cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8032878
title: Experimental study dataset: "Enhancing Touch Sensibility with Sensory Electrical Stimulation and Sensory Retraining"

description: Experimental study dataset: "Enhancing Touch Sensibility with Sensory Electrical Stimulation and Sensory Retraining".


This research was supported by the Swiss National Science Foundation through the grant PP00P2 163800. This work was also supported by SENACYT and IFARHU, the Panamanian Government.


Files and data to upload:



	
Description of variables 
	
Continue robot data (pickles)
	
Discontinue robot data (task performance)
	
EEG data
description: Disclaimer: please be aware that the EEG data needs some preprocessing to effectively select the trials that are relevant for each experiment phase.
DOI: 10.5281/zenodo.8032879
title: Experimental study dataset: "Enhancing Touch Sensibility with Sensory Electrical Stimulation and Sensory Retraining"

description: Experimental study dataset: "Enhancing Touch Sensibility with Sensory Electrical Stimulation and Sensory Retraining".


This research was supported by the Swiss National Science Foundation through the grant PP00P2 163800. This work was also supported by SENACYT and IFARHU, the Panamanian Government.


Files and data to upload:



	
Description of variables 
	
Continue robot data (pickles)
	
Discontinue robot data (task performance)
	
EEG data
description: Disclaimer: please be aware that the EEG data needs some preprocessing to effectively select the trials that are relevant for each experiment phase.
DOI: 10.25402/pgs.14572389.v1
title: Supplementary Materials and Methods. Pharmacogenetic testing in Psychiatry and Neurology: An Overview of Reviews

description: PubMed search
strategy and General characteristics of the included reviews.
DOI: 10.6084/m9.figshare.25664445
title: Inverted device architecture for high efficiency single-layer organic light-emitting diodes with imbalanced charge transport

description: Source data of the figures in the article.
DOI: 10.25402/pgs.17205983.v1
title: Supplementary Table 2: Pharmacogenetic loci for rosuvastatin are associated with intima-media thickness change and coronary artery disease risk.docx

description: <b>Supplementary
 Table 2.</b> Call rate for genotyped SNPs and number of cases, included into
 analyses of associations with total cholesterol and low-density lipoprotein
 cholesterol change, baseline carotid intima-media thickness, and its change
 during rosuvastatin therapy.
DOI: 10.6084/m9.figshare.25635051
title: Serological evidence of zoonotic filovirus exposure among bushmeat hunters in Guinea

description: RAW data for ELISA, Luminex, neutralisation and western blots
DOI: 10.6084/m9.figshare.23620155
title: Optogenetic activation of dorsal raphe serotonin neurons induces brain-wide activation

description: Figures for optogenetic activation of dorsal raphe nucleus with fMRI under awake and anesthetized states.
DOI: 10.25402/pgs.14572389
title: Supplementary Materials and Methods. Pharmacogenetic testing in Psychiatry and Neurology: An Overview of Reviews

description: PubMed search
strategy and General characteristics of the included reviews.
DOI: 10.15468/dl.jq2p9v
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lutra felina (Molina, 1782)"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021332-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25402/pgs.19195805.v1
title: Supplementary tables 1A & B: Pharmacogenetics research in Brazil: a systematic review

description: Table
 S1-A: Noticeable updates of this study when compared with Rodrigues-Soares et
 al. (2018) - doi: 10.1038/s41397-018-0015-7.
 
 
 




Table S1-B: Information considering all articles
included in this review.
DOI: 10.25402/pgs.19212891.v2
title: Supplementary tables 1: Differential correlation network analysis of rectal transcriptomes reveals cystic fibrosis-related disturbance

description: Supplementary
 Figure 1. A STRING protein interaction network created from genes included in
 the differential correlation network based on expression microarray data from
 CF and control rectal tissue.
 Supplementary
 Table 1. Result of cf Pearson annoatated.
 
 




Supplementary Table 2. Overlap results.
DOI: 10.25402/pgs.19212891
title: Supplementary tables 1: Differential correlation network analysis of rectal transcriptomes reveals cystic fibrosis-related disturbance

description: Supplementary
 Figure 1. A STRING protein interaction network created from genes included in
 the differential correlation network based on expression microarray data from
 CF and control rectal tissue.
 Supplementary
 Table 1. Result of cf Pearson annoatated.
 
 




Supplementary Table 2. Overlap results.
DOI: 10.25402/fca.19596775.v1
title: Supplementary table 1: Aortic valve intervention for aortic stenosis and cardiac amyloidosis: a systematic review and meta-analysis.docx

description: Supplementary Table 1.
DOI: 10.25402/fsg.20037077.v1
title: Supplementary material: Association of GDF-15, hs-cTnT and NT-proBNP with coronary artery disease in patients undergoing elective angiography

description: Supplementary material: Association of GDF-15, hs-cTnT and NT-proBNP with coronary artery disease in patients undergoing elective angiography
DOI: 10.25402/pgs.20496204.v1
title: ARG2 single-nucleotide polymorphism rs3742879 affects plasma arginase 2 levels, nitric oxide formation and antihypertensive therapy response in preeclampsia: supplementary files

description: Aim: This work examined whether ARG1 (rs2781659, rs2781667, rs2246012 and rs17599586) and ARG2
(rs3742879 and rs10483801) single-nucleotide polymorphisms (SNPs) are associated with antihypertensive
therapy responsiveness in preeclampsia (PE) and their effects on arginase isoforms and nitrite
concentrations in responsive and nonresponsive patients. Methods: SNP genotypes were determined by
TaqMan assays. Plasma arginase levels were measured by ELISA and nitrite concentrations were measured
using an ozone-based chemiluminescence assay. Results: The G allele for ARG2 rs3742879 (A&gt;G) was less
frequent in nonresponsive compared with responsive patients (15.5% vs 24.7%) and the G carriers of the
nonresponsive subgroup had lower arginase 2 (9.2 ± 7.5 ng/ml vs 19.1 ± 17.3 ng/ml) and higher nitrite
concentrations (110.2 ± 52.8 nM vs 78.5 ± 37.9 nM) than carriers of the AA genotype (all p &lt; 0.05).
Conclusion: ARG2 SNP rs3742879 is associated with diminished arginase 2 levels and increased nitric oxide
formation in nonresponsive PE patients.
DOI: 10.5281/zenodo.11207119
title: Multiscale Bayesian Simulations Reveal Functional Chromatin Condensation of Gene Loci

description: Chromatin, the complex assembly of DNA and associated proteins, plays a pivotal role in orchestrating various genomic functions. To aid our understanding of the principles underlying chromatin organization, we introduce Hi-C metainference, a Bayesian approach that integrates Hi-C contact frequencies into multiscale prior models of chromatin. This approach combines both bottom-up (the physics-based prior) and top-down (the data-driven posterior) strategies to characterize the 3D organization of a target genomic locus. We first demonstrate the capability of this method to accurately reconstruct the structural ensemble and the dynamics of a system from contact information. We then apply the approach to investigate the Sox2, Pou5f1, and Nanog loci of mouse embryonic stem cells using a bottom-up chromatin model at 1kb resolution. We observe that the studied loci are conformationally heterogeneous and organized as crumpled globules, favoring contacts between distant enhancers and promoters. Using nucleosome-resolution simulations, we then reveal how the Nanog gene is functionally organized across the multiple scales of chromatin. At the local level, we identify diverse tetranucleosome folding motifs with a characteristic distribution along the genome, predominantly open at cis-regulatory elements and compact in between. At the larger scale, we find that enhancer-promoter contacts are driven by the transient condensation of chromatin into compact domains stabilized by extensive inter-nucleosome interactions. Overall, this work highlights the condensed, but dynamic nature of chromatin in vivo, contributing to a deeper understanding of gene structure-function relationships.
DOI: 10.5281/zenodo.11207120
title: Multiscale Bayesian Simulations Reveal Functional Chromatin Condensation of Gene Loci

description: Chromatin, the complex assembly of DNA and associated proteins, plays a pivotal role in orchestrating various genomic functions. To aid our understanding of the principles underlying chromatin organization, we introduce Hi-C metainference, a Bayesian approach that integrates Hi-C contact frequencies into multiscale prior models of chromatin. This approach combines both bottom-up (the physics-based prior) and top-down (the data-driven posterior) strategies to characterize the 3D organization of a target genomic locus. We first demonstrate the capability of this method to accurately reconstruct the structural ensemble and the dynamics of a system from contact information. We then apply the approach to investigate the Sox2, Pou5f1, and Nanog loci of mouse embryonic stem cells using a bottom-up chromatin model at 1kb resolution. We observe that the studied loci are conformationally heterogeneous and organized as crumpled globules, favoring contacts between distant enhancers and promoters. Using nucleosome-resolution simulations, we then reveal how the Nanog gene is functionally organized across the multiple scales of chromatin. At the local level, we identify diverse tetranucleosome folding motifs with a characteristic distribution along the genome, predominantly open at cis-regulatory elements and compact in between. At the larger scale, we find that enhancer-promoter contacts are driven by the transient condensation of chromatin into compact domains stabilized by extensive inter-nucleosome interactions. Overall, this work highlights the condensed, but dynamic nature of chromatin in vivo, contributing to a deeper understanding of gene structure-function relationships.
DOI: 10.25402/pgs.20746726.v1
title: Characterization of POR haplotype distribution in African populations and comparison with other global populations: Supplementary tables

description: Background & aim: POR is an enzyme that mediates electron transfer to enable the drug-metabolizing
activity of CYP450 proteins. However, POR has been understudied in pharmacogenomics despite this vital
role. The authors aimed to characterize the genetic variation in POR across African populations and
to compare the star allele (haplotype) distribution with that in other global populations. Materials &
methods: POR star alleles were called from whole-genome sequencing data using the StellarPGx pipeline.
Results: In addition to the common POR*1 and *28 haplotypes (defined by rs1057868), five novel rare
haplotypes were computationally inferred. No significant frequency differences were observed among
the majority of African populations. However, POR*28 was observed at a higher frequency in individuals
of non-African ancestry. Conclusion: This study highlights the distribution of POR alleles in Africa and
across global populations with a view toward informing future precision medicine implementation.
DOI: 10.25402/pgs.21695132.v1
title: Breast cancer pharmacogenetics: a systematic review - Supplementary Material

description:   
<strong>Supplementary Material 1. Table indicating the frequencies of analyzed polymorphisms in cases+controls, cases and controls.</strong>
<br>
  
<strong>Supplementary Material 2. Haplotypes and treatment regimens description.</strong>
DOI: 10.25402/pgs.23211965.v1
title: Supplementary data: SLCO1B1 gene-based clinical decision support reduces statin-associated muscle symptoms risk with simvastatin

description: Supplementary data
DOI: 10.25402/pgs.23259650.v1
title: Pharmacogenetics of pain management in Zimbabwean patients with sickle cell disease: Supplementary Table

description: Supplementary Table 1
DOI: 10.25402/pgs.21378144
title: Association between genetic variants and the risk of nivolumab-induced immune-related adverse events (irAEs) - Supplementary material

description: Supplementary Table 1. Patient demographics and clinical characteristics (nivolumab-induced hypothyroidism).
Supplementary Table 2. Profile of nivolumab-induced irAEs.
Supplementary Table 3.  Association results of 90 SNPs which showed smaller P values in combined analysis than those in GWAS.
DOI: 10.25402/pgs.23694576
title: Attitudes about pharmacogenomic testing vary by healthcare specialty

description: Supplementary data
DOI: 10.25402/pgs.21488145.v1
title: Pharmacogenomics of medications given via nonconventional administration routes: a scoping review - Supplementary Information

description:   
<strong>Table S1: </strong>Characteristics of included pharmacogenomics studies involving intramuscular administration routes 
  
<strong>Table S2: </strong>Outcomes and results of included pharmacogenomics studies on intramuscular administration routes
  
<strong>Table S3: </strong>Characteristics of included pharmacogenomic studies on intrathecal/intraventricular administration routes
  
<strong>Table S4: </strong>Outcomes and results of included pharmacogenomics studies on intrathecal/intraventricular administration routes
  
<strong>Table S5: </strong>Characteristics of included pharmacogenomics studies on intrahepatic arterial, intratympanic, and subcutaneous administration routes
  
<strong>Table S6: </strong>Outcomes and results of included pharmacogenomics studies on intrahepatic arterial, intratympanic, and subcutaneous administration routes
  
<strong>Table S7: </strong>Characteristics of included pharmacogenomics studies on topical/intralesional and transdermal administration routes
  
<strong>Table S8: </strong>Outcomes and results of included pharmacogenomics studies on topical/intralesional administration routes
  
<strong>Table S9: </strong>Outcomes and results of included pharmacogenomics studies on transdermal administration routes
  
<strong>Table S10</strong>: Recommendations for Medications Given via a Non-Conventional Administration Route Provided by Pharmacogenomic Associations
<br>
DOI: 10.25402/pgs.23798709.v1
title: Carbamazepine cutaneous adverse reactions and HLA gene variation in the Chinese population: a systematic review and meta-analysis

description: This study was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement. The PRISMA checklist is described in Supplementary Table 1. The literature search strategy is shown in Supplementary Material II.The quality range of all included studies, evaluated by Newcastle–Ottawa scoring, is six to nine (Supplementary Table 2). Egger’s test shows that there is no publication bias (Egger’s test, t = 3.32, p = 0.004, Supplementary Figure 4). The publication bias verification is performed using the clipping method, and the result of clipping method indicates that there were no indications of publication with the Duval’s trim and fill method (no new studies added); the results are robust (Supplementary Figure 4). Sensitivity analysis was conducted on 16 meta-results of HLA-B*15:02 and CBZ-SJS/TEN in Figure 3. The combined effect of 16 meta-results did not change significantly after being excluded from the study one by one (Supplementary Figure 5). The distribution of the funnel diagram was relatively symmetrical (Supplementary Figure 6)
DOI: 10.25402/fca.20131703
title: Supplementary material: Coenzyme Q10 supplementation for the treatment of statin-associated muscle symptoms

description: Supplementary material:  STUDY PARTICIPANT QUESTIONNAIRE #1
DOI: 10.25402/pgs.22316716.v1
title: IL16 and Factor V gene variations are associated with the asparaginase-related thrombosis in childhood ALL patients - Supplementary material

description:  Supplemental Table 1. Distribution of SNPs in investigated genes in entire cohort of  childhood ALL patients with and without thrombosis 
 Supplemental Table 2. Identity of polymorphisms, details of PCR and ASO  hybridization 
<br>
 Supplemental Figure 1. IL16 rs11556218 in relation to mRNA expression
DOI: 10.25402/pgs.22551634.v1
title: Effects of ADIPOQ & NOS3 SNP/haplotypes on blood pressure control in patients with adherence to antihypertensive therapy - Supplementary Material

description:   
<strong>Supplementary Table S1</strong>. Frequency of antihypertensive drug classes and quantity used by the hypertensive subjects grouped according to blood pressure control.
DOI: 10.25402/pgs.22698784.v1
title: Patient Satisfaction with Return of Pharmacogenomic Results Utilizing a Patient Portal Message - supplementary material

description: Supporting Materials: Table 1: List of all questions and answer options included in this survey.
Figure Supporting Materials 2: Answers to the question: Who contacted you about your Pharmacogenomics (PGx) results?
Figure Supporting Materials 3: Answers to the question I was given written information explaining what the results mean to me.
Figure Supporting Materials 4: Answers to the question: I was given access to a video explaining what the results mean to me.
Figure Supporting Materials 5: Answers to the question: If a friend was interested in having Pharmacogenomics (PGx) testing, how likely are you to recommend they have it done?
Figure Supporting Materials 6: Discrete answers to the question: How do you prefer to be contacted with Pharmacogenomics (PGx) results? (Please select all that apply)
Figure Supporting Materials 7: Comparison of the text of the PRM sent prior to adjusting the process of sending the message to all panel-based testing patients.
DOI: 10.25402/pgs.23130968.v1
title: Supplementary Tables: Profiling of pharmacogenomic variants in CYP2D6 and DPYD in indigenous Arab breastcancer patients

description: Supplementary Table
DOI: 10.25402/fca.20792632
title: Supplementary Table 2: Anticoagulation and BMI: effect of high body weight on the safety and efficacy of direct oral anticoagulants.docx

description:   
<strong>Supplemental Table 2. Inclusion and Exclusion Criteria of Clinical Trials, and Relevant Weight Stratifications. </strong>
DOI: 10.25402/pgs.23131523.v2
title: Supplementary Tables: The frequency of major ABCG2, SLCO1B1 and CYP2C9 variants in Asian, Native Hawaiian and Pacific Islander women subgroups: implications for personalized statins dosing

description: Supplementary Tables
DOI: 10.15468/dl.cd68k5
title: Occurrence Download

description: A dataset containing 1751 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Megaptera novaeangliae (Borowski, 1781)"
 ]
}

 The dataset includes 1751 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021333-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25402/fca.21062944.v1
title: Supplementary Material 2: Outcomes in cardiac implantable electronic device-related infective endocarditis: a systematic review of current literature.docx

description:   
<strong>Supplementary material 2. </strong>The complete search strategy per database
DOI: 10.25402/pgs.23798727.v1
title: Single-nucleotide polymorphisms in ABC drug transporters alter expression and circulating tenofovir in healthy South African women exposed to pre-exposure prophylaxis

description: <b>Supplementary Figure 1. Comparison of Fold-X computed (∆∆</b><b>G</b><b>) and ENCoM-computed (∆∆</b><b>S</b><b>vib</b><b>).</b> Each haplotype is represented by a maroon square and their defining missense variants are represented by circles. Figure points that fall within the highlighted region are expected to have neutral effects on protein stability [1]. ∆∆G predicts most of the variants and haplotypes as destabilising to the protein encoded protein structures. Both ∆∆G and ∆∆S<sub>vib</sub> seem to exhibit a destabilising bias for both haplotype and variants. However, ∆∆S<sub>vib</sub> predicted more haplotypes and variants to have neutral effects on protein stability than ∆∆G (see also Figure 3A).<b>Supplementary Table 1. </b>This table presents all 261 missense variants analysed in this study, together with their FoldX and ENCoM-derived energy scores. A combined ∆∆G (combination of ENCoM and FoldX) is presented, from which a prediction of the effect of each variant is made based on the threshold (-0.5 &lt; combined ∆∆G &lt; 0.5) [1]. Predictions from commonly used Ensembl Variant Effect Predictor (VEP; https://www.ensembl.org/ToolsVEP) [2] plugins as well as a consensus (2 from 3 rule) has been included for comparison with combined ∆∆G predictions<b>Supplementary Table 2. CYP star allele/haplotype NMA analysis.</b><i> </i>This table presents 92 CYP star alleles together with the defining missense variants for each star allele. Moreover, a CPIC functional classification is included together with the NMA-based combined ∆∆G analysis.<b>Supplementary Table 3. SWAAT analysis of CYP missense variant structural consequence.</b>
DOI: 10.25402/fca.21062947.v1
title: Supplementary Material 1: Outcomes in cardiac implantable electronic device-related infective endocarditis: a systematic review of current literature.docx

description: PRISMA checklist
DOI: 10.25402/pgs.23904450
title: Pharmacogenomic variation in the Malagasy population: implications for the antimalarial drug primaquine metabolism

description: In the present study, the authors performed genome-wide SNP typing of 55 Malagasy samples with the Infinium Multi-Ethnic Genotyping Array (MEGA) and analyzed data with a focus on a set of 28 pharmacogenes (Supplementary Table 1).QC steps were followed as recommended by Illumina [42,45] and have been described by various authors [46,47] (Supplementary Document 1). The MAF distribution of the polymorphic SNPs in four classes (rare, &lt;1%; low, 1–5%; moderate, &gt;5–10%; and high, &gt;10%) is presented in Supplementary Table 2For the polymorphic SNPs, their locations, SNP IDs, genomic sequence positions and variant impacts, the star alleles/suballeles they represent and their MAFs, are presented in Supplementary Table 3 in chromosomal order.The majority of these SNPs are intronic (n = 384), whereas 110 are in coding regions or impact splicing; the latter are presented separately in Supplementary Table 4.Their distribution, CNV confidence scores and sizes are presented in Supplementary Table 5.The same CNVs were identified in more than one Malagasy sample; examples and selected results are presented in Supplementary Table 6
DOI: 10.15468/dl.syadf4
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Mesoplodon peruvianus Reyes, Mead & Van Waerebeek, 1991"
 ]
}

 The dataset includes 23 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021335-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/m6wg96kxfw.2
title: Primordial Prevention of Gestational Diabetes Mellitus A Novel Approach

description: Objective: Pregnant women should be tested for Post-Prandial Blood Glucose(PPBG) by the 8th week (2 months) with the value of 2hr PPBG 110 mg/dl as a Cut-off so that adequate time is available to control blood glucose within this range otherwise; fetal insulin will start secreting if blood glucose goes beyond 110 mg/dl by 11th week, and therefore within this crucial period blood glucose can be controlled with medical nutrition therapy(MNT), exercise, and Metformin 250 mg twice daily throughout pregnancy.