cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12496529
title: Supplementary Material for: Prognostic Effect of Preoperative Apolipoprotein B Level in Surgical Patients with Clear Cell Renal Cell Carcinoma

description: <b><i>Background:</i></b> The aim of this study was to assess the prognostic value of the preoperative apolipoprotein B (ApoB) level in surgical patients with clear cell renal cell carcinoma (ccRCC). <b><i>Materials and Methods:</i></b> The study included 307 ccRCC patients receiving radical or partial nephrectomy between 2003 and 2012 in our center. The correlations among the preoperative ApoB, clinicopathological parameters, and overall survival (OS) were evaluated. <b><i>Results:</i></b> A total of 193 males (62.9%) and 114 females (37.1%) with ccRCC who underwent radical or partial nephrectomy were enrolled in the present study. The OS at 5 years after the operation was 90.6% for all patients, 87.4% for the lower ApoB group, and 97.0% for the higher-ApoB group. The cause-specific survival (CSS) at 5 years after surgery was 90.2% for all patients, 86.7% for the lower-ApoB group, and 97.0% for the higher-ApoB group. A higher-ApoB level was related to a better OS and CSS in ccRCC patients (<i>p</i> = 0.001 and <i>p</i> &lt; 0.001, respectively). In multivariate analysis, age &gt;60 years (<i>p</i> = 0.008 and <i>p</i> = 0.023) and a lower Apo B level (<i>p</i> = 0.019 and <i>p</i> = 0.018) were independent prognostic factors for OS and CSS, respectively. <b><i>Conclusions:</i></b> In the Apo apolipoprotein family, the preoperative ApoB level had an important clinical significance for predicting the prognosis and survival rate of ccRCC patients.
DOI: 10.6084/m9.figshare.12496556.v1
title: Characterization and removal of biofouling from reverse osmosis membranes (ROMs) from a desalination plant in Northern Chile, using <i>Alteromonas</i> sp. Ni1-LEM supernatant

description: Biofouling control in reverse osmosis membranes (ROMs) is challenging due to the high cost of treatments, and reduction in the life of ROMs. This study characterizes the biofouling in the ROMs from a desalination plant and reports its effective removal using the supernatant obtained from <i>Alteromonas</i> sp. strain Ni1-LEM. The characterization of the bacterial community revealed that the most abundant taxa in ROMs were the genera <i>Fulvivirga</i> and <i>Pseudoalteromonas</i>, and unclassified species of the families Flavobacteriaceae and Sphingomonadaceae. This bacterial community significantly decreased upon treatment with the supernatant from <i>Alteromonas</i> sp. Ni1-LEM, resulting in the prevalence of the genus <i>Pseudoalteromonas</i>. Furthermore, this bacterial supernatant significantly inhibited cell adhesion of seven benthic microalgae isolated from ROMs as well as promoting cell detachment of the existing microbial biofilms. The study showed that the extracellular supernatant modified the conformation of extracellular polymeric substances (EPS) in the biofouling of ROMs without any biocidal effects.
DOI: 10.6084/m9.figshare.12496529.v1
title: Supplementary Material for: Prognostic Effect of Preoperative Apolipoprotein B Level in Surgical Patients with Clear Cell Renal Cell Carcinoma

description: <b><i>Background:</i></b> The aim of this study was to assess the prognostic value of the preoperative apolipoprotein B (ApoB) level in surgical patients with clear cell renal cell carcinoma (ccRCC). <b><i>Materials and Methods:</i></b> The study included 307 ccRCC patients receiving radical or partial nephrectomy between 2003 and 2012 in our center. The correlations among the preoperative ApoB, clinicopathological parameters, and overall survival (OS) were evaluated. <b><i>Results:</i></b> A total of 193 males (62.9%) and 114 females (37.1%) with ccRCC who underwent radical or partial nephrectomy were enrolled in the present study. The OS at 5 years after the operation was 90.6% for all patients, 87.4% for the lower ApoB group, and 97.0% for the higher-ApoB group. The cause-specific survival (CSS) at 5 years after surgery was 90.2% for all patients, 86.7% for the lower-ApoB group, and 97.0% for the higher-ApoB group. A higher-ApoB level was related to a better OS and CSS in ccRCC patients (<i>p</i> = 0.001 and <i>p</i> &lt; 0.001, respectively). In multivariate analysis, age &gt;60 years (<i>p</i> = 0.008 and <i>p</i> = 0.023) and a lower Apo B level (<i>p</i> = 0.019 and <i>p</i> = 0.018) were independent prognostic factors for OS and CSS, respectively. <b><i>Conclusions:</i></b> In the Apo apolipoprotein family, the preoperative ApoB level had an important clinical significance for predicting the prognosis and survival rate of ccRCC patients.
DOI: 10.6084/m9.figshare.12496517
title: indivPlots.tgz

description: This item contains plots of summary statistics calculated from individual simulation replicates from Dan Schrider's paper comparing patterns of variation produced by hitchhiking to those produced by background selection. For more information see the manuscript (doi: https://doi.org/10.1101/2019.12.13.876136), and the code used to produce these simulations (https://github.com/SchriderLab/posSelVsBgs).
DOI: 10.6084/m9.figshare.12496520
title: Underlying Data: A Quantitative Analysis of 3D Printed Face Shields and Masks During COVID-19

description: This is the underlying data supporting a study titled "A Quantitative Analysis of 3D Printed Face Shields and Masks During COVID-19" (https://doi.org/10.35241/emeraldopenres.13815.1).<br>37 face shields and 31 face masks suitable for fused filament fabrication (FFF) were analysed from a fabrication perspective, documenting factors such as filament use, time to print and geometric qualities. <br>
DOI: 10.6084/m9.figshare.12496523.v1
title: Supplementary Material for: Left Atrial Volume Index Predicts New-Onset Atrial Fibrillation and Stroke Recurrence in Patients with Embolic Stroke of Undetermined Source

description: <b><i>Introduction:</i></b> It is unclear which surrogate of atrial cardiopathy best predicts the risk of developing a recurrent ischemic stroke in embolic stroke of undetermined source (ESUS). Left atrial diameter (LAD) and LAD index (LADi) are often used as markers of left atrial enlargement in current ESUS research, but left atrial volume index (LAVi) has been found to be a better predictor of cardiovascular outcomes in other patient populations. <b><i>Objective:</i></b> We aim to compare the performance of LAVi, LAD, and LADi in predicting the development of new-onset atrial fibrillation (AF) and stroke recurrence in ESUS. <b><i>Methods:</i></b> Between October 2014 and October 2017, consecutive patients diagnosed with ESUS were followed for new-onset AF, ischemic stroke recurrence, and a composite outcome of occult AF and stroke recurrence. LAVi and LADi were measured by transthoracic echocardiogram; “high” LAVi was defined as ≥35 mL/m<sup>2</sup> in accordance with American Society of Echocardiography guidelines. <b><i>Results:</i></b> 185 ischemic stroke patients with ESUS were recruited and followed for a median duration of 2.1 years. Increased LAVi was associated with new-onset AF detection (aOR 1.08; 95% CI 1.03–1.14; <i>p</i> = 0.003) and stroke recurrence (aOR 1.05; 95% CI 1.01–1.10; <i>p</i> = 0.026). Patients with “high” LAVi had a higher likelihood of developing a composite of AF detection and stroke recurrence (HR 3.45; 95% CI 1.55–7.67; <i>p</i> = 0.002). No significant association was observed between LADi and either occult AF or stroke recurrence. <b><i>Conclusions:</i></b> LAVi is associated with new-onset AF and stroke recurrence in ESUS patients and may be a better surrogate of atrial cardiopathy.
DOI: 10.6084/m9.figshare.12496010
title: flyHubDFE.tgz

description: This item contains all forward simulations of background selection under Drosophila-like parameters from Dan Schrider's paper comparing patterns of variation produced by hitchhiking to those produced by background selection. For more information see the manuscript (doi: https://doi.org/10.1101/2019.12.13.876136), and the code used to produce these simulations (https://github.com/SchriderLab/posSelVsBgs). <br><br>Note: the large-scale simulation output is not included here, but the windowed statistics and logs (which contain random seeds for reproducibility) from these simulations are present.<br>
DOI: 10.6084/m9.figshare.12496517.v1
title: indivPlots.tgz

description: This item contains plots of summary statistics calculated from individual simulation replicates from Dan Schrider's paper comparing patterns of variation produced by hitchhiking to those produced by background selection. For more information see the manuscript (doi: https://doi.org/10.1101/2019.12.13.876136), and the code used to produce these simulations (https://github.com/SchriderLab/posSelVsBgs).
DOI: 10.6084/m9.figshare.12495914
title: Species diversity and seasonal variation in zooplankton in the Sanmenxia Reservoir characterized by the 18S rRNA and COI metabarcoding methods

description: Species diversity and seasonal variation in zooplankton in the Sanmenxia Reservoir characterized by the 18S rRNA and COI metabarcoding methods.
DOI: 10.6084/m9.figshare.12496004
title: PeerTeach online decision making data

description: This data is referenced in the report, Each one teach one: Teaching learners to do learner-centered teaching. This file includes online decision making during virtual tutoring. "Predeci" represents decisions made pre-intervention. "Postdeci" represents decisions made post-intervention. 1 represents that an elicitive teaching move was selected. The total number of elicitive teaching moves selected is shown in the "total" columns.
DOI: 10.6084/m9.figshare.12496010.v1
title: flyHubDFE.tgz

description: This item contains all forward simulations of background selection under Drosophila-like parameters from Dan Schrider's paper comparing patterns of variation produced by hitchhiking to those produced by background selection. For more information see the manuscript (doi: https://doi.org/10.1101/2019.12.13.876136), and the code used to produce these simulations (https://github.com/SchriderLab/posSelVsBgs). <br><br>Note: the large-scale simulation output is not included here, but the windowed statistics and logs (which contain random seeds for reproducibility) from these simulations are present.<br>
DOI: 10.6084/m9.figshare.12495881
title: PeerTeach assessment data with exit ticket scores

description: This data is referenced in the report, Each one teach one: Teaching learners to do learner-centered teaching. This file includes exit ticket scores for tutors, showing their content knowledge before tutoring.
DOI: 10.6084/m9.figshare.12496004.v1
title: PeerTeach online decision making data

description: This data is referenced in the report, Each one teach one: Teaching learners to do learner-centered teaching. This file includes online decision making during virtual tutoring. "Predeci" represents decisions made pre-intervention. "Postdeci" represents decisions made post-intervention. 1 represents that an elicitive teaching move was selected. The total number of elicitive teaching moves selected is shown in the "total" columns.
DOI: 10.6084/m9.figshare.12495881.v1
title: PeerTeach assessment data with exit ticket scores

description: This data is referenced in the report, Each one teach one: Teaching learners to do learner-centered teaching. This file includes exit ticket scores for tutors, showing their content knowledge before tutoring.
DOI: 10.6084/m9.figshare.12495656
title: peerteach_post_assessment_data.csv

description: This is the post assessment data referenced in the report, Each one teach one: Teaching learners to do learner-centered teaching. Group1 is the WISE training, Group2 is the Talk Moves training, and Group3 is the control students.
DOI: 10.6084/m9.figshare.12495656.v1
title: peerteach_post_assessment_data.csv

description: This is the post assessment data referenced in the report, Each one teach one: Teaching learners to do learner-centered teaching. Group1 is the WISE training, Group2 is the Talk Moves training, and Group3 is the control students.
DOI: 10.6084/m9.figshare.12495734
title: JVASP-10370 to JVASP-11300

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12495914.v1
title: Species diversity and seasonal variation in zooplankton in the Sanmenxia Reservoir characterized by the 18S rRNA and COI metabarcoding methods

description: Species diversity and seasonal variation in zooplankton in the Sanmenxia Reservoir characterized by the 18S rRNA and COI metabarcoding methods.
DOI: 10.6084/m9.figshare.12495473
title: Supplementary Data 2

description: Source data for the bar charts in Figure 2b (Cell dry mass), Figure 2c (% of MaSp1 in total proteins), Figure 2d (MaSp1 yield) and exact <i>p</i>-values obtained from statistical analysis using one-way ANOVA.
DOI: 10.6084/m9.figshare.12495479
title: Additional file 1 of In vivo absolute quantification of striatal and extrastriatal D2/3 receptors with [123I]epidepride SPECT

description: Additional file 1. Supplemental Materials and Methods
DOI: 10.6084/m9.figshare.12495431
title: Additional file 1 of A prognostic model based on cell-cycle control predicts outcome of breast cancer patients

description: Additional file 1. Details of IHC for detecting Securin, Separase, Cdc20, Pttg1IP, SA2, Cdk1 and CyclinB1 and routine clinical biomarkers of breast cancer ER, PR, Ki-67 and HER2. The datasheet contains the details of the immunohistochemical methods used in this study.
DOI: 10.6084/m9.figshare.12495419
title: Additional file 1 of The TNF/TNFR2 signaling pathway is a key regulatory factor in endothelial progenitor cell immunosuppressive effect

description: Additional file 1: Supplementary Figure 1. Flow cytometry representative of proliferation assay. Supplementary Figure 2. ECFCs can modulate CD4+ T cell activation markers. Supplementary Figure 3. ECFCs can modulate CD8+ T cell activation markers. Supplementary Figure 4. ECFCs immunosuppressive effect is entirely abolished when T cells are incapable of TNFα production. Supplementary Figure 5. Expression of TNFR1 and TNFR2 on different endothelial cells.
DOI: 10.6084/m9.figshare.12495431.v1
title: Additional file 1 of A prognostic model based on cell-cycle control predicts outcome of breast cancer patients

description: Additional file 1. Details of IHC for detecting Securin, Separase, Cdc20, Pttg1IP, SA2, Cdk1 and CyclinB1 and routine clinical biomarkers of breast cancer ER, PR, Ki-67 and HER2. The datasheet contains the details of the immunohistochemical methods used in this study.
DOI: 10.6084/m9.figshare.12495413
title: Additional file 3 of Activity-based protein profiling guided identification of urine proteinase 3 activity in subclinical rejection after renal transplantation

description: Additional file 2. List of all proteins identified by mass spectromety in the urine samples from patients undergoing clinical rejection.
DOI: 10.6084/m9.figshare.12495416
title: Additional file 4 of Activity-based protein profiling guided identification of urine proteinase 3 activity in subclinical rejection after renal transplantation

description: Additional file 3. List of all proteins identified by mass spectromety in the urine samples from patients undergoing subclinical rejection.
DOI: 10.6084/m9.figshare.12495413.v1
title: Additional file 3 of Activity-based protein profiling guided identification of urine proteinase 3 activity in subclinical rejection after renal transplantation

description: Additional file 2. List of all proteins identified by mass spectromety in the urine samples from patients undergoing clinical rejection.
DOI: 10.6084/m9.figshare.12495416.v1
title: Additional file 4 of Activity-based protein profiling guided identification of urine proteinase 3 activity in subclinical rejection after renal transplantation

description: Additional file 3. List of all proteins identified by mass spectromety in the urine samples from patients undergoing subclinical rejection.
DOI: 10.6084/m9.figshare.12495419.v1
title: Additional file 1 of The TNF/TNFR2 signaling pathway is a key regulatory factor in endothelial progenitor cell immunosuppressive effect

description: Additional file 1: Supplementary Figure 1. Flow cytometry representative of proliferation assay. Supplementary Figure 2. ECFCs can modulate CD4+ T cell activation markers. Supplementary Figure 3. ECFCs can modulate CD8+ T cell activation markers. Supplementary Figure 4. ECFCs immunosuppressive effect is entirely abolished when T cells are incapable of TNFα production. Supplementary Figure 5. Expression of TNFR1 and TNFR2 on different endothelial cells.
DOI: 10.6084/m9.figshare.12495407
title: Additional file 9 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 9 : Table S4. ΔACL/iΔACS transcriptome. Excel spreadheet summarising the transcriptome data set from the RNA-seq analysis. Transcripts which are significantly up- or downregulated in ΔACL/iΔACS parasites are highlighted. Abbreviations: ACL: ATP-citrate lyase; ACS: acetyl-CoA synthetase.
DOI: 10.6084/m9.figshare.12495398
title: Additional file 7 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 7 : Table S3. ΔBCKDH acetytlome. Excel spreadheet summarising the acetylome data set from the nanoLC-MS/MS analysis. Sites and proteins which are significantly hypo- or hyper-acetylated in ΔBCKDH parasites are highlighted. Abbreviations: BCKDH: branched-chain α-keto acid dehydrogenase-complex; LC-MS/MS: liquid chromatography-tandem mass spectrometry.
DOI: 10.6084/m9.figshare.12495407.v1
title: Additional file 9 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 9 : Table S4. ΔACL/iΔACS transcriptome. Excel spreadheet summarising the transcriptome data set from the RNA-seq analysis. Transcripts which are significantly up- or downregulated in ΔACL/iΔACS parasites are highlighted. Abbreviations: ACL: ATP-citrate lyase; ACS: acetyl-CoA synthetase.
DOI: 10.6084/m9.figshare.12495398.v1
title: Additional file 7 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 7 : Table S3. ΔBCKDH acetytlome. Excel spreadheet summarising the acetylome data set from the nanoLC-MS/MS analysis. Sites and proteins which are significantly hypo- or hyper-acetylated in ΔBCKDH parasites are highlighted. Abbreviations: BCKDH: branched-chain α-keto acid dehydrogenase-complex; LC-MS/MS: liquid chromatography-tandem mass spectrometry.
DOI: 10.6084/m9.figshare.12495395
title: Additional file 6 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 6 : Table S2. ΔACL/iΔACS acetytlome. Excel spreadheet summarising the acetylome data set from the nanoLC-MS/MS analysis. Sites and proteins which are significantly hypo- or hyper-acetylated in ΔACL/iΔACS parasites are highlighted. Abbreviations: ACL: ATP-citrate lyase; ACS: acetyl-CoA synthetase; LC-MS/MS: liquid chromatography-tandem mass spectrometry.
DOI: 10.6084/m9.figshare.12495395.v1
title: Additional file 6 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 6 : Table S2. ΔACL/iΔACS acetytlome. Excel spreadheet summarising the acetylome data set from the nanoLC-MS/MS analysis. Sites and proteins which are significantly hypo- or hyper-acetylated in ΔACL/iΔACS parasites are highlighted. Abbreviations: ACL: ATP-citrate lyase; ACS: acetyl-CoA synthetase; LC-MS/MS: liquid chromatography-tandem mass spectrometry.
DOI: 10.6084/m9.figshare.12495365
title: Additional file 2 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 2 : Table S1. ΔACL/iΔACS metabolome. Excel spreadheet summarising the metabolomic data set from the LC-MS analysis. Metabolites which are significantly decreased or increased in ΔACL parasites, iΔACS parasites and ΔACL/iΔACS parasites are highlighted. Abbreviations: ACL: ATP-citrate lyase; ACS: acetyl-CoA synthetase; LC-MS: liquid chromatography-mass spectrometry.
DOI: 10.6084/m9.figshare.12495365.v1
title: Additional file 2 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 2 : Table S1. ΔACL/iΔACS metabolome. Excel spreadheet summarising the metabolomic data set from the LC-MS analysis. Metabolites which are significantly decreased or increased in ΔACL parasites, iΔACS parasites and ΔACL/iΔACS parasites are highlighted. Abbreviations: ACL: ATP-citrate lyase; ACS: acetyl-CoA synthetase; LC-MS: liquid chromatography-mass spectrometry.
DOI: 10.6084/m9.figshare.12495353
title: Additional file 14 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 14 : Table S8. Primers. Excel spreadsheet providing an overview of the primers used in this publication including their sequences.
DOI: 10.6084/m9.figshare.12495347
title: Additional file 12 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 12 : Table S7. ΔBCKDH proteome. Excel spreadheet summarising the proteome data set from the nano-LC-MS/MS analysis. Proteins which are significantly up- or downregulated in ΔBCKDH parasites are highlighted. Abbreviations: BCKDH: branched-chain α-keto acid dehydrogenase-complex; LC-MS/MS: liquid chromatography-tandem mass spectrometry.
DOI: 10.6084/m9.figshare.12495341
title: Additional file 11 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 11 : Table S6. ΔBCKDH transcriptome. Excel spreadheet summarising the transcriptome data set from the RNA-seq analysis. Transcripts which are significantly up- or downregulated in ΔBCKDH parasites are highlighted. Abbreviations: BCKDH: branched-chain α-keto acid dehydrogenase-complex.
DOI: 10.6084/m9.figshare.12495353.v1
title: Additional file 14 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 14 : Table S8. Primers. Excel spreadsheet providing an overview of the primers used in this publication including their sequences.
DOI: 10.6084/m9.figshare.12495335
title: Additional file 10 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 10 : Table S5. ΔACL/iΔACS proteome. Excel spreadheet summarising the proteome data set from the nano-LC-MS/MS analysis. Proteins which are significantly up- or downregulated in ΔACL/iΔACS parasites are highlighted. Abbreviations: ACL: ATP-citrate lyase; ACS: acetyl-CoA synthetase; LC-MS/MS: liquid chromatography-tandem mass spectrometry.
DOI: 10.6084/m9.figshare.12495341.v1
title: Additional file 11 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 11 : Table S6. ΔBCKDH transcriptome. Excel spreadheet summarising the transcriptome data set from the RNA-seq analysis. Transcripts which are significantly up- or downregulated in ΔBCKDH parasites are highlighted. Abbreviations: BCKDH: branched-chain α-keto acid dehydrogenase-complex.
DOI: 10.6084/m9.figshare.12495347.v1
title: Additional file 12 of Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

description: Additional file 12 : Table S7. ΔBCKDH proteome. Excel spreadheet summarising the proteome data set from the nano-LC-MS/MS analysis. Proteins which are significantly up- or downregulated in ΔBCKDH parasites are highlighted. Abbreviations: BCKDH: branched-chain α-keto acid dehydrogenase-complex; LC-MS/MS: liquid chromatography-tandem mass spectrometry.