cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/7cwf6mf33z.1
title: Metabolomic and Fluxomic data for: Control of redox potential in a novel continuous bioelectrochemical system led to remarkable metabolic and energetic responses of Clostridium pasteurianum grown on glycerol 

description: This data repository contains data and information in relation with the following scientific research paper:

Arbter P, Widderich N, Utesch T, Hong Y, Zeng AP. Control of redox potential in a novel continuous bioelectrochemical system led to remarkable metabolic and energetic responses of Clostridium pasteurianum grown on glycerol. Microbial Cell Factories (submitted).

The repository consists of three folders: the first folder contains the metabolomic data (displayed in Figure 3 of the paper). The second folder contains the results of the metabolic flux analysis (MFA, Figure 2) and the metabolic model. The metabolic model is given as the stoichiometric matrix, in .sbml format exported from CellNetAnalyzer, and also the model folder for import and use with the software. The MFA folder does also contain a short description of the model with explanations and additional references from literature. The third folder contains all files related to the symbolic metabolic control analysis (symMCA) and regulation analysis (RA, Figure 6).

The exact method for generation of the metabolomic data (sampling, extractions, and LC-MS/MS quantification) is described in detail in a previous paper:

Arbter P, Widderich N, Utesch T, Hong Y, Zeng AP. Metabolomic and kinetic investigations on the electricity-aided production of butanol by Clostridium pasteurianum strains. Eng Life Sci. 2021; 21: 181– 195. https://doi.org/10.1002/elsc.202000035
DOI: 10.4225/03/59ed402437518
title: Founders and Survivors: Life Course Ships Project

description: Dataset of 25,000 convicts who were transported to Van Diemen's Land (Tasmania) on 126 convict ships, 1812-1853. Contains around 100 variables on early life, crime and sentence, behaviour and punishment under sentence, family formation, post-sentence life, descendants, and date and details of death. Sources include convict records; birth, death and marriage registrations; census records; newspapers; police gazettes; and other administrative and historical sources. Part of the larger 'Founders and Survivors' Project.
DOI: 10.21338/ess6e02_4
title: ESS6 - integrated file, edition 2.4
DOI: 10.5281/zenodo.6618953
title: MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl2 part 1

description: MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl<sub>2</sub> part 1 (0-500ns) Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms), input files (.cfg, .msj, .cms), and other files For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl200_x-xns.tar.gz) Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectories are as 100 ns pieces for analysis since simulation did not equilibrate during 1000 ns. System: POPC bilayer in water Number of lipids: 200 (100/leaflet) Number of waters: 8880 Salt: CaCl<sub>2</sub> Concentration: 200 mM Number of cations: 32 Simulation time: 1000 ns (in this dataset 0-500ns) Simulation engine: Desmond 2019-4 Temperature: 300 K Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl<sub>2</sub> part 2
DOI: 10.23645/epacomptox.6062479.v4
title: ToxCast and Tox21 Summary Files

description: Data for a single chemical endpoint pair for thousands of chemicals and 821 assay endpoints for 20 variables such as the activity or hit call/activity concentrations/whether the chemical was tested in a specific assay/etc.
DOI: 10.5281/zenodo.1403225
title: Data For: Why Do Phylogenomic Analyses Of Early Animal Evolution Continue To Disagree? Sites In Different Structural Environments Yield Different Answers

description: Supporting data for "Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers" submitted by A Pandey and EL Braun. File is a gzipped tarball including protein multiple sequence alignments, phylogenetic trees, and other supporting data; see included README for details.
DOI: 10.5281/zenodo.6347982
title: MD simulation of POPC bilayer with OPLS3e force field, 100 mM CaCl2 part 2

description: MD simulation of POPC bilayer with OPLS3e force field, 100 mM CaCl<sub>2</sub> part 2 (500-1000ns) Dataset contains trajectories (_trj) for the last 500ns of the 1000ns trajectory, topology (-out.cms) and other files. For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl100_x-xns.tar.gz) System: POPC bilayer in water Number of lipids: 200 (100/leaflet) Number of waters: 8880 Salt: CaCl<sub>2</sub> Concentration: 100 mM Number of cations: 16 Simulation time: 1000 ns (in this dataset 500-1000ns) Simulation engine: Desmond 2019-4 Temperature: 300 K Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 100 mM CaCl<sub>2</sub> part 1
DOI: 10.5281/zenodo.6618982
title: MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl2 part 1

description: MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl<sub>2</sub> part 1 Dataset contains trajectories (_trj) for the first 500ns of the 1000ns trajectory, topology (-out.cms) and input files (.cfg, .msj, .cms). For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl500_x-xns.tar.gz) Dataset also contains Gromacs converted files (.xtc, .gro and .top). Converted trajectories are as 100 ns pieces for analysis since simulation did not equilibrate during 1000 ns. System: POPC bilayer in water Number of lipids: 200 (100/leaflet) Number of waters: 8880 Salt: CaCl<sub>2</sub> Concentration: 500 mM Number of cations: 80 Simulation time: 1000 ns (in this dataset 0-500ns) Simulation engine: Desmond 2019-4 Temperature: 300 K Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl<sub>2</sub> part 2
DOI: 10.5281/zenodo.6886226
title: Dataset for A Revision of the Formation Conditions of the Vredefort Crater.

description: Dataset associated with Allen et al. 2022 - <em>A Revision of the Formation Conditions of the Vredefort Crater. </em>Contained are all of our input asteroid.inp files, along with their associated material.inp file (the same of which was used for all of the simulations), the full jdata.dat file for our Model A, and a movie of our three discussed models over the full time of the simulation. All simulations were created using iSALE (https://isale-code.github.io/), and some python code showing potential visualization techniques for the data can be found at https://github.com/natalieallen/iSALE_scripts.
DOI: 10.1285/i1825229xv7n2p159
title: Phytoplankton composition in six Northern Scotland lagoons (Orkney Islands)

description: 1 - Transitional waters are ecotones between freshwater, marine and terrestrial ecosystems and include a number of different ecosystem types, one of which is constituted by lagoons.
2 - Lagoons are important patches in the coastal landscapes, which constitute for their ecological relevance a priority habitat (1150) in the EC Nature 2000 Directive.
3 - In the Northern part of Scotland and in the Scottish islands, lagoons are typical coastal ecosystems, while estuaries dominate the Southern Scottish coast.
4 - In this study, we investigate the phytoplankton communities in six Scottish lagoons in Orkney Islands (Kirwall, Ouse, Oyce of Isbister, Point of Backaquoy, Skaith and Loch of Stenness), describing their taxonomic composition and abundance.
5 - The taxonomic list consists of 9 phyla and 16 classes, including 160 taxa, which are evenly distributed among classes. Generally, the higher taxonomical abundance in the studied lagoons is reached by Bacillariophyceae, Chlorophyceae, Coscinodiscophyceae and Dinophyceae. The dominant groups among all the systems in terms of number of cells are: small undetermined phytoplankton and phytoflagellates, which are numerically abundant in all the six Scottish lagoons, Bacillariophyceae, Chlorophyceae, Coscinodiscophyceae, Cyanophyceae and Fragilariophyceae.
DOI: 10.5285/0779002b-b95d-432f-b035-b952c36aa5c9
title: Medium resolution vector contours for Antarctica

description: A continuous, smoothed contour dataset at 500 m intervals for all land south of 60S, excluding the Balleny Islands. The vertical datum of the contours is EGM2008. Contours are extracted primarily from the PGC Reference Elevation Model of Antarctica (REMA) v1.1 with certain islands filled from Copernicus WorldDEM. Peter I Oy contours are from the Norwegian Polar Institute. Sources of individual line segments are contained in the attribute table and full compilation information is given in the lineage statement.
description: All processing described here was performed in ArcGIS Pro version 2.6. A composite Digital Elevation Model (DEM) was created comprising of three datasets from the Reference Elevation Model of Antarctica v1.1: REMA_100m_peninsula_dem_filled, REMA_100m_dem and REMA_200m_dem_filled. These DEMs were first converted from ellipsoidal height to height above EGM2008 geoid and then mosaicked together in respective order at 100 m spatial resolution. This 100 m DEM was smoothed by performing Focal Statistics using a 40x40 cell size. 500 m contours were extracted and all contours with a height &lt;1m were deleted, as well as erroneous offshore contours. In certain locations, primarily some islands on the Antarctic Peninsula, REMA data was insufficient to produce contours. In these places, contours were produced from the 'Copernicus WorldDEM 90m' DEM and smoothed by 4 km using a PAEK smoothing algorithm. Contours for Peter I y were incorporated from the Norwegian Polar Institute Data at 100 m intervals: 500 m intervals were extracted and smoothed by 800 m, to match the appropriate resolution of the main contours. All contours were merged together and lines &lt;5 km in length were deleted. Further lines &lt;20 km were deleted in non-mountainous regions, so as to avoid deleting small mountain peak contours but to still simplify the main dataset. These regions were interpreted manually using the hillshade of the DEM used to produce the contours.
DOI: 10.6084/m9.figshare.20072687
title: Supplementary Material for: Conventional or drug-eluting beads? Randomized study of chemo-embolization for hepatocellular carcinoma: JIVROSG-1302

description: Introduction With the advent of effective systemic therapy, transarterial chemoembolization (TACE) is established as a highly effective locoregional treatment modality for carefully selected patients of hepatocellular carcinoma (HCC). This randomized controlled trial was conducted to clarify whether selective TACE with drug-eluting beads loaded with epirubicin (DEB-TACE) or selective conventional TACE with epirubicin-ethiodized oil (cTACE) might be more effective for obtaining complete response (CR) in patients with HCC. Methods Between March 2016 and May 2019, Child-Pugh class A or B patients with unresectable HCC who were scheduled to receive selective TACE were randomly assigned at a 1:1 ratio to the DEB-TACE arm or the cTACE arm. The primary endpoint was the CR rate at 3 months, as evaluated according to the modified Response Evaluation Criteria in Solid Tumors (mRECIST) by an independent review committee, and the secondary endpoints were the CR rate at 1 month and incidences of adverse events. Results A total of 200 patients (DEB-TACE, 99 patients; cTACE, 101 patients) were enrolled in the study. The CR rates at 3 months and 1 month were significantly higher in the cTACE arm (75.2%, 84.2%) as compared with the DEB-TACE arm (27.6%, 35.7%). However, the frequencies of adverse events of any grade, including pyrexia (DEB-TACE vs. cTACE, 19.4% vs. 45.5%, p=0.0001), fatigue (5.1% vs. 15.8%, p=0.0194), malaise (11.1% vs. 25.7%, p=0.0103), appetite loss (12.1% vs. 28.7%, p=0.0048), abdominal pain (12.1% vs. 23.8%, p=0.0423), increased serum bilirubin (22.2% vs. 48.5%, p=0.0002), hypoalbuminemia (43.4% vs. 60.3%, p=0.0154), increased serum aspartate aminotransferase (35.7% vs. 81.2%, p&lt;0.0001), and increased serum alanine aminotransferase (35.7% vs. 77.2%, p&lt;0.0001), were also significantly higher in the cTACE arm than in the DEB-TACE arm. Conclusions Selective cTACE appeared to have higher CR rates for local tumor control as compared to selective DEB-TACE for HCC. However, the frequency of post-embolization syndrome was also significantly higher in the cTACE group than in the DEB-TACE group. Thus, to achieve CR, cTACE may be selected over DEB-TACE in patients who can be expected to tolerate post-embolization syndrome.
DOI: 10.34740/kaggle/dsv/4038241
title: ALEV400P FINGERLINGS
DOI: 10.6084/m9.figshare.20067194
title: Supplementary Material for: Systemic treatments with tyrosine kinase inhibitor and platinum-based chemotherapy in patients with unresectable or metastatic hepatocholangiocarcinoma

description: Backgrounds and aims: Even if no systemic treatment is currently validated for unresectable hepato-cholangiocarcinoma (cHCC-CCA), tyrosine kinase inhibitors (TKI), and platinum-based chemotherapy are frequently used in clinical practice. Our study aims to describe the effectiveness of first-line systemic treatments in patients with cHCC-CCA. Patients and Methods: Patients with histological diagnosis of unresectable or metastatic cHCC-CCA confirmed by a centralized review (WHO classification 2019) and who received systemic treatment from 2009 to 2020 were included retrospectively in 11 centers. The outcomes of patients with cHCC-CCA were compared with patients with hepatocellular carcinoma (HCC) treated by sorafenib (n=117) and with intrahepatic cholangiocarcinoma (iCCA, n=94) treated mainly by platinum-based chemotherapy using a frailty Cox model. The efficacy of tyrosine kinase inhibitors and platinum-based chemotherapies in patients with cHCC-CCA was assessed using a doubly robust estimator. Results: A total of 83 patients with cHCC-CCA were included and were predominantly male (72%) with underlying cirrhosis (55%). 67% of patients had extrahepatic metastases and 31% macrovascular tumor invasion. cHCC-CCAs were more often developed on cirrhosis (55.4%) than iCCA (26.6%) but less frequently than HCC (80.2%)(p &lt;0.001). Both HCC (36.8% and cHCC-CCA (66.2%) had less frequent extrahepatic metastases than iCCA (81%)(P&lt;0.001). Unadjusted overall survival (OS) was better in iCCA (13 months) compared to cHCC-CCA (12 months) and HCC (11 months) (p=0.130). In multivariable analysis, after adjustment by a Cox frailty model, patients with cHCC-CCA had the same survival as HCC and iCCA (HR=0.67, CI95%:0.37-1.22, p=0.189 and HR=0.66, CI95%:0.43-1.02, p=0.064 respectively). ALBI score (HR=2.15; CI95%:1.23-3.76; p=0.009), ascites (HR=3.45, CI95%:1.31-9.03, p=0.013) and tobacco use (HR=2.29, CI95%:1.08-4.87, p=0.032) were independently associated with OS in cHCC-CCA. Among patients with cHCC-CCA, 25 patients treated with TKI were compared with 54 patients who received platinum-based chemotherapies. Patients treated with TKI had a median OS of 8.3 months compared to 11.9 months for patients treated with platinum-based chemotherapy (p=0.86). After a robust doubly adjustment on tumor number and size, vascular invasion, ALBI, MELD, and cirrhosis, the type of treatment did not impact OS (HR=0.92, 95%CI:0.27-3.15, p=0.88) or progression-free survival (HR=1.24, 95%CI:0.44-3.49, p=0.67). Conclusions: First-line systemic treatments with tyrosine kinase inhibitors or platinum-based chemotherapies have similar efficacy in patients with unresectable/metastatic cHCC-CCA. The ALBI score predicts overall survival.
DOI: 10.7910/dvn/lejuqz/1uoami
title: Codebook.pdf

description: Codebook
DOI: 10.17614/q4nf0v
title: [nitroso(phosphonomethyl)amino]acetic acid
DOI: 10.5066/f7w66jrh
title: Data release for results of societal exposure to California's volcanic hazards (ver. 3.0, November 2019)
DOI: 10.6084/m9.figshare.20191982
title: Supplementary Material for: Efficacy of Early Video Capsule Endoscopy for Acute Overt Lower Gastrointestinal Bleeding with Colonic Diverticulosis: A Prospective Observational Study

description: <b><i>Background/Aims:</i></b> Although most patients with presumptive colonic diverticular bleeding (CDB) do not undergo a small bowel investigation in clinical practice, no prospective study supports this management. We evaluated the utility of early small bowel capsule endoscopy (CE) after negative colonoscopy results. <b><i>Methods:</i></b> This prospective study evaluated the diagnostic yield of early small bowel CE (≤3 days from visit) for consecutive patients with acute-onset hematochezia, when colonoscopy found colonic diverticulosis but did not identify the definite bleeding source (<i>n</i> = 51; presumptive CDB). As a matched control for comparing clinical outcomes, presumptive CDB patients without CE (<i>n</i> = 51) were retrospectively extracted. <b><i>Results:</i></b> On CE for the prospective cohort, the rates of total positive findings, P2 findings (high bleeding potential according to the P classification), and blood pooling in the colon were 57%, 12% (ulceration, 8%; angioectasia, 4%), and 24%, respectively. The rates of rebleeding within 30 and 365 days were 16% and 29% in the prospective cohort with CE, respectively, and were not significantly different from those in the retrospective cohort without CE (10% and 25%, respectively). In addition, thromboembolism and mortality within 30 and 365 days were not significantly different between those with and without CE. <b><i>Conclusion:</i></b> Early CE detected a suspected small bowel bleeding source in 12% of acute-onset presumptive CDB patients but did not significantly improve major clinical outcomes. Therefore, routine CE is unnecessary for presumptive CDB patients after colonoscopy (UMIN000026676).
DOI: 10.6084/m9.figshare.20765755
title: Supplementary Material for: Mortality in a Multiethnic Population Attending a One-Stop TIA Clinic

description: <b><i>Introduction:</i></b> Studies indicate a 13–27% mortality rate following a transient ischaemic attack (TIA). However, outcomes following TIA/minor stroke since the introduction of rapid-access TIA clinics and prompt vascular risk factor intervention are not known. Specifically, there is paucity of data comparing outcomes between people who are diagnosed with an “acute cerebrovascular” (CV) event or an alternative non-cardiovascular diagnosis (non-CV) in a rapid-access TIA clinic. We aimed to assess the mortality in such a setting. <b><i>Methods:</i></b> A retrospective observational study was undertaken at the Leicester rapid-access secondary care TIA clinic. Data included information collected at the first clinic visit (including comorbidities, and primary diagnosis, categorized as CV and non-CV) and the date of death for people dying during follow-up. <b><i>Results:</i></b> 11,524 subjects were included with 33,164 years of follow-up data; 4,746 (41.2%) received a CV diagnosis. The median follow-up time was 2.75 years (interquartile range 1.36–4.32). The crude mortality rate was 37.3 (95% CI: 35.3–39.5) per 1,000 person-years (PTPY). The mortality rate was higher following a CV diagnosis (50.8 [47.2–54.7] PTPY) compared to a non-CV diagnosis (27.9 [25.7–30.4] PTPY), and for males, older people, those of white ethnicity, and people with orthostatic hypotension (OH). <b><i>Discussion:</i></b> This study identified possible risk factors associated with a higher mortality in TIA clinic attendees, who may benefit from specific intervention. Future research should explore the underlying causes and the effect of specific targeted management strategies.
DOI: 10.18112/openneuro.ds003639.v1.0.0
title: In-scanner head motion and structural covariance networks
DOI: 10.25318/3210035201-eng
title: Crushing statistics of major oilseeds

description: Data on the production of the crushing of seed, oil and meal.
DOI: 10.4121/uuid:29614991-345e-4ffd-be22-2930912a2798
title: Daily maxima of total water levels from the Global Tide and Surge Reanalysis (GTSR) dataset

description: GTSR (Global Tide and Surge Reanalysis) is the first global reanalysis of storm surges and extreme sea levels based on hydrodynamic modelling. GTSR covers the entire world's coastline and provides time-series of tides and storm surge from 1979-2014. Tides are simulated with FES2012, while storm surges are simulated by forcing the Global Tide and Surge Model (GTSM) with wind and pressure fields from ERA-Interim. In addition to timeseries, GTSR also provides estimates of extreme sea levels for various return period based on the Gumbel distribution
DOI: 10.5066/f76h4gpx
title: Annual estimates of suspended-sediment concentration and load to support trend analysis on the Mississippi River and Atchafalaya River, 1980-2015

description: This data release contains annual estimates of suspended-sediment concentration and load for the Mississippi River, St. Francisville site and the Atchafalaya River, Melville site from 1980-2015. Annual estimates and flow-normalized estimates were generated using the Weighted Regressions on Time, Season and Discharge (WRTDS) model. Input data for the model included suspended-sediment concentrations publicly available from the U.S. Geological Survey (USGS)'s National Water Information System (U.S. Geological Survey, 2016) and daily-mean streamflow estimates from the Army Corps of Engineers (2016) and USGS. These annual concentrations and loads are used to support trend analyses and provide estimates of sediment availability to the Gulf of Mexico. See companion publication for more details (Mize, S.V., Murphy, J.C., Diehl, T.H., and Demcheck, D.K., 2018, Suspended-sediment concentrations and loads in the lower Mississippi and Atchafalaya Rivers decreased by half between 1980 and 2015, Journal of Hydrology, In review). References U.S. Army Corp of Engineers, 2016, Water levels of Rivers and Lakes data available on the World Wide Web at RiverGages.com, accessed June 10, 2016, at URL http://rivergages.mvr.usace.army.mil U.S. Geological Survey, 2016, National Water Information SystemWeb interface, accessed November 8, 2017, at http://dx.doi.org/10.5066/F7P55KJN.