cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5823597
title: The contribution of genetic and environmental effects to Bergmann's rule and Allen's rule in house mice

description: Data associated with the manuscript, "The contribution of genetic and environmental effects to Bergmann's rule and Allen's rule in house mice". <strong>Abstract</strong>: Distinguishing between genetic, environmental, and genotype-by-environment effects is central to understanding geographic variation in phenotypic clines. Two of the best-documented phenotypic clines are Bergmann's rule and Allen's rule, which describe larger body sizes and shortened extremities in colder climates, respectively. Although numerous studies have found inter- and intraspecific evidence for both ecogeographic patterns, we still have a poor understanding of the extent to which these patterns are driven by genetics, environment, or both. Here, we measured the genetic and environmental contributions to Bergmann's rule and Allen's rule across introduced populations of house mice (<em>Mus musculus domesticus</em>) in the Americas. First, we documented clines for body mass, tail length, and ear length in natural populations, and found that these conform to both Bergmann's rule and Allen's rule. We then raised descendants of wild-caught mice in the lab and showed that these differences persisted in a common environment and are heritable, indicating that they have a genetic basis. Finally, using a full-sib design, we reared mice under warm and cold conditions. We found very little plasticity associated with body size, suggesting that Bergmann's rule has been shaped by strong directional selection in house mice. However, extremities showed considerable plasticity, as both tails and ears grew shorter in cold environments. These results indicate that adaptive phenotypic plasticity as well as genetic changes underlie major patterns of clinal variation in house mice and likely facilitated their rapid expansion into new environments across the Americas. Supplemental data files are provided below. Code associated with the analysis of these data can be found on GitHub at https://github.com/malballinger/Ballinger_allenbergmann_AmNat_2021.
DOI: 10.5281/zenodo.5823586
title: The contribution of genetic and environmental effects to Bergmann's rule and Allen's rule in house mice

description: Data associated with the manuscript, "The contribution of genetic and environmental effects to Bergmann's rule and Allen's rule in house mice". <strong>Abstract</strong>: Distinguishing between genetic, environmental, and genotype-by-environment effects is central to understanding geographic variation in phenotypic clines. Two of the best-documented phenotypic clines are Bergmann's rule and Allen's rule, which describe larger body sizes and shortened extremities in colder climates, respectively. Although numerous studies have found inter- and intraspecific evidence for both ecogeographic patterns, we still have a poor understanding of the extent to which these patterns are driven by genetics, environment, or both. Here, we measured the genetic and environmental contributions to Bergmann's rule and Allen's rule across introduced populations of house mice (<em>Mus musculus domesticus</em>) in the Americas. First, we documented clines for body mass, tail length, and ear length in natural populations, and found that these conform to both Bergmann's rule and Allen's rule. We then raised descendants of wild-caught mice in the lab and showed that these differences persisted in a common environment and are heritable, indicating that they have a genetic basis. Finally, using a full-sib design, we reared mice under warm and cold conditions. We found very little plasticity associated with body size, suggesting that Bergmann's rule has been shaped by strong directional selection in house mice. However, extremities showed considerable plasticity, as both tails and ears grew shorter in cold environments. These results indicate that adaptive phenotypic plasticity as well as genetic changes underlie major patterns of clinal variation in house mice and likely facilitated their rapid expansion into new environments across the Americas. Supplemental data files are provided below. Code associated with the analysis of these data can be found on GitHub at https://github.com/malballinger/Ballinger_allenbergmann_AmNat_2021.
DOI: 10.6084/m9.figshare.17912932
title: Additional file 1 of Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration

description: Additional file 1.
DOI: 10.6084/m9.figshare.17912932.v1
title: Additional file 1 of Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration

description: Additional file 1.
DOI: 10.6084/m9.figshare.17912935
title: Additional file 2 of Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration

description: Additional file 2.
DOI: 10.6084/m9.figshare.17912941.v1
title: Additional file 3 of Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration

description: Additional file 3.
DOI: 10.6084/m9.figshare.17912941
title: Additional file 3 of Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration

description: Additional file 3.
DOI: 10.6084/m9.figshare.17912935.v1
title: Additional file 2 of Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration

description: Additional file 2.
DOI: 10.6084/m9.figshare.17912947
title: Additional file 4 of Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration

description: Additional file 4.
DOI: 10.6084/m9.figshare.17912953.v1
title: Additional file 5 of Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration

description: Additional file 5.
DOI: 10.6084/m9.figshare.17912947.v1
title: Additional file 4 of Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration

description: Additional file 4.
DOI: 10.6084/m9.figshare.17912953
title: Additional file 5 of Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration

description: Additional file 5.
DOI: 10.6084/m9.figshare.17912986
title: Additional file 3 of Avian haemosporidian parasites of accipitriform raptors

description: Additional file 3: Table S1. CytB sequences used in the present study (including GenBank accession numbers, MalAvi lineage names, localities, host species, and references).
DOI: 10.6084/m9.figshare.17912986.v1
title: Additional file 3 of Avian haemosporidian parasites of accipitriform raptors

description: Additional file 3: Table S1. CytB sequences used in the present study (including GenBank accession numbers, MalAvi lineage names, localities, host species, and references).
DOI: 10.6084/m9.figshare.17913051
title: Additional file 3 of Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial

description: Additional file 3: Table S1. Clinicopathological information for pembrolizumab-treated HCC patients.
DOI: 10.6084/m9.figshare.17913051.v1
title: Additional file 3 of Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial

description: Additional file 3: Table S1. Clinicopathological information for pembrolizumab-treated HCC patients.
DOI: 10.6084/m9.figshare.17913057
title: Additional file 5 of Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial

description: Additional file 5: Table S4. CTNNB1 mutations detected in pembrolizumab-treated patients.
DOI: 10.6084/m9.figshare.17913057.v1
title: Additional file 5 of Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial

description: Additional file 5: Table S4. CTNNB1 mutations detected in pembrolizumab-treated patients.
DOI: 10.6084/m9.figshare.17913088
title: Additional file 1 of Poliovirus immunity among adults in the Democratic Republic of the Congo: a cross-sectional serosurvey

description: Additional file 1: Table S1. Comparison of DRC 2013–2014 adult DHS respondent demographics across sample split. Table S2. To test for intra-household correlation in seropositivity, we merged the adult and child datasets, and assessed whether any child and/or any adult in the household was seropositive for each type of polio. The table below summarizes the results across households. Using Pearson’s Chi-squared test, we find that sero-status has a mild positive association for Type 2 (p = 0.01), but there is little evidence for within household correlation for Types 1 and 3. Figure S1. Study design flowchart for dried blood spot (DBS) sampling, testing, and analysis. From a total of 8713 DBS collected in the field, 5526 (63.4%) were successfully processed and merged to DHS questionnaire data for inclusion in this analysis.
DOI: 10.6084/m9.figshare.17913088.v1
title: Additional file 1 of Poliovirus immunity among adults in the Democratic Republic of the Congo: a cross-sectional serosurvey

description: Additional file 1: Table S1. Comparison of DRC 2013–2014 adult DHS respondent demographics across sample split. Table S2. To test for intra-household correlation in seropositivity, we merged the adult and child datasets, and assessed whether any child and/or any adult in the household was seropositive for each type of polio. The table below summarizes the results across households. Using Pearson’s Chi-squared test, we find that sero-status has a mild positive association for Type 2 (p = 0.01), but there is little evidence for within household correlation for Types 1 and 3. Figure S1. Study design flowchart for dried blood spot (DBS) sampling, testing, and analysis. From a total of 8713 DBS collected in the field, 5526 (63.4%) were successfully processed and merged to DHS questionnaire data for inclusion in this analysis.
DOI: 10.6084/m9.figshare.17913094
title: Additional file 3 of Poliovirus immunity among adults in the Democratic Republic of the Congo: a cross-sectional serosurvey

description: Additional file 3. Serology data for poliovirus among adults surveyed and sampled in the 2013-2014 DHS in the Democratic Republic of Congo.
DOI: 10.6084/m9.figshare.17913094.v1
title: Additional file 3 of Poliovirus immunity among adults in the Democratic Republic of the Congo: a cross-sectional serosurvey

description: Additional file 3. Serology data for poliovirus among adults surveyed and sampled in the 2013-2014 DHS in the Democratic Republic of Congo.
DOI: 10.6084/m9.figshare.17913221
title: Additional file 2 of The clinical significance of adenomatous polyposis coli (APC) and catenin Beta 1 (CTNNB1) genetic aberrations in patients with melanoma

description: Additional file 2. Individual Patient Data for the UNC-CH/Vanderbilt/California Pacific Medical Research Institute. Abbreviations: F, female; M, male; MM, metastatic melanoma; f/u, follow-up; immunotx, immunotherapy; n/a, non applicable; n/a(CNA), copy number alteration not tested; †, ‡, § next generation sequencing of corresponding genes from the Foundation One CDx assay was not tested (Illumina 26-gene panel).
DOI: 10.6084/m9.figshare.17913221.v1
title: Additional file 2 of The clinical significance of adenomatous polyposis coli (APC) and catenin Beta 1 (CTNNB1) genetic aberrations in patients with melanoma

description: Additional file 2. Individual Patient Data for the UNC-CH/Vanderbilt/California Pacific Medical Research Institute. Abbreviations: F, female; M, male; MM, metastatic melanoma; f/u, follow-up; immunotx, immunotherapy; n/a, non applicable; n/a(CNA), copy number alteration not tested; †, ‡, § next generation sequencing of corresponding genes from the Foundation One CDx assay was not tested (Illumina 26-gene panel).
DOI: 10.6084/m9.figshare.17913224
title: Additional file 1 of Evaluation of CRISPR gene-editing tools in zebrafish

description: Additional file 1: Supplementary Figure 1. Editing efficiencies across 50 gRNAs with different GC content. Supplementary Figure 2. Mosaicism predicted using Illumina sequencing of G0 mutant larvae. Supplementary Figure 3. Network analyses of the shared differentially expressed genes in Cas9 enzyme and Cas9 mRNA injected larvae. Supplementary Table 1. Oligonucleotides utilized for all assays performed throughout the project. Supplementary Table 2. On-target efficiency scores for the 50 gRNAs obtained from different in silico prediction tools, empirical cleavage scores in vivo using Sanger sequencing and sequence deconvolution tools (TIDE and ICE), from the in vitro assay CIRCLE-seq (RPMN), and Illumina sequencing using the CrispRVariants software. Supplementary Table 3. Description of the off-targets predicted by CRISPRScan and CIRCLE-seq for the 50 evaluated gRNAs. The percentage of sites intersecting genes from the CRISPRScan tool was obtained from the top 30 predicted off-targets since the tool only provides detailed information from these. Supplementary Table 4. List of the frameshift variants identified in protein-coding genes in samples injected with either Cas9 enzyme or Cas9 mRNA using uninjected batch-siblings as reference. Supplementary Table 5. Illumina mosaicism percentages observed in larvae injected with Cas9 (enzyme or mRNA), catalytically dead Cas9 (dCas9), scrambled gRNA, uninjected batch siblings, and a finclip from their crossing parents. Supplementary Table 6. List of DE genes observed in Cas9-injected samples relative to uninjected batch-siblings and siblings from another batch. Supplementary Table 7. List of gene ontology terms enriched in upregulated genes found in both injection treatments (Cas9 enzyme and Cas9 mRNA).
DOI: 10.6084/m9.figshare.17913224.v1
title: Additional file 1 of Evaluation of CRISPR gene-editing tools in zebrafish

description: Additional file 1: Supplementary Figure 1. Editing efficiencies across 50 gRNAs with different GC content. Supplementary Figure 2. Mosaicism predicted using Illumina sequencing of G0 mutant larvae. Supplementary Figure 3. Network analyses of the shared differentially expressed genes in Cas9 enzyme and Cas9 mRNA injected larvae. Supplementary Table 1. Oligonucleotides utilized for all assays performed throughout the project. Supplementary Table 2. On-target efficiency scores for the 50 gRNAs obtained from different in silico prediction tools, empirical cleavage scores in vivo using Sanger sequencing and sequence deconvolution tools (TIDE and ICE), from the in vitro assay CIRCLE-seq (RPMN), and Illumina sequencing using the CrispRVariants software. Supplementary Table 3. Description of the off-targets predicted by CRISPRScan and CIRCLE-seq for the 50 evaluated gRNAs. The percentage of sites intersecting genes from the CRISPRScan tool was obtained from the top 30 predicted off-targets since the tool only provides detailed information from these. Supplementary Table 4. List of the frameshift variants identified in protein-coding genes in samples injected with either Cas9 enzyme or Cas9 mRNA using uninjected batch-siblings as reference. Supplementary Table 5. Illumina mosaicism percentages observed in larvae injected with Cas9 (enzyme or mRNA), catalytically dead Cas9 (dCas9), scrambled gRNA, uninjected batch siblings, and a finclip from their crossing parents. Supplementary Table 6. List of DE genes observed in Cas9-injected samples relative to uninjected batch-siblings and siblings from another batch. Supplementary Table 7. List of gene ontology terms enriched in upregulated genes found in both injection treatments (Cas9 enzyme and Cas9 mRNA).
DOI: 10.6084/m9.figshare.17913227
title: Additional file 1 of Anti-infection roles of miR-155-5p packaged in exosomes secreted by dendritic cells infected with Toxoplasma gondii

description: Additional file 1: Table S1. Primers and siRNA, inhibitors, mimics sequences list.
DOI: 10.6084/m9.figshare.17913227.v1
title: Additional file 1 of Anti-infection roles of miR-155-5p packaged in exosomes secreted by dendritic cells infected with Toxoplasma gondii

description: Additional file 1: Table S1. Primers and siRNA, inhibitors, mimics sequences list.
DOI: 10.6084/m9.figshare.17913246.v1
title: Additional file 5 of Under-nutrition and associated factors among children infected with human immunodeficiency virus in sub-Saharan Africa: a systematic review and meta-analysis

description: Additional file 5.
DOI: 10.6084/m9.figshare.17913246
title: Additional file 5 of Under-nutrition and associated factors among children infected with human immunodeficiency virus in sub-Saharan Africa: a systematic review and meta-analysis

description: Additional file 5.
DOI: 10.5517/ccdc.csd.cc28y7fx
title: CCDC 2113469: Experimental Crystal Structure Determination

description: Related Article: Katharina Bleher, Peter Comba, Michael Gast, Sandra Kronenberger, Thomas Josephy|2022|Inorg.Chim.Acta|532|120752|doi:10.1016/j.ica.2021.120752
DOI: 10.5517/ccdc.csd.cc28y7gy
title: CCDC 2113470: Experimental Crystal Structure Determination

description: Related Article: Katharina Bleher, Peter Comba, Michael Gast, Sandra Kronenberger, Thomas Josephy|2022|Inorg.Chim.Acta|532|120752|doi:10.1016/j.ica.2021.120752
DOI: 10.5517/ccdc.csd.cc28y7hz
title: CCDC 2113471: Experimental Crystal Structure Determination

description: Related Article: Katharina Bleher, Peter Comba, Michael Gast, Sandra Kronenberger, Thomas Josephy|2022|Inorg.Chim.Acta|532|120752|doi:10.1016/j.ica.2021.120752
DOI: 10.5517/ccdc.csd.cc28y7j0
title: CCDC 2113472: Experimental Crystal Structure Determination

description: Related Article: Katharina Bleher, Peter Comba, Michael Gast, Sandra Kronenberger, Thomas Josephy|2022|Inorg.Chim.Acta|532|120752|doi:10.1016/j.ica.2021.120752
DOI: 10.5517/ccdc.csd.cc28y7k1
title: CCDC 2113473: Experimental Crystal Structure Determination

description: Related Article: Katharina Bleher, Peter Comba, Michael Gast, Sandra Kronenberger, Thomas Josephy|2022|Inorg.Chim.Acta|532|120752|doi:10.1016/j.ica.2021.120752
DOI: 10.5517/ccdc.csd.cc28y7l2
title: CCDC 2113474: Experimental Crystal Structure Determination

description: Related Article: Katharina Bleher, Peter Comba, Michael Gast, Sandra Kronenberger, Thomas Josephy|2022|Inorg.Chim.Acta|532|120752|doi:10.1016/j.ica.2021.120752
DOI: 10.5517/ccdc.csd.cc28y7m3
title: CCDC 2113475: Experimental Crystal Structure Determination

description: Related Article: Katharina Bleher, Peter Comba, Michael Gast, Sandra Kronenberger, Thomas Josephy|2022|Inorg.Chim.Acta|532|120752|doi:10.1016/j.ica.2021.120752
DOI: 10.5517/ccdc.csd.cc28y7n4
title: CCDC 2113476: Experimental Crystal Structure Determination

description: Related Article: Katharina Bleher, Peter Comba, Michael Gast, Sandra Kronenberger, Thomas Josephy|2022|Inorg.Chim.Acta|532|120752|doi:10.1016/j.ica.2021.120752
DOI: 10.5517/ccdc.csd.cc28y7p5
title: CCDC 2113477: Experimental Crystal Structure Determination

description: Related Article: Katharina Bleher, Peter Comba, Michael Gast, Sandra Kronenberger, Thomas Josephy|2022|Inorg.Chim.Acta|532|120752|doi:10.1016/j.ica.2021.120752
DOI: 10.5517/ccdc.csd.cc28y7q6
title: CCDC 2113478: Experimental Crystal Structure Determination

description: Related Article: Katharina Bleher, Peter Comba, Michael Gast, Sandra Kronenberger, Thomas Josephy|2022|Inorg.Chim.Acta|532|120752|doi:10.1016/j.ica.2021.120752
DOI: 10.5517/ccdc.csd.cc28y7r7
title: CCDC 2113479: Experimental Crystal Structure Determination

description: Related Article: Katharina Bleher, Peter Comba, Michael Gast, Sandra Kronenberger, Thomas Josephy|2022|Inorg.Chim.Acta|532|120752|doi:10.1016/j.ica.2021.120752
DOI: 10.25345/c5mg4f
title: MassIVE MSV000088648 - HDXMS of Target binding to human Argonaute-2
title: HDX-MS data collected in collaboration with Brianna Bibel, Elad Elkayam, and Leemor Joshua-Tor
DOI: 10.5517/ccdc.csd.cc28x5p2
title: CCDC 2112454: Experimental Crystal Structure Determination

description: Related Article: Yuan Zhang, Zhiqi Liu, Tingyu Zhu, Ying Huang, Weibin Fan, Deguang Huang|2021|Org.Biomol.Chem.|20|415|doi:10.1039/D1OB02043A
DOI: 10.5517/ccdc.csd.cc28x5q3
title: CCDC 2112455: Experimental Crystal Structure Determination

description: Related Article: Yuan Zhang, Zhiqi Liu, Tingyu Zhu, Ying Huang, Weibin Fan, Deguang Huang|2021|Org.Biomol.Chem.|20|415|doi:10.1039/D1OB02043A
DOI: 10.5281/zenodo.5823610
title: Predicting dry matter intake in Canadian Holstein dairy cattle using milk mid-infrared reflectance spectroscopy and other commonly available predictors via artificial neural networks

description: Supplementary Tables
DOI: 10.5281/zenodo.5813380
title: Year-round observations of stable carbon isotopic composition of diacids and related compounds in fine aerosols at Tianjin, North China – Data set

description: To better understand the origins and photochemical processing of water-soluble organic aerosols in the Tianjin region, North China, we studied the stable isotopic composition (δ<sup>13</sup>C) of diacids, oxoacids, α-dicarbonyls, citric acid and fatty acids in fine aerosols (PM<sub>2.5</sub>) collected at an urban (Nankai District, ND; <em>n</em> = 121) and a suburban (Haihe Education Park, HEP; <em>n</em> = 40) sites in Tianjin from 5 July 2018 to 4 July 2019. The δ<sup>13</sup>C of diacids and related compounds were measured using a capillary gas chromatography (Agilent 7890B) coupled with isotope ratio mass spectrometry (GC-irMS) system. Based on seasonal variations in δ<sup>13</sup>C of selected species and linear relations with their concentrations and mass ratios, we found that the diacids and related compounds were mainly derived from fossil fuel including coal combustion and biomass burning and photochemical processing, preferably in gaseous- and aqueous-phases in warm (March-September) and cold (October-February) periods, respectively, in Tianjin, North China.
description: Acknowledgements. This study was partly supported by the National Key R&D Program of China (2017YFC0212700) and National Natural Science Foundation of China (NSFC) through Grant-in-Aid number: 41775120.