cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3811314.v1
title: Stress-associated radiation effects in pygmy wood mouse <i>Apodemus uralensis</i> (Muridae, Rodentia) populations from the East-Urals Radioactive Trace

description: This work is based on the comparative analysis of data obtained in the course of monitoring pygmy wood mouse populations (<i>Apodemus uralensis</i> Pallas, 1811) in the East-Urals Radioactive Trace (EURT) area and background territories. The effect of population size and its interaction with the radioactivity on biochemical parameters in the spleen and adrenal glands was studied. The concentrations of total lipids, proteins, DNA and RNA, activity of glucose-6-phosphate isomerase and catalase as well as the level of lipid peroxidation (LPO) were evaluated. The functional-metabolic shifts seen with large population sizes were characterized by delipidisation of adrenocortical cells, increased LPO as the main mechanism for steroidogenesis, growth of the protein components of the adrenal glands to maintain their hyperfunction, as well as immunosuppression associated with the restriction of carbohydrates providing splenocytes, reduction of DNA synthesis, and the development of a pro-/antioxidant imbalance. Reactivity of the neuroendocrine and hematopoietic systems of animals experiencing a high population density was higher in the EURT zone compared with the reference group. This difference can be explained by the additional stress from the chronic radiation exposure. The level of LPO, catalase activity, and DNA/protein ratio in the spleen and the total protein content in the adrenal glands were the most sensitive to the interaction of population size and radiation exposure. The harmful effect (distress) of the interaction of non-radiation and radiation factors can manifest when there is a population abundance above 30 ind./100 trap–day and a radiation burden which exceeds the lower boundary of the Derived Consideration Reference Levels, which is above 0.1 mGy/day.
DOI: 10.6084/m9.figshare.3811308
title: SNP calls in VCF format

description: SNP calls in VCF format. As used in for:<br>Jeffares DC et al (2015). The Genomic and Phenotypic Diversity of Schizosaccharomyces pombe. Nature Genetics 47(3):235-241. doi: 10.1038/ng.3215.<br>http://www.ncbi.nlm.nih.gov/pubmed/25665008. <br>File: Schizosaccharomyces-pombe-snps.2012-12-12.filt3c.all.snps-only.anno4.vcf.gz<br>
DOI: 10.6084/m9.figshare.3811308.v1
title: SNP calls in VCF format

description: SNP calls in VCF format. As used in for:<br>Jeffares DC et al (2015). The Genomic and Phenotypic Diversity of Schizosaccharomyces pombe. Nature Genetics 47(3):235-241. doi: 10.1038/ng.3215.<br>http://www.ncbi.nlm.nih.gov/pubmed/25665008. <br>File: Schizosaccharomyces-pombe-snps.2012-12-12.filt3c.all.snps-only.anno3.vcf.gz<br>
DOI: 10.6084/m9.figshare.3811305
title: indel calls in VCF format

description: Indel calls in VCF 4.1 format.<br>File: Schizosaccharomyces-pombe-indels.gatk.union.genotyped.filter2.vcf.gz<br>
DOI: 10.6084/m9.figshare.3811305.v1
title: indel calls in VCF format

description: Indel calls in VCF 4.1 format.<br>File: Schizosaccharomyces-pombe-indels.gatk.union.genotyped.filter.vcf.gz<br>
DOI: 10.6084/m9.figshare.3811299
title: numeric trait data

description: All numeric trait data, both raw data values and normalised.<br>File: Schizosaccharomyces-pombe-numeric-trait-data.tar.gz
DOI: 10.6084/m9.figshare.3811293
title: structural variant calls in VCF format

description: Structural variant calls for the 113 curated variants in VCF 4.1 format.<br>File: Schizosaccharomyces-pombe-113-curated-SV-calls-Jeffares-2016.vcf.gz
DOI: 10.6084/m9.figshare.3811293.v1
title: structural variant calls in VCF format

description: Structural variant calls for the 113 curated variants in VCF 4.1 format.<br>File: Schizosaccharomyces-pombe-113-curated-SV-calls-Jeffares-2016.vcf.gz
DOI: 10.6084/m9.figshare.3811290
title: Supplementary tables

description: Supplementary tables in Excel format.
DOI: 10.6084/m9.figshare.3811290.v1
title: Supplementary tables

description: Supplementary tables in Excel format.
DOI: 10.6084/m9.figshare.3811287
title: BiOCURA-metabolomic profiles and clinical parameters

description: Patients were selected from the observational BiOCURA study in which patients were enrolled between 2009 and 2015. Serum samples from selected subjects were measured on three targeted LC-MS platforms, covering a broad spectrum of pre-defined metabolites. The lipid platform targets low abundance lipid species, including free fatty acids (FAs) and phospholipid derivates, such as lysophosphatidylcholines (LPCs) and lysophosphatidylethanolamines (LPEs); the oxylipins platform covers oxygenated metabolites derived from polyunsaturated fatty acids through enzymatic and non-enzymatic oxidation processes; the amine platform targets amino acids and biogenic amines.Demographic, clinical, and laboratory parameters of patients at baseline were obtained, including age, gender, menopausal status, body mass index (BMI), disease duration, any previously used bDMARD (biological naivety), currently used csDMARDs and non-anti-rheumatic drugs, 28 tender joint count (TJC), 28 swollen joint count (SJC), a 100mm visual analogue scale on general health (VAS-GH), erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), rheumatoid factor (RF), and anti-citrullinated protein antibody (ACPA). Disease activity was assessed at baseline and at follow-up visits, using DAS28 (disease activity score based on a 28-joint count) to evaluate therapeutic responses.
DOI: 10.6084/m9.figshare.3811287.v1
title: BiOCURA-metabolomic profiles and clinical parameters

description: Patients were selected from the observational BiOCURA study in which patients were enrolled between 2009 and 2015. Serum samples from selected subjects were measured on three targeted LC-MS platforms, covering a broad spectrum of pre-defined metabolites. The lipid platform targets low abundance lipid species, including free fatty acids (FAs) and phospholipid derivates, such as lysophosphatidylcholines (LPCs) and lysophosphatidylethanolamines (LPEs); the oxylipins platform covers oxygenated metabolites derived from polyunsaturated fatty acids through enzymatic and non-enzymatic oxidation processes; the amine platform targets amino acids and biogenic amines.Demographic, clinical, and laboratory parameters of patients at baseline were obtained, including age, gender, menopausal status, body mass index (BMI), disease duration, any previously used bDMARD (biological naivety), currently used csDMARDs and non-anti-rheumatic drugs, 28 tender joint count (TJC), 28 swollen joint count (SJC), a 100mm visual analogue scale on general health (VAS-GH), erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), rheumatoid factor (RF), and anti-citrullinated protein antibody (ACPA). Disease activity was assessed at baseline and at follow-up visits, using DAS28 (disease activity score based on a 28-joint count) to evaluate therapeutic responses.
DOI: 10.6084/m9.figshare.3811284
title: S4 Table (Performance Assessment of Four Chimeric Trypanosoma cruzi Antigens Based on Antigen-Antibody Detection for Diagnosis of Chronic Chagas Disease).xlsx

description: Performance Assessment of Four Chimeric Trypanosoma cruzi Antigens Based on Antigen-Antibody Detection for Diagnosis ofChronic Chagas Disease<br>S4 Table. IBMP sequence details<br>
DOI: 10.6084/m9.figshare.3811284.v2
title: S4 Table (Performance Assessment of Four Chimeric Trypanosoma cruzi Antigens Based on Antigen-Antibody Detection for Diagnosis of Chronic Chagas Disease).xlsx

description: Performance Assessment of Four Chimeric Trypanosoma cruzi Antigens Based on Antigen-Antibody Detection for Diagnosis ofChronic Chagas Disease<br>S4 Table. IBMP sequence details<br>
DOI: 10.6084/m9.figshare.3811284.v1
title: S4 Table.xlsx

description: Performance Assessment of Four Chimeric Trypanosoma cruzi Antigens Based on Antigen-Antibody Detection for Diagnosis ofChronic Chagas Disease<br>S4 Table. IBMP sequence details<br>
DOI: 10.6084/m9.figshare.3811281
title: structural variant, SNP and indel calls used for GWAS in PLINK format

description: All structural variant, SNP and indel calls used for GWAS.<br>All filtered to have minor allele count at least 5, and in PLINK format.<br>File: Schizosaccharomyces-pombe-variants-plink-minor-allele-count5-Jeffares2016.tar.gz<br><br>
DOI: 10.6084/m9.figshare.3811254
title: Differential abundance of bacterial families (based on their relative abundance) - Related to Fig. 3

description: Differential abundance of bacterial families (based on their respective relative abundance). Pairwise comparison by DNA extraction method was performed using the relative abundance of each family and their log2-fold difference (column vs. rows). This figure relates to the article: <br>Berith E. Knudsen, Lasse Bergmark, Patrick Munk, Oksana Lukjancenko, Anders Priemé, Frank M. Aarestrup, Sünje J. Pamp (2016) Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition. <b><i>mSystems</i></b> Oct 2016, 1 (5) e00095-16; DOI: 10.1128/mSystems.00095-16 http://msystems.asm.org/content/1/5/e00095-16
DOI: 10.6084/m9.figshare.3811254.v1
title: Differential abundance of bacterial families (based on their relative abundance) - Related to Fig. 3

description: Differential abundance of bacterial families (based on their respective relative abundance). Pairwise comparison by DNA extraction method was performed using the relative abundance of each family and their log2-fold difference (column vs. rows). This figure relates to the article: <br>Berith E. Knudsen, Lasse Bergmark, Patrick Munk, Oksana Lukjancenko, Anders Priemé, Frank M. Aarestrup, Sünje J. Pamp (2016) Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition. <b><i>mSystems</i></b> Oct 2016, 1 (5) e00095-16; DOI: 10.1128/mSystems.00095-16 http://msystems.asm.org/content/1/5/e00095-16
DOI: 10.6084/m9.figshare.3811251
title: Differential abundance analysis workflow (16S rRNA gene profiling data) - Example

description: In order to test for the differential abundance of taxa that may drive the differences observed between inferred microbial communities derived from the different DNA isolation procedures, we performed DESeq2 analyses. Here we provide an example for such an analysis from human fecal specimen, examined using 16S rRNA gene profiling. This workflow relates to the article: <br>Berith E. Knudsen, Lasse Bergmark, Patrick Munk, Oksana Lukjancenko, Anders Priemé, Frank M. Aarestrup, Sünje J. Pamp (2016) Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition. <b><i>mSystems</i></b> Oct 2016, 1 (5) e00095-16; DOI: 10.1128/mSystems.00095-16 http://msystems.asm.org/content/1/5/e00095-16
DOI: 10.6084/m9.figshare.3811251.v1
title: Differential abundance analysis workflow (16S rRNA gene profiling data) - Example

description: In order to test for the differential abundance of taxa that may drive the differences observed between inferred microbial communities derived from the different DNA isolation procedures, we performed DESeq2 analyses. Here we provide an example for such an analysis from human fecal specimen, examined using 16S rRNA gene profiling. Related to Knudsen et al., “Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition”.
DOI: 10.6084/m9.figshare.3811212
title: Natural variation in brain gene expression profiles of aggressive and nonaggressive individual sticklebacks

description: Lists of the differentially expressed genes between aggressive and nonaggressive individuals in each region
DOI: 10.6084/m9.figshare.3811212.v1
title: Natural variation in brain gene expression profiles of aggressive and nonaggressive individual sticklebacks

description: Lists of the differentially expressed genes between aggressive and nonaggressive individuals in each region
DOI: 10.6084/m9.figshare.3811098
title: Syntheses, crystal structures, and properties of optically active Lu(III) and Yb(III) complexes of <i>N,N′</i>-bis(2-hydroxybenzyl)-<i>N,N′</i>-bis(2-pyridylmethyl)-<i>R</i>-1,2-propanediamine with chloride or thiocyanate

description: The reaction of <i>N,N′</i>-bis(2-hydroxybenzyl)-<i>N,N′</i>-bis(2-pyridylmethyl)-<i>R</i>-1,2-propanediamine (<i>R</i>-bbppnH<sub>2</sub>) with LnCl<sub>3</sub>∙6H<sub>2</sub>O (Ln: Lu, Yb) stereoselectively gave an optically active complex, [LnCl(<i>R</i>-bbppn)], which crystallizes in the acentric space group of <i>P</i>2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>. The central lutetium(III) is coordinated by two oxygens from two phenolates, four nitrogens from two pyridines, and one bidentate propanediamine of <i>R</i>-bbppn<sup>2−</sup>, one chloride to form a seven-coordinate distorted pentagonal bipyramidal geometry. Although two optical isomers, ΔΛΔ and ΛΔΛ, are possible for such a structure, the absolute configuration of the complex is stereoselectively unified to ΔΛΔ. The coordinated chloride of the complex is readily replaced by other ligands, and hence the reaction with thiocyanate results in formation of another seven-coordinate complex, [Ln(NCS)(<i>R</i>-bbppn)].
DOI: 10.6084/m9.figshare.3811098.v1
title: Syntheses, crystal structures, and properties of optically active Lu(III) and Yb(III) complexes of <i>N,N’</i>-bis(2-hydroxybenzyl)-<i>N,N’</i>-bis(2-pyridylmethyl)-<i>R</i>-1,2-propanediamine with chloride or thiocyanate

description: The reaction of <i>N,N’</i>-bis(2-hydroxybenzyl)-<i>N,N’</i>-bis(2-pyridylmethyl)-<i>R</i>-1,2-propanediamine (<i>R</i>-bbppnH<sub>2</sub>) with LnCl<sub>3</sub>∙6H<sub>2</sub>O (Ln: Lu, Yb) stereoselectively gave an optically active complex, [LnCl(<i>R</i>-bbppn)], which crystallizes in the acentric space group of <i>P</i>2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>. The central lutetium(III) is coordinated by two oxygens from two phenolates, four nitrogens from two pyridines and one bidentate propanediamine of <i>R</i>-bbppn<sup>2−</sup>, one chloride to form a seven-coordinate distorted pentagonal bipyramidal geometry. Although two optical isomers, ΔΛΔ and ΛΔΛ, are possible for such a structure, the absolute configuration of the complex is stereoselectively unified to ΔΛΔ. The coordinated chloride of the complex is readily replaced by other ligands, and hence the reaction with thiocyanate results in formation of another seven-coordinate complex, [Ln(NCS)(<i>R</i>-bbppn)].
DOI: 10.6084/m9.figshare.3811098.v2
title: Syntheses, crystal structures, and properties of optically active Lu(III) and Yb(III) complexes of <i>N,N′</i>-bis(2-hydroxybenzyl)-<i>N,N′</i>-bis(2-pyridylmethyl)-<i>R</i>-1,2-propanediamine with chloride or thiocyanate

description: The reaction of <i>N,N′</i>-bis(2-hydroxybenzyl)-<i>N,N′</i>-bis(2-pyridylmethyl)-<i>R</i>-1,2-propanediamine (<i>R</i>-bbppnH<sub>2</sub>) with LnCl<sub>3</sub>∙6H<sub>2</sub>O (Ln: Lu, Yb) stereoselectively gave an optically active complex, [LnCl(<i>R</i>-bbppn)], which crystallizes in the acentric space group of <i>P</i>2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>. The central lutetium(III) is coordinated by two oxygens from two phenolates, four nitrogens from two pyridines, and one bidentate propanediamine of <i>R</i>-bbppn<sup>2−</sup>, one chloride to form a seven-coordinate distorted pentagonal bipyramidal geometry. Although two optical isomers, ΔΛΔ and ΛΔΛ, are possible for such a structure, the absolute configuration of the complex is stereoselectively unified to ΔΛΔ. The coordinated chloride of the complex is readily replaced by other ligands, and hence the reaction with thiocyanate results in formation of another seven-coordinate complex, [Ln(NCS)(<i>R</i>-bbppn)].
DOI: 10.6084/m9.figshare.3811071
title: A Study about Non-Volatile Memories.pdf

description: This paper presents an upcoming nonvolatile memories (NVM) overview. Non-volatile memory devices are electrically programmable and erasable to store charge in a location within the device and to retain that charge when voltage supply from the device is disconnected. The non-volatile memory is typically a semiconductor memory comprising thousands of individual transistors configured on a substrate to form a matrix of rows and columns of memory cells. Non-volatile memories are used in digital computing devices for the storage of data. In this paper we have given introduction including a brief survey on upcoming NVM's such as FeRAM, MRAM, CBRAM, PRAM, SONOS, RRAM, Racetrack memory and NRAM. In future Nonvolatile memory may eliminate the need for comparatively slow forms of secondary storage systems, which include hard disks.
DOI: 10.6084/m9.figshare.3811071.v1
title: A Study about Non-Volatile Memories.pdf

description: This paper presents an upcoming nonvolatile memories (NVM) overview. Non-volatile memory devices are electrically programmable and erasable to store charge in a location within the device and to retain that charge when voltage supply from the device is disconnected. The non-volatile memory is typically a semiconductor memory comprising thousands of individual transistors configured on a substrate to form a matrix of rows and columns of memory cells. Non-volatile memories are used in digital computing devices for the storage of data. In this paper we have given introduction including a brief survey on upcoming NVM's such as FeRAM, MRAM, CBRAM, PRAM, SONOS, RRAM, Racetrack memory and NRAM. In future Nonvolatile memory may eliminate the need for comparatively slow forms of secondary storage systems, which include hard disks.
DOI: 10.5281/zenodo.4013847
title: Finland COVID-19 R-value estimate March - August

description: This dataset contains the time-dependent effective reproduction number R<sub>t</sub> of the COVID-19 epidemic in Finland for the period Feb 27th 2020 - August 14th 2020. The reproduction number was estimated using the daily new coronavirus cases in the infectious diseases registry of Finland with an unscented RTS smoother and the SEIR epidemic model. The SEIR model was defined as<br> \(S(t+1) = S(t) - \frac{R_t(t)}{T_i} I(t) \frac{S(t)}{N} + \omega_{S}\\ E(t+1) = E(t) + \frac{R_t(t)}{T_i} I(t) \frac{S(t)}{N} - \frac{E(t)}{T_e} + \omega_{E}\\ I(t+1) = I(t) + \frac{E(t)}{T_e}-\frac{I(t)}{T_i} + \omega_{I} \\ R_t(t+1) = R_t(t) + \omega_{R_t}\) with S, E, and I being the susceptible, exposed, and infective populations, R<sub>t</sub> the time-dependent effective reproduction number, and ωs are normally distributed random numbers with zero mean and small (1e-8) variance except for ω<sub>Rt</sub> whose variance was set to 0.00025. The exposed state duration was set to T<sub>e</sub>=3 days and infective state duration T<sub>i</sub>=5 days. The measurement model (from the SEIR state to observed daily new cases) was defined as<br> \(P_\text{new cases}(k) \propto \mathcal{N}\left[ \alpha \frac{R_t(t-5 days)}{T_i}I(t-5\text{days}) \frac{S(t-5\text{days})}{N}, \sigma_\text{new cases}^2(t) \right]\), i.e., via a time-delayed gaussian process whose variance was computed by the observed daily new cases with a 7-day rolling mean. Here the detection rate α is set to 10%, but has no significant affect on the computed R-values. The data is a CSV-format file with the columns date = ISO 8601 date string Rt = maximum a posteriori estimate of R<sub>t</sub> Rt_lower50 = lower limit of the 50% credible interval for R<sub>t</sub> Rt_upper50 = upper limit of the 50% credible interval for R<sub>t</sub> Rt_lower90 = lower limit of the 90% credible interval for R<sub>t</sub> Rt_upper90 = upper limit of the 90% credible interval for R<sub>t</sub>
DOI: 10.5281/zenodo.4013846
title: Finland COVID-19 R-value estimate March - August

description: This dataset contains the time-dependent effective reproduction number R<sub>t</sub> of the COVID-19 epidemic in Finland for the period Feb 27th 2020 - August 14th 2020. The reproduction number was estimated using the daily new coronavirus cases in the infectious diseases registry of Finland with an unscented RTS smoother and the SEIR epidemic model. The SEIR model was defined as<br> \(S(t+1) = S(t) - \frac{R_t(t)}{T_i} I(t) \frac{S(t)}{N} + \omega_{S}\\ E(t+1) = E(t) + \frac{R_t(t)}{T_i} I(t) \frac{S(t)}{N} - \frac{E(t)}{T_e} + \omega_{E}\\ I(t+1) = I(t) + \frac{E(t)}{T_e}-\frac{I(t)}{T_i} + \omega_{I} \\ R_t(t+1) = R_t(t) + \omega_{R_t}\) with S, E, and I being the susceptible, exposed, and infective populations, R<sub>t</sub> the time-dependent effective reproduction number, and ωs are normally distributed random numbers with zero mean and small (1e-8) variance except for ω<sub>Rt</sub> whose variance was set to 0.00025. The exposed state duration was set to T<sub>e</sub>=3 days and infective state duration T<sub>i</sub>=5 days. The measurement model (from the SEIR state to observed daily new cases) was defined as<br> \(P_\text{new cases}(k) \propto \mathcal{N}\left[ \alpha \frac{R_t(t-5 days)}{T_i}I(t-5\text{days}) \frac{S(t-5\text{days})}{N}, \sigma_\text{new cases}^2(t) \right]\), i.e., via a time-delayed gaussian process whose variance was computed by the observed daily new cases with a 7-day rolling mean. Here the detection rate α is set to 10%, but has no significant affect on the computed R-values. The data is a CSV-format file with the columns date = ISO 8601 date string Rt = maximum a posteriori estimate of R<sub>t</sub> Rt_lower50 = lower limit of the 50% credible interval for R<sub>t</sub> Rt_upper50 = upper limit of the 50% credible interval for R<sub>t</sub> Rt_lower90 = lower limit of the 90% credible interval for R<sub>t</sub> Rt_upper90 = upper limit of the 90% credible interval for R<sub>t</sub>
DOI: 10.6084/m9.figshare.3810960
title: The Feedback-Related Negativity and the P300 brain potential are sensitive to price expectation violations in a virtual shopping task. (PLOS One)

description: This is a set of files containing the data from a paper to appear soon in PLOS One (as of September 2016). The paper is authored by Alexandre Schaefer, Luciano G Buratto, Nobuhiko Goto and Emilie Brotherhood, and it shows that two brain event-related potentials - the Feedback-Related Negativity and the P300 - are sensitive to price expectation violations during a simulated shopping context. The actual accepted paper is included amongst the files.
DOI: 10.4225/03/57d78bc040fe1
title: Wolbachia-mediated blocking of dengue virus in mosquito cells is due in part to the action of the RNAi pathway

description: The first dataset examines the effect of Wolbachia infection on genes representing the major innate immune pathways in Aedes aegypti cells. <br>The second data set reports the effects of siRNA designed to target these genes on their expression and on dengue virus loads in Wolbachia infected and Wolbachia free cells. <br>The last dataset reports the effects of treatment with combinations of siRNAs targeting multiple immune pathways on the genes expression and dengue virus loads in Wolbachia infected and Wolbachia free cells. <br>