cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4470104
title: Gradients2-MGL1704-HPLC_2020-03-25_v1.0

description: Cruise: Gradients 2, MGL1704 Project Name: Simons Foundation Gradients 2 NPSG Description: Samples were processed to detect and quantify phytoplankton pigments using a modified version of the high-performance liquid chromatography (HPLC) method of Wright et al. (1991) as described by Bidigare et al. (2005). HPLC samples were collected by semi-automated and sequential filtration of the ship's underway flow through seawater onto Whatman GF/F filters (0.7 µm nominal pore size) and stored at -80°C until analysis. Filters were extracted in 100% acetone for 24 h at 4°C. Extracts were processed in reverse-phase on a 250 mm C18 column using a Waters separations module and photodiode detector array. Empower chromatography software was used for integration and pigment quantification. The instrument was calibrated using chlorophyll a from Anacystis nidulans (Sigma USA) and mixed pigment standards were obtained from DHI in Denmark.
DOI: 10.5281/zenodo.3735501
title: Gradients2-MGL1704-HPLC_2020-03-25_v1.0

description: Cruise: Gradients 2, MGL1704 Project Name: Simons Foundation Gradients 2 NPSG Description: Samples were processed to detect and quantify phytoplankton pigments using a modified version of the high-performance liquid chromatography (HPLC) method of Wright et al. (1991) as described by Bidigare et al. (2005). HPLC samples were collected by semi-automated and sequential filtration of the ship's underway flow through seawater onto Whatman GF/F filters (0.7 µm nominal pore size) and stored at -80°C until analysis. Filters were extracted in 100% acetone for 24 h at 4°C. Extracts were processed in reverse-phase on a 250 mm C18 column using a Waters separations module and photodiode detector array. Empower chromatography software was used for integration and pigment quantification. The instrument was calibrated using chlorophyll a from Anacystis nidulans (Sigma USA) and mixed pigment standards were obtained from DHI in Denmark.
DOI: 10.15785/sbgrid/817
title: 2-Oxo-acid Dehydrogenase Complex component proteins from C. thermophilum

description: Structural models of the E1 and E2 proteins of Pyruvate Dehydrogenase Complex (PDHc), 2-Oxoglutarate Dehydrogenase (OGDHc), and Branched-Chain alpha-Keto Acid Dehydrogenase Complex (BCKDHc), E3BP of PDHc and E3, shared among all three complexes. In addition, a cif-file of E1, E2, E3BP, and E3 of PDHc modeled from cryoEM data is provided. Models were generated by homology modeling using MODELLER and refined using HADDOCK webserver.
description: N/A
DOI: 10.5281/zenodo.4307459
title: Genetic and transcriptional contributions to relapse in acute myeloid leukemia

description: Raw data (Cellranger feature-barcode matrices) and assorted supplementary analysis for "Genetic and epigenetic contributions to relapse in acute myeloid leukemia." Each mutant cell is listed, along with the mutation it contains and read coverage spanning the mutant site.
DOI: 10.6084/m9.figshare.13646012
title: Internet-based cognitive behavioral therapy for tinnitus in the United States (ICBT US Study): A Randomized Clinical Trial

description: This data set was generated as a part of the clinical trial to examine the efficacy of the Internet-based cognitive behavioural therapy for tinnitus in the US population (Clinicaltrials.gov registration no NCT04004260). A prospective two-arm delayed intervention efficacy trial with a 2-month follow-up was implemented. Participants were randomized to the <i>Experimental group</i> (n=79) who received the ICBT intervention for 8-weeks, or the <i>Control group</i> (n=79) were monitored weekly during this 8-week period. During Phase I the experimental group completed the intervention. Following this, both groups completed T1 outcome measures. During Phase II, the control group underwent the same ICBT intervention while the experimental group had an 8 week waiting period. After the control group completed the intervention both groups were invited to complete T2 outcomes. <br>The attached documents include the dataset, demographic questionnaire and metadata which provide additional details about the dataset.
DOI: 10.5281/zenodo.4470108
title: Gradients 2 - MGL1704 - PCPN

description: Cruise: Gradients 2, MGL1704 Project Name: Simons Foundation Gradient NPSG The carbon and nitrogen content of particulate material (PC and PN) was collected from rosette niskin bottles at specific depths and filtered at low vacuum through a combusted glass fiber filter. Following filtration, filters were folded in half and placed in combusted aluminum foil and stored at -80°C for later analysis. Post-cruise, all filters were thawed and dried overnight at 60°C. Samples were then balled into Sn boats and plated for analysis. Organic carbon and total nitrogen content was analyzed using high-temperature combustion (1020 C) on a ThermoQuest NC 2500 elemental analyzer. Three standards with known %C and %N were weighed, folded in tin boats, and analyzed with the samples to develop the calibration equation for each run. The calibration equation was then used to calculate the mass (mg) of carbon and nitrogen in each sample using EAS Clarity Chromatography Station software. The standards are Cystine (Elemental Microanalysis, B2035, 11.66 %TN, 29.99 %TC), Atropine (Elemental Microanalysis, B2002, 4.84 %TN, 70.56%TC), and GoniLab Secondary Standard (low %C)-A1 (an internal standard of sediment from the Gulf of Mexico, MV0803, with low carbon - 0.12 %N, 1.3 %C).
DOI: 10.5281/zenodo.4470107
title: Gradients 2 - MGL1704 - PCPN

description: Cruise: Gradients 2, MGL1704 Project Name: Simons Foundation Gradient NPSG The carbon and nitrogen content of particulate material (PC and PN) was collected from rosette niskin bottles at specific depths and filtered at low vacuum through a combusted glass fiber filter. Following filtration, filters were folded in half and placed in combusted aluminum foil and stored at -80°C for later analysis. Post-cruise, all filters were thawed and dried overnight at 60°C. Samples were then balled into Sn boats and plated for analysis. Organic carbon and total nitrogen content was analyzed using high-temperature combustion (1020 C) on a ThermoQuest NC 2500 elemental analyzer. Three standards with known %C and %N were weighed, folded in tin boats, and analyzed with the samples to develop the calibration equation for each run. The calibration equation was then used to calculate the mass (mg) of carbon and nitrogen in each sample using EAS Clarity Chromatography Station software. The standards are Cystine (Elemental Microanalysis, B2035, 11.66 %TN, 29.99 %TC), Atropine (Elemental Microanalysis, B2002, 4.84 %TN, 70.56%TC), and GoniLab Secondary Standard (low %C)-A1 (an internal standard of sediment from the Gulf of Mexico, MV0803, with low carbon - 0.12 %N, 1.3 %C).
DOI: 10.5281/zenodo.3743881
title: Gradients2-MGL1704-PPPCPN-UW_2020-03-11_v1.0

description: Cruise: Gradients 2, MGL1704 Project Name: Simons Foundation Gradient NPSG, SCOPE The phosphorus content of particulate material (PP) was collected by semi-automated and sequential filtration of the ship’s underway flow through seawater onto acid-washed and combusted GFF filters. Select samples had a piggybacked GFF filter holder in sequence for collection of dissolved organic material and/or evaluation of trapping efficiency of GFF. Following filtration, filters were placed in histoprep capsules and stored at -80°C for later analysis. Post-cruise, all filters were thawed overnight, combusted at 450°C for 4.5 hours, then extracted with 0.15 M HCl for 1 hour at 60°C. PP was then analyzed spectrophotometrically as SRP in a 1.0 cm cell at 880 nm following Strickland and Parsons (1972). Recovery efficiency was assessed from the analysis of a known dry weight of certified reference material (National Institute of Standards, NIST 1515, apple leaves, certified 0.159% P by weight). The carbon and nitrogen content of particulate material (PC, PN) was collected by semi-automated and sequential filtration of the ship’s underway flow through seawater onto a combusted GFF filter. Select samples had a piggybacked GFF filter holder in sequence for collection of dissolved organic material and/or evaluation of trapping efficiency of GFF. Following filtration, filters were folded in half and placed in combusted aluminum foil and stored at -80°C for later analysis. Post-cruise, all filters were thawed, acidified, and dried overnight at 60°C. Samples were then balled into Ag and Sn boats and plated for analysis. Organic carbon and total nitrogen content was analyzed using high-temperature combustion (1020 C) on a ThermoQuest NC 2500 elemental analyzer. Three standards with known %C and %N were weighed, folded in tin boats, and analyzed with the samples to develop the calibration equation for each run. The calibration equation was then used to calculate the mass (mg) of carbon and nitrogen in each sample using EAS Clarity Chromatography Station software. The standards are Cystine (Elemental Microanalysis, B2035, 11.66 %TN, 29.99 %TC), Atropine (Elemental Microanalysis, B2002, 4.84 %TN, 70.56%TC), and GoniLab Secondary Standard (low %C)-A1 (an internal standard of sediment from the Gulf of Mexico, MV0803, with low carbon - 0.12 %N, 1.3 %C). The ship’s location, sea surface temperature and salinity from ship’s underway instrumentation are matched to the mid-point of each PCPN filtration time, and PP data were matched to the closest PCPN filtration. Samples were corrected for DOC/DON/DOP. Depth of 5m refers to the depth of the seawater intake on the R/V Marcus G. Langseth.
DOI: 10.6084/m9.figshare.13645889
title: Determinants of Insurance Companies’ Profitability in Montenegro

description: <b>Descriptions of columns:</b> f1 – Return on assets (ROA) (%) f2 – Insurer age f3 – Logarithm of insurer age f4 – Gross premium (€) f5 – Logarithm of gross premium f6 – Liquidity ratio f7 – Debt ratio f8 – Solvency margin (thousands of €) f9 – Logarith of solvency margin f10 – GDP (thousands of €) f11 – Logarithm of GDP f12 – Inflation rate (%) f13 – Loans interest rate (%) Data of ROA, insurer age, gross premium, liquidity and debt ratio are taken from the annual financial reports of insurance companies in Montenegro including the reports of the external auditor published by the Insurance Supervision Agency (http://www.ano.me/en/) Data of GDP and inflation rate are taken from the reports of Statistical Office of Montenegro MONSTAT (https://www.monstat.org/eng/index.php) Loans interest rate data are taken from the official macroeconomic (annual) reports of Central bank of Montenegro (https://www.cbcg.me/en)
DOI: 10.6084/m9.figshare.13645889.v1
title: Determinants of Insurance Companies’ Profitability in Montenegro

description: <b>Descriptions of columns:</b> f1 – Return on assets (ROA) (%) f2 – Insurer age f3 – Logarithm of insurer age f4 – Gross premium (€) f5 – Logarithm of gross premium f6 – Liquidity ratio f7 – Debt ratio f8 – Solvency margin (thousands of €) f9 – Logarith of solvency margin f10 – GDP (thousands of €) f11 – Logarithm of GDP f12 – Inflation rate (%) f13 – Loans interest rate (%) Data of ROA, insurer age, gross premium, liquidity and debt ratio are taken from the annual financial reports of insurance companies in Montenegro including the reports of the external auditor published by the Insurance Supervision Agency (http://www.ano.me/en/) Data of GDP and inflation rate are taken from the reports of Statistical Office of Montenegro MONSTAT (https://www.monstat.org/eng/index.php) Loans interest rate data are taken from the official macroeconomic (annual) reports of Central bank of Montenegro (https://www.cbcg.me/en)
DOI: 10.5281/zenodo.4470112
title: Gradients3-KM1906-15N13C_2020-03-25_v1.0

description: Cruise: Gradients 3, KM1906 Project Name: Simons Foundation, Gradient NPSG Dataset Description: Standard protocols were used to measure in vitro primary productivity via the 13C radiotracer method [Lengendre et al., 1996] and N2-fixation rate measurements via 15N2 isotopic gas method described by Montoya et al., 1996. Briefly, water samples were collected before dawn in 4.3L polycarbonate bottles, a total of 120ml of cold enriched 15N2 seawater was added via syringe by inserting bevline tubing to the bottom of the sample bottle and slowly injecting the volume while overflowing. Bottles were then sealed with caps fitted with septum and injected with 0.5ml of 47mM 13C bicarbonate stock and gently mixed by inversion. Bottles were incubated on deck in incubators screened to 48% of surface irradiance and plumbed with flow through surface seawater for temperature regulation. All bottles were incubated for ~ 24hr at 48% light level. Duplicate light bottles were paired with dark bottles and time final bottles that received no enrichment. Time zero bottles were also collected and sacrificed for each station. Following dawn to dawn incubations, each sample was filtered onto a combusted 25mm glass fiber filter, filters were folded in half and placed in combusted aluminum foil and stored at -80°C for later analysis. Post-cruise, all filters were thawed and dried overnight at 60°C. Samples were then balled into Sn boats and plated for analysis. The carbon and nitrogen isotopic composition (13C and 15N, respectively) were analyzed by continuous-flow isotope ratio mass spectrometry by the Stable Isotope Facility at UC Davis (https://stableisotopefacility.ucdavis.edu/13cand15n.html).
DOI: 10.5281/zenodo.3750387
title: Gradients3-KM1906-15N13C_2020-03-25_v1.0

description: Cruise: Gradients 3, KM1906 Project Name: Simons Foundation, Gradient NPSG Dataset Description: Standard protocols were used to measure in vitro primary productivity via the 13C radiotracer method [Lengendre et al., 1996] and N2-fixation rate measurements via 15N2 isotopic gas method described by Montoya et al., 1996. Briefly, water samples were collected before dawn in 4.3L polycarbonate bottles, a total of 120ml of cold enriched 15N2 seawater was added via syringe by inserting bevline tubing to the bottom of the sample bottle and slowly injecting the volume while overflowing. Bottles were then sealed with caps fitted with septum and injected with 0.5ml of 47mM 13C bicarbonate stock and gently mixed by inversion. Bottles were incubated on deck in incubators screened to 48% of surface irradiance and plumbed with flow through surface seawater for temperature regulation. All bottles were incubated for ~ 24hr at 48% light level. Duplicate light bottles were paired with dark bottles and time final bottles that received no enrichment. Time zero bottles were also collected and sacrificed for each station. Following dawn to dawn incubations, each sample was filtered onto a combusted 25mm glass fiber filter, filters were folded in half and placed in combusted aluminum foil and stored at -80°C for later analysis. Post-cruise, all filters were thawed and dried overnight at 60°C. Samples were then balled into Sn boats and plated for analysis. The carbon and nitrogen isotopic composition (13C and 15N, respectively) were analyzed by continuous-flow isotope ratio mass spectrometry by the Stable Isotope Facility at UC Davis (https://stableisotopefacility.ucdavis.edu/13cand15n.html).
DOI: 10.6084/m9.figshare.13635185.v1
title: Evaluation of Early Markers of Ischemia Reperfusion Injury and Preservation Solutions in a Hindlimb Model of Vascularized Composite Allotransplantation

description: These data includes1- Immunohistochemistry staining of cleaved caspase 3 in muscle, skin, vessel, nerve and bone.2- Immunohistochemistry staining of laminin in muscle, skin, vessel and nerve.3- Immunohistochemistry staining of CD31 in vessel.4- Quantification of TUNEL-positive cells in muscle, skin, vessel, nerve and bone.5- Quantification of HMGB1 concentration in muscle and skin.6- Quantification of TUNEL-positive cells in allogeneic group vs syngeneic group.
DOI: 10.6084/m9.figshare.13646108.v1
title: Experiment 1 LC/MS raw files

description: Experiment 1 LC/MS raw MS and MS/MS data output.
DOI: 10.6084/m9.figshare.13646108
title: Experiment 1 LC/MS raw files

description: Experiment 1 LC/MS raw MS and MS/MS data output.
DOI: 10.6084/m9.figshare.13646126
title: Experiment 2 LC/MS raw files

description: Experiment 2 LC/MS raw MS and MS/MS data output.
DOI: 10.6084/m9.figshare.13646126.v1
title: Experiment 2 LC/MS raw files

description: Experiment 2 LC/MS raw MS and MS/MS data output.
DOI: 10.6084/m9.figshare.12501461
title: Experiment 1 % coverage.xlsx

description: To determine how DEX treatment in WT and MKO mice leads to muscle atrophy, we measured muscle protein fractional synthesis rates using shot-gun LC-MS/MS analysis after <i>in vivo</i> <sup>2</sup>H<sub>2</sub>O labeling . Mice were treated with PBS or DEX for 10 days. During the final 7 days, mice were also labeled with <sup>2</sup>H<sub>2</sub>O. The sample size for wild type controls treated with PBS (WT-PBS, n=6), wild type treated with DEX (WT-DEX, n=6), MKO treated with PBS (MKO-PBS, n=5) and MKO treated with DEX (MKO-DEX, n=5). The rational for biological replicates of n=5 -6 were used to ensure accurate comparison among each group. Biological replicates were chosen to asses biological variability rather than sole reliance on technical replicates. Controls included WT-PBS treated mice (n=6). Two separate dynamic proteomic experiments were completed and combined for final data analysis. This consisted of experiment 1 that included WT-PBS (n=4) and WT-DEX (n=4). Experiment 2 included the final biological replicates of WT-PBS (n=2), WT-DEX (n=2), MKO-PBS (n=5) and MKO-DEX (n=5). The data sets were combined and annotated as described by the following.<br>Entry name, accession number, group number, sub group number, number of spectra, number of unique peptides, unique score, percent coverage, coverage map, total intensity, protein molecular weight, database, parent charge, score, sequence, chromatographic peak width, parent mass to charge ratio, delta parent mass and delta parent mass in ppm are shown. <br>
DOI: 10.6084/m9.figshare.12501461.v3
title: Experiment 1 % coverage.xlsx

description: To determine how DEX treatment in WT and MKO mice leads to muscle atrophy, we measured muscle protein fractional synthesis rates using shot-gun LC-MS/MS analysis after <i>in vivo</i> <sup>2</sup>H<sub>2</sub>O labeling . Mice were treated with PBS or DEX for 10 days. During the final 7 days, mice were also labeled with <sup>2</sup>H<sub>2</sub>O. The sample size for wild type controls treated with PBS (WT-PBS, n=6), wild type treated with DEX (WT-DEX, n=6), MKO treated with PBS (MKO-PBS, n=5) and MKO treated with DEX (MKO-DEX, n=5). The rational for biological replicates of n=5 -6 were used to ensure accurate comparison among each group. Biological replicates were chosen to asses biological variability rather than sole reliance on technical replicates. Controls included WT-PBS treated mice (n=6). Two separate dynamic proteomic experiments were completed and combined for final data analysis. This consisted of experiment 1 that included WT-PBS (n=4) and WT-DEX (n=4). Experiment 2 included the final biological replicates of WT-PBS (n=2), WT-DEX (n=2), MKO-PBS (n=5) and MKO-DEX (n=5). The data sets were combined and annotated as described by the following.<br>Entry name, accession number, group number, sub group number, number of spectra, number of unique peptides, unique score, percent coverage, coverage map, total intensity, protein molecular weight, database, parent charge, score, sequence, chromatographic peak width, parent mass to charge ratio, delta parent mass and delta parent mass in ppm are shown. <br>
DOI: 10.6084/m9.figshare.12501461.v2
title: Experiment 1 % coverage.xlsx

description: To determine how DEX treatment in WT and MKO mice leads to muscle atrophy, we measured muscle protein fractional synthesis rates using shot-gun LC-MS/MS analysis after <i>in vivo</i> <sup>2</sup>H<sub>2</sub>O labeling . Mice were treated with PBS or DEX for 10 days. During the final 7 days, mice were also labeled with <sup>2</sup>H<sub>2</sub>O. The sample size for wild type controls treated with PBS (WT-PBS, n=6), wild type treated with DEX (WT-DEX, n=6), MKO treated with PBS (MKO-PBS, n=5) and MKO treated with DEX (MKO-DEX, n=5). The rational for biological replicates of n=5 -6 were used to ensure accurate comparison among each group. Biological replicates were chosen to asses biological variability rather than sole reliance on technical replicates. Controls included WT-PBS treated mice (n=6). Two separate dynamic proteomic experiments were completed and combined for final data analysis. This consisted of experiment 1 that included WT-PBS (n=4) and WT-DEX (n=4). Experiment 2 included the final biological replicates of WT-PBS (n=2), WT-DEX (n=2), MKO-PBS (n=5) and MKO-DEX (n=5). The data sets were combined and annotated as described by the following.<br>Entry name, accession number, group number, sub group number, number of spectra, number of unique peptides, unique score, percent coverage, coverage map, total intensity, protein molecular weight, database, parent charge, score, sequence, chromatographic peak width, parent mass to charge ratio, delta parent mass and delta parent mass in ppm are shown. <br>
DOI: 10.5281/zenodo.4470126
title: Replication package for the paper "What do Developers Discuss about Code Comment Conventions"

description: <pre><code class="language-markdown"># RP-commenting-conventions-multiple-sources Replication Package for the paper "What do Developers Discuss about Code Comment Conventions?" ## Structure ``` Appendix.pdf RQ1/ LDA_input/ stackoverfow_raw_dataset.csv LDA_output/ Mallet/ output_csv/ docs-in-topics.csv topic-words.csv topics-in-docs.csv topics-metadata.csv output_html/ all_topics.html Docs/ Topics/ RQ2/ datasource_rawdata/ mailing_lists_selection_criteria.csv quora.csv stackoverflow.csv manual_analysis_output/ stackoverflow_quora_taxonomy.xlsx ``` ## Contents of the Replication Package --- - **Appendix.pdf**- Appendix of the paper containing supplement tables - **RQ1/** - contains the data used to answer RQ1 - **LDA_input/** - input data used for LDA analysis - `stackoverfow_raw_dataset.csv` - stackoverflow questions used to perform LDA analysis - **LDA_output/** - **Mallet/** - contains the LDA output generated by MALLET tool - **output_csv/** - `docs-in-topics.csv` - documents per topic - `topic-words.csv` - most relevant topic words - `topics-in-docs.csv` - topic probability per document - `topics-metadata.csv` - metadata per document and topic probability - **output_html/** - Browsable results of mallet output - `all_topics.html` - `Docs/` - `Topics/` - **RQ2/** - contains the data used to answer RQ2 - **datasource_rawdata/** - contains the raw data for each source - `mailing_lists_selection_criteria.csv` - criteria used to select mailing_lists. - `quora.csv` - contains the processed dataset (like removing HTML tags). To know more about the preprocessing steps, please refer to the reproducibility section in the paper. The data is preprocessed using [Makar](https://github.com/maethub/makar) tool. - `stackoverflow.csv` - contains the processed Stack Overflow dataset. To know more about the preprocessing steps, please refer to the reproducibility section in the paper. The data is preprocessed using [Makar](https://github.com/maethub/makar) tool. - **manual_analysis_output/** - `stackoverflow_quora_taxonomy.xlsx` - contains the classified dataset of Stack Overflow and quora and a description of taxonomy. - `Taxonomy` - contains the description of the first dimension and second dimension categories. Second dimension categories are further divided into levels, separated by `|` symbol. - `stackoverflow-posts` - the questions are labelled relevant or irrelevant and categorized into the first dimension and second dimension categories. - `quota-posts` - the questions are labelled relevant or irrelevant and categorized into the first dimension and second dimension categories. --- </code></pre>