardization, systems biology
A large variety of molecular interactions occurs between biomolecular components in cells. When one or a cascade of molecular interactions results in a regulatory effect, by one component onto a downstream component, a so-called 'causal interaction' takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g., gene regulation) need to be described with a careful appreciation of molecular interactions that occur between entities. A proper description of this information enables archiving, sharing, and reuse by humans and for computational science. Various representations of causal relationships between biological components are currently used in a variety of resources. Here, we propose a checklist that accommodates current representations, and call it the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while assuring uniformity and interoperability of the data across resources.
Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network
Hiroko X. Kondo, Hiroyuki Iizuka, Gen Masumoto, Yuichi Kabaya, Yusuke Kanematsu, Yu Takano
Subject: Life Sciences, Biochemistry Keywords: structure–function correlation; active site conformation; convolutional neural network; machine learning
Structure–function relationships in proteins have been one of the crucial scientific topics. Heme proteins have diverse and pivotal biological functions. Therefore, clarifying their structure–function correlation is significant to understand their functional mechanism and is informative for various fields of science. In this study, we constructed convolutional neural network models for predicting protein functions from the tertiary structures of heme-binding sites (active sites) of heme proteins to examine the structure–function correlation. As a result, we succeeded in the classification of oxygen-binding protein (OB), oxidoreductase (OR), proteins with both functions (OB–OR), and electron transport protein (ET) with high accuracy. Although the misclassification rate for OR and ET was high, the rates between OB and ET and between OB and OR were almost zero, indicating that the prediction model works well between protein groups with very different functions. However, predicting the function of proteins modified with amino acid mutation(s) remains a challenge. Our findings indicate a structure–function correlation in the active site of heme proteins. This study is expected to be applied to the prediction of more detailed protein functions such as catalytic reactions.
Direct Interaction of Mitochondrial Cytochrome c Oxidase with Thyroid Hormones: Evidence for Two Binding Sites
Ilya P. Oleynikov, Natalia V. Azarkina, Tatiana V. Vygodina
Subject: Life Sciences, Biochemistry Keywords: cytochrome oxidase; thyroid hormones; steroid hormones; Bile Acids Binding Site; regulation
Thyroid hormones regulate tissue metabolism establishing an energy balance in the cell, in particular by affecting oxidative phosphorylation. Their long-term impact is mainly associated with changes in gene expression, while the short-term effects may differ in mechanism. Our work is devoted to short-term effects of hormones T2, T3, and T4 on mitochondrial cytochrome c oxidase (CcO) mediated by a direct contact with the enzyme. The data obtained indicate the existence of two separate sites of CcO interaction with thyroid hormones differing in location, affinity and specificity to hormone binding. It is shown that T3 and T4 but not T2 inhibit oxidase activity of CcO in solution and on membrane preparations with Кi≈100–200 M. In solution, T3 and T4 compete in a 1:1 ratio with the detergent dodecyl-maltoside for binding to the enzyme. Peroxidase and catalase partial activities of CcO are not sensitive to hormones while electron transfer from heme a to the oxidized binuclear center is affected. We believe that T3 and T4 are ligands of the Bile Acid Binding Site found in the 3D structure of CсO by Ferguson-Miller's group, and hormone induced inhibition is associated with dysfunction of the K- proton channel. Similar conclusion we made recently with regard to steroid-like compounds. It is found that T2, T3, and T4 inhibit superoxide generation by oxidized CcO in the presence of excess Н2О2. Inhibition is characterized by Ki values of 0.3 – 5 M and apparently affects the formation of О2• at the protein surface. The second binding site for thyroid hormones presumably coincides with the point of tight T2 binding on the Va subunit described in the literature.
Preprint SHORT NOTE | doi:10.20944/preprints202106.0121.v1
SARS-CoV-2 Origin: An Affair of Codons?
Antonio Ramón Romeu, Enric Ollé
Subject: Biology, Anatomy & Morphology Keywords: SARS-CoV-2 origin; Furin Cleavage Site; Arginine Codon Usage; Bioinformatics
Online: 4 June 2021 (08:00:03 CEST)
The furin cleavage site, with an arginine doublet (RR), is one of the clues of the SARS-CoV-2 origin. This furin-RR is encoded by the CGG-CGG sequence. Because arginine can be encoded by six codons, in a previous work we found that in SARS-CoV-2, CGG was the minority arginine codon (3%). Also, analyzing the RR doublet from a large sample of furin cleavage sites of several kinds of viruses, we found that none of them were encoded by CGG-CGG. Here, we come back to the core of the matter, but from the perspective that in the human genome, in contrast, CGG is the majoroty arginine codon (21%). Here, we highlighted that the 6 arginine codons provide genetic markers to a traceability on the RR origin in the furin site, as well as, to weigh the probability of the theories about the origin of the virus.
Applicability of Large-Span Structures for Presentations of Archaeological Sites
Natasa C Zivaljevic-Luxor, Hartmut Pasternak
Subject: Engineering, Automotive Engineering Keywords: archaeological site, roof, shelter, bridge, sustainability, aesthetics, heritage presentation, decision making
The purpose of the study was to provide support in the decision-making process for architects and engineers regarding large-spans structures for the presentation of archaeological sites in situ - construction of roofs, shelters, and bridges. We examined existing practice and analyzed their engineering classifications looking for a pattern in their application regarding sustainability and relation between type of cultural heritage site and type of applied large span structure. Contemporary engineering structures at built heritage sites create a sharp contrast between old and new. A presentation of cultural heritage in situ requires an understanding of heritage theory and internationally accepted doctrine which exceeds common engineering education. Nevertheless, application of large-span structures, which often take advantages of state-of-art construction-technologies nowadays, is also an aesthetical statement that affects the appearance of the site. Therefore, we gave an overview of the theoretical background of aesthetical issues and the overall ethics of the decision-making process in such sensitive cases. Within the framework of heritage-presentation, engineering and architectural issues, and selected case studies, we concluded in favor of the application of large-span structures under certain conditions.
Preprint CONCEPT PAPER | doi:10.20944/preprints201810.0773.v2
A Comparative Study of the AHP and TOPSIS Techniques for Dam Site Selection Using GIS: A Case Study of Sistan and Baluchestan Province, Iran
Ali Jozaghi, Babak Alizadeh, Mohsen Hatami, Ian Flood, Mohammad Khorrami, Nastaran Khodaei, Erfan Ghasemi Tousi
Subject: Engineering, Civil Engineering Keywords: multi-criteria decision-making; TOPSIS; AHP; water resources; dam site selection
The application of multiple criteria decision-making (MCDM) techniques in real-life problems has increased in recent years. The need to build advanced decision models with higher capabilities that can support decision making in a broad spectrum of applications, promotes the integration of MCDM techniques with applicable systems, including artificial intelligence, and Geographic Information Systems (GIS). The Analytic Hierarchy Process (AHP) and Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) are amongst the most widely adopted MCDM techniques capable of resolving water resources challenges. A critical problem associated with water resource management is dam site selection. This paper presents a comparative analysis of TOPSIS and AHP in the context of decision making using GIS for dam site selection. The comparison was made based on geographic and water quality criteria. A ratio estimation procedure was used to determine the weights of these criteria. Both methods were applied for selection of optimal sites for dams in the Sistan and Baluchestan province, Iran. The results show that the TOPSIS method is better suited to the problem of dam site selection for this case study. Actual locations of dams constructed in the area were used to verify the results of both methods.
Preprint HYPOTHESIS | doi:10.20944/preprints202206.0409.v1
Evolutionary Honing in and Mutational Replacement: How Long-Term Directed Mutational Responses to Specific Environmental Pressures Are Possible
Adi Livnat, Daniel Melamed
Subject: Life Sciences, Genetics Keywords: Non random mutation; interaction-based evolution; hemoglobin S; directed mutation; parallelism; genome organization
Recent results have shown that the human malaria-resistant hemoglobin S mutation originates de novo more frequently in the gene and in the population where it is of adaptive significance, namely, in the hemoglobin subunit beta gene compared to the non-resistant but otherwise identical 20A>T mutation in the hemoglobin subunit delta gene, and in sub-Saharan Africans, who have been subject to intense malarial pressure for many generations, compared to Northern Europeans, who have not. This finding raises a fundamental challenge to the traditional notion of accidental mutation. Here we address this finding with the replacement hypothesis, according to which pre-existing genetic interactions can lead directly and mechanistically to mutations that simplify and replace them. Thus, a gradual evolutionary process under selection can hone in on interactions of importance for the currently evolving adaptations, from which large-effect mutations follow that are relevant to these adaptations. We exemplify this hypothesis using multiple types of mutation, including gene fusion mutations, gene duplication mutations, A>G mutations in RNA-edited sites and transcription-associated mutations, and place it in the broader context of a system-level view of mutation origination called Interaction-based Evolution. Potential consequences include that similarity of mutation pressures may contribute to parallel evolution in genetically related species, that the evolution of genome organization may be driven by mutational mechanisms, that transposable element movements may also be explained by replacement, and that long-term directional mutational responses to specific environmental pressures are possible. Such responses need to be further tested by future studies in natural and artificial settings.
Determination of Location-Specific Solidification Cracking Susceptibility for a Mixed Dissimilar Alloy Processed by Wire-Arc Additive Manufacturing
Soumya Sridar, Noah Sargent, Xin Wang, Michael A. Klecka, Wei Xiong
Subject: Materials Science, Metallurgy Keywords: functionally graded alloy; directed energy deposition; solidification cracking susceptibility; ICME; CALPHAD; high entropy.
Solidification cracking is a major obstacle when joining dissimilar alloys using additive manufacturing. In this work, location-specific solidification cracking susceptibility has been investigated using an integrated computational materials engineering (ICME) approach for a graded alloy formed by mixing P91 steel and Inconel 740H superalloy. An alloy derived from a mixture of 26 wt.% P91 steel and 74 wt.% Inconel 740H, with high configurational and total entropy, was fabricated using wire-arc additive manufacturing. Microstructure characterization revealed intergranular solidification cracks, which increased in length along with the build height. With inputs from experiments, such as secondary dendrite arm spacing, the DICTRA (diffusion-controlled transformations) module within the Thermo-Calc software was used to model location-specific solidification cracking susceptibility. The top region, with the highest cooling rate, has the highest solidification cracking susceptibility and is in good agreement with the experimentally observed crack length. From Scheil simulations, it was deduced that pronounced segregation of Nb and Cu within the cracks increased the solidification range by suppressing the solidus temperature. The overall solidification cracking susceptibility and freezing range was highest for the 26 wt.% P91 alloy amongst the mixed compositions between P91 steel and 740H superalloy, proving that solidification characteristics play a major role in alloy design for additive manufacturing.
MOOCs at the Crossroads: A Literature Review and Reflection Drawing upon Discourse Analysis
Laila Mohebi, Marcelo F. Ponce
Subject: Social Sciences, Education Studies Keywords: MOOCs; distance education; self-directed learning; self-defined learning pathways; 21st century abilities
This study is a synthesis of 159 articles that were selected for their relevance to comprehend key aspects of the Massive Open Online Courses (MOOCs) phenomenon, from a discourse analysis perspective. Since 2011, MOOCs are expanding worldwide so that the number of subscribers outpointed 101 million at the end of 2018. This paper explores the question whether the MOOCs are the embodiment of the global one-world classroom or whether, instead, they represent a low-cost alternative tailored to a segment that doesn´t have enough time or resources to attend a brick-and-mortar college. In addition, the review tackles the link between motivation and low completion rates. Finally, we discuss the need to devise better methods to assess the pedagogical value of MOOCs.
Improve Ubiquitination-site Prediction Using Physicochemical Properties and Machine Learning with Grid Search
Xiaoye Mo, Samuel Cho, Xia Jiang
Subject: Biology, Other Keywords: ubiquitination; ubiquitination-site; PCP; protein physicochemical properties; prediction; machine learning; grid search
ABSTRACT Background Ubiquitination plays an important role in protein post-translational processes and has been found to be involved in a number of regulatory functions including proteasome degradation, DNA repair, transcription, signal transduction, endocytosis, and sorting. As the identification of ubiquitination site is critical to furthering our understanding of the mechanism of ubiquitination, various experimental and machine learning methods have been used to conduct this task. It has been an important but challenging task to improve the accuracy of ubiquitination site prediction. In this research, we explore the possibility of improving the prediction performance of machine learning by incorporating grid search in the training process. Method We developed grid search procedures for each of six widely used machine learning methods including NB, LR, DT, SVM, LASSO, and KNN, and applied them to ubiquitination site prediction using the six PCP datasets that were previously developed. For each of the ML methods, we developed a set of values for each of the tunable hyperparameters available to the method. These sets of values then can be combined to form a large grid of hyperparameter settings, and each of these settings is used in the grid search. We integrated 5-fold cross-validation in grid search to train and test ML models and applied an additional independent validation procedure by conducting a pre-training 80-20 sample split. We evaluated the performance of the six methods by comparing them side by side for each of the six datasets. We also compared the grid search results with the results that were previously published without doing grid search. To optimize the prediction performance, we trained 1.1 million ML models in total through grid search. Results We compared the overall prediction performance of these six methods, as well as their prediction performance when working with balanced vs. imbalanced data, and large-scale vs. small-scale data. From the perspective of dataset, we find that the overall performance of every PCP dataset has been significantly improved in this study compared to the previous study, with the percentage increase of the average AUC of all six datasets ranging from 7.9% (PCP-4) up to 17.0% (PCP-1). From the perspective of method, we find that three out of four methods significantly benefit from grid search comparing to their previously published non-grid search results, with the maximum AUC improvement as high as 47% (LASSO on PCP-5), 43.3% (NB on PCP-1), and 33.7% (SVM on PCP-6). SVM overall ranks number one, followed by KNN as the number two performer based on their average AUCs on all datasets. But these two also ranked the top two (KNN 76 days and SVM 15 days) in terms of the total running time that they need to do grid search. We also find that SVM, KNN, and DT tend to handle small-scale and imbalanced datasets better, while LR, and LASSO are doing well with large-scale and balanced datasets. NB is more sensitive to data imbalance while less sensitive to the size of a dataset. Conclusions Our results show that using grid search has improved the performance of ubiquitination prediction significantly. We find that the performance of a method is closely related to its hyperparameter setting and the type of data it handles. Even though SVM is on average an outperformer, none of the methods can provide the best performance for all datasets. When sufficient computing resources are well accessible, grid search is an effective way to identify both a top performing model for a machine learning method and a suitable machine learning method for a particular dataset.
Estimation of Annual Effective Dose Due to Ingestion of 210Pb and 210Po in Crops from A Site of Coal Mining and Processing in Southwest China
Chenxiao Wang, Qifan Wu, Ziqiang Pan, Senlin Liu, Zhonggang Cao, Yilin Yu
Subject: Earth Sciences, Environmental Sciences Keywords: Natural radioactivity; risk assessment; 210Pb and 210Po; radiological impact; polluted mine site.
Since the exploitation of mineral resources results in the release of radionuclides, and consuming radionuclides affects public health in the short and long term. A case study of the environmental radiation impact from coal mining and germanium processing was carried out in southwest China. The coal mines contain germanium and uranium and have been exploited for more than 40 years. The farmlands around the site of coal mining and germanium processing have been contaminated by the solid waste and mine water in some extend since then. Samples of crops have been collected from contaminated farmlands in research area. The research area covers a radius of 5 km, in which there are 2 coal mines located. 210Pb and 210Po have been analyzed as the key radionuclides during monitoring program. The average activity concentrations of 210Pb and 210Po in the crops were 1.38 and 1.32 Bq/kg in cereals, 4.07 and 2.19 Bq/kg in leafy vegetables and 1.63 and 1.32 Bq/kg in root vegetables. The annual effective doses due to the ingestion of 210Pb and 210Po in consumed crops have been estimated for adult residents living in research area. The average annual effective dose was 0.336mSv/a, while the minimum was 0.171 mSv/a and the maximum was 0.948 mSv/a. The results show that crops grown on contaminated farmland contained an enhanced level of radioactivity concentration. Ingestion doses of local residents in research area were significantly higher than the China average level of 0.112 mSv/a, and the world average level of 0.042 mSv/a through 210Pb and 210Po in crops intake respectively.
Non-Uniform Aspects of SARS-CoV-2 Intraspecies Evolution Reopen Questions on Its Origin
Sk Sarif Hassan, Vaishnavi Kodakandla, Elrashdy M. Redwan, Kenneth Lundstrom, Pabitra Pal Choudhury, Ángel Serrano-Aroca Aroca, Gajendra Kumar Azad, Alaa A.A. Aljabali, Giorgio Palu, Tarek Mohamed Abd El-Aziz, Debmalya Barh, Bruce D. Uhal, Parise Adadi, Kazuo Takayama, Nicolas G. Bazan, Murtaza Tambuwala, Samendra P. Sherchan, Amos Lal, Gaurav Chauhan, Wagner Baetas-da-Cruz, Vladimir N. Uversky
Subject: Life Sciences, Biochemistry Keywords: SARS-CoV-2; Mutations; Furin Cleavage Site (FCS); Evenly-uneven; Invariant regions
Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no hypothesis has managed to identify the origin, and the issue has resurfaced. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins across different continents comprising 24 geo-locations. The results showed an evenly uneven distribution of unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across the 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations we have considered. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and to be prepared to meet the challenges of potential future pandemics.
A Furin Cleavage Site Inserted into the Spike Protein of SARS-CoV-2: A Structural Implication?
Subject: Life Sciences, Biophysics Keywords: COVID-19; SARS-CoV-2; furin cleavage site (FCS); salt bridging analysis
One notable features of the SARS-CoV-2 genome is that the spike protein of SARS-CoV-2 has a functional polybasic (furin) cleavage site (RRAR) at the S1–S2 boundary through the insertion of 12 nucleotides encoding PRRA. To date, the furin cleavage site (FCS) remains an experimentally uncharted territory both structurally and functionally. For instance, whether or not FCS is actually cleaved, before or after viral cell entry or exit, still remains to be experimentally investigated. With currently available structural data, this article presents a computational structural characterization of the FCS inserted into SARS-CoV-2 spike glycoprotein, and puts forward a set of structural hypothesis against the hypothesis of SARS-CoV-2 from purposeful manipulation: (1), the inserted FCS does not alter, neither stabilize nor de-stabilize, the overall structure of SARS-CoV-2 spike glycoprotein; (2), the net structural consequence of FCS is the insertion of a furin cleavage site into SARS-CoV-2 spike glycoprotein, whose S1 and S2 subunits will still be bonded together even if the FCS is actually cleaved by furin protease.
The Extracellular and Intracellular Biomineralization Induced by Bacillus licheniformis DB1-9 at Different Mg/Ca Molar Ratios
Zuozhen Han, Xiao Gao, Hui Zhao, Maurice E. Tucker, Yanhong Zhao, Huaxiao Yan
Subject: Earth Sciences, Environmental Sciences Keywords: Mg/Ca; biominerliazation; nucleation site; Bacillus licheniformis DB1-9; carbonic anhydrase; ammonia
Biomineralization has become a research hotspot and attracted widespread attention in the field of carbonate sedimentology. In this study, Bacillus licheniformis DB1-9 was used to induce the calcium carbonate precipitation at different magnesium calcium molar ratios in the laboratory to further explore the biomineralization mechanism. Phylogenetic tree shows that the bacteria belongs to Bacillus licheniformis species. The ammonia and carbonic anhydrase can be released by this bacteria, resulting in the pH increase, and the carbonic anhydrase can also promote the hydration reaction of carbon dioxide and subsequently produce the bicarbonate and carbonate ions to elevate the supersaturation of calcium carbonate in the liquid culture medium to facilitate the precipitation of carbonate minerals. The calcites have a shape of rhombohedron, dumbell, and elongation, and aragonite often appears in the form of mineral aggregates, besides that there are also the spherical and the fusiform minerals. FTIR result shows there are some organic functional groups, such as C-O-C and C=O, beside of the characteristic peaks of the calcite and the aragonite, indicating that microbial metabolism is closely related to the mineral formation. The superthin slices of the bacteria analyzed by HRTEM, SAED, EDS and STEM show that the surface and EPS can adsorb a large number of calcium ions and magnesium ions and EPS may act as the nucleation sites, what's more, the intracellular nanometer-scale sphere areas show the amorphous structures, and the intracellular calcium ions and magnesium ions suggeste that they can be transported from the outside to inside the cell by diffusion along the concentration grade from high to low. This study may provide some references to further understand the biomineralization mechanism induced by microorganisms in the laboratory and the field, and also helps to explore the reason of the transition of calcite sea to aragonite sea in the geological history.
Spatial Differentiation of the Public Transport Modal Split for Integration into the Location Analysis for Charging Infrastructure
Waldemar Brost, Teresa Funke, Michael Lembach
Subject: Engineering, Civil Engineering Keywords: site identification; electric charging infrastructure; electromobility; spatial analysis; modal split; public transport
The spread of charging infrastructure (CIS) for battery electric vehicles is crucial for coping with the increasing number of electric vehicles. Therefore, the selection of ideal (fast-) charging locations determines acceptance, utilization and, thus, the economic viability of a single site or the whole charging network. The methodology of the Integrated Model Approach STELLA[1] for site identification of CIS uses proven methods of traffic modeling such as the classic four-step traffic modeling in a new context to enable statements regarding the positioning of CIS. Based on different spatial analyzes and characterizations of urban quarters, traffic generated by individuals is calculated using the FGSV approach of 2010. Because only (electric) motorized individual traffic is of importance for CIS, the share of trips is calculated by differentiating the modal split between various transport groups. One approach is to concretize the modal split share of public transport based on analyzes of different criteria and data sets, e.g. the accessibility of stops. The model approach STELLA, which also combines various extensive data (e.g. transport networks and traffic volumes, settlement structures, vehicle characteristics, power supply data and user requirements), is currently developed for a planning area covering the entire territory of the Federal Republic of Germany. [1] STELLA is the acronym for the German term "STandortfindungsmodell für ELektrische LAdeinfrastruktur".
Expanding the Myxochelin Natural Product Family by Nicotinic Acid Containing Congeners
Nicolas A. Frank, Márió Széles, Sergi H. Akone, Sari Rasheed, Stephan Hüttel, Simon Frewert, Mostafa M. Hamed, Jennifer Herrmann, Soeren M. M. Schuler, Anna K. H. Hirsch, Rolf Müller
Subject: Chemistry, Analytical Chemistry Keywords: Myxobacteria; myxochelin; nicotinic acid; secondary metabolites; natural product discovery; precursor-directed biosynthesis; total synthesis
Myxobacteria represent a viable source of chemically diverse and biologically active secondary metabolites. The myxochelins are a well-studied family of catecholate-type siderophores produced by various myxobacterial strains. Here, we report the discovery, isolation and structure elucidation of three new myxochelins N1–N3 from the terrestrial myxobacterium Corallococcus sp. MCy9049, featuring an unusual nicotinic acid moiety. Precursor-directed biosynthesis (PDB) experiments and total synthesis were performed in order to confirm structures, improve access to pure compounds for bioactivity testing and to devise a biosynthesis proposal. The combined evaluation of metabolome and genome data covering myxobacteria supports the notion that the new myxochelin congeners reported here are in fact frequent side products of the known myxochelin A biosynthetic pathway in myxobacteria.
Inflamm-Aging: Why Older Men Are the Most Susceptible to SARS-Cov-2 Complicated Outcomes
Massimiliano Bonafè, Francesco Prattichizzo, Angelica Giuliani, Gianluca Storci, Jacopo Sabbatinelli, Fabiola Olivieri
Subject: Medicine & Pharmacology, Pathology & Pathobiology Keywords: SARS-CoV-2; COVID-19; IL-6; inflamm-aging; immune senescence; host-directed therapies
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is characterized by a high mortality of elderly men with age-related comorbidities. In most of these patients, uncontrolled local and systemic hyperinflammation induces severe and often lethal outcomes. The aging process is characterized by the gradual development of a chronic subclinical systemic inflammation (inflamm-aging) and by acquired immune system impairment (immune senescence). Here, we advance the hypothesis that some key features of aging contribute to the disproportionate SARS-CoV-2 mortality suffered by elderly men. At least four well-recognized aging-related characteristics that are strongly expressed in older men go some way towards explaining why these patients account for the vast majority of fatalities: i. the presence of subclinical systemic inflammation without overt disease, ii. a blunted acquired immune system and type I interferon response due to the chronic inflammation; iii. the downregulation of ACE2 (SARS-CoV-2 receptor), which triggers inflammation, particularly in patients with age-related comorbid diseases such as type II diabetes; and iv. accelerated biological aging, as measured by epigenetic and senescence markers (e.g. telomere shortening) associated to the chronic inflammatory state. Though typical of the aged, especially of elderly men, it is conceivable that these features are also shared by some subsets of the younger population. The high mortality rate of SARS-CoV-2 infection suggests that clarification of the mechanisms of inflamm-aging and immune senescence can help combat not only age-related disorders but also SARS-CoV-2 infection.
Latest Developments in Industrial Hybrid Machine Tools That Combine Additive and Subtractive Operations
Magdalena Cortina, Jon Iñaki Arrizubieta, Jose Exequiel Ruiz, Eneko Ukar, Aitzol Lamikiz
Subject: Engineering, Industrial & Manufacturing Engineering Keywords: hybrid machines; hybrid manufacturing; additive manufacturing; subtractive manufacturing; Directed Energy Deposition; Powder Bed Fusion
Hybrid machine tools combining additive and subtractive processes have arisen as a solution to the increasing manufacture requirements, boosting the potentials of both technologies, while compensating and minimizing their limitations. Nevertheless, the idea of hybrid machines is relatively new and there is a notable lack of knowledge in the field. Therefore, in the present paper, an insight into the advancements of hybrid machines is given, identifying their real capabilities, together with the latest developments from an industrial context. In addition, the current situation and future perspectives of hybrid machines from the point of view of process planning, monitoring and inspection are discussed. Finally, the challenges that must be overcome and the opportunities that the hybrid machines will provide in the forthcoming years are presented.
iPReditor-CMG: Improving Predictive RNA Editor for Crop Mitochondrial Genomes Using Genomic Sequence Features and Optimal Support Vector Machine
Sidong Qin, Yanjun Fan, Shengnan Hu, Yongqiang Wang, Ziqi Wang, Yixiang Cao, Qiyuan Liu, Siqiao Tan, Zhijun Dai, Wei Zhou
Subject: Biology, Plant Sciences Keywords: iPReditor-CMG; RNA editing site; Mitochondrial genomes; genomic sequence feature; support vector machine
Cytosine (C) to uracil (U) RNA editing is one of the most important post-transcriptional processes, however exploring C-to-U editing events efficiently within the crop mitochondrial genome remains a challenge. An improving predictive RNA editor for crop mitochondrial genomes, iPReditor-CMG, was proposed, which was based on SVM, three common crop mitochondrial genomes and self-sequenced tobacco mitochondrial ATPase. After multi-combination feature extracting, high-dimension feature screening and multi-test independent predicting, the results showed that the average accuracy of intraspecific prediction was 0.85, and the highest value even up to 0.91, which outperformed the previous reference models. While the prediction accuracies were 0.78 between dicotyledons and no more than 0.56 between dicotyledons and monocotyledons, implying a possible similarity in C-to-U editing mechanisms among close relatives. The best model was finally identified with an independent test accuracy of 0.91 and an area under the curve of 0.88, and further suggested that five unreported feature sequences TGACA, ACAAC, GTAGA, CCGTT and TAACA were closely associated with the editing phenomenon. Multiple evaluation findings supported that the iPReditor-CMG could be effectively applied to predict crop mitochondrial editing sites, which may contribute to insight into their recognition mechanisms and even other post-transcriptional events in crop mitochondria.
metaRE R Package for Meta-analysis of Transcriptome Data to Identify the Cis-regulatory Code behind the Transcriptional Reprogramming
Daria Novikova, Yana Sizentsova, Pavel Cherenkov, Victoria Mironova
Subject: Life Sciences, Genetics Keywords: meta-analysis; transcription factor; binding site; genomics; transcriptomics; chilling stress; CBF; DREB; CAMTA
At the molecular level, response to an external factor or an internal condition causes reprogramming of temporal and spatial transcription. When an organism undergoes physiological and/or morphological changes, several signaling pathways are activated simultaneously. Examples of such complex reactions are the response to temperature changes, dehydration, various biologically active substances, and others. Synergistic action of multiple pathways greatly complicates the experimental study of the molecular genetic mechanisms of the organism's reactions. As a result, a significant part of the regulatory ensemble in such complex reactions remains unidentified. We developed metaRE, an R package for the systematic search for cis-regulatory elements enriched in the promoters of the genes significantly changed their transcription in a complex reaction. metaRE mines multiple expression profiling datasets generated to test the same organism's response and identifies simple and composite cis-regulatory elements systematically associated with differential expression of genes. Here we showed metaRE performance for identification of cold stress-responsive cis-regulatory code in Arabidopsis thaliana. MetaRE identified potential binding sites for known as well as unknown cold response regulators. Software with source files, documentation, and example data files are freely available online at the repository (https://github.com/cheburechko/MetaRE).
Changes in Lower Layers Biodiversity Caused by Polish Pony in Old Growth Scots Pine Stands
Sergii Boiko, Ernest Bielinis, Zbigniew Sierota, Anna Zawadzka, Maciej Nasiadko, Jakub Borkowski
Subject: Biology, Forestry Keywords: Polish primitive horse, forest site type, herb layer, undergrowth layer, understory layer, biodiversity
The study was conducted in coniferous and deciduous old growth forests in two forest complexes located in: i) the fenced area of the Popielno Research Station of the Polish Academy of Sciences, with free-living Polish pony [Polish primitive horse (Equus ferus caballus)], and ii) open Maskulińskie Forest District managed (harvested) forest, without horses. The impact of forest animals on ground cover layer as well as on understory shrub layer and undergrowth, in i) area (horses and other forest animals) was compared with the results in ii) area (forest animals without horses). Very significant differences in the understory and undergrowth (above 0,5 m) layer vegetation communities structure between both areas and type of stands were found. The results suggest that the presence of the Polish horse substantially changed the species composition and increased the species diversity of the ground layer and shrub layer both on coniferous forest and in the deciduous forest habitats. The height of the shrub layer trees was lower by 30% in the area with the Polish horse.
An Overview of Physical Phenomena Involved in the Laser Powder Directed Energy Deposition Process
Gabriele Piscopo, Eleonora Atzeni, Abdollah Saboori, Alessandro Salmi
Subject: Engineering, Industrial & Manufacturing Engineering Keywords: additive manufacturing; directed energy deposition; laser metal deposition; powder stream; melt pool; microstructure; residual stresses
Laser Powder Directed Energy Deposition (LP-DED) is an Additive Manufacturing process in which a laser beam is used to generate a melt pool onto a substrate. The additional material, in form of powder material, is fed into the generated melt pool and a raised track is obtained. The LP-DED process is very powerful for different applications such as the repair operations and the production of functionally graded material, however the application is still limited and one of the main reasons is related to the lack of knowledge in the physics of the process mechanisms. The process is influenced by a huge number of parameters and three main mechanisms can be identi-fied. These mechanisms are the powder flow, the generation of the molten pool and the solidifica-tion process and for each of these mechanisms the process parameters have a different relevance. In this paper, a review of the main mechanisms and the relationship between the process parame-ters and the outcome of each step of the process is presented.
Clinical Outcomes of the Endoscopic Step-Up Approach With or Without Radiology-Guided Percutaneous Drainage for Symptomatic Walled-Off Pancreatic Necrosis
Tanawat Pattarapuntakul, Tummarong Charoenrit, Thanawin Wong, Nisa Netinatsunton, Bancha Ovartlarnporn, Thanapon Yaowmaneerat, Teeravut Tubtawee, Pattira Boonsri, Pimsiri Sripongpun
Subject: Medicine & Pharmacology, Gastroenterology Keywords: Directed endoscopic necrosectomy; endoscopic step-up approach; endoscopic transluminal drainage; percutaneous drainage; walled-off pancreatic necrosis
Abstract: Background and objectives: Symptomatic walled-off pancreatic necrosis is a serious local complication of acute necrotising pancreatitis. The endoscopic step-up approach is the standard treatment for symptomatic walled-off pancreatic necrosis; however, adjunctive radiologic percu-taneous drainage for this condition is controversial. This study compared the clinical and radio-logic resolution of walled-off pancreatic necrosis achieved with the endoscopic step-up approach with or without radiology-guided percutaneous drainage. Material and Methods: This retrospective, single-center cohort study enrolled patients with symp-tomatic walled-off pancreatic necrosis who underwent endoscopic transmural drainage (ETD) followed by directed endoscopic necrosectomy (DEN) with or without radiology-guided drainage. A total of 34 patients (endoscopic approach, n=22; combined modality approach, n=12) underwent the endoscopic step-up approach (ETD followed by DEN). Baseline characteristics, clinical success, and resolution of necrosis were compared between groups. Results: All patients achieved symptom resolution from walled-off pancreatic necrosis. The mean patient age was 58.4 years, and 21 (61.8%) were men. After treatment with the endoscopic approach and combined modality approach, clinical success was achieved in 90.9% of patients within 11.5 days, and 66.7% of patients within 16.5 days, respectively. Both the total hospital stay (55 days vs 71 days; p=0.071) and time to complete radiologic resolution were shorter (93 days vs 124 days; p=0.23) in the endoscopic approach group. Conclusion: The endoscopic step-up approach resulted in the clinical resolution of symptomatic walled-off pancreatic necrosis comparable to that of the combined modality drainage. However, the endoscopic approach alone allows higher clinical success, early clinical and radiologic resolution, and a shorter hospital stay.
Self-Direction in Physics Graduate Education: David J. Rowe's Career-Long Commitment
Carol Nash
Subject: Physical Sciences, Nuclear & High Energy Physics Keywords: self-directed learning; graduate education; flow; David J. Rowe; open mindedness; mentoring; symmetry; narrative research; STEM
The ability to self-direct a research program determines graduate degree completion. Yet, research on incompletion of graduate physics programs assume students' present level of self-direction adequate and neglects to recognize a lack of self-directed learning as key. One theoretical mathematical physicist focused on changing this challenge of physics graduate education by promoting self-directed learning through the type research flow that has been found to bring the greatest satisfaction to researchers with respect to their insights. This he provided through his space, time, open mindedness and theoretical contributions with his students and in collaboration with his colleagues. A self-directed learner himself, David J. Rowe developed methods of mentoring for encouraging physics graduate students to recognize symmetry as valuable in identifying solutions to problems quickly—helping these students take the lead in finding insightful resolutions to complex, multidimensional, mathematical physics uncertainties. How Rowe set about supporting self-directed learning in his graduate physics education interactions will be examined with the use of narrative research to interpret the texts and conversations with the author he made available. His techniques will be presented and recommendations made regarding how Rowe's work in this regard can be modeled to improve self-direction in STEM graduate education.
Anatomical Study of Type Classification and Surface Area of Attachment Sites for Tibialis Anterior Tendon
Tomoki Hirai, Mutsuaki Edama, Ryoya Togashi, Haruki Osanami, Rina Saito, Koyo Kato, Mayuu Shagawa, Chie Sekine, Hirotake Yokota, Ryo Hirabayashi, Tomonobu Ishigaki, Hiroshi Akuzawa, Yuki Yamada, Taku Toriumi, Ikuo Kageyama
Subject: Physical Sciences, Other Keywords: tibialis anterior tendon; attachment site area; three-dimensional; medial cuneiform bone; first metatarsal bone
The purpose of this study was to clarify the attachment types of the tibialis anterior tendon (TAT) in Japanese fixed cadavers and to determine the attachment site area in three dimensions. We examined 100 feet from 50 Japanese cadavers. The TAT was classified according to differences in the number of fiber bundles as: Type I, with one fiber bundle; Type II, with two fiber bundles; and Type III, with three fiber bundles. The attachment site area of the TAT was measured using a three-dimensional scanner. Cases were Type II in 95% and Type III in 5%, with no cases of Type I identified. In Type II, mean attachment site areas were 85.2 ± 18.2 mm2 for the medial cuneiform bone (MCB) and 72.4 ± 19.0 mm2 for the first metatarsal bone (1MB), showing a significantly larger area for MCB than for 1MB. These findings suggest the possibility of ethnic differences in TAT attachment types and suggest that TAT attachments in Japanese individuals are highly likely to be Type II, with rare cases of Type III. Accurate measurement of attachment site areas is possible with appropriate three-dimensional measurements.
Long-Term Tree Survival and Diversity of Highway Tree Planting Projects
Allyson B. Salisbury, Jason W. Miesbauer, Andrew K. Koeser
Subject: Biology, Plant Sciences Keywords: drought tolerance; roadside woody vegetation; Simpson diversity; site conditions; tree mortality; tree planting initiatives
Online: 4 March 2022 (17:04:27 CET)
Long-term, multi-decade research on planted tree survival in urban settings is sparse. One understudied urban environment is highway rights-of-way (ROW), lands adjacent to high-speed, unsignalized roadways. We conducted a re-inventory of tree planting cohort in northern Illinois, U.S. on a 48 km-long highway near Chicago which were 10-, 21-, and 30-years old to evaluate long-term patterns of survival and diversity. Using each randomly selected planting site along the highway as a unit of observation and analysis, we compared the number of trees documented in record drawing to the number of trees currently alive to determine percent survival. We evaluated 224 planting sites which originally contained 2,944 trees and collected data about the planting site location. For the oldest cohort, 26% of trees were still alive in 2018 (median survival by species = 16%, Q1 = 0%, Q3 = 48%), while 31% of the 21-year-old cohort (med. = 6%, Q1 = 0%, Q3 = 47%) and 86% of the 10-year-old cohort were still alive (med. = 85%, Q1 = 74%, Q3 = 96%). The survival of the 21- and 30-year-old cohort matches urban tree survival estimates by other researchers, while the 10-year-old survival is higher than expected. The only planting location characteristic that significantly affected survival was traffic islands (areas between the highway and entrance/exit ramps). Species with low drought tolerance were less likely to be alive for the 10-year-old cohort. Waterlogging tolerant species were more likely to be alive in the 10-year-old cohort. Since some species in the 21- and 30-year-old cohorts had very low survival, the tree species richness and diversity s in study areas declined between the initial record drawings and reinventory. This study demonstrates the challenges of maintaining long-term survival and diversity in the highway ROW and emphasizes the importance of species selection.
BIM Approach in Construction Safety – A Case Study
Fernanda Rodrigues, J. Santos Baptista, Débora Pinto
Subject: Engineering, Civil Engineering Keywords: Building Information Modelling; Construction safety; Planning; Safety Elements; Construction Site Management; Falls from height.
As is known, the construction industry has one of the highest occupational accidents incidence rates among all economic sectors. Currently, Building Information Modeling (BIM) appears as a tool that addresses occupational safety issues throughout the construction life cycle projects, avoiding hazards and risks and, consequently, increasing safety. This work investigates BIM methodology and related technologies application for building safety planning in construction and demonstrates the potential of this technology for the integrated implementation of safety measures during the design phase and the construction site management. The first step consisted of a literature review on the application of BIM in safety in the design and planning phases. Following, to show the potentialities of construction simulation, a case study based on BIM 4D to prevent falls from height was developed. With BIM 4D, it is possible to follow the construction process over time, giving the construction safety technicians', designers, supervisors and managers the capability to analyse, in each phase, the potential risks and which safety measures should be implemented. BIM can effectively integrate safety measures from the design phase to the construction and use phase and do integrated safety planning within construction planning, leading to reliable safety management throughout the construction process.
Enhancing the Cell-Free Expression of Native Membrane Proteins by in-Silico Optimisation of the Coding Sequence - An Experimental Study of the Human Voltage-Dependent Anion Channel
Sonja Zayni, Samar Damiati, Susana Moreno-Flores, Fabian Amman, Ivo Hofacker, Eva Kathrin Ehmoser
Subject: Life Sciences, Biochemistry Keywords: cell-free membrane protein expression; translation enhancer; translation initiation; ribosome docking site; sequence design.
The investigation of membrane proteins, key constituents of cells, is hampered by the difficulty and complexity of their in vitro synthesis, of unpredictable yield. Cell-free synthesis is herein employed to unravel the impact of the expression construct on gene transcription and translation, without the complex regulatory mechanisms of cellular systems. Through the systematic design of plasmids in the immediacy of the start of the target gene, it was possible to identify translation initiation and the conformation of mRNA as the main factors governing the cell-free expression efficiency of the human voltage dependent anion channel (VDAC), a relevant membrane protein in drug-based therapy. A simple translation initiation model was developed to quantitatively assess the expression potential for the designed constructs. A scoring function is proposed that quantifies the feasibility of formation of the translation initiation complex through the ribosome-mRNA hybridization energy and the accessibility of the mRNA segment binding to the ribosome. The scoring function enables to optimize plasmid sequences and semi-quantitatively predict protein expression efficiencies. This scoring function is publicly available as webservice XenoExpressO at rna.tbi.univie.ac.at.
Impact of Charcoal Canker on Oak Trees at a Site of Community Importance: Case Study of the Relict Castelfidardo Forest (SIC Area IT520008, Castelfidardo, AN, Italy)
Sergio Murolo, Jonathan Concas, Alessandro Salerno, Fedele Maiorano, Lorenzo Cingolani, Francesca Carloni, Salvatore Moricca, Gianfranco Romanazzi
Subject: Life Sciences, Biochemistry Keywords: Biscogniauxia mediterranea; oak decline; dieback; Site of Community Importance (S.I.C.); tree competition; warming conditions
Oaks are a dominant and key tree species in Mediterranean forest ecosystems. However, in recent decades, oak forests have been heavily impacted by oak decline, a worldwide phenomenon exacerbated by climate change. The charcoal disease agent Biscogniauxia mediterranea is involved in the decline of Mediterranean oak formations in a variety of contexts. Here, we investigated the impact and role of B. mediterranea in decline of oaks in Castelfidardo Forest, a relict wood of the late Holocene and a Site of Community Importance. We established five plots within which we recorded the tree positions, any symptoms and signs of decline, association of B. mediterranea to declining trees, and the deadwood and associated mycota. Of 471 oaks inspected, 7.0% showed brownish exudates on the stems, 46.9% showed epicormic shoots along the main trunk, and 24.4% showed black carbonaceous stromata on diseased branches and trunks. The decline was most severe for Quercus cerris, which comprised plots #4 and #5, at 50.0% (81/162 trees) and 29.0% (33/114), respectively; then for Quercus robur for plot #3, at 40.0% (38/95); and finally for Quercus pubescens for plots #1 and #2, at 13.7% (7/51) and 12.3% (6/49), respectively. Bark tissue was collected from trees with charcoal cankers, with microscopy examination and identification by mycological and molecular methods. This investigation revealed close association between oaks with pronounced reduction of vitality and incidence of B. mediterranea. The deadwood was equally distributed among the five plots, and was heavily colonized by Basidiomycota. The high incidence of this oak-weakening pathogen B. mediterranea appears to be related to stress conditions (e.g., water scarcity, prolonged drought). However, absence of silvicultural management, high competition among physiologically mature trees, and the geographic isolation of this residual forest might have predisposed these oaks to decline.
Triglycine-Based Approach for Identifying the Substrate Recognition Site of an Enzyme
Ki Hyun Nam
Subject: Biology, Other Keywords: protein-protein interaction; protein-peptide interaction; triglycine; substrate binding site; peptide; inhibitor; Proteinase K
Various peptides or non-structural amino acids are recognized by their specific target proteins and perform biological role in various pathways in vivo. Understanding the interactions between target protein and peptides (or non-structural amino acids) provides key information on the molecular interactions, which can be potentially translated to the development of novel drugs. However, it is experimentally challenging to determine the crystal structure of protein-peptide complexes. To obtain structural information on substrate recognition of peptide-recognizing enzyme, X-ray crystallographic studies were performed using triglycine (Gly-Gly-Gly) as main-chain of peptide. The crystal structure of Parengyodontium album Proteinase K in complex with triglcyine was determined at 1.4 Å resolution. Two different bound conformations of triglycine were observed at the substrate recognition site. The triglycine backbone forms stable interactions with β5-α4 and α5-β6 loops of main-chain. One of the triglycine-binding conformations was identical with the binding mode of a peptide-based inhibitor from a previously reported crystal structure of Proteinase K. Triglycine has potential application X-ray crystallography to identify substrate recognition sites in peptide binding enzymes.
Spleen, as an Optimal Site for Islet Transplantation and a Source of Mesenchymal Stem Cells
Naoaki Sakata, Gumpei Yoshimatsu, Shohta Kodama
Subject: Medicine & Pharmacology, General Medical Research Keywords: spleen; islet transplantation; transplant site; immunity; tolerance; regeneration; diabetes mellitus; mesenchymal stem cell; Sjogren's syndrome; HOX
In this review, we show the unique potential of spleen as an optimal site for islet transplantation and a source of mesenchymal stem cells. Islet transplantation is a cellular replacement therapy to treat severe diabetes mellitus, but its clinical outcome is unsatisfactory at present. One factor in clinical success of this therapy is selection of the most appropriate transplantation site. The spleen has been studied for a long time as a candidate site for islet transplantation. Its advantages include physiological insulin drainage and regulation of immunity. Recently it has also been shown that the spleen contributes to the regeneration of transplanted islets. The efficacy of transplantation is not as high as that obtained with intraportal transplantation, which is the current representative method of clinical islet transplantation. Safer and more effective methods of islet transplantation need to be established before the spleen can be effectively used in the clinic. Spleen also has an interesting aspect as a mesenchymal stem cell reservoir. The splenic mesenchymal stem cells contribute to tissue repair in damaged tissue, and thus, the infusion can be a promising therapy for autoimmune diseases, including type 1 diabetes mellitus and Sjogren's syndrome.
An Engineering Theory of Evolution
Simeon Castle, Claire Grierson, Thomas Gorochowski
Subject: Life Sciences, Biotechnology Keywords: evolution; evotype; engineering theory; genotype-phenotype maps; directed evolution; selection; synthetic biology; bioengineering; evolvability; self-adaptive systems
Biological technologies are fundamentally unlike any other because biology evolves. Bioengineering therefore requires novel design methodologies with evolution at their core. Knowledge about evolution is currently applied to the design of biosystems ad hoc. Unless we have a unified engineering theory of evolution, we will neither be able to meet evolution's potential as a design tool, nor understand or limit its unintended consequences on our designs. Our concept of the evotype offers a conceptual framework for engineering the evolutionary potential of biosystems. We show how a biosystem's evolutionary properties might be rationally designed by engineering aspects of genetic variation, designed function, and natural selection. This idea could apply to all biosystems – from individual proteins to communities of whole-cells or even entire ecosystems – whether the goal is to direct evolution in the design process, or to limit its impacts during application. These principles could even be used beyond the realm of bioengineering to design entirely synthetic evolving auto-adaptive technologies.
Transitional Channel Flow: A Minimal Stochastic Model
Paul Manneville, Masaki Shimizu
Subject: Physical Sciences, Acoustics Keywords: transition to/from turbulence; wall-bounded shear flow; plane Poiseuille flow; spatiotemporal intermittency; directed percolation; critical phenomena
In line with Pomeau's conjecture about the relevance of directed percolation (DP) to turbulence onset/decay in wall-bounded flows, we propose a minimal stochastic model dedicated to the interpretation of the spatially intermittent regimes observed in channel flow before its return to laminar flow. Numerical simulations show that a regime with bands obliquely drifting in two stream-wise symmetrical directions bifurcates into an asymmetrical regime, before ultimately decaying to laminar flow. The model is expressed in terms of a probabilistic cellular automaton evolving von Neumann neighbourhoods with probabilities educed from a close examination of simulation results. It implements band propagation and the two main local processes: longitudinal splitting involving bands with the same orientation, and transversal splitting giving birth to a daughter band with orientation opposite to that of its mother. The ultimate decay stage observed to display one-dimensional DP properties in a two-dimensional geometry is interpreted as resulting from the irrelevance of lateral spreading in the single-orientation regime. The model also reproduces the bifurcation restoring the symmetry upon variation of the probability attached to transversal splitting, which opens the way to a study of the critical properties of that bifurcation, in analogy with thermodynamic phase transitions.
Discovery of Multi-Target-Directed Ligands by Targeting Host-specific SARS-CoV-2's Structurally Conserved Main Protease
Rakesh Joshi, Shounak Jagdale, Sneha Bansode, S. Shiva Shankar, Meenakshi Tellis, Vaibhav Kumar Pandya, Ashok Giri, Mahesh Kulkarni
Subject: Life Sciences, Biotechnology Keywords: coronavirus; COVID-19; hACE-2; MPro; multi-target-directed ligand; protease inhibito; RdRp; SARS-CoV-2 virus
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the current COVID-19 pandemic. Worldwide this disease has infected around 1.5 million individuals with a mortality rate ranging from 5 to 10%. It has also imposed extreme challenges on global health, economy, and social behavior. Due to the unavailability of therapeutics, several efforts are going on in the drug discovery to control the SARS-CoV-2 viral infection. The main protease (MPro) plays a critical role in viral replication and maturation, thus can serve as the primary drug target. To understand the structural evolution of MPro, we have performed phylogenetic and SSN analysis, that depicted divergence of Coronaviridae MPro in five clusters specific to viral hosts. This clustering was also corroborated with the comparison of MPro structures. Furthermore, it has been observed that backbone and binding site conformations are conserved despite variation in some of the residues. This conservation can be exploited to repurpose available viral protease inhibitors against SARS-CoV-2 MPro. In agreement with this, we performed screening of the custom-made library of ~7100 molecules including active ingredients present in the Ayurvedic anti-tussive medicines, anti-viral phytochemicals and synthetic anti-virals against SARS-CoV-2 MPro as the primary target. We identified several natural molecules that strongly binds to SARS-CoV-2 MPro among which top seven molecules are d-Viniferin, Myricitrin, Taiwanhomoflavone A, Lactucopicrin 15-oxalate, Nympholide A, Biorobin and Phyllaemblicin B. Most of the predicted lead molecules are from Vitis vinifera, also reported for anti-tussive and/or antiviral activities. These molecules also showed strong binding with other main targets RdRp and hACE-2. We anticipate that our approach for identification of multi-target-directed ligand will provide new avenues for drug discovery against SARS-CoV-2 infection.
Perioperative Goal Directed Therapy During Kidney Transplantation: An Impact Evaluation on the Major Postoperative Complications
Marco Cavaleri, Massimiliano Veroux, Filippo Palermo, Francesco Vasile, Mirko Mineri, Joseph Palumbo, Lorenzo Salemi, Marinella Astuto, Paolo Murabito
Subject: Medicine & Pharmacology, Cardiology Keywords: perioperative goal-directed fluid therapy; haemodynamics monitoring; fluid management; kidney transplantation; major postoperative complications; outcome of surgery
Background: Kidney transplantation is considered the first-choice therapy in ESRD patients. Despite recent improvements in terms of outcomes and graft survival in recipients, postoperative complications still concern health-care providers involved in the management of those patients. Particularly challenging are cardiovascular complications. Perioperative goal-directed fluid-therapy (PGDT) and hemodynamic optimization are widely used in high-risk surgical patients, and are associated with a significant reduction in postoperative complication rates and length of stay (LOS). The aim of this work is to compare the effects of perioperative goal-directed therapy (PGDT) with conventional fluid therapy (CFT), and to determine whether there are any differences in major postoperative complications rates and delayed graft function (DGF) outcomes. Methods: Prospective study with historical controls. Two groups, a PGDT- and a CFT- group were used: the stroke volume (SV) optimization protocol was applied in PGDT group throughout the procedure. Conventional fluid therapy with fluids titration at a central venous pressure (CVP) 8-12 mmHg and mean arterial pressure (MAP) >80mmHg was applied to the control-group. Postoperative data collection including vital signs, weight, urinary output, serum creatinine, blood urea nitrogen, serum potassium, and assessement of volemic status and the signs and symptoms of major postoperative complications occurred at 24h, 72h, 7 days and 30 days after transplantation. Results: Among the 66 patients enrolled, 33 were in each group and both groups had similar physical characteristics. Good fuctional recovery was evident in the 94% of patients. The statistical analysis has showed a difference in postoperative complications as follows: significant reduction of cardiovascular complications, DGF episodes (p<0.05) and surgical complications (p<0.01). There were no significant differences in pulmonary or other complication. Conclusions: PGDT and SV optimization effectively influenced the rate of major postoperative complications, reducing the overall morbidity and thus the mortality in patients receiving kidney transplantation.
Microclimatic Effects on the Preservation of Finds in the Visitor Centre of the Archaelological Site 1a Imperial Palace Sirmium
Aleksandra Ugrinović, Budimir Sudimac, Željko Savković
Subject: Engineering, Other Keywords: protective structures; microclimatic monitoring; microbiological deterioration of architectural finds; Archaeological site 1a Imperial Palace Sirmium
Online: 8 September 2021 (11:24:50 CEST)
For the purpose of this paper, the actual air temperature and air humidity values were monitored in the Visitor Centre of the Archaeological site 1a Imperial Palace Sirmium, designated cultural heritage of exceptional importance. The contamination level of archaeological finds in the site was microbiologically analysed. The findings showed that during the phase of microclimatic monitoring (February–April 2021), air humidity was almost constantly above the levels set by standards and recommendations for museum collections (&gt;60%). The highest levels of air humidity, amounting to 93%, were recorded in February, with daily oscillations of up to 30%; the lowest recorded temperature was 0.3°C, with the maximum daily oscillations of 6°C. Microbiological analysis revealed great diversity in the deterioration level of the finds, which can be attributed to the time lapse between the last conservation and the present. The comparative analysis of microclimatic monitoring and microbiological analysis results identified high levels of relative air humidity as the dominant factor in the increased microbiological contamination of the finds. The findings also pointed to the necessity of continuous microclimatic monitoring during the actual usage of the facility in order to provide the sustainable display and preservation of the finds on the premises.
Inhomogeneous Poisson Point Process for Species Distribution Models: Relative Performance of Methods Accounting for Sampling Bias and Imperfect Detection
Yannick MUGUMAARHAHAMA, Adandé Belarmain FANDOHAN, Arsene Ciza MUSHAGALUSA, Idelphonse Akoeugnigan SODE, Romain GLELE KAKAÏ
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: Integrated Species distribution models; Maximum likelihood; Point-counts; Presence-only data; Site-Occupancy; species abundance
Species distribution models have become tools of great importance in ecology since the advanced knowledge of suitable habitat of species is needed in the process of the world's biodiversity conservation. Models that use presence-only data are of great interests and are widely used in ecology due to their easy access. However, these models do not estimate accurately the true spatial species distribution based solely on presence-only data since they do not account for biases induced by the sampling techniques used and imperfect detection. To address this gap, Hierarchical integrated models have been recently introduced. Through this study, we assessed the relative performance of these new SDMs models using simulated data. The performance of the models was tested by comparing the estimates of parameters of the distribution models they provide with parameters used to simulate the distribution of the virtual species. The best model was the one whose estimates were close to the true distribution parameters of the virtual species. Results showed that analyzing Presence-only data in conjunction with Point-counts data through the Dorazio's Hierarchical model produced estimates of the coe cients of the species intensity models with high precision and less bias while the Koshkina integrated model showed poor performance. Site-occupancy data, being not informative of species abundance, did not allow reducing biases in Presence-only data. The Dorazio's Hierarchical model produced estimates with high precision even with low detection probability. We have also found that the species rarity tends to in ate the variability of the models' estimates making modelling abundant species to be more accurate than modelling less abundant species. Hence, to model the species distribution with high precision based on Presence-only data, additional Point-counts data are required to account for sampling bias and imperfect detection.
Label-Free Biosensors Based Onto Monolithically Integrated Onto Silicon Optical Transducers
Michailia Angelopoulou, Sotirios Kakabakos, Panagiota Petrou
Subject: Engineering, Biomedical & Chemical Engineering Keywords: integrated optical sensors; monolithic integration; broad-band interferometers; label-free; multiplexed detection; on-site determinations
The article reviews the current status of label-free integrated optical sensors focusing on the evolution over the years of their analytical performance. At first a short introduction to the evanescent wave optics is provided followed by detailed description of the main categories of label-free optical sensors including sensors based on surface plasmon resonance (SPR), grating coupler, photonic crystals, ring resonators and interferometric transducers. After a short reference to SPR techniques, including localized SPR, integrated optical sensors i.e., grating-couplers, interferometers, photonic crystals, microring resonators are reviewed. For each type of sensor, the detection principle is first provided followed by description of the different transducer configurations so far developed and their performance as biosensors. Finally, a short discussion about the current limitations and future perspectives of integrated label-free biosensors optical sensors is provided
An on-site, ultra-sensitive, quantitative sensing method for the determination of total aflatoxin in peanut and rice based on quantum dot nanobeads strip
Suiyan Ouyang, Zhaowei Zhang, Ting He, Peiwu Li, Qi Zhang, Xiaomei Chen, Du Wang, Hui Li, Xiaoqian Tang, Wen Zhang
Subject: Chemistry, Food Chemistry Keywords: total aflatoxin; quantum dot nanobead; test strip; on-site; peanut and rice; agro-food safety
An on-site, ultra-sensitive, and quantitative sensing method was developed based on quantum dot nanobeads (QDNBs) and test strip for the determination of total aflatoxins (AFTs) in rice and peanut. The monoclonal antibody against AFT (mAbAFT) was home-made and labeled with QDNB. After the pre-coating of the AFT antigen on the test line (T line), the competitive immunoreactions were conducted between AFT and AFT antigen on the T line with QDNBs-mAbAFT. Under optimal conditions, this approach allowed a rapid response towards AFT with a considerable sensitivity of 1.4 pg/mL and 2.9 pg/mL in rice and peanut matrices, respectively. The put-in and put-out duration were within 10 min. The recoveries for AFT in rice and peanut samples matrices were recorded from 86.25–118.0% with the relative deviations (RSD) below 12%. The assay was further validated via the comparison between this QDNB strip and the conventional HPLC method using spiked samples. Thus, the design provided a potential alternative for on-site, ultra-sensitive, and quantitative sensing of AFT that could also be expanded to other chemical contaminants for food safety.
Do the Flexible Employment Arrangements Increase Job Satisfaction and Employee Loyalty? Evidence from Bayesian Networks and Instrumental Variables
Eleftherios Giovanis
Subject: Social Sciences, Econometrics & Statistics Keywords: Bayesian networks; directed acyclic graphs; employee loyalty; employment arrangements; flexi-time; job satisfaction; teleworking; workplace employment relations survey
This study explores the relationship between job satisfaction, employee loyalty and two types of flexible employment arrangements; teleworking and flexi-time. The analysis relies on data derived by the Workplace Employee Relations Survey (WERS) in 2004 and 2011. A propensity score matching and least squares regressions are applied. Furthermore, Bayesian Networks (BN) and Directed Acyclic Graphs (DAGs) are employed in order to confirm the causality between employment types explored and the outcomes of interest. Finally, an instrumental variables (IV) approach based on the BN framework is proposed and applied in this study. The results support that there is a positive causal effect from these employment arrangements on job satisfaction and employee loyalty.
Preprint BRIEF REPORT | doi:10.20944/preprints202110.0080.v2
SARS-CoV-2 and MERS-CoV Share the Furin Site CGG-CGG Genetic Footprint
Antonio R. Romeu
Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; MERS-CoV; arginine dimer; polybasic furin cleavage site; aginine codon; Markov model; bioinformatics
The SARS-CoV-2 polybasic furin cleavage site is still a missing link. Remarkably, the two arginine residues of this protease recognition site are encoded by the CGG codon, which is rare in Betacoronavirus. However, the arginine pair is common at viral furin cleavage sites, but are not CGG-CGG encoded. The question is: Is this genetic footprint unique to the SARS-CoV-2? To address the issue, using Perl scripts, here I dissect in detail the NCBI Virus database in order to report the arginine dimers of the Betacoronavirus proteins. The main result reveals that a group of Middle East respiratory syndrome-related coronavirus (MERS-CoV) (isolates: camel/Nigeria/NVx/2016, host: Camelus dromedarius) also have the CGG-CGG arginine pair in the spike protein polybasic furin cleavage region. In addition, CGG-CGG encoded arginine pairs were found in the orf1ab polyprotein from HKU9 and HKU14 Betacoronavirus, as well as, in the nucleocapsid phosphoprotein from few SARS-CoV-2 isolates. To quantify the probability of finding the arginine CGG-CGG codon pair in Betacoronavirus, the likelihood ratio (LR) and a Markov model were defined. In conclusion, it is highly unlikely to find this genetic marker in betacoronaviruses wildlife, but they are there. Collectively, results shed light on recombination as origin of the virus CGG-CGG arginine pair in the S1/S2 cleavage site.
Transpositional Recombination and Site-Specific Recombination May Be Initiated by Copy Choice during DNA Synthesis Rather Than Break/Join Mechanism
Lei Jia, Jingyun Li
Subject: Life Sciences, Cell & Developmental Biology Keywords: transpositional recombination; site-specific recombination; meiotic recombination; the intertwinement model; branched structure; Holliday junction; copy choice
Types of DNA recombination include homologous recombination and nonhomologous recombination. Homologous DNA recombination is a general term that includes exchange of information between chromatids: (reciprocal) crossing-over, gene conversion, and post-meiotic segregation. Gene conversion is now thought to be a type of non-Mendelian segregation of heterozygous markers near the recombination initiation site. Thus, it includes both gene conversion and post-meiotic segregation previously described. DNA non-HR including transpositional recombination and site-specific recombination. Our understanding of the molecular mechanism by which DNA recombination occurs has significantly increased in the past decades. Currently The synthesis-dependent strand annealing model is now thought to give rise to most or all noncrossovers, with the double-strand-break repair model forming mainly crossovers. The Shapiro model proposed by Dr. J. Shapiro explains the molecular mechanism of transpositional recombination. Site-specific recombination results from another distinct model. We previously proposed a novel theory which can provide a more reasonable and simpler explanation accounting for DNA HR including the 3 classes of recombinogenic events described above. In the new supplementedly molecular model, DNA meiotic recombination can be initiated by a copy choice mechanism, that is, copying part of 1 single-stranded DNA template, followed by DNA polymerase switching to another single-stranded DNA template, and then resuming the following DNA synthesis along the new template. The current review suggests that transpositional recombination and site-specific recombination should be initiated by copy choice during DNA synthesis rather than break/join mechanism. The work indicates that review of DNA nonhomologous recombination are very necessary. The novel theory would challenge earlier models accounting for transpositional recombination and site-specific recombination and would be critical to the understanding of the mechanisms. We hope copy choice initiating DNA nonhomologous recombination will be one of the concepts that are explored. Proper and specific experiments are required to reconstruct the detailed mechanism described here.
Online Meeting Challenges in a Research Group Resulting from COVID-19 Limitations
Subject: Social Sciences, Education Studies Keywords: academic meetings; video conferencing; Zoom; private Facebook group; narrative research; COVID-19; self-directed learning; team mindfulness; democratic meetings
The online learning necessitated by COVID-19 social distancing limitations has resulted in the utilization of hybrid online formats focused on maintaining visual contact among learners and teachers. The preferred option of video conferencing for academic meetings has become that of Zoom. The needs of one voluntary, democratic, self-reflective university research group—grounded in responses to writing prompts—differed in learning focus. Demanding a safe space to encourage and record both self-reflection and creative questioning of other participants, the private Facebook group was chosen over video conferencing to maintain the concentration on group members' written responses rather than how they saw themselves (and thought others saw them) on screen. A narrative research model initiated in 2015, the 2020/21 interaction of the group in the year's worth of Facebook entries, and the yearend feedback received from group participants, will be compared with previous years when the weekly group met in-person. The results in relation to COVID-19 limitations indicate that an important aspect of self-directed learning related to trust that comes from team mindfulness is lost when face-to-face interaction is eliminated regarding the democratic nature of these meetings. With online meetings the new standard, maintaining trust requires improvements to online virtual meeting spaces.
Cancer clinic redesign: Opportunities for Resource Optimization
Michael Fung-Kee-Fung, Rachel S. Ozer, Bill Davies, Stephanie Pick, Kate Duke, David J. Stewart, M. Neil Reaume, Marcus Ward, Katelyn Balchin, Robert M. MacRae, Shannon Nelson, Julie Renaud, Dennis Garvin, Suzanne Madore, Jason R. Pantarotto
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: learning health system; ambulatory clinic; block schedule; disease site teams; interdisciplinary care; cancer operations; oncology value stream
Abstract: Ambulatory cancer centers face fluctuating patient demand and deploy specialized personnel who have variable availability. This undermines operational stability through misa-lignment of resources to patient needs, resulting in overscheduled clinics, budget deficits, and wait times exceeding provincial targets. We describe deployment of a Learning Health System framework for operational improvements within the entire ambulatory center. Known methods of value stream mapping, operations research and statistical process control were applied to achieve organizational high performance that is data-informed, agile and adaptive. We transitioned from a fixed template model by individual physician to a caseload management by disease site model that is realigned quarterly. We adapted a block schedule model for the ambulatory oncology clinic to align the regional demand for specialized services with optimized human and physical resources. We demonstrated improved utilization of clinical space, increased weekly consistency and im-proved distribution of activity across the workweek. Increased value, represented as the ratio of monthly encounters per nursing worked hours, and increased percentage of services delivered by full-time nurses were benefits realized in our cancer system. The creation of a data-informed demand capacity model enables application of predictive analytics and business intelligence tools that will further enhance clinical responsiveness..
Changes in Risk in Medium Business Plants Following Revision of the Korean Chemical Accident Prevention System, Focusing on Plating and Paint Manufacturing Industries
Hyo Eun Lee, Min-Gyu Kim, Seok J. Yoon, Da-An Huh, Kyong Whan Moon
Subject: Chemistry, Chemical Engineering Keywords: Preparation of Off-Site Consequence Analyses; Chemicals Control Act; Risk Assessment; Paint Manufacturing Plant; Plating Industry Plant
: Chemical accidents can occur anywhere. The need for chemical management in Korea was realized following the 2012 Gumi hydrofluoric acid accident in 2012. The Chemicals Control Act was enacted in 2015. This system evaluates the risks (high, medium, low) and consequent safety management at all plants that handle hazardous chemical substances. However, the system was criticized as excessive when most plants were designated high-risk without considering their size. Thus, laboratories and hospitals handling very small quantities were subject to regulation. Accordingly, in 2021 Korea revised the system to include off-site consequence analyses and a Korean-style risk analysis. Plants handling very small quantities, such as laboratories and hospitals, were exempt from regulation. In this study, plating and paint manufacturing companies, which were classified as high-risk in the previous system, even though they were medium-size business plants, were re-evaluated as low-risk plants. In the Korean-style risk analysis, it is possible to see at a glance what is lacking in the plants, such as cooperation between local residents and local governments and the construction of safety facilities according to the type of accident scenario. The revised system is a reasonable regulation for medium business plants.
Highly Graphitized Fe-N-C Electrocatalysts Prepared from Chitosan Hydrogel Frameworks
Giorgia Daniel, Tomasz Kosmala, Federico Brombin, Marco Mazzucato, Alessandro Facchin, Maria Chiara Dalconi, Denis Badocco, Paolo Pastore, Gaetano Granozzi, Christian Durante
Subject: Chemistry, Analytical Chemistry Keywords: ORR; PGM-free; iron; chitosan; biomass, acid electrolyte; iron-nitrogen-doped carbon; graphitization, site density, Fe-Nx
The development of platinum group metal-free (PGM-free) electrocatalysts derived from cheap and environmentally friendly biomasses for oxygen reduction reaction (ORR) is a topic of relevant interest, particularly from the point of view of sustainability. Fe-nitrogen-doped carbon materials (Fe-N-C) have attracted particular interest as alternative to Pt-based materials, due to the high activity and selectivity of Fe-Nx active sites, the high availability and good tolerance to poisoning. Recently, many studies focused on developing synthetic strategies, which could transform N-containing biomasses into N-doped carbons. In this paper chitosan was employed as a suitable N-containing biomass for preparing Fe-N-C catalyst in virtue of its high N content (7.1%) and unique chemical structure. Moreover, the major application of chitosan is based on its ability to strongly coordinate metal ions, a precondition for the formation of Fe-Nx active sites. The synthesis of Fe-N-C consists in a double step thermochemical conversion of a dried chitosan hydrogel. In acidic aqueous solution, the preparation of physical cross-linked hydrogel allows to obtain sophisticated organization, which assure an optimal mesoporosity before and after the pyrolysis. After the second thermal treatment at 900 °C, a highly graphitized material was obtained, which has been fully characterized in term of textural, morphological and chemical properties. RRDE technique was used for understanding the activity and the selectivity of the material versus the ORR in 0.5 M H2SO4 electrolyte. Special attention was put in the determination of the active site density according to nitrite electrochemical reduction measurements. It was clearly established that the catalytic activity expressed as half wave potential linearly scales with the number of Fe-Nx sites. It was also established that the addition of the iron precursor after the first pyrolysis step leads to an increased activity because of both an increased number of active sites and of a hierarchical structure, which improves the access to active sites. At the same time, the increased graphitization degree, and a reduced density of pyrrolic nitrogen groups are helpful to increase the selectivity toward the 4e- ORR pathway.
Working Paper REVIEW
Antivirals against the Chikungunya Virus
Verena Battisti, Ernst Urban, Thierry Langer
Subject: Medicine & Pharmacology, Other Keywords: Chikungunya virus; alphavirus; antiviral therapy; direct-acting antivirals; host-directed antivirals; in silico screening; in vivo validation; antiviral drug development
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that has re-emerged in recent decades, causing large-scale epidemics in many parts of the world. CHIKV infection leads to a febrile disease known as chikungunya fever (CHIKF), which is characterised by severe joint pain and myalgia. As many patients develop a painful chronic stage and neither antiviral drugs nor vaccines are available, the development of a potent CHIKV inhibiting drug is crucial for CHIKF treatment. A comprehensive summary of current antiviral research and development of small-molecule inhibitor against CHIKV is presented in this review. We highlight different approaches used for the identification of such compounds and further discuss the identification and application of promising viral and host targets.
Preprint DATA DESCRIPTOR | doi:10.20944/preprints202108.0295.v3
Sustainable Building Plan-Design, Construction, Performance, and Renovation Criteria
Puthearath Chan, Khemony Khoeng, Hang Kheang Ung, Teksim Tang, Kimsong Eung, Suysoklin Uth, Sovanrany Meng, Leng Sun, Sereyphut Em, Hon Toum, Oudomkitya Phok, Ratha Sry, Limdavid Mok, Rothvisal Lo, Chanmakara Vat, Sunleng Phay, Otdom Hor, Chey Vithyea Cheath, Mengheang Lim, Pichbormey An, Mardy Sareun, Sothet Sot, Sievminh Va, Yiheang Chea, Molly Ratana Piseth
Subject: Engineering, Other Keywords: sustainability; sustainable building criteria; sustainable building planning and design; sustainable site selection; sustainable construction; performance and renovation criteria.
Published data or available literature on sustainable building plan-design, construction, performance, and renovation criteria have covered some stages or some parts of each stage. These data usually have been published partially in many different papers―there have not been any papers that published these data together. Hence, this paper aims to collectively review these data and publish them together. The collection and review of these data were carried out by our twenty-five team members who specialized in sustainable urban, architectural, and civil engineering and construction management. The gathered and reviewed outputs were combined and validated based on a general group consensus. This consensus decision-making proceeded through two major group meetings with several follow-up meetings. The first major meeting was to combine and improve the gathered reviewed sustainable building criteria for Cambodia. The second major meeting was to validate the improved reviewed sustainable building criteria for Cambodia. The several follow-up meetings were to discuss the relevance and importance of the validated data "criteria and their classifications and descriptions" in all stages and more focused on their importance and applicability to Cambodia. The collective reviewed data in this paper would be useful to researchers in the fields. They could also be useful collective knowledge and information for policymakers from governmental agencies and development partners, particularly for sustainable building and construction companies.
The SARS-CoV-2 Spike Protein D614G Mutation Shows Increasing Dominance and May Confer a Structural Advantage to the Furin Cleavage Domain
Leyan Tang, Allison Schulkins, Chun-Nan Chen, Kurt Deshayes, John S. Kenney
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; spike protein; D614G mutation; genotype distribution; furin cleavage site; secondary structure; sequence analysis; homology modeling
We analyzed the SARS-CoV-2 spike (S) protein amino acid sequence extracted from 11,542 viral genomic sequences submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database through April 27, 2020. Consistent with prior reports, we found a major S protein mutation, D614 to G614, that was represented in 56% of all the analyzed sequences. All other mutations combined were less than 10%. After parsing the data geographically, we found most of the Chinese patient samples showed D614 (97%). By contrast, most patient samples in many European countries showed G614 (51 to 88%). In the United States, the genotypic distribution in California and Washington was similar to Asian countries, while the distribution in other US states was comparable to Europe. We observed a dramatic increase in the frequency of G614 over time in multiple regions, surpassing D614 when both were present, suggesting G614 S protein virus outcompetes D614 S protein virus. To gain insight into the consequences of the D614G mutation, homology modeling using a multi-template threading mechanism with ab initio structural refinement was performed for a region of the S protein (S591 to N710) spanning the D614G mutation and the S1 furin cleavage site. Molecular models of this region containing D614 or G614 revealed a major difference in secondary structure at the furin domain (RRARS, R682 to S686). The D614 model predicted a random coil structure in the furin domain whereas the G614 model predicted an alpha helix. Critical residues in the cleavage domain of G614 model were found to better align with the PDB structure of a furin inhibitor. Thus, homology modeling studies suggest a potential mechanism whereby the D614G mutation may confer a competitive advantage at the furin binding domain that may contribute to the rise of the D614G SARS-CoV-2 mutant.
Assessment of Enzyme Inhibition: A Review with Examples from the Development of Monoamine Oxidase and Cholinesterase Inhibitory Drugs
Rona R. Ramsay, Keith F. Tipton
Subject: Chemistry, Medicinal Chemistry Keywords: affective disorders; alzheimer's disease; l-Deprenyl (Selegiline); donepezil; galantamine; value; inhibitor constant; mechanism-based inhibition; multitarget-directed ligand (MTDL); rasagiline; rivastigmine
The actions of many drugs involve enzyme inhibition. This is exemplified by the inhibitors of monoamine oxidases (MAO) and the cholinsterases (ChE) that have been used for several pharmacological purposes. This review describes key principles and approaches for the reliable determination of enzyme activities and inhibition as well as some of the methods that are in current use for such studies with these two enzymes. Their applicability and potential pitfalls arising from their inappropriate use are discussed. Since inhibitor potency is frequently assessed in terms of the quantity necessary to give 50% inhibition (the IC50 value), the relationships between this and the mode of inhibition is also considered, in terms of the misleading information that it may provide. Incorporation of more than one functionality into the same molecule to give a multi-target-directed ligands (MTDLs) requires careful assessment to ensure that the specific target effects are not significantly altered and that the kinetic behaviour remains as favourable with the MTDL as it does with the individual components. Such factors will be considered in terms of recently developed MTDLs that combine MAO and ChE inhibitory functions.
Performance Assessment for Short-Term Water Demand Forecasting Models at an End-Use Level in Korea
Kang Min Koo, Kuk Heon Han, Kyung Soo Jun, Gyumin Lee, Jung Sik Kim, Kyung Taek Yum
Subject: Engineering, Automotive Engineering Keywords: smart water grid; advanced metering infrastructure; short-term water demand forecasting; end-use level; on-site sodium hypochlorite generator
It is crucial to forecast the water demand accurately for supplying water efficiently and stably in a water supply system. In particular, accurately forecasting short-term water demand helps in saving energy and reducing operating costs. With the introduction of the Smart Water Grid (SWG) in a water supply system, the amount of water consumption is obtained in real time through an advanced metering infrastructure (AMI) sensor, which can be used for forecasting the short-term water demand. The models widely used for water demand forecasting include the autoregressive integrated moving average, radial basis function-artificial neural network, quantitative multi-model predictor plus, and long short-term memory. However, there is a lack of research on assessing the performance of models and forecasting the short-term water demand by applying the data on the amount of water consumption by purpose and the pipe diameter of an end-use level of the SWG demonstration plant in each demand forecasting model. Therefore, in this study, the short-term water demand was forecasted for each model using the data collected from the AMI, and the performance of each model was assessed. The Smart Water Grid Research Group installed ultrasonic-wave-type AMI sensors in the block 112 located in YeongJong Island, Incheon, and the actual data used for operating the SWG demonstration plant were adopted. The performance of the model was assessed by using the residual, root mean square error (RMSE), normalized root mean square error (NRMSE), Nash–Sutcliffe efficiency (NSE), and Pearson correlation coefficient (PCC) as indices. The water demand forecast was slightly underestimated in models that employed the assessment results based on the RMSE and NRMSE. Furthermore, the forecasting accuracy was low for the NSE due to a large number of negative values; the correlation between the observed and forecasted values of the PCC was not high, and it was difficult to forecast the peak amount of water consumption. Therefore, as the short-term water demand forecasting models using only time and the amount of water consumption have limitations in reflecting the characteristics of consumers, a water supply system can be managed more precisely if other factors (weather, customer behavior, etc.) influencing the water demand are applied.
A Conceptual Design Approach for Archeological Structures, a Challenging Issue Between Innovation and Conservation: A Studied Case in the Ancient Pompeii
Vincenzo Calvanese, Alessandra Zambrano
Subject: Engineering, Automotive Engineering Keywords: cultural heritage; masonry rehabilitation; seismic device; steel structure; basalt fiber; grout injections; archeological site; rubber-bearing; non-destructive testing
The preservation of the authenticity of a building artefact is a responsible practice. On the other side, the need to save the building artefact from the natural and anthropic degradation, to ensure the structural reliability to the different actions, to define an efficient maintenance program are big challenges, that involves the cooperation of several professionals, responsible use of innovative techniques and materials that are nowadays available. This paper focuses on a specific design approach for the rehabilitation works of ancient constructions in archaeological sites. The proposed conceptual design approach implies different steps that allow the optimization of the design at an increasing level of knowledge on the existing structures and their materials. The design procedure on historical constructions generally includes the following steps: the collection of data, the structural identification, hazard, and vulnerability analysis, damage and risk analysis, a cost-benefit analysis, so only at the end of the process, the final design is achieved. In the archaeological area, some important design aspects cannot be defined before the execution work phase, since some elements could be revealed and identified during work execution, as a consequence, the final design has been often optimized after all this information has been acquired. A studied case in the archaeological site of Pompeii is herein presented to prove the efficiency of the proposed approach.
Functional Analysis of the Acinetobacter baumannii XerC and XerD Site-Specific Recombinases: Potential Role in Dissemination of Resistance Genes
David L. Lin, German M. Traglia, Rachel Baker, David J. Sherratt, Maria S. Ramirez, Marcelo E. Tolmasky
Subject: Biology, Other Keywords: site-specific recombination; carbapenemase; ESKAPE; Acinetobacter; plasmid; Xer; dif; pdif; Re27; gene transfer; gene dissemination; horizontal transfer; horizontal dissemination
Modules composed of a resistance gene flanked by Xer site-specific recombination sites, the vast majority of which were found in Acinetobacter baumannii, are thought to behave as elements that facilitate horizontal dissemination. The A. baumannii xerC and xerD genes were cloned, and the recombinant clones used to complement the cognate Escherichia coli mutants. The complemented strains supported resolution of plasmid dimers, and, as is the case with E. coli and Klebsiella pneumoniae plasmids, the activity was enhanced when cells were growing in low osmolarity growth medium. Binding experiments showed that partially purified A. baumannii XerC and XerD proteins (XerCAb and XerDAb) bound synthetic Xer site-specific recombination sites, some of them with a nucleotide sequence deduced from existing A. baumannii plasmids. Incubation with suicide substrates resulted in covalent attachment of DNA to a recombinase, probably XerCAb, indicating that the first step in the recombination reaction took place. The results described show that XerCAb and XerDAb are functional proteins and support the hypothesis that they participate in horizontal dissemination of resistant genes among bacteria.
Molecular Analyses of Over Hundred Sixty Clinical Isolates of SARS-CoV-2: Insights on Likely Origin, Evolution and Spread, and Possible Intervention
Salma Jamal, Jasdeep Singh, Javaid Ahmad Sheikh, Hina Singh, Mohd Khubaib, Sunil Kohli, Ulrich Dobrindt, Syed Asad Rahman, Nasreen Zafar Ehtesham, Seyed Ehtesham Hasnain
Subject: Life Sciences, Virology Keywords: envelope protein; furin cleavage site; hydrophobic aggregation and rapid transmission; immediate ancestor; pangolins coronaviruses; SARS-CoV-2; spike protein
We are witnessing the severe third outbreak mediated by coronaviruses affecting global public health with unprecedented economic consequences. A better understanding of its phylogenetics, exploration of sequence features and mutational changes could unveil its genealogy to gain insights into the mechanism of transmission and development of possible interventions. Our comparative genomic analyses of >160 isolates of SARS-CoV-2 reveal phylogenetic kinship with other coronaviruses and emergence of evolutionary divergence in clinical isolates. t-SNE-based clustering revealed different clades but no continent specific clusters. Amino acid substitutions at RBD of spike protein provide possible reasons for rapid transmission. Few proteins specific to SARS-CoV-2 were identified which could have implications as therapeutic targets and diagnostic biomarkers. Virtual screening identified repurposed drugs, known nutraceuticals, for specific interventions. These phylogenetic observations reveal the ancestry and computational studies reveal the emergency measures to interject this emerging pathogen that pose threat to whole of mankind.
Potassium Supplying Capacity of Diverse Soils and K-Use Efficiency of Maize in South Asia
Saiful Islam, Jagadish Timsina, Muhammad Salim, Kaushik Majumdar, Mahesh K Gathala
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Site-specific K management, Soil K supply, Maize yield response to K, Maize Crop Manager, Nutrient Expert for Maize.
Increased nutrient withdrawal by rapidly expanding intensive cropping systems, in combination with imbalanced fertilization, is leading to potassium (K) depletion from agricultural soils in Asia. There is an urgent need to better understand the soil K-supplying capacity and K-use efficiency of crops to address this issue. Maize is increasingly being grown in rice-based systems in South Asia, particularly in Bangladesh and North East India. The high nutrient extraction, especially K, however, causes concerns for the sustainability of maize production systems in the region. The present study was designed to estimate, through a plant-based method, the magnitude, and variation in K-supplying capacity of a range of soils from the maize-growing areas and the K-use efficiency of maize in Bangladesh. Eighteen diverse soils were collected from several upazillas (or sub-districts) under 11 agro-ecological zones to examine their K-supplying capacity from the soil reserves and from K fertilization (@ 100 mg K kg-1 soil) for successive seven maize crops grown up to V10-V12 in pots inside a net house. A validation field experiment was conducted with five levels of K (0, 40, 80, 120 and 160 kg ha-1) and two fertilizer recommendations based on "Nutrient Expert for Maize-NEM" and "Maize Crop Manager-MCM" decision support tools (DSSs) in 12 farmers' fields in Rangpur, Rajshahi and Comilla districts in Bangladesh. Grain yield and yield attributes of maize responded significantly (P < 0.001) to K fertilizer, with grain yield increase from 18 to 79% over control in all locations. Total K uptake by plants not receiving K fertilizer, considered as potential K-supplying capacity of the soil in the pot experiment, followed the order: Modhukhali >Mithapukur >Rangpur Sadar >Dinajpur Sadar >Jhinaidah Sadar >Gangachara >Binerpota >Tarash >Gopalpur >Daudkandi >Paba >Modhupur >Nawabganj Sadar >Shibganj >Birganj >Godagari >Barura >Durgapur. Likewise in the validation field experiment, the K-supplying capacity of soils was 83.5, 60.5 and 57.2 kg ha-1 in Rangpur, Rajshahi, and Comilla, respectively. Further, the order of K-supplying capacity for three sites was similar to the results from pot study confirming the applicability of results to other soils and maize-growing areas in Bangladesh and similar soils and areas across South Asia. Based on the results from pot and field experiments, we conclude that the site-specific K management using the fertilizer DSSs can be the better and more efficient K management strategy for maize.
Validation of Sustainable Building Planning and Design Criteria for Cambodia: A Delphi Study
Puthearath Chan
Subject: Engineering, Other Keywords: Delphi methods; consensus decision analysis; building sustainability plan and design; Cambodia urban buildings; sustainable site selection; sustainable building shape design
Buildings can generate heats which are mostly generated from the machinery using inside the buildings, and these heats generally released to the atmosphere. Buildings can also block the wind flow by their canopies and trap the heat by using low albedo materials. These causes pointedly contribute to urban heat island and greenhouse effects. Likewise, urban development and building construction in Cambodia are growing rapidly. The construction has been recognized as a key development sector while thousands of buildings are being built and have been operated in the main cities. However, those buildings mostly have not been considered to incorporate sustainability concepts while the major final energy consumers in the country are buildings. The buildings' energy consumption is also projected to increase more than double until 2040. Hence, sustainable building promotion in Cambodia is necessary, and sustainable building criteria are completely required. This research aims to find out significant sustainable building criteria for Cambodia and focused on planning and design criteria because having proper planning and design is a smart start leading to achieving building sustainability in all stages. This research used the Delphi methods to validate the relevant sustainable building criteria available in the literature and then select the significant ones for Cambodia based on the Delphi consensus. The results showed that ninety-nine consensus planning and design criteria were found to be significant for sustainable buildings in Cambodia.
Analysis of Default Mode Network in Social Anxiety Disorder: EEG Resting-State Effective Connectivity Study
Abdulhakim Al-Ezzi, Nidal Kamel, Ibrahima Faye, Esther Gunaseli
Subject: Engineering, Automotive Engineering Keywords: Effective connectivity network, Partial directed coherence (PDC), Social Anxiety Disorder (SAD), Default Mode Network (DMN), Electrophysiological biomarkers (EEG), Resting state network (RSN), Granger
Recent brain imaging findings by using different methods (e.g., fMRI and PET) have suggested that social anxiety disorder (SAD) is correlated with alterations in regional or network-level brain function. However, due to many limitations associated with these methods, such as poor temporal resolution and limited number of samples per second, neuroscientists could not quantify the fast dynamic connectivity of causal information networks in SAD. In this study, SAD-related changes in brain connections within the default mode network (DMN) were investigated using eight electroencephalographic (EEG) regions of interest. Partial directed coherence (PDC) was used to assess the causal influences of DMN regions on each other and indicate the changes in the DMN effective network related to SAD severity. The DMN is a large-scale brain network basically composed of the mesial prefrontal cortex (mPFC), posterior cingulate cortex (PCC)/precuneus, and lateral parietal cortex (LPC). The EEG data were collected from 88 subjects (22 control, 22 mild, 22 moderate, 22 severe) and used to estimate the effective connectivity between DMN regions at different frequency bands: delta (1–3 Hz), theta (4–8 Hz), alpha (8–12 Hz), low beta (13–21 Hz), and high beta (22–30 Hz). Among the healthy control (HC) and the three considered levels of severity of SAD, the results indicated a higher level of causal interactions for the mild and moderate SAD groups than for the severe and HC groups. Between the control and the severe SAD groups, the results indicated a higher level of causal connections for the control throughout all the DMN regions. We found significant increases in the mean PDC in the delta (p = 0.009) and alpha (p = 0.001) bands between the SAD groups. Among the DMN regions, the precuneus exhibited a higher level of causal influence than other regions. Therefore, it was suggested to be a major source hub that contributes to the mental exploration and emotional content of SAD. In contrast to the severe group, HC exhibited higher resting-state connectivity at the mPFC, providing evidence for mPFC dysfunction in the severe SAD group. Furthermore, the total Social Interaction Anxiety Scale (SIAS) was positively correlated with the mean values of the PDC of the severe SAD group, r (22) = 0.576, p = 0.006 and negatively correlated with those of the HC group, r (22) = −0.689, p = 0.001. The reported results may facilitate greater comprehension of the underlying potential SAD neural biomarkers and can be used to characterize possible targets for further medication.
Mscligan- A Structure-Informed Generative Adversarial Model for Multi-Site Statistical Downscaling of Extreme Precipitation -Using Multi-Model Ensemble
Chiranjib Chaudhuri, Colin Robertson
Subject: Earth Sciences, Atmospheric Science Keywords: Multi-site statistical downscaling; Generative Adversarial Network; Combination of Errors; Convolutional Neural Network; Struc-tural Similarity Index; Wasserstein GAN; extreme precipitation
Although the statistical methods of downscaling climate data have progressed significantly, the development of high-resolution precipitation products continues to be a challenge. This is especially true when interest centres on downscaling value over several study sites. In this paper , we report a new downscaling method termed the multi-site Climate Generative Adversarial Network (MSCliGAN), which can simulate annual maximum precipitation to the regional scale during the 1950-2010 period in different cities in Canada by using different AOGCM's from the Coupled Model Inter-Comparison Project 6 (CMIP6) as input. Auxiliary information provided to the downscaling model included topography and land-cover. The downscaling framework uses a convolution encoder-decoder U-net network to create a generative network and a convolution encoder network to create a critic network. An adversarial training strategy is used to train the model. The critic/discriminator used Wasserstein distance as a loss measure and on the other hand the generator is optimized using a summation of content loss on Nash-Shutcliff Model Efficiency (NS), structural loss on structural similarity index (SSIM), and adversarial loss Wasserstein distance. Downscaling results show that downscaling AOGCMs by incorporating topography and land-use/land-cover can produce spatially coherent fields close to observation over multiple-sites. We believe the model has sufficient downscaling potential in data sparse regions where climate change information is often urgently needed.
Rapid on-site Detection of Illicit Drugs in Smuggled Samples with a Portable Electrochemical Device
Marc Parrilla, Amorn Slosse, Robin Van Echelpoel, Noelia Felipe Montiel, Amelia R Langley, Filip Van Durme, Karolien De Wael
Subject: Chemistry, Analytical Chemistry Keywords: Electrochemical sensors; square-wave voltammetry; screen-printed electrodes; electrochemical profiling; illicit drugs; forensic analysis; Raman spectrometer; on-site detection; FTIR spectrometer
Illicit drug consumption is posing critical concerns in our society causing health issues, crime-related activities, and the disruption of border trade. The smuggling of illicit drugs urges the development of new tools for rapid on-site identification in cargos. Current methods used by law enforcement officers rely on presumptive color tests and portable spectroscopic techniques. However, these methods sometimes exhibit inaccurate results due to commonly used cutting agents, the colorful nature of the sample or because the drugs are smuggled (hidden or mixed) in common goods. Interestingly, electrochemical sensors can deal with these specific problems. Herein, an electrochemical device is presented that uses affordable screen-printed electrodes for the electrochemical profiling of illicit drugs by square-wave voltammetry (SWV). The identification of the illicit compound is based on the oxidation potential of the analyte. Hence, a library of electrochemical profiles is built upon the analysis of illicit drugs and common cutting agents. This library allows the design of a tailor-made script that enables the identification of each drug through a user-friendly interface (laptop or mobile phone). Importantly, the electrochemical test is compared by analyzing 48 confiscated samples with other portable devices based on Raman and FTIR spectroscopy as well as a laboratory standard method (i.e. gas chromatography – mass spectrometry). Overall, the electrochemical results obtained through the analysis of different samples from confiscated cargos at an end-user site, present a promising alternative to current methods, offering low-cost and rapid testing in the field.
Indicator Minerals, Pathfinder Elements, and Portable Analytical Instruments in Mineral Exploration Studies
Balaram V., Sawant S. S.
Subject: Earth Sciences, Geochemistry & Petrology Keywords: Portable instruments; indicator minerals; pathfinder elements; core scanners; pXRF; pXRD; pNIR-SWIR spectrometer; μRaman spectrometer; LIBS; mineral exploration; on-site analysis
Until recently, the classic approach to mineral exploration studies is to bring the field samples/drill cores collected during field studies to the laboratory followed by laborious analysis procedures to generate the analytical data. This is very expensive, time consuming and difficult for exploring vast areas. But rapid technological advances in field portable analytical instruments such as portable ultraviolet–visible and near-infrared spectrophotometers, gamma ray spectrometer, pXRF, pXRD, pLIBS, and µRaman spectrometer have changed this scenario completely and increased their on-site applications in mineral exploration studies. These instruments are currently providing direct, rapid, on-site, real-time, non-destructive, cost-effective identification, and determination of target elements, indicator minerals and pathfinder elements in rock, soil, and sediment samples. These portable analytical instruments are currently helping to obtain accurate chemical and mineralogical information directly in field with minimal or no sample preparation, and providing decision-making support during field work as well as during drilling operations in several successful mineral exploration programs. In this article, the developments in these portable devices, and their contributions in the platinum group elements (PGE), rare earth elements (REE), gold, base metals, and lithium exploration studies both on land and on ocean bed have been summarized with examples.
Long-term Results after Autologous Breast Reconstruction with DIEP Versus PAP Flaps based on Quality of Life and Aesthetic Outcome Analysis
Angela Augustin, Evi M. Morandi, Selina Winkelmann, Ines Schoberleitner, Daniel Egle, Magdalena Ritter, Thomas Bauer, Tanja Wachter, Dolores Wolfram
Subject: Medicine & Pharmacology, Other Keywords: breast cancer; mastectomy; autologous breast reconstruction; PAP flap; DIEP flap; donor-site morbidity; quality of life; aesthetic outcome; scar quality; Breast Q
(1) Background: This work aimed to conduct the first comparative study providing long-term data about patient reported outcome measures as well as donor-site scar assessment and aesthetic evaluation of the reconstructed breasts in patients with DIEP versus PAP flap breast reconstruction. (2) Methods: This prospective, single-center, matched cohort study included a total of 36 patients after DIEP and PAP flap breast reconstruction. Evaluation was done using the Breast-Q and POSAS questionnaire as well as the Breast Aesthetic Scale for cosmetic analysis by four plastic surgeons. (3) Results: Post-operative Breast-Q evaluation revealed no significant differences between both patient groups for the categories physical well-being donor-site, physical well-being breast and satisfaction with the breast. Scar evaluation of the donor-site region showed equivalent results for the thigh and the abdomen concerning the overall opinion of patients and observers. There was no significant difference between both methods of reconstruction for all aspects of breast aesthetics. (4) Conclusions: Similar results of donor-site morbidity, scar quality and aesthetic outcome of the breast in both the DIEP and PAP patient group have been demonstrated. Hence, in cases suitable for both types of reconstruction, the decision can be based on factors such as patients' lifestyle, leisure activities and preferences.
Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV) Reduced Virus Fitness in Chickens which is Restored by Reassortment with Highly Pathogenic H5N1 AIV
Marcel Gischke, Reiner Ulrich, Olanrewaju I. Fatola, David Scheibner, Ahmed H. Salaheldin, Beate Crossley, Eva Böttcher-Friebertshäuser, Jutta Veits, Thomas Mettenleiter, El-Sayed Abdelwhab
Subject: Life Sciences, Molecular Biology Keywords: Highly Pathogenic Avian Influenza Virus, Low Pathogenic Avian Influenza Virus, Evolution, Virulence Determinants, non-H5/H7, Cleavage Site, Chicken-to-Chicken Transmission, Virulence, Protease
Highly pathogenic (HP) avian influenza viruses (AIVs) are naturally restricted to H5 and H7 subtypes with a polybasic cleavage site (CS) in the hemagglutinin (HA) and any AIV with an intravenous pathogenicity index (IVPI) ≥1.2. Only few non-H5/H7 viruses fulfill the criteria of HPAIVs; nevertheless, it remains unknown why these viruses did not spread in domestic birds. In 2012, a unique H4N2 virus with a polybasic CS 322PEKRRTR/G329 was isolated from quails in California which, however, was avirulent in chickens. This is the only known non-H5/H7 virus with four basic amino acids in the HACS. Here, we investigated the virulence of this virus in chickens after expansion of the polybasic CS by substitution of T327R (322PEKRRRR/G329) or T327K (322PEKRRKR/G329) with or without reassortment with HPAIVs H5N1 and H7N7. The impact of single mutations or reassortment on virus fitness in vitro and in vivo was studied. Efficient cell culture replication of T327R/K carrying H4N2 viruses increased by trypsin, particularly in MDCK cells, and reassortment with HPAIV H5N1. Likewise, replication, virus excretion and bird-to-bird transmission of H4N2 was remarkably compromised by the CS mutations, but restored after reassortment with HPAIV H5N1, although not with HPAIV H7N7. Viruses carrying the H4-HA with or without R327 or K327 mutations and the other gene segments from HPAIV H5N1 exhibited high virulence and efficient transmission in chickens. Together, increasing the number of basic amino acids in the H4N2 HACS was detrimental for viral fitness particularly in vivo but compensated by reassortment with HPAIV H5N1. This may explain the absence of non-H5/H7 HPAIVs in poultry.
Thin-Layer Chromatography (TLC) in Screening of Botanicals – its Versatile Potential and Selected Applications
Teresa Kowalska, Mieczysław Sajewicz
Subject: Chemistry, Analytical Chemistry Keywords: TLC screening of plants; TLC screening of psychoactive plants; TLC-direct bioautography; effect directed detection; chemotaxonomy of plants; quality control of medicinal plants; quality control of alimentary products; quality control of cosmetic products
The aim of this paper is to present a comprehensive overview of the main aims and scopes in screening of botanicals, a task which thin-layer chromatography (TLC) is on an everyday basis confronted with and engaged in. Stunning omnipresence of this modest analytical technique (both in its standard format (TLC) and the high-performance one (HPTLC), either hyphenated or not) for many analysts might at a first glance appear chaotic and random, with an auxiliary rather than leading role in research, and not capable of issuing meaningful final statements. Based on these reflections, our purpose is not to present a general review paper on TLC in screening of botanicals, but a blueprint rather (illustrated with a selection of practical examples), which highlights a sovereign and important role of TLC in accomplishing the following analytical tasks: (i) solving puzzles related to chemotaxonomy of plants, (ii) screening a wide spectrum of biological properties of plants, (iii) providing quality control of herbal medicines and alimentary and cosmetic products of biological origin, and (iv) tracing psychoactive plants under forensic surveillance.