cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5433145
title: Secondary ionization mass spectrometry. Age and petrogenesis of the Lundy granite: Paleocene intraplate peraluminous magmatism in the Bristol Channel, UK

description: Table S3. Secondary ionization mass spectrometry.
DOI: 10.6084/m9.figshare.5433148.v1
title: London Ambulance Service NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433154.v1
title: London North West Healthcare NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433139
title: Liverpool Heart and Chest NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433145.v1
title: Secondary ionization mass spectrometry. Age and petrogenesis of the Lundy granite: Paleocene intraplate peraluminous magmatism in the Bristol Channel, UK

description: Table S3. Secondary ionization mass spectrometry.
DOI: 10.6084/m9.figshare.5433130
title: Liverpool Community Health NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433130.v1
title: Liverpool Community Health NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433139.v1
title: Liverpool Heart and Chest NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433124
title: Lincolnshire Partnership NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433118
title: Lincolnshire Community Health Services NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433115
title: Lewisham and Greenwich NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433124.v1
title: Lincolnshire Partnership NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433115.v1
title: Lewisham and Greenwich NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433118.v1
title: Lincolnshire Community Health Services NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433112
title: Leicestershire Partnership NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433097
title: Leeds Teaching Hospitals NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433094
title: Leeds Community Healthcare NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433097.v1
title: Leeds Teaching Hospitals NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433112.v1
title: Leicestershire Partnership NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433061
title: Lancashire Care NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433076
title: Lancashire Teaching Hospitals NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.<br>
DOI: 10.6084/m9.figshare.5433076.v1
title: Lancashire Teaching Hospitals NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.<br>
DOI: 10.6084/m9.figshare.5433091
title: Leeds and York Partnership NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433094.v1
title: Leeds Community Healthcare NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433061.v1
title: Lancashire Care NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433091.v1
title: Leeds and York Partnership NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433031
title: L. infantum JPCM5

description: FASTQ files
DOI: 10.6084/m9.figshare.5433043
title: Kingston Hospital NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433043.v1
title: Kingston Hospital NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5433031.v1
title: L. infantum JPCM5

description: FASTQ files
DOI: 10.6084/m9.figshare.5432899
title: Probing the toxicity of nanoparticles: a unified <i>in silico</i> machine learning model based on perturbation theory

description: Nanoparticles (NPs) are part of our daily life, having a wide range of applications in engineering, physics, chemistry, and biomedicine. However, there are serious concerns regarding the harmful effects that NPs can cause to the different biological systems and their ecosystems. Toxicity testing is an essential step for assessing the potential risks of the NPs, but the experimental assays are often very expensive and usually too slow to flag the number of NPs that may cause adverse effects. <i>In silico</i> models centered on quantitative structure–activity/toxicity relationships (QSAR/QSTR) are alternative tools that have become valuable supports to risk assessment, rationalizing the search for safer NPs. In this work, we develop a unified QSTR-perturbation model based on artificial neural networks, aimed at simultaneously predicting general toxicity profiles of NPs under diverse experimental conditions. The model is derived from 54,371 NP-NP pair cases generated by applying the perturbation theory to a set of 260 unique NPs, and showed an accuracy higher than 97% in both training and validation sets. Physicochemical interpretation of the different descriptors in the model are additionally provided. The QSTR-perturbation model is then employed to predict the toxic effects of several NPs not included in the original dataset. The theoretical results obtained for this independent set are strongly consistent with the experimental evidence found in the literature, suggesting that the present QSTR-perturbation model can be viewed as a promising and reliable computational tool for probing the toxicity of NPs.
DOI: 10.6084/m9.figshare.5432869
title: Salinity responses of benthic diatoms inhabiting tidal flats

description: We performed culture experiments using intertidal benthic diatoms collected from a river mouth tidal flat (Fujimae Tidal Flats, Nagoya, Japan) to study their responses to salinity. The six species examined were <i>Navicula</i> aff. <i>erifuga, Karayevia amoena</i>, <i>Tryblionella apiculata</i>, <i>Planothidium delicatulum</i>, <i>Melosira moniliformis</i> var. <i>octogona,</i> and <i>Entomoneis japonica.</i> Clones were grown at ten salinity levels from 0 to 50 psu. Three species were unable to grow at low salinities (0 and 0.1 psu), but all were able to grow, though at a reduced rate, in hypersaline conditions (50 psu). All species had wider tolerance ranges than the salinity range of their original habitat (4–16 psu). Two species, <i>T. apiculata</i> and <i>K. amoena</i>, were essentially euryhaline, while the other four showed various constraints on their salinity response. Two species, <i>P. delicatulum</i> and <i>M. moniliformis</i> var. <i>octogona</i>, showed optimal growth outside the range of the salinities normally occurring in the environment from which they were isolated.
DOI: 10.6084/m9.figshare.5432869.v1
title: Salinity responses of benthic diatoms inhabiting tidal flats

description: We performed culture experiments using intertidal benthic diatoms collected from a river mouth tidal flat (Fujimae Tidal Flats, Nagoya, Japan) to study their responses to salinity. The six species examined were <i>Navicula</i> aff. <i>erifuga, Karayevia amoena</i>, <i>Tryblionella apiculata</i>, <i>Planothidium delicatulum</i>, <i>Melosira moniliformis</i> var. <i>octogona,</i> and <i>Entomoneis japonica.</i> Clones were grown at ten salinity levels from 0 to 50 psu. Three species were unable to grow at low salinities (0 and 0.1 psu), but all were able to grow, though at a reduced rate, in hypersaline conditions (50 psu). All species had wider tolerance ranges than the salinity range of their original habitat (4–16 psu). Two species, <i>T. apiculata</i> and <i>K. amoena</i>, were essentially euryhaline, while the other four showed various constraints on their salinity response. Two species, <i>P. delicatulum</i> and <i>M. moniliformis</i> var. <i>octogona</i>, showed optimal growth outside the range of the salinities normally occurring in the environment from which they were isolated.
DOI: 10.6084/m9.figshare.5432749
title: Amino acid residues critical for DNA binding and inducer recognition in CbnR, a LysR-type transcriptional regulator from <i>Cupriavidus necator</i> NH9

description: CbnR, a LysR-type transcriptional regulator from <i>Cupriavidus necator</i> NH9, activates the transcription of chlorocatechol-degradative enzymes. To activate the transcription, CbnR needs to bind not only to the <i>cbnA</i> promoter but also to the inducer. In this study, the transcriptional activity and DNA-binding activity of twenty-five mutants of CbnR were analyzed. Of the 17 mutants of the DNA-binding domain, 11 mutants lost their ability to activate transcription. While most mutants without transcriptional activation did not show DNA-binding activity, Asn17Ala, Gln29Ala, and Pro30Ala retained DNA-binding activity, suggesting that transcriptional activation by CbnR requires more than its binding to promoter DNA. Of the 8 mutants of the regulatory domain, 6 mutants changed their responses to the inducer, when compared with wild-type CbnR. Interestingly, Arg199Ala and Val246Ala induced constitutive expression of the <i>cbnA</i> promoter without the inducer, suggesting that these mutations brought about a conformational change mimicking that induced by the inducer molecule. Mutational analysis of a LysR-type transcriptional regulator, CbnR, revealed critical amino acids in regulatory domain (A and B) and DNA-binding domain (C and D).
DOI: 10.6084/m9.figshare.5432749.v1
title: Amino acid residues critical for DNA binding and inducer recognition in CbnR, a LysR-type transcriptional regulator from <i>Cupriavidus necator</i> NH9

description: CbnR, a LysR-type transcriptional regulator from <i>Cupriavidus necator</i> NH9, activates the transcription of chlorocatechol-degradative enzymes. To activate the transcription, CbnR needs to bind not only to the <i>cbnA</i> promoter but also to the inducer. In this study, the transcriptional activity and DNA-binding activity of twenty-five mutants of CbnR were analyzed. Of the 17 mutants of the DNA-binding domain, 11 mutants lost their ability to activate transcription. While most mutants without transcriptional activation did not show DNA-binding activity, Asn17Ala, Gln29Ala, and Pro30Ala retained DNA-binding activity, suggesting that transcriptional activation by CbnR requires more than its binding to promoter DNA. Of the 8 mutants of the regulatory domain, 6 mutants changed their responses to the inducer, when compared with wild-type CbnR. Interestingly, Arg199Ala and Val246Ala induced constitutive expression of the <i>cbnA</i> promoter without the inducer, suggesting that these mutations brought about a conformational change mimicking that induced by the inducer molecule. Mutational analysis of a LysR-type transcriptional regulator, CbnR, revealed critical amino acids in regulatory domain (A and B) and DNA-binding domain (C and D).
DOI: 10.6084/m9.figshare.5432746
title: Flavonoid compounds related to seed coat color of wheat

description: In red wheat, reddish-brown pigments accumulate in testa of mature seeds. Half-cut wheat seeds were immersed in <i>p</i>-dimethylaminocinnamaldehyde (DMACA) reagent that stains flavanol structures blue. Testa of 10–40 days after flowering (DAF) in red wheat (“Norin 61” and “Satonosora”) seeds were stained blue and the reagent color changed to blue with 10–25 DAF seeds. No blue staining was observed in white wheat (“Tamaizumi”) seeds during maturation. “Norin 61” seed coats at 10 DAF contained dihydroquercetin, dihydromyricetin, (+)-catechin, procyanidin B3, and prodelphinidin B3, which were identified by HPLC-diode array detector and LC-MS/MS analyses. These five components began accumulating 7 DAF, reached maxima at 10 or 15 DAF, and then decreased in red wheat seeds, but were not detected in white wheat seeds. These results suggest that flavanol and proanthocyanidins are possible precursors of the reddish-brown pigments of red wheat seeds, and are converted to insoluble compounds as the seeds mature. Dihydroflavonols, flavanol, and proanthocyanidin dimers accumulated in immature red wheat seeds, whose mature seed coat has reddish-brown pigments, but not in white wheat seeds.
DOI: 10.6084/m9.figshare.5432746.v1
title: Flavonoid compounds related to seed coat color of wheat

description: In red wheat, reddish-brown pigments accumulate in testa of mature seeds. Half-cut wheat seeds were immersed in <i>p</i>-dimethylaminocinnamaldehyde (DMACA) reagent that stains flavanol structures blue. Testa of 10–40 days after flowering (DAF) in red wheat (“Norin 61” and “Satonosora”) seeds were stained blue and the reagent color changed to blue with 10–25 DAF seeds. No blue staining was observed in white wheat (“Tamaizumi”) seeds during maturation. “Norin 61” seed coats at 10 DAF contained dihydroquercetin, dihydromyricetin, (+)-catechin, procyanidin B3, and prodelphinidin B3, which were identified by HPLC-diode array detector and LC-MS/MS analyses. These five components began accumulating 7 DAF, reached maxima at 10 or 15 DAF, and then decreased in red wheat seeds, but were not detected in white wheat seeds. These results suggest that flavanol and proanthocyanidins are possible precursors of the reddish-brown pigments of red wheat seeds, and are converted to insoluble compounds as the seeds mature. Dihydroflavonols, flavanol, and proanthocyanidin dimers accumulated in immature red wheat seeds, whose mature seed coat has reddish-brown pigments, but not in white wheat seeds.
DOI: 10.6084/m9.figshare.5432722
title: Calculating the Malliavin Derivative of some numerical models using the Malliavin Weight Sampling method

description: The Malliavin calculus suggests a methodology, called the Malliavin Weight Sampling method, for computing the derivative of an expected quantity of a stochastic system with respect to the parameters of its underlying stochastic variable. This repository shows how to apply this method to some problems found in classical mechanics, including problems solved using numerical methods like finite elements (FEniCS) and finite differences.<br>This code was used to generate the results in the paper:<br>Calculating the Malliavin derivative of some stochastic mechanics problems, Hauseux P, Hale JS, Bordas SPA (2017) PLOS ONE 12(12): e0189994 https://doi.org/10.1371/journal.pone.0189994<br><br>This repository is for archive purposes. Please see the bitbucket repository below for the latest version.
DOI: 10.6084/m9.figshare.5432737
title: Inhibition of phosphatidylinositide 3-kinase impairs the benzyl isothiocyanate-induced accumulation of autophagic molecules and Nrf2 in human colon cancer cells

description: The regulating role of phosphatidylinositide 3-kinase (PI3K) in benzyl isothiocyanate (BITC)-induced Nrf2 activation, contributing to the inducible expression of cytoprotective genes, was investigated. BITC significantly enhanced the accumulation of Nrf2 as well as autophagic molecules in human colorectal cancer HCT-116 cells. Experiments using a PI3K-specific inhibitor suggested that PI3K plays the key role in the non-canonical Nrf2 activation by BITC.
DOI: 10.6084/m9.figshare.5432737.v1
title: Inhibition of phosphatidylinositide 3-kinase impairs the benzyl isothiocyanate-induced accumulation of autophagic molecules and Nrf2 in human colon cancer cells

description: The regulating role of phosphatidylinositide 3-kinase (PI3K) in benzyl isothiocyanate (BITC)-induced Nrf2 activation, contributing to the inducible expression of cytoprotective genes, was investigated. BITC significantly enhanced the accumulation of Nrf2 as well as autophagic molecules in human colorectal cancer HCT-116 cells. Experiments using a PI3K-specific inhibitor suggested that PI3K plays the key role in the non-canonical Nrf2 activation by BITC.
DOI: 10.6084/m9.figshare.5432665
title: Biologic drugs in adult onset Still’s disease: a systematic review and meta-analysis of observational studies

description: <b>Background</b>: Biological drugs, mainly interleukin (IL)-1 and IL-6 antagonists, but also tumor necrosis factor (TNF) inhibitors, have been used in the treatment of adult onset Still’s disease patients (AOSD). <b>Methods</b>: We summarised the available evidence for the effectiveness of biologic drugs in AOSD. A systematic review of the literature was performed in order to identify all the available data concerning the effectiveness of biologic drugs in AOSD. The proportion of patients achieving complete remission or any clinical response was calculated. The meta-analysis was thus performed using a random-effects model accounting for the expected high level of heterogeneity. <b>Results</b>: Nineteen observational published studies were included in the meta-analysis. The pooled analysis under a random-effects model showed an overall rate of clinical response of 0.85 (95% CI: 0.77–0.91, p 2 = 68.23%). <b>Conclusions</b>: Our meta-analysis suggests that AOSD patients may experience a clinical response and/or a complete remission when treated with biologic drugs. Specifically designed and powered studies are needed to fully investigate the role of such medications in the management of AOSD patients.
DOI: 10.6084/m9.figshare.5432662
title: Augmentative and alternative communication practices: a descriptive study of the perceptions of South African speech-language therapists

description: Speech-language therapists (SLTs) have direct contact with a wide variety of individuals who require augmentative and alternative communication (AAC) and they are therefore considered to have a primary role in the assessment, selection, and implementation of AAC symbols, techniques, aids, and strategies. Limited information is available with regard to SLTs’ practices in the field of AAC, and there is a particular paucity of information about developing country contexts such as South Africa. The aim of this study was to determine how South African SLTs perceive their current AAC practices. Specifically, the study aimed to investigate SLTs’ assessment and intervention practices, their choice and use of graphic symbols, and display layouts for aided AAC systems. An online survey was developed, using the Qualtrics Research Suite™ online survey software. The survey included open-ended questions (analyzed using thematic analysis) and closed questions (analyzed using descriptive statistics). The responses indicated that SLTs in South Africa currently use a limited variety of assessment and intervention approaches. The data suggest that current practices are informed by previous experience with various technologies and AAC systems and that the primary caseloads of SLTs do not appear to inform specific approaches to assessment and AAC implementation.
DOI: 10.6084/m9.figshare.5432665.v1
title: Biologic drugs in adult onset Still’s disease: a systematic review and meta-analysis of observational studies

description: <b>Background</b>: Biological drugs, mainly interleukin (IL)-1 and IL-6 antagonists, but also tumor necrosis factor (TNF) inhibitors, have been used in the treatment of adult onset Still’s disease patients (AOSD). <b>Methods</b>: We summarised the available evidence for the effectiveness of biologic drugs in AOSD. A systematic review of the literature was performed in order to identify all the available data concerning the effectiveness of biologic drugs in AOSD. The proportion of patients achieving complete remission or any clinical response was calculated. The meta-analysis was thus performed using a random-effects model accounting for the expected high level of heterogeneity. <b>Results</b>: Nineteen observational published studies were included in the meta-analysis. The pooled analysis under a random-effects model showed an overall rate of clinical response of 0.85 (95% CI: 0.77–0.91, p 2 = 68.23%). <b>Conclusions</b>: Our meta-analysis suggests that AOSD patients may experience a clinical response and/or a complete remission when treated with biologic drugs. Specifically designed and powered studies are needed to fully investigate the role of such medications in the management of AOSD patients.
DOI: 10.6084/m9.figshare.5432662.v1
title: Augmentative and alternative communication practices: a descriptive study of the perceptions of South African speech-language therapists

description: Speech-language therapists (SLTs) have direct contact with a wide variety of individuals who require augmentative and alternative communication (AAC) and they are therefore considered to have a primary role in the assessment, selection, and implementation of AAC symbols, techniques, aids, and strategies. Limited information is available with regard to SLTs’ practices in the field of AAC, and there is a particular paucity of information about developing country contexts such as South Africa. The aim of this study was to determine how South African SLTs perceive their current AAC practices. Specifically, the study aimed to investigate SLTs’ assessment and intervention practices, their choice and use of graphic symbols, and display layouts for aided AAC systems. An online survey was developed, using the Qualtrics Research Suite™ online survey software. The survey included open-ended questions (analyzed using thematic analysis) and closed questions (analyzed using descriptive statistics). The responses indicated that SLTs in South Africa currently use a limited variety of assessment and intervention approaches. The data suggest that current practices are informed by previous experience with various technologies and AAC systems and that the primary caseloads of SLTs do not appear to inform specific approaches to assessment and AAC implementation.
DOI: 10.6084/m9.figshare.5432656
title: Correlations between Mendeley readers and Scopus citations for 323 narrow Scopus fields

description: An Excel spreadsheet of correlations between Mendeley readers and Scopus citations for 323 narrow Scopus fields for articles published in 2012, using reader count and citation count data from August/September 2017.Supporting material for the journal article, "Are Mendeley Reader Counts Useful Impact Indicators in all Fields?"