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JCEM Manuscript Supplemental Information
<p>This supplementary dataset includes supplemental tables and figures for the article <strong>Utility of In-vivo Magnetic Resonance Imaging of Gestational Diabetes Mellitus during Early Pregnancy: Prediction Possibilities.</strong></p>
JCEM Supplemental Materials
<p>Supplemental Materials for "<strong>Utility of <em>In-vivo</em> Magnetic Resonance Imaging in Gestational Diabetes Mellitus during Early Pregnancy".</strong></p> <p>Includes: Supplemental Figures and Tables, Raw Data File</p>
Avalon: A Benchmark for RL Generalization Using Procedurally Generated Worlds - Data Supplement
<p>This is the data supplement for <em>Avalon: A Benchmark for RL Generalization Using Procedurally Generated Worlds</em>.</p> <p>This version corresponds to the latest round of human player data collection.</p> <ul> <li><strong>avalon__agent_eval_worlds.tar.gz</strong> contains all the evaluation worlds on which agents are scored</li> <li><strong>avalon__human_eval_worlds.tar.gz</strong> contains all the evaluation worlds on which humans are scored (same as agent worlds, just some minor visual differences e.g. the colors are slightly modified for human comfort)</li> <li><strong>avalon__human_data.tar.gz </strong>contains all the metadata, actions, inputs, and observations for the human players</li> <li><strong>avalon__human_scores.json</strong> contains the scores for the human players</li> </ul>
Supplemental Data for Generalized Testing for Finite State Specifications
<p>Additional supplemental data for <em>Generalized Testing for Finite State Specifications</em>.</p> <p>Files in this dataset:<br> - `edge-pair-analysis.tgz` contains all data from analysis done in Section III-B (On the bugginess of mined specs).<br> - `preliminary-study-mined-fsms.tgz` contains all mined FSMs used for analysis in Section III-B (On the bugginess of mined specs).<br> - `temari-study-data.tgz` contains all Temari experiment data for RQ1 (How generalizable is Temari?).</p>
Stowaways Supplement Table S2. Ma'agan Mikhael B Rattus rattus Skeletal Element Identification (NISP) Datasheet
<p>Number of identified specimens of black rat (Rattus rattus) skeletal elements recovered from the early Islamic period shipwreck Ma'agan Mikhael B (Israel). Dataset includes catalogue number, skeletal element, side, part, epiphyseal fusion status, and tooth wear stage (TWS; following Armitage in Morales & Rodríguez [1997]).</p> <p>***Version 2 added two new specimens from the September 2022 excavation season.</p>
Supplemental material for "Statins, type 2 diabetes and body mass index: a univariable and multivariable Mendelian randomization study"
<p>Supplemental material for "Statins, type 2 diabetes and body mass index: a univariable and multivariable Mendelian randomization study" by Guoyi Yang and C Mary Schooling.</p>
LMAS Supplemental Material
<p><a href="https://github.com/cimendes/LMAS">LMAS</a> is an automated workflow enabling the benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities.</p> <p>As proof of concept, the eight bacterial genomes and four plasmids, in tripled form, of the ZymoBIOMICS Microbial Community Standards are made available to be used as reference. Simulated raw sequence data of the mock communities with evenly distributed reads, generated from the reference genomes, with and without error, were obtained with <a href="https://github.com/HadrienG/InSilicoSeq">inSilicoSeq</a>.</p> <p>Project repository: <a href="https://github.com/cimendes/LMAS">https://github.com/cimendes/LMAS</a></p>
Supplemental documents for: Temperature-associated selection linked to putative chromosomal inversions in king scallop (Pecten maximus)
<p>The genomic landscape of divergence – the distribution of differences among populations or species across the genome – is increasingly characterized to understand the role that microevolutionary forces such as natural selection and recombination play in causing and maintaining genetic divergence. This line of inquiry has also revealed chromosome structure variation to be an important factor shaping the landscape of adaptive genetic variation. Due to a high prevalence of chromosome structure variation and the strong pressure for local adaptation necessitated by their sessile nature, bivalve molluscs are an ideal taxon for exploring the relationship between chromosome structure variation and local adaptation. Here, we report a population genomic survey of king scallop (<em>Pecten</em> <em>maximus</em>) across its natural range in the northeastern Atlantic Ocean, utilizing a recent chromosome-level genome assembly. We report the presence of at least three large (12-22 Mb), putative chromosomal inversions associated with sea surface temperature and whose frequencies are in contrast to neutral population structure. These results highlight a potentially large role for recombination-suppressing chromosomal inversions in local adaptation and suggest a hypothesis to explain the maintenance of differences in reproductive timing found at relatively small spatial scales across king scallop populations.</p>
Supplement table for Sparano et al.: Classic and follicular variant of papillary thyroid microcarcinoma: two different phenotypes beyond tumour size. Journal of the Endocrine Society, 2022.
<p>Sparano <em>et al.</em> Supplement to: Classic and follicular variant of papillary thyroid microcarcinoma: two different phenotypes beyond tumour size. <em>Journal of the Endocrine Society</em>, 2022.</p>
Supplemental information for "Single-Molecule Dynamics of Surface Lipoproteins in Bacteroides Indicate Similarities and Cooperativity"
<p>Supplemental Movies 1 - 3</p> <p><strong>SI Movie S1 - Representative movie of SusG-HT dynamics in <em>Bt</em> cells grown in amylopectin.</strong> The <em>Bt</em> cell outlines (white) are determined from the corresponding phase-contrast image. The single-molecule localization fits (circles) and corresponding trajectories (lines) are overlaid with the same colors as in Figure 1c. Below the scale bar is the date of the experiment, the movie number, the number of the photo-activation pulse that the sequence follows (in parentheses), and the frame number. These indicators are displayed in green during the imaging frames and in red during the photo-activation pulse. Scale bar: 1 µm; imaging rate: 20 ms/frame.</p> <p><strong>SI Movie S2 - Representative movie of SusG-HT dynamics in <em>Bt</em> cells grown in maltose.</strong> The <em>Bt</em> cell outlines (white) are determined from the corresponding phase-contrast image. The single-molecule localization fits (circles) and corresponding trajectories (lines) are overlaid with the same colors as in Figure 1c. Below the scale bar is the date of the experiment, the movie number, the number of the photo-activation pulse that the sequence follows (in parentheses), and the frame number. These indicators are displayed in green during the imaging frames and in red during the photo-activation pulse. Scale bar: 1 µm; imaging rate: 20 ms/frame.</p> <p><strong>SI Movie S3 - Representative movie of SusG-HT dynamics in <em>Bt</em> cells grown in glucose.</strong> The <em>Bt</em> cell outlines (white) are determined from the corresponding phase-contrast image. The single-molecule localization fits (circles) and corresponding trajectories (lines) are overlaid with the same colors as in Figure 1c. Below the scale bar is the date of the experiment, the movie number, the number of the photo-activation pulse that the sequence follows (in parentheses), and the frame number. These indicators are displayed in green during the imaging frames and in red during the photo-activation pulse. Scale bar: 1 µm; imaging rate: 20 ms/frame.</p>
Supplement 1 of High fidelity anthropomorphic 3D printed models – accuracy, precision and quality control
<p>Raw data for "High fidelity anthropomorphic 3D printed models – accuracy, precision and quality control" presented at EHB2022e</p>
Supplemental data for: Development and validation of a polygenic risk score for stroke in the Chinese population
<div class="WordSection1"> <div class="WordSection1"> <strong>Objective</strong>: To construct a polygenic risk score (PRS) for stroke and evaluate its utility in risk stratification and primary prevention for stroke.</div> <div class="WordSection1"> </div> <div class="WordSection1"> <strong>Methods</strong>: Using meta-analytic approach and large genome-wide association results for stroke and stroke-related traits in East Asians, we generated a combined PRS (metaPRS) by incorporating 534 genetic variants in a training set of 2,872 patients with stroke and 2,494 controls. We then validated its association with incident stroke using Cox regression models in large Chinese population-based prospective cohorts comprising 41,006 individuals.</div> <div class="WordSection1"> </div> <div class="WordSection1"> <strong>Results</strong>: During a total of 367,750 person-years (mean follow-up 9.0 years), 1,227 participants developed stroke before age of 80 years. Individuals with high polygenic risk had an about 2-fold higher risk of incident stroke compared with those with low polygenic risk (HR: 1.99, 95% CI: 1.66-2.38), with the lifetime risk of stroke being 25.2% (95% CI: 22.5%-27.7%) and 13.6% (95% CI: 11.6%-15.5%), respectively. Individuals with both high polygenic risk and family history displayed the lifetime risk as high as 41.1% (95% CI: 31.4%-49.5%). Moreover, individuals with high polygenic risk achieved greater benefits in terms of absolute risk reductions from adherence to ideal fasting blood glucose and total cholesterol than those with low polygenic risk. Maintaining favorable cardiovascular health (CVH) profile could substantially mitigate the increased risk conferred by high polygenic risk to the level of the low polygenic risk (from 34.6 % to 13.2%).</div> <div class="WordSection1"> </div> <div class="WordSection1"> <strong>Conclusions</strong>: Our metaPRS has great potential for risk stratification of stroke and identification of individuals who may benefit more from maintaining ideal CVH. </div> <div class="WordSection1"> </div> <div class="WordSection1"> <strong>Classification of Evidence</strong>: This study provides Class I evidence that a meta-polygenic risk score is predictive of stroke risk.</div> <p> </p> </div>
Calculating the sustainability of products based on their efficiency and function. Supplemental Data.
<p>Supplemental data for article "Calculating the sustainability of products based on their efficiency and function".</p>
Supplemental Video 1 to Vanzella et al paper: A passive, camera-based head-tracking system for real-time, three-dimensional estimation of head position and orientation in rodents
<p>This video shows how the head tracker described in the manuscript "<strong>A passive, camera-based head-tracking system for real-time, three-dimensional estimation of head position and orientation in rodents" </strong>can track in real time the pose of the head of rat engaged in a perceptual discrimination task.</p>
Supplementary material 1 from: Sim IMW, Wilkinson NI, Scridel D, Anderson D, Roos S (2015) Food supplementation does not increase demographic rates in a passerine species of conservation concern. Nature Conservation 10: 25-43. https://doi.org/10.3897/natureconservation.10.4556
Supplementary Information: Explanation note: Details of the models predicting adult ring ouzel provisioning rate to nestlings, fledging success, brood size at fledging in successful nests, nestling BCI at fledging, within-brood variation in nestling BCI at fledging, and juvenile survival probability for up to 100 days post-fledging.
Supplemental material: Comparing approaches for evolving high-level robot control based on behaviour repertoires
<p>Supplemental material for the paper:</p> <p>Comparing approaches for evolving high-level robot control based on behaviour repertoires<br> Jorge Gomes, Anders Lyhne Christensen</p> <p>Videos of the highest-performing solutions evolved with each method. In all videos, the schematic of the robot indicates the current wheel angles and robot speed. In the repertoire-based methods, the visualization on the bottom left indicates which primitives are being executed.</p> <p><strong>vid_evorbc_2_4_f1.12.mp4 </strong><br> Evolved by NEAT-EvoRBC. The blue cross indicates the behaviour selection vector.</p> <p><strong>vid_gp_2_2_f1.12_best.mp4</strong><br> Evolved by GP-DT. The primitives highlighted in green are the ones that exist in the decision tree.</p> <p><strong>vid_gp_8_4_f0.92_paper.mp4 </strong><br> Evolved by GP-DT. Smallest tree with fitness above 0.9. Shown in the paper.</p> <p><strong>vid_neatsub_9_5_f0.89.mp4 </strong><br> Evolved by NEAT-Subset. Only the primitives that are in the subset are shown. The numbers near each primitive indicate the activation level of the corresponding output (or maximum activation level if there are multiple outputs corresponding to the same primitive).</p> <p><strong>vid_neattr_24_f0.28.mp4 </strong><br> Evolved by NEAT-TR.</p> <p>The videos have been verified to reproduce correctly with the <strong>VLC player</strong>. But any other modern player should handle them.</p>
Supplemental Material: Effects of Environmental Sustainability Enhancing Architectural Patterns and Tactics on different Quality Attributes
<p>These are the additional resources to the thesis with the same title.</p> <p>Context: Environmental sustainability is increasingly vital amid global challenges,<br>as IT presents both solutions and threats to the environment. Integrating environ-<br>mental sustainability into software engineering practices is essential, necessitating a<br>comprehensive understanding of environmental sustainability design decisions and<br>how they impact sustainability and other quality attributes within software architec-<br>tures.<br>Objectives: This research aims to address two primary objectives: firstly, to elicit environ-<br>mental sustainability scenarios and patterns and tactics from domain experts, and secondly,<br>to assess the tradeoffs of these design decisions in the context of a case study. Through qual-<br>itative insights garnered from a workshop and quantitative analysis via experiments, this<br>study seeks to offer nuanced insights into these tradeoffs.<br>Methodology: Utilizing a case study approach in collaboration with an industrial partner,<br>this work employs a combination of qualitative and quantitative analysis methods.<br>Qualitative insights are gathered through an Architecture Tradeoff Analysis Method<br>(ATAM) workshop with industrial partners, aimed at eliciting environmental sustainability<br>scenarios, design decisions, and their tradeoffs. Afterward, quantitative experiments<br>are conducted based on the workshop results using the Goal-Question-Metric (GQM)<br>approach, to measure the impact of environmental sustainability design decisions on<br>specific quality attributes in a mock implementation based on the industrial partner’s<br>system.<br>Results: We were able to capture eight environmental sustainability scenarios and<br>patterns and tactics and tradeoffs for five of them during the workshop. In the ex-<br>periments we implemented two tactics, expecting them to negatively impact the per-<br>formance. The experimentation provided empirical data, revealing nuanced insights,<br>sometimes contradicting initial hypotheses, highlighting the importance of empirical<br>validation.<br>Conclusion: This study underscores the complexity of balancing environmental sustain-<br>ability with other quality attributes in software design. It emphasizes the complementary<br>role of qualitative and quantitative analysis in understanding tradeoffs and making informed<br>decisions. By integrating insights from both approaches, this research contributes to ad-<br>vancing discussions on sustainability in software engineering, benefiting both researchers<br>and practitioners. Continued collaboration between academia and industry is crucial for<br>furthering sustainable software engineering practices.</p> <p> </p>
Supplemental Material for Context Switch Sensitive Fault Localization
Open the record for dataset details and reuse information.
Supplemental information of "Transitioning from food waste disposal to treatment and reuse can achieve meaningful reductions in food's climate and resource burdens"
<p>(1) Source data (Data 1) for bootstrapping analysis to compute means and 95% CIs of carbon footprint and product metrics of food waste treatments, as well as food waste landfill emissions</p> <p>(2) Source data (Data 2) for food waste management schemes of US, EU, and China for emission estimation as well as emission mitigation analyses</p> <p>(3) STATA output report</p> <p>(4) List of studies selected from a systematic literature review</p>
Supplemental datasets for the brittle star A. filiformis genome
<p>This repository stores the supplemental datasets for the brittle star <i>Amphiura filiformis</i> genome manuscript.</p>
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.