cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5104507.v1
title: Supplementary Material for: Impact of low copy repeats on the generation of balanced and unbalanced chromosomal aberrations in mental retardation

description: Low copy repeats (LCRs) are stretches of duplicated DNA that are more than 1 kb in size and share a sequence similarity that exceeds 90%. Non-allelic homologous recombination (NAHR) between highly similar LCRs has been implicated in numerous genomic disorders. This study aimed at defining the impact of LCRs on the generation of balanced and unbalanced chromosomal rearrangements in mentally retarded patients. A cohort of 22 patients, preselected for the presence of submicroscopic imbalances, was analysed using submegabase resolution tiling path array CGH and the results were compared with a set of 41 patients with balanced translocations and breakpoints that were mapped to the BAC level by FISH. Our data indicate an accumulation of LCRs at breakpoints of both balanced and unbalanced rearrangements. LCRs with high sequence similarity in both breakpoint regions, suggesting NAHR as the most likely cause of rearrangement, were observed in 6/22 patients with chromosomal imbalances, but not in any of the balanced translocation cases studied. In case of chromosomal imbalances, the likelihood of NAHR seems to be inversely related to the size of the aberration. Our data also suggest the presence of additional mechanisms coinciding with or dependent on the presence of LCRs that may induce an increased instability at these chromosomal sites.
DOI: 10.6084/m9.figshare.5104522.v1
title: Supplementary Material for: Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density

description: <i>Objective:</i> Analyze the information contained in homozygous haplotypes detected with high density genotyping. <i>Methods:</i> We analyze the genotypes of ∼2,500 markers on chr 22 in 12 population samples, each including 200 individuals. We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments characterized by non-random homozygosity (NRH), taking into account allele frequencies, missing data, genotyping error, and linkage disequilibrium. <i>Results:</i> We show how our measure of linkage disequilibrium based on homozygosity leads to results comparable to those of <i>R</i><sup>2</sup>, as well as the importance of correcting for small sample variation when evaluating <i>D</i>′. We observe that the regions that harbor NRH segments tend to be consistent across populations, are gene rich, and are characterized by lower recombination. <i>Conclusions:</i> It is crucial to take into account LD patterns when interpreting long stretches of homozygous markers.
DOI: 10.6084/m9.figshare.5104501
title: Supplementary Material for: Prospective Controlled Cohort Studies on Long-Term Therapy of Breast Cancer Patients with a Mistletoe Preparation (Iscador®)

description: Mistletoe preparations such as Iscador® (Weleda, Schwäbisch Gmünd, Germany) are commonly used in complementary and alternative / anthroposophic medicine for many cancer indications, particularly for solid cancers. Efficacy of this complementary therapy is still controversial. Objective: Does long-term therapy with Iscador show any effect on survival, tumor progression and psychosomatic self-regulation of patients with breast cancer? Patients and Methods: Prospective recruitment and long-term follow-up of two controlled cohort studies: (1) Randomized matched-pair study (38 pairs): breast cancer patients without any recurrences or metastases and no mistletoe therapy were matched for prognostic factors. By pairwise random allocation, one of the patients was suggested mistletoe therapy to be applied by the attending physician. (2) Non-randomized matched-pair study (84 pairs): breast cancer patients without recurrences or metastases that already received mistletoe therapy were matched to control patients without Iscador therapy. Results: For overall survival, the nonrandomized study shows significant effects in favor of Iscador therapy: hazard ratio HR estimate and 95% confidence interval CI: 0.43 (0.27-0.68). The effect of long-term Iscador therapy on tumor progression as measured by the time to local recurrences, lymphatic or distant metastases in breast cancer patients without any such events at first diagnosis, is in most cases significant in favor of the Iscador group, in the randomized as well as in the non-randomized study. Psychosomatic self-regulation in the Iscador group improves significantly within 12 months compared with the control group in the randomized as well as in the non-randomized study: estimate of the median difference and 95% CI: 0.35 (0.05-0.60), respectively 0.20 (0-0.35). Conclusion: Iscador shows a clinically relevant effect on breast tumor progression as measured by overall survival as well as by the time to recurrences, lymphatic or distant metastases. In the short term, psychosomatic self-regulation increases more markedly under complementary Iscador therapy than under conventional therapy alone
DOI: 10.6084/m9.figshare.5104504
title: Supplementary Material for: Decreased Growth Rate of Lung Metastatic Lesions after Splenectomy in Mice

description: <i>Background:</i> The effect of splenectomy on hematogenous metastases of malignant tumors remains controversial. The aim of this study was to clarify the effect of splenectomy on hematogenous metastases in an animal model. <i>Methods:</i> Colon 26 cancer cells were inoculated into the lateral tail vein of 90 mice. The mice were then assigned to a splenectomy group or a control group. Lung weight, number of lung metastases, size of metastatic nodules, and serum vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF) levels after the surgical procedure were measured and compared between the two groups. <i>Results:</i> The lung nodules were significantly smaller in the splenectomy group than in the control group. In both groups, the serum VEGF levels increased on day 1 and then decreased. The serum VEGF levels on day 5 were significantly lower in the splenectomy group than in the control group. The serum bFGF levels were significantly lower in the splenectomy group than in the control group on days 1 and 5. Immunohistochemical study showed that bFGF was produced by reticuloendothelial cells of the spleen. <i>Conclusion:</i> The growth rate of hematogenous metastatic lesions appears to decrease after splenectomy and may be associated with decreases in serum levels of VEGF and bFGF induced by splenectomy.
DOI: 10.6084/m9.figshare.5104492
title: Supplementary Material for: Calreticulin as a new histone binding protein in mitotic chromosomes

description: Calreticulin (CRT) is a multifunctional Ca<sup>2+</sup>-binding protein that mainly functions in the endoplasmic reticulum as a molecular chaperone for newly synthesized proteins. Recently we reported the protein composition of human metaphase chromosomes (Uchiyama et al., 2004), which included CRT. Here we describe new characteristics of CRT in vitro as well as its localization on the surface of metaphase chromosomes in vivo. CRT was detected in the chromosomal fraction by Western blotting and its binding partners were identified as core and linker histones by ligand overlay assay. Surface plasmon resonance sensor analyses revealed that CRT is bound to chromatin fibers. Moreover, we found that CRT has both supercoiling activity, which assists core histone assembly into chromatin fibers, and binding ability to histone H2A/H2B dimers and histone H3/H4 tetramers. Unlike the chromosome scaffold proteins, indirect immunofluorescent staining revealed that CRT is located on the surface of metaphase chromosomes. These results suggest that CRT plays a role which involves chromatin dynamics on the surface of mitotic chromosomes.
DOI: 10.5061/dryad.8gg5mk2/2
title: greenhouse_competition_soil_extract_experiment

description: Plant biomass and nodulation data in a greenhouse experiment manipulating competition and soil extracts.
DOI: 10.5061/dryad.8gg5mk2/3
title: fuc_mdn_nodC_field2015

description: OTU counts of nodC genotypes measured on nodules from experimental plants in the field.
DOI: 10.5061/dryad.8gg5mk2/4
title: clean_nodC_field2015_OTU_seqs

description: OTU sequences of nodC genotypes measured on nodules from experimental plants in the field.
DOI: 10.5061/dryad.8gg5mk2/5
title: soil_chemistry

description: Soil chemistry data in relation to the distribution of our three Trifolium species.
DOI: 10.5061/dryad.8j88573/1
title: FASTQ files for Experiments 1 and 2

description: FASTQ files for Experiments 1 and 2. List of libraries in Table S4 with the manuscript.
DOI: 10.5061/dryad.8j88573/2
title: eDNA-capture-scripts
DOI: 10.5061/dryad.ck70sj0/1
title: Supplementary Table 1: Evaluation of pathogenicity of all SYNGAP1 variants
DOI: 10.5061/dryad.ck70sj0/2
title: Supplemental Table 2: Phenotypes of individuals with SYNGAP1 variants
DOI: 10.5061/dryad.cv270/1
title: phylogeny_aln.tar

description: The gene sequence alignments (codon-forced; FASTA format) used for phylogeny reconstruction, introgression and genetic distance analyses.
DOI: 10.5061/dryad.cv270/2
title: Jalt_noSolyc_codon.tar

description: The mvf file used for PhyloGWAS analysis on Jaltomata lineages. Tomato (the outgroup) sequences were not included in this dataset.
DOI: 10.5061/dryad.cv270/3
title: paml_aln_noCap.tar

description: The gene sequence alignments (codon-forced; FASTA format) used for PAML branch-site and clade analyses within Jaltomata lineages.
DOI: 10.5061/dryad.cv270/5
title: paml_aln_wtCap.tar

description: The gene sequence alignments (codon-forced; FASTA format) used for PAML branch-site on the ancestral branch of Jaltomata lineages with Capsicum as outgroup.
DOI: 10.5061/dryad.f0s23r8/100
title: Donor124: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 124.
DOI: 10.5061/dryad.f0s23r8/101
title: Donor128: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 128.
DOI: 10.5061/dryad.f0s23r8/102
title: Donor131: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 131.
DOI: 10.5061/dryad.f0s23r8/94
title: Donor94_Part2/2: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 94.
DOI: 10.5061/dryad.f0s23r8/95
title: Donor215: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 215.
DOI: 10.5061/dryad.f0s23r8/96
title: Donor206: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 206.
DOI: 10.5061/dryad.f0s23r8/97
title: Donor198: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 198.
DOI: 10.5061/dryad.f0s23r8/98
title: Donor141: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 141.
DOI: 10.5061/dryad.f0s23r8/99
title: Donor120: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 120.
DOI: 10.5061/dryad.g81sd47/1
title: Model source code

description: Contains C++ files used to model inbreeding depression in autotetraploids
DOI: 10.5061/dryad.jg81r80/13
title: RAD19_fastq

description: Fastq dataset associated with RAD19 barcode file
DOI: 10.5061/dryad.jg81r80/14
title: RAD20_fastq

description: Fastq dataset associated with RAD20 barcode file
DOI: 10.5061/dryad.jg81r80/15
title: RAD21_fastq

description: Fastq dataset associated with RAD21 barcode file
DOI: 10.5061/dryad.jg81r80/16
title: RAD22-1_fastq (1 of 2)

description: Partial fastq dataset associated with RAD22 barcode file. Combine with RAD22-2 prior to analysis.
DOI: 10.5061/dryad.jg81r80/17
title: RAD22-2_fastq

description: Partial fastq dataset associated with RAD22 barcode file. Combine with RAD22-1 prior to analysis.
DOI: 10.5061/dryad.jg81r80/18
title: RAD24_fastq

description: Fastq dataset associated with RAD24 barcode file
DOI: 10.5061/dryad.jg81r80/19
title: RAD26_fastq

description: Fastq dataset associated with RAD26 barcode file
DOI: 10.5061/dryad.jg81r80/20
title: RAD28_fastq

description: Fastq dataset associated with RAD28 barcode file
DOI: 10.5061/dryad.jg81r80/21
title: RAD30A_fastq

description: Fastq dataset associated with RAD30A barcode file
DOI: 10.5061/dryad.k0n0676/2
title: Reference_membrane_colony_density_second_experiment

description: Second replicate of the Infection efficiency experiment. The data was collected from the reference membranes used to measure viable spore densities during the inoculation spraying. The first column, "treatment", contains numbers giving the spore concentration in the inoculated spore suspension, spores/ml. The second column, "position" refers to position of the membrane on the infection plate so that number 1 was at one end, number 2 next to it and so on, from 1 to 5. The third column, "number" identifies the counting square used to sample the colony density, arbitrary numbering of up to two squares in the first and up to three squares in the second experiment. The fourth column, "colony", gives the number of colonies counted in the square. The fifth column, "percm", gives the density of colonies within a square, colonies/cm^2. The sixth column, "size", gives the size of a square, always "1", except for highest concentration treatment of the second experiment, cm^2. Tab delimited .txt file.
DOI: 10.5061/dryad.k0n0676/3
title: Lesion_appearance_data_first_experiment

description: Lesion appearance on each leaf in the first replicate. The data was collected from daily photos by recording newly appeared lesions for every day. The first column, "treatment", contains numbers giving the spore concentration in the inoculated spore suspension, spores/ml. The second column, "density" gives the estimated vaible spore density calculated based on the reference membranes on two sides of the leaf set, spore/cm^2. The third column, "timepoint", gives the timepoint of the recording, days after inoculation. The fourth column, "leafset", identifies four leaf sets belonging to each treatment, from 1 to 4. The fifth column, "leafnumber", identifies each leaf in a leaf set, up to 8 leaves per set. The sixth column, "lesion", gives number of observed separate lesions on the image of the leaf at that date. The seventh column, "lesionappear", gives number of newly appearing lesions since the previous time point. The eighth column, "lesiontot", gives total number of appeared single lesions by that date, based on sum of appearance data of each timepoint. The ninth column, "leafsize", gives size of each leaf estimated from photos of the leaf sets taken on the day of inoculation, cm^2. The tenth column, "colony", gives estimated number of spores that landed on that leaf during the inoculation. The eleventh column, "leaflesion", gives density of all lesions appeared on the leaf (column "lesiontot"), lesions/cm^2. Tab delimited .txt file.
DOI: 10.5061/dryad.k0n0676/4
title: Lesion_appearance_data_second_experiment

description: Lesion appearance on each leaf in the second replicate. The data was collected from daily photos by recording newly appeared lesions for every day. The first column, "treatment", contains numbers giving the spore concentration in the inoculated spore suspension, spores/ml. The second column, "density" gives the estimated vaible spore density calculated based on the reference membranes on two sides of the leaf set, spore/cm^2. The third column, "timepoint", gives the timepoint of the recording, days after inoculation. The fourth column, "leafset", identifies four leaf sets belonging to each treatment, from 1 to 4. The fifth column, "leafnumber", identifies each leaf in a leaf set, up to 8 leaves per set. The sixth column, "lesion", gives number of observed separate lesions on the image of the leaf at that date. The seventh column, "lesionappear", gives number of newly appearing lesions since the previous time point. The eighth column, "lesiontot", gives total number of appeared single lesions by that date, based on sum of appearance data of each timepoint. The ninth column, "leafsize", gives size of each leaf estimated from photos of the leaf sets taken on the day of inoculation, cm^2. The tenth column, "colony", gives estimated number of spores that landed on that leaf during the inoculation. The eleventh column, "leaflesion", gives density of all lesions appeared on the leaf (column "lesiontot"), lesions/cm^2. Tab delimited .txt file.
DOI: 10.5061/dryad.ng473mj/1
title: Supplemental Materials - A Theory for Polymicrogyria and Brain Arteriovenous Malformations in HHT

description: Methods, Table e-1, and Figures e-1, e-2, and e-3 for manuscript
DOI: 10.5061/dryad.q2r3b1f/1
title: R scripts and data files
DOI: 10.5061/dryad.qm114cj/3
title: R Script

description: R script for all analyses
DOI: 10.5061/dryad.qt6535q/1
title: Data on phocid seals natural history parameters and code for Bayesian hierarchical models

description: The datafile was compiled based on publicly available published sources cited in Trukhanova et al 2018 Appendix S1. The associated R files contain a code for data analysis. For detailed data description please see README file.
DOI: 10.5061/dryad.t358vv1.1
title: Data from: Impacts of inference method and dataset filtering on phylogenomic resolution in a rapid radiation of ground squirrels (Xerinae: Marmotini)
DOI: 10.5061/dryad.t358vv1.1/1.1
title: zipped
DOI: 10.5061/dryad.t358vv1.2/10.2
title: svdquartets_empirical_trees

description: SVDQuartets species trees from empirically filtered datasets with support values from 100 bootstrap replicates and rooted on Aplodontia rufa. Trees are named with the filtering level used (e.g., 5var = at least 5 percent variable sites per locus) followed by the number of resulting UCE loci in each dataset
DOI: 10.5061/dryad.vh6t0c7/10
title: hap_chr8.txt

description: Chromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.
DOI: 10.5061/dryad.vh6t0c7/11
title: hap_chr9.txt

description: Chromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.
DOI: 10.5061/dryad.vh6t0c7/12
title: hap_chr7.txt

description: Chromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.
DOI: 10.5061/dryad.vh6t0c7/13
title: hap_chr6.txt

description: Chromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.
DOI: 10.5061/dryad.vh6t0c7/14
title: hap_chr4.txt

description: Chromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.
DOI: 10.5061/dryad.vh6t0c7/15
title: hap_chr3.txt

description: Chromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.
DOI: 10.5061/dryad.vh6t0c7/16
title: hap_chr13.part1.txt

description: Chromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.
DOI: 10.5061/dryad.vh6t0c7/9
title: hap_chr14.txt

description: Chromopainter results for Duroc haplotypes separated by tab. Each haplotype has two columns separated by a space, indicating ancestry from Meishan and Bamaxiang.
DOI: 10.17632/4njhpyrrjj.1
title: Data for: Design of high resistivity light-rare-earth-based PrFe1.93 magnetostrictive alloys: Si doping and high-pressure annealing

description: XRD+M-H+Electrical resistivity+Magnetostriction
DOI: 10.5061/dryad.1cf2fb0/1
title: List of specimens studied.

description: Details about the fossil specimens studied.
DOI: 10.5061/dryad.1cf2fb0/2
title: Calculation of body length of Pahvantia hastata

description: Measurements and method used to calculate the maximum body lengths of the specimens of Pahvantia hastata.
DOI: 10.5061/dryad.1cf2fb0/3
title: Calculation of maximum body lengths of selected radiodonts.

description: Measurements and method used to calculate the maximum body sizes reached in selected radiodonts.
DOI: 10.5061/dryad.1cf2fb0/4
title: Matrix of characters used in the cladistic analyses.
DOI: 10.5061/dryad.2bs69.2
title: Data from: Threshold effect of growth rate on population variability of Escherichia coli cell lengths
DOI: 10.5061/dryad.2h63d10/1
title: Carbon storage, bird community, and vegetation metrics from riparian study areas in the Cosumnes River Preserve, California
DOI: 10.5061/dryad.2h63d10/2
title: Presence/absence data for landbirds in riparian study areas in the Cosumnes River Preserve, California
DOI: 10.5061/dryad.3c7pd3g/1
title: Code for the model

description: This is a Berkeley Madonna file.
DOI: 10.5061/dryad.4q8r207/1
title: Dataset_Breech_FRABAT
DOI: 10.5061/dryad.54bg04m/2
title: Data for Henningsson et al 2018-J R Soc Interface-Part 1

description: Sequences 1 to 4 of the data
DOI: 10.5061/dryad.54bg04m/3
title: Data for Henningsson et al 2018-J R Soc Interface-Part 2

description: Sequences 5 to 7 of the data
DOI: 10.5061/dryad.54bg04m/4
title: Data for Henningsson et al 2018-J R Soc Interface-Part 3

description: Sequences 8 to 10 of the data
DOI: 10.5061/dryad.56s5d84/1
title: Database for publication

description: Database used for analyses
DOI: 10.5061/dryad.56s5d84/2
title: Legend and references for database

description: Legend and references for database
DOI: 10.5061/dryad.5ft0368/1
title: Moth occurrence dataset before removal of pseudoreplicates

description: Occurrence records from the Pacific Northwest Moths (http://pnwmoths.biol.wwu.edu) database used for analyses in this paper. The Pacific Northwest Moths database is largely built from natural history collection specimen records, but it also includes some records from field notes, the literature, and photograph-vouchered specimens. See README.txt for information about the column headings.
DOI: 10.5061/dryad.5n0c3.2
title: Data from: Species pool functional diversity plays a hidden role in generating β-diversity
DOI: 10.5061/dryad.5n0c3.2/1.2
title: Watershed Invertebrate Diversity Data for 1995 MBSS

description: Data accompanying the analyses in Patrick & Brown 2017, Species pool functional diversity plays a hidden role in generating β-diversity.  Eight columns by 266 rows.  Each row corresponds to a community type in a particular watershed.  Community type is designated by the "group" column (P= Predator, H=Herbivore, F=Filterer, C=Collector-Gatherer, S = Shredder, all = Whole Community).  Watershed is denoted in the "MDE8Digit" column by a code referring to a Maryland 8 Digit watershed code (corresponds to USGS HUC12).  The average within stream alpha richness for the watershed is in the "alpha" column.  The total gamma richness for the watershed is in the "gamma" column.  The functional diversity, expressed as RaoQ, for the species pool of the watershed is in the "fdiv" column. The beta diversity, expressed as mean bray curtis dissimilarity, of the watershed is in the "bdiv" column.  The environmental dispersion, expressed as multivariate dispersion among environmental variables, is in the "envdisp" column.  Please see Patrick & Brown 2017 for detailed methods.
DOI: 10.5061/dryad.7n6f407/1
title: Baden_VvNesting_Microhabitat

description: Microhabitat data from control and nest/park sites
DOI: 10.5061/dryad.7n6f407/2
title: Baden_VvNesting_Total_nest_locations

description: UTM locations for all nest and park sites included in this study, along with the identity for who constructed nest sites, whether nest/park sites were used, and if used, whether sites were used singly or communally, and the number and identities of users.