cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8269721.v1
title: Blue whale home range shapefiles from: Spatial and temporal occurrence of blue whales off the U.S. West Coast, with implications for management.

description: This data repository contains an Arc Package for Esri ArcGIS software with shapefiles of home ranges estimated for 53 blue whales (Balaenoptera musculus) tracked with Argos satellite tags off the U.S. West Coast between 1994 and 2008. Home ranges were calculated with an LSCV kernel density estimator for tracks at least 30 d in duration as documented in Irvine et al 2014 (see reference link). The raw tracking data that was used to produce these home ranges are deposited as a Movebank Repository (Mate et al. 2019; see second reference link).<br>
DOI: 10.6084/m9.figshare.8269604
title: Predicting factors for disappearance of anti-mutated citrullinated vimentin antibodies in sera of patients with rheumatoid arthritis

description: <b>Objectives:</b> We aimed to determine the predicting factors for disappearance of anti-mutated citrullinated vimentin antibody (anti-MCV Ab) in sera from rheumatoid arthritis (RA) patients. <b>Methods:</b> In 2013, 95 RA patients whose Disease Activity Score with erythrocyte sedimentation rate were moderate to severe (DAS28-ESR ≥3.2) at baseline were enrolled. Titers of anti-MCV Ab and anti-cyclic citrullinated peptide (anti-CCP) Ab for 2013 and 2014 were measured. The association of anti-MCV disappearance with disease activity, treatment, interstitial lung disease (ILD), and serum markers of ILD were retrospectively examined. Predicting factors of anti-MCV disappearance were determined by multivariable analysis. <b>Results:</b> While anti-CCP positivity rate did not change during the year, anti-MCV Ab changed from positive to negative in 18 patients (=19.0%). Continuous biological disease-modifying anti-rheumatic drug use, prednisolone dose (≥5.0 mg daily), and low KL-6 level (&lt;191 U/mL) were determined as predicting factors of anti-MCV disappearance by multivariable analysis. In our cohort, anti-MCV Ab disappearance was not linked to clinical and radiological improvement. <b>Conclusion:</b> Different from anti-CCP Ab, anti-MCV Ab in sera from RA patients can disappear in a year. Some predicting factors for such negative seroconversion were found, whereas clinical significance of anti-MCV Ab disappearance was undetermined.
DOI: 10.6084/m9.figshare.8269598
title: Isotopic markers indicate that foraging on landfills may favour carotenoid-based coloration and reproductive investment in Yellow-legged gulls

description: <i>δ</i><sup>13</sup>C and <i>δ</i><sup>15</sup>N isotope signatures<br>
DOI: 10.6084/m9.figshare.8269604.v1
title: Predicting factors for disappearance of anti-mutated citrullinated vimentin antibodies in sera of patients with rheumatoid arthritis

description: <b>Objectives:</b> We aimed to determine the predicting factors for disappearance of anti-mutated citrullinated vimentin antibody (anti-MCV Ab) in sera from rheumatoid arthritis (RA) patients. <b>Methods:</b> In 2013, 95 RA patients whose Disease Activity Score with erythrocyte sedimentation rate were moderate to severe (DAS28-ESR ≥3.2) at baseline were enrolled. Titers of anti-MCV Ab and anti-cyclic citrullinated peptide (anti-CCP) Ab for 2013 and 2014 were measured. The association of anti-MCV disappearance with disease activity, treatment, interstitial lung disease (ILD), and serum markers of ILD were retrospectively examined. Predicting factors of anti-MCV disappearance were determined by multivariable analysis. <b>Results:</b> While anti-CCP positivity rate did not change during the year, anti-MCV Ab changed from positive to negative in 18 patients (=19.0%). Continuous biological disease-modifying anti-rheumatic drug use, prednisolone dose (≥5.0 mg daily), and low KL-6 level (&lt;191 U/mL) were determined as predicting factors of anti-MCV disappearance by multivariable analysis. In our cohort, anti-MCV Ab disappearance was not linked to clinical and radiological improvement. <b>Conclusion:</b> Different from anti-CCP Ab, anti-MCV Ab in sera from RA patients can disappear in a year. Some predicting factors for such negative seroconversion were found, whereas clinical significance of anti-MCV Ab disappearance was undetermined.
DOI: 10.6084/m9.figshare.8269598.v1
title: Isotopic markers indicate that foraging on landfills may favour carotenoid-based coloration and reproductive investment in Yellow-legged gulls

description: <i>δ</i><sup>13</sup>C and <i>δ</i><sup>15</sup>N isotope signatures<br>
DOI: 10.6084/m9.figshare.8269388
title: Forestry bird assemblages in Europe

description: Forest bird community point count data. Point counts are from native oak forests and conifer plantations in Ireland, France and Portugal.
DOI: 10.6084/m9.figshare.8269388.v1
title: Forestry bird assemblages in Europe

description: Forest bird community point count data. Point counts are from native oak forests and conifer plantations in Ireland, France and Portugal.
DOI: 10.6084/m9.figshare.8268989
title: Data and R code for "False memory for pictorial scripted material: the role of distinctiveness and negative emotion"

description: Dataset and R code for the statistical analysis of the manuscript titled "False memory for pictorial scripted material: the role of distinctiveness and negative emotion"
DOI: 10.6084/m9.figshare.8268791
title: Processed Data Required for the Associated Scripts

description: Processed data required for implementation of scrips in File S1, S3 and S4 associated with the collection Bacterial community shifts in streams receiving treated wastewater effluent
DOI: 10.6084/m9.figshare.8268791.v1
title: Processed Data Required for the Associated Scripts

description: Processed data required for implementation of scrips in File S1, S3 and S4 associated with the collection Bacterial community shifts in streams receiving treated wastewater effluent
DOI: 10.6084/m9.figshare.8268704
title: File S4: code for SeqENV Analysis

description: Code required to implement SeqENV Analysis.
DOI: 10.6084/m9.figshare.8268704.v1
title: File S4: code for SeqENV Analysis

description: Code required to implement SeqENV Analysis.
DOI: 10.6084/m9.figshare.8268674
title: Study data from Developmental plasticity of cardiac anoxia-tolerance in juvenile common snapping turtles (<i>Chelydra serpentina</i>)

description: His file contains the data used to create the figures and tables
DOI: 10.6084/m9.figshare.8268674.v1
title: Study data from Developmental plasticity of cardiac anoxia-tolerance in juvenile common snapping turtles (<i>Chelydra serpentina</i>)

description: His file contains the data used to create the figures and tables
DOI: 10.6084/m9.figshare.8268599
title: File S3: Processing the 16S Data using Phyloseq for the Amplicon Sequencing Variants Version.

description: Processing the 16S Data using Phyloseq for the Amplicon Sequencing Variants Version.
DOI: 10.6084/m9.figshare.8268569
title: File S1: Processing the 16S Data using Phyloseq

description: Code for processing the 16S Data using Phyloseq.
DOI: 10.6084/m9.figshare.8268569.v1
title: File S1: Processing the 16S Data using Phyloseq

description: Code for processing the 16S Data using Phyloseq.
DOI: 10.22023/mdx.8268548
title: Piper .pdf

description: This project is part of Ceres Artists in Residence at The Museum of Domestic Design & Architecture (MoDA). The aim of the residency was to use objects from MoDA's collection as a starting point for exploration of natural prints and dyes with the aim of raising the awareness of sustainability in design research.<b><br></b><b><br></b><b>Piper design</b><br>One-colour repeat, with overprinting and papercut out details. This design produced by Lara Mantell <br> Piper is my response to the work of the designer John Piper; in particular a piece of fabric called Stones of Bath, manufactured by Arthur Sanderson & Sons Ltd. I was captivated by the depth of colour, the intensity of the pattern, and the abstract qualities of the design. My design originated from drawings, collaged textures and mark-making. I made this into a one-colour repeat, that was further embellished by over-printing using cut-paper stencils. The images show the design printed in three different colourways, onto hemp-silk and wool, and silk.<br>Far left fabric:Silk-hemp: Red onion, Brazilwood, Chlorophyllin, Indigo, Buckthorn, Iron, and Madder. Middle fabric:Silk: Red onion, Iron, Brazilwood, Soda Ash, Buckthorn, Indigo, and Chlorophyllin. Far right fabric:Wool: Red onion, Brazilwood, Chlorophyllin, and Soda Ash. The design is printed, steamed to fix the dye-pastes, and washed by hand.After steaming and washing out the dye colours change in brightness and intensity. All fabric was mordanted prior to the print process. All the print pastes were made using combinations of bio-waste and plant extracts.
DOI: 10.22023/mdx.8268548.v1
title: Piper .pdf

description: This project is part of Ceres Artists in Residence at The Museum of Domestic Design & Architecture (MoDA). The aim of the residency was to use objects from MoDA's collection as a starting point for exploration of natural prints and dyes with the aim of raising the awareness of sustainability in design research.<b><br></b><b><br></b><b>Piper design</b><br>One-colour repeat, with overprinting and papercut out details. This design produced by Lara Mantell <br> Piper is my response to the work of the designer John Piper; in particular a piece of fabric called Stones of Bath, manufactured by Arthur Sanderson & Sons Ltd. I was captivated by the depth of colour, the intensity of the pattern, and the abstract qualities of the design. My design originated from drawings, collaged textures and mark-making. I made this into a one-colour repeat, that was further embellished by over-printing using cut-paper stencils. The images show the design printed in three different colourways, onto hemp-silk and wool, and silk.<br>Far left fabric:Silk-hemp: Red onion, Brazilwood, Chlorophyllin, Indigo, Buckthorn, Iron, and Madder. Middle fabric:Silk: Red onion, Iron, Brazilwood, Soda Ash, Buckthorn, Indigo, and Chlorophyllin. Far right fabric:Wool: Red onion, Brazilwood, Chlorophyllin, and Soda Ash. The design is printed, steamed to fix the dye-pastes, and washed by hand.After steaming and washing out the dye colours change in brightness and intensity. All fabric was mordanted prior to the print process. All the print pastes were made using combinations of bio-waste and plant extracts.
DOI: 10.6084/m9.figshare.8268530
title: Mechanism of resistance to acyclovir in thymidine kinase mutants from Herpes simplex virus type 1: a computational approach

description: Herpes simplex virus type 1 (HSV-1) infections affect about two-thirds of the world population, and the standard treatment consists of acyclovir (ACV) and its analogs, which interact with thymidine kinase (TK) blocking viral replication. Lately, the emergence of ACV-resistant strains has been reported, especially associated with TK mutations. In this context, ACV therapy fails against isolates encoding Y172C and Y53H/R163H TK mutants, but the molecular mechanism of drug resistance remains unclear. Thus, we examined the effects of these mutations on ACV and the cofactor ATP binding through molecular modeling approaches. We showed that Y172C prevents the anchoring of the aromatic ring of ACV through π–π stacking interactions, leading to an inversed binding mode and different interactions. On the other hand, Y53H/R163H remarkably affected the cofactor binding mode which shifted away from its binding site and also influenced the interaction network of ACV. This is likely due to the loss of polar interactions with R163 residue. Unlike what was observed in the wild-type complex, both drug and cofactor binding poses were not well positioned to allow the phosphorylation reaction which explains the resistance observed. Moreover, energy analysis corroborated the experimental data and showed lower theoretical affinity of ACV with mutant enzymes resulted from energetic loss in polar solvation in Y172C and electrostatic terms in Y53H/R163H mutant enzyme. Therefore, our study shed light on the resistance mechanism toward ACV of two mutant TKs identified in clinical HSV-1 strains and may further support the development of new anti-herpetic drugs to treat resistant infections. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8268530.v2
title: Mechanism of resistance to acyclovir in thymidine kinase mutants from Herpes simplex virus type 1: a computational approach

description: Herpes simplex virus type 1 (HSV-1) infections affect about two-thirds of the world population, and the standard treatment consists of acyclovir (ACV) and its analogs, which interact with thymidine kinase (TK) blocking viral replication. Lately, the emergence of ACV-resistant strains has been reported, especially associated with TK mutations. In this context, ACV therapy fails against isolates encoding Y172C and Y53H/R163H TK mutants, but the molecular mechanism of drug resistance remains unclear. Thus, we examined the effects of these mutations on ACV and the cofactor ATP binding through molecular modeling approaches. We showed that Y172C prevents the anchoring of the aromatic ring of ACV through π–π stacking interactions, leading to an inversed binding mode and different interactions. On the other hand, Y53H/R163H remarkably affected the cofactor binding mode which shifted away from its binding site and also influenced the interaction network of ACV. This is likely due to the loss of polar interactions with R163 residue. Unlike what was observed in the wild-type complex, both drug and cofactor binding poses were not well positioned to allow the phosphorylation reaction which explains the resistance observed. Moreover, energy analysis corroborated the experimental data and showed lower theoretical affinity of ACV with mutant enzymes resulted from energetic loss in polar solvation in Y172C and electrostatic terms in Y53H/R163H mutant enzyme. Therefore, our study shed light on the resistance mechanism toward ACV of two mutant TKs identified in clinical HSV-1 strains and may further support the development of new anti-herpetic drugs to treat resistant infections. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8268530.v1
title: Mechanism of resistance to acyclovir in thymidine kinase mutants from Herpes simplex virus type 1: a computational approach

description: Herpes simplex virus type 1 (HSV-1) infections affect about two-thirds of the world population, and the standard treatment consists of acyclovir (ACV) and its analogs, which interact with thymidine kinase (TK) blocking viral replication. Lately, the emergence of ACV-resistant strains has been reported, especially associated with TK mutations. In this context, ACV therapy fails against isolates encoding Y172C and Y53H/R163H TK mutants, but the molecular mechanism of drug resistance remains unclear. Thus, we examined the effects of these mutations on ACV and the cofactor ATP binding through molecular modeling approaches. We showed that Y172C prevents the anchoring of the aromatic ring of ACV through π–π stacking interactions, leading to an inversed binding mode and different interactions. On the other hand, Y53H/R163H remarkably affected the cofactor binding mode which shifted away from its binding site and also influenced the interaction network of ACV. This is likely due to the loss of polar interactions with R163 residue. Unlike what was observed in the wild-type complex, both drug and cofactor binding poses were not well positioned to allow the phosphorylation reaction which explains the resistance observed. Moreover, energy analysis corroborated the experimental data and showed lower theoretical affinity of ACV with mutant enzymes resulted from energetic loss in polar solvation in Y172C and electrostatic terms in Y53H/R163H mutant enzyme. Therefore, our study shed light on the resistance mechanism toward ACV of two mutant TKs identified in clinical HSV-1 strains and may further support the development of new anti-herpetic drugs to treat resistant infections. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8268407
title: Clinical response to fecal microbiota transplantation in patients with diarrhea-predominant irritable bowel syndrome is associated with normalization of fecal microbiota composition and short-chain fatty acid levels

description: <b>Objectives:</b> Irritable bowel syndrome (IBS) may be associated with disturbances in gut microbiota composition and functions. We recently performed a study of fecal microbiota transplantation (FMT) in diarrhea-predominant IBS (IBS-D) and found that IBS symptoms improved and the gut microbiota profile changed following FMT. We now aimed to explore the effects of FMT on the gut microenvironment in further detail by using 16S rRNA sequencing for more extended microbiota profiling and analyzing bacterial fermentation products (SCFAs: short chain fatty acids). <b>Materials and methods:</b> The study included 13 patients (four females and nine males) with IBS-D according to Rome III criteria and 13 healthy donors. Freshly donated feces were administered into duodenum via gastroscopy. The patients completed symptom and quality of life (QoL) questionnaires and delivered feces before and 1, 3, 12 and 20/28 weeks after FMT. Microbiota analysis was performed by sequencing 16S rRNA gene with Illumina Miseq technology. Fecal concentrations of SCFAs were analyzed by vacuum distillation followed by gas chromatography. <b>Results:</b> Several gut microbiota taxa and SCFAs were significantly different in the patients at baseline compared to their donors. These differences normalized by the third week following FMT in parallel with significant improvement in symptoms and QoL. Responders had different gut microbiota profile and SCFAs than nonresponders. Significant correlations were found between the gut microenvironment and IBS symptoms. No adverse effects were reported. <b>Conclusions:</b> FMT restores alterations of the gut microenvironment in IBS-D patients during the first 3 weeks and improves their symptoms for up to 28 weeks. <b>ClinicalTrials.gov ID:</b> NCT03333291. <b>Trial registration:</b>ClinicalTrials.gov identifier: NCT03333291.
DOI: 10.6084/m9.figshare.8268407.v2
title: Clinical response to fecal microbiota transplantation in patients with diarrhea-predominant irritable bowel syndrome is associated with normalization of fecal microbiota composition and short-chain fatty acid levels

description: <b>Objectives:</b> Irritable bowel syndrome (IBS) may be associated with disturbances in gut microbiota composition and functions. We recently performed a study of fecal microbiota transplantation (FMT) in diarrhea-predominant IBS (IBS-D) and found that IBS symptoms improved and the gut microbiota profile changed following FMT. We now aimed to explore the effects of FMT on the gut microenvironment in further detail by using 16S rRNA sequencing for more extended microbiota profiling and analyzing bacterial fermentation products (SCFAs: short chain fatty acids). <b>Materials and methods:</b> The study included 13 patients (four females and nine males) with IBS-D according to Rome III criteria and 13 healthy donors. Freshly donated feces were administered into duodenum via gastroscopy. The patients completed symptom and quality of life (QoL) questionnaires and delivered feces before and 1, 3, 12 and 20/28 weeks after FMT. Microbiota analysis was performed by sequencing 16S rRNA gene with Illumina Miseq technology. Fecal concentrations of SCFAs were analyzed by vacuum distillation followed by gas chromatography. <b>Results:</b> Several gut microbiota taxa and SCFAs were significantly different in the patients at baseline compared to their donors. These differences normalized by the third week following FMT in parallel with significant improvement in symptoms and QoL. Responders had different gut microbiota profile and SCFAs than nonresponders. Significant correlations were found between the gut microenvironment and IBS symptoms. No adverse effects were reported. <b>Conclusions:</b> FMT restores alterations of the gut microenvironment in IBS-D patients during the first 3 weeks and improves their symptoms for up to 28 weeks. <b>ClinicalTrials.gov ID:</b> NCT03333291. <b>Trial registration:</b>ClinicalTrials.gov identifier: NCT03333291.
DOI: 10.6084/m9.figshare.8268407.v1
title: Clinical response to fecal microbiota transplantation in patients with diarrhea-predominant irritable bowel syndrome is associated with normalization of fecal microbiota composition and short-chain fatty acid levels

description: <b>Objectives:</b> Irritable bowel syndrome (IBS) may be associated with disturbances in gut microbiota composition and functions. We recently performed a study of fecal microbiota transplantation (FMT) in diarrhea-predominant IBS (IBS-D) and found that IBS symptoms improved and the gut microbiota profile changed following FMT. We now aimed to explore the effects of FMT on the gut microenvironment in further detail by using 16S rRNA sequencing for more extended microbiota profiling and analyzing bacterial fermentation products (SCFAs: short chain fatty acids). <b>Materials and methods:</b> The study included 13 patients (four females and nine males) with IBS-D according to Rome III criteria and 13 healthy donors. Freshly donated feces were administered into duodenum via gastroscopy. The patients completed symptom and quality of life (QoL) questionnaires and delivered feces before and 1, 3, 12 and 20/28 weeks after FMT. Microbiota analysis was performed by sequencing 16S rRNA gene with Illumina Miseq technology. Fecal concentrations of SCFAs were analyzed by vacuum distillation followed by gas chromatography. <b>Results:</b> Several gut microbiota taxa and SCFAs were significantly different in the patients at baseline compared to their donors. These differences normalized by the third week following FMT in parallel with significant improvement in symptoms and QoL. Responders had different gut microbiota profile and SCFAs than nonresponders. Significant correlations were found between the gut microenvironment and IBS symptoms. No adverse effects were reported. <b>Conclusions:</b> FMT restores alterations of the gut microenvironment in IBS-D patients during the first 3 weeks and improves their symptoms for up to 28 weeks. <b>ClinicalTrials.gov ID:</b> NCT03333291.
DOI: 10.6084/m9.figshare.8268110
title: Earthquake catalogue of the network 3A.

description: Catalogue of the earthquakes of magnitude larger than 3.0 and distance less than 30km from Amatrice (Latitude 42.63, Longitude 13.29) recorded by the network 3A during the working period. The epicentral localization are given by the INGV web service, accessible from http://terremoti.ingv.it/en.
DOI: 10.6084/m9.figshare.8268110.v1
title: Earthquake catalogue of the network 3A.

description: Catalogue of the earthquakes of magnitude larger than 3.0 and distance less than 30km from Amatrice (Latitude 42.63, Longitude 13.29) recorded by the network 3A during the working period. The epicentral localization are given by the INGV web service, accessible from http://terremoti.ingv.it/en.
DOI: 10.6084/m9.figshare.8268020
title: ARIMA.zip

description: ARIMA and STI data for UAE climate
DOI: 10.6084/m9.figshare.8267984
title: Wave fetch GIS layer for Orkney at 22m resolution

description: This data layer gives values of summed wave fetch in 32 angular sectors around focal cells, using a model modified from that given in Burrows et al (2012 - see reference). Wave fetch is the distance to the nearest land in a defined direction. The model performs a three-scale search for land around each cell in the model, sparsely (every 4.4km) up to 200km, every 440m up to 20km away, and every 22m up to 220m distant. <br>Values represent the summed number of grid cells to the nearest land across all 32 11.5° sectors. The file is a GeoTIFF using the WGS84 UTM 30N projection.
DOI: 10.6084/m9.figshare.8268005
title: forecastARIMA.xlsx

description: data for STI and ARIMA assessment of UAE climate
DOI: 10.6084/m9.figshare.8268020.v1
title: ARIMA.zip

description: ARIMA and STI data for UAE climate