Input: Claim: Vaccination programs have significantly reduced the global incidence of diseases like measles and polio. [SEP] Text: In addition, one study mentioned the resistance of participants living in Pakistan due to the lack of basic health facilities in their communities [20]. This lack of infrastructure was a primary cause of mistrust, and, consequently, resistance to OPV. Moreover, this study also discussed refusal of intervention uptake as a means of protest against the government in order to address their political and economic problems. One study described increased trust in government health services and thus acceptance of vaccination when improvements were made to these services across seven countries (and Angola) [23]. A frontline worker from this study stated that “one manifestation of this trust [in government health services] was acceptance of vaccination” (p. 15) [23]. Infrastructure. Infrastructure was another theme identified in the implementation of polio programs. General infrastructural issues impeded effective implementation and limited efforts to reach vulnerable populations. Conversely, in the presence of good infrastructure and resource mobilization, the implementation of polio programs was deemed successful. Under this theme, nine studies mentioned a total of five barriers, and three studies mentioned a total of three facilitators. One study highlighted that in Nigeria, the general lack of basic necessities, including drug availability in hospitals and water service, is a barrier to future immunization uptake [15]. Eight studies highlighted available resources as a challenge to the effective implementation of polio programs [14, 17, 18, 21, 23–26]. The lack of access to healthcare was mentioned by one study in Niger, where the majority of respondents noted inaccessibility as impeding routine immunizations and acute flaccid paralysis surveillance [24]. Two additional studies highlighted financial, organizational, operational, logistical, and quality barriers to the delivery of immunization services across several countries, including and Angola [14, 23]. The study conducted in Ethiopia listed “shortage of vaccine and supplies, non-functionality of refrigerators, lack of training, cancellation of immunization sessions, and unavailability of health posts to deliver the services” (p. 33) as possible reasons for low immunization [14]. Moreover, the unavailability of eligible children was considered a barrier by four studies across Pakistan, Afghanistan, and India [17, 19, 25, 27]. Children were frequently missed during polio vaccination visits and were not followed up with at a later time.

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: We have included this information in the revised manuscript Results section. 4) Much of the interpretive material is confusing or questionable. – The sentence “Taken together, these results indicate that while many of the sequences we identified were shared between related bacterial genera, our approach also identified sequences that were identical in the genomes of distantly related pathogens. ” took about four reads before I decided it simply meant there was a lot of sharing among close genera, and some sharing among more distant genera. A more parallel structure to the sentence could clarify (if that is indeed what it means). A reference to Figure 2 could also help. We apologize for the confusion. This sentence has been removed from the revised manuscript. – Discussion section: "generate biased interpretations of the driving forces": I don't see any interpretation of the driving forces behind HGT (or as I imagine driving forces, behind the success of lineages which have undergone HGT, such as transmissibility or antimicrobial selection pressure or the like) in this paper, and moreover, biased interpretations can be biased only relative to some defined estimand. This seems like unduly vague language, and maybe should be replaced with "incomplete accounts of the extent of HGT" or something similar. We agree and have modified this sentence accordingly. – Discussion paragraph three is somewhat peculiar. It seems to rest on the premise that if an element moves to a new host, it will be selected to change its sequence to adapt to that host, but then undermines that premise with hypotheses 2 and 3. This may be just a matter of wording, but it seems confusing. Maybe sequences are adapted to generic functions (e. g. neutralizing a drug) rather than to the bacterial host. At a minimum the wording should be changed; better would be, instead of giving one example of each, to try to classify the clusters based on these explanations. Again, this is part of the distance between "comprehensive analysis" and the more descriptive tone of the paper. We thank the reviewer for this helpful feedback. The three possible causes that we listed are hypotheses that might help explain our observations, and for which we have some (very limited) evidence in our dataset. We chose to offer some speculation regarding what we feel is the strongest example supporting each hypothesis; formally testing each one, especially in a dataset of this size, would require significant additional work that we feel would be better suited to future studies.

Output: pass


Input: Claim: HIV treatment can reduce viral load to undetectable levels. [SEP] Text: She was clinically stable after completion of the treatment for neurosyphilis and was discharged to the nursing home. She remained clinically stable for over a year, and recently died from COVID-19 complications. Informed consent was obtained from her family for the publication of this case report. incidence of syphilis has declined since the introduction of penicillin. In early the 2000s the US rate of reported cases of diagnosed primary and secondary syphilis was 2. 1 cases/100 000 people, which was the lowest rate since reporting began in 1941. Since then, the reported cases of syphilis in the US have increased almost every year in African Americans, Hispanics, and men who have sexual intercourse with men [3,4]. In developed countries, the increasing number of new cases are due to the occurrence of syphilis in patients with HIV. Neurosyphilis causes diverse clinical manifestations, including mood disorders, psychotic behaviors, emotional instability with the loss of social awareness, poor judgement, and different forms of memory deficits [1]. Our patient’s mental status began a progressive decline over a 1-month period; however, her medical history and clinical presentation were not suggestive of primary or secondary syphilis. She was treated for HIV with emtricitabine, dolutegravir, and tenofovir alafenamide, and her recent CD4 count was above 350 cells/mL with an undetectable HIV VL. This was in addition to a medical history of controlled schizophrenia with tardive dyskinesia treated with benztropine, risperi-done, and valproic acid. Primary dementia was ruled out as she had a rapid decline in mental function from the baseline of being independent in activities of daily living. The brain CT and EEG suggested that her altered mentation was not likely to be secondary to a space-occupying lesion, seizures, cerebral edema, other forms of oncotic cerebral damage, or acute ischemic changes. The results of the initial and repeated routine blood tests, hepatitis panel, and UDS test were unremarkable and not suggestive of metabolic or infectious encephalopathy. In the literature, many case reports discuss patients with HIV who have early syphilis and are at increased risk for neurologic complications that range from mild cognitive impairment to psychosis and worsened altered mental status [1].

Output: corroborate


Input: Claim: Vaccination programs have significantly reduced the global incidence of diseases like measles and polio. [SEP] Text: In a 2017 study in Pakistan, “38 percent of children were not vaccinated with OPV,” and the most frequent reason given was “the unavailability of children at home during polio vaccinator visits” (p. 29) [19]. Lack of general infrastructure, including access to hard-to-reach flood plains, weak health infrastructures, and insufficient financing for strategy implementation, impeded effective polio implementation in one study [26]. Furthermore, three studies listed the availability of resources as a facilitator in some settings [25, 28, 29]. First, one study highlighted a good social mobilization system in Afghanistan, where mobilizers visited over “90 percent of targeted, low-performing communities in the South” (p. 170) prior to the program’s implementation [25]. In addition, the finding and mapping of marginalized populations across seven countries in and sub-facilitated the targeting of children who may have been missed during polio visits in one study [28]. Lastly, one study in Uganda highlighted increased accessibility to immunization due to close Days (NID) posts as facilitating individuals’ participation in routine immunization campaigns, citing “NID posts very near and within a short walking distance” from their homes (p. 367) [29]. Beliefs about the intervention. The most prominent theme discovered in the implementation of polio programs surrounded beliefs related to the intervention. Negative beliefs about the polio vaccine emerged from cultural beliefs, religious conceptions, and inadequate awareness of the vaccine’s purpose and effectiveness. However, increased knowledge and positive beliefs about the vaccine’s efficacy against disease facilitated program implementation in other settings. Under this theme, 11 barriers from 15 studies, and four facilitators from seven studies were identified. Anti-immunization debates were thought to negatively contribute to the community’s trust in the vaccine. For instance, anti-immunization debates challenged the immunization program in India [30]. The authors of this study highlight that frequent debates challenging immunization programs “began to influence the community’s trust in the vaccines” (p. 7). When considering the presence of particular beliefs about the intervention, 14 studies mentioned a total of nine barriers. An additional seven studies listed a total of four facilitators. Propaganda and mistrust against vaccines and their efficacy were mentioned by two studies as the reasons for parental vaccine refusal in India [17, 31].

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: We have nonetheless modified this section of the manuscript accordingly. – "both plasmids…from the same patient were nearly identical to one another, suggesting that they were indeed transferred shortly before the bacteria were isolated" – over what timescale might we expect difference to occur in plasmids and of what magnitude? This is an important point to consider. Unfortunately, careful estimates of mutation rates among mobile elements are currently lacking. We have revised this section of the manuscript accordingly. – "underscores how quickly MGEs can move" – this makes no sense. MGEs move by for example conjugation which has been measured in the lab as taking minutes. The literal movement is of course fast. I think finding evidence of transfer that is close together in space and time is unremarkable; finding persistence over time is more remarkable. This is a fair point and we have modified this sentence accordingly. – Some of the other conclusions seem a bit unsupported by the analyses that are conducted – e. g. "the fact we only observed plasmids in closely related bacterial lineages suggests that they are well-adapted to these lineages, and if they were transmitted to other STs they were likely lost due to instability and/or fitness costs". I would think this could easily be affected by sampling strategy used, with only invasive samples of select species. This is also a fair point, and we have removed this sentence from the revised manuscript. – Figure 1D and E just show the proportion of clusters with X gene type or Y AME gene, respectively, but underlying cluster sizes range from 2-52 – shared across all samples. Is there a way authors can standardize by cluster size, as I am not sure a cluster of 2 should have the same weight as a cluster of 52 in these analyses? We agree that cluster size might affect how we interpret the contents of each cluster. We now include a table that summarizes the number of isolates and genetic contents of each cluster (Supplementary file 2), which will allow readers to access this information directly. – Authors required a minimum of 5Kb and 100% identity on nucmer and state these cut-offs were arbitrary (Discussion) – did authors examine any other cut-offs and how do their findings change if these are adjusted?

Output: pass


Input: Claim: HIV treatment can reduce viral load to undetectable levels. [SEP] Text: To determine the prevalence and associated factors with chronic kidney disease (CKD) in a cohort of HIV-positive individuals with undetectable viral load on HAART. March, 2009 to September 2009, 213 individuals between 18-70 years, period on HAART ≥12 months, viral load < 50 copies/mm3, and CD4 ≥ 200 cells/mm3, were consecutively enrolled at the outpatient clinic of Hospital de Clínicas, Porto Alegre, Brazil. Exclusion criteria were obesity, malnourishment, amputee, paraplegic, previous history of renal disease, pregnancy and hepatic insufficiency. Renal function was determined by estimated glomerular filtration rate (eGFR) assessed by the modification of diet in renal disease. CKD was defined as an eGFR less or equal than 60 ml/min/1. 73 m2, for a period of at least 3 months. Poisson regression was used to determine factors associated with CKD. Results CKD was diagnosed in 8. 4% of the population, and after adjustment, the risk factors were hypertension (RR = 3. 88, 95%CI, 1. 84 - 8. 16), time on HAART (RR = 1. 15, 95%CI,1. 03–1. 27) and tenofovir exposure (RR = 2. 25, 95%CI, 1. 04–4. 95). Higher weight (RR =0. 88 95%CI, 0. 82–0. 96) was associated to normal function. Conclusions CKD was a common finding in this cohort of patients and was related to hypertension, time on HAART and tenofovir exposure. We suggest a more frequent monitoring of renal function, especially for those with risk factors to early identify renal impairment. Citation: (2011) Prevalence and Associated to Disease in HIV-on HAART and Load in Brazil. 6(10): e26042. Kallas, University of Sao Paulo, BrazilReceived: June 28, 2011; Accepted: September 16, 2011; Published: October 12, 2011Copyright: © 2011 Menezes et al. This is an open-access 4. 7% to 7. 6% according to several studies [5]–[8].

Output: corroborate


Input: Claim: Vaccination programs have significantly reduced the global incidence of diseases like measles and polio. [SEP] Text: An additional study identified the importance of cultural beliefs in the decision to reject the vaccine in Niger [24]. Categorized under knowledge and beliefs about the intervention, seven studies mentioned refusal of polio program uptake due to a lack of information, ignorance, and illiteracy across Pakistan, Nigeria, India, and the of America [15–17, 19, 21, 27, 32]. For instance, in Nigeria, the majority of refusal respondents mentioned “drinking of clean water as a way to avoid polio virus, [while] others identified [that] ways to protect against polio included proper care and belief in God” (p. 3326) [15]. The belief that vaccination was unnecessary was cited as an indicator of refusal and thus a barrier to intervention uptake across four studies [15, 21, 23, 25]. Moreover, a study in India identified vaccine-resistant areas in a particular district as a barrier [30]. Safety and religious misconceptions regarding the vaccine were mentioned by two studies, which included witchcraft accusations and Westernized medicines that threaten religious credentials [19, 23]. In Pakistan, the misconception that “the vaccine is not ‘halal’ or [that it is] impermissible in the Islamic Law” (p. 27) [19] was a major reason for vaccine refusal. The perception of age, particularly being “too old,” and lax or disinterested parents were deemed as reasons by participants in one study to avoid polio vaccination in the of America [33]. Additionally, the reliance on religious leaders that oppose OPV uptake fueled skepticism and resistance in one study in Pakistan [20]. Lastly, one study mentioned mothers avoiding OPV by running away with their children as a barrier to polio campaigns in India [17]. Parents’ moral obligation to vaccinate their children and their belief that they cannot be deviant was mentioned by one study as a facilitator to polio intervention use in India [31]. Additionally, four studies across the of America, Uganda, India, and Pakistan highlighted the belief in the vaccine’s ability to protect against polio as a facilitator [20, 21, 29, 30]. Participants of one study in Uganda said that “the major aim [of the vaccine] was to ‘weaken’ the disease and/or ‘strengthen’ the children’s capability in fighting diseases” (p. 367) [29].

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: DNA was extracted using 100/G (Qiagen, USA) or (MoBio, USA). Illumina library preparation and sequencing were performed at by the facility. Pacbio library preparation and sequencing were performed by the University of. De novo hybrid assembly was performed using SPAdes (v3. 5. 0) (Bankevich et al. , 2012). Genomes were annotated using the Review (IMG/ER) annotation pipeline (Markowitz et al. , 2012). In addition, we also sequenced eight additional rind isolates of Brachybacterium (strains 341. 9, 738. 10, 862. 8, 876. 9, 900. 8, 908. 11, 947. 1, 962. 10) and Brevibacterium (strains 341. 13, 738. 8, 862. 7, 876. 7, 900. 6, 908. 7, 947. 7, 962. 8) and three additional isolates of Glutamicibacter (strains BW77, 78, 80) from different cheeses in a broad geographic distribution. For these isolates, we prepared draft genomes using Illumina short-read sequencing and assembled with CLC genomics workbench. The annotated genomes used can be found on Zenodo (Bonham et al. , 2016) Phylogenetic trees Request a detailed protocol 16S sequences were retrieved from the sequenced genomes and aligned using the structure-based aligner, Infernal v1. 1rc4 (Nawrocki and Eddy, 2013), as implemented in the Project release 11 (Cole et al. , 2009). The alignment was imported into Geneious v9 (Biomatters, LTD), and a tree was calculated using the maximum likelihood method PHYML (GTR model)(Guindon et al. , 2003). The tree was rooted using Thermus thermophilus. The tree was then uploaded to of Life (iTOLv3) (Letunic and Bork, 2016) to enable mapping of HGT data (connections and group abundance profiles). RNa detailed protocol Four replicate transcriptomes from two treatments were sequenced: (1) G. arilaitensis alone and (2) G. arilaitensis + Penicillium.

Output: pass


Input: Claim: HIV treatment can reduce viral load to undetectable levels. [SEP] Text: Risks that have already been associated include the “traditional” factors related to ageing, diabetes mellitus (DM) and hypertension [5], [6]. Besides that, other features such as the virus itself and some of the antiretrovirals (ARVs) currently used, such as indinavir (IDV) and tenofovir (TDF) have already been linked with nephrotoxicity in these individuals [5], [7], [8]. The first stage of renal impairment is silent and only detectable through laboratory analysis [9]. Although the most used biomarker for renal dysfunction diagnosis, the measurement of serum creatinine has limitations, such as the relatively low sensitivity, which underestimates the underlying renal status, and therefore, its values could be in the “normal range”, even after the loss of 50–60% of the glomerular filtration rate (GFR) [9], [10]. Although not clearly validated to HIV-infected individuals, equations adjusting for muscle mass, age, weight, ethnicity and sex, provide a more sensitive estimation of the true renal function, and have been used in general population (eGFR)[11], [12]. Currently, the most common formulas to estimate the GFR are Modification of Diet in formula (MDRD) [13], [14], Cockcroft-Galt (CG) [14], [15] and Collaboration (CKD-epi) [16]. The objectives of our study were to describe the prevalence of CKD and to determine the risk factors associated to the development of renal disease in a cohort of HIV infected individuals on HAART, undetectable viral load, and not severely immunosupressed (CD4 count > 200 cells/mm3), which would better resemble the general population, in Brazil. Materials and Two hundred fifty five patients attended in the HIV/AIDS outpatient clinic at Hospital de Clínicas, Porto Alegre, Brazil, were consecutively enrolled from March, 2009 through September, 2009. To be included, patients needed to be on HAART and undetectable viral load (<50 copies/ml) for a period equal or greater than 12 months, CD4 counts higher than 200 cells/mm3 and age between 18 and 70 years.

Output: corroborate


Input: Claim: Eating only organic foods guarantees a toxin-free diet. [SEP] Text: People today experience “modern malnutrition”, which is caused by modern diet habits such as high intakes of sugar, fat, fast food, and soda [8, 11, 48,49,50]. This type of diet is typically found in solitary eating. If people continue to eat alone, they will have potential risks of developing obesity and metabolic syndromes [11, 45]. The new social phenomena of an increase in one-person households creates public isolation, which can affect public health [14], but at the same time, we need to acknowledge that we have been ignoring the potential risk that another party could have. We were able to infer that, along with changes in our daily lifestyle, products that supplement diet balance for people who live alone may be beneficial. However, people who live together, mostly with family [25] consider their meals better than others even when they eat alone. Similar to that idea, people who are in a higher social stratum are considered more able to maintain their health by themselves. As we discovered from our analyses, poor meal quality does not appear only among the socially disadvantaged or those who live alone. The results indicate that we should promote nutritional health awareness to the lower socioeconomic class yet we should discriminate to improve diet quality for the entire population as the result of subgroup analysis shown. ConclusionsThis study provides evidence to promote interventions to improve the quality of the diet of the public. adults are experiencing low diet quality when they eat alone. The number of people who eat alone is increasing along with the changes of lifestyle. Also, the people who were considered as upper socio-economic status, such as who have high income, education level and white collar occupation status, are also experiencing issues in diet quality. Our study is highly recommended to policy-makers to utilize it as evidence to develop and improve social welfare services for the general population. AbbreviationsBMI: Body mass index GLM: Generalized linear model : Health and : Mean adequacy ratio NAR: The nutrient adequacy ratio RDA: Recommended dietary allowance 71. p. 1–41. 8. 71. New York: York; 2013. p. 89–100. 9. Korea Statistics; 2017. Accessed 7 Apr 2017. . Social relationships and healthful dietary behaviour: evidence from over-50s in the EPIC cohort, UK. Med. 2014;100:167–75. Seoul: Nutrition Society; 2015. 91. 10.

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: We used a strain of Penicillium solitum that was isolated from a natural rind cheese and was used for experiments in Wolfe et al. (2014). For each experimental unit, approximately 80,000 CFUs of Glutimicibacter arilaitensis were spread across the surface of a 100 mm Petri dish containing 20 mL of cheese curd agar (10% freeze-dried fresh cheese, 3% NaCl, 1. 7% agar, 0. 5% xanthan gum) (Wolfe et al. , 2014). For the + Penicillium treatment, approximately 100,000 CFUs were co-inoculated onto the plates with the Glutimicibacter. Plates were incubated in a bin with moist paper towel (>90% relative humidity) at 24°C for 5 days. Rind biofilms were then harvested by scraping the cheese curd surface and stored in RNA(Qiagen) to stabilize mRNA frozen at −80°C. RNA was extracted using a standard phenol-chloroform protocol used for many different fungal and bacterial species, which has been adopted from transcriptomics work in gut microbiomes (see [David et al. , 2014]). This protocol uses a standard bead-beating step in a lysis buffer to release cell contents from biofilms stored in RNAProtect. DNA was removed from the samples using a -free kit (Life Technologies), and 5S tRNA and large rRNA was depleted using MEGAClear (Life Technologies) and RiboZero (Illumina) kits, respectively. To remove both fungal and bacterial large rRNA, we used an equal mixture of Ribo-and Bacteria rRNA Removal Solution. To confirm that the samples were free of DNA contaminants, a PCR of the 16S rRNA gene was performed with standard primers (27 f and 1492 r). Overall quantity and quality of the RNA preps were confirmed by Nanodrop and Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit. RNA-seq libraries were constructed from purified mRNA using the for Illumina (Biolabs) where each library received a unique six base pair barcode for demultiplexing after the sequencing run. Each library was run on an Agilent 2100 chip to confirm that primer dimers and adapter dimers were not present in the sample and to determine the size of the library.

Output: pass


Input: Claim: HIV treatment can reduce viral load to undetectable levels. [SEP] Text: In plasma, median values of p24-antigen were 148 pg/ml (IQR 105–152). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 1. Plasma viral load and p24-antigen in plasma and erythrocytes from individuals with detectable plasma viral load in at least one sample during the year prior to the study. addition, we found pVL<10,000 copies/ml in 32 out of the 71 patients evaluated and pVL≥10,000 copies/ml in the remaining 39. No p24-antigen in plasma was detected in any of the 32 individuals with pVL<10,000 copies/ml, while Ag-E was detected in 22 out of these 32 individuals. Indeed, four out of these 22 individuals presented pVL<50 copies/ml, and three out of these four exhibited Ag-E levels above 110 pg p24-antigen/ml. Eleven out of the 39 individuals with pVL≥10,000 copies/ml presented both Ag-E and Ag-P, whereas two showed absence of Ag-E and presence of Ag-P and 18 showed presence of Ag-E without detectable Ag-P. Finally, p24-antigen was not detected at all in the remaining eight individuals (Table 1). To note, eight out of the 13 cases where Ag-P was detectable showed higher levels of Ag-P than of Ag-E (Table 1). It is important to highlight that p24-antigen was never detected in the supernatant of the last wash of purified erythrocytes (see Methods section), showing that Ag-E determination was not affected by Ag-P. With the aim to elucidate the relationship between pVL and the presence of Ag-E and Ag-P, the 71 individuals studied were assigned to four groups according to their pVL at the moment of the study: 1) <1,000 copies/ml (n = 20), 2) 1,000–9,999 copies/ml (n = 12), 3) 10,000–49,999 copies/ml (n = 21), 4) ≥50,000 copies/ml (n = 18), and the percentage of individuals with p24-antigen detection in plasma and in erythrocytes was evaluated (Figure 1).

Output: corroborate


Input: Claim: Eating only organic foods guarantees a toxin-free diet. [SEP] Text: This is because even if an “obesity prevention” product were very effective, anyone forced to eat it only would grow sick of the taste after a few days and prefer to starve to death than eat nothing but that product for the rest of their lives. Unlike with medicine, people grow tired of the taste of food over time. Even now, Korean bureaucrats continue to include “preventing something” as part of indexes for evaluating projects, despite the fact that this is based on a false understanding of foods. This is a foolish policy. Developing foods that can satisfy the diverse cultural, biological, and lifestyle needs of consumers is the key to global success in the future, but bureaucrats seem hell-bent on promoting the development of monotonous foods rooted in an outdated industrial era mindset. food industry will struggle to develop unless this changes. It is regrettable that this line of thinking still underpins many government projects. The government needs to rapidly abandon its corporate-oriented food policy and replace it with one that caters to the public. Because consumers make hundreds of choices about foods every year, choice is the key for both lifestyle and life itself. It needs to be recognized that Korea’s current approach to product development and production is undermining growth in the food industry. Life style science and Technology for the PublicAs discussed earlier, the food industry is an integral part of our lives. Accordingly, even if every other industry developed by humanity falls by the wayside, the food industry will remain as long as humans still exist on earth. Although ordinary people are the end consumers of smart-phones and cars, these industries are not considered part of life science. This is because once a person has decided between buying an Apple or Samsung phones, it has very little impact on their life thereafter. The same applies to choosing between different brands of cars. On the other hand, decisions about food need to be made every day, and the foods a person chooses to eat will influence their taste, health, life, and even happiness. This is why the food industry is one of the life style sciences [8], and why this industry should be approached from the perspective of life style science technology that can enrich people’s lives and make them happier and healthier, instead of industrial technology with a focus on production. Such an approach focuses on foods that are tastier and healthier and help people to live happy and healthy lives.

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: Scripts to import and store genome information and blast results and to analyze results are available on github (Bonham, 2016; A copy is archived at Genomic average nucleotide identity (ANI) was calculated using the ‘ani. rb’ script from the enveomics collection (commit ‘e8faed01ff848222afb5820595cccc4e50c89992’) with default settings (Rodriguez-R and Konstantinidis, 2016). a detailed protocol Shotgun metagenomic data from (Wolfe et al. , 2014) and (Kastman et al. , 2016) were assembled with CLC 8. 0. Representative sequences for or were compared with assembled metagenomes by BLAST. Hits with >97% similarity were considered to be positive hits for target regions. Accession numbers Request a detailed protocol Newly sequenced genomes were registered with NCBI with the bioproject 387187.

Output: pass


Input: Claim: HIV treatment can reduce viral load to undetectable levels. [SEP] Text: p24-antigen associated to erythrocytes was detected in HIV-positive individuals with undetectable plasma viral load for one year After demonstrating the presence of p24-antigen in purified erythrocytes from HIV-positive individuals, it was important to note that we found this Ag-E in patients with pVL<1,000 copies/ml at the moment of the study. Therefore, we wondered whether Ag-E might also be detected in individuals with undetectable pVL for one year prior to the study. To this end, we used 41 samples from HIV-positive individuals with undetectable pVL in three determinations for 12 months before the study. Eight out of the 41 individuals showed detectable pVL (median: 112 copies/ml; IQR 77–403) at the moment of the study and all of them presented Ag-E (median: 25 pg p24-antigen/ml; IQR 20–76) (Table 2). In contrast, 33 out of the 41 individuals presented undetectable pVL at the moment of the study, and five out of these 33 showed Ag-E (median: 38 pg p24-antigen/ml; IQR 31–97). When analyzing both groups, a significant positive relationship between detectable pVL and the presence of Ag-E was found (p<0. 00001) (Table 2). p24-antigen was not detected in plasma of any sample or in the supernatant of the last wash of each sample of purified erythrocytes from the 41 individuals. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 2. p24-antigen associated to erythrocytes in individuals with consecutive undetectable plasma viral load for one year. results show that Ag-E was present in individuals with undetectable pVL for one year. Furthermore, pVL detection at the moment of the study is related to the presence of Ag-E, suggesting that Ag-E determination could be a possible indicator for viral expression.

Output: corroborate


Input: Claim: Eating only organic foods guarantees a toxin-free diet. [SEP] Text: However, the result of the study should be interpreted cautiously condifring the limitations of the study such as the cross-sectional design of the study, which limits the ability to determine cause-and-effect relationships. Moreover, other factors such as anxiety and depression may also play a predictive role in EDs risk [48], which we were limited in considering in the relationship between EDs and adherence to a GFD. In this study, we did not use serum markers such as tTG-IgA to measure compliance with GFD, although the previous study have shown that CDAT is highly correlated with antibody levels [24]. In addition, we did not assess other barriers such as physical and economic access to gluten-free products and the psychological status of participants. Nonetheless, we believe that our findings increase the understanding of EDs and body image disturbances in patients with CD. They also highlight the importance of adhering to GFD in reducing their prevalence. ConclusionThe study found that 43. 5% of people with celiac disease (CD) also have eating disorders (EDs). Moreover, 65. 9% of CD patients suffer from body image dissatisfaction, and 41. 1% experience body image distortion. On the other hand, following a gluten-free diet (GFD) was found to have a negative association with the development of EDs. Therefore, it is recommended that CD patients receive psychological interventions, such as cognitive or self-management therapies, to address the high prevalence of EDs and body image dissatisfaction. Also, nutritionists should be aware of the potential psychological barriers that may hinder adherence to a GFD. However, the study has certain limitations, and more longitudinal studies are needed to confirm these findings. These studies should also take into account other potential factors, such as economic status, anxiety, and depression, to gain a more comprehensive understanding of the relationship between CD, EDs, and body image issues. Data availability The data are available from the corresponding author upon request.

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: Biosample accession numbers for individual genomes are shown in Supplementary file 1a, and are as follows: Brevibacterium linens 341_13: SAMN07141149, Brevibacterium linens 738_8: SAMN07141150, Brevibacterium linens 862_7: SAMN07141151, Brevibacterium linens 876_7: SAMN07141152, Brevibacterium linens 900_6: SAMN07141153, Brevibacterium linens 908_7: SAMN07141154, Brevibacterium linens 947_7: SAMN07141155, Brevibacterium linens 962_8: SAMN07141156, Brachybacterium alimentarium 341_9: SAMN07141157, Brachybacterium alimentarium 738_10: SAMN07141158, Brachybacterium alimentarium 862_8: SAMN07141159, Brachybacterium alimentarium 876_9: SAMN07141160, Brachybacterium alimentarium 900_8: SAMN07141161, Brachybacterium alimentarium 908_11: SAMN07141162, Brachybacterium alimentarium 947_11: SAMN07141163, Brachybacterium alimentarium 962_10: SAMN07141164, Glutamicibacter sp. BW77: SAMN07141165, Glutamicibacter sp. BW78: SAMN07141166, Glutamicibacter sp. BW80: SAMN07141167, Microbacterium sp. JB110: SAMN07141168, Halomonas sp JB37: SAMN07141169, Brevibacterium linens JB5: SAMN07141170, Psychrobacter sp. JB193: SAMN07141171, Brachybacterium sp. JB7: SAMN07141172, Sphingobacterium sp.

Output: pass


Input: Claim: HIV treatment can reduce viral load to undetectable levels. [SEP] Text: Open in figure viewer Figure 1 Routine viral load testing algorithm. Abbreviations: ART: antiretroviral therapy. In routine care, current WHO guidelines recommend that VL testing be done at six and 12 months after initiation of ART and repeated every 12 months thereafter. If the VL is detectable at any time (1000 copies/mL or greater), it is recommended that a patient undergoes intensive adherence support and repeat VL testing three to six months later. If the VL is still detectable and non‐adherence can be ruled out, a clinician may then decide to change to second‐line therapy (WHO 2013; WHO 2016). In this review, we will focus on the accuracy of a single POC VL test done at one time point (for example, at six or 12 months after ART initiation). We believe that this evidence may be extrapolated to provide evidence that may guide the use of the test at other time points. Alternative test(s) tests include non‐nucleic acid tests (non‐molecular tests) that detect HIV viral enzymes (reverse transcriptase) and HIV viral proteins (p24 antigen); markers that can be correlated to. These tests indirectly reflect VL concentration and are currently not commonly used (2015). Alternative methods for monitoring response to ART include immunological monitoring through CD4 testing and clinical monitoring through WHO clinical staging. For example, in adults, a persistent CD4 count less than 100 cells/mm3 or a new or recurrent clinical condition indicative of WHO clinical stage 4 after six months of treatment is regarded as treatment failure. However, these methods are less sensitive and specific than VL testing and are not recommended as the first‐line approach for monitoring response to ART (Rutherford 2014). This may lead to delayed detection of treatment failure or lead to unnecessary therapy switches. In addition, the WHO revised its guidelines in 2013 to recommend that all HIV‐positive people be started on ART regardless of CD4 count and clinical status (WHO 2013). In this regard, using these criteria to monitor response to therapy will not be an accurate measure of treatment failure. Nonetheless, these alternative tests may still be used in areas that do not have access to VL testing (WHO 2013).

Output: corroborate


Input: Claim: Eating only organic foods guarantees a toxin-free diet. [SEP] Text: Skip to main content Explore journals Get published About BMC My account Search all BMC 2020. In addition, the global market for spices and herbs will grow at a considerable speed during the forecast period between 2020 and 2026 [14]. Over the years, the global spice trade showed a significant and differentiated product development. With production industrialization, the industry of spices became more consolidated. Moreover, thanks to the development of Information and (ICT) and Business (BToB) activities, the demand and supply of spices increased rapidly within importing and exporting countries; this contributed to enhance the whole trade of spices and make the spice market more and more competitive. Nevertheless, according to literature [15] there are around 40-50 spices of global economic and culinary importance and many lesser known spices used in traditional cooking that have little or no international trade value. Herbs and spices help to vary dishes and to emphasize the national particularities of ethnic cuisines (e. g. , turmeric in Indian cuisine; basil, garlic, and oregano in Italian and Greek cuisines; wasabi in Japanese cuisine; and paprika powder in Hungarian cuisine). At the same time, spices enrich food with important nutrients for the body, and in some cases, they are used to lengthen the time storage of food [16]. Additionally, spices are very valuable for the cosmetic industry and are used for medical solutions or as dietary supplements. In fact, spices are used for their high antioxidant activity [17] in different forms, like essential oils, aqueous or methanolic extracts, resins, whole, and oleoresins in food. In fact, spices have a large number of bioactive compounds such as flavonoids, phenolic compounds, sulfur-based compounds, tannins, alkaloids, and vitamins [18, 19]. Furthermore, today some spices are classified as superfoods, although there is not a standard definition of these special foods, and generally, they are considered a sub-category of “functional foods. ” Principally, superfoods have a high nutritional content with benefic properties to which the concept of quality is linked, which is absent in functional synthetic foods [20]. Superfoods have a vegetable origin, and thanks to the particular intrinsic characteristics, they give the human body a large amount of vitamins, minerals, essential and non-essential amino acids, fatty acids, and useful phytochemicals [21].

Output: pass


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: JB170: SAMN07141173, Vibrio casei JB196: SAMN07141174, Arthrobacter sp. JB182: SAMN07141175, Corynebacterium sp. JB4: SAMN07141176, Pseudoalteromonas sp. JB197: SAMN07141177. Add a comment + Open annotations. The current annotation count on this page is being calculated. Data availability The following data sets were generated (2016) Datasets associated with Bonham et al. Publicly available at Zenodo ( (2017) Datasets associated with Bonham et al. Publicly available at the (accession no: PRJNA387187). The following previously published data sets were used (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524487. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524500. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524498. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524496. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524502. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524495. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524488. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524490. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524499. 3).

Output: pass


Input: Claim: HIV treatment can reduce viral load to undetectable levels. [SEP] Text: 2014, the on HIV/AIDS () declared the 90‐90‐90 target; it aimed to have at least 90% of HIV‐positive people diagnosed, at least 90% of those diagnosed receiving ART, and at least 90% of those receiving ART having suppressed viral replication by 2020 (WHO 2016). POC VL tests being developed to detect and treatment failure in HIV‐positive people on ART in resource‐limited settings will be instrumental in checking if the third target will be met effectively. If these POC VL tests have a high level of accuracy, they can replace or complement laboratory‐based testing platforms because they are quicker to use and may minimize delays in initiating therapy or changing therapy in cases of treatment failure (2014; 2015). A high sensitivity is required because false‐negative results will lead to a delay in detecting treatment failure or adherence concerns related to treatment. This will ultimately lead to progression to AIDS and mortality. A high specificity is also required because false‐positive results will lead to unnecessary switching to costly second‐line therapy. A test with an optimal combination of sensitivity and specificity is thus needed. estimate the diagnostic accuracy of point‐of‐care tests to detect high viral load levels in HIV‐positive people on ART. Secondary objectives To investigate sources of heterogeneity in test accuracy estimates including age (children versus adults), test type (commercially available versus in‐house assays), sample type (whole blood versus plasma), test threshold (1000 copies/mL or greater versus other thresholds), location of testing (true‐POCs versus near‐POCs), geographical location (sub‐versus other regions), and methodological quality (high versus low risk of bias). for considering studies for this review Types of studies We will include any primary study that compares the results of the index test to that of a reference standard (cross‐sectional, prospective, and retrospective study designs or diagnostic accuracy studies performed within randomized trials), and those that provide sufficient data to create the 2 × 2 table to calculate sensitivity, specificity, and negative and positive predictive values. We will exclude ecological studies and diagnostic case‐control studies in which the test performance was compared in participants with the target condition versus healthy controls, as specificity will be overestimated (Macaskill 2010). We will exclude studies without a reference standard, case reports and case‐series studies, animal or laboratory studies, reviews, discussion papers, non‐research letters, commentaries, or editorials.

Output: corroborate


Input: Claim: Drinking alkaline water has scientifically proven benefits for cancer prevention. [SEP] Text: Abstract Background: Standard therapy are saying that cancer recurrence prevention is difficult. Shelton L. N. reported that cancer cell is grown up in the presence of both glucose and glutamine. So, dietary energy restriction (DER) is useful tool of recurrence prevention. As the second item, I have exploited herbal medicine (Sun Advance) which inhibit the hallmarks of carcinogenesis. have employed detoxifying therapy. As the 4th method, high dose of vitamin C therapy which promotes the increasing of hydro-peroxide in cancer cell. I applied these 4 combinations of intervention method on the high risk of postoperative cancer patients. Method: Among 500 post-operative patients, I have selected 131 candidates who were classified into tumor stage IV and tumor stage V. Among them, 104 members are intervened, and 27 patients are classified into control group. Results: In control group, 55% have tendency to aggravating change. Among intervened 104 members, 7. 7% are not prevented. Keywords dietary energy restriction (DER), herbal medicine (Sun Advance), high dose of vitamin C, detoxifying therapy, recurrence prevention program said that there is no correct barometer for cancer prevention and recurrence prevention. So as to solve this problem, we have reported tumor marker combination assay (TMCA) in Cancer (1994) [1]. By utilizing TMCA, I have classified cancer risk assessment into 5 tumor stages among 500 postoperative cancer patients and I have selected 131 high risk group, who are classified into TSIV and TSV. I have intervened by 4 methods against high risk groups. Shelton LN et al. [2-4] reported that VM-M3 cancer cell is grown up in the presence of both glucose and glutamine. So, wise dietary energy restriction (DER) has induced from this knowledge as the nutritional counter measure for cancer prevention [5-8]. Youngman LD reported that the combination of carcinogen and high protein diet highly promote the carcinogenesis. As the second item, I have exploited herbal medicine (Sun Advance) [9-10] which inhibit selectively mitochondrial oxygen respiration on cancer cell and which inhibit its hallmarks of carcinogenesis of culture cell.

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524497. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524491. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524493. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524501. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524482. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524489. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524483. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524505. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524494. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524486. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524504. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524485. 3). (2014) shotgun metagenomic data from cheese rinds used in Figure 4 Publicly available at MG-RAST (accession no: 4524484. 3). 1101. PubMed 143. 477. PubMed 124. PubMed 386. PubMed 589. PubMed 421. PubMed 875.

Output: pass


Input: Claim: HIV treatment can reduce viral load to undetectable levels. [SEP] Text: Skip to main content Skip to main navigation menu Skip to site footer the 10. 3396/ijic. v19. 20588 Keywords: human immunodeficiency virus, knowledge, antiretroviral therapy, viral load, sustained virologic response, transmission, Background: Knowledge of ‘Undetectable HIV viral load (VL) is Untransmittable’ (U=U) motivates optimal adherence to antiretroviral therapy (ART). Objective: This study assessed factors associated with knowledge about U=U among Zambian people living with HIV on ART. Design: The study used questionnaires and in-depth interviews (IDIs) concurrently between December 2018 and January 2019. Three high volume health facilities, Chilenje, Chipata, and Kalingalinga, were selected. A single proportion of 63. 4% of HIV VL suppression (VLS) in was used to calculate a sample size of 362 respondents. Probability proportional to size procedure was used to apportion the sample to the study sites while a simple random technique was employed in selecting respondents aged 18–59 years and on ART for over 9 months. Stata 14 was used to run descriptive and chi-square statistical analyses. Fifty-five respondents were drawn from 362 respondents for IDIs. The selection was based on varied VL levels. Interviews were audio-recorded, transcribed and analysed thematically, and the findings merged in the discussion. Results: Approximately, 34. 5% of the 362 respondents (n = 125) had knowledge about U=U. The VLS status was significantly associated with U=U knowledge (P = 0. 01). Discussion: Diverse information sources, symbiotic understanding of VL, and treatment-as-prevention benefits were enablers of acquiring more knowledge about U=U, while inadequate health discussion about VL and congestion and waiting time were barriers. Conclusions: The findings suggest that increased information sharing on the implication of suppressed VL being able to prevent HIV transmission could motivate people living with HIV to adhere to ART, thus sustaining VLS. data is not yet available. 10. doi: 10. 7448/IAS. 20. 1. 21803 Assefa Y, Gilks CF.

Output: corroborate


Input: Claim: Drinking alkaline water has scientifically proven benefits for cancer prevention. [SEP] Text: have employed detoxifying therapy which is utilized in old type of Japanese therapy as CAM, which is mainly composed of (Apparatus: WA: 57B (686) Yamato (KK, Ehime prefecture, Japan) of exercise and sweeping of intestinal canal which eliminate immunosuppressive substances from bloods and elevate immune activity utilizing detoxifying medicine. As the fourth method, high dose of vitamin C therapy will inhibit angiogenesis of cancer tissue and promote increasing of hydro-peroxide in cancer cell [11-12]. Materials and Methods Post-operative cancer patients are as follows. Gastric cancer: 20, colon cancer:28, liver cancer: 3, breast cancer: 27, lung cancer: 17, prostate: 11, sarcoma: 2, kidney cancer: 2, ovarium cancer: 3, esophageal cancer: 3, uterine cancer 14, skin cancer: 1, Among them, 104 candidates were contributed to as an intervened group. Others: 27 patients are served to be as a control group. Detoxifying and immune-therapy is composed of intestinal sweeping by detoxifying medicine and Nishi type exercise utilizing apparatus (Apparatus: WA: 57B (686) Yamato (KK, Ehime prefecture, Japan). As for cancer recurrence prevention, 4 types of intervened method are prepared and applied to 104 candidates: DER, high dose of vitamin C (20g), Herbal medicine (Sun Advance, Chiba city, Japan) and detoxification therapy are applied step by step. As to herbal medicine, SA 1. 6g was prescribed daily. As for control group (herbal medicine 5g as Kudzu Decoction) prescription was applied as placebo. TMCA examination was carried out in everyone month and checked their risk assessment? Detoxifying therapy is composed of Nishi type [Apparatus : WA: 57B(686) Yamato(KK, Ehime prefecture? Japan)] of exercise for 20 minutes and detoxifying therapy medicine for 6 hours which is sweeping of intestinal canal which eliminate detoxifying medicine [intake of the mixture of citric acid (12g), lactulose ( Kowa, Tokyo) (24g), magnesium hydroxide(30g) and 50 ml of water], total body massage, hot and cold water dipping each time for 1 minute alternatively, 7 time repeating) stimulation for autonomic nervous system and sauna bathing at 39?

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: Accordingly, the vast majority of self-mobilizable MGEs—89% of the prophages and 90% of ICEs—were identified in hotspots (set 3 and Supplementary Fig. 7). On the other hand, only around 9% of the hotspots encoded ICEs or integrative mobilizable elements (IMEs), and only 23% encoded prophages (Fig. 5). Integrons were even rarer (present in 1% of the hotspots). Non-self-transferable MGEs lack conjugation or virion structural genes, but usually encode integrases. The vast majority of integrases was identified in hotspots, but less than half (45%) of the hotspots encoded an integrase and only 29% encoded tRNA or tmRNA genes (Fig. 5). Hence, although most self-mobilizable MGEs are in hotspots, most hotspots lack them (Supplementary Fig. 8). Fig. 5Genetic mobility of hotspots. We represent the percentage of hotspots containing the different genetic elements (top) and the percentage of spots containing such elements that are hotspots (bottom). Note that hotspots are only 1. 2% of all the spots. The analysis includes MGEs (prophages, integrons), mobility-associated proteins (MAPs) (), and tRNA/tmRNA, rRNA. Also, shown in colored bins are the observed/expected (log10O/E) number of hotspots that contain the abovementioned elements, when the null model was computed from the distribution of coldspots containing the same type of elements. Expected values were obtained by multiplying the number of hotspots by the fraction of spots containing each type of elementFull size imageInsertion sequences (ISs) encoding DDE recombinases (transposases) are frequent within MGEs, and we found them in many hotspots (56%). The integration of these elements has low-sequence specificity, which explains why hotspots accounted for a small fraction of the locations with ISs (19%), unlike what we observed for self-mobilizable MGEs and integrases. Altogether, half of the hotspots lacked evidence for the presence of MGEs and 27% lacked any of the mobility-associated proteins (MAPs, integrases and transposases) that we searched for.

Output: pass


Input: Claim: HIV treatment can reduce viral load to undetectable levels. [SEP] Text: 0114 Understanding the time needed to link to care and start ART in seven HPTN 071 (PopART) study communities in Zambia and South Africa. AIDS Behav. 20189; 23(4): 929–46071(0123456789). doi: 10. 1007/s10461-018-2335-7 Orne- Addressing social issues in a universal HIV test and treat intervention trial (ANRS 12249 TasP) in South Africa: methods for appraisal. BMC Public Health. Published online 2015; 15: 209. doi: 10. 1186/s12889-015-1344-y Undetectable equals untransmittable (U = U): aAwareness and associations with health outcomes among people living with HIV in 25 countries. Infect. 2021; 97(1): 18–26. doi: 10. 1136/sextrans-2020-054551 Kim H-. The effect of partner HIV status on motivation to take antiretroviral and isoniazid preventive therapies: a conjoint analysis. AIDS Care. 2018; 30(10): 1298–1305. doi: 10. 1080/09540121. 2018. 1455958. Decreases in community viral load are accompanied by reductions in new HIV infections in San Francisco. PLoS One. 2010; 5(6): e11068. doi: 10. 1371/journal. pone. 0011068 Belief in treatment as prevention and its relationship to HIV status and behavioral risk. J Defic Syndr. 2018; 77(1): 8–16. doi: 10. 1097/QAI. 0000000000001557. HIV viral load and transmissibility of HIV infection: undetectable equals untransmittable. JAMA. 2019; 321(5): 451–452. doi: 10. 1001/jama. 2018. 21167 Hayes R. HPTN 071 demonstrates community-wide HIV prevention strategy can reduce new infections. In: Conference on Retroviruses and (CROI); 2019. Available from: doi: [cited 15 December 2019]. How ‘place’ matters for addressing the HIV epidemic: evidence from the HPTN 071 (PopART) cluster-randomised controlled trial in Zambia and South Africa. Trials. 2021; 22(1): 1–13.

Output: corroborate


Input: Claim: Drinking alkaline water has scientifically proven benefits for cancer prevention. [SEP] Text: 5% Thirdly, among them, I have randomly selected one post-operative colon cancer patient (72 yrs. ) and followed for 12 years. In this patient, I have intervened by 2 methods: herbal medicine (Sun Advance) and detoxifying treatment therapy. When risk assessment by TMCA become higher risk, detoxifying therapy (in another name is Refreshment therapy) or mix-intervention of herbal medicine (Sun Advance) and detoxifying therapy (Figure 2) were applied. This patient could be prevented his cancer recurrence by these intervened methods for 12 years. Figure 2. Post -operative colon cancer patient (72 years old) was followed up by the combination intervention of herbal medicine and detoxifying treatment. Among the postoperative cancer patients (131), we have carried out intervention treatment by 4 methods which promote natural healing power against higher risk group. We have succeeded in cancer recurrence prevention program in 93%. cancer tissue will develop just look like fetus development, we should carry out suitable cancer recurrence prevention program by means which solve cancer nutritional control, solve lowering immune activity, inhibit cancer angiogenesis and solve mitochondria respiratory dysfunction because neoplasm is appeared by immunological decreasing disease. Before clinical neoplasm will be appeared, complementary and alternatively medicine or holistic medicine would be effective for cancer recurrence prevention. In this paper I have failed cancer recurrence prevention in 7. 7%. But as to this 7. 7%, I have applied immune-thermo-chemotherapy (ITC) [13] on those who have not succeeded in cancer recurrence prevention program after consent. Utilizing ITC, I have succeeded in cancer recurrence prevention in 99 %( not published). In ordinal standard western medicine, 60~70% of cancer patients would be recurred up to now. So, my reported recurrence prevention programs are good intervention which are depended upon the activation of natural healing power different from chemotherapy and radiotherapy. We should change the treatment not cancer attacking invasive treatment but contributed to promote natural healing power. Most of cancer sacrifices are derived from cancer recurrence in 60~70%. If our cancer recurrence prevention program is applied to the postoperative patients with high risk, cancer patients will be secured. is no funding in this paper. am grateful to my co-worker: Hayashida Shgeru. Conflict of interest No confliction. 1953.

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: These results confirm that hotspots concentrate most MGEs and integrases, but not the majority of ISs. They also show that regions with high concentration of HTgenes often lack recognizable MGEs, suggesting that other mechanisms are implicated in their genesis and turnover. The chromosomal context of hotspotsWe then searched to identify the preferential genetic contexts of hotspots, since they might illuminate constraints associated with the chromosomal organization of HGT. We analyzed whether the distribution of hotspots was random relative to the function of the neighboring core genes. Interestingly, these core genes showed an overrepresentation of several functions, notably replication, recombination/repair, and transcription (Fig. 4a). In contrast, cell cycle control genes were underrepresented. Hence, hotspots are preferentially associated with specific functions of neighboring core genes. We then tested whether hotspots were randomly distributed in genomes. Since replication drives much of the large-scale organization of bacterial genomes8, we analyzed the position of hotspots relative to the distance to the origin of replication along the replichore. These results showed that the frequency of hotspots including prophages, as previously shown in E. coli13, increases linearly along the ori-> ter replication axis (Fig. 6a). Interestingly, this does not seem to be the case for ICEs and IMEs, nor for the very large category of hotspots that lack and prophages. Fig. 6Chromosomal context of hotspots. a Number of hotspots containing prophages, ICEs/IMEs, and none of the above along the origin–terminus axis of replication. Linear regression and the confidence limits (shaded area) for the expected value (mean) were indicated for each category. The number of hotspots including prophages increases linearly with the distance to the origin of replication (Spearman’s ρ = 0. 87, P < 10−3), but this is not the case for the other two categories (both P > 0. 05). b Heatmap of odds ratios of co-localizations in hotspots of MGEs, mobility-associated proteins (MAPs) and RNAs. ***P < 10−3; **P < 10−2; *P < 0.

Output: pass


Input: Claim: The WHO monitors and supports global public health initiatives. [SEP] Text: From a of Digital Covid-19 Fidelia Cascini1*Causio1Giovanna Failla2Andriy Melnyk1Valeria Puleo1Luca Regazzi1Walter Ricciardi1,3 1Section of Hygiene and Public Health, Department of Università Cattolica del Sacro Cuore, Roma, Italy 2Department of Public Health, University of Verona, Verona, Italy 3mobility is one of the highest priorities of the current globalized society after being greatly hampered by the Covid-19 pandemic. Worldwide, much effort has been put into revitalizing non-essential travel (e. g. , for tourism), while also preserving safety. In fact, an increasing number of national and international initiatives have been launched to facilitate a mutual recognition of Covid-19 status certificates amongst countries1. Countries have been invited by the Organization (WHO) to adopt an omni-comprehensive risk-based approach. This is based on lifting public health measures, such as testing and/or quarantine requirements, and requires travelers to be fully vaccinated with WHO-approved vaccines, have documented proof of past infection, or to have been tested negative to WHO-approved rRT-PCR tests or antigen detection rapid diagnostic tests (Ag-RDTs)2. However, the rapid increase of Covid-19 certificates worldwide is showing differences in the governance of issuing and validation processes and has raised challenges such as the reliability of the certificates and trustworthiness of certifying bodies or authorities, the data protection guarantees, and the interoperability prospects. 2021, the WHO has been promoting the use of the of Vaccination and Prophylaxis (ICVP) to record the SARS-CoV-2 vaccination proof. It proposed a solution to leverage public key infrastructures (i. e. , the same used for credit card transactions) to establish a cryptographically supported trust framework for Covid-19 certificates. This would be used between member states, with the WHO in the role of trust broker3. However, different Digital Covid-19 Certificates (DCC) are currently available worldwide, possibly affecting international mobility for safe people. Digital Covid-19 31, 2021, the proposed to update the on the coordination of free movement limitations in the (EU).

Output: corroborate


Input: Claim: Drinking alkaline water has scientifically proven benefits for cancer prevention. [SEP] Text: Log in or to journalnew issue alertsGet alerts Enter your Email address: Subscribe to e2002. | DOI: 10. 1097/01. EEM. 0000334240. 85179. 07 of thousands of individuals have undergone and continue to undergo chelation therapy for a variety of reasons, despite the lack of credible evidence of the effectiveness of this modality. Clinics all over the country hawk the so-called benefits of chelation therapy for such diverse afflictions as elevated cholesterol, diabetes, stroke, coronary heart disease, osteoporosis, and arthritis. For this final column of the series examining chelation therapy, I went to the web site of a prominent chelation therapy clinic, and investigated the assertions they make and the appeal these have for patients. The site I visited claimed that “chelation therapy is a safe and effective IV procedure that improves circulation, reversing the symptoms of serious cardiovascular disorders such as arteriosclerosis, angina, and hypertension. ” They also state that “chelation therapy provides relief from many other ailments that stem from decreased circulation. ” Specifically, they list elevated cholesterol, diabetes, stroke, coronary heart disease, osteoporosis, and arthritis as a partial compendium of the conditions that can be helped through chelation therapy. The web site I visited indicated that chelation was first used in the 1940s to remove lead and other metals from the body, and that following administration of chelation therapy, “doctors found that patients experienced vast improvement in stamina and that blood pressure and cholesterol levels were lowered. ” They further said these patients “had fewer episodes of angina; even their diabetic symptoms were reduced. ” They summarize by stating that “in general, there was a marked improvement in all problems related to poor circulation. ” One web site touts chelation therapy to reverse the symptoms of serious arteriosclerosis, angina, and hypertension The defining principle of the chelationist is stated on the web site as follows: “The condition of the circulatory system also affects how fast and how well we age. If the arteries are kept supple and prevented from hardening and narrowing, we slow down aging.

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: Further work is needed to understand if there are other organizational traits that constrain the distribution of hotspots in the chromosome, and in particular in those devoid of recognizable MGEs. Knowing these traits might facilitate large-scale genetic engineering and should lead to a better understanding of the evolutionary interactions between horizontal gene transfer and genome organization. Finally, our study focused on the dynamics of hotspots and how they contribute to genome diversification, but left unanswered the questions related to their origin and fate. Previous studies identified common prophage hotspots between E. coli and Salmonella enterica13. Hence, we will have to study taxonomical units broader than the species level to unravel their origin. As for their fate, long-term adaptive HTgenes may become fixed in the population, explaining the patterns of nestedness of certain hotspots, and leading eventually to the split of the hotspot into two new (eventually hot) spots. MethodsDataThe sequences and annotations of 932 bacterial genomes from 80 bacterial species were retrieved from (ftp://ftp. ncbi. nih. gov/genomes, last accessed in February 2014)41. We made no selection on the species that were to be analyzed, except that we required a minimum of four complete genomes per species. We have made no attempt to re-define species: we used the information presented in GenBank. Their list is available in set 1. We excluded CDS annotated as partial genes, as well as those lacking a stop codon or having stop codons within the reading frame. Core genomes and phylogenetic reconstructions were obtained from our previous work27 (set 2). Our data set includes several species from the same genera. It also includes species with diverse numbers of genomes and HTgenes. To minimize the effects of these unavoidable biases most of our analyses are non-parametric and each species has the same weight. When they were done on the data cumulated from all species, we made a control where each species is analyzed separately. We also made complementary analyses where we aggregated the results per genus. The 27. These core genomes were built for clades with at least four complete genomes available in GenBank RefSeq (set 1, Supplementary Fig. 1).

Output: pass


Input: Claim: The WHO monitors and supports global public health initiatives. [SEP] Text: It is a favored pastime of medical editors and journalists (including ourselves) to criticize the Organization (WHO) for, among other things, its “fossilized bureaucracy,” its lack of clear direction and priorities, the dysfunctional relationship between its headquarters and regional offices, and its faltering steps towards building partnerships [1,2]. But with the arrival of so many new players on the global health scene, and the subsequent fragmentation of global health governance, we surely need WHO more than ever [3]. It is the best placed of all health agencies to coordinate the disparate, often overlapping global health initiatives and to set global norms and standards in health care, and its convening power (its ability to bring together experts) is unparalleled. Two recent WHO initiatives on preparing for and responding to global public health threats show the organization at its best, although there are, as always, some important caveats. The first initiative, described by Holger Schünemann and colleagues in this issue of PLoS Medicine, is the development and pilot testing of the new [4]. WHO's standard process for guideline development typically takes years of consultations and endless rounds of revisions, a process that is wholly inadequate for dealing with emergency health threats such as severe acute respiratory syndrome (SARS) or H5N1 avian influenza. In response to requests for advice from frontline clinicians and public health professionals on how to treat H5N1 infections, WHO convened a new type of panel to issue rapid, evidence-based advice. It took one month to convene an expert team, and five weeks for the team to summarize the evidence and prepare draft guidelines. The guidelines were then discussed at a two-day meeting, after which a draft manuscript for publication was prepared within 10 days. In WHO terms, this time scale was miraculously quick, but there is clearly room for improvement—an even quicker time frame is likely to be needed for future health emergencies. The process could be expedited, say the authors, by identifying or establishing collaborating centers skilled in producing evidence-based guidelines and by building in-house capacity to reduce the time needed to organize a review team. It will also be vital for this new rapid advice group to make its process of panel selection as transparent as possible if the group is to garner the trust of the public health community. WHO has previously come under fire for allowing industry to unduly influence its expert committees, and for failing to ensure that committee members declare their competing interests [3].

Output: corroborate


Input: Claim: Drinking alkaline water has scientifically proven benefits for cancer prevention. [SEP] Text: At the same time, we lessen the threat of contracting diseases associated with the aging process — forms of cardiovascular degeneration, arthero- and arteriosclerosis, peripheral circulatory dysfunction, some types of kidney disease, hypertension, stroke, and premature senility. ” These claims, quite simply, never have been validated or scientifically proven. Nonetheless, these are the sorts of claims being made all over the country with regard to chelation therapy. Tens of thousands of patients buy into these concepts, some in desperation, some out of distrust for the traditional medical system, and others because of sheer naivete. The web site goes on to say that “one of the substances most affected by chelation is calcium. If inappropriately present in the body tissue (on the surface of a joint, as in arthritis, or in the lining of an artery), deposits of calcium can be detrimental to your health, the site says. Chelation therapy removes these deposits, causing the plaque in the arteries to soften, and at the same time, encouraging re-calcification of the bones. EDTA also helps reduce free radical damage, a constant irritant to the cell walls and membranes, by binding with toxins on a cellular level. Chelation removes these irritants, which allows the cell walls to heal, the web site says. Chelation promotes health by correcting the underlying cause of arterial blockage. These are the principles espoused by chelationists. The lack of credible evidence to support these claims, however, creates a potentially serious hazard to the unsuspecting patient. In an attempt to appeal to the large numbers of patients with coronary artery disease, the chelationists who operate the Internet site I visited claimed that “bypass surgery is the mechanical repair of only a small portion of the arterial system. Chelation improves blood flow throughout the entire vascular system. And it costs just a fraction of the cost of bypass surgery. ” They emphasize that “chelation therapy is among the safest of all medical procedures, and that more than 28 million people have successfully received chelation during the past 50 years. ” Perhaps the most telling information about how chelation therapy is marketed is the treatment recommendations made by the site: “A course of chelation consists of 10 to 30 sessions depending on the condition being treated. Chelation is done in our center in a comfortable setting, and usually lasts approximately 1. 5 to 2 hours.

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: Briefly, a preliminary list of orthologs was identified as reciprocal best hits using end-gap-free global alignment, between the proteome of a reference genome (pivot, typically the first completely sequenced isolate) and each of the other strain’s proteomes. Hits with < 80% similarity in amino-acid sequence or >20% difference in protein length were discarded. This list of orthologs was then refined for every pairwise comparison using information on the conservation of gene neighborhood. Thus, positional orthologs were defined as bi-directional best hits adjacent to at least four other pairs of bi-directional best hits within a neighborhood of 10 genes (five upstream and five downstream). These parameters (four genes being less than half of the diameter of the neighborhood) allow retrieving orthologs at the edge of rearrangement breakpoints (positions where intervals were split by events of chromosome rearrangement) and therefore render the analysis robust to the presence of a few rearrangements. The core genome of each clade was defined as the intersection of pairwise lists of positional orthologs. Definitions of interval and spotThe core genome is the collection of all gene families present in one and only one copy in each genome of a clade (Supplementary Fig. 2). Let CX and CY be two families of core genes in a clade with N taxa where one of the taxa is a pivot (reference genome, see above). We call CAX and CAY contiguous core genes in a given chromosome A if they are adjacent in the list of core genes sorted in terms of the position in the chromosome. We defined an interval (IAX, AY) as the location between the pair of contiguous core genes CAX and CAY in chromosome A. The content of an interval is the set of accessory genes in the interval. The HTgenes content of an interval is the number of genes that were acquired by HGT in the interval. Multiple chromosomes, when present, were treated independently. Intervals flanked by the same core gene families (CX, CY) as the pivot genome were defined as syntenic intervals (i. e. , the members of the core gene families X and Y were also contiguous in the pivot). The intervals that do not satisfy this constraint were classed as breakpoint intervals and excluded from our analysis. They contain < 2% of all genes.

Output: pass


Input: Claim: The WHO monitors and supports global public health initiatives. [SEP] Text: The rapid advice group must not sacrifice transparency in the interests of urgency. We surely need WHO more than ever. The second initiative is the long overdue 2005 revision of the Regulations (IHR 2005), which comes into force next month [5]. These regulations are an international legal instrument designed to ensure maximum protection against the international spread of infectious disease while minimizing restrictions on travel and trade. Up until the 2005 revision, the regulations in force since 1969 (IHR 1969) required notification of just three diseases: yellow fever, cholera, and plague. The instrument was therefore hopelessly outdated for dealing with the new infectious diseases that have emerged at a rate of about one per year over the last 20 years [6], or indeed for dealing with established threats such as pandemic influenza. IHR 1969 had several other limitations—for example, surveillance relied totally upon individual governments notifying WHO and there were no specific strategies to help build the capacity of resource-poor countries to monitor or respond to outbreaks [7]. Compliance was poor, in part because countries feared that reporting of outbreaks would lead to unwarranted and damaging travel and trade restrictions [5]. China's initial reluctance to disclose the SARS pandemic was motivated by such fears [7]. Under IHR 2005, WHO member states are now required to notify WHO of “all events which may constitute a public health emergency of international concern,” which can include noninfectious events (such as chemical or radiation hazards) [5]. A new algorithm has been devised to aid states in determining what constitutes such an emergency. Criteria for reporting are whether the public health impact of the event is serious, whether it is unusual or unexpected, whether there is a risk of international spread, and whether there is a risk of international restrictions to trade and travel. The algorithm includes a long list of specific diseases that must always be notified, such as viral hemorrhagic fevers, SARS, and human influenza caused by a new subtype. IHR 2005 requires all states to develop “core surveillance and response capacities” and requires WHO to assist in this development process. Each country must now have a “” to maintain communications between WHO and the member state. When an event is reported, WHO will guide the appropriate response by issuing time-limited recommendations to the member state tailored to the assessed risk of the event.

Output: corroborate


Input: Claim: Drinking alkaline water has scientifically proven benefits for cancer prevention. [SEP] Text: It is recommended that two to three sessions be done per week for maximum benefit. ” I decided to call the chelation site whose web address I had accessed. I asked the woman who answered the phone how much chelation treatments would cost, and was told treatments are sold in blocks of 10. Each block of 10 goes for $1200. The usual treatment regimen according to this person was “about 30. ” She said that decision would be up to the doctor who runs the clinic, and often patients need to have even 60 treatments or more. She then spent about 15 minutes telling me how wonderful people feel immediately after undergoing their treatment. asked about the doctor's specific credentials and qualifications, I was told that he is “a full MD” and “a bio-chemical specialist or something. ” Somehow, I was not reassured. Sadly, I suspect that similar answers to similar questions would be forthcoming at virtually all chelation clinics currently operating in this country. These clinics are, quite simply, money-making operations. Beyond the well described placebo effect, these treatments offer little chance for the reversal or prevention of organic disease. At worst, these clinics may harm patients by the uncontrolled use of chelation therapy. At best, they probably neither cure nor prevent illness. The bottom line here is that chelation therapy requires vastly more study before it can be recommended for conditions other than heavy metal intoxication. In fact, government regulators and insurers need to take a hard look at these chelation operations and hold them to the same standards of practice that apply to all other health care providers. Rendering useless or unproven treatments should be condemned. Thousands buy into the concept of chelation therapy, some in desperation, others from naivete Until that happens, chelationists will continue their unproven practice, and patients may be at risk. Emergency physicians should remain vigilant to recognize that patients undergoing chelation treatments may well present to the emergency department and manifest complications deriving from those treatments. And emergency physicians must be prepared to report to state health authorities and professional societies any chelation operation that may be causing harm to the public's health. for Eighty-seven percent of respondents in a nationally representative survey of more than 2,600 U. S. physicians indicated that overall morale in their profession has waned in the past five years.

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: For every interval in the pivot genome, we defined spot as the set of syntenic intervals flanked by members of the same pair of core gene families (Supplementary Fig. 2). Identification of spot pan-genomesThe pan-genome is the full complement of homologous gene families in a clade. We built a pan-genome for each species using the gene repertoire of each genome. Initially, we determined a preliminary list of putative homologous proteins between pairs of genomes (excluding plasmids) by searching for sequence similarity between each pair of proteins with v. 2. 2. 28+ (default parameters). We then used the e-values (<10−4) of the output to cluster them using SILIX (v1. 2. 8, We set the parameters of SILIX such that two proteins were clustered in the same family if the alignment had at least 80% identity and covered >80% of the smallest protein (options –I 0. 8 and –r 0. 8). We computed the diversity of gene families observed in each spot. The spot pan-genome is the set of gene families present in the intervals associated with the spot (Supplementary Fig. 2). Reconstruction of the evolution of gene repertoiresWe assessed the evolutionary dynamics of gene repertoires of each clade using Count43 (downloaded in April 2015). This program uses birth-death models to identify the rates of gene deletion, duplication, and loss in each branch of a phylogenetic tree. We used the spots’ pan-genomes matrices, and the phylogenetic birth-and-death model of Count, to evaluate the most likely scenario for the evolution of a given gene family on the clade’s tree. Rates were computed with default parameters, assuming a Poisson distribution for the family size at the tree root, and uniform gain, loss, and duplication rates. One hundred rounds of rate optimization were computed with a convergence threshold of 10−3. After optimization of the branch-specific parameters of the model, we performed ancestral reconstructions by computing the branch-specific posterior probabilities of evolutionary events, and inferred the gains in the terminal branches of the tree. The posterior probability matrix was converted into a binary matrix of presence/absence of HTgenes using a threshold probability of gain higher than 0. 95 at the terminal branches and excluding gains occurring in the last common ancestor with a probability higher than 0. 5.

Output: pass


Input: Claim: The WHO monitors and supports global public health initiatives. [SEP] Text: An important new feature of IHR 2005 is that WHO can now use information about health emergencies not just from governments but from a range of sources, including nongovernmental organizations and the media. WHO can also raise the alarm itself about an emergency even when a country has not voluntarily notified the organization. IHR 2005 is undoubtedly “a great step forward for international public health practice” [8]. On paper at least, the radical revision to the IHR, which took ten years to finalize, gives WHO the teeth it needs to prepare for and respond to any global health threat. But WHO will have to address several important concerns if IHR 2005 is to become a real force for strengthening our collective defenses against public health threats. The first, and most obvious, concern is that many developing countries lack the financial resources to build core surveillance and response capacity. These countries will be unable to comply with IHR 2005 through no fault of their own. Unless WHO helps to mobilize new funding, an upgraded global surveillance and response system will remain just an aspiration. Donors have taken an interest in preparing for at least one “public health emergency of international concern”—pandemic influenza—but without a way of ensuring equitable distribution of funds, it is the donor countries themselves that will largely benefit from these extra resources. For example, in December 2005 the congress allocated $US3. 8 billion to help prepare for the next pandemic, of which $US3. 3 billion went to the Department of Health and [9]. Three-quarters of this departmental funding is allocated to the stockpiling of antiviral drugs and vaccines for use in the US, while only 3. 8% is dedicated to “international activities. ” Poor countries are understandably concerned that the stockpiling of tools for pandemic influenza control will be the preserve of the rich world. A related concern is that IHR 2005 appears to have no remit to help developing countries deal with national public health emergencies. The event must be “of international concern” for the IHR machinery to kick in. It would arguably be better for a country to adopt a precautionary principle rather than to wait until a disease has crossed its borders to become an “international” epidemic. The woolly language of IHR 2005 also leaves the regulations open to the criticism that they are there simply to prevent infectious diseases of the poor world from encroaching upon rich countries.

Output: corroborate


Input: Claim: Mental health issues are more frequently diagnosed in high-income countries due to greater healthcare access. [SEP] Text: Investing for population mental health in low and middle income countries—where and why? Download PDF Download eeOpen access Published: 11 August 2022 Investing for population mental health in low and middle income countries—where and why? Melvyn Freeman1 of Systems 16. 5% [3]. Importantly for this paper, around 2% of the population were assessed to have severe mental disorder, while the remainder had a range of conditions frequently referred to as common mental disorders including depression, anxiety and substance abuse disorders. While no national data is available, the 12-month prevalence of child and adolescent mental disorders in the is reported to be 17% [4]. allocates around 5% of its health budget to mental health—this being USD615. 3 million in the 2016/17 financial year [5]. This amounts to USD13. 3 per capita of the uninsured population. Inpatient care accounts for 86% of mental healthcare expenditure, with nearly half of total mental health spending occurring at the psychiatric hospital-level. The vast majority of admissions are for severe mental health conditions. Only around 8% of the mental health budget is spent within primary health care [5]. This includes down referrals from hospitals for people with severe mental disorders into primary care in clinics and community health centres and includes costs of medicines. As with hospital care (in psychiatric and general hospitals where psychiatric care is provided), the vast majority of primary care mental health expenditure is spent on treatment for people with severe mental disorder. Hence despite the high prevalence of common mental health conditions, expenditure on people with these conditions is minimal. Moreover, it is evident that given the very high of percentage of the health budget spent on in-patient care, very little expenditure is on prevention and promotion. Funding for improved mental healthIt is widely recognized that mental health is neglected, under-resourced and underfunded, particularly in low and middle income countries (LMICs) [6, 7]. The treatment gap—that is the absolute difference between the true prevalence of a disorder and the treated proportion of individuals affected by the disorder [8]—exceeds 50% in all countries, approaching 90% in the least resourced countries [9, 10].

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: Identification of hotspotsWe made simulations to obtain the expected distribution of HTgenes in the spots given the numbers of HTgenes and spots (Supplementary Fig. 4). We made the null hypothesis that the distribution of these genes was constrained by the frequency of genes in operons, and followed a uniform distribution in all other respects. Previous works have shown that two-third of the genes are in operons and one-third are in mono-cistronic units44, with little inter-species variation for the average length of poly-cistronic units (3. 15 ± 0. 06)45. Hence, given N HTgenes per clade we created two groups of elements: N/3 isolated genes and 2 N/3 in operons with three genes. These elements were then randomly placed among the spots following a uniform distribution. For each of the 1000 simulations (per species), we recorded the maximal value of genes within a single spot (MaxHTg,i), which was used to identify the value of the 95th percentile (T95%) of the distribution of MaxHTg,i. Hence, 95% of the simulations have no spot with more than T95% genes (set 1). Spots (in the real genomes) with more than T95% HTgenes were regarded as hotspots. Spots lacking accessory genes were called empty spots. The other spots were called coldspots. As a control, we also made simulations considering that HTgenes were acquired independently of the structure in operons (i. e. , considering N isolated genes). The values of T95% of the two analyses were highly correlated (Spearman’s ρ = 0. 89, P < 10−4, set 1), but those of the latter were smaller (linear regression: T95% isolated = −0. 62 + 0. 66 T95% operons, R2 = 0. 87). This is expected because the operon structure should increase the variance of the genes per spot, and thus increase T95%. Measures of gene repertoire diversitySince most spots have few or no genes, and most gene families have few (or no gene) per genome, we computed the genetic diversity of spots using matrices of presence/absence of gene families (computed from the pan-genome).

Output: pass


Input: Claim: The WHO monitors and supports global public health initiatives. [SEP] Text: There are other potential barriers to the success of IHR 2005. The division of power within federations may make it difficult for them to meet the surveillance and reporting requirements of IHR 2005 [10]. It is unclear whether the instrument will have any power to assist states that are not members of WHO, such as Taiwan, which suffered a major SARS outbreak in 2003 and which is at risk of pandemic influenza. It is too soon to tell how IHR 2005 will interact with other guidelines on public health emergencies. Union, for example, already has its own network for reporting unusual events that may constitute a public health emergency [11]—does this network supersede the IHR 2005? And it is too soon to tell whether IHR 2005 gives countries enough of an incentive to report epidemics or whether compliance will be just as poor as with IHR 1969. IHR 2005 has been hailed as “a governance regime unlike anything in the history of international law on public health” [7]. Margaret Chan, WHO's Director-General, believes that the new regulations give the organization the preemptive powers it needs to detect an outbreak early and stop it at its source [12]. IHR 2005 certainly gives the health community a new tool that could promote collective action against global health threats, but the tool will be weakened unless the technical, logistical, and, most crucially, financial hurdles are overcome.

Output: corroborate


Input: Claim: Mental health issues are more frequently diagnosed in high-income countries due to greater healthcare access. [SEP] Text: Over a number of studies the median untreated rate for schizophrenia and other non-affective psychosis has been found to be 32%, major depression 56%, dysthymia 56%, bipolar disorder 50%, GAD 58% and OCD 60%, alcohol abuse and dependence 78% [2]. (SASH) found a treatment gap of 75% for common mental disorders [11]. However, a more recent analysis suggests that the gap for mental disorders, epilepsy and intellectual disability is close to 92% [5]. The vast majority of untreated disorders are persons with common mental disorder. Given that country budgets are finite and in demand from many competing sectors, including from areas that affect mental health such as poverty alleviation, job creation, housing, education, social security, safety, nutrition [12], making a case for investment in mental health requires careful deliberation and weighing up of evidence from a wide range of perspectives. Allocating more resources to treatment at the expense of social determinants or vice versa might widen rather than narrow the treatment gap. Closing the gap through more efficient and effective (including cost effective) approaches, as well as by eliminating wasteful expenditure, is necessary and possible. For example, resources can be spread through decentralization using task shifting or task sharing approaches [13, 14] or through more competitive tendering for purchasing of medication or equipment [15, 16]. The treatment gap can also be narrowed through coverage initiatives such as Insurance that allows more equitable distribution of human and financial resources and hence wider service coverage [17]. As essential as these innovations are though, and as much as the treatment gap also arises as a result of stigma [18], and cultural factors [19] that prevent people seeking treatment, for most LMICs additional resources are required to adequately redress unmet need. Two key question then arise. Where should current resources that are allocated to mental health be spent to achieve optimal outcomes? And, to which areas should additional resources be allocated should these be come available for mental health,? Given global fiscal constraints and an area of health that has relatively low mortality, is not infectious and has high stigma, it is critical that resource allocation—if not to be based on pure science alone and is not merely the whim of a donor or politician—must be carefully thought through and debated. Ideally, fiscal decisions by governments should be based on comparative analyses and evidence in which a wide array of investment proposals across different sectors are weighed against each other.

Output: contrast


Input: Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: 547 with a predefined tree (i. e. , the clade’s tree), default priors R/θ = 10−1, 1/δ = 10−3, and ν = 10−1, and 100 pseudo-bootstrap replicates, as previously suggested47. Mean patristic branch lengths were computed with the R package “ape” v3. 348, and transition/transversion ratios were computed with the R package “PopGenome” v2. 1. 649. The priors estimated by this mode were used as initialization values to rerun CFML under the “per-branch model” mode with a branch dispersion parameter of 0. 1. Functional assignmentGene functional assignment was performed by searching for protein similarity with HMMer (hmmsearch) on the bactNOG subset of the eggNOG v4. 5 database50 (downloaded in March 2016). We have considered the pivot (reference) genomes as good representatives of each clade, and limited our analysis to these. We have kept hits with an e-value lower than 10−5, a minimum alignment coverage of 50%, and when the majority (>50%) of non-supervised orthologous groups (NOGs) attributed to a given gene pertained to the same functional group. Hits corresponding to poorly characterized or unknown functional groups were discarded. Identification of MGEs and proteins associated to mobilityTemperate phages integrated in the bacterial chromosome (prophages) were identified using v4. 651 (stringent option). Prophages with > 25% of the predicted genes belonging to ISs, and partially degraded prophages (shorter than 30 kb) were removed52. Integrons were identified using IntegronFinder v. 1. 4 with the –local_max option53. Integrative conjugative elements (ICEs) and integrative mobilizable elements (IMEs) were identified using MacSyFinder v. 1. 0. 254 with TXSScan profiles55. Elements with a full conjugative apparatus were classed as ICE, the others as IME (see ref. 33 for criteria).

Output: pass