cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9736532.v1
title: Prevalence of the parasite Loxothylacus panopaei on host crab Rhithropanopeus harrisii along the East and Gulf coasts of the Atlantic: Survey data

description: Detailed sampling strategy outlined in the associated paper (listed above).<br>Each row is a single crab; all crabs &gt;= 2 mm were removed from crab collectors. Detail on sampling sites and times are given in the associated "RL_site_metadata.csv" metadata file.<br>Columns:Site = estuary code (coordinates in metadata)<br>Status = parasite status (Native, Invasive, Absent)<br>Subsite = subsite code (coordinates in metadata)Trap = 1-2 traps deployed at each subsite<br>Time = sampling date<br>Species = crab species<br>Sex = crab sex: M(ale), F(emale), I(ndeterminate)<br>Ovigerous = crab ovigery: Y(es), N(o)<br>Loxo = parasite presence: Y(es), N(o)Loxo_bin = binary parasite presence: 1 (present), 0 (absent)Virgin = number of virgin parasite externae<br>Mature = number of mature parasite externae<br>Scar = number of parasite externae scars<br>CW = carapace width of crab<br>
DOI: 10.6084/m9.figshare.9736379.v1
title: Authentication of 2-(4'-chlorophenyl)-1,4-benzoquinone

description: Authentication of 2-(4'-chlorobiphenyl)-1,4-benzoquinone by GC-MS. This compound was synthesized from 1,4-benzoquinone adn diazotized 4-chloroaniline using the Meerwein arylation reactions as described previously. This compound is &gt; 99% pure by GC-MS.
DOI: 10.6084/m9.figshare.9736337
title: Plasmid maps for AAVS1 targeting

description: Plasmid maps for CRISPR Cas9 targeted knock-in of R-GECO1.0 to the AAVS1 locus
DOI: 10.6084/m9.figshare.9736340
title: Authentication of 3,3',4,4',5-pentachlorobiphenyl

description: Authentication of 3,3',4,4',5-pentachlorobiphenyl (PCB 126) by GC-MS. This compound was synthesized via Suzuki-Cross-Coupling reaction, from 3,4,5-trichlorobromobenzene and 3,4-dichlorophenylboronic acid under the calalysis of Pd(dba)2/DPDB system.
DOI: 10.6084/m9.figshare.9736340.v1
title: Authentication of 3,3',4,4',5-pentachlorobiphenyl

description: Authentication of 3,3',4,4',5-pentachlorobiphenyl (PCB 126) by GC-MS. This compound was synthesized via Suzuki-Cross-Coupling reaction, from 3,4,5-trichlorobromobenzene and 3,4-dichlorophenylboronic acid under the calalysis of Pd(dba)2/DPDB system.
DOI: 10.6084/m9.figshare.9736337.v1
title: Plasmid maps for AAVS1 targeting

description: Plasmid maps for CRISPR Cas9 targeted knock-in of R-GECO1.0 to the AAVS1 locus
DOI: 10.6084/m9.figshare.9736241
title: Table S2 from A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure

description: Table S2. Kinetoplastid-like proteins identified in this study.
DOI: 10.6084/m9.figshare.9736241.v1
title: Table S2 from A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure

description: Table S2. Kinetoplastid-like proteins identified in this study.
DOI: 10.6084/m9.figshare.9736238
title: Table S1 from A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure

description: Table S1. Information on taxa used in phylogenomic analysis, including gene coverages and sources.
DOI: 10.6084/m9.figshare.9736238.v1
title: Table S1 from A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure

description: Table S1. Information on taxa used in phylogenomic analysis, including gene coverages and sources.
DOI: 10.6084/m9.figshare.9736139
title: data.zip

description: Data used in "An Examination of the Distribution of White-Collar Worker Residences in Tokyo and Osaka during the Modernizing Period"<br>
DOI: 10.6084/m9.figshare.9736028
title: Consentimiento informado

description: Consentimiento informado
DOI: 10.6084/m9.figshare.9736139.v1
title: data.zip

description: Data used in "An Examination of the Distribution of White-Collar Worker Residences in Tokyo and Osaka during the Modernizing Period"<br>
DOI: 10.6084/m9.figshare.9736022
title: Bacterial Diversity in the Metal-Rich Terrestrial Deep Subsurface Sediments of Krishna Godavari Basin, India

description: Krishna Godavari (KG) basin, located in the eastern continental margin of India, is a geological region well known for the abundance of economically important minerals. However, less is known about the microbial ecology of its subsurface sediments. The present study is the first report on the comprehensive culture-independent census of bacterial communities of deep subsurface of KG basin and their relationship with the geochemical environment. Elemental and mineralogical characterization of the sediments highlighted the presence of carbon and nitrogen deprived conditions along with the abundance of metalliferous minerals, especially rich in valuable elements like zirconium, vanadium, cesium, and rare earth elements. Diversity analysis based on Illumina MiSeq high-throughput sequencing platform revealed the predominance of Firmicutes (44.24%), Proteobacteria (34.17%), Bacteroidetes (15.18%), and Actinobacteria (3.81%) in the deep subsurface of this basin. ‘Abundant’ and ‘rare’ sub-communities analysis indicated that a large number of phyla like Acidobacteria, Armatimonadetes, Chloroflexi, and Deinococcus-Thermus were exclusively present as a rare community. Statistical analyses demonstrated that geochemical parameters, especially depth, pH, and metal content, showed significant influence on the microbial community structure. The present study should help future investigations for microbial mediated sustainable utilization of mineral-rich sediments of the region.
DOI: 10.6084/m9.figshare.9736022.v1
title: Bacterial Diversity in the Metal-Rich Terrestrial Deep Subsurface Sediments of Krishna Godavari Basin, India

description: Krishna Godavari (KG) basin, located in the eastern continental margin of India, is a geological region well known for the abundance of economically important minerals. However, less is known about the microbial ecology of its subsurface sediments. The present study is the first report on the comprehensive culture-independent census of bacterial communities of deep subsurface of KG basin and their relationship with the geochemical environment. Elemental and mineralogical characterization of the sediments highlighted the presence of carbon and nitrogen deprived conditions along with the abundance of metalliferous minerals, especially rich in valuable elements like zirconium, vanadium, cesium, and rare earth elements. Diversity analysis based on Illumina MiSeq high-throughput sequencing platform revealed the predominance of Firmicutes (44.24%), Proteobacteria (34.17%), Bacteroidetes (15.18%), and Actinobacteria (3.81%) in the deep subsurface of this basin. ‘Abundant’ and ‘rare’ sub-communities analysis indicated that a large number of phyla like Acidobacteria, Armatimonadetes, Chloroflexi, and Deinococcus-Thermus were exclusively present as a rare community. Statistical analyses demonstrated that geochemical parameters, especially depth, pH, and metal content, showed significant influence on the microbial community structure. The present study should help future investigations for microbial mediated sustainable utilization of mineral-rich sediments of the region.
DOI: 10.6084/m9.figshare.9735908
title: Supplementary Material for: Selenium and Other Trace Elements in the Etiology of Parkinson’s Disease: A Systematic Review and Meta-Analysis of Case-Control Studies

description: <b><i>Background:</i></b> Parkinson’s disease (PD) is the most common neurodegenerative disease after Alzheimer’s dementia. Whereas the exact etiology of PD remains unknown, risk of developing PD seems to be related to a combination of genetic and environmental factors. This also includes abnormal exposure to trace elements of nutritional and toxicological interest. <b><i>Objectives:</i></b> In this systematic review and meta-analysis, we summarized the results of case–control studies comparing levels of selenium, copper, iron, and zinc in PD patients and controls in either blood (whole blood, serum/plasma) or cerebrospinal fluid (CSF). <b><i>Methods:</i></b> We performed a systematic PubMed search selecting studies reporting trace element levels in different specimens of patients and controls. We performed a meta-analysis using a random-effect model to compute the weighted mean differences (WMD) and corresponding 95% CI of selenium, copper, iron, and zinc levels in the blood or CSF of patients and their matched controls. <b><i>Results:</i></b> We retrieved 56 papers reporting data for selenium (cases/controls: 588/721), copper (2,190/2,522), iron (2,956/3,469), and zinc (1,798/1,913) contents in CSF and blood. Cases showed considerably higher levels of selenium in CSF compared with controls (+51.6%; WMD 5.49; 95% CI 2.82 to 8.15), while levels in serum were similar (–0.2%; WMD –0.22; 95% CI –8.05 to 7.62). For copper, cases showed slightly higher levels in CSF and slightly lower concentrations in serum (+4.5%; WMD 1.87; 95% CI –3.59 to 7.33, and –4.5%; WMD –42.79; 95% CI –134.35 to 48.76, respectively). A slight increase was also found for CSF iron ­levels (+9.5%; WMD 9.92; 1.23 to 18.61), while levels were ­decreased in serum/plasma (–5.7%; WMD –58.19; 95% CI –106.49 to –9.89) and whole blood (–10.8%; WMD –95.69; 95% CI –157.73 to –33.65). Conversely, for zinc cases exhibited lower levels both in CSF (–10.8%; WMD –7.34; 95% CI –14.82 to 0.14) and serum/plasma (–7.5%; WMD –79.93; 95% CI –143.80 to –16.06). A longer duration of the disease tends to be associated with overall lower trace element levels in either CSF or blood. <b><i>Conclusions:</i></b> Due to the study findings and the greater relevance of the CSF compartment compared with the circulating peripheral ones, this meta-analysis suggests that overexposure in the central nervous system to selenium, and possibly to copper and iron, may be a risk factor of the disease, while zinc might have a protective ­effect.
DOI: 10.6084/m9.figshare.9735866
title: Dataset for: Proteins required for vacuolar function are targets of lysine polyphosphorylation in yeast

description: Polyphosphates (polyP) are long chains of inorganic phosphates that can be attached to lysine residues of target proteins as a non-enzymatic post-translational modification. This modification, termed polyphosphorylation, may be particularly prevalent in bacterial and fungal species that synthesize large quantities of polyP. In this study, we evaluated the polyphosphorylation status of over 200 candidate targets in S. cerevisiae. We report 8 new polyphosphorylated proteins that interact genetically and physically with previous targets implicated in ribosome biogenesis. The expanded target network includes vacuolar proteins Prb1 and Apl5, whose modification with polyP suggests a model for feedback regulation of polyP synthesis, while raising questions regarding the location of polyphosphorylation in vivo.
DOI: 10.6084/m9.figshare.9735866.v1
title: Dataset for: Proteins required for vacuolar function are targets of lysine polyphosphorylation in yeast

description: Polyphosphates (polyP) are long chains of inorganic phosphates that can be attached to lysine residues of target proteins as a non-enzymatic post-translational modification. This modification, termed polyphosphorylation, may be particularly prevalent in bacterial and fungal species that synthesize large quantities of polyP. In this study, we evaluated the polyphosphorylation status of over 200 candidate targets in S. cerevisiae. We report 8 new polyphosphorylated proteins that interact genetically and physically with previous targets implicated in ribosome biogenesis. The expanded target network includes vacuolar proteins Prb1 and Apl5, whose modification with polyP suggests a model for feedback regulation of polyP synthesis, while raising questions regarding the location of polyphosphorylation in vivo.
DOI: 10.6084/m9.figshare.9735800
title: Wave fetch GIS layers for Chile at 100m scale

description: This data layer gives values of summed wave fetch in 32 angular sectors around focal cells, using a model modified from that given in Burrows et al (2012 - see reference). Wave fetch is the distance to the nearest land in a defined direction. The model performs a three-scale search for land around each cell in the model, sparsely (every 10km) up to 200km, every 1km up to 20km away, and every 100m up to 1km distant.<br>Values represent the summed number of grid cells to the nearest land across all 32 11.5° sectors. The file is a GeoTIFF using the WGS84 projection.
DOI: 10.6084/m9.figshare.9735722
title: Alcohol and drug use prior to liver transplantation: more common than expected in patients with non-alcoholic liver disease

description: <b>Objective:</b> Liver transplantation (LT) is a life-saving procedure for patients with end-stage liver disease, acute liver failure or hepatocellular carcinoma (HCC). Patients with known alcoholic liver cirrhosis (ALC) are usually assessed by an addiction specialist, but patients with other liver diseases may also exhibit harmful drinking. This study aims to assess the drinking habits in LT-recipients with or without a diagnosis of ALC. <b>Patients and methods:</b> Between April 2012 and December 2015, 190 LT-recipients were interviewed using the Lifetime Drinking History (LDH) and the Addiction Severity Index (ASI). Patients were categorized according to their diagnoses: ALC (group A, <i>n</i> = 39), HCC or hepatitis C (group B, <i>n</i> = 56) or other liver diseases (group C, <i>n</i> = 95). Data were analysed using descriptive statistic methods. <b>Results:</b> Fifteen of 95 patients (15.8%) in group C – a cohort without suspected addiction problems – had either alcohol consumption or binge drinking within the upper quartile of the overall cohort. The aetiology of liver disease in this subgroup included mainly cholestatic and cryptogenic liver disease. Illicit drugs had been used by 35% of all patients. Cannabis and amphetamine were the most common drugs and had the longest duration of regular use. <b>Conclusions:</b> LT candidates without known alcohol or drug use may have a clinically significant consumption of alcohol and previous illicit drug use. Efforts should be put on identification of these patients during LT evaluation. The use of structured questionnaires such as the ASI and the LDH could facilitate detection of alcohol and drug problems.
DOI: 10.6084/m9.figshare.9735719
title: Database of an association study between SNPs in IGF-1 and myopia .sav

description: It's the database collecting from an association study in a young Chinese population, aiming to find whether the SNPs in IGF-1 gene were associated with myopia among Chinese children and adolescents.
DOI: 10.6084/m9.figshare.9735722.v1
title: Alcohol and drug use prior to liver transplantation: more common than expected in patients with non-alcoholic liver disease

description: <b>Objective:</b> Liver transplantation (LT) is a life-saving procedure for patients with end-stage liver disease, acute liver failure or hepatocellular carcinoma (HCC). Patients with known alcoholic liver cirrhosis (ALC) are usually assessed by an addiction specialist, but patients with other liver diseases may also exhibit harmful drinking. This study aims to assess the drinking habits in LT-recipients with or without a diagnosis of ALC. <b>Patients and methods:</b> Between April 2012 and December 2015, 190 LT-recipients were interviewed using the Lifetime Drinking History (LDH) and the Addiction Severity Index (ASI). Patients were categorized according to their diagnoses: ALC (group A, <i>n</i> = 39), HCC or hepatitis C (group B, <i>n</i> = 56) or other liver diseases (group C, <i>n</i> = 95). Data were analysed using descriptive statistic methods. <b>Results:</b> Fifteen of 95 patients (15.8%) in group C – a cohort without suspected addiction problems – had either alcohol consumption or binge drinking within the upper quartile of the overall cohort. The aetiology of liver disease in this subgroup included mainly cholestatic and cryptogenic liver disease. Illicit drugs had been used by 35% of all patients. Cannabis and amphetamine were the most common drugs and had the longest duration of regular use. <b>Conclusions:</b> LT candidates without known alcohol or drug use may have a clinically significant consumption of alcohol and previous illicit drug use. Efforts should be put on identification of these patients during LT evaluation. The use of structured questionnaires such as the ASI and the LDH could facilitate detection of alcohol and drug problems.
DOI: 10.6084/m9.figshare.9735719.v1
title: Database of an association study between SNPs in IGF-1 and myopia .sav

description: It's the database collecting from an association study in a young Chinese population, aiming to find whether the SNPs in IGF-1 gene were associated with myopia among Chinese children and adolescents.
DOI: 10.6084/m9.figshare.9735479
title: Deepening our understanding of HDL proteome

description: <b>Introduction</b>: High-density lipoprotein (HDL) particles are heterogeneous and their proteome is complex and distinct from HDL cholesterol. However, it is largely unknown whether HDL proteins are associated with cardiovascular protection. <b>Areas covered</b>: HDL isolation techniques and proteomic analyses are reviewed. A list of HDL proteins reported in 37 different studies was compiled and the effects of different isolation techniques on proteins attributed to HDL are discussed. Mass spectrometric techniques used for HDL analysis and the need for precise and robust methods for quantification of HDL proteins are discussed. <b>Expert opinion</b>: Proteins associated with HDL have the potential to be used as biomarkers and/or help to understand HDL functionality. To achieve this, large cohorts must be studied using precise quantification methods. Key factors in HDL proteome quantification are the isolation methodology and the mass spectrometry technique employed. Isolation methodology affects what proteins are identified in HDL and the specificity of association with HDL particles needs to be addressed. Shotgun proteomics yields imprecise quantification, but the majority of HDL studies relied on this approach. Few recent studies used targeted tandem mass spectrometry to quantify HDL proteins, and it is imperative that future studies focus on the application of these precise techniques.
DOI: 10.6084/m9.figshare.9735476
title: 100 instances

description: A small dataset of videos to perform instance level recognition<br>
DOI: 10.6084/m9.figshare.9735479.v1
title: Deepening our understanding of HDL proteome

description: <b>Introduction</b>: High-density lipoprotein (HDL) particles are heterogeneous and their proteome is complex and distinct from HDL cholesterol. However, it is largely unknown whether HDL proteins are associated with cardiovascular protection. <b>Areas covered</b>: HDL isolation techniques and proteomic analyses are reviewed. A list of HDL proteins reported in 37 different studies was compiled and the effects of different isolation techniques on proteins attributed to HDL are discussed. Mass spectrometric techniques used for HDL analysis and the need for precise and robust methods for quantification of HDL proteins are discussed. <b>Expert opinion</b>: Proteins associated with HDL have the potential to be used as biomarkers and/or help to understand HDL functionality. To achieve this, large cohorts must be studied using precise quantification methods. Key factors in HDL proteome quantification are the isolation methodology and the mass spectrometry technique employed. Isolation methodology affects what proteins are identified in HDL and the specificity of association with HDL particles needs to be addressed. Shotgun proteomics yields imprecise quantification, but the majority of HDL studies relied on this approach. Few recent studies used targeted tandem mass spectrometry to quantify HDL proteins, and it is imperative that future studies focus on the application of these precise techniques.
DOI: 10.6084/m9.figshare.9735314
title: Microbiota-derived peptide mimics drive lethal inflammatory cardiomyopathy

description: The data here deposited correspond to 16S rRNA microbiome analysis from the murine samples included in the manuscript.Two mapping files with metadata are included describing in the details the characteristics of each sample.
DOI: 10.6084/m9.figshare.9735302
title: Supplementary Material for: MCH Neuron Activity Is Sufficient for Reward and Reinforces Feeding

description: <b><i>Background:</i></b> Melanin-concentrating hormone (MCH)-expressing neurons have been implicated in regulation of energy homeostasis and reward, yet the role of their electrical activity in short-term appetite and reward modulation has not been fully understood. <b><i>Objectives:</i></b> We investigated short-term behavioral and physiological effects of MCH neuron activity manipulations. <b><i>Methods:</i></b> We used optogenetic and chemogenetic approaches in <i>Pmch-cre</i> transgenic mice to acutely stimulate/inhibit MCH neuronal activity while probing feeding, locomotor activity, anxiety-like behaviors, glucose homeostasis, and reward. <b><i>Results:</i></b> MCH neuron activity is neither required nor sufficient for short-term appetite unless stimulation is temporally paired with consumption. MCH neuronal activation does not affect short-term locomotor activity, but inhibition improves glucose tolerance and is mildly anxiolytic. Finally, using two different operant tasks, we showed that activation of MCH neurons alone is sufficient to induce reward. <b><i>Conclusions:</i></b> Our results confirm diverse behavioral/physiological functions of MCH neurons and suggest a direct role in reward function.
DOI: 10.6084/m9.figshare.9735299
title: Supplementary Material for: Identification of Genes and Pathways Associated with Acne Using Integrated Bioinformatics Methods

description: <b><i>Background:</i></b> Acne is the most common skin inflammatory condition. The pathogenesis of acne is not fully understood. <b><i>Aims:</i></b> We performed weighted gene co-expression network analysis (WGCNA) to select acne-associated genes and pathways. <b><i>Methods:</i></b> GSE53795 and GSE6475 datasets including data from lesional and nonlesional skin of acne patients were downloaded from the NCBI Gene Expression Omnibus. Differentially expressed genes (DEGs) in lesions were identified following a false discovery rate &lt;0.05 and | log2 fold change | ≥0.5. DEG-associated biological processes and pathways were identified. WGCNA analysis was performed to identify acne-associated modules. DEGs in the acne-associated modules were used for protein-protein interaction (PPI) network construction and Gene Set Enrichment Analysis (GSEA). Acne-associated candidate DEGs and pathways were identified together with items in the Comparative Toxicogenomics Database (CTD). <b><i>Results:</i></b> A total of 2,140 and 1,190 DEGs were identified in GSE53795 and GSE6475 datasets, respectively, including 716 overlapping DEGs with similar expression profiles in the two datasets, which were clustered into 10 consensus modules. Two modules (brown and turquoise, 359 genes) were associated with acne phenotype. Of these 359 DEGs, 254 were enrolled in the PPI network. GSEA showed that these DEGs were associated with chemokine signaling pathway, cytokine-cytokine receptor interaction, and natural killer cell-mediated cytotoxicity. After identification in CTD, one pathway Cytokine-cytokine receptor interaction and 24 acne-associated DEGs, including IL1R1, CXCL1, CXCR4, CCR1, CXCL2 and IL1β, were identified as candidates associated with acne. <b><i>Conclusion:</i></b> Our results highlight the important roles of the proinflammatory cytokines including IL1β, CXCL1, CXCL2, CXCR4, and CCR1 in acne pathogenesis or therapeutic management.