cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12010257.v1
title: Additional file 10 of Altered secretory and neuroprotective function of the choroid plexus in progressive multiple sclerosis

description: Additional file 10: Supplementary Table 6. Gene ontology enrichment analysis. Table displays the GO category ID, the name of the term, the number of differentially expressed (DE) genes in the category and the total number of genes in the category.
DOI: 10.6084/m9.figshare.12010182
title: Additional file 9 of Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

description: Additional file 9. Accession numbers for individual MAGs deposited in NCBI database.
DOI: 10.6084/m9.figshare.12010182.v1
title: Additional file 9 of Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

description: Additional file 9. Accession numbers for individual MAGs deposited in NCBI database.
DOI: 10.6084/m9.figshare.12010173
title: Additional file 8 of Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

description: Additional file 8: Table S7. Identified proteins in the adjacent mudstone.
DOI: 10.6084/m9.figshare.12010170
title: Additional file 7 of Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

description: Additional file 7: Table S6. Identified proteins in dinosaur fossil bone
DOI: 10.6084/m9.figshare.12010170.v1
title: Additional file 7 of Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

description: Additional file 7: Table S6. Identified proteins in dinosaur fossil bone
DOI: 10.6084/m9.figshare.12010173.v1
title: Additional file 8 of Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

description: Additional file 8: Table S7. Identified proteins in the adjacent mudstone.
DOI: 10.6084/m9.figshare.12010161
title: Additional file 5 of Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

description: Additional file 5: Table S4. Relative abundance of MAGs in each metagenome
DOI: 10.6084/m9.figshare.12010161.v1
title: Additional file 5 of Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

description: Additional file 5: Table S4. Relative abundance of MAGs in each metagenome
DOI: 10.6084/m9.figshare.12010155
title: Additional file 4 of Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

description: Additional file 4: Table S3. Taxonomic classification based on the GTDB-Tk tool.
DOI: 10.6084/m9.figshare.12010155.v1
title: Additional file 4 of Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

description: Additional file 4: Table S3. Taxonomic classification based on the GTDB-Tk tool.
DOI: 10.5281/zenodo.4000852
title: Replication package of "Revisiting Test Smells in Automatically Generated Tests: Limitations, Pitfalls, and Opportunities"

description: <strong>Abstract:</strong><br> Test smells attempt to capture design issues in test code that reduce their maintainability. Previous work found such smells to be highly common in automatically generated test-cases, but based this result on specific static detection rules; although these are based on the original definition of “test smells”, a recent empirical study showed that developers perceive these as overly strict and non-representative of the maintainability and quality of test suites. This leads us to investigate how effective such test smell detection tools are on automatically generated test suites. In this paper, we build a dataset of 2,340 test cases automatically generated by EVOSUITE for 100 Java classes. We performed a multi-stage, cross-validated manual analysis to identify six types of test smells and label their instances. We benchmark the performance of two test smell detection tools: one widely used in prior work, and one recently introduced with the express goal to match developer perceptions of test smells. Our results show that these test smell detection strategies poorly characterized the issues in automatically generated test suites; the older tool’s detection strategies, especially, misclassified over 70% of test smells, both missing real instances (false negatives) and marking many smell-free tests as smelly (false positives). We identify common patterns in these tests that can be used to improve the tools, refine and update the definition of certain test smells, and highlight as of yet uncharacterized issues. Our findings suggest the need for (i) more appropriate metrics to match development practice; and (ii) more accurate detection strategies, to be evaluated primarily in industrial contexts.
DOI: 10.5281/zenodo.4000851
title: Replication package of "Revisiting Test Smells in Automatically Generated Tests: Limitations, Pitfalls, and Opportunities"

description: <strong>Abstract:</strong><br> Test smells attempt to capture design issues in test code that reduce their maintainability. Previous work found such smells to be highly common in automatically generated test-cases, but based this result on specific static detection rules; although these are based on the original definition of “test smells”, a recent empirical study showed that developers perceive these as overly strict and non-representative of the maintainability and quality of test suites. This leads us to investigate how effective such test smell detection tools are on automatically generated test suites. In this paper, we build a dataset of 2,340 test cases automatically generated by EVOSUITE for 100 Java classes. We performed a multi-stage, cross-validated manual analysis to identify six types of test smells and label their instances. We benchmark the performance of two test smell detection tools: one widely used in prior work, and one recently introduced with the express goal to match developer perceptions of test smells. Our results show that these test smell detection strategies poorly characterized the issues in automatically generated test suites; the older tool’s detection strategies, especially, misclassified over 70% of test smells, both missing real instances (false negatives) and marking many smell-free tests as smelly (false positives). We identify common patterns in these tests that can be used to improve the tools, refine and update the definition of certain test smells, and highlight as of yet uncharacterized issues. Our findings suggest the need for (i) more appropriate metrics to match development practice; and (ii) more accurate detection strategies, to be evaluated primarily in industrial contexts.
DOI: 10.6084/m9.figshare.12010083
title: Additional file 2 of Longitudinal analysis of the capacities of community health workers mobilized for seasonal malaria chemoprevention in Burkina Faso

description: Additional file 2. CBD responses at each round.
DOI: 10.6084/m9.figshare.12010083.v1
title: Additional file 2 of Longitudinal analysis of the capacities of community health workers mobilized for seasonal malaria chemoprevention in Burkina Faso

description: Additional file 2. CBD responses at each round.
DOI: 10.6084/m9.figshare.12010077
title: Additional file 1 of Longitudinal analysis of the capacities of community health workers mobilized for seasonal malaria chemoprevention in Burkina Faso

description: Additional file 1. Participation pattern of the panel.
DOI: 10.6084/m9.figshare.12010077.v1
title: Additional file 1 of Longitudinal analysis of the capacities of community health workers mobilized for seasonal malaria chemoprevention in Burkina Faso

description: Additional file 1. Participation pattern of the panel.
DOI: 10.6084/m9.figshare.12009789
title: 1 microsecond simulation of nCoV 6LU7 using the dimeric form,

description: This protein was simulated without its cocrystallized ligand. Simulation time was 1 microsecond. The protein was parametrized using ff19SB and OPC water. <br>Trajectories are shared as dcd charms files without water or counterion molecules.
DOI: 10.17608/k6.auckland.12009615
title: SHR Midwall Collagen

description: 3D TIFF file of SHR rat LV midwall stained with PSR for collagen. Imaged on the Extended-Volume Imaging rig at 0.4µm isotropic pixel size.<br>
DOI: 10.17608/k6.auckland.12009615.v1
title: SHR Midwall Collagen

description: 3D TIFF file of SHR rat LV midwall stained with PSR for collagen. Imaged on the Extended-Volume Imaging rig at 0.4µm isotropic pixel size.<br>
DOI: 10.17608/k6.auckland.12009612
title: WKY Midwall Collagen

description: 3D TIFF file of WKY rat LV midwall stained with PSR for collagen. Imaged on the Extended-Volume Imaging rig at 0.4µm isotropic pixel size.<br>
DOI: 10.17608/k6.auckland.12009612.v1
title: WKY Midwall Collagen

description: 3D TIFF file of WKY rat LV midwall stained with PSR for collagen. Imaged on the Extended-Volume Imaging rig at 0.4µm isotropic pixel size.<br>
DOI: 10.6084/m9.figshare.12009603
title: Supplements

description: These materials are supplements to a manuscript.
DOI: 10.6084/m9.figshare.12009600
title: Test dataset for https://arxiv.org/abs/2002.05534v1

description: This is the test dataset for our paper（Please read "ReadMe.pdf" to know the data structure of "Breathing_TEST.csv"）: Wang Y L, Hu M H*, Li Q L, Zhang X P, Zhai G T, Yao N. Abnormal respiratory patterns classifier may contribute to large-scale screening of people infected with COVID-19 in an accurate and unobtrusive manner [J]. arXiv preprint arXiv:2002.05534, 2020.
DOI: 10.6084/m9.figshare.12009603.v1
title: Supplenmental Figure 1.doc

description: These materials are supplements to a manuscript.
DOI: 10.6084/m9.figshare.12009603.v2
title: Supplenments

description: These materials are supplements to a manuscript.
DOI: 10.6084/m9.figshare.12009603.v4
title: Supplements

description: These materials are supplements to a manuscript.
DOI: 10.6084/m9.figshare.12009603.v3
title: Supplements

description: These materials are supplements to a manuscript.
DOI: 10.25374/mcri.12009564
title: Data and do files

description: This zip folder has the raw data, do files and outputs for the section Kate Francis did for the Nature paper.
DOI: 10.25374/mcri.12009564.v1
title: Data and do files

description: This zip folder has the raw data, do files and outputs for the section Kate Francis did for the Nature paper.
DOI: 10.6084/m9.figshare.12009516
title: An experimental test of the ecological mechanisms driving density-mediated carry-over effects in a seasonal population

description: This dataset includes reproductive output and individual dry masses from replicate populations of Drosophila melanogaster. These populations were maintained under an experimental seasonal regime, in which distinct periods of breeding and non-breeding occur. Population density (low = LD, high = HD) and per capita food availability (low = LF, high = HF) were independently manipulated during the non-breeding period, and body condition and reproductive output were sampled the following breeding period.
DOI: 10.6084/m9.figshare.12009516.v1
title: An experimental test of the ecological mechanisms driving density-mediated carry-over effects in a seasonal population

description: This dataset includes reproductive output and individual dry masses from replicate populations of Drosophila melanogaster. These populations were maintained under an experimental seasonal regime, in which distinct periods of breeding and non-breeding occur. Population density (low = LD, high = HD) and per capita food availability (low = LF, high = HF) were independently manipulated during the non-breeding period, and body condition and reproductive output were sampled the following breeding period.
DOI: 10.6084/m9.figshare.12009492
title: Dataset Microbiota AG y2020m03

description: <b>Gut microbiota in hospitalized children under 5 years with acute infective gastroenteritis caused by virus or bacteria in a regional Peruvian hospital<br></b><b><br></b><b>ABSTRACT</b>Objective: The main objective of this study was to describe the prevalence of 13 representative bacteria from the gut microbiota (GM) in stools samples from children under 5 years of age with acute infective gastroenteritis (AIG) as well as to describe clinical and demographic features from our study population.Results: The most commonly isolated bacteria from the GM were Firmicutes (63.2%) Bacteriodetes (62.4%), Lactobacillus (59.8%), Prevotella (57.3%), Proteobacterium (53.8%), regardless of the etiological agent responsible for the AIG. Interestingly, despite the high prevalence of Firmicutes, Bacteroidetes, Lactobacillus, and Prevotella across all samples, a visible reduction of these agents was observed especially among patients with a single bacterial infection or even bacteria – bacteria coinfections when compared to viral etiologies. Patients with exclusive or mixed breastfeeding registered the highest amount of gut microbiota bacteria, in contrast to infants who received formula or were not breastfed.
DOI: 10.6084/m9.figshare.12009372
title: Computational Search for Magnetic and Non-magnetic 2D Topological Materials using Unified Spin-orbit Spillage Screening

description: Two-dimensional topological materials (TMs) have a variety of properties that make them attractive for applications including spintronics and quantum computation. However, there are only a few such experimentally known materials. To help discover new 2D TMs, we develop a unified and computationally inexpensive approach to identify magnetic and non-magnetic 2D TMs, including gapped and semi-metallic topological classifications, in a high-throughput way using density functional theory-based spin-orbit spillage, Wannier-interpolation, and related techniques. We first compute the spin-orbit spillage for the ~1000 2D materials in the JARVIS-DFT dataset (https://www.ctcms.nist.gov/~knc6/JVASP.html ), resulting in 122 materials with high-spillage values. Then, we use Wannier-interpolation to carry-out Z<sub>2</sub>, Chern-number, anomalous Hall conductivity, Curie temperature, and edge state calculations to further support the predictions. We identify various topologically non-trivial classes such as quantum spin-hall insulators (QSHI), quantum anomalous-hall insulators (QAHI), and semimetals. For a few predicted materials, we run G<sub>0</sub>W<sub>0</sub>+SOC and DFT+U calculations. We find that as we introduce many-body effects, only a few materials retain non-trivial band-topology, suggesting the importance of high-level DFT methods in predicting 2D topological materials. However, as an initial step, the automated spillage screening and Wannier-approach provide useful predictions for finding new topological materials and to narrow down candidates for experimental synthesis and characterization.
DOI: 10.6084/m9.figshare.12009375
title: Datafile Peeters et al. (2020) - Separate effects of BoNT-A and casting.xlsx

description: This data was collected for the investigation of Peeters et al (2020) - Joint and Muscle Assessments of the Separate Effects of Botulinum NeuroToxin-A and Lower-Leg Casting in Children With Cerebral Palsy.This data file contains baseline characteristics, muscle morphology and joint hyper-resistance parameters.
DOI: 10.6084/m9.figshare.12009372.v1
title: Computational Search for Magnetic and Non-magnetic 2D Topological Materials using Unified Spin-orbit Spillage Screening

description: Two-dimensional topological materials (TMs) have a variety of properties that make them attractive for applications including spintronics and quantum computation. However, there are only a few such experimentally known materials. To help discover new 2D TMs, we develop a unified and computationally inexpensive approach to identify magnetic and non-magnetic 2D TMs, including gapped and semi-metallic topological classifications, in a high-throughput way using density functional theory-based spin-orbit spillage, Wannier-interpolation, and related techniques. We first compute the spin-orbit spillage for the ~1000 2D materials in the JARVIS-DFT dataset (https://www.ctcms.nist.gov/~knc6/JVASP.html ), resulting in 122 materials with high-spillage values. Then, we use Wannier-interpolation to carry-out Z<sub>2</sub>, Chern-number, anomalous Hall conductivity, Curie temperature, and edge state calculations to further support the predictions. We identify various topologically non-trivial classes such as quantum spin-hall insulators (QSHI), quantum anomalous-hall insulators (QAHI), and semimetals. For a few predicted materials, we run G<sub>0</sub>W<sub>0</sub>+SOC and DFT+U calculations. We find that as we introduce many-body effects, only a few materials retain non-trivial band-topology, suggesting the importance of high-level DFT methods in predicting 2D topological materials. However, as an initial step, the automated spillage screening and Wannier-approach provide useful predictions for finding new topological materials and to narrow down candidates for experimental synthesis and characterization.
DOI: 10.6084/m9.figshare.12009372.v2
title: Computational Search for Magnetic and Non-magnetic 2D Topological Materials using Unified Spin-orbit Spillage Screening

description: Two-dimensional topological materials (TMs) have a variety of properties that make them attractive for applications including spintronics and quantum computation. However, there are only a few such experimentally known materials. To help discover new 2D TMs, we develop a unified and computationally inexpensive approach to identify magnetic and non-magnetic 2D TMs, including gapped and semi-metallic topological classifications, in a high-throughput way using density functional theory-based spin-orbit spillage, Wannier-interpolation, and related techniques. We first compute the spin-orbit spillage for the ~1000 2D materials in the JARVIS-DFT dataset (https://www.ctcms.nist.gov/~knc6/JVASP.html ), resulting in 122 materials with high-spillage values. Then, we use Wannier-interpolation to carry-out Z<sub>2</sub>, Chern-number, anomalous Hall conductivity, Curie temperature, and edge state calculations to further support the predictions. We identify various topologically non-trivial classes such as quantum spin-hall insulators (QSHI), quantum anomalous-hall insulators (QAHI), and semimetals. For a few predicted materials, we run G<sub>0</sub>W<sub>0</sub>+SOC and DFT+U calculations. We find that as we introduce many-body effects, only a few materials retain non-trivial band-topology, suggesting the importance of high-level DFT methods in predicting 2D topological materials. However, as an initial step, the automated spillage screening and Wannier-approach provide useful predictions for finding new topological materials and to narrow down candidates for experimental synthesis and characterization.
DOI: 10.6084/m9.figshare.12008850
title: Stepwise progressive parametric multiple testing procedure with correlated normal test statistics

description: Multiple testing problems are often seen in clinical trials. An appropriate testing procedure should be specified to deal with the potential inflation of type I error rate due to multiplicity. In this article, we propose a stepwise progressive parametric multiple (SPPM) testing procedure, which constructs the testing using the products of all the combinations of local p-values and the critical values are determined by numerical integrations progressively using the closure principle. We have compared the performance of SPPM to several other procedures, and demonstrate the advantage of SPPM procedure, in terms of power, for the certain situations of multiple testing.
DOI: 10.6084/m9.figshare.12008850.v1
title: Stepwise progressive parametric multiple testing procedure with correlated normal test statistics

description: Multiple testing problems are often seen in clinical trials. An appropriate testing procedure should be specified to deal with the potential inflation of type I error rate due to multiplicity. In this article, we propose a stepwise progressive parametric multiple (SPPM) testing procedure, which constructs the testing using the products of all the combinations of local p-values and the critical values are determined by numerical integrations progressively using the closure principle. We have compared the performance of SPPM to several other procedures, and demonstrate the advantage of SPPM procedure, in terms of power, for the certain situations of multiple testing.
DOI: 10.6084/m9.figshare.12008790
title: Sequences of mitochondrial contigs for Adineta vaga individuals L1-L11

description: Sequences of mitochondrial contigs for <i>A. vaga </i>individuals L1-L11 extracted from whole-genome assemblies using the mitochondrial contig from the first published <i>A. vaga</i> genome assembly (Flot et al., 2013) as the query for blastn search. For L1, mitochondrial contigs were extracted from the MiSeq-based L1 diploid assembly (N50=22,073 bp). For individuals L2-L11, highly fragmented assemblies (with N50 in the range ~1,600-4,300 bp) were generated with SPAdes (version 3.6.0) from HiSeq reads. Mitochondrial sequences for each individual, L1-L11, are in separate FASTA files.
DOI: 10.6084/m9.figshare.12007257
title: Resultado do IMI

description: Este <i>dataset</i> refere-se ao cálculo final do índice de multi/interdisciplinairdade - IMI da tese de Vívian Costa Alves. <br>
DOI: 10.6084/m9.figshare.12007257.v1
title: Resultado do IMI

description: Este <i>dataset</i> refere-se ao cálculo final do índice de multi/interdisciplinairdade - IMI da tese de Vívian Costa Alves. <br>
DOI: 10.6084/m9.figshare.12008790.v1
title: Sequences of mitochondrial contigs for A. vaga individuals L1-L11

description: Sequences of mitochondrial contigs for <i>A. vaga </i>individuals L1-L11 extracted from whole-genome assemblies using the mitochondrial contig from the first published <i>A. vaga</i> genome assembly (Flot et al., 2013) as the query for blastn search. For L1, mitochondrial contigs were extracted from the MiSeq-based L1 diploid assembly (N50=22,073 bp). For individuals L2-L11, highly fragmented assemblies (with N50 in the range 1,600-3,400 bp) were generated with SPAdes (version 3.6.0) from HiSeq reads. Mitochondrial sequences for each individual, L1-L11, are in separate FASTA files.
DOI: 10.6084/m9.figshare.12006783
title: CA29_reference_genome

description: Alternate reference genome of the paternal strain (CA29) used in the introgression scheme.
DOI: 10.6084/m9.figshare.12006783.v1
title: CA29_reference_genome

description: Alternate reference genome of the paternal strain (CA29) used in the introgression scheme.