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397 results for “Study design”
FIGURE 1 in RNames, a stratigraphical database designed for the statistical analysis of fossil occurrences - the Ordovician diversification as a case study
FIGURE 1. Simplified structure of the RNames Database (rnames.luomus.fi/). The database contains eight related tables (blue and red objects) of which the object "Relations" is central. In "Relations" correlated stratigraphic units are listed by reference. Three output tables (yellow objects) list time binned stratigraphic units based on a search algorithm that uses "Relations" via R-Package RMySQL (the scripts are available under https://github.com/bjoekroe/ RNames). Global Stages after Cooper et al. (2012). Abbreviations: ID, identifier; StS, Stage Slice (Bergström et al., 2009); TS, Time Slice (Webby et al., 2004)
FIGURE 5 in RNames, a stratigraphical database designed for the statistical analysis of fossil occurrences - the Ordovician diversification as a case study
FIGURE 5. Quality of PaleobioDB data used for diversity calculations. 1. Number of collections available per time bin. 2. Mean stratigraphic range of collections through time bins. Diamonds, two-time-bin resolution; triangles, one-time bin resolution; squares, all collections. Red, Global Stages after Cooper et al. (2012), green; Stage Slices, Bergström et al. (2009); blue, Time Slices, Webby et al. (2004).
FIGURE 4 in RNames, a stratigraphical database designed for the statistical analysis of fossil occurrences - the Ordovician diversification as a case study
FIGURE 4. Ordovician genus-level diversity trends of PaleobioDB occurrence data, based on three different time binning approaches. 1. Total mean standing diversity (after Cooper, 2004). 2. Rarefied diversity with time bins of <100 collections culled, with quota 600. Diamonds, two-time-bin resolution; triangles, one-time bin resolution; stars, all collections. Red, Global Stages after Cooper et al. (2012), green; Stage Slices, Bergström et al. (2009); blue, Time Slices, Webby et al. (2004). Error bars reflect 95% confidence interval.
Supplementary data for study on "Superplastic 3D printed nitinol woven metamaterials lead to dramatic variations of mechanical properties by design"
<p>Raw and processed data from experimental compression testing of 3D printed nitinol lattices and wovens are provided as supplementary materials for the mentioned study, submitted for evaluation to the journal of Virtual and Physical Prototyping.</p>
Figures 15–22 in Parajulid milliped studies XII: Initial assessment of Ptyoiulus Cook 1895 and neotype designations for Julus impressus Say 1821 and J. montanus Cope 1869 (Diplopoda: Julida)
Figures 15–22. Gonopodal variation in P. montanus. 15) Distal extremity of right anterior gonopod of male from Montgomery Co., Virginia, caudal view. 16) The same of male from Tishomingo Co., Mississippi. 17) The same of male from DeKalb Co., Georgia. 18) The same of male from Craighead Co., Arkansas. 19) The same of male from Clay Co., Arkansas. 20) Right posterior gonopod of male from Mason Co., Tennessee, lateral view. 21) The same of male from Tishomingo Co., Mississippi. 22) The same of male from Montgomery Co., Virginia. Abbreviations as in Fig. 5–6.
Figures 7–13 in Parajulid milliped studies XII: Initial assessment of Ptyoiulus Cook 1895 and neotype designations for Julus impressus Say 1821 and J. montanus Cope 1869 (Diplopoda: Julida)
Figures 7–13. Gonopodal variation in P. impressus. 7) Distal extremity of right anterior gonopod of neotype, caudal view. 8) The same of male from Rabun Co., Georgia. 9) The same of male from Liberty Co., Florida. 10) The same of male from Leon Co., Florida. 11) The same of male from Greene Co., Arkansas. 12) Right posterior gonopod of male from Rabun Co., Georgia, lateral view. 13) The same of male from Greene Co., Arkansas. Abbreviations as in Fig. 5–6.
Figure 14 in Parajulid milliped studies XII: Initial assessment of Ptyoiulus Cook 1895 and neotype designations for Julus impressus Say 1821 and J. montanus Cope 1869 (Diplopoda: Julida)
Figure 14. Distributions of species of Ptyoiulus. Black dots, P. impressus. Open black circle in southeastern Pennsylvania, denoted by the black arrow, is the neotype locality. Red dots, P. montanus. Open red circle in central North Carolina, denoted by the red arrow, is the neotype locality. Blue dots, geographically significant samples lacking adult males and presently unidentifiable to species.
Figures 5–6. Ptyoiulus spp. anterior gonopods, caudal views. 5 in Parajulid milliped studies XII: Initial assessment of Ptyoiulus Cook 1895 and neotype designations for Julus impressus Say 1821 and J. montanus Cope 1869 (Diplopoda: Julida)
Figures 5–6. Ptyoiulus spp. anterior gonopods, caudal views. 5) P. impressus. 6) P. montanus. at, anterior gonopod telopodite; ca, calyx; cp, coxal process stem.
Figure 4 in Parajulid milliped studies XII: Initial assessment of Ptyoiulus Cook 1895 and neotype designations for Julus impressus Say 1821 and J. montanus Cope 1869 (Diplopoda: Julida)
Figure 4. Distributions of Ptyoiulus/Ptyoiulinae plotted against the maximal extent of the Western Interior Seaway during the Cretaceous Period, Mesozoic Era. All land areas shown are in the eastern land mass, Appalachia, which was separated from western Laramidia by the vertical, latitudinal arm of the Seaway (not shown), which segregated Ptyoiulus from bollmaniulinines in Laramidia but is irrelevant to Ptyoiulus itself. The Seaway spread eastward south of Appalachia and when it receded, P. impressus spread southward into the formerly inundated area. 1, large, contiguous main range area. 2, small, disjunct northernmost population extending from Montreal, Québec, to northern Vermont. 3, disjunct population along the southwestern coast of Lake Michigan. 4, disjunct area in northeastern/eastcentral Arkansas. 5, point locality in northeastern Louisiana vouchered by females. The transect denoted by the red lines near the center of the distribution is the band occupied by both P. montanus and P. impressus; the latter occurs alone to the north and south.
Figures 1–3 in Parajulid milliped studies XII: Initial assessment of Ptyoiulus Cook 1895 and neotype designations for Julus impressus Say 1821 and J. montanus Cope 1869 (Diplopoda: Julida)
Figures 1–3. Pilosity and epiproct variation on caudalmost rings of Ptyoiulus impressus. 1) Specimen from Morgan Co., Ohio. 2) Specimen from Allen Co., Kentucky. 3) Specimen from Leon Co., Florida. e, epiproct; h, hypoproct; lp, left paraproct.
Datasets of the manuscript "Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons"
<p><strong>DATASETS</strong></p> <p>Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons</p> <p>Liliane S. Oliveira, Alejandro Reyes, Bas E. Dutilh and Arthur Gruber<sup>*</sup></p> <p>* Correspondence: <a href="mailto:argruber@usp.br">argruber@usp.br</a> (AG); Tel. +55 11 3091 7274</p> <p> </p> <p>Here we provide different data of <em>Microviridae</em>, <em>Flavivirus</em> and casposons used throughout the work:</p> <ul> <li>Microviridae folder <ul> <li>conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for <em>Microviridae</em></li> <li>discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for <em>Microviridae</em></li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>Microviridae_113-seq_training_set.fasta - 113 VP1 sequences covering diversity of the <em>Microviridae</em> family</li> <li>Microviridae_113-seq.aln – multiple sequence alignment of the 113-protein dataset</li> <li>Microviridae_1836-seq_testset.fasta - 1,836 sequence dataset covering 1,836 sequences of the major capsid protein (VP1) comprising 501 <em>Alpavirinae</em> sequences, 1,040 <em>Gokushovirinae</em> sequences and 295 <em>Pichovirinae</em> sequences</li> <li>Microviridae_1866-seq.aln - multiple sequence alignment of the 1,866-protein <em>Microviridae</em> dataset used in the experiment of Figure 4</li> </ul> </li> </ul> </li> <li>Flavivirus folder <ul> <li>conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for <em>Flavivirus</em></li> <li>discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for <em>Flavivirus</em> <ul> <li>full-length – models constructed from full-length protein sequences</li> <li>short - models constructed from selected short alignment blocks of the protein sequences</li> </ul> </li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>Flavivirus_127-seq_training_set.fasta - 127 polyprotein sequences covering species diversity of the genus <em>Flavivirus</em></li> <li>Flavivirus_127-seq.aln – multiple sequence alignment of the 127-protein dataset</li> <li>Flavivirus_6364-seq_testset.fasta - 6,364 sequence dataset covering species diversity of <em>Flavivirus</em>, including 3,919 of dengue virus (DENV), 327 of Zika virus (ZIKV), 63 of yellow fever virus (YFV), and the remaining 2,055 sequences covering other available flaviviruses</li> <li>Flavivirus_6364-seq.aln - multiple sequence alignment of the 6,364-protein <em>Flavivirus</em> dataset</li> </ul> </li> </ul> </li> <li>Casposons folder <ul> <li>casposon_generic_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the generic detection of all casposons and discrimination from CRISPRs.</li> <li>casposon_family_discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the specific discrimination among casposon families and from CRISPRs.</li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>casposons_crisprs.fasta – 106 Cas1 <em>bona fide</em> sequences derived from 52 CRISPRs and 54 casposons</li> <li>casposon_family_discrimination.aln - multiple sequence alignment of 52 <em>bona fide</em> CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for the discrimination of each casposon family.</li> <li>casposons_crisprs_discrimination.aln - multiple sequence alignment of 52 <em>bona fide</em> CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for discrimination of CRISPRs and casposons.</li> </ul> </li> </ul> </li> </ul>
Data from: Potentials of closed contour analysis in species differentiation and holotype designation: a case study on lower Norian (Upper Triassic) conodonts
<p><span>Geometric morphometric approaches become increasingly applied in the fields of biology and paleontology. Taxonomy is a good example, where a long-standing intention of scientists is to eliminate subjectivity as much as possible. In the case of biostratigraphically important conodont elements, the application of such methods is not widespread. Indeed, only a handful of studies attempted to deal with the morphological variance of conodont elements from this aspect. The detailed description of five lower Norian (Upper Triassic) taxa (<em>Ancyrogondolella quadrata, A. rigoi, A. triangularis, A. uniformis</em> and <em>Metapolygnathus mazzai</em>) is presented here based on landmarks and Fourier analysis of the P1 element and keel outlines. Both methods led to similar outcomes regarding taxonomic differentiation and exposing shape variability. Consensus shapes were generated to objectively reveal the typical contour shape of each taxon, which allowed their comparison with each other, and with the members of their respective sample population including the holotypes. The results pointed out that the holotype of a taxon is generally not an average representative, but rather a peripheral form with well-separable morphological characteristics. <em>Ancyrogondolella quadrata</em> and <em>A. rigoi</em> turned out to represent a morphological continuum with ample transitional forms between these two end-members that may cause bias in their biostratigraphic applicability; however, their combined shape variance seems to be too large for uniting them into a single species. Given the results that may be too subtle to realize based solely on qualitative observations, future taxonomic studies and type material designation could greatly benefit from the application of similar methodologies.</span></p>
Practical Cell Design for PTMA-Based Organic Batteries: an Experimental and Modeling Study - Supporting Dataset
<p>The cycling and impedance data used in the work "Practical Cell Design for PTMA-Based Organic Batteries: an Experimental and Modeling Study" are provided in this repository.<br> The data are reported both as original .txt files with the raw data from the instruments and as processed Matlab files, where the data are structured in cycles.<br> The Excel sheet "Metadata" explains the type of battery associated to each code and file(s).</p> <p><br> </p>
LOGiC - Lapatinib Optimization Study in ErbB2 (HER2) Positive Gastric Cancer: A Phase III Global, Blinded Study Designed to Evaluate Clinical Endpoints and Safety of Chemotherapy Plus Lapatinib
ClinicalTrials.gov study NCT00680901. IPD Sharing: YES. Countries: 23. Publications: 2.
A Medical Research Study Designed to Determine if Venglustat Can be a Future Treatment for ADPKD Patients
ClinicalTrials.gov study NCT03523728. IPD Sharing: YES. Countries: 23. Publications: 3.
Data from: Potentials of closed contour analysis in species differentiation and holotype designation: a case study on lower Norian (Upper Triassic) conodonts
Open the record for dataset details and reuse information.
Empirical Study of the Relationship between Design Patterns and Code Smells
<p>Software systems are often developed in such a way that good practices in the object-oriented paradigm are not met, causing the occurrence of specific disharmonies which are sometimes called code smells. Design patterns catalogue best practices for developing object-oriented software systems. Although code smells and design patterns are widely divergent, there might be a co-occurrence relation between them. The objective of this paper is to empirically evaluate if the presence of design patterns is related to the presence of code smells at different granularity levels. We performed an empirical replication study using 20 design patterns and 13 code smells in ten small-size to medium-size, open-source Java-based systems. We applied statistical analysis and association rules. Results confirm that classes participating in design patterns have less smell-proneness and smell frequency than classes not participating in design patterns. We also noticed that every design pattern category act in the same way in terms of smell-proneness in the subject systems. However, we observed, based on the association rules learning and the proposed validation technique, that some patterns may be linked with certain smells in some cases. For instance, Command patterns can co-occur with God Class, Blob and External Duplication smell.</p> <p><strong>The published data set contains the following:</strong></p> <ol> <li>List of the selected systems (source code files)</li> <li>The P-MARt: the design pattern repository as XML for the selected systems. </li> <li>Data of design patterns and code smells: We processed this data by parsing the design pattern XML file and running the smell detection tool (inFusion).</li> <li>The data of the data mining analysis.</li> </ol>
Weight loss, insulin resistance, and study design confound results in a meta-analysis of animal models of fatty liver
The classical drug development pipeline necessitates studies using animal models of human disease to gauge future efficacy in humans, however there is a low conversion rate from success in animals to humans. Non-alcoholic fatty liver disease (NAFLD) is a complex chronic disease without any established therapies and a major field of animal research. We performed a meta-analysis with meta-regression of 603 interventional rodent studies (10,364 animals) in NAFLD to assess which variables influenced treatment response. Weight loss and alleviation of insulin resistance were consistently associated with improvement in NAFLD. Multiple drug classes that do not affect weight in humans caused weight loss in animals. Other study design variables, such as age of animals and dietary composition, influenced the magnitude of treatment effect. Publication bias may have increased effect estimates by 37-79%. These findings help to explain the challenge of reproducibility and translation within the field of metabolism.
Supplementary Material for the Paper "Design Recommendations for Self-Monitoring in the Workplace: Studies in Software Development"
<p>Contains the supplementary material for the paper "Design Recommendations for Self-Monitoring in the Workplace: Studies in Software Development" submitted to CSCW'18. All contents are explained in the file README.txt.</p> <p>Abstract:<br> One way to improve the productivity of knowledge workers is to increase their self-awareness about productivity at work through self-monitoring. Yet, little is known about expectations of, the experience with and the impact of self-monitoring in the workplace. To address this gap, we studied software developers, as one community of knowledge workers. We used an iterative, feedback-driven development approach (N=20) and a survey (N=413) to infer design elements for workplace self-monitoring, which we then implemented as a technology probe called WorkAnalytics. We field-tested these design elements during a three-week study with software development professionals (N=43). Based on the results of the field study, we present design recommendations for self-monitoring in the workplace, such as using experience sampling to increase the awareness about work and to create richer insights, the need for a large variety of different metrics to retrospect about work, and that actionable insights, enriched with benchmarking data from co-workers, are likely needed to foster productive behavior change at work.</p>
Global Sensitivity Analysis is Not Always Beneficial for Evolutionary Computation: A Study in Engineering Design
<p>This Zenodo repository contains all the results generated for the book chapter "Global Sensitivity Analysis is Not Always Beneficial for Evolutionary Computation: A Study in Engineering Design".</p>
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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.