cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5488039
title: Distribution and genotyping of antibiotic resistant strains of Acinetobacter baumannii isolated from aquatic environment categorized by ERIC-PCR.

description: The original ERIC-PCR image and the raw data of Antibiotic susceptibility for <i>Acinetobacter baumannii </i>isolates in this study.
DOI: 10.6084/m9.figshare.5488039.v2
title: Distribution and genotyping of antibiotic resistant strains of Acinetobacter baumannii isolated from aquatic environment categorized by ERIC-PCR.

description: The original ERIC-PCR image and the raw data of Antibiotic susceptibility for <i>Acinetobacter baumannii </i>isolates in this study.
DOI: 10.6084/m9.figshare.5487316
title: sample.rar

description: SCCP
DOI: 10.6084/m9.figshare.5487310
title: Flow curves for 7 wt% waste activated sludge at various temperatures (80 - 145 ˚C).

description: This submission contains the raw rheometer files from flow curve measurements of waste activated sludge (total solids content = 7wt%). The sludge samples were measured at various elevated temperature conditions (80, 90, 100, 120, 130 and 145 °C). The flow curves were generated from the sludge sample first at room temperature, then periodically across 60 minutes at constant set point elevated temperature. After 60 minutes, the sample was allowed to cool down room temperature, and another flow curve was generated.<br>The measurements were carried out on a DHR-3 rheometer (TA-Instruments), equipped with a pressure cell geometry.<br>Measurement protocol summary:<br>1) Waste activated sludge samples loaded into pressure cell.2) Nitrogen gas used to purge air from pressure cell.3) Nitrogen gas used to pressurise pressure cell to 5 bar.4) Flow curve generated for sample at 25 °C. Flow curves were generated by presetting a decreasing logarithmic shear-rate sweep.5) Sample heated to desired set point (80 °C).6) Once reached, flow curves were generated periodically at constant temperature (80 °C) over a 60 minute period.7) Sample cooled down to 25 °C and final flow curve generated.8) Sample replaced and repeat at new desired temperature (80 - 140 °C).<br>Detailed experimental protocol is recorded in the .tri (TRIOS) file attached with each data set. This file can be read using the TRIOS software made available on TA-Instruments website (http://www.tainstruments.com/support/software-downloads-support/downloads/). Rheometer geometry dimensions and other details are also obtainable from these files.<br>Please contact authors for access to files.<br><br>Contact:<br><br>nicky.eshtiaghi@rmit.edu.auRMITrheologygroup@gmail.com <br><br><br><br>Licence:<br>CC BY-NC
DOI: 10.6084/m9.figshare.5487310.v1
title: Flow curves for 7 wt% waste activated sludge at various temperatures (80 - 145 ˚C).

description: This submission contains the raw rheometer files from flow curve measurements of waste activated sludge (total solids content = 7wt%). The sludge samples were measured at various elevated temperature conditions (80, 90, 100, 120, 130 and 145 °C). The flow curves were generated from the sludge sample first at room temperature, then periodically across 60 minutes at constant set point elevated temperature. After 60 minutes, the sample was allowed to cool down room temperature, and another flow curve was generated.<br>The measurements were carried out on a DHR-3 rheometer (TA-Instruments), equipped with a pressure cell geometry.<br>Measurement protocol summary:<br>1) Waste activated sludge samples loaded into pressure cell.2) Nitrogen gas used to purge air from pressure cell.3) Nitrogen gas used to pressurise pressure cell to 5 bar.4) Flow curve generated for sample at 25 °C. Flow curves were generated by presetting a decreasing logarithmic shear-rate sweep.5) Sample heated to desired set point (80 °C).6) Once reached, flow curves were generated periodically at constant temperature (80 °C) over a 60 minute period.7) Sample cooled down to 25 °C and final flow curve generated.8) Sample replaced and repeat at new desired temperature (80 - 140 °C).<br>Detailed experimental protocol is recorded in the .tri (TRIOS) file attached with each data set. This file can be read using the TRIOS software made available on TA-Instruments website (http://www.tainstruments.com/support/software-downloads-support/downloads/). Rheometer geometry dimensions and other details are also obtainable from these files.<br>Please contact authors for access to files.<br><br>Contact:<br><br>nicky.eshtiaghi@rmit.edu.auRMITrheologygroup@gmail.com <br><br><br><br>Licence:<br>CC BY-NC
DOI: 10.6084/m9.figshare.5487253
title: Phylogenetic relationships of millipedes in the subclass Penicillata (Diplopoda) with a key to the genera

description: Bristly millipedes (subclass Penicillata, order Polyxenida) are minute diplopods characterised by uncalcified cuticle and a body covered with unique tufts of bristles. The order is found worldwide and comprises less than 200 described species divided into three families, with many of the species and genera being poorly known. The first evolutionary analysis of the order presented here utilises both molecular (COI, 18S rRNA and 16S rRNA) and morphological data to examine monophyly of the families and subfamilies and the evolutionary relationships between them. Maximum likelihood analysis was based on molecular data only, whereas parsimony analyses were based on molecular data as well as combined morphological and molecular data. The results of these analyses with two different optimality criteria were incongruent in many aspects. Unlike parsimony, the likelihood result found strong support for a basal position of the family Synxenidae and separation of the order into two monophyletic clades corresponding to the two superfamilies Synxenoidea, containing the family Synxenidae, and Polyxenoidea, containing the families Polyxenidae and Lophoproctidae. Parsimony results did not support the existence of the two superfamilies. Both analyses resolved the family Synxenidae as monophyletic and Polyxenidae as polyphyletic, whereas the family Lophoproctidae was shown to be paraphyletic in likelihood and monophyletic in parsimony analysis. The subfamilies Monographinae and Polyxeninae were found to be monophyletic in the likelihood tree but parsimony suggested paraphyly of both. The results suggest that further revision of the systematics of the Polyxenida may be necessary. However, a much larger molecular data set will be necessary to clarify and provide stronger nodal support for phylogenetic trees and to confirm the relationships, particularly of the families Polyxenidae and Lophoproctidae. Molecular identification is likely to be an important tool for this taxonomically challenging order in future. A simplified key to the genera is provided.
DOI: 10.6084/m9.figshare.5487253.v1
title: Phylogenetic relationships of millipedes in the subclass Penicillata (Diplopoda) with a key to the genera

description: Bristly millipedes (subclass Penicillata, order Polyxenida) are minute diplopods characterised by uncalcified cuticle and a body covered with unique tufts of bristles. The order is found worldwide and comprises less than 200 described species divided into three families, with many of the species and genera being poorly known. The first evolutionary analysis of the order presented here utilises both molecular (COI, 18S rRNA and 16S rRNA) and morphological data to examine monophyly of the families and subfamilies and the evolutionary relationships between them. Maximum likelihood analysis was based on molecular data only, whereas parsimony analyses were based on molecular data as well as combined morphological and molecular data. The results of these analyses with two different optimality criteria were incongruent in many aspects. Unlike parsimony, the likelihood result found strong support for a basal position of the family Synxenidae and separation of the order into two monophyletic clades corresponding to the two superfamilies Synxenoidea, containing the family Synxenidae, and Polyxenoidea, containing the families Polyxenidae and Lophoproctidae. Parsimony results did not support the existence of the two superfamilies. Both analyses resolved the family Synxenidae as monophyletic and Polyxenidae as polyphyletic, whereas the family Lophoproctidae was shown to be paraphyletic in likelihood and monophyletic in parsimony analysis. The subfamilies Monographinae and Polyxeninae were found to be monophyletic in the likelihood tree but parsimony suggested paraphyly of both. The results suggest that further revision of the systematics of the Polyxenida may be necessary. However, a much larger molecular data set will be necessary to clarify and provide stronger nodal support for phylogenetic trees and to confirm the relationships, particularly of the families Polyxenidae and Lophoproctidae. Molecular identification is likely to be an important tool for this taxonomically challenging order in future. A simplified key to the genera is provided.
DOI: 10.6084/m9.figshare.5487247
title: Science Gateway Patterns and Practices: Experiences Deploying Web Portals for Science at the NERSC Supercomputing Center

description: p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Times New Roman"; }p.MsoFootnoteText, li.MsoFootnoteText, div.MsoFootnoteText { margin: 0in 0in 0.0001pt; text-align: justify; text-indent: 10.1pt; font-size: 8pt; font-family: "Times New Roman"; }p.Abstract, li.Abstract, div.Abstract { margin: 1pt 0in 0.0001pt; text-align: justify; text-indent: 10.1pt; font-size: 11pt; font-family: "Times New Roman"; font-style: italic; }span.FootnoteTextChar { }.MsoChpDefault { font-size: 10pt; }div.WordSection1 { In this work we catalog patterns, practices and trends we have seen from our experiences deploying science gateways at the NERSC supercomputing center. We cover the following topics: Sharing Data Over The Web, Web Frameworks for Science, Web IDEs and Interactive HPC, HTTP APIs, Federated Identity and Single Sign-On, Edge Services, Data Transfer Services, Cloud Hosted Portals, and Containers. This is our attempt to share what we have learned with the community, and to identify key aspects of science gateway deployment and development.
DOI: 10.6084/m9.figshare.5487235
title: MacLean et al. Journal of Neuroscience Methods 2017 data

description: Correlation matrix for measures of oxytocin and vasopressin using different ELISA kits and HPLC-MS published in:<br>10.1016/j.jneumeth.2017.08.033<br>
DOI: 10.6084/m9.figshare.5487235.v1
title: MacLean et al. Journal of Neuroscience Methods 2017 data

description: Correlation matrix for measures of oxytocin and vasopressin using different ELISA kits and HPLC-MS published in:<br>10.1016/j.jneumeth.2017.08.033<br>
DOI: 10.6084/m9.figshare.5487223
title: Clinical meta-data for DCE-MRI data set

description: Clinical meta-data for the 15 oropharyngeal cancer patients, representing our cohort. Patients, disease and treatment identifiers are detailed in this *.csv file.
DOI: 10.6084/m9.figshare.5487220
title: ReadMe_Clinical meta-data

description: Supplemental information about the headings of the columns in the clinical data set file.
DOI: 10.6084/m9.figshare.5487223.v1
title: Clinical meta-data for DCE-MRI data set

description: Clinical meta-data for the 15 oropharyngeal cancer patients, representing our cohort. Patients, disease and treatment identifiers are detailed in this *.csv file.
DOI: 10.6084/m9.figshare.5487211
title: Arterial Input Function

description: Arterial input function (AIF) created from 10 patients with head and neck squamous cell carcinoma DCE-MRI scans.
DOI: 10.6084/m9.figshare.5487211.v1
title: Arterial Input Function

description: Arterial input function (AIF) created from 10 patients with head and neck squamous cell carcinoma DCE-MRI scans.
DOI: 10.6084/m9.figshare.5487214.v3
title: The Art of Microbiology: A Laboratory Manual

description: This PDF contains the course materials for our "Art of Microbiology" laboratory course, intended for undergraduate biology majors. Students isolate soil bacteria and use them to create living works of art, then use the observations of interactions within the art as a platform for developing their own research projects.<br>These materials are definitely works in progress, and contain large gaps that are filled in practice with a variety of handouts and materials from other sources. We plan to continue updating this lab manual over time; future versions will be posted here in version control.
DOI: 10.6084/m9.figshare.5487145
title: Latombe et al. scripts and data

description: Code and data for the downscaling of a paleoclimatic model. Latombet et al.
DOI: 10.6084/m9.figshare.5487088
title: Transcriptome analysis reveals the molecular mechanism of hepatic fat metabolism disorder caused by Muscovy duck reovirus infection

description: The aim of this work was to clarify the molecular mechanism underlying the fatty degeneration of livers infected with Muscovy duck reovirus (MDRV), which produces obvious white necrotic foci in the liver. Transcriptome data for MDRV-infected Muscovy duck livers and control livers were sequenced, assembled, and annotated with Illumina<sup>®</sup> HiSeq 2000. The differentially expressed genes were screened and their functions were analysed. We also determined and confirmed the molecular mechanism of the hepatic fat metabolism disorder caused by MDRV infection. The expression of 4190 genes was higher in the infected livers than in the control livers, and the expression of 1113 genes was reduced. A Gene Ontology analysis showed that these genes were involved in 48 biological functions, and were significantly enriched in 237 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The free fatty acid content was significantly higher in the livers of infected Muscovy ducks than in the control livers (<i>P</i> <b>Abbreviations:</b> ABC: ATP binding cassette transport; ACADVL: acyl-CoA dehydrogenase, very long chain; ACAT: mitochondrial-like acetyl-CoA acetyltransferase A; ACAT2: acetyl-CoA acyltransferase 2; ACNAT2: acyl-coenzyme A amino acid N-acyltransferase 2-like; ACOT1: acyl-CoA thioesterase 1; ACOT7: acyl-CoA thioesterase 7; ACOX1: acyl-CoA oxidase 1, palmitoyl; ACSBG2: acyl-CoA synthetase bubblegum family member 2; ACSL1: acyl-CoA synthetase long-chain family member 1; ADH1: alcohol dehydrogenase 1; APOA4: apolipoprotein A-IV; ARV: avian reovirus; cDNA: complementary deoxyribonucleic acid; COG: Clusters of Orthologous Groups; DEG: differentially expressed gene; DGAT: diacylgycerol acyltransferase; DNA: deoxyribonucleic acid; ECI2: enoyl-CoA delta isomerase 2; EHHADH: enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase; FDR: false discovery rate; GCDH<i>: Pseudopodoces humilis</i> glutaryl-CoA dehydrogenase; GO: Gene Ontology; HADHA: hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit; I-FABP: intestinal fatty acid binding protein; KEGG: Kyoto Encyclopedia of Genes and Genomes; L-FABP: liver fatty acid binding protein; MDRV: Muscovy duck reovirus; MOI: multiplicity of infection; NPC1L1: Niemann-Pick C1-like 1; qPCR: real-time quantitative polymerase chain reaction; RNA: ribonucleic acid; RNase: ribonuclease; RNA-seq: RNA sequencing technology; RPKM: reads per kilobase per million mapped reads; SR-B1: scavenger receptor class b type 1.
DOI: 10.6084/m9.figshare.5487040
title: Appendix-A

description: For each of the subject programs, this document lists: 1) Descriptions of the faulty code locations. 2) The resulting defects, which could involve more than one faulty location. 3) For each defect, a yes/no flag indicating whether there exists a SliceP element that occurs in at least one failure due the defect, but does not occur in any passing runs nor in failures due to other defects.
DOI: 10.6084/m9.figshare.5487088.v1
title: Transcriptome analysis reveals the molecular mechanism of hepatic fat metabolism disorder caused by Muscovy duck reovirus infection

description: The aim of this work was to clarify the molecular mechanism underlying the fatty degeneration of livers infected with Muscovy duck reovirus (MDRV), which produces obvious white necrotic foci in the liver. Transcriptome data for MDRV-infected Muscovy duck livers and control livers were sequenced, assembled, and annotated with Illumina<sup>®</sup> HiSeq 2000. The differentially expressed genes were screened and their functions were analysed. We also determined and confirmed the molecular mechanism of the hepatic fat metabolism disorder caused by MDRV infection. The expression of 4190 genes was higher in the infected livers than in the control livers, and the expression of 1113 genes was reduced. A Gene Ontology analysis showed that these genes were involved in 48 biological functions, and were significantly enriched in 237 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The free fatty acid content was significantly higher in the livers of infected Muscovy ducks than in the control livers (<i>P</i> <b>Abbreviations:</b> ABC: ATP binding cassette transport; ACADVL: acyl-CoA dehydrogenase, very long chain; ACAT: mitochondrial-like acetyl-CoA acetyltransferase A; ACAT2: acetyl-CoA acyltransferase 2; ACNAT2: acyl-coenzyme A amino acid N-acyltransferase 2-like; ACOT1: acyl-CoA thioesterase 1; ACOT7: acyl-CoA thioesterase 7; ACOX1: acyl-CoA oxidase 1, palmitoyl; ACSBG2: acyl-CoA synthetase bubblegum family member 2; ACSL1: acyl-CoA synthetase long-chain family member 1; ADH1: alcohol dehydrogenase 1; APOA4: apolipoprotein A-IV; ARV: avian reovirus; cDNA: complementary deoxyribonucleic acid; COG: Clusters of Orthologous Groups; DEG: differentially expressed gene; DGAT: diacylgycerol acyltransferase; DNA: deoxyribonucleic acid; ECI2: enoyl-CoA delta isomerase 2; EHHADH: enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase; FDR: false discovery rate; GCDH<i>: Pseudopodoces humilis</i> glutaryl-CoA dehydrogenase; GO: Gene Ontology; HADHA: hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit; I-FABP: intestinal fatty acid binding protein; KEGG: Kyoto Encyclopedia of Genes and Genomes; L-FABP: liver fatty acid binding protein; MDRV: Muscovy duck reovirus; MOI: multiplicity of infection; NPC1L1: Niemann-Pick C1-like 1; qPCR: real-time quantitative polymerase chain reaction; RNA: ribonucleic acid; RNase: ribonuclease; RNA-seq: RNA sequencing technology; RPKM: reads per kilobase per million mapped reads; SR-B1: scavenger receptor class b type 1.
DOI: 10.6084/m9.figshare.5487025
title: Note.docx

description: Note
DOI: 10.6084/m9.figshare.5487028
title: Experimental data files.csv

description: Experimental data
DOI: 10.6084/m9.figshare.5487025.v1
title: Note.docx

description: Note
DOI: 10.6084/m9.figshare.5487040.v2
title: Appendix-A

description: For each of the subject programs, this document lists: 1) Descriptions of the faulty code locations. 2) The resulting defects, which could involve more than one faulty location. 3) For each defect, a yes/no flag indicating whether there exists a SliceP element that occurs in at least one failure due the defect, but does not occur in any passing runs nor in failures due to other defects.
DOI: 10.6084/m9.figshare.5487040.v1
title: Appendix-A.pdf

description: For each of the subject programs, this document lists: 1) Descriptions of the faulty code locations. 2) The resulting defects, which could involve more than one faulty location. 3) For each defect, a yes/no flag indicating whether there exists a SliceP element that occurs in at least one failure due the defect, but does not occur in any passing runs nor in failures due to other defects.
DOI: 10.6084/m9.figshare.5484916
title: TIPA Supplementary Files

description: A spreadsheet demonstrating the TIPA phase shift estimation process on each of the 3,600 simulations used in our analysis, as well as the R code used to generate the simulations.
DOI: 10.6084/m9.figshare.5484916.v1
title: TIPA Supplementary Files

description: A spreadsheet demonstrating the TIPA phase shift estimation process on each of the 3,600 simulations used in our analysis, as well as the R code used to generate the simulations.
DOI: 10.6084/m9.figshare.5484838
title: train.txt

description: This data set contains data of 2606 patients: their vitamin B12 measurements, kidney function measurements (CKD-EPI) and MMA measusrements
DOI: 10.6084/m9.figshare.5484841
title: test.txt

description: This data set contains data of 300 patients: their vitamin B12 measurements, kidney function measurements (CKD-EPI) and MMA measusrements
DOI: 10.6084/m9.figshare.5484841.v1
title: test.txt

description: This data set contains data of 300 patients: their vitamin B12 measurements, kidney function measurements (CKD-EPI) and MMA measusrements
DOI: 10.6084/m9.figshare.5484838.v1
title: train.txt

description: This data set contains data of 2606 patients: their vitamin B12 measurements, kidney function measurements (CKD-EPI) and MMA measusrements
DOI: 10.6084/m9.figshare.5484838.v3
title: train.txt

description: This data set contains data of 2606 patients: their vitamin B12 measurements, kidney function measurements (CKD-EPI) and MMA measusrements
DOI: 10.6084/m9.figshare.5484838.v2
title: train.txt

description: This data set contains data of 2606 patients: their vitamin B12 measurements, kidney function measurements (CKD-EPI) and MMA measusrements
DOI: 10.6084/m9.figshare.5484658
title: Supplementary Material for: The Missing Link in the Pathophysiology of Vascular Cognitive Impairment: Design of the Heart-Brain Study

description: <b><i>Background:</i></b> Hemodynamic balance in the heart-brain axis is increasingly recognized as a crucial factor in maintaining functional and structural integrity of the brain and thereby cognitive functioning. Patients with heart failure (HF), carotid occlusive disease (COD), and vascular cognitive impairment (VCI) present themselves with complaints attributed to specific parts of the heart-brain axis, but hemodynamic changes often go beyond the part of the axis for which they primarily seek medical advice. The Heart-Brain Study hypothesizes that the hemodynamic status of the heart and the brain is an important but underestimated cause of VCI. We investigate this by studying to what extent hemodynamic changes contribute to VCI and what the mechanisms involved are. Here, we provide an overview of the design and protocol. <b><i>Methods:</i></b> The Heart-Brain Study is a multicenter cohort study with a follow-up measurement after 2 years among 645 participants (175 VCI, 175 COD, 175 HF, and 120 controls). Enrollment criteria are the following: 1 of the 3 diseases diagnosed according to current guidelines, age ≥50 years, no magnetic resonance contraindications, ability to undergo cognitive testing, and independence in daily life. A core clinical dataset is collected including sociodemographic factors, cardiovascular risk factors, detailed neurologic, cardiac, and medical history, medication, and a physical examination. In addition, we perform standardized neuropsychological testing, cardiac, vascular and brain MRI, and blood sampling. In subsets of participants we assess Alz­heimer biomarkers in cerebrospinal fluid, and assess echocardiography and 24-hour blood pressure monitoring. Follow-up measurements after 2 years include neuropsychological testing, brain MRI, and blood samples for all participants. We use centralized state-of-the-art storage platforms for clinical and imaging data. Imaging data are processed centrally with automated standardized pipelines. <b><i>Results and Conclusions:</i></b> The Heart-Brain Study investigates relationships between (cardio-)vascular factors, the hemodynamic status of the heart and the brain, and cognitive impairment. By studying the complete heart-brain axis in patient groups that represent components of this axis, we have the opportunity to assess a combination of clinical and subclinical manifestations of disorders of the heart, vascular system and brain, with hemodynamic status as a possible binding factor.