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Screening of ~7000 coronavirus-specific compounds for anti-SARS-CoV-2 activity
<p>This short report describes the most relevant results of screening selected compounds with potential activity against SARS-CoV-2 in a VeroE6 cell-based anti-SARS-CoV-2 assay.</p>
Quantitative Evaluation of COVID-19 Pneumonia Lung Extension by Specific Software and Correlation with Patient Clinical Outcome
<p>Quantitative Evaluation of COVID-19 Pneumonia Lung Extension by Specific Software and Correlation with Patient Clinical Outcome</p> <p>Dataset regarding lung extension of covid 19 </p>
Figure 1 in A theoretical composite model for population sex-specific shell size dynamics in Strombidae (Gastropoda, Neostromboidae)
Figure 1. Modelling male and females population distribution curves showing the mean size (μ) of each sex and the (1) Sex dependant factors: a) time to maturity; b) intra-male competition; c) femalespecific sexual selection; d) fecundity; (2) Inter-sex dependant factors: e) time to maturity; f) sex bias towards larger numbers of females; and (3) Population factors: g) environmental conditions; and h) universal size regulators that affect the size ratio between females and males.
Fig. 2. A in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 2. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among five novel Limosilactobacillus species, six L. reuteri subspecies and other recognized species in the genus Limosilactobacillus. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S rRNA gene sequences. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].
Fig. 3. A in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 3. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among six L. reuteri subspecies. The tree was reconstructed using 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp. murium, n=10 for L. reuteri subsp. reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium) and L. balticus BG-AF3-AT was used as an outgroup. Further information on the involved genome sequences is listed in Table S1. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. The tree was drawn with iTOL [54].
Fig. 4 in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 4. Pairwise average nucleotide identity values (ANI; %) of genome sequences belonging to the same or different L. reuteri subspecies. ANI values within the same subspecies and between different subspecies were calculated for 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp. murium, n=10 for L. reuteri subsp. reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium). Further information on the involved genome sequences is listed in Table S1.
Neuronal activity in sensory cortex predicts the specificity of learning
<p>Learning to avoid dangerous signals while preserving normal responses to safe stimuli is essential for everyday behavior and survival. Following identical experiences, subjects exhibit fear specificity ranging from high (specializing fear to only the dangerous stimulus) to low (generalizing fear to safe stimuli), yet the neuronal basis of fear specificity remains unknown. Here, we identified the neuronal code that underlies inter-subject variability in fear specificity using longitudinal imaging of neuronal activity before and after differential fear conditioning in the auditory cortex of mice. Neuronal activity prior to, but not after learning predicted the level of specificity following fear conditioning across subjects. Stimulus representation in auditory cortex was reorganized following conditioning. However, the reorganized neuronal activity did not relate to the specificity of learning. These results present a novel neuronal code that determines individual patterns in learning. Keywords: fear conditioning, auditory cortex, sensory systems, learning, computational model, imaging, sensory cortex, tuning curve, neurobiology, population coding.</p>
Direct and legacy-mediated drought effects on plant performance are species-specific and depend on soil community composition
Droughts affect plant communities, but their impacts may be mediated by soil biota. Soil communities may ameliorate drought stress, and droughts may leave legacies of altered soil communities that may affect future plant growth. However, it is not yet understood which groups of soil biota in particular affect plant performance under drought, nor which groups contribute to drought-legacy effects on future plant growth. We hypothesized that increasing soil-community complexity ameliorates drought stress and that drought-legacy effects are species-specific and soil-community-dependent. To test these hypotheses, we performed a two-phase experiment with six grassland species. In the first phase, we examined plant performance under drought and ambient conditions, in soils inoculated with a sterilized inoculum, or increasingly complex soil communities created by wet-sieving through 20-, 40-, and 200-µm mesh sieves. In the second phase, we examined drought-legacy effects on conspecific plant performance. We separately analysed plant performance in both phases, and integrated data from both phases using structural equation models. Drought effects on first-phase root biomass depended on soil inoculum, and this interaction differed among plant species, while effects on shoot biomass differed among species, but did not depend on inoculum. Only one species experienced drought-stress-ameliorating effects of soil biota. Drought-legacy effects on plant performance were positive, but depended on soil inoculum in case of root biomass, and on soil inoculum and species identity in case of shoot biomass. Drought-legacy effects were often mediated by first-phase biomass. In some species this effect was independent of inoculum, suggesting an abiotic legacy effect. In others, low first-phase biomass corresponded with high second-phase performance in presence of the most complex soil community. We conclude that drought-legacy effects on plant performance were soil-community-dependent but positive, suggesting that plants establishing after drought may benefit from increased nutrient availability and more positive impacts of soil biota.
Sex-specific influence of communal breeding experience on parenting performance and fitness in a burying beetle
<p>Communal breeding, wherein multiple conspecific individuals live and reproduce together during a single breeding event, may generate immediate benefits in terms of defence and reproduction. However, the carry-over effects of events in communal breeding on individual behaviour and fitness remain less studied. We experimentally tested the immediate and carry-over effects of communal breeding on parenting performance and fitness in the burying beetle (<em><span>Nicrophorus vespilloides</span></em>). These beetles bury carcasses as food resource for their offspring and themselves, and provide extended care to the developing larvae on the buried carcass. We subjected individuals of varying sizes to communal (i.e. group-breeding) or non-communal breeding (i.e. pair-breeding) experience during their first breeding event, and subsequently to non-communal breeding during their second breeding event, and measured parental effort and reproductive success during both breeding events. In communal groups, large individuals became dominant and monopolized the carcass. At the first breeding attempt, large males in communal groups spent more time providing care than large males in non-communal groups, while such a difference was not observed for large females and small females or males in communal and non-communal groups. Reproductive success was similar for individuals that bred in communal and non-communal groups during their first reproductive event, indicating no significant immediate benefits of communal breeding in terms of reproduction. Compared to males that originated from non-communal groups, males from communal groups produced a similar number, but heavier larvae during their second breeding attempt, whereas such an effect was not observed for females. Our results provide evidence for sex-specific effects of communal breeding experience on parenting performance and fitness. Such observed sex differences in carry-over effects of communal breeding on fitness may generate sexual conflict over parental effort in social animals.</p>
Global analysis of cell behavior and protein localization dynamics reveals region-specific functions for Shroom3 and N-cadherin during neural tube closure
<p>Failures of neural tube closure are common and serious birth defects, yet we have a poor understanding of the interaction of genetics and cell biology during neural tube closure. Additionally, mutations that cause neural tube defects (NTDs) tend to affect anterior or posterior regions of the neural tube but rarely both, indicating a regional specificity to NTD genetics. To better understand the regional specificity of cell behaviors during neural tube closure, we analyzed the dynamic localization of actin and N-cadherin via high-resolution tissue-level time-lapse microscopy during Xenopus neural tube closure. To investigate the regionality of gene function, we generated mosaic mutations in shroom3, a key regulator or neural tube closure This approach elucidates new differences between cell behaviors during cranial/anterior and spinal/posterior neural tube closure, provides mechanistic insight into the function of shroom3 and demonstrates the ability of tissue-level imaging and analysis to generate cell-biological mechanistic insights into neural tube closure.</p>
Observational evidence of herbivore-specific associational effects between neighboring conspecifics in natural, dimorphic populations of Datura wrightii
Associational effects – in which the vulnerability of a plant to herbivores is influenced by its neighbors – have been widely implicated in mediating plant-herbivore interactions. Studies of associational effects typically focus on interspecific interactions or pest-crop dynamics. However, associational effects may also be important for species with intraspecific variation in defensive traits. In this study, we observed hundreds of Datura wrightii – which exhibits dimorphism in its trichome phenotype – from over 30 dimorphic populations across California. Our aim was to determine whether a relationship existed between the trichome phenotype of neighboring conspecifics and the likelihood of being damaged by four species of herbivorous insects. We visited plants at three timepoints to assess how these effects vary both within and between growing seasons. We hypothesized that the pattern of associational effects would provide rare-morphs (i.e. focal plants that are a different morph than their neighbors) with an advantage in the form of reduced herbivory, thereby contributing to the negative frequency-dependent selection previously documented in this system. We found the best predictor of herbivory/herbivore presence on focal plants was the phenotype of the focal plant. However, we also found some important neighborhood effects. The total number of plants near a focal individual predicted the likelihood and/or magnitude of herbivory by Tupiochoris notatus, Lema daturaphila, and Manduca sexta. We also found that velvety focal plants with primarily sticky neighbors are more susceptible to infestation by Tupiochoris notatus and Lema daturaphila. This does not align with the hypothesis that associational effects at the near-neighbor scale contribute to a rare-morph advantage in this system. Overall the results of our study show that the number and trichome-morph composition of neighboring conspecifics impact interactions between D. wrightii and insect herbivores.
Allele-specific chromatin accessibility for 23 cancer types and weight files for Regulome Wide Association-Studies (RWAS)
<p><strong>stratAS_results.tar.gz</strong></p> <p>This folder contains the results of analyses of allele-specific chromatin accessibility for 23 cancer types + pan-cancer using the stratAS software. The analyses identified allelically imbalanced genomic regions from 406 cancer ATAC-Seq samples. The files are named after each cancer type (or “pancancer” for the pan-cancer analysis) and contain the following columns:</p> <p>CHR - Chromosome<br> POS - Position of test<br> SNP RSID - ID of test SNP<br> P0 - Start of gene/peak<br> P1 - End of gene/peak<br> NAME - Name of gene/peak<br> CENTER - Center position of peak (or TSS for gene)<br> N.HET - Number of heterozygous individuals tested N.READS - Number of reads tested in total<br> ALL.AF - Allelic fraction estimate from beta binomial test across both conditions<br> ALL.BBINOM.P - Beta-binomial test for imbalance across both conditions<br> C0.AF - Allelic fraction estimate from condition 0<br> C0.BBINOM.P - Beta-binomial test for imbalance in condition 0<br> C1.AF - Allelic fraction estimate from condition 1<br> C1.BBINOM.P - Beta-binomial test for imbalance in condition 1<br> DIFF.BBINOM.P - Beta-binomial test for difference between conditions<br> IND.C0 - Number of each condition 0 individual included in this test (comma separated)<br> IND.C0.COUNT.REF - condition 0 REF allele counts of each individual included in this test (comma separated)<br> IND.C0.COUNT.ALT - condition 0 ALT allele counts of each individual included in this test (comma separated)<br> IND.C1 - Number of each condition 1 individual included in this test (comma separated)<br> IND.C1.COUNT.REF - condition 1 REF allele counts of each individual included in this test (comma separated)<br> IND.C1.COUNT.ALT - condition 1 ALT allele counts of each individual included in this test (comma separated)</p> <p>In our analysis, samples that belong to a cancer type that is analyzed for allelic imbalance are assigned to Condition 1 (C1) while samples belonging to the remaining 22 cancer types are assigned to Condition 0 (C0). For the pan-cancer analysis, samples from all 23 cancer types are assigned to C1. P-values denoting the significance of allelic imbalance in a given cancer type (or pan-cancer analysis) are listed in the column C1.BBINOM.P. P-values denoting the significance of differential allelic imbalance between a given cancer type and the remaining 22 cancer types are listed in column DIFF.BBINOM.P (set to NA for pan-cancer analysis since all samples are assigned to C1).</p> <p>More information about stratAS and its output format can be found at https://github.com/gusevlab/stratAS.</p> <p>The conducted analyses are described in detail in the methods section of Grishin D. and Gusev A. Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms (2022).</p> <p><strong>RWAS_weights.tar.gz</strong></p> <p>This folder contains weight files that can be used together with GWAS summary statistics to conduct Regulome Wide Association-Studies (RWAS) using the FUSION software package.</p> <p>Each weight file corresponds to a single accessible element in the FUSION format. Instructions on how to use FUSION for RWAS can be found at http://gusevlab.org/projects/fusion/. RWAS is conducted in the same manner as TWAS using these RWAS weights.</p> <p>The weight files were generated using a pan-cancer peak set. A BED file containing pan-cancer peaks can be found in the peaks_hg19 folder along with other BED files containing cancer-type specific peaks. Cancer-type specific peak files can be used to restrict the RWAS analysis to regulatory elements active in specific cancer types.</p> <p>The conducted analyses are described in detail in the methods section of Grishin D. and Gusev A. Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms (2022).</p>
Impacts of using different standard populations in calculating age-standardized death rates when age-specific death rates in the populations being compared do not have a consistent relationship: A cross-sectional population-based observational study on US state HIV death rates
<p><strong>Objective</strong>: To examine if the rankings of state HIV age-standardized death rates (ASDRs) changed if different standard population (SP) was used.</p> <p><strong>Design</strong>:<strong> </strong>A cross-sectional population-based observational study. Setting 36 states in the United States.</p> <p><strong>Participants</strong>: People died from 2015 to 2019.</p> <p><strong>Main outcome measures</strong>: State HIV ASDR using 4 SPs, namely WHO2000, US2000, US2mor020, and Eur2011–2030.</p> <p><strong>Results</strong>: The rankings of 19 states did not change when ASDRs were calculated using US2000 and US2020. Of the 17 states whose rankings changed, the rankings of 9 states calculated using US2000 were higher than those calculated using US2020; in 8 states, the rankings were lower. The states with the greatest changes in rankings between US2000 and US2020 were Kentucky (12th and 9th, respectively) and Massachusetts (8th and 11th, respectively).</p> <p><strong>Conclusions</strong>: State ASDRs calculated using the current official SP (US2000) weigh middle-age HIV death rates more heavily than older-age HIV death rates, resulting in lower ASDRs among states with higher older-age HIV death rates.</p>
Design specifications
<p>This data was used for the redaction of the project deliverable "D2.5: Design specifications". Designing specifications for promising food markets for each targeted packaging technology of MYPACK.</p> <p>Moreover, this data is from the scientific publication "<a href="https://www.sciencedirect.com/science/article/pii/S0272494421001778?via%3Dihub%22%20l%20%22ack001"><strong>A meaningful reminder on sustainability: When explicit and implicit packaging cues meet</strong></a>”.</p>
Data from: Evidence for tissue-specific defense-offense interactions between milkweed and its community of specialized herbivores
<p>Input data used to generate the results for the manuscript under publication. It contains: 1) the residual enzymatic activity (absorbance) of 3 cardenolide-tolerant insects and the non tolerant fruit fly to 5 tissue extracts from Asclepias curassavica (roots, leaves, flower buds, seeds and latex); 2) The dilution level required to inhibit the enzymes by 50% (IC50); 3) The amount of tissue used to prepare the extracts for the enzymatic assay, as well as their cardenolide concentration to standardize the IC50 estimates by tissue mass and plant defense concentration; 4) The dataset of the chemical characterization by HPLC of the different plant parts of Asclepias curassavica; 5) The latex data used to estimate dry/wet mass ratio to correct for our latex samples.</p>
Distribution. Manus, New Britain, Duke of York, and Umboi Is; a specimen from Wetar I was identified as this species, but specific status of this specimen needs to be confirmed. in Vespertilionidae
Distribution. Manus, New Britain, Duke of York, and Umboi Is; a specimen from Wetar I was identified as this species, but specific status of this specimen needs to be confirmed.
Separating the effects of paternal age and mating history: evidence for sex-specific paternal effect in eastern mosquitofish
<p>Paternal age and past mating effort by males are often confounded, which can affect our understanding of a father's age effects. To our knowledge, only a few studies have standardized mating history when testing for effects of paternal age, and none has simultaneously disentangled how paternal age and mating history might jointly influence offspring traits. Here, we experimentally manipulated male mating history to tease apart its effects from those of paternal age on female fertility and offspring traits in the eastern mosquitofish (<em>Gambusia holbrooki</em>). Male age did not affect female fertility. However, males with greater past mating effort produced significantly larger broods. Paternal age and mating history interacted to affect sons' body size: sons sired by old-virgin males were larger than those sired by old-mated males, but this was not the case for younger fathers. Intriguingly, however, sons sired by old-virgin males tended to produce fewer sperms than those sired by old-mated males, indicating a potential trade-off in beneficial paternal effects. Finally, neither paternal age nor mating history affected daughter's fitness. Our results highlight that variation in offspring traits attributed to paternal age effect could partly arise due to a father's mating history, and not simply to his chronological age.</p>
FIGURE 9 in Notes on the specific identity of Synotis damiaoshanica (Compositae, Senecioneae), with clarification of the confusing identities of S. guizhouensis and S. sinica
FIGURE 9. Distribution map of Synotis guizhouensis (☆), S. damiaoshanica (★), S. austroyunnanensis (▲) and S. sinica (●).
FIGURE 6 in Notes on the specific identity of Synotis damiaoshanica (Compositae, Senecioneae), with clarification of the confusing identities of S. guizhouensis and S. sinica
FIGURE 6. Synotis guizhouensis [Guiding (location of the holotype S. guizhouensis), Guizhou, China]. A. Habitat. B and C. Habit. D. Adaxial (left) and abaxial surface (right) of leaf blades. E. Inflorescence. F. Capitula (side view, noting that left with 8 phyllaries while right with 12 phyllaries). G. Capitulum (top view). Notes: Red arrow in B showing the young plant with its leaves subrosulate on the uppermost stem; yellow arrows in E, F and G showing the inconspicuous revolute ray florets.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.