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Quantitative metaproteomics and activity-based protein profiling of patient fecal microbiomes identifies host and microbial serine-type endopeptidase activity associated with ulcerative colitis
<p>Supplemental files associated with patient ulcerative colitis metaproteomics study including protein fasta files, protein group (CD-HIT cluster) files, label free quantification output, de novo-database peptide comparison output tables, ComPIL database search output PSM files, 16S amplicon sequencing data, and Interproscan annotations.</p>
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Sarah Williams, <a href="https://orcid.org/0000-0002-2644-9952">https://orcid.org/0000-0002-2644-9952</a>. Claims were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Data from: Investigating human repeatability of a computer vision based task to identify meristems on a potato plant (Solanum tuberosum)
<p>Labelled training data in artificial intelligence (AI) is used to teach so-called 'supervised learning models'. However, such data may contain error or bias, which can impact model prediction accuracy. Thus, obtaining accurate training data is of high importance. In applications of AI, such as in classification and detection problems, raw training data is not always made available in published research. Likewise, the process of obtaining labelled data is not always documented well enough to enable reproducibility. This training data set captures a repeatability exercise in AI training data collection for a task that is difficult for humans to perform, delineating a bounding box in a two-dimensional image of a growing apical meristem in potato plants.</p>
Figure 2 from: Srisuka W, Aupalee K, Otsuka Y, Fukuda M, Takaoka H, Saeung A (2022) A new species of Simulium (Gomphostilbia) (Diptera, Simuliidae) from Thailand, with a key to identify females of 14 species of the Simulium varicorne species-group. ZooKeys 1083: 1-12. https://doi.org/10.3897/zookeys.1083.77428
Figure 2 Female of Simulium khelangense sp. nov. A antenna (left side; dorsal view) B third palpal segment with sensory vesicle (right side; front view) C cibarium D mid tibia (left side; outer view) E hind tibia (left side; outer view) F hind basitarsus and second tarsomere (left side; outer view) G claw of hind tarsus (lateral view) H eighth sternite and ovipositor valves (ventral view) I genital fork (ventral view) J, K paraprocts and cerci (right side; J ventral view K lateral view) L spermatheca. Scale bars: 0.1 mm (D–F); 0.05 mm (A); 0.02 mm (B, C, H–L); 0.01 mm (G).
Figure 1 from: Srisuka W, Aupalee K, Otsuka Y, Fukuda M, Takaoka H, Saeung A (2022) A new species of Simulium (Gomphostilbia) (Diptera, Simuliidae) from Thailand, with a key to identify females of 14 species of the Simulium varicorne species-group. ZooKeys 1083: 1-12. https://doi.org/10.3897/zookeys.1083.77428
Figure 1 Neighbor-joining tree of the four Thai species in the S. chumpornense subgroup of the S. varicorne species-group based on 658 bp COI gene sequences. Bootstrap and posterior probability values (NJ/BI) are shown above each branch. The scale bar represents 0.01 substitutions per nucleotide position. Sequences in bold type are generated in this study.
Network Analysis to Identify Critical Links for Relief Activities During Extreme Weather Events
<p>As one of the principal lifeline systems, transportation networks are crucial for evacuation and delivering essential resources and services during the response and recovery phases of extreme weather events and must remain intact to enhance regional resiliency. The conventional evaluation measures that estimate the vulnerability or criticality of road network based on travel time or link volumes do not capture the community impacts due to disruptions. This study seeks to develop a framework to evaluate road network infrastructure criticality during extreme weather events by introducing measures that evaluate the vulnerability of roads users, rather than the physical aspects of link importance. The research develops an innovative approach that integrates three important concepts including hurricane evacuation behavior, community impacts, and road criticality to identify the critical links. Results show that the critical links for vulnerable populations during evacuation do not always align with conventional link-based measures. This highlights the importance of using a performance measure that takes the social vulnerability of road users into consideration when identifying the criticality of a road network and planning for fortification of links to avoid irreversible consequences for vulnerable population groups. Furthermore, decision-making that considers the risks to different communities may lead to a more effective distribution of resources and help support a timely and safe evacuation from disaster events by strengthening the preservation of critical infrastructure links.</p>
Identifying biotic drivers of population dynamics in a benthic–pelagic community
Benthic species and communities are linked to pelagic zooplankton through life-stages encompassing both benthic and pelagic habitats and through a mutual dependency on primary producers as a food source. Many zooplankton taxa contribute to the sedimentary system as benthic eggs. Our main aim was to investigate the nature of the population level biotic interactions between and within these two seemingly independent communities, both dependent on the pelagic primary production, while simultaneously accounting for environmental drivers (salinity, temperature and oxygen conditions). To this end we applied multivariate autoregressive state-space models to long (1966–2007) time-series of annual abundance data, comparing models with and without interspecific interactions, as well as models with and without environmental variables included. We were not able to detect any direct coupling between sediment-dwelling benthic taxa and pelagic copepods and cladocerans on the annual scale, but the most parsimonious model indicated that interactions within the benthic community are important. There were also positive residual correlations between the copepods and cladocerans potentially reflecting the availability of a shared resource or similar seasonal dependence, whereas both groups tended to correlate negatively with the zoobenthic taxa. The most notable single interaction within the benthic community was a tendency for a negative effect of <i>Limecola balthica</i> on the amphipods <i>Monoporeia affinis</i> and <i>Pontoporeia femorata</i>, which can help explain the observed decrease of amphipods due to increased competitive interference.
Data from: Identifying 'vital attributes' for assessing disturbance-recovery potential of seafloor communities
<p>Soft-sediment macrofaunal community data used in "Identifying 'vital attributes' for assessing disturbance-recovery potential of seafloor communities" in <em>Ecology and Evolution</em>.</p> <p>Data is macrofauna community data from two soft-sediment disturbance recovery experiments conducted in the Tvärminne-Hanko Archipelago in the Baltic Sea, and Kawau Bay in New Zealand.</p>
Genome-wide DNA methylation analysis in monozygotic twins identifies potential biomarkers of fasting plasma glucose
<p><strong><span>Purpose:</span></strong><span> An epigenome-wide association study (EWAS) was conducted to detect specific epigenetic variants potentially related to fasting plasma glucose (FPG) in middle-aged and elderly Chinese monozygotic twins.</span></p> <p><span><strong>Methods:</strong> </span><span>Association between DNA methylation (DNAm) of single CpG and FPG was tested by applying generalized estimation equation in 52 twin pairs. Differentially methylated regions (DMRs) were identified by</span><em> <span>comb-P</span></em> <span>approach</span><span>. Inference about Causation through Examination of Familial Confounding (ICE FALCON) was utilized to perform the causal inference. Candidate CpGs were quantified using Sequenom MassARRAY platform in a community population. Weighted gene co-expression network analysis (WGCNA) was conducted using gene expression data. </span></p> <p><span><strong>Results</strong>: </span><span>The relationship between DNAm of 30 top CpGs and FPG reached <em>P</em>-value</span><span><</span><span>1×10<sup>-6</sup></span><span> level. Thirty-two DMRs within 24 genes, such as TLCD1, MRPS31P5, </span><span>CASZ1 </span><span>and CXADRP3, were identified. Causal relationship of 20 top CpGs within <em>TLCD1, MZF1, PTPRN2, SLC6A18, ASTN2, IQCA1, GRIN1</em>, and <em>PDE2A </em>with FPG were further identified. Pathways related to FPG such as mitogen-activated protein kinase p38 binding were found. Three CpGs mapped to <em>SLC6A18 </em>were</span><span> validated in a community population, with </span><span>a hypermethylated direction in type 2 diabetes cases. The gene expression levels of 18 genes where the top CpGs and DMRs located, such as <em>SLC6A18 </em>and <em>TLCD1</em>, were positively correlated with FPG. Besides, common biological pathways, such as dopamine binding, regulation of biosynthetic process, and neuron fate specification, were found in methylation and gene expression analyses.</span></p> <p><span><strong>Conclusion</strong>: </span><span>Our findings showed that</span> <span>multiple methylated CpGs and regions, crucial genes, and biological pathways were underlyingly associated with FPG and diabetes.</span></p>
Using phenome-wide association studies and the SF-12 quality of life metric to identify profound consequences of adverse childhood experiences on adult mental and physical health in a northern Nevadan population
<p>In this research, we examine and identify the implications of Adverse Childhood Experiences (ACEs) on a range of health outcomes, with particular focus on a number of mental health disorders. Many previous studies observed that traumatic childhood events are linked to long-term adult diseases using the standard Adverse Childhood Experience Questionnaire. The study cohort was derived from the Healthy Nevada Project, a volunteer-based population health study in which each adult participant is invited to take a retrospective questionnaire that includes the Adverse Childhood Experience Questionnaire, the 12-item Short Form Survey measuring quality of life, and self-reported incidence of nine mental disorders. Using participants' cross-referenced electronic health records, a phenome-wide association analysis of 1,703 phenotypes and the incidence of ACEs examined links between traumatic events in childhood and adult disease. These analyses showed that many mental disorders were significantly associated with ACEs in a dose-response manner. Similarly, a dose-response between ACEs and obesity, chronic pain, migraine, and other physical phenotypes was identified. An examination of the prevalence of self-reported mental disorders and incidence of ACEs showed a positive relationship. Furthermore, participants with less adverse childhood events experienced a higher quality of life, both physically and mentally. The whole-phenotype approach confirms that ACEs are linked with many negative adult physical and mental health outcomes. With the nationwide prevalence of ACEs as high as 67%, these findings suggest a need for new public health resources: ACE-specific interventions and early childhood screenings.</p>
An Analysis of Transcriptomic Burden Identifies Biological Progression Roadmaps for Hematological Malignancies and Solid Tumors
<p>Supplementary materials for review.</p>
Supplementary material 6 from: Jay C, Haines R, Vigo M, Matentzoglu N, Stevens R, Boyle J, Davies A, Del Vescovo C, Gruel N, Le Blanc A, Mawdsley D, Mellor D, Mikroyannidi E, Rollins R, Rowley A, Vega J (2017) Identifying the challenges of code/theory translation: report from the Code/Theory 2017 workshop. Research Ideas and Outcomes 3: e13236. https://doi.org/10.3897/rio.3.e13236
Lightning Talk: Richard Rollins
Supplementary material 5 from: Jay C, Haines R, Vigo M, Matentzoglu N, Stevens R, Boyle J, Davies A, Del Vescovo C, Gruel N, Le Blanc A, Mawdsley D, Mellor D, Mikroyannidi E, Rollins R, Rowley A, Vega J (2017) Identifying the challenges of code/theory translation: report from the Code/Theory 2017 workshop. Research Ideas and Outcomes 3: e13236. https://doi.org/10.3897/rio.3.e13236
Lightning Talk: Dale Mellor
Supplementary material 4 from: Jay C, Haines R, Vigo M, Matentzoglu N, Stevens R, Boyle J, Davies A, Del Vescovo C, Gruel N, Le Blanc A, Mawdsley D, Mellor D, Mikroyannidi E, Rollins R, Rowley A, Vega J (2017) Identifying the challenges of code/theory translation: report from the Code/Theory 2017 workshop. Research Ideas and Outcomes 3: e13236. https://doi.org/10.3897/rio.3.e13236
Lightning Talk: David Mawdsley
Supplementary material 3 from: Jay C, Haines R, Vigo M, Matentzoglu N, Stevens R, Boyle J, Davies A, Del Vescovo C, Gruel N, Le Blanc A, Mawdsley D, Mellor D, Mikroyannidi E, Rollins R, Rowley A, Vega J (2017) Identifying the challenges of code/theory translation: report from the Code/Theory 2017 workshop. Research Ideas and Outcomes 3: e13236. https://doi.org/10.3897/rio.3.e13236
Lightning Talk: Nicolas Gruel
Supplementary material 7 from: Jay C, Haines R, Vigo M, Matentzoglu N, Stevens R, Boyle J, Davies A, Del Vescovo C, Gruel N, Le Blanc A, Mawdsley D, Mellor D, Mikroyannidi E, Rollins R, Rowley A, Vega J (2017) Identifying the challenges of code/theory translation: report from the Code/Theory 2017 workshop. Research Ideas and Outcomes 3: e13236. https://doi.org/10.3897/rio.3.e13236
Lightning Talk: Andrew Rowley
Supplementary material 1 from: Jay C, Haines R, Vigo M, Matentzoglu N, Stevens R, Boyle J, Davies A, Del Vescovo C, Gruel N, Le Blanc A, Mawdsley D, Mellor D, Mikroyannidi E, Rollins R, Rowley A, Vega J (2017) Identifying the challenges of code/theory translation: report from the Code/Theory 2017 workshop. Research Ideas and Outcomes 3: e13236. https://doi.org/10.3897/rio.3.e13236
Lightning Talk: Jonathan Boyle
Supplementary material 2 from: Jay C, Haines R, Vigo M, Matentzoglu N, Stevens R, Boyle J, Davies A, Del Vescovo C, Gruel N, Le Blanc A, Mawdsley D, Mellor D, Mikroyannidi E, Rollins R, Rowley A, Vega J (2017) Identifying the challenges of code/theory translation: report from the Code/Theory 2017 workshop. Research Ideas and Outcomes 3: e13236. https://doi.org/10.3897/rio.3.e13236
Lightning Talk: Chiara Del Vescovo
Supplementary material 4 from: Chen R, Fang C, Shih F, King C (2016) A Scoring System for Identifying Severe Cases of Influenza-like Illness by Comorbidity and Age - A Nationwide Cohort Analysis. Research Ideas and Outcomes 2: e9648. https://doi.org/10.3897/rio.2.e9648
The poster presented in the Conference.
Supplementary material 5 from: Chen R, Fang C, Shih F, King C (2016) A Scoring System for Identifying Severe Cases of Influenza-like Illness by Comorbidity and Age - A Nationwide Cohort Analysis. Research Ideas and Outcomes 2: e9648. https://doi.org/10.3897/rio.2.e9648
The dataset used for in Stata 14 format. The other datasets are available upon request.
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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.