cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5955898
title: Supplementary Material for: Cinacalcet for Treatment of Chronic Kidney Disease-Mineral and Bone Disorder: A Meta-Analysis of Randomized Controlled Trials

description: <b><i>Background:</i></b> Cinacalcet could decrease serum calcium, phosphate, and parathyroid hormone (PTH) in previous meta-analyses. However, the effect of cinacalcet on the new biomarkers such as fibroblast growth factor-23 (FGF-23), bone markers, and vascular calcification are still unestablished. We conducted a meta-analysis to examine the effects of cinacalcet on all laboratory and clinical spectrums of chronic kidney disease-mineral bone disorders (CKD-MBD). <b><i>Methods:</i></b> A systematic literature search was conducted in MEDLINE, Scopus, Cochrane Central Register of Controlled Trials, and Clinical Trials.gov to identify randomized controlled trials (RCTs) comparing the effect of cinacalcet relative to standard treatment on CKD-MBD surrogate markers and clinical outcomes. Random-effect models were used to compute the weighted mean difference for continuous variables and the risk ratio for binary variables. <b><i>Results:</i></b> Twenty-four RCTs (10,031 dialysis patients) were identified. Besides lowering effects on calcium, phosphate, and PTH, cinacalcet significantly reduced bone resorptive marker (tartrate-resistant acid phosphatase 5b) but unaltered bone formation markers (bone alkaline phosphatase and osteocalcin). Cinacalcet also resulted in significant higher risk of hypocalcemia, nausea, vomiting, and diarrhea. Cinacalcet significantly lowered serum FGF-23 level, although unaltered all-cause mortalities. <b><i>Conclusions:</i></b> Use of cinacalcet in dialysis patients improves several CKD-MBD-related surrogate markers. However, the benefit on all-cause mortalities was not demonstrated.
DOI: 10.6084/m9.figshare.5955898.v1
title: Supplementary Material for: Cinacalcet for Treatment of Chronic Kidney Disease-Mineral and Bone Disorder: A Meta-Analysis of Randomized Controlled Trials

description: <b><i>Background:</i></b> Cinacalcet could decrease serum calcium, phosphate, and parathyroid hormone (PTH) in previous meta-analyses. However, the effect of cinacalcet on the new biomarkers such as fibroblast growth factor-23 (FGF-23), bone markers, and vascular calcification are still unestablished. We conducted a meta-analysis to examine the effects of cinacalcet on all laboratory and clinical spectrums of chronic kidney disease-mineral bone disorders (CKD-MBD). <b><i>Methods:</i></b> A systematic literature search was conducted in MEDLINE, Scopus, Cochrane Central Register of Controlled Trials, and Clinical Trials.gov to identify randomized controlled trials (RCTs) comparing the effect of cinacalcet relative to standard treatment on CKD-MBD surrogate markers and clinical outcomes. Random-effect models were used to compute the weighted mean difference for continuous variables and the risk ratio for binary variables. <b><i>Results:</i></b> Twenty-four RCTs (10,031 dialysis patients) were identified. Besides lowering effects on calcium, phosphate, and PTH, cinacalcet significantly reduced bone resorptive marker (tartrate-resistant acid phosphatase 5b) but unaltered bone formation markers (bone alkaline phosphatase and osteocalcin). Cinacalcet also resulted in significant higher risk of hypocalcemia, nausea, vomiting, and diarrhea. Cinacalcet significantly lowered serum FGF-23 level, although unaltered all-cause mortalities. <b><i>Conclusions:</i></b> Use of cinacalcet in dialysis patients improves several CKD-MBD-related surrogate markers. However, the benefit on all-cause mortalities was not demonstrated.
DOI: 10.6084/m9.figshare.5955886
title: Code and data for -1 programmed ribosomal frameshifting's effect on codon usage bias analysis.

description: Here we share the code with which we investigated the presence of a cost of -1 programmed ribosomal frameshifting to translation. With this code, we also analyzed how -1 programmed ribosomal frameshifting might affect estimates of codon usage bias in mRNA. <br>
DOI: 10.6084/m9.figshare.5955886.v1
title: Code and data for -1 programmed ribosomal frameshifting's effect on codon usage bias analysis.

description: Here we share the code with which we investigated the presence of a cost of -1 programmed ribosomal frameshifting to translation. With this code, we also analyzed how -1 programmed ribosomal frameshifting might affect estimates of codon usage bias in mRNA. <br>
DOI: 10.6084/m9.figshare.5955880
title: Inside out: microbiota dynamics during host-plant adaptation of whiteflies - Supplementay Material

description: <br>While most insect herbivores are selective feeders, a small proportion of them feed on a wide range of plants. This polyphagous habit requires overcoming a remarkable array of defenses, which often necessitates an adaptation period. Efforts for understanding the mechanisms involved mostly focus on the insect’s phenotypic plasticity. Here, we hypothesized that the adaptation process might partially rely on transient associations with bacteria. To test this, we followed in a field-like experiment, the adaptation process of <i>Bemisia tabaci</i>, a generalist sap-feeder, to pepper (a less-suitable host), after switching from watermelon (a suitable host). Amplicon sequencing of 16S rRNA transcripts from hundreds of dissected guts revealed the presence of active “core” and “transient” bacterial communities, dominated by the phyla Proteobacteria, Actinobacteria, and Firmicutes, and increasing differences between populations grown on watermelon and pepper. Insects grown on pepper for over two generations, presented a significant increase in specific genera, mainly <i>Mycobacterium</i>, with a predicted enrichment in degradative pathways of xenobiotics and secondary metabolites. This result correlated with a significant increase in the insect’s survival on pepper. Taken together, our findings suggest that gut-associated bacteria can provide an additional flexible metabolic “tool-box” to generalist sap-feeders for facilitating a quick host switching process.
DOI: 10.6084/m9.figshare.5955880.v1
title: Inside out: microbiota dynamics during host-plant adaptation of whiteflies - Supplementay Material

description: <br>While most insect herbivores are selective feeders, a small proportion of them feed on a wide range of plants. This polyphagous habit requires overcoming a remarkable array of defenses, which often necessitates an adaptation period. Efforts for understanding the mechanisms involved mostly focus on the insect’s phenotypic plasticity. Here, we hypothesized that the adaptation process might partially rely on transient associations with bacteria. To test this, we followed in a field-like experiment, the adaptation process of <i>Bemisia tabaci</i>, a generalist sap-feeder, to pepper (a less-suitable host), after switching from watermelon (a suitable host). Amplicon sequencing of 16S rRNA transcripts from hundreds of dissected guts revealed the presence of active “core” and “transient” bacterial communities, dominated by the phyla Proteobacteria, Actinobacteria, and Firmicutes, and increasing differences between populations grown on watermelon and pepper. Insects grown on pepper for over two generations, presented a significant increase in specific genera, mainly <i>Mycobacterium</i>, with a predicted enrichment in degradative pathways of xenobiotics and secondary metabolites. This result correlated with a significant increase in the insect’s survival on pepper. Taken together, our findings suggest that gut-associated bacteria can provide an additional flexible metabolic “tool-box” to generalist sap-feeders for facilitating a quick host switching process.
DOI: 10.6084/m9.figshare.5955847
title: Supplementary Material for: Prophylactic Effect of Dexamethasone on Regorafenib-Related Fatigue and/or Malaise: A Randomized, Placebo-Controlled, Double-Blind Clinical Study in Patients with Unresectable Metastatic Colorectal Cancer (KSCC1402/HGCSG1402)

description: <b><i>Background:</i></b> Regorafenib is an oral multikinase inhibitor with a proven survival benefit for metastatic colorectal cancer patients. The KSCC1402/HGCSG1402 study investigated the prophylactic effect of oral dexamethasone (DEX) on regorafenib-related fatigue and/or malaise. <b><i>Patients and Methods:</i></b> Patients who progressed after standard chemotherapy were randomized 1: 1 to a DEX group (2 mg/day; days 1–28) with regorafenib or a placebo group with regorafenib. The primary endpoint was the incidence of fatigue and/or malaise, based on version 4.0 of the National Cancer Institute’s CTCAE (Common Terminology Criteria for Adverse Events). One of the secondary endpoints was the in­cidence of fatigue and/or malaise based on the CTCAE assessed by patient-reported outcome (PRO). <b><i>Results:</i></b> The incidence of any grade of fatigue and/or malaise assessed by the investigators was 58.8% in the DEX group and 61.1% in the placebo group (<i>p</i> = 0.8101), and that assessed by PRO was 47.2 and 58.3%, respectively (<i>p</i> = 0.3450). The incidence of grade ≥2 fatigue and/or malaise, as assessed by the investigators, was 19.4% for the DEX group and 38.9% for the placebo group (<i>p</i> = 0.0695), and that assessed by PRO was 27.8 and 52.8%, respectively (<i>p</i> = 0.0306). <b><i>Conclusion:</i></b> Our results suggest that prophylactic oral DEX is clinically effective in improving regorafenib-related fatigue and/or malaise.
DOI: 10.6084/m9.figshare.5955847.v1
title: Supplementary Material for: Prophylactic Effect of Dexamethasone on Regorafenib-Related Fatigue and/or Malaise: A Randomized, Placebo-Controlled, Double-Blind Clinical Study in Patients with Unresectable Metastatic Colorectal Cancer (KSCC1402/HGCSG1402)

description: <b><i>Background:</i></b> Regorafenib is an oral multikinase inhibitor with a proven survival benefit for metastatic colorectal cancer patients. The KSCC1402/HGCSG1402 study investigated the prophylactic effect of oral dexamethasone (DEX) on regorafenib-related fatigue and/or malaise. <b><i>Patients and Methods:</i></b> Patients who progressed after standard chemotherapy were randomized 1: 1 to a DEX group (2 mg/day; days 1–28) with regorafenib or a placebo group with regorafenib. The primary endpoint was the incidence of fatigue and/or malaise, based on version 4.0 of the National Cancer Institute’s CTCAE (Common Terminology Criteria for Adverse Events). One of the secondary endpoints was the in­cidence of fatigue and/or malaise based on the CTCAE assessed by patient-reported outcome (PRO). <b><i>Results:</i></b> The incidence of any grade of fatigue and/or malaise assessed by the investigators was 58.8% in the DEX group and 61.1% in the placebo group (<i>p</i> = 0.8101), and that assessed by PRO was 47.2 and 58.3%, respectively (<i>p</i> = 0.3450). The incidence of grade ≥2 fatigue and/or malaise, as assessed by the investigators, was 19.4% for the DEX group and 38.9% for the placebo group (<i>p</i> = 0.0695), and that assessed by PRO was 27.8 and 52.8%, respectively (<i>p</i> = 0.0306). <b><i>Conclusion:</i></b> Our results suggest that prophylactic oral DEX is clinically effective in improving regorafenib-related fatigue and/or malaise.
DOI: 10.6084/m9.figshare.5955838
title: FinancialNews.tar.gz

description: Financial-News dataset used in <i>Studying thematic evolution over time using Dynamic Topic Vectors.</i> Raw data is available at https://github.com/philipperemy/financial-news-dataset.<br>The data folder contains document embeddings for each Financial-News articles between 2006-2013. Each yearly folder contains pickled python objects for each train/test set:<br><br>document matrix: *_FinNews_{year}_corpus_N_*.p<br>document dictionaries: *_FinNews_{year}_doc_dict_N_*.p<br>document dictionaries for all empty articles: *_FinNews_{year}_doc_dict_empty_N_*.p
DOI: 10.6084/m9.figshare.5955838.v1
title: FinancialNews.tar.gz

description: Financial-News dataset used in <i>Studying thematic evolution over time using Dynamic Topic Vectors.</i> Raw data is available at https://github.com/philipperemy/financial-news-dataset<br>
DOI: 10.6084/m9.figshare.5955817
title: Experiment 3: Electrical circuit composed of human skin memristors

description: This experiment demonstrates a possible application of the human skin memristor in an electrical circuit. This circuit functioned as a frequency doubler or half-wave rectifier under certain conditions.<br> <br><b>Experimental Design</b><br>Two sinusoidal voltages of opposite signs (randomized order) and the same frequency and amplitude as 1 V were applied to the skin for two periods. Resulting current, i, was measured. This procedure was performed three times for frequencies of 0.005 Hz, 0.05 Hz and 0.5 Hz in randomized order. The time during which no signal was applied between runs was 4 seconds. <br><br><b>File information</b><br>The Samples 1 to 1001 in each line reflect 2 periods of the corresponding signal. Sample 1 of each measurement run was distorted by the instrumentation and was set to NaN (not a number) which can be handled by Matlab. Variant A (CC1-electrode at the earlobe) was chosen for subjects 1 - 12. Variant B (CC1-electrode at the forehead) was chosen for subjects 13 - 28.<br>
DOI: 10.6084/m9.figshare.5955817.v1
title: Experiment 3: Electrical circuit composed of human skin memristors

description: This experiment demonstrates a possible application of the human skin memristor in an electrical circuit. This circuit functioned as a frequency doubler or half-wave rectifier under certain conditions.<br> <br><b>Experimental Design</b><br>Two sinusoidal voltages of opposite signs (randomized order) and the same frequency and amplitude as 1 V were applied to the skin for two periods. Resulting current, i, was measured. This procedure was performed three times for frequencies of 0.005 Hz, 0.05 Hz and 0.5 Hz in randomized order. The time during which no signal was applied between runs was 4 seconds. <br><br><b>File information</b><br>The Samples 1 to 1001 in each line reflect 2 periods of the corresponding signal. Sample 1 of each measurement run was distorted by the instrumentation and was set to NaN (not a number) which can be handled by Matlab. Variant A (CC1-electrode at the earlobe) was chosen for subjects 1 - 12. Variant B (CC1-electrode at the forehead) was chosen for subjects 13 - 28.<br>
DOI: 10.6084/m9.figshare.5955748
title: Supplementary Material 2 from Analysis of wild macaque stone tools used to crack oil palm nuts

description: Dimensional and UAI data for all hammerstones studied
DOI: 10.6084/m9.figshare.5955748.v1
title: Supplementary Material 2 from Analysis of wild macaque stone tools used to crack oil palm nuts

description: Dimensional and UAI data for all hammerstones studied
DOI: 10.6084/m9.figshare.5955730
title: Supplementary Material for: Real-World Scenario Improvements in Serum Phosphorus Levels and Pill Burden in Peritoneal Dialysis Patients Treated with Sucroferric Oxyhydroxide

description: <b><i>Background:</i></b> A database analysis was conducted to assess the effectiveness of sucroferric oxyhydroxide (SO) on lowering serum phosphorus and phosphate binder (PB) pill burden among adult peritoneal dialysis (PD) patients prescribed SO as part of routine care. <b><i>Methods:</i></b> Adult PD patients (<i>n</i> = 258) prescribed SO through a renal pharmacy service were analyzed. Baseline was 3 months before SO prescription. SO-treated follow-up was for 6 months or until either a new PB was prescribed, SO was not refilled, PD modality changed, or patient was discharged. In-range serum phosphorus was defined as ≤5.5 mg/dL. <b><i>Results:</i></b> At baseline, mean serum phosphorus was 6.59 mg/dL with 10 prescribed PB pills/day. The proportion of patients achieving in-range serum phosphorus increased by 72% from baseline to month 6. Prescribed PB pills/day decreased by 57% (10 at baseline to 4.3 at SO follow-up, <i>p</i> &lt; 0.0001). The mean length of SO follow-up was 5.1 months; SO follow-up ended for 38, 27, and 50 patients at months 4, 5, and 6, respectively, due to no further PB fills, and for 10, 11, and 4 patients at months 4, 5, and 6, respectively, due to another PB prescribed. In patients with baseline serum phosphorus &gt;5.5 mg/dL who achieved in-range serum phosphorus during SO follow-up for ≥1 quarter, a notable improvement in serum phosphorus (6.54 to 5.10 mg/dL, <i>p</i> &lt; 0.0001) was observed, and there was a 53% reduction in PB pill burden (9.9 to 4.7, <i>p</i> &lt; 0.0001). <b><i>Conclusion:</i></b> Among PD patients prescribed SO as part of routine care, improvements in serum phosphorus control and &gt;50% reduction in PB pills/day were observed.
DOI: 10.5281/zenodo.4008356
title: COVID-19 Mobility Data Aggregator

description: <strong>Description</strong> This repository includes:<br> 1) Data scraper of Google, Apple and Waze Mobility data<br> 2) Preprocessed mobility reports in different formats<br> 3) Merged mobility reports in summary files <strong>About data</strong> About Google COVID-19 Community Mobility Reports About Apple COVID-19 Mobility Trends Reports About Waze COVID-19 local driving trends <strong>Description of data files</strong> <em><strong>Google reports (located in google_reports directory):</strong></em> The raw report in ZIP format: Global_Mobility_Report.zip<br> Data for the worldwide (only 1st level of subregions): mobility_report_countries (CSV and Excel formats available)<br> Data for Brazil: mobility_report_brazil (CSV and Excel formats available)<br> Data for Europe: mobility_report_europe (CSV and Excel formats available)<br> Data for Asia + Africa: mobility_report_asia_africa (CSV and Excel formats available)<br> Data for North and South America + Oceania (Brazil and US excluded): mobility_report_america_oceania (CSV and Excel formats available) <em><strong>Apple reports (located in apple_reports directory):</strong></em> Raw report: applemobilitytrends.csv<br> Data for the worldwide: apple_mobility_report (Google Sheets, CSV and Excel formats available)<br> Data for the US: apple_mobility_report_US (CSV and Excel formats available) <em><strong>Waze reports (located in waze_reports directory):</strong></em> Raw CSV files: Waze_Country-Level_Data.csv, Waze_City-Level_Data.csv<br> Preprocessed report: waze_mobility (Google Sheets, CSV and Excel formats available) <em><strong>Summary reports (located in summary_reports directory)</strong></em> These are merged Apple and Google reports. Report by regions: summary_report_regions (CSV and Excel formats available)<br> Report by countries: summary_report_countries (Google Sheets, CSV and Excel formats available)<br> Report for the US: summary_report_US (CSV and Excel formats available) <strong>License</strong> See LICENSE.txt <strong>Credits</strong> If you use this dataset, please also cite the original data sources: 1. Google LLC <em>"Google COVID-19 Community Mobility Reports"</em>. https://www.google.com/covid19/mobility/ Accessed: &lt;date&gt; 2. Apple Inc. "<em>Apple COVID-19 Mobility Trends Reports"</em>. https://www.apple.com/covid19/mobility Accessed: &lt;date&gt; 3. Waze Ltd "<em>Waze COVID-19 Impact Dashboard". </em>https://www.waze.com/covid19 Accessed: &lt;date&gt;
DOI: 10.5281/zenodo.3977029
title: COVID-19 Mobility Data Aggregator

description: <strong>Description</strong> This repository includes:<br> 1) Data scraper of Google, Apple and Waze Mobility data<br> 2) Preprocessed mobility reports in different formats<br> 3) Merged mobility reports in summary files <strong>About data</strong> About Google COVID-19 Community Mobility Reports About Apple COVID-19 Mobility Trends Reports About Waze COVID-19 local driving trends <strong>Description of data files</strong> <em><strong>Google reports (located in google_reports directory):</strong></em> The raw report in ZIP format: Global_Mobility_Report.zip<br> Data for the worldwide (only 1st level of subregions): mobility_report_countries (CSV and Excel formats available)<br> Data for Brazil: mobility_report_brazil (CSV and Excel formats available)<br> Data for Europe: mobility_report_europe (CSV and Excel formats available)<br> Data for Asia + Africa: mobility_report_asia_africa (CSV and Excel formats available)<br> Data for North and South America + Oceania (Brazil and US excluded): mobility_report_america_oceania (CSV and Excel formats available) <em><strong>Apple reports (located in apple_reports directory):</strong></em> Raw report: applemobilitytrends.csv<br> Data for the worldwide: apple_mobility_report (Google Sheets, CSV and Excel formats available)<br> Data for the US: apple_mobility_report_US (CSV and Excel formats available) <em><strong>Waze reports (located in waze_reports directory):</strong></em> Raw CSV files: Waze_Country-Level_Data.csv, Waze_City-Level_Data.csv<br> Preprocessed report: waze_mobility (Google Sheets, CSV and Excel formats available) <em><strong>Summary reports (located in summary_reports directory)</strong></em> These are merged Apple and Google reports. Report by regions: summary_report_regions (CSV and Excel formats available)<br> Report by countries: summary_report_countries (Google Sheets, CSV and Excel formats available)<br> Report for the US: summary_report_US (CSV and Excel formats available) <strong>License</strong> See LICENSE.txt <strong>Credits</strong> If you use this dataset, please also cite the original data sources: 1. Google LLC <em>"Google COVID-19 Community Mobility Reports"</em>. https://www.google.com/covid19/mobility/ Accessed: &lt;date&gt; 2. Apple Inc. "<em>Apple COVID-19 Mobility Trends Reports"</em>. https://www.apple.com/covid19/mobility Accessed: &lt;date&gt; 3. Waze Ltd "<em>Waze COVID-19 Impact Dashboard". </em>https://www.waze.com/covid19 Accessed: &lt;date&gt;
DOI: 10.6084/m9.figshare.5955694
title: Supplementary_Data from Same length, different shapes: ants collectively choose a straight foraging path over a bent one

description: In socials insects, exploration is fundamental for the discovery of food resources and determines decision-making. We investigated how the interplay between the physical characteristics of the paths leading to food sources and the way it impacts the behaviour of individual ants affects their collective decisions. Colonies of different sizes of <i>Lasius niger</i> had access to two equal food sources through two paths of equal length but of different geometries: one was straight between the nest and the food source, and the other involved an abrupt change of direction at the midway point (135°). Both the food sources were discovered simultaneously, but the food source at the end of the straight path was preferentially exploited by ants. Based on experimental and theoretical results, we show that a significantly shorter duration of nestbound travel on the straight path, which rapidly leads to a stronger pheromone trail, is at the origin of this preference.
DOI: 10.6084/m9.figshare.5955694.v1
title: Supplementary_Data from Same length, different shapes: ants collectively choose a straight foraging path over a bent one

description: In socials insects, exploration is fundamental for the discovery of food resources and determines decision-making. We investigated how the interplay between the physical characteristics of the paths leading to food sources and the way it impacts the behaviour of individual ants affects their collective decisions. Colonies of different sizes of <i>Lasius niger</i> had access to two equal food sources through two paths of equal length but of different geometries: one was straight between the nest and the food source, and the other involved an abrupt change of direction at the midway point (135°). Both the food sources were discovered simultaneously, but the food source at the end of the straight path was preferentially exploited by ants. Based on experimental and theoretical results, we show that a significantly shorter duration of nestbound travel on the straight path, which rapidly leads to a stronger pheromone trail, is at the origin of this preference.
DOI: 10.6084/m9.figshare.5955655
title: Paroedura_picta_gene.v1.gff

description: The gene annotations of the Madagascar ground gecko (<i>Paroedura picta</i>) genome.