Input: Claim: Some ant species can farm fungi as a food source. [SEP] Text: View 29. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph. D. dissertation, of Texas at Austin. Available: 30. Rambaut A, Drummond AJ (2007) Tracer v1. 4 [updated to v1. 5]. Available: Accessed 20 October 2012. 31. (2004) AWTY: A system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Available: Accessed 22 October 2012. 32. Tamura K, (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Evol 10: 512–526. View 33. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Evol 28: 2731–2739. View 34. (1891) Les Formicides. [part]. In: Grandidier A, editor. Histoire physique, naturelle, et politique de XX Histoire naturelle des Hyménoptères, Deuxième partie (28e fascicule). Paris: Hachette et Cie,. v +237. 35. Wheeler WM (1922) Ants of the Congo expedition. A contribution to the myrmecology of Africa. IX. A synonymic list of the ants of the Malagasy region. Hist 45: 1005–1055. View 36. (1922) Hymenoptera, fam. Formicidae, subfam. Myrmicinae. 174B: 95–206. View 37. (1995) A new general catalogue of the ants of the world. Cambridge, Massachusetts: Press. 504 p. 38. (1894) Mission scientifique de M. Ch. Alluaud aux îles Séchelles (mars, avril, mai 1892). 2e mémoire. Formicides. 63: 67–72. View 39. André E (1887) Description de quelques fourmis nouvelles ou imparfaitement connues. Revue d’Entomologie (Caen) 6: 280–298. View 40.

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: DOI: [PubMed] Hattar, S; Liao, HW; Takao, M; Berson, DM; Yau, KWMelanopsin-containing retinal ganglion cells: architecture, projections, and intrinsic photosensitivity Science 295: 1065–1070, DOI: [PubMed] Panda, S; Sato, TK; Castrucci, AM; Rollag, MD; DeGrip, WJ; Hogenesch, JB; Provencio, I; Kay, SAMelanopsin (Opn4) requirement for normal light-induced circadian phase shifting Science 298: 2213–2216, DOI: [PubMed] Cermakian, N; Sassone-Corsi, PEnvironmental stimulus perception and control of circadian clocks Neurobiol 12: 359–365, DOI: [PubMed] Schibler, U; Ripperger, J; Brown, SAPeripheral circadian oscillators in mammals: time and food J 18: 250–260, DOI: [PubMed] Yoo, SH; Yamazaki, S; Lowrey, PL; Shimomura, K; Ko, CH; Buhr, ED; Siepka, SM; Hong, HK; Oh, WJ; Yoo, OJ; Menaker, M; 2::real-time reporting of circadian dynamics reveals persistent circadian oscillations in mouse peripheral tissues 101: 5339–5346, DOI: [PubMed] Damiola, F; Le Minh, N; Preitner, N; Kornmann, B; Fleury-Olela, F; Schibler, URestricted feeding uncouples circadian oscillators in peripheral tissues from the central pacemaker in the suprachiasmatic nucleus 14: 2950–2961, DOI: [PubMed] Stokkan, KA; Yamazaki, S; Tei, H; Sakaki, Y; Menaker, MEntrainment of the circadian clock in the liver by feeding Science 291: 490–493, DOI: [PubMed] Balsalobre, A; Marcacci, L; Schibler, UMultiple signalling pathways elicit circadian gene expression in cultured rat-1 fibroblasts 10: 1291–1294, DOI: [PubMed] Brown, S

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan.Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: Table 7 Summary of a linear mixed effects analysis on the response of bacterial diversity across the body sites using the full data set and then filtered to include just adults Age groupBody siteFixed effectsRandom effectsModelΔAICPr(Chi)AllPalms (L&R)Dog + Cat + Sex + KidBS + Ag + Fa + FS + Pl + LaFull0NA(−)Dog2. 910. 027(−)Cat−5. 601(−)Sex1. 730. 053(−)Kid−5. 621ForeheadDog + Cat + Sex + KidAg + Fa + FS + Pl + LaFull0NA(−)Dog0. 570. 11(−)Cat−5. 251(−)Sex0. 970. 085(−)Kid−4. 221FecalDog + Cat + Sex + KidAg + Fa + FS + Pl + LaFull0NA(−)Dog−0. 0490. 16(−)Cat−0. 150. 17(−)Sex0. 330. 13(−)Kid−0. 130. 17OralDog + Cat + Sex + KidAg + Fa + FS + Pl + LaFull0NA(−)Dog1. 220. 072(−)Cat−1. 950. 82(−)Sex−1. 880. 73(−)Kid−1. 780. 64AdultsPalms (L&R)Dog + Cat + Sex + KidBS + Fa + FS + Pl + LaFull0NA(−)Dog4. 090. 014(−)Cat−5. 291(−)Sex4. 110. 013(−)Kid−5. 691ForeheadDog + Cat + Sex + KidFa + FS + Pl + LaFull0NA(−)Dog2. 520. 033(−)Cat−4. 991(−)Sex−0. 370. 20(−)Kid−4. 381FecalDog + Cat + Sex + KidFa + FS + Pl + LaFull0NA(−)Dog0. 300. 13(−)Cat0. 240. 13(−)Sex−1. 440. 45(−)Kid−0. 420. 21OralDog + Cat + Sex + KidFa + FS + Pl + LaFull0NA(−)Dog−0. 290.

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: 1 IntroductionThe waggle dance is a pattern of movement performed by successful honey bee foragers within the nest to recruit colony mates to forage on a profitable food source. This honey bee “dance language”, discovered by the pioneering work of Karl von Frisch (von Frisch 1967), is drawing renewed scientific interest as new tools allow novel insights into the remarkable sophistication of the signal, its mechanism of information transfer, and the effect of the signal’s message on the dynamic organization of honey bee foraging (see reviews by Dyer 2002; Grüter and Farina 2009). Recently, solid-phase microextraction (SPME) coupled with gas chromatography and mass spectrometry (GC/MS) analysis added an entirely new facet to the waggle dance signal by revealing a suite of four semi-volatile hydrocarbons (Z-(9)-tricosene, tricosane, Z-(9)-pentacosene, and pentacosane) emitted by waggle-dancing bees (Thom et al. 2007). When a synthetic mixture of this suite of volatile compounds was released into the hives of foraging colonies, it caused bees to exit the hive, suggesting that this suite of volatile compounds stimulates a colony’s foraging efforts (Thom et al. 2007). It would not be surprising for a semiochemical to play a role in organizing foraging within honey bee colonies. Olfactory communication is important in the foraging of other social insects (e. g. , Free and Williams 1983; Kerr 1994; and Alonso 1998; Steinmetz et al. 2003; Stout et al. 1998) and in organizing non-foraging tasks within honey bee colonies (Free 1987). Determining the role of the waggle-dance compounds in the foraging behavior of the honey bee, agriculture’s most important pollinator, should be considered a priority. Here we seek to further our understanding of the waggle-dance compounds beyond the single published account of their discovery (Thom et al. 2007). First, not revealed by experiments to date, is whether the bees that exit the hive in response to the waggle-dance compounds are foragers. Second, if these bees are foragers, then do they subsequently engage in foraging behavior following their departure?

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: [PubMed] Kalsbeek, A; Buijs, RMOutput pathways of the mammalian suprachiasmatic nucleus: coding circadian time by transmitter selection and specific targeting Res 309: 109–118, DOI: [PubMed] Buijs, RM; Wortel, J; Van Heerikhuize, JJ; Feenstra, MGP; Ter Horst, GJ; Romijn, HJ; Kalsbeek, AAnatomical and functional demonstration of a multisynaptic suprachiasmatic nucleus adrenal (cortex) pathway Neurosci 11: 1535–1544, DOI: [PubMed] Schibler, U; Sassone-Corsi, PA web of circadian pacemakers Cell 111: 919–22, DOI: [PubMed] Yagita, K; Tamanini, F; Horst, GT van Der; Okamura, HMolecular mechanisms of the biological clock in cultured fibroblasts Science 292: 278–281, DOI: [PubMed] Shearman, LP; Sriram, S; Weaver, DR; Maywood, ES; Chaves, I; Zheng, B; Kume, K; Lee, CC; Horst, GT van der; Hastings, MH; Reppert, SMInteracting molecular loops in the mammalian circadian clock Science 288: 1013–1019, DOI: [PubMed] Takahashi, JSFinding new clock components: past and future J 19: 339–347, DOI: [PubMed] Gekakis, N; Staknis, D; Nguyen, HB; Davis, FC; Wilsbacher, LD; King, DP; Takahashi, JS; Weitz, CJRole of the CLOCK protein in the mammalian circadian mechanism Science 280: 1564–9, DOI: [PubMed] Ueda, HR; Hayashi, S; Chen, W; Sano, M; Machida, M; Shigeyoshi, Y; Iino, M; Hashimoto, SSystem-level identification of transcriptional circuits underlying mammalian circadian clocks 37: 167–192, DOI: Doi, M; Hirayama, J; Sassone-Corsi, PCircadian regulator CLOCK is a histone acetyltransferase Cell 125: 497–508, DOI

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: Antibodies used to label each cell type: NeuN for granule cells, ITPR1 for Purkinje cells, SORCS3 for basket cells, GFAP labels the cell bodies and process of astrocytes, MOG labels the cell bodies and process of oligodendrocyte. (B) Fluorescence activated sorting of stained nuclei from five cell types. Antibodies used for staining are indicated on the x- and y-axes. Percentage of each cell type based on the positive population is indicated. (C) Browser view showing examples of gene that are specifically expressed in each of the five cell types. (D) Heatmap of FPKM levels for example genes in each of the five cell types (granule – green, Purkinje – red, basket – orange, astrocyte – blue, oligodendrocytes - cyan). (E-F) Examples of labeled cerebellar nuclei using cell-type specific antibodies. Nuclei are counterstained with DAPI, a marker for heterochromatin. (E) Nuclei labeled with antibodies against ITPR1 and NeuN. Itpr1, an endoplasmic reticulum membrane protein, is localized at the nuclear membrane, while NeuN, a splicing factor, is localized at euchromatin inside the nucleus. (F) Antibodies against the basket cell marker SORCS3 and astrocyte marker EAAT1, two cellular membrane proteins, show labeling of the nuclear membrane. Antibodies against the oligodendrocyte marker and transcription factor OLIG2 show labeling in euchromatin. (G) Heatmap showing the pairwise Pearson’s correlation coefficient of GFP- (G) and antibody- (A) sorted nuclei. Hierarchical clustering is performed on the 250 most variable genes across all conditions. See also Figure 1—figure supplement 1, Figure 1—figure supplement 2. Nuclear RNA profiles generated from sorted nuclei are cell-type specific We next produced gene expression profiles for each of the five cerebellar cell types by isolating RNA from the sorted nuclei and performing RNA-seq. To evaluate the purity of these profiles, we checked the expression of known markers for each cell type of interest. In all cases, we observed high expression of markers only in the appropriate cell type.

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: If the hydrocarbons emitted by waggle-dancing bees play a role in foraging communication, then their application to the hive must be shown to affect a colony’s foraging activity. The first part of the present study tests this hypothesis by exposing bees to the waggle-dance compounds and then measuring the number of visits by bees to a sucrose feeder to which they had been trained. The second part of the present study investigates the mechanism by which the waggle-dance compounds might stimulate foraging. Recruitment pheromones such as ant trail pheromones and bumblebee footprint pheromones often function outside the nest (and Alonso 1998; Stout et al. 1998). The results of the experiments by Thom et al. (2007), however, suggest that the waggle-dance compounds may have behavioral effects within the nest, similar to the recruitment pheromone of bumblebees (Dornhaus and Chittka 2001; Dornhaus et al. 2003; Granero et al. 2005). The waggle-dance compounds may function within the nest to alter the behavior of any or all of the many behavioral-task groups associated with foraging activities. Preliminary data gathered by the authors in 2008 (not presented here) suggested that one task group that might respond to the waggle-dance compounds is the pool of bees that have previously foraged but are currently inactive, hereafter referred to as unemployed experienced foragers following the terminology of Biesmeijer and de Vries (2001). The second part of the present study tests the hypothesis that the waggle-dance compounds stimulate foraging by reactivating unemployed experienced foragers to exploit known food sources. We predicted that foragers which have been trained to a sugar-water feeder and marked to allow for individual identification will increase their foraging activity following introduction of the waggle-dance compounds even when the feeder is empty. Emptying the feeder will eliminate recruitment to it, so that any arriving bees must be experienced foragers familiar with the food source. Also investigated is whether the predicted dance-compound induced boost in visits to the food source can be accounted for by increases in the number of reactivated foragers, or by increases in the foraging rate of reactivated foragers, or both. 2 Materials and methods2.

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: : [PubMed] Kume, K; Zylka, MJ; Sriram, S; Shearman, LP; Weaver, DR; Jin, X; Maywood, ES; Hastings, MH; 1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop Cell 98: 193–205, DOI: [PubMed] Sato, TK; Yamada, RG; Ukai, H; Baggs, JE; Miraglia, LJ; Kobayashi, TJ; Welsh, DK; Kay, SA; Ueda, HR; Hogenesch, JBFeedback repression is required for mammalian circadian clock function 38: 312–319, DOI: [PubMed] Hirayama, J; Sahar, S; Grimaldi, B; Tamaru, T; Takamatsu, K; Nakahata, Y; Sassone--mediated acetylation of BMAL1 controls circadian function Nature 450: 1086–1090, DOI: [PubMed] Nakahata, Y; Kaluzova, M; Grimaldi, B; Sahar, S; Hirayama, J; Chen, D; Guarente, LP; Sassone-+-dependent deacetylase SIRT1 modulates CLOCK-mediated chromatin remodeling and circadian control Cell 134: 329–340, DOI: [PubMed] Asher, G; Gatfield, D; Stratmann, M; Reinke, H; Dibner, C; Kreppel, F; Mostoslavsky, R; Alt, FW; 1 regulates circadian clock gene expression through PER2 deacetylation Cell 134: 317–328, DOI: [PubMed] Guillaumond, F; Dardente, H; Giguere, V; Cermakian, NDifferential control of Bmal1 circadian transcription by REV-ERB and ROR nuclear receptors J 20: 391–403, DOI: [PubMed] Sato, TK; Panda, S; Miraglia, LJ; Reyes, TM; Rudic, RD; McNamara, P; Naik, KA; FitzGerald, GA; Kay, SA; Hogenesch, JBA functional genomics strategy reveals Rorα as a component of the mammalian circadian clock Neuron 43: 5

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: subdivide their basket neurons into four subpopulations, non-Bergmann glia astrocytes into two subpopulations, and oligodendrocytes into two subpopulations; we also examined the expression of our human and mouse-enriched genes for these cell types in all subpopulations. We found that for all cell types and for both measures of expression, the expression of human-enriched genes in human single nuclei data is significantly higher than the expression of mouse-enriched genes (Figure 3—figure supplement 3C). Concordantly, the expression of mouse-enriched genes in mouse single cell data is higher than the expression of human-enriched genes for all cell types, including subpopulations of each cell type (Figure 3—figure supplement 3D). For both measures of expression, the distributions of expression for mouse- and human-enriched genes are statistically different for all cell types except for OPCs, which is likely due to sample size as Saunders et al. only identified eight cerebellar OPCs. These results confirm that the genes we have identified as differentially expressed between human and mouse are likely to be true species differences, and do not arise as a result of sorting different subpopulations in the two species. We next performed (GO) analysis of species-specific genes to understand whether their expression might reflect changes that occur independently, or arise due to transcriptional programs that are altered between species. GO analysis of human-enriched genes from granule neurons, astrocytes, oligodendrocytes, and OPCs do not have significantly associated GO categories, suggesting species differences in these cell types contribute to a wide range of pathways and functions. The majority of human-enriched genes in basket cells are also unrelated functionally, although there was significant enrichment for the cellular component sub-ontology cell projection membrane. GO analysis of mouse-enriched genes from astrocytes revealed weak enrichment for genes with phosphoric diester hydrolase/phospholipase activity, while mouse-enriched genes from granule neurons, basket neurons, oligodendrocytes, and OPCs revealed enrichment for genes with transporter activity or those involved in neuronal development (Supplementary file 9). These data indicate that evolutionary divergence between mouse and human cell types involves both frequent alterations in regulatory mechanisms impacting single genes (Villar et al.

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: 1 Experiment 1Experiments were performed during July and August, 2008, using one colony of approximately 7,500 workers of the Carniolan variety (Apis mellifera carnica) housed in a five-frame hive in an uncultivated field in North Haledon, New Jersey. Foragers were trained to a feeder containing unscented sugar water located approximately 100 m from the hive. Training consisted of attracting to the feeder foragers at the entrance of the hive, then gradually moving the feeder to the final location (von Frisch 1967). Care was taken to eliminate foragers from foreign colonies by marking the initial recruits with a dot of paint and then subsequently killing any unmarked bees that visited the feeder. Upon completion of training, two replicates were conducted each day, one in the morning from 09:30 to 10:30, and one in the late afternoon from 16:00 to 17:00. Immediately before each experimental replicate, and only at this time, the feeder was filled with sugar solution. To account for fluctuations in the favorability of foraging conditions, the concentration of the sugar solution was adjusted between 5% and 11% to prevent overcrowding of the feeder dish (7-cm diameter) by recruited bees. Each replicate began when the first bee arrived at the feeder station, which typically occurred within 5 min of filling the dish at the feeder station. Thereafter, we counted for 40 min the number of bee visits to the feeder station for the duration of every other minute (a total of 20 counts per trial). A visit was defined as a bee landing on the dish and extending her proboscis to the feeder reservoir. Following their visit, the majority of bees flew directly toward the hive after a single looping flight. However, because bees were not individually identifiable in this experiment, it is possible that some bees were counted more than once within a particular 60-s count. Over counting of visits was minimized by watching the flight of each bee departing from the feeder and excluding any visits by bees returning to the feeder immediately after departure. Another observer simultaneously counted the number of worker exits from the hive for the duration of every other minute. At minute 10, either 300 μl of waggle-dance compound mixture or 300 μl of pure ethyl ether was introduced into the hive.

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: 27–537, DOI: [PubMed] Akashi, M; Takumi, TThe orphan nuclear receptor RORα regulates circadian transcription of the mammalian core-clock Bmal1 12: 441–448, DOI: [PubMed] Preitner, N; Damiola, F; Lopez-Molina, L; Zakany, J; Duboule, D; Albrecht, U; Schibler, UThe orphan nuclear receptor REV-ERBα controls circadian transcription within the positive limb of the mammalian circadian oscillator Cell 110: 251–260, DOI: [PubMed] Triqueneaux, G; Thenot, S; Kakizawa, T; Antoch, MP; Safi, R; Takahashi, JS; Delaunay, F; Laudet, VThe orphan receptor Rev-erbα gene is a target of the circadian clock pacemaker J 33: 585–608, DOI: [PubMed] Reick, M; Garcia, JA; Dudley, C; 2: an analog of clock operative in the mammalian forebrain Science 293: 506–509, DOI: [PubMed] Amir, S; Lamont, EW; Robinson, B; Stewart, JA circadian rhythm in the expression of 2 protein reveals a novel SCN-controlled oscillator in the oval nucleus of the bed nucleus of the stria terminalis J Neurosci 24: 781–790, DOI: [PubMed] Lamont, EW; Robinson, B; Stewart, J; Amir, SThe central and basolateral nuclei of the amygdala exhibit opposite diurnal rhythms of expression of the clock protein Period2 102: 4180–4184, DOI: [PubMed] Harms, E; Kivimae, S; Young, MW; Saez, LPosttranscriptional and posttranslational regulation of clock genes J 19: 361–373, DOI: [PubMed] Meyer, P; Saez, L; -TIM interactions in living Drosophila cells: an interval timer for the circadian clock Science 31: 226–229, DOI: Dunlap, JCRunning a clock requires quality time together Science 311: 184–186, DOI: [PubMed] Xu, Y; Padiath, QS; Shapiro, RE; Jones, CR; Wu, SC;

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: Despite the lack of data for late spermatids, our results suggest that many errors are at least partially repaired before the completion of spermatid maturation. Alternatively, cell death could have removed mutated cells before spermatid maturation if a lesion could not be repaired. Our data cannot distinguish between the death of mutated cells and successful repair of lesions. The variants we have found are either DNA lesions that have escaped repair, or the lesions that have been selected through competition among cells (Loewe and Hill, 2010). It is likely that some of these substitutions would result in inviable offspring and would never be observed in an adult population. Our result suggests that mutational load varies between different cell divisions, consistent with previous work that suggests a variable lesion rate between cell types (Gao et al. , 2011; Gao et al. , 2014). Mutational load is the net product of damage and repair, and further characterization of how lesions occur and accumulate in the germline is needed to better understand the evolutionary ramifications of this process (Moorjani et al. , 2016). It appears that the cell types with the highest mutational load are germline stem cells/early spermatogonia, the earliest germ cells. This indicates that by the time germline stem cells enter spermatogenesis, they carry a relatively high mutational burden. This could be due to the fact that germline stem cells cycle many times, dividing asymmetrically to produce spermatogonia and a replenished germline stem cell. This cycle, repeated enough times, could cause a buildup of variants in germline stem cells as they continue to produce spermatogonia. Such a scenario would necessitate a mechanism to remove high level of lesions from maturing gametes. This mechanism must be an equilibrium removing enough lesions to prevent the accumulation of harmful phenotypes. However, the population-level mutation rate never reaches zero, otherwise adaptive evolution will cease (Lynch, 2010). Since we observed that the transcription of 211 DNA repair genes drops during meiotic stages, we suspect that DNA repair gene products are translated early and continue to repair lesions throughout spermatogenesis. After meiosis, however, the gametes become haploid, and there is no longer a template strand to facilitate homology-directed repair. This should constrain the types of DNA damage repair available in late spermatogenesis.

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: The waggle-dance compound mixture contained Z-(9)-tricosene, tricosane, and pentacosane, each diluted 1:100 in ether and mixed at a ratio of 1:2:3, respectively (this ratio produced chromatograms with peak heights that approximately matched those from samples of waggle dancers; Thom et al. 2007), and then further diluted 1:10 in ether. The substance was introduced into the hive by pipetting an aliquot of 100 μl onto each of three watch glasses (6-cm diameter) attached to a wooden strip, which was then immediately inserted into the entrance of the hive, effectively centering the three dishes on the bottom of the hive. The dishes remained in the hive until the experimental replicate was complete. To avoid contamination of the solvent dish, a separate but identical set of introduction apparatus was used for the ether and waggle-dance compound introductions. To control for presentation order and time-of-day effects, the order of the substance introduced (waggle-dance compounds or solvent) was alternated each day. To prevent observer bias, the identity of the substance introduced in each replicate was not revealed to the experimenter recording bee visits to the feeder station. The identity of the substance introduced in each replicate was known, however, by the experimenter recording hive departures because this individual also performed the substance introductions. A total of 15 solvent and 14 waggle-dance compound replicates were performed. To determine whether exposure to waggle-dance compounds increased the number of hive departures, the mean number of bee departures for solvent and waggle-dance compound replicates was compared using a two-sample T test. A similar comparison was made for bee arrivals at the feeder. Before each of these comparisons was made, the data was adjusted in three ways. First, to account for daily fluctuations in foraging conditions, the data for each replicate were normalized by dividing each 1-min count by the average number of hive departures per minute during the 10 min immediately preceding the experiment (for hive departure data) or by dividing each 1-min count by the number of feeder arrivals during the minute immediately preceding substance exposure (for feeder arrival data; the average was not used here because there was a predictable increase in bees arriving from minute 1 to minute 9).

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: , A; Dulong, S; Innominato, PF; Clairambault, JCircadian timing in cancer treatments 50: 377–421, DOI: [PubMed] Lévi, F; Schibler, UCircadian rhythms: Mechanisms and therapeutic implications 47: 593–628, DOI: [PubMed] Mormont, MC; Lévi, FCancer chronotherapy: Principles, applications, and perspectives Cancer 97: 155–169, DOI: [PubMed] Lévi, FRedfern P, Lemmer B(1997).

Output: pass


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: For example, images can be acquired faster from mammalian neural tissue than from Drosophila, both because its stronger contrast and fewer small processes. Figure 6 Download asset Open asset Improved FIB-SEM resolution reveals more detailed cellular structures in biological samples. Typical images of (a) Drosophila central complex and (b) Chlamydomonas reinhardtii, using standard 8 × 8 × 8 nm3 voxel imaging condition are shown in the top panels. The bottom panels show the corresponding high-resolution images at 4 × 4 × 4 nm3 voxel. Scale bar, 1 µm. Inset scale bar, 200 nm. An 8 × 8 × 8 µm3 high-resolution data set from the Drosophila central complex acquired over 10 days illustrates clearly delineated processes, and synapses with well-defined postsynaptic densities (see Figure 7 and Video 4). This high-quality data provides significantly more accurate estimates of synaptic connectivity than possible for lower-resolution stacks. Moreover, data of this quality will permit highly automated reconstruction, thus greatly reducing the time required for manual proofreading. In contrast, it would take only ~2 hr to acquire a comparable dataset using the high-throughput mode of acquisition, but it would require hundreds of man-hours of proofreading to correct the dataset because of the small neurites in Drosophila. High-resolution data also provides an accurate ‘gold standard’ for the higher throughput data, helping to interpret the larger dataset and perhaps also serving as a reference for machine learning. The actual resolution of this high-resolution mode can be objectively quantified by intracellular structures of known dimensions. For example, in Figure 7b, the resolved hollow core of the 25 nm outer-diameter/17 nm inner-diameter microtubule confirms a resolution of <3. 5 nm (referenced to a 25–75% step edge rise resolution criteria, consistent with an alternative definition for resolution of (spatial period = 21 nm/2π). Figure 7 Download asset Open asset A high-resolution image (4 × 4 × 4 nm3) of a Drosophila protocerebral bridge (in the central complex) reveals fine details of various organelles.

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: Second, all data were natural-log transformed to yield normally distributed sample groups with equal variances. Third, data from morning and afternoon trials were pooled because time of day did not impact behavior at the feeder; the mean bee count just before substance exposure was almost identical between morning (8. 5 bees/min, 95% CI ± 2. 7) and afternoon (8. 9 bees/min, 95% CI ± 2. 8) replicates. 2. 2 Experiment 2Experiments were conducted between June 25 and August 18, 2009, using two colonies of approximately 7,500 workers of the Italian variety (Apis mellifera ligustica) housed in a five-frame hive in an uncultivated field in North Haledon, New Jersey. Foragers were trained, as described for Section 2. 1, to a feeder containing unscented sugar water located approximately 100 m from the hive. Following training of the bees to the feeder, but before experimental replicates began, we marked each bee visiting the feeder with a unique color combination to allow individual identification of the foragers experienced with the feeder-dish food source. Thereafter, the feeder was filled only once each day so that the bees remain trained to it, but this was done at a random time of day to prevent the bees from learning to visit the feeder at a particular time. During each daily feeding, which lasted approximately 60 min, additional foragers were marked to ensure that the majority of visitors to the feeder during each experimental replicate were marked for individual identification. The total number of marked bees by the end of the experiment was approximately 84 for colony 1 and 92 for colony 2. Each replicate of this experiment consisted of recording for 60 min the time and identity (“unknown” for unmarked bees, never more than 10% of the visiting bees) of each forager visiting the empty feeder dish. A visit was defined as a bee landing on the feeder dish, no matter how briefly. Any repeat visits by a bee within 60 s of the bee’s first visit were not considered visits. Introduced into the hive at minute 30 was 300 μl of either waggle-dance compound mixture or this mixture’s solvent, ethyl ether. Introduction procedures and composition of the waggle-dance compound mixture were identical to those described for Section 2.

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Journal of Circadian RhythmsStart SubmissionBecome a ReviewerReading: Weak evidence of bright light effects on human LH and (US English)PDF (US English)Alt. DisplayShareShareResearch 10. 1186/1740-3391-8-5Submitted on Feb 27, 2010Accepted on May 11, 2010Published on May 11, 20104. 0 generations of scientists have studied photoperiodism extensively throughout the biological world. One of the most dramatic photoperiodic responses in birds is a massive increase in luteinizing hormone (LH) appearing within a few hours of stimulatory light exposure at a critical time of night [1]. Likewise, in small mammals, light at critical times of night produces large increases in LH and follicle stimulating hormone (FSH), resulting in growth of gonads [2 - 4]. These increases in gonadotropins prepare animals for seasonal breeding [5]. There is a preponderance of evidence that light at night functions to decrease the duration of melatonin secretion, causing the nights to be interpreted as shorter (complementing a longer summer-like day) [6 - 8]. However, some evidence for critical time intervals for light (or melatonin) sensitivity at night suggests a more complex mechanism [9,10]. Moreover, in hamsters, light may stimulate LH at times outside the normal interval of melatonin secretion [4]. In mammals, neurobiologic responses to light are intrinsically bound to the circadian timing system [4,5,11]. The relationships between melatonin peak duration and LH stimulation are species-specific and may be somewhat different in large mammals, whose gestation period may require autumn-winter breeding for births to occur in the spring. LH is regulated photoperiodically in sheep, but short days (longer nights) stimulate LH in order to implement autumn-winter breeding, which results in spring births [12]. Nonhuman primates are also photoperiodic breeders, but the situation is complex, as some primates breed (and show LH peaks) in autumn or winter [13]. In female rhesus monkeys, light increased multiunit activity of hypothalamic neurons (which were presumably those GnRH neurons which stimulate LH release) [14]. Although seasonal elevations of LH may occur at various times of year, depending on the seasonal breeding adaptation, prolactin elevations occur in summer in both summer-breeding and most winter-breeding mammals [15].

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: (a) an 8 × 8 µm2 area overview; (b) end-on and side views of microtubule, indicated by green arrows; (c) polyribosomes attached to the endoplasmic reticulum, indicated by blue arrows; and (d) synaptic vesicles, presynaptic T-bar, and postsynaptic density, shown in two different z planes. Video 4 shows the corresponding full z stack. Scale bar, 1 µm in (a) and 500 nm in (b)-(d). Video 4 Download asset This video cannot be played in place because your browser does support HTML5 video. You may still download the video for offline viewing. Download as MPEG-4 Download as WebM Download as of synapse in Drosophila protocerebral bridge showing multiple post synaptic contacts. FIB-SEM for cell biology Further improvement in resolution/volume for FIB-SEM should pay substantial dividends for cell biology, just as previous two-fold resolution improvements in fluorescence microscopy have enabled important scientific advances by rendering finer details. Here, we illustrate the potential of this approach for cellular neurobiology with data from the nucleus accumbens, a region of the mammalian forebrain involved in reward processing (see Figure 8a and Video 5). This dataset encompasses much of the soma of one neuron, along with the surrounding neuropil. The endoplasmic reticulum (ER) is well resolved and easily segmented, allowing its full 3D structure to be extracted; one is no longer relying on sampling from 2D EM sections to infer its 3D organization. For example, the frequency of ER-to-plasma membrane and ER-to-mitochondrion contacts can be quantified across a whole cell (Wu et al. , 2017), providing new insight into contact-dependent processes such as lipid transfer. Dendrites with readily-segmentable organelles, and synapses with all vesicles countable are plentiful and could be mined for statistics, for example, quantitative comparisons among synapses from the same axon, or onto the same dendrite. Figure 8 Download asset Open asset Isotropic high-resolution data offer easy visualization of 3D structures through arbitrary slices. (a) Two orthoslices (x–y and x–z) from nucleus accumbens in a sample of adult mouse brain.

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: 1 Also recorded was the number of departures of bees from the hive, which was sampled for 60 s every fourth minute. Each replicate of the experiment was conducted at one of the following times of day: 09:00, 11:00, 13:00, 15:00, or 17:00, determined randomly. Because the feeder must remain empty during data collection, the daily feeding was scheduled so as to not coincide with the experiment. A single replicate was performed each day to insure that each substance exposure was independent of previous exposures. The type of replicate (solvent control or waggle-dance compounds) was determined by coin toss each day, and to avoid observer bias, this information was withheld from the observer at the feeder. Two colonies were used for the experiment. Only a single colony was set up at any one time to prevent competition and drifting among colonies that might obfuscate results. Eleven replicates (six waggle-dance compound and five solvent control introductions) were conducted with colony 1, and another 11 replicates (five waggle-dance compound and six solvent control introductions) were conducted with colony 2. The data generated by the experiment described above yielded three variables upon which we focused our analysis. 1. Number of Visits to Feeder: the total number of bee arrivals at the feeder, including unmarked bees (n = 11 replicates for colony 1, n = 11 replicates for colony 2) 2. Number of Visitors to Feeder: the number of unique visitors (i. e. , different individuals) that arrived at the feeder, excluding unmarked bees (n = 11 replicates for colony 1, n = 11 replicates for colony 2) 3. Number of per Bee: the number of visits to the feeder by each individual bee, including only those marked bees that participated in at least one dance-compound replicate and one solvent-control replicate (n = 34 bees for colony 1, n = 42 bees for colony 2) To investigate the effects of the dance compounds on each of these three variables, we calculated the difference between the Number of Visits/Number of Visitors/Number of Visits per Bee for the 30 min before substance introduction compared to the 30 min after substance introduction.

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Humans may be an exception [16]. Much progress has been made in understanding the mechanisms of mammalian photoperiodism. The light stimulus is probably transmitted from retinal neurons containing the photopigment melanopsin and supplying the axons of the retino-hypothalamic tract [17 - 20], which synapse within the suprachiasmatic nucleus (SCN), releasing neurotransmitters PACAP, glutamate, and perhaps acetylcholine [21]. Accessory pathways to the SCN may be involved, including pathways from the serotonin-releasing cells of the midbrain and the intergeniculate leaflet cells releasing NPY and GABA. SCN cell-surface receptors regulate the transcription of circadian clock genes through complex pathways [20,22]. The SCN appears to be a crucial center of photoperiodic control [23]. The timing of dawn and dusk influences SCN functional circadian organization, apparently through differential entrainment effects on morning and evening circadian oscillator components [24 - 26]. It is possible that separate evening and morning components are represented in the molecular circadian clock, e. g. , by PER1, PER2, and the cryptochromes, the circadian phase relationships of which, somehow mediate photoperiodism [27 - 30]. Thus, the timing of light exposure may influence the dynamics of the SCN molecular circadian clock. An important output of the SCN controls the nocturnal release of melatonin from the pineal. The secretion of melatonin is longer in long nights (short days), but may be abbreviated by brief light exposures during the night [6]. There is much evidence that the pineal and melatonin are necessary for the inhibition of gonadal function produced by short days. It appears that melatonin effects on hypothalamic synthesis of active T3 and reverse T3 may mediate some of these responses [31,32]. Regulation of LH and FSH is responsive to the circadian timing of light, to the absolute photoperiod, and also to the history of change in photoperiod [4,33]. Pituitary release of LH is largely governed by the frequency of pulsatile releases of gonadotropin releasing hormone (GnRH) into the portal circulation [34]. Part of the response involves sensitivity to negative feedback of gonadal hormones (such as estrogen) upon GnRH cells [35]. There is considerable interspecies variation in the anatomy and connections of GnRH cells.

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: Many details in the structure of the nucleus, mitochondria, ER, and Golgi are visible. Of particular interest is the large cup-shaped chloroplast and the associated light-sensing eyespot and the ‘pyrenoid,’ a Rubisco-rich structure involved in the first major step of carbon fixation. All these structures are clearly distinguishable; their overall organization and interplay, in various functional conditions and in light-sensitive mutants, would provide new light on mechanisms of photosynthesis. C. reinhardtii flagella have also been extensively studied to understand cell motility. Zooming into the flagellar base (see inset Figure 6b and Videos 6 and 7), the nine-fold doublet microtubule structure becomes clearly visible, and details of the mature basal body pair and two probasal bodies are revealed. The latter form during basal body replication, at a very early stage of cell division in C. reinhardtii. After cytokinesis, the daughter cell will contain one mature basal body and one newly-formed one from which the flagella pair will grow (Silflow and Lefebvre, 2001; Preble et al. , 2000). Our imaging of this stage illustrates how recording a large data set that includes a population of cells allows the researcher to capture a variety of details through the cell cycle, as well as being more statistically meaningful than a single tomogram of a thin section of a single cell could ever be. Video 6 Download asset This video cannot be played in place because your browser does support HTML5 video. You may still download the video for offline viewing. Download as MPEG-4 Download as WebM Download as Chlamydomonas reinhardtii. Video 7 Download asset This video cannot be played in place because your browser does support HTML5 video. You may still download the video for offline viewing. Download as MPEG-4 Download as WebM Download as structure of a Chlamydomonas reinhardtii. Video 8 Download asset This video cannot be played in place because your browser does support HTML5 video. You may still download the video for offline viewing. Download as MPEG-4 Download as WebM Download as of volume stitch test in Drosophila protocerebral bridge region between hot knife sections #26 and #27. The wealth of structural data yielded by this approach merits the application of data mining tools.

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: The general linear model was used to determine whether replicate type (solvent control or dance compounds) and colony identity (colony 1 or colony 2) were significant factors with respect to the first two variables (Number of Visits and Number of Visitors). The differences used in the general linear model are expressed as percent changes in Figure 2a, b for ease of comparison. Because the data for the third variable (Number of per Bee) were self-paired, a repeated measures ANOVA was used to determine the effect of replicate type and colony identity. The repeated measures ANOVA used as subjects the 76 individual bees which visited during both solvent control and dance compound replicates. In cases where an individual bee participated in more than one replicate of either type, we calculated the average difference between visits before and after exposure and used this average in the T test. All three variables were normally distributed with equal variances between both factors. 3 Results3. 1 Experiment 1: number of bee departures from hiveThe average number of departures from the hive following substance exposure depended on whether waggle-dance compounds or solvent was introduced (Figure 1a). The time course of this effect can be divided into three distinct phases: before substance exposure (minutes 1–9), immediately following substance exposure (minutes 11–19), and the second half of the experiment (minutes 21–39). Before substance exposure, there was no difference in departures between waggle-dance compound and control exposures (two sample T test of average number of departures between minutes 1 and 9—T value = 1. 47, P value = 0. 153, df = 27). Immediately following substance exposure, there was a momentary decrease in the number of departures, which was more quickly recovered from during waggle-dance compound than control replicates (Figure 1a, minute 13), though the overall trend for this period of the experiment did not significantly favor waggle-dance over control exposures (two sample T test, minutes 13–19—T value = −1. 74, P value = 0. 094, df = 27; minute 11 removed from analysis to avoid artifacts of the disturbance resulting from introduction of the compounds into the hive).

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: In a small study of 11 healthy young men, our laboratory found that 1000 lux bright light from 0500-0600 in the morning for 5 mornings could increase daily LH production as much as 65% [54]. This dramatic augmentation of LH production by bright light needed replication. It also raised many additional questions: What would happen with light treatment at other times of day? What would happen with longer durations of daily treatment? What would happen after several weeks of treatment? Will similar responses occur in older men who may be more in need of LH-testosterone augmentation? Would similar responses occur in women, in whom there is preliminary evidence that light may augment LH, FSH, and ovulation [55]? Would the effect in women depend upon menstrual cycle phase or upon menopause? To seek data relevant to these questions, we assayed LH and FSH in samples from three human studies undertaken for other goals. 1, PRseries of experiments were performed to examine light circadian phase-response curves (PRCs), contrasting adult women and men of young and older ages [56]. Baseline circadian phase was assessed by monitoring subjects for 30-48 hours in the laboratory while they underwent an ultra-short 90-min sleep-wake cycle, consisting of a 30 min. lights-out-sleep period followed by a 60 min. lights-on-wake interval in 50 lux. Urine samples collected by the participants were frozen every 90 min. (2 ml) for later assays, to measure urinary aMT6s (6-sulfatoxymelatonin), the primary metabolite of melatonin. After aMT6s was assayed, the refrozen samples were subsequently rethawed for urinary LH assays. Using stratified randomization, subjects were assigned to receive 3000 lux light treatment for 3 hours on each of 3 consecutive days at one of 8 times of day, while continuing the 90-min ultra-short sleep-wake cycle. Because of variability in baseline circadian phase adjustment, light treatments were effectively administered randomly throughout the 360-degree circadian cycle. Then a 30-hour follow-up assessment was made with further urine collections every 90 minutes. LH was assayed in rethawed baseline and follow-up samples with the DSL-10-460 ActiveR LH Elisa, an enzymatically amplified "one-step" sandwich-type immunoassay (Laboratories, Inc. , Webster, TX.

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: a detailed protocol Fault-tolerant protected facilities with layers of backups were implemented on all utilities to provide uninterrupted and stable power, cooling water, compressed air, room temperature, air handling, etc. These back-up utilities were further tuned so that any transition would not produce a damaging fluctuation. For example, switching from a failed main air handler to an auxiliary unit will produce a transient in room temperature of <0. 5°C. Although costly, these facility upgrades are the foundation of stable long-term operation. A second layer of protection is achieved by monitoring environmental parameters like room temperature, so that the system can be paused quickly in the event of an anomalous excursion. In-line image auto-optimization Request a detailed protocol During extended image acquisition, SEM focus, stigmation, and aperture alignment must be optimized periodically to correct drift of various components. Traditionally, these adjustments are performed manually off-line, causing interrupts to the continuous milling and imaging process. Besides increasing overhead, this approach introduces further errors by disturbing the steady state of milling and imaging cycles. The in-line optimization procedure described below effectively overcomes the deficiencies in conventional methods. Recognizing these problems, a functionally similar approach was previously described (Binding et al. , 2013). In our approach, a ‘focus index’ (FI) based on the strength of the highest spatial frequency components is calculated to assess the focus quality for each acquired image. FI=[∑i=0n−1(I∗S1−I∗S2)2]/n, where the original 2D image I is smoothed by 2D Gaussian functions of a shorter (S1) and a longer (S2) length scale that straddles the resolution limit. Typical standard deviation values for Gaussian distributions S1 and S2 are 1 and 4 pixels, respectively. The total root mean square pixel-to-pixel difference between those two smoothed images averaged over the total number of pixels (n) is assigned to the original image as a focus index, where i is the index of each pixel. A higher focus index indicates more high spatial frequency content, and therefore a better-focused image. The focus index value depends upon the highest spatial frequency features of the sample, the actual focus of the electron beam spot, and the signal intensity.

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: During the last half of the experiment, there was little change in the average number of departures, but there were significantly more departures during waggle-dance compound exposures than during control exposures (two sample T test, minutes 21–39—T value = −2. 11, P value = 0. 044, df = 27). Figure 1Mean normalized number of bee departures from the hive and arrivals at a feeder station for two treatments over the course of 29 40-min trials. At minute 10, either the waggle-dance compound mixture or the mixture’s solvent, ether, was introduced into the hive. Error bars indicate one standard error. a Bee departures from the hive. Counts for each replicate were normalized to the average number of bees departing between minutes 1 and 9. b Bee arrivals at feeder station. Counts for each replicate were normalized to the number of bees arriving at minute 9. Full size image 3. 2 Experiment 1: number of bee arrivals at feederThe average number of arrivals at the feeder following substance exposure depended greatly upon whether waggle-dance compounds or solvent was introduced (Figure 1b). The time course of this effect can be divided into the same three phases as above: before substance introduction (minutes 1–9), immediately following substance introduction (minutes 11–19), and the second half of the experiment (minutes 21–39). Before substance introduction, there was again no difference in arrivals between waggle-dance compound and control exposures (two sample T test of the average number of arrivals between minutes 1 and 9—T value = −0. 52, P value = 0. 610, df = 27). Immediately following substance introduction at minute 10, feeder arrivals remained unchanged (Figure 1b, minute 11), but then increased significantly more quickly during waggle-dance compound than during control exposures (two sample T test, minutes 11 to 19—T value = −3. 80, P value ≤ 0. 001, df = 27). During the last half of the experiment, feeder arrivals increased slowly for both types of substance introductions, but by this point arrivals during waggle-dance compound exposures outnumbered those during control exposures by nearly a factor of two (two sample T test, minutes 21 to 39—T value = −3. 61, P value ≤ 0. 001, df = 27).

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: In pilot studies, adult women with PMDD exhibited an abnormal phase shift to early morning light, suggesting some disorder of the circadian system. This study contrasted the phase-shifting responses to early-night and early-morning bright light in women with DSM-with the responses of normal controls. The age range was 20-45 years. First, the women underwent extensive diagnostic evaluations and preliminary Center admissions to determine their dim light melatonin onset (DLMO) in the follicular and luteal menstrual phases. DLMO is that time of evening when the onset of melatonin secretion occurs, an excellent circadian timing marker, which is used to insure that each subject can be exposed to bright light at standardized phases of the circadian rhythm, even though circadian rhythms differ in phase-timing from one subject to another. Then, in separate months, each woman underwent two Center admissions to test bright light responses, once in the follicular menstrual phase (8 ± 2 days after the onset of menses) and once in the luteal menstrual phase (2-4 days before the date of next expected menses, over a month later). Each of these Center admissions included a baseline urine-sampling night, a bright light treatment night, and an additional follow-up night for urine sampling to determine hormonal results of light treatment. Apart from the treatment, subjects were maintained in dim light or darkness. Fractional urine specimens were measured and sampled both during the baseline (6 PM to 11 AM) and during the follow-up (6 PM to 11 AM). Part of each group (PMDD and controls) received bright 6000 lux light for 3 hours early in the night, starting 3 hours after the DLMO (approximately 24:00-0300). Also, the other half of each group (PMDD and controls) received similar bright light early in the morning starting 8 hours after the DLMO (approximately 05:00-08:00). Blood and urine samples were assayed for melatonin, to determine the phase of the circadian system, which is indicated well by the nocturnal rise and morning fall of melatonin. The bright light administered starting 3 hours after the DLMO was expected to be phase-delaying. The bright light starting 8 hours after the DLMO was expected to be phase-advancing in controls, but possibly not among PMDD patients. Urinary LH and FSH data were analyzed in SPSS 12.

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: Effect of landing energy on signal and contrast Request a detailed protocol The dependence of the fraction of backscattered electrons on the energy of the primary beam is summarized in the table of Figure 15a for both modeled and measured values, for the three reference samples and for a modeled lipid-osmium sample. The parameter of interest is the staining contrast for a known percentage of highly scattering heavy metal. This is tabulated for contrast between epoxy to Pt[(C6H5)3P]4 for both modeled and measured values, and also between lipid membrane with 0 and 1 molarity of osmium stain. In all cases, the best contrast is at the highest energies of 1. 2 keV, and drops over a factor of 2 with lower landing energies of about 600 eV, reflecting the increased relative backscattering cross-section of carbon vs. osmium at low energies, Figure 15b. For typical samples with ~100 low Z (mainly hydrogen, carbon and oxygen) atoms for every high Z osmium atom, this explains why contrast vanishes below 600 eV, when the weighted contrast ratio falls to unity. Effect of landing energy on the point spread function Request a detailed protocol The landing energy determines the resolution, since higher energy electrons scatter further and explore larger volumes of the sample before they backscatter. This can be quantified by the model in Figure 17a,b, which shows such a distribution of scattering locations for primary electron energies of 0. 8 and 1. 2 keV in a sample not stained with osmium, and approximates the Function (PSF) for signal. The spatial distribution difference between stained and unstained samples is relatively small, Figure 17a,c. These figures of scattering location can be misleading in estimating the contribution to PSF arising from the distribution of scattering locations. Any differential contrast will also be heavily weighted by the higher energy scattering events, which are concentrated even more to the center in the red (highest energy backscattered electrons) region. Figure 17 Download asset Open asset Effect of landing energy on the point spread function based on simulations. (a,b,c). simulation of backscattered electrons at different landing energies. Lower landing energy generates smaller sampling volume (implying better resolution), but with reduced contrast and SNR, as discussed in (d,e).

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: This difference between waggle-dance compounds and control exposures remained through to the end of the experiment, 30 min after substance introduction (Figure 1b, minute 39). 3. 3 Experiment 2: number of visits to feederThe number of visits to the empty feeder dish was significantly greater following exposure to the waggle-dance compounds compared to the solvent control (general linear model, F = 14. 69, P ≤ 0. 001, df = 1,19), while colony was not a significant factor affecting the number of visits (F = 0. 02, P = 0. 895, df = 1,19). Data from the two colonies are therefore pooled into one data set, and this is displayed as percentage changes in Figure 2a. Figure 2Comparison of changes in foraging behavior following exposure to waggle-dance compounds and a solvent control. Change is the difference between the bees’ behavior during the 30 min prior to substance introduction and the 30 min following substance introduction. Error bars indicate one standard error. a The number of total visits to the feeder station (n is the number of replicates of each type). b The number of marked unique individual bees visiting the feeder (n is the number of replicates of each type). c The number of feeder visits per marked unique individual bee (n is the number of unique individual bees that participated in at least one of each type of replicate). Full size image 3. 4 Experiment 2: number of visitors to feederThe number of unique visitors to the empty feeder was significantly greater following exposure to the waggle-dance compounds compared to the solvent control (general linear model, F = 6. 42, P = 0. 020, df = 1,19), while colony was not a significant factor affecting the number of visits (F = 0. 28, P = 0. 606, df = 1,19). Data from the two colonies are therefore pooled into one data set, and this is displayed as percentage changes in Figure 2b. 3. 5 Experiment 2: number of feeder visits per beeThe number of feeder visits per bee was significantly greater following exposure to the waggle-dance compounds compared to the solvent control (repeated measures = 14. 28, P = 0. 0003, df = 1,75) while colony was not a significant factor (F = 2. 58, P = 0.

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Therefore, we cannot exclude that the increases in LH were due to various placebo and nonspecific experimental effects, as well as the passage of time. For example, suggestion and hope often produce positive placebo responses in a wide variety of trials. If a clinical trial commenced with subjects in a heightened state of anxiety or depression, spontaneous remission might lead to endocrine changes such as enhancements of LH and FSH production. In a separate study, our group demonstrated a significant increase in FSH after early morning stimulations with bright green light, as compared to dim light placebo, but this effect was not very robust [65]. We are left with tantalizingly suggestive evidence that bright light stimulates LH and FSH in human subjects, but there is a need for much more convincing evidence. These studies had a number of limitations. In the first study, the light stimuli were administered for only 3 days at a level of only 3000 lux, whereas, a longer duration of brighter stimulation might have produced a greater gonadotropic response. In the second study, though 10,000 lux bright light stimuli were randomized for 4 weeks, we were uncertain of the compliance of these very depressed and elderly study participants, particularly since there was only weak evidence for circadian phase-shifting effect in the experimental groups and no persuasive evidence of a favorable mood effect. Only data from the morning light treatments were analyzed because of lack of evidence that the evening treatments had any physiologic or mood effects. In the third study, the numbers of subjects were extremely small, and the light stimulation was given only on a single day, which may have been insufficient to produce a large effect. A light stimulus intended to produce a phase shift may not be optimal for stimulating LH and FSH. Though we were able to obtain data from these studies which had been organized for other goals, the numbers of participants yielding usable data was unexpectedly small in the second and third studies. There is also concern that the several years that the urine samples were frozen, and the freezing and thawing processes, might have introduced inaccuracy into the assays. studies organized specifically to measure bright light effects on gonadotropins may be needed to verify the potential of bright light regulation for the reproductive endocrine system. Longer durations of exposure should be tested. Competing interests The authors declare that they have no competing interests. Authors' contributions DFK participated in design, acquisition of data, interpretation and statistics, and manuscript preparation.

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: A model for ribosome biogenesis that includes DNA replication, transcription, translation, and ribosome assembly in slow growing E. coli has already been developed (Earnest et al. , 2015; Earnest et al. , 2016). As its components have on average 50% sequence identity to those genetic information processing genes in JCVI-syn3A, this model is assumed to be applicable to JCVI-syn3A as well. Hence, the next important step in modeling JCVI-syn3A is the reconstruction of its metabolic network. The metabolic reconstruction presented here is based on the curated genome annotation, extensive experimental information from the literature on M. mycoides capri and other mycoplasma species, and accompanying transposon insertion and proteomics data. Our model features 338 reactions organized in nine subsystems (see Supplementary file 1B), involving 304 metabolites, catalyzed by gene products of 155 genes, thus covering a third of the genes of JCVI-syn3A. The reconstruction process enabled us to suggest several annotation refinements and updates, and yielded a metabolic network that is fairly complete. Together with the reconstructed biomass composition of JCVI-syn3A and estimates of its reaction flux constraints and energy expenses, the reconstructed metabolic network was cast into a flux-balance analysis (FBA) model (Orth et al. , 2010). FBA yields the set of steady-state reaction fluxes through a metabolic network that maximize a pre-defined objective function, for example production of cellular biomass. The solution space of possible fluxes is constrained not only by the steady-state assumption, but also by specific flux limits accounting for maximal uptake/secretion rates or cellular energy expenses. If these flux limits are not known, the network stochiometry predicts the biomass yield achieved by the cell, that is gram biomass produced/gram carbon source taken up (or equivalently biomass production rate/carbon substrate uptake rate). If flux constraints, in particular substrate uptake rates are known or can be assumed, the yield as growth rate per uptake rate can be converted to an absolute growth rate. While measurements to derive such flux constraints are not available yet for JCVI-syn3A, some measurements are available from other mycoplasmas and bacteria that have the same high-affinity glucose transporter (PtsG) found in JCVI-syn3A. Using the glucose uptake rate measured in M.

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: 1107, df = 1,75). The mean difference for all 76 bees (from both colonies) between the number of visits before and after substance introduction for solvent control exposures was −0. 75, and for dance-compound exposures was −0. 07. These means are displayed in Figure 2c. 3. 6 Experiment 2: number of bee departures from hiveThe results concerning the number of bee departures from the hive do not directly relate to the hypothesis under investigation in the second part of this study, so they are only summarized here. This summary is included to verify the effect of the dance compounds on hive departures observed in a single colony in Section 2. 1. Two approaches were taken to assess the effect of the dance compounds on the number of departures from the hive. First, the number of bee departures from ten replicates using colony 1 and 12 replicates using colony 2 were pooled. For each replicate, we tallied the number of departures for minutes 30–40 (i. e. , the 10 min following substance introduction) and the number of departures for minutes 41–60 (i. e. , through to the end of the experiment). The percent change was then calculated by comparing these two time intervals to the number of departures during minutes 0–29 (i. e. , before substance introduction). The mean percent changes for solvent control replicates was −43% and −22% for minutes 30–40 and minutes 41–60, respectively, while the mean percent changes for waggle-dance compound replicates were −30% and +12% for minutes 30–40 and minutes 41–60, respectively. Second, a general linear model using changes in departures and incorporating replicate type (waggle-dance compound or control), time interval (minutes 30–40 or minutes 41–60), and colony (1 or 2) showed both replicate type and time interval as highly significant factors while colony was not (F = 10. 54, P = 0. 002 for replicate type; F = 21. 7, P ≤ 0. 001 for time interval; and F = 0. 01, P = 0. 941 for colony; all df = 1,40). 4 DiscussionThe results from the two experiments presented here suggest two major conclusions. First, the hydrocarbons emitted by waggle-dancing bees affect the behavior of bees by stimulating foraging activity.

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: DOI: [PubMed] Hattar, S; Liao, H-W; Takao, M; Berson, DM; Yau, K-WMelanopsin-containing retinal ganglion cells: Architecture, projections, and intrinsic photosensitivity Science 295: 1065–1070, DOI: [PubMed] Berson, DM; Dunn, FA; Takao, MPhototransduction by retinal ganglion cells that set the circadian clock Science 295: 1070–1074, DOI: [PubMed] Gillette, MU; Mitchell, JWSignaling in the suprachiasmatic nucleus: selectively responsive and integrative Res 309: 99–107, DOI: [PubMed] Reppert, SM; Weaver, DRCoordination of circadian timing in mammals Nature 418: 935–941, DOI: [PubMed] Schwartz, WJ; de la Iglesia, HO; Zlomanczuk, P; within the mammalian brain: Photoperiodic orchestration through the suprachiasmatic nucleus J 16: 302–311, DOI: [PubMed] Jagota, A; de la Iglesia, HO; Schwartz, WJMorning and evening circadian oscillations in the suprachiasmatic nucleus in vitro 3: 372–376, DOI: [PubMed] vanderLeest, HT; Houben, T; Michel, S; Deboer, T; Albus, H; Vansteensel, MJ; Block, GD; Meijer, JHSeasonal encoding by the circadian pacemaker of the SCN 17: 468–473, DOI: [PubMed] Naito, E; Watanabe, T; Tei, H; Yoshimura, T; Ebihara, SReorganization of the suprachiasmatic nucleus coding for day length J 23: 140–149, DOI: [PubMed] Daan, S; Albrecht, U; Horst, GTJ van der; Illnerova, H; Roenneberg, T; Wehr, TA; Schwartz, WJAssembling a clock for all seasons: Are there M and E oscillators in the genes?

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: ACP carries a 4′-phosphopantetheine moiety in its holo form, and including the holoenzyme in the biomass equation enforces flux through the corresponding prosthetic group attachment reaction. dUTPase is included for technical reasons discussed in Section 'Nucleotide metabolism'. We use cellular abundances of 138 (ACP) and 10 (dUTPase), derived from the proteomics experiments. The resulting mass fractions are then subtracted from the total protein mass fraction. Lipids and capsule Based on the experimental lipid composition of M. mycoides capri serovar capri PG3 (Archer, 1975) and M. mycoides capri LC Y (Plackett, 1967a), the model includes the phospholipids phosphatidylglycerol and cardiolipin, the glycolipid monogalactosyl-diacylglycerol (Gal-DAG), cholesterol, diacylglycerol and free fatty acids. For fatty acids, palmitic acid (C16:0) and oleic acid (C18:1 cis-9) are considered to be the two most important representatives, and an average ‘fatty acid’ with a molecular weight averaged between palmitate and oleate is used in all lipid species. In addition, a galactan polysaccharide capsule is included in the biomass. M. mycoides capri LC GM12 (the strain from which JCVI-syn3A is derived) is known to produce a galactan polysaccharide (specifically, poly-β−1→6-galactofuranose) (Schieck et al. , 2016); while it is not yet experimentally known whether the minimal cell still produces this galactan, genetic features suggest it does. As other M. mycoides capri LC strains form a polysaccharide capsule but secrete negligible amounts of polysaccharide (Bertin et al. , 2015), the JCVI-syn3A galactan is assumed to form a capsule as well and is included as polygalactosyl-diacylglycerol (lipogalactan).

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: This was shown in the first experiment by the immediate rise and sustained high level of bee departures from the hive (Figure 1a) and bee arrivals at the feeder (Figure 1b) following exposure to a blend of three waggle-dance compounds. Some of this rise in foraging activity following exposure was no doubt due to natural waggle-dance recruitment to the sucrose solution available at the feeder, but comparison to control exposures shows that bee departures increased over control levels by as much as 46% and bee arrivals increased by as much as 106%. These increases in foraging activity over control levels must be due to the effect of the waggle-dance compounds. The difference in arrivals between dance compound and solvent control treatments was highly significant for the single colony tested in Section 2. 1. Similar results were obtained in Section 2. 2 for two additional colonies of a different subspecies during a different year (Figure 2a; shown are comparisons of before and after substance introduction, not the timescale of difference as in Figure 1). The observed responses of bees to the waggle-dance compounds are therefore not likely idiomatic, suggesting that the waggle-dance compounds play an important role in organizing foraging tasks within honey bee colonies. The second major conclusion to be drawn from the experiments described in this study is that the hydrocarbons emitted by waggle-dancing bees increase foraging activity at least partly by means of reactivation, i. e. , by stimulating foragers with knowledge of a food site to depart the hive and fly to the location of the food. Following exposure to the waggle-dance compounds, foragers visited an empty feeder in greater numbers (Figure 2b) and more often (Figure 2c) than following exposure to the solvent control. Because the feeder was empty, these increases over control levels cannot possibly be explained by enhanced recruitment to the feeder, but must be due to stimulation of foragers with experience foraging at the feeder. These experienced foragers are not only reactivated by the dance compounds but also stimulated to forage at a faster rate than the bees visiting the feeder during control replicates, which were either inspectors spontaneously checking known food sources or experienced foragers reactivated by a stimulus other than the introduced dance compounds. This increase in foraging rate (i. e.

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Journal of Circadian RhythmsStart SubmissionBecome a ReviewerReading: Phase delaying the human circadian clock with a single light pulse and moderate delay of the sleep/dark episode: no influence of iris colorDownloadXML (US English)PDF (US English)Alt. DisplayShareShareResearch 1. 3 ± 0. 6 h, with a maximum delay of ~2 hours, and was similar for subjects with blue and brown irises. There were no significant correlations between any of the iris color variables and the magnitude of the phase delay. Conclusion: A single 2-hour bright light pulse combined with a moderate delay of the sleep/dark episode delayed the circadian clock an average of ~1. 5 hours. There was no evidence that iris color influenced the magnitude of the phase shift. Future studies are needed to replicate our findings that iris color does not impact the magnitude of light-induced circadian phase shifts, and that the previously reported differences may be due to race. Year: 2009Page/10. 1186/1740-3391-7-8Submitted on Jun 3, 2009Accepted on Jul 17, 2009Published on Jul 17, 20094. 0 exposure can shift the human circadian clock in a phase-dependent manner. Light exposure during the evening hours or early in the habitual sleep episode produces phase delays, while light exposure late in the habitual sleep episode or morning hours produces phase advances [1 - 4]. The crossover point at which the phase shift in response to light exposure changes from delays to advances is estimated to occur near the body temperature minimum (Tmin) [1]. The rate at which the circadian clock can be shifted with light exposure is dependent on the spectral composition of the light source [5 - 8], the light level [9,10], and the duration and pattern of the light pulse(s) [11 - 14]. As the converse of light exposure, the timing or duration of the sleep/dark episode can also phase shift the circadian clock [15 - 19]. Many studies have measured the phase delay produced by bright light exposure administered over successive days (e. g. [20 - 23]). Some studies have also administered phase delaying light pulses on a single day. Understanding how much a single pulse of light can delay the circadian clock is important because practical constraints in the real world may limit the ability of individuals to adhere to several consecutive days of light treatment.

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan.Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: The product DAG serves as the lipid moiety for the synthesis of lipogalactan (catalyzed by epsG/0113 and cps/0114, see Section 'Biomass composition and reaction') and Gal-DAG. Lacking further evidence, Gal-DAG is assumed to be formed by either of the two glycosyltransferases, cps/0114 and 0697. Possibly related to lipid metabolism, the existing annotation lists a putative choline/ethanolamine kinase (0906); however, as M. mycoides capri LC is experimentally known to not produce phosphatidylcholine (Plackett, 1967a), we assume that this kinase has some yet to be determined substrate and do not include it in the model. Macromolecules and amino acids Schematics of the macromolecular and amino acid reaction networks are provided in Figure 11 and Figure 12. The genome of JCVI-syn3A contains a putative oligopeptide ABC importer (Opp/Ami, oppB/0165 through oppA/0169). lactis, the Opp system has been found to import peptides of four to at least 35 amino acids with little dependence of uptake rates on peptide length or amino acid composition (Detmers et al. , 1998; Doeven et al. , 2004). For the sake of simplicity, peptides imported are assumed to be representative homotetrapeptides of all amino acids except cysteine, since cysteine contained in peptides cannot be easily utilized by mycoplasmas (Yus et al. , 2009). The model assumes that any of four peptidases (ietS/0133, 0305, 0444, and 0479) can split these peptides into individual amino acids. Figure 11 Download asset Open asset Macromolecule metabolism in JCVI-syn3A. Map components and labels as in Figure 5. The detailed (amino acid-specific) stoichiometry of the protein synthesis and degradation reactions can be found in Supplementary file 4. Protein synthesis reactions for the proteins explicitly included in the model (apo-ACP, dUTPase and PdhC) are analogous to the translation reaction shown and are therefore not included in the map. Figure 12 Download asset Open asset Amino acid metabolism in JCVI-syn3A.

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: , number of visits per bee over 30 min) was relative rather than absolute. The absolute change in foraging rate for 76 bees when exposed to the dance compounds was not different from zero (Figure 2c). However, when compared to the control treatment, which contained the same amount of the solvent, the waggle-dance compounds had a significant stimulating effect (P = 0. 001). The depressant effect of the solvent on foraging behavior, which is seen throughout the data presented here, appears to be working in opposition to the stimulating effect of the dance compounds. Temporary disruption of foraging is not a particularly surprising response to ether, but use of such a solvent was unavoidable given the nature of the waggle-dance compounds. The conclusions from the experiments described in this study imply that the hydrocarbons emitted by waggle-dancing bees are a semiochemical that functions in concert with the information contained in the waggle dance to speedily and efficiently direct foragers to exploit available food sources. While the waggle dance advertises profitable food locations, the compounds emitted by the dancers may advertise to a wider audience favorable foraging conditions. A close comparison might be drawn to the foraging pheromone of bumblebees, which is released by bumblebee foragers upon returning from a successful foraging trip (Dornhaus and Chittka 2001; Dornhaus et al. 2003; Granero et al. 2005) and appears to act as a general foraging activation signal, indicating favorable foraging conditions. This pheromone, a collection of terpenes (Granero et al. 2005), is not chemically related to the long-chain hydrocarbons produced by honey bee waggle dancers. Similarity in function may therefore indicate convergent evolution. Within a honey bee nest, foragers with current memories of profitable food sites would be an important task group receiving and responding to a signal indicating favorable foraging conditions. Stimulation of experienced foragers by the waggle-dance compounds might explain why previous studies have found that experienced foragers can become reactivated after following dances very briefly (<5 s) or not at all (Gil and Farina 2002; Biesmeijer and Seeley 2005). However, we do not yet know whether a forager needs to follow a dance to be stimulated by the waggle-dance compounds, so this connection remains tentative.

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Phase delays of up to one hour per day can be produced when a phase delaying light pulse is combined with awakening at the usual time the next morning [24 - 26]. However, holding wake time constant would likely constrain phase delays of the circadian clock because morning light exposure on the advance portion of the light PRC would oppose the delaying effect of the evening/nighttime light pulse. When a very long single light pulse is combined with 2 days of a large abrupt shift of the sleep episode, the circadian clock can be delayed as much as three hours [9,27,28]. Although these delays can be quite large, delaying the sleep episode that much is not practical for most individuals trying to phase shift their circadian rhythms at home. When a phase-delaying evening light pulse is used in the field, it may be most practical to combine it with a moderate delay of the sleep/dark episode (e. g. [29,30]). The first goal of this study was thus to measure the phase delay produced by a single 2-hour light pulse before bedtime combined with a moderate delay of the sleep episode. A number of studies have shown large individual differences in the magnitude of the phase shift produced within the same protocol (e. g. [8,12,24,31,32]). Factors that may contribute to these individual differences include light exposure history, iris color and/or race. Light history has been shown to influence light-induced melatonin suppression [33,34], and these findings have recently been extended to circadian phase shifting [32,35]. One study found that light-eyed subjects had earlier sleep times and more "morningness" on a chronotype questionnaire [36], which could suggest that light-eyed subjects are more sensitive to the phase-advancing effects of morning light exposure. Light-induced melatonin suppression has been reported to be greater for light-eyed Caucasian than dark-eyed Asian subjects [37]. In this latter study it could not be determined whether iris color, race, or both accounted for the group differences. Differences in intraocular straylight as a result of iris color could influence non-image-forming responses such as melatonin suppression and circadian phase shifts. Intraocular straylight (light scattering) is the name for the phenomenon in which the retina receives light at locations that do not optically correspond to the direction light is coming from, but that nonetheless could trigger phototransduction.

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: An estimated 92,000 colonies were harvested from the plates in 20 ml of SP4 media (passage zero, P0) and a 45 µl sample was added to 45 ml SP4 media containing puromycin 2 µg/ml and grown for 24 hr (passage one, P1). A 45-µl sample of P1 culture was added to 45 ml of fresh SP4 media (P2) and grown for 48 hr. Two more passages (P3 and P4) were done. DNA preparations from each passage were done as described in Hutchison et al. (2016a), and DNA preparations were additionally purified by gel electrophoresis. library preparation kit was used for paired-end library construction (Illumina, San Diego, CA) by the manufacturer’s protocol with the following change. A forward primer 5′-designed by us and the reverse primer from the kit were used for the PCR amplification to achieve marker-specific sequencing (Wright et al. , 2017). To locate points of Tn5 insertion in the JCVI-syn3A genome, sequence reads were searched for the Tn5 19 bp terminus followed by an exact 30 bp match to genome sequence. The Tn5 to genome junction point identified the insertion location. ‘Duplicate insertions’ (i. e. insertions found in sequences repeated in the genome) were ignored in all further analyses since they could not be unequivocally assigned to a single gene. Tn5 insertions were displayed using CLC (). Classification of genes Request a detailed protocol To place genes into ‘essential’, ‘quasi-essential’, and ‘non-essential’ classifications, a simple statistical model of transposon insertion was used. It assumes that the positions of insertions within a gene are unbiased (Poisson distributed) and that the number of insertions in a particular gene is described by one of two possible distributions. The two distributions separate the genes into groups with few and many insertions. The probability to observe ni insertions for gene i, which has a sequence length of ℓi is (1) P(ni|ℓi)=ploekloℓi(kloℓi)nini!

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: Reception of the waggle-dance semiochemical may also explain why exposure of a non-foraging honey bee colony to the dance-floor odors of a foraging colony increases the number of foragers visiting an empty feeder (Thom and Dornhaus 2007), and why, in response to dancers indicating an unknown food source with an unfamiliar scent, most bees (82%) fly to previously visited food sites (Grüter et al. 2008). Floral food-source odors, which are known to reactivate experienced but inactive foragers in much the same way as the waggle-dance compounds (Reinhard et al. 2004), may be an alternative explanation for the former result (i. e. , Thom and Dornhaus 2007), but cannot explain the latter (i. e. , Grüter et al. 2008) because the food odor emanating from the dancer did not match the site with which the foragers were familiar. The discovery of the waggle-dance compounds’ role in the reactivation of nectar foragers also reinforces Grüter and Farina’s (2009) emphases regarding (a) the importance in honey bee foraging of private information about food sources, and (b) the clarification that the waggle-dance language is only one component of the multimodal, multicomponent waggle-dance signal and synonymous use of these terms should be avoided.

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Studies in which a single long duration bright light pulse (> 6 hours, up to ~10,000 lux) was paired with 2 days of a large delay (>8 hours) in the sleep/dark episode have reported phase delays of up to 3 hours [9,12,27,28]. Although a 3 hour phase delay from a single day of light treatment is robust, such a large shift in the sleep schedule may not be appealing or feasible for individuals using light treatment at home. The present study, which incorporated a compromise between not delaying wake time at all and completely inverting the sleep/dark episode, yielded large phase delays in a protocol that is more practical for real world applications. We found that phase delays of the DLMO for subjects with blue and brown irises were similar. Light exposure measurements while subjects were sitting in front of the light box were not different between subjects with blue versus brown irises, and were close to the targeted light levels. The light levels in the 3 subjects in the blue-eyed group that had smallest phase delays were still at or close to the targeted light levels, suggesting that variability in the light levels reaching the cornea did not account for the variability in phase shifts of the DLMO. Caucasian subjects in the Higuchi et al. melatonin suppression study [37] had iris colors including blue, green and light brown, while all the Asian subjects had dark brown irises. We only enrolled subjects with blue or brown irises, but we could not clearly differentiate between subjects with light versus dark brown irises by visual inspection because there were continuous gradations in iris color. We therefore quantified iris color using individual color axes and lightness scales derived from each subject's iris photographs. Although the blue and brown-eyed groups were distinguished by several color dimensions derived from the iris photographs, none of these dimensions were associated with phase shift of the DLMO, or were even in the predicted direction. It is nonetheless possible that differences in phase shifting due to iris color might have been observed at lower light levels or with a different light source than used in the present study. It is also possible that, via disparate mechanisms, iris color influences light-induced melatonin suppression, but not circadian phase shifting. The greater light-induced melatonin suppression in light-eyed Caucasians compared to dark-eyed Asians reported by Higuchi et al.

Output: corroborate


Input: Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan.Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: Spectra used for quantitation had to meet the requirements of greater than 10 average signal-to-noise per label and isolation interference of less than 25% (Ting et al. , 2011). Data were normalized as previously described (Lapek et al. , 2017b; Lapek et al. , 2017a). In order to convert relative protein abundances obtained from the mass spectrometry data to absolute cellular abundances (i. e. number of molecules per cell for each protein species), the average protein length and amino acid composition, and hence average molecular weight, were calculated from the relative abundances and known protein sequences. The molecular weight of the average JCVI-syn3A protein was then used to estimate the total number of all proteins in JCVI-syn3A based on the protein dry mass fraction and cellular dry weight (see Section 'Biomass composition and reaction'). This estimated total number of proteins was used to scale relative abundances of proteins in the proteome to absolute abundances in the average cell of JCVI-syn3A. The mass spectrometry data has been deposited on MassIVE with accession number 000081687 (ftp://massive. ucsd. edu/MSV000081687). The ProteomeXchange accession number is PXD008159. (Lapek and Gonzalez, 2017). Omics scale visualization Request a detailed protocol Voronoi treemaps (Figures 1, 3 and 17a) were constructed following (Liebermeister et al. , 2014). Briefly, the genetic loci were associated with a KEGG orthology (KO) identifier (Kanehisa et al. , 2015). Mappings between KO identifiers and locus tags were acquired from KEGG Genomes for M. pneumoniae (T00006) and E. coli (T00944). A mapping between genes and KO identifiers for JCVI-syn3A was derived from the locus tag/KO map for M. mycoides capri LC str. 95010 (T01478) by matching M. mycoides capri genes to JCVI-syn3A genes using a reciprocal best hit BLASTp search (Altschul et al. , 1990).

Output: pass


Input: Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: in through your institution issue and search term Advance 10. 1093/beheco/arq218 Published: 25 February 2011 10. 1093/beheco/arq218 Select format. ris (Mendeley, Papers, Zotero). enw (EndNote). bibtex (BibTex). txt (Medlars, RefWorks) Download citation issue and search term issue and search term study investigates variation in collective behavior in a natural population of colonies of the harvester ant, Pogonomyrmex barbatus. Harvester ant colonies regulate foraging activity to adjust to current food availability; the rate at which inactive foragers leave the nest on the next trip depends on the rate at which successful foragers return with food. This study investigates differences among colonies in foraging activity and how these differences are associated with variation among colonies in the regulation of foraging. Colonies differ in the baseline rate at which patrollers leave the nest, without stimulation from returning ants. This baseline rate predicts a colony's foraging activity, suggesting there is a colony-specific activity level that influences how quickly any ant leaves the nest. When a colony's foraging activity is high, the colony is more likely to regulate foraging. Moreover, colonies differ in the propensity to adjust the rate of outgoing foragers to the rate of forager return. Naturally occurring variation in the regulation of foraging may lead to variation in colony survival and reproductive success. A first step in understanding the evolution of behavior is to investigate variation among individuals in their responses to changing conditions (Sih et al. 2004; Dingemanse et al. 2009). Many social animals engage in collective decision making (Conradt et al. 2009). In social insect colonies, individual workers, using local information, perform and regulate colony tasks collectively (e. g. , Pratt and Sumpter 2006; Gordon 2010). Because social insect colonies produce new colonies, the colony can be considered to be a reproductive individual. Ant colonies vary in the distribution of worker sizes (e. g. , Beshers and Traniello 1994; Powell 2008), and differences among colonies in genetic diversity or number of patrilines (e. g. , Sundstrom 1993; Ross and Keller 1995; Crozier and Pamilo 1996; DeHeer and Herbers 2004) are associated with differences in behavior (Snyder 1993; Wiernasz et al. 2008).

Output: pass


Input: Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: How to trick mother nature into letting you fly around or stay up all night J 20: 353–365, [PubMed] DOI: Wright, HR and Lack, LC (2001). Effect of light wavelength on suppression and phase delay of the melatonin rhythm 18: 801–808, [PubMed] DOI: and Kennaway, DJ (2004). Differential effects of light wavelength in phase advancing the melatonin rhythm J 36: 140–144, [PubMed] DOI: and Skene, DJ (2003). Phase advancing human circadian rhythms with short wavelength light 342: 37–40, [PubMed] DOI: and Czeisler, CA (2003). High sensitivity of the human circadian melatonin rhythm to resetting by short wavelength light J Metab 88: 4502–4505, [PubMed] DOI: and Czeisler, CA (2000). Sensitivity of the human circadian pacemaker to nocturnal light: melatonin phase resetting and suppression J Physiol 526 Pt 3: 695–702. [PubMed] and Czeisler, CA (1996). Dose-response relationships for resetting of human circadian clock by light Nature 379: 540–542, [PubMed] DOI: and Czeisler, CA (2000). Dynamic resetting of the human circadian pacemaker by intermittent bright light 279: R1574–R1579. [PubMed] and Czeisler, CA (2004). Efficacy of a single sequence of intermittent bright light pulses for delaying circadian phase in humans Metab 287: E174–E181, [PubMed] DOI: and Eastman, CI (2003). Preflight adjustment to eastward travel: 3 days of advancing sleep with and without morning bright light J 18: 318–328, [PubMed] DOI: 'Hermite-Baleriaux, M and Zee, PC (2003). Effect of increasing light intensity vs. increasing light duration on phase shifts of the circadian clock of humans Sleep 26: A103. and Eastman, CI (1997). Conflicting bright light exposure during night shifts impedes circadian adaptation J 12: 5–15, [PubMed] DOI: 'and Birnbaum, J (2001). A single dose of melatonin prevents the phase delay associated with a delayed weekend sleep pattern Sleep 24: 272–281.

Output: corroborate