cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10000391.v1
title: Supplementary Material for: Adalimumab Dose Intensification in Recalcitrant Hidradenitis Suppurativa/Acne Inversa

description: <b><i>Background:</i></b> Adalimumab is the only approved compound for the treatment of adult patients with moderate-to-severe hidradenitis suppurativa (HS) who did not respond to a systemic classical treatment. Despite its significant short- and long-term efficacy, a percentage of patients do not respond sufficiently. Moreover, some primary responders experience a response loss with time. <b><i>Objective:</i></b> To analyse the effectiveness of adalimumab dose intensification in HS patients. <b><i>Methods:</i></b> A case series of adalimumab 80 mg/week subcutaneously (s.c.) compassionate use in patients with HS, who did not respond sufficiently or in primary responders with progressive response loss to the registered adalimumab dose of 40 mg/week s.c. Patients were collected and evaluated retrospectively. Patients’ data were extracted from medical records. <b><i>Results:</i></b> The 14 patients collected were Caucasian with HS of Hurley stage II–III and moderate or severe International HS Severity Score System (IHS4) stage. Adalimumab dose intensification significantly improved IHS4 score, Pain Index, HS-Physician Global Assessment, pain, and Cardiff Dermatology Life Quality Index. Two young female patients with HS and Crohn’s disease developed psoriatic lesions during the treatment with adalimumab 80 mg/week s.c. <b><i>Conclusion:</i></b> An enhanced level of effectiveness was assessed in the majority of the HS patients treated with adalimumab dose intensification (80 mg/week s.c.). Larger studies are required to evaluate this observation.
DOI: 10.6084/m9.figshare.10000349
title: Meteoric10Be_concentrations.xlsx

description: This data sheet contains new meteoric 10Be concentration data from marine sediment (biogenic muds) recovered during International Ocean Drilling Program Expedition 343 (JFAST) that help constrain the age, origin, and internal structure of the frontal prism at the Japan trench in the vicinity of the 2011 Tohoku-oki M9 earthquake rupture. Core data for IODO Expedition 343 can be fpound at http://sio7.jamstec.go.jp. Meteoric 10Be was extracted from sediment at the University of Vermont Cosmogenic laboratory in 2013. AMS measurements were made at the Scotish Universities Enviornmental Research Center (SUERC) in 2013. <br>
DOI: 10.6084/m9.figshare.10000352
title: Contrasting effects of land-use changes on herbivory and pollination networks

description: Data for plant community composition and plant–insect interactions (herbivory and pollination) in semi-natural grasslands on edges of rice fields in Japan.Species IDs in this dataset follow the supplemental information of the manuscript.
DOI: 10.6084/m9.figshare.10000382
title: Supplementary Material for: Post-Progression Treatment Eligibility of Unresectable Hepatocellular Carcinoma Patients Treated with Lenvatinib

description: <b><i>Background/Aim:</i></b> Post-progression treatment following tyrosine-kinase inhibitor (TKI) failure in patients with unresectable hepatocellular carcinoma (u-HCC) is important to prolong post-progression survival (PPS), which has a good correlation with overall survival (OS). This study aimed to elucidate the clinical features of progressive disease (PD) in patients treated with lenvatinib (LEN). <b><i>Materials/Methods:</i></b> From March 2018 to June 2019, 156 u-HCC patients with Child-Pugh A were enrolled (median age: 71 years, Child-Pugh score 5:6 = 105:51, BCLC A:B:C = 8:56:92, modified albumin-bilirubin grade (mALBI) 1:2a:2b = 59:42:55, past history of sorafenib:regorafenib = 57:17). Clinical features were retrospectively evaluated. <b><i>Results:</i></b> The median observation period was 8.5 months. Median OS was not obtained, while median time to decline to Child-Pugh B (CPB) was 11.4 months, median time to progression (TTP) was 8.4 months, and the period of LEN administration was 7.3 months. When we compared predictive values for time to decline to CPB based on Child-Pugh score and mALBI, values for Akaike information criterion (AIC) score and c-index of mALBI were superior as compared to Child-Pugh score (AIC: 592.3 vs. 599.7) (c-index: 0.655 vs. 0.597). Of the 73 patients with PD, 32 (43.8%) showed no decline to CPB or death. After excluding 3 without alpha-fetoprotein data at PD determination, only 14 (20.0%) of 70 showed REACH-2 eligibility. Non-mALBI 1/2a at the start of LEN was a significant risk factor for decline to CPB during LEN treatment (HR 2.552, 95% CI: 1.577–4.129; <i>p</i> &lt; 0.001). <b><i>Conclusion:</i></b> Introduction of TKI therapy including LEN for u-HCC patients with better hepatic function (mALBI 1/2a: ALBI score ≤–2.27), when possible, increases the chance of undergoing post-progression treatment, which can improve PPS.
DOI: 10.6084/m9.figshare.10000388.v1
title: Raw data Bioassays.xlsx

description: The data provided are insecticide bioassays using a series of transgenic An. gambiae mosquitoes overexpressing a number of metabolic resistance genes
DOI: 10.6084/m9.figshare.10000313
title: Data_Interactions.csv

description: Data for herbivory and pollination interactions between plant and insect species in semi-natural grasslands on edges of rice fields in Japan.Species IDs in this dataset follow the supplemental information of the manuscript.<br>
DOI: 10.6084/m9.figshare.10000349.v1
title: Meteoric10Be_concentrations.xlsx

description: This data sheet contains new meteoric 10Be concentration data from marine sediment (biogenic muds) recovered during International Ocean Drilling Program Expedition 343 (JFAST) that help constrain the age, origin, and internal structure of the frontal prism at the Japan trench in the vicinity of the 2011 Tohoku-oki M9 earthquake rupture. Core data for IODO Expedition 343 can be fpound at http://sio7.jamstec.go.jp. Meteoric 10Be was extracted from sediment at the University of Vermont Cosmogenic laboratory in 2013. AMS measurements were made at the Scotish Universities Enviornmental Research Center (SUERC) in 2013. <br>
DOI: 10.6084/m9.figshare.10000304
title: Validation of OpenGeoSys by Henry Saltwater Intrusion Problem

description: This is the dataset for modeling Henry Problem by OpenGeoSys
DOI: 10.6084/m9.figshare.10000313.v1
title: Data_Interactions.csv

description: Data for herbivory and pollination interactions between plant and insect species in semi-natural grasslands on edges of rice fields in Japan.Species IDs in this dataset follow the supplemental information of the manuscript.<br>
DOI: 10.6084/m9.figshare.10000301
title: Data_Plant_Composition.csv

description: Plant community composition data in semi-natural grasslands on edges of rice fields in Japan
DOI: 10.6084/m9.figshare.10000304.v1
title: Validation of OpenGeoSys by Henry Saltwater Intrusion Problem

description: This is the dataset for modeling Henry Problem by OpenGeoSys
DOI: 10.5281/zenodo.4001917
title: Dataset for "Atmospheric oxygen isotopic fractionation in clouds: a bin–resolved microphysics model approach"

description: This dataset contains the raw model outputs for the paper titled "Atmospheric oxygen isotopic fractionation in clouds: a bin–resolved microphysics model approach" by Thibault Hiron and Andrea Flossmann. The structure of the data and the explaination for the filenames are to be found in the ReadMe.txt file.
description: Research funded by Project AC-AHC2 grant number ANR-15-CE01-0015 of the French National Agency of Research (ANR).
DOI: 10.5281/zenodo.3479448
title: Dataset for "Atmospheric oxygen isotopic fractionation in clouds: a bin–resolved microphysics model approach"

description: This dataset contains the raw model outputs for the paper titled "Atmospheric oxygen isotopic fractionation in clouds: a bin–resolved microphysics model approach" by Thibault Hiron and Andrea Flossmann. The structure of the data and the explaination for the filenames are to be found in the ReadMe.txt file.
description: Research funded by Project AC-AHC2 grant number ANR-15-CE01-0015 of the French National Agency of Research (ANR).
DOI: 10.6084/m9.figshare.10000301.v1
title: Data_Plant_Composition.csv

description: Plant community composition data in semi-natural grasslands on edges of rice fields in Japan
DOI: 10.6084/m9.figshare.10000280.v1
title: Supplementtable_revised

description: Additional information of paper
DOI: 10.6084/m9.figshare.9999941
title: KIM_JGR_2019.zip

description: The executable MATLAB code used for estimating model calculation results (i.e., wave amplitude, wave normal angle, and plasmapause location), the data file for the solar wind parameters and geomagnetic indices used as model inputs, the coefficients, along with the minimum and maximum values for normalization procedure of input and output parameters, for each model of hiss waves, and the coefficients for the plasmapause location model
DOI: 10.6084/m9.figshare.9999887
title: Selected articles

description: This is the list of selected articles according to the inclusion and exclusion criteria defined in the paper.<br>
DOI: 10.6084/m9.figshare.9999941.v1
title: KIM_JGR_2019.zip

description: The executable MATLAB code used for estimating model calculation results (i.e., wave amplitude, wave normal angle, and plasmapause location), the data file for the solar wind parameters and geomagnetic indices used as model inputs, the coefficients, along with the minimum and maximum values for normalization procedure of input and output parameters, for each model of hiss waves, and the coefficients for the plasmapause location model
DOI: 10.6084/m9.figshare.9999863
title: railroads shapefile for Bray, CA

description: The contemporary railroads shapefile covered Bray, CA, downloaded from US census website.
DOI: 10.6084/m9.figshare.9999863.v2
title: railroads shapefile for Bray, CA

description: The contemporary railroads shapefile covered Bray, CA, downloaded from US census website.
DOI: 10.6084/m9.figshare.9999863.v1
title: Trans_RailFeature_clip_proj.dbf

description: The contemporary railroads shapefile covered Bray, CA, downloaded from US census website.
DOI: 10.6084/m9.figshare.9999887.v1
title: Selected articles

description: This is the list of selected articles according to the inclusion and exclusion criteria defined in the paper.<br>
DOI: 10.17608/k6.auckland.9999749
title: Publications making use of the Auckland Optotypes

description: A list of publications making use of the Auckland Optotypes
DOI: 10.6084/m9.figshare.9999740
title: CA_Bray_100414_2001_24000_geo.tif

description: The georeferenced USGS topographic historical map covered Bray, CA, circa 2001
DOI: 10.17608/k6.auckland.9999749.v1
title: Publications making use of the Auckland Optotypes

description: A list of publications making use of the Auckland Optotypes
DOI: 10.6084/m9.figshare.9999728
title: Treatment with commonly used antiretroviral drugs induces a type I/III interferon signature in the gut in the absence of HIV infection: ISG15 microscopy

description: The purpose of this data set was to measure how the expression of ISG15 in rectal and duodenal biopsies is affected by use of oral tenofovir disoproxil fumarate/emtricitabine for prevention of HIV infection. ISG15 expression was measured by immunofluorescence microscopy from samples taken from the ACTU3500 study at baseline and after two months of daily oral tenofovir disoproxil fumarate/emtricitabine.<br>The complete methods and results are described here: https://doi.org/10.1101/701961
DOI: 10.6084/m9.figshare.9999740.v1
title: CA_Bray_100414_2001_24000_geo.tif

description: The georeferenced USGS topographic historical map covered Bray, CA, circa 2001
DOI: 10.6084/m9.figshare.9999629
title: Data and analysis scripts for "Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow"

description: Phenotypic, genotype, and analysis scripts for "Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow"<br>Main growth analysis of the 5,051 seedlings can be reproduced by running the "04a-fit-full-model.R" script and loading the "full growth analysis.Rdata" dataset in R<br>Data for GEBV estimation with cross-validation not across families is contained within the directories in: run_642454_tmax_sum_dif_rgr_10fold_notacross_seed300.zip<br>Data for GEBV estimation with cross-validation across families is in: run_648224_tmax_sum_dif_rgr_10fold_acrossfams_seed300.zip<br>To reproduce the GEBV estimation and analysis, download the corresponding zip files that contains the R environment and datasets and use the "04d-analyze-models-cluster.R" script<br>"valley oak growth data - all seedlings.csv" contains the relative growth rates and relevant covariates for the 5,051 seedlings in an easy to read format<br>"gbs451_FIL-4_noLD.recode.vcf" contains the genotypes of each maternal tree in the study in VCF format<br><br>All data preparation and analysis scripts are available on Github: https://github.com/lukembrowne/Valley-oak-common-garden-growth-analysis<br><br><br><br>
DOI: 10.6084/m9.figshare.9999728.v2
title: Treatment with commonly used antiretroviral drugs induces a type I/III interferon signature in the gut in the absence of HIV infection: ISG15 microscopy

description: The purpose of this data set was to measure how the expression of ISG15 in rectal and duodenal biopsies is affected by use of oral tenofovir disoproxil fumarate/emtricitabine for prevention of HIV infection. ISG15 expression was measured by immunofluorescence microscopy from samples taken from the ACTU3500 study at baseline and after two months of daily oral tenofovir disoproxil fumarate/emtricitabine.<br>The complete methods and results are described here: https://doi.org/10.1101/701961
DOI: 10.6084/m9.figshare.9999431
title: A new approach for discriminating calcite and dolomite by ASTER imagery in arid and semi-arid regions

description: The supplementary zip file contains several files and folders. There is a pdf file inside the zip file which describes where each file can be found. <br>These data include, but are not limited to the following items:<br>- The ArcGIS shapefile (.shp) which shows the study area;<br>- The classification map produced by the mapping method introduced in the article for classifying carbonate rocks into dolomite and calcite in the study area (in shapefile format);<br>- A lithologic map of the study area (in shapefile format);<br>- The high-resolution spectra of rock samples collected during fieldwork (in ENVI spectral library format);<br>- A compilation of the spectral materials downloaded from ASTER spectral library (in ENVI spectral library format). These spectra include that of dolomite, calcite, limestone, dolostone, epidote, vegetation, shale, and soil.
DOI: 10.6084/m9.figshare.9999728.v1
title: ISG15_microscopy.xlsx

description: The purpose of this data set was to measure how the expression of ISG15 in rectal and duodenal biopsies is affected by use of oral tenofovir disoproxil fumarate/emtricitabine for prevention of HIV infection. ISG15 expression was measured by immunofluorescence microscopy from samples taken from the ACTU3500 study at baseline and after two months of daily oral tenofovir disoproxil fumarate/emtricitabine.<br>The complete methods and results are described here: https://www.biorxiv.org/content/10.1101/701961v1
DOI: 10.6084/m9.figshare.9998468
title: The complete IAS network

description: The Integrated Association Score (IAS) network from integrating 127 raw interaction networks of different data types (physical, co-mRNA expression, co-protein expression, co-dependence, sequence similarity), supervised by the annotation similarity (Resnik score) of the Gene Ontology.
DOI: 10.6084/m9.figshare.9999431.v1
title: A new approach for discriminating calcite and dolomite by ASTER imagery in arid and semi-arid regions

description: The supplementary zip file contains several files and folders. There is a pdf file inside the zip file which describes where each file can be found. <br>These data include, but are not limited to the following items:<br>- The ArcGIS shapefile (.shp) which shows the study area;<br>- The classification map produced by the mapping method introduced in the article for classifying carbonate rocks into dolomite and calcite in the study area (in shapefile format);<br>- A lithologic map of the study area (in shapefile format);<br>- The high-resolution spectra of rock samples collected during fieldwork (in ENVI spectral library format);<br>- A compilation of the spectral materials downloaded from ASTER spectral library (in ENVI spectral library format). These spectra include that of dolomite, calcite, limestone, dolostone, epidote, vegetation, shale, and soil.
DOI: 10.6084/m9.figshare.9997208
title: Supplementary_Tables.xlsx

description: Supplementary tables of Nespolo et al.<br>
DOI: 10.6084/m9.figshare.9997208.v1
title: Supplementary_Tables.xlsx

description: Supplementary tables of Nespolo et al.<br>
DOI: 10.6084/m9.figshare.9998468.v1
title: The complete IAS network

description: The Integrated Association Score (IAS) network from integrating 127 raw interaction networks of different data types (physical, co-mRNA expression, co-protein expression, co-dependence, sequence similarity), supervised by the annotation similarity (Resnik score) of the Gene Ontology.
DOI: 10.6084/m9.figshare.9998468.v3
title: The complete IAS network

description: The Integrated Association Score (IAS) network from integrating 127 raw interaction networks of different data types (physical, co-mRNA expression, co-protein expression, co-dependence, sequence similarity), supervised by the annotation similarity (Resnik score) of the Gene Ontology.
DOI: 10.6084/m9.figshare.9998468.v2
title: The complete IAS network

description: The Integrated Association Score (IAS) network from integrating 127 raw interaction networks of different data types (physical, co-mRNA expression, co-protein expression, co-dependence, sequence similarity), supervised by the annotation similarity (Resnik score) of the Gene Ontology.
DOI: 10.6084/m9.figshare.9996203
title: Performance enhancement and sample throughput increase of a multiresidue pesticides method in fruits and vegetables using Data-Dependent MS acquisition

description: Due to the growing number of analysed pesticide residues, analytical strategies have evolved for the data processing of 100s of pesticides in a single analysis. We present herein a LC-MS/MS method based on triple quadrupole technology capable of detecting concentrations at 5 ng/g and confirming 381 pesticides in a single injection. Confirmatory analysis is performed using data-dependent acquisition that compares full MS/MS spectra of candidates to a fast library interrogation within the same injection. A comparison on more than 200 samples of fruits and vegetables (representing principal types: normal, pigmented, and fatty) with pre-existing workflow based on single MRM analysis per compound was performed to validate this approach. A fast turnaround time was demonstrated due to more-unambiguous identification suppressing the need for reinjection to confirm candidates. The automated library searching and confirmation only of putative hits also allowed focusing on the manual verification and validation steps just for putative candidates which hence also increased overall throughput and results quality. Superior robustness of the method due partially to a reduced volume injected was also one of the key points achieved using this methodology. An interesting feature is also the capability to enrich the library and the number of pesticides screened with ease.
DOI: 10.6084/m9.figshare.9996146
title: Carbonyl compounds and furan derivatives with toxic potential evaluated in the brewing stages of craft beer

description: Carbonyl compounds and furan derivatives may form adducts with DNA and cause oxidative stress to human cells, which establishes the carcinogenic potential of these compounds. The occurrence of these compounds may vary according to the processing characteristics of the beer. The objective of this study was, for the first time, to investigate the free forms of target carbonyl compounds [acetaldehyde, acrolein, ethyl carbamate (EC) and formaldehyde] and furan derivatives [furfural and furfuryl alcohol (FA)] during the brewing stages of ale and lager craft beers. Samples were evaluated using headspace-solid phase microextraction and gas chromatography with mass spectrometric detection in selected ion monitoring mode (HS-SPME-GC/MS-SIM). Acetaldehyde, acrolein, formaldehyde and furfuryl alcohol were found in all brewing stages of both beer types, while EC and furfural concentrations were below the LOD and LOQ of the method (0.1 and 0.01 µg L<sup>−1</sup>, respectively). Boiling and fermentation of ale brewing seem to be important steps for the formation of acrolein and acetaldehyde, respectively, while boiling resulted in an increase of FA in both types of beer. Conversely, pasteurisation and maturation reduced the levels of these compounds in both types of beer. An increase in concentration of acrolein has not been verified in lager brew probably due to the difference in boiling time between these two types of beer (60 and 90 min for ale and lager, respectively).
DOI: 10.6084/m9.figshare.9996146.v1
title: Carbonyl compounds and furan derivatives with toxic potential evaluated in the brewing stages of craft beer

description: Carbonyl compounds and furan derivatives may form adducts with DNA and cause oxidative stress to human cells, which establishes the carcinogenic potential of these compounds. The occurrence of these compounds may vary according to the processing characteristics of the beer. The objective of this study was, for the first time, to investigate the free forms of target carbonyl compounds [acetaldehyde, acrolein, ethyl carbamate (EC) and formaldehyde] and furan derivatives [furfural and furfuryl alcohol (FA)] during the brewing stages of ale and lager craft beers. Samples were evaluated using headspace-solid phase microextraction and gas chromatography with mass spectrometric detection in selected ion monitoring mode (HS-SPME-GC/MS-SIM). Acetaldehyde, acrolein, formaldehyde and furfuryl alcohol were found in all brewing stages of both beer types, while EC and furfural concentrations were below the LOD and LOQ of the method (0.1 and 0.01 µg L<sup>−1</sup>, respectively). Boiling and fermentation of ale brewing seem to be important steps for the formation of acrolein and acetaldehyde, respectively, while boiling resulted in an increase of FA in both types of beer. Conversely, pasteurisation and maturation reduced the levels of these compounds in both types of beer. An increase in concentration of acrolein has not been verified in lager brew probably due to the difference in boiling time between these two types of beer (60 and 90 min for ale and lager, respectively).