cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7649483.v1
title: DGFs_after_filtering

description: Digital Genomic Footprints after DNAseI cutting bias correction
DOI: 10.7284/107306
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise EN473 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.12885033.v1
title: Weighted gene coexpression network analysis identifies critical genes in different subtypes of acute myeloid leukaemia

description: Acute myeloid leukaemia (AML) is a common blood cancer with rapid progression and a high death rate. The aim of this study was to illustrate the molecular mechanism and identify potential prognostic genes by performing weighted gene coexpression network analysis (WGCNA) of AML. WGCNA of AML was performed with R software based on GDC The Cancer Genome Atlas (TCGA) Acute Myeloid Leukaemia (LAML) RNA-seq data from TCGA database. The gene modules showing significant correlation with the M0-M7 subtypes and the NPMc mutation were analysed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. Hub genes from the key modules were identified using the cytoHubba package, and the prognostic values of these hub genes were analysed with a Cox proportional hazards model based on TCGA clinical data. A total of 151 patients from the TCGA database with RNA-seq data were included in the present study. The weighted gene coexpression network contained 21 coexpression modules. Three modules (blue, yellow and purple) were highly correlated with AML subtypes and the NPMc mutation. In total, six key hub genes were identified from the AML subtype- and NPMc mutation-related modules: <i>TLR8</i>, <i>SLC15A3</i>, <i>ADAP2</i>, <i>HOXA6</i> and <i>HOXA10</i>. Kaplan–Meier curve analysis showed that the five hub genes in the gene expression network are significantly associated with AML prognosis. WGCNA of AML performed in the present study revealed potential prognostic genes that not only have important clinical significance for prognosis but also provide important clues for identifying effective targets in AML therapeutic strategies.
DOI: 10.6084/m9.figshare.7649468
title: Supplementary Material for: Effects of Peritoneal Dialysis on Clinical Factors and Functional Performance

description: <b><i>Background:</i></b> We investigated the longitudinal trend of functional performance in peritoneal dialysis (PD) patients over 1 year after PD commencement and its related clinical parameters. <b><i>Methods:</i></b> One hundred and ninety-six PD patients were enrolled in this study. Karnofsky Performance Status Scale(KPSS) scores were used to assess functional performance. Patients were stratified into 3 groups according to the changes in KPSS from baseline to 1 year. A logistic regression analysis was performed to examine the associations of clinical parameters with KPSS changes. <b><i>Results:</i></b> Patients with KPSS declined showed older age and higher serum albumin concentration reduction within 1 year than those in KPSS improved and stable changes. Age was the significant risk factor for KPSS decline, while male and diabetes were significantly associated with non-declined KPSS by multivariable logistic regression analysis. <b><i>Conclusion:</i></b> The main determinants of KPSS trend were age, sex, and diabetes in new PD patients.
DOI: 10.6084/m9.figshare.7649486.v1
title: Block-matrix-based approach for the hybrid vehicle routing problem with fuzzy travel time and transportation type selection

description: In this study, we propose a novel hybrid model for the vehicle routing problem that combines fuzzy travel time and transportation type selection between milk-run and cross-dock strategies to derive an optimal transportation plan. Furthermore, we present a novel block-matrix-based approach for the hybrid model to explore optimal transportation plans in an intuitive, reasonable, effective, and efficient form. The proposed block-matrix-based approach derives an optimal transportation plan by solving a hybrid vehicle routing problem that considers not only fuzzy travel time, but also transportation type selection between milk-run and cross-dock strategies. An extended biogeography-based optimization (BBO) algorithm is proposed to effectively derive a transportation plan with the optimal degree of plant satisfaction by extending the operators of migration and mutation, and introducing a novel self-adaptive mutation rate, as well as a secondary mutation operator.
DOI: 10.6084/m9.figshare.12885033
title: Weighted gene coexpression network analysis identifies critical genes in different subtypes of acute myeloid leukaemia

description: Acute myeloid leukaemia (AML) is a common blood cancer with rapid progression and a high death rate. The aim of this study was to illustrate the molecular mechanism and identify potential prognostic genes by performing weighted gene coexpression network analysis (WGCNA) of AML. WGCNA of AML was performed with R software based on GDC The Cancer Genome Atlas (TCGA) Acute Myeloid Leukaemia (LAML) RNA-seq data from TCGA database. The gene modules showing significant correlation with the M0-M7 subtypes and the NPMc mutation were analysed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. Hub genes from the key modules were identified using the cytoHubba package, and the prognostic values of these hub genes were analysed with a Cox proportional hazards model based on TCGA clinical data. A total of 151 patients from the TCGA database with RNA-seq data were included in the present study. The weighted gene coexpression network contained 21 coexpression modules. Three modules (blue, yellow and purple) were highly correlated with AML subtypes and the NPMc mutation. In total, six key hub genes were identified from the AML subtype- and NPMc mutation-related modules: <i>TLR8</i>, <i>SLC15A3</i>, <i>ADAP2</i>, <i>HOXA6</i> and <i>HOXA10</i>. Kaplan–Meier curve analysis showed that the five hub genes in the gene expression network are significantly associated with AML prognosis. WGCNA of AML performed in the present study revealed potential prognostic genes that not only have important clinical significance for prognosis but also provide important clues for identifying effective targets in AML therapeutic strategies.
DOI: 10.6084/m9.figshare.7649450
title: DGF_before_filtering

description: Digital Genomic Footrpints before correction for DNAseI cutting bias
DOI: 10.6084/m9.figshare.7649444
title: Supplementary Material for: Differential Molecular Modeling Predictions of Mid and Conventional Dialysate Flows

description: <b><i>Background:</i></b> High dialysate flow rates (Q<sub>D</sub>) of 500–800 mL/min are used to maximize urea removal during conventional hemodialysis. There are few data describing hemodialysis with use of mid-rate Q<sub>D</sub> (300 mL/min). <b><i>Methods:</i></b> We constructed uremic solute (urea, beta<sub>2</sub>-microglobulin and phosphate) kinetic models at varying volumes of distribution and blood flow rates to predict solute clearances at Q<sub>D</sub> of 300 and 500 mL/min. <b><i>Results:</i></b> Across a range of volumes of distribution a Q<sub>D</sub> of 300 mL/min generally yields a predicted urea spKt/V greater than 1.2 during typical treatment times with a small difference in urea spKt/V between a Q<sub>D</sub> of 300 and 500 mL/min. A larger urea KoA dialyzer and 15 min of additional time narrows the urea spKt/V difference. No substantial differences were observed regarding the kinetics of beta<sub>2</sub>-microglobulin and phosphate for Q<sub>D</sub> of 300 vs. 500 mL/min. <b><i>Conclusion:</i></b> A Q<sub>D</sub> of 300 mL/min can achieve urea clearance targets. Hemodialysis systems using mid-rate Q<sub>D</sub> can be expected to provide adequate hemodialysis, as currently defined.
DOI: 10.7284/108616
title: Fluorometer data collected during research cruise EN473 using a Turner 10-AU instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7649432
title: Suppl Table S3.xlsx“Transcriptome-proteome integration of archival human renal cell carcinoma biopsies enables identification of molecular mechanisms”

description: <b>Supplementary Table for "Transcriptome-proteome integration of archival human renal cell carcinoma<br>biopsies enables identification of molecular mechanisms", Koch et al., 2019, AJPRP<br></b>
DOI: 10.6084/m9.figshare.7649444.v1
title: Supplementary Material for: Differential Molecular Modeling Predictions of Mid and Conventional Dialysate Flows

description: <b><i>Background:</i></b> High dialysate flow rates (Q<sub>D</sub>) of 500–800 mL/min are used to maximize urea removal during conventional hemodialysis. There are few data describing hemodialysis with use of mid-rate Q<sub>D</sub> (300 mL/min). <b><i>Methods:</i></b> We constructed uremic solute (urea, beta<sub>2</sub>-microglobulin and phosphate) kinetic models at varying volumes of distribution and blood flow rates to predict solute clearances at Q<sub>D</sub> of 300 and 500 mL/min. <b><i>Results:</i></b> Across a range of volumes of distribution a Q<sub>D</sub> of 300 mL/min generally yields a predicted urea spKt/V greater than 1.2 during typical treatment times with a small difference in urea spKt/V between a Q<sub>D</sub> of 300 and 500 mL/min. A larger urea KoA dialyzer and 15 min of additional time narrows the urea spKt/V difference. No substantial differences were observed regarding the kinetics of beta<sub>2</sub>-microglobulin and phosphate for Q<sub>D</sub> of 300 vs. 500 mL/min. <b><i>Conclusion:</i></b> A Q<sub>D</sub> of 300 mL/min can achieve urea clearance targets. Hemodialysis systems using mid-rate Q<sub>D</sub> can be expected to provide adequate hemodialysis, as currently defined.
DOI: 10.6084/m9.figshare.7649426
title: Suppl Table S2.xlsx“Transcriptome-proteome integration of archival human renal cell carcinoma biopsies enables identification of molecular mechanisms”

description: Supplementary Table to "Transcriptome-proteome integration of archival human renal cell carcinoma<br>biopsies enables identification of molecular mechanisms", Koch et al., 2019, AJPRP<br>
DOI: 10.6084/m9.figshare.7649429
title: Suppl Table S1.xlsx“Transcriptome-proteome integration of archival human renal cell carcinoma biopsies enables identification of molecular mechanisms”

description: Supplementary table S1 to the manuscript <b>"Transcriptome-proteome integration of archival human renal cell carcinoma<br>biopsies enables identification of molecular mechanisms",</b><b>Koch et al, 2019, AJPRJ<br></b>
DOI: 10.7284/107303
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN473 using a Furuno GP-90D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7649417
title: Supplementary Material for: Improved Control of Secondary Hyperparathyroidism in Hemodialysis Patients Switching from Oral Cinacalcet to Intravenous Etelcalcetide, Especially in Nonadherent Patients

description: <b><i>Background:</i></b> Etelcalcetide is a novel second-generation calcimimetic that, because of its intravenous administration, could improve treatment adherence in secondary hyperparathyroidism (SHPT). The aim of this study was to evaluate the effectiveness of etelcalcetide compared with that of cinacalcet in controlling SHPT in patients under hemodialysis. <b><i>Methods:</i></b> A prospective observational study was performed in 29 patients with SHPT under hemodialysis who switched from cinacalcet to etelcalcetide with a follow-up of 6 months. A survey was conducted of adherence to the oral calcimimetic. The primary end-point of the study was to assess whether etelcalcetide was more effective than cinacalcet in controlling SHPT. <b><i>Results:</i></b> After the switch of treatment, none of the patients developed clinical intolerance or new adverse effects. Etelcalcetide was more effective than cinacalcet in controlling intact parathyroid hormone (iPTH), with an overall decrease in iPTH levels that was significant from the second month. Average calcium levels remained within the normal range, with a higher percentage of hypocalcemia with etelcalcetide (6.9 vs. 13.8%), which was asymptomatic in all cases. Patients who were nonadherent to cinacalcet (38%) showed a significant reduction in calcium and iPTH during follow-up with etelcalcetide. The adherent group (62%) also showed a trend to lower iPTH levels reaching statistical significance after 5 months of follow-up. The dose conversion factor for the switch from cinacalcet to etelcalcetide was etelcalcetide/session = 0.111*mg cinacalcet/day + 0.96, <i>R</i><sup>2</sup> = 0.57. <b><i>Conclusions:</i></b> Etelcalcetide was more effective than cinacalcet in this patient population, especially in the nonadherent subgroup, leading to better SHPT control without adverse effects.
DOI: 10.6084/m9.figshare.7649432.v2
title: Suppl Table S3.xlsx“Transcriptome-proteome integration of archival human renal cell carcinoma biopsies enables identification of molecular mechanisms”

description: <b>Supplementary Table for "Transcriptome-proteome integration of archival human renal cell carcinoma<br>biopsies enables identification of molecular mechanisms", Koch et al., 2019, AJPRP<br></b>
DOI: 10.7284/111985
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN473 using a Trimble NT-300D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7649417.v1
title: Supplementary Material for: Improved Control of Secondary Hyperparathyroidism in Hemodialysis Patients Switching from Oral Cinacalcet to Intravenous Etelcalcetide, Especially in Nonadherent Patients

description: <b><i>Background:</i></b> Etelcalcetide is a novel second-generation calcimimetic that, because of its intravenous administration, could improve treatment adherence in secondary hyperparathyroidism (SHPT). The aim of this study was to evaluate the effectiveness of etelcalcetide compared with that of cinacalcet in controlling SHPT in patients under hemodialysis. <b><i>Methods:</i></b> A prospective observational study was performed in 29 patients with SHPT under hemodialysis who switched from cinacalcet to etelcalcetide with a follow-up of 6 months. A survey was conducted of adherence to the oral calcimimetic. The primary end-point of the study was to assess whether etelcalcetide was more effective than cinacalcet in controlling SHPT. <b><i>Results:</i></b> After the switch of treatment, none of the patients developed clinical intolerance or new adverse effects. Etelcalcetide was more effective than cinacalcet in controlling intact parathyroid hormone (iPTH), with an overall decrease in iPTH levels that was significant from the second month. Average calcium levels remained within the normal range, with a higher percentage of hypocalcemia with etelcalcetide (6.9 vs. 13.8%), which was asymptomatic in all cases. Patients who were nonadherent to cinacalcet (38%) showed a significant reduction in calcium and iPTH during follow-up with etelcalcetide. The adherent group (62%) also showed a trend to lower iPTH levels reaching statistical significance after 5 months of follow-up. The dose conversion factor for the switch from cinacalcet to etelcalcetide was etelcalcetide/session = 0.111*mg cinacalcet/day + 0.96, <i>R</i><sup>2</sup> = 0.57. <b><i>Conclusions:</i></b> Etelcalcetide was more effective than cinacalcet in this patient population, especially in the nonadherent subgroup, leading to better SHPT control without adverse effects.
DOI: 10.6084/m9.figshare.7649387
title: Block-matrix-based approach for the hybrid vehicle routing problem with fuzzy travel time and transportation type selection

description: In this study, we propose a novel hybrid model for the vehicle routing problem that combines fuzzy travel time and transportation type selection between milk-run and cross-dock strategies to derive an optimal transportation plan. Furthermore, we present a novel block-matrix-based approach for the hybrid model to explore optimal transportation plans in an intuitive, reasonable, effective, and efficient form. The proposed block-matrix-based approach derives an optimal transportation plan by solving a hybrid vehicle routing problem that considers not only fuzzy travel time, but also transportation type selection between milk-run and cross-dock strategies. An extended biogeography-based optimization (BBO) algorithm is proposed to effectively derive a transportation plan with the optimal degree of plant satisfaction by extending the operators of migration and mutation, and introducing a novel self-adaptive mutation rate, as well as a secondary mutation operator.
DOI: 10.6084/m9.figshare.7649429.v1
title: Suppl Table S1.xlsx“Cross-omics analysis of archival human renal cell carcinoma biopsies opens possibilities for emerging treatment avenues”

description: Supplementary table S1 to the manuscript <b>"Transcriptome-proteome integration of archival human renal cell carcinoma<br>biopsies enables identification of molecular mechanisms",</b><b>Koch et al, 2019, AJPRJ<br></b>
DOI: 10.7284/108611
title: Gyrocompass data collected during research cruise EN473 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7649387.v2
title: Block-matrix-based approach for the hybrid vehicle routing problem with fuzzy travel time and transportation type selection

description: In this study, we propose a novel hybrid model for the vehicle routing problem that combines fuzzy travel time and transportation type selection between milk-run and cross-dock strategies to derive an optimal transportation plan. Furthermore, we present a novel block-matrix-based approach for the hybrid model to explore optimal transportation plans in an intuitive, reasonable, effective, and efficient form. The proposed block-matrix-based approach derives an optimal transportation plan by solving a hybrid vehicle routing problem that considers not only fuzzy travel time, but also transportation type selection between milk-run and cross-dock strategies. An extended biogeography-based optimization (BBO) algorithm is proposed to effectively derive a transportation plan with the optimal degree of plant satisfaction by extending the operators of migration and mutation, and introducing a novel self-adaptive mutation rate, as well as a secondary mutation operator.
DOI: 10.6084/m9.figshare.7649387.v1
title: Untitled Item

description: In this study, we propose a novel hybrid model for the vehicle routing problem that combines fuzzy travel time and transportation type selection between milk-run and cross-dock strategies to derive an optimal transportation plan. Furthermore, we present a novel block-matrix-based approach for the hybrid model to explore optimal transportation plans in an intuitive, reasonable, effective, and efficient form. The proposed block-matrix-based approach derives an optimal transportation plan by solving a hybrid vehicle routing problem that considers not only fuzzy travel time, but also transportation type selection between milk-run and cross-dock strategies. An extended biogeography-based optimization (BBO) algorithm is proposed to effectively derive a transportation plan with the optimal degree of plant satisfaction by extending the operators of migration and mutation, and introducing a novel self-adaptive mutation rate, as well as a secondary mutation operator.
DOI: 10.7284/108612
title: Gyrocompass data collected during research cruise EN473 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7649216
title: Remembering with a Friend or a Stranger: Comparing Acquainted and Unacquainted Pairs in Collaborative Eyewitness Interviews

description: Previous findings show that collaborative interviews with pairs of eyewitnesses can result in more accurate testimony than individual interviews, and that partners remember more together if they acknowledge, repeat, rephrase and elaborate upon each other’s contributions. In the present study, we investigated whether these findings differ for pairs of acquainted and unacquainted partners, respectively. Participants viewed a violent movie in the cinema and took part in three eyewitness interviews approximately five days later. The first and the last interview were always individual. The second interview was individual in the nominal condition (<i>N </i>= 22 pairs), collaborative with a known partner in the acquainted condition (<i>N </i>= 21 pairs), or collaborative with a stranger in the unacquainted condition (<i>N </i>= 20 pairs). We replicated benefits of collaborative eyewitness interviews, in terms of error pruning as well as delayed cross-cuing. However, we found no significant differences between acquainted and unacquainted pairs, neither in recall performance nor in retrieval strategies during the collaborative interview. Regardless of acquaintance, pairs who listened to and elaborated upon each other’s contributions during the collaborative interview, remembered more together. The findings are evaluated within the theoretical framework of transactive memory. Practical implications for investigative interviewers are discussed.
DOI: 10.7284/107305
title: Singlebeam Echosounder data collected during research cruise EN473 using a Knudsen 320B/R instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7649201
title: <i>Aeromonas hydrophila</i> biofilm, exoprotease, and quorum sensing responses to co-cultivation with diverse foodborne pathogens and food spoilage bacteria on crab surfaces

description: The effects of dual species interactions on biofilm formation by <i>Aeromonas hydrophila</i> in the presence of <i>Pseudomonas aeruginosa</i>, <i>Pseudomonas fluorescens</i>, <i>Pectobacterium carotovorum</i>, <i>Salmonella</i> Typhimurium, and <i>Listeria monocytogenes</i> were examined. High-performance liquid chromatography and liquid-chromatography-mass spectrometry were performed to identify <i>N</i>-acyl homoserine lactone (AHL) molecules secreted by monocultures and dual cultures grown in crab broth. Field emission scanning electron microscopy was performed to observe attachment and biofilm formation. <i>P. aeruginosa</i> and <i>P. fluorescens</i> inhibited biofilm formation by <i>A. hydrophila</i> on the crab surface, without affecting their own biofilm-forming abilities. Dual biofilms of <i>S.</i> Typhimurium, <i>L. monocytogenes</i>, or <i>P. carotovorum</i> did not affect <i>A. hydrophila</i> biofilm formation. Exoprotease, AHL, and AI-2 levels were significantly reduced in dual cultures of <i>P. aeruginosa</i> and <i>P. fluorescens</i> with <i>A. hydrophila</i>, supporting the relationship between quorum sensing and biofilm formation. Dual-species biofilms were studied in their natural environment and in the laboratory.