cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8180765.v1
title: Endoscopic biliary drainage in patients with cholangiocarcinoma – self-expanding metal <i>versus</i> polyethylene stents

description: <b>Background:</b> Endoscopic biliary drainage is the standard of care for patients with cholangiocarcinoma (CCA)-induced, obstructive jaundice. Self-expanding metal stents are supposed to be superior to polyethylene stents in terms of reduction of interventions and costs. So far, there are only few real-life data with respect to stent selection and survival in this patient cohort. <b>Methods:</b> In this study, we retrospectively analyzed patients with CCA treated with endoscopic biliary drainage from 2000 to 2015 at Hannover Medical School, Germany. The aim of this study was to analyze whether metal stenting reduces the frequency of interventions and influences survival in a large, real-life cohort. <b>Results:</b> Overall, 422 patients with CCA were included in this study. Indication for endoscopic biliary drainage was most often obstructive jaundice (<i>n</i> = 397; 94.1%). Among these patients, 20 patients (5%) were initially treated with a metal stent and 38 (9.6%) received a metal stent in the subsequent course. Median number of interventions per month was 2.4-fold reduced following metal stenting. Patients first treated with a metal stent had a more advanced tumor stage and a significantly shorter median overall survival (mOS) compared to patients who received a metal stent subsequently (7.5 months <i>vs</i>. 15.2 months; <i>p</i>=.019). There was no difference in mOS for metal <i>vs</i>. polyethylene stenting following a propensity score match for the confounders curative resection and chemotherapy (13.2 <i>vs</i>. 13.7 months, <i>p</i>=.555). <b>Conclusions:</b> Our data confirm that metal stenting reduces the frequency of interventions, but does not influence OS. Metal stenting should be considered specifically in younger patients who are suitable for chemotherapy.
DOI: 10.6084/m9.figshare.8180915
title: Small Sample Analysis of Modern Slavery Statements in Cocoa and Garment Sectors

description: In advance of fieldwork to examine what impact, if any, the relatively new Transparency in Supply Chain (TISC) requirement is having on working conditions in garment and cocoa sectors supply chains, where there are known issues around exploitation and child labour, a small sample analysis of 40 Modern Slavery Act statements produced in the UK garment and cocoa sectors was undertaken by the University of Liverpool Clothes, Chocolate and Children Project.
DOI: 10.6084/m9.figshare.8181917.v1
title: Training final year medical students in telephone communication and prioritization skills: An evaluation in the simulated environment

description: <b>Introduction:</b> Receiving clinical tasks via the telephone and correctly prioritizing job lists are integral to patient safety. However, structured training on these skills is currently lacking in many medical curriculums. This study evaluated the impact of telephone communication and prioritization training on the ability of final year medical students to carry out these skills during an on-call simulation. <b>Methods:</b> Twenty-five final year King’s College London medical students underwent a training session focused on telephone communication and task prioritization (group A). The performance of group A students in an on-call simulation involving these tasks was compared with twenty-five untrained final year students (group B). All participants completed a questionnaire about their training and/or simulation experience. <b>Results:</b> Group A compared to B students asked for more task-related information during each simulated call and correctly prioritized the resultant job list on significantly more occasions. Significantly more group A students reported being confident in answering calls and prioritizing their lists. The majority of students supported the addition of telephone communication and prioritization training into the medical curriculum. <b>Conclusions:</b> This study demonstrates the educational benefit of structured teaching on the ability of final year medical students to receive telephone handovers and prioritize job lists.
DOI: 10.6084/m9.figshare.8181587
title: Identification of promising anti-DNA gyrase antibacterial compounds using <i>de novo</i> design, molecular docking and molecular dynamics studies

description: The rapidly increasing rate of antibiotic resistance is of great concern. Approximately two million deaths result annually from bacterial infections worldwide. Therefore, there is a paramount requirement to develop innovative and novel antibacterial agents with new mechanisms of action and activity against resistant bacterial strains. For this purpose, a set of benzothiazole and <i>N</i>-phenylpyrrolamides derivatives reported as DNA Gyrase B (GyrB) inhibitors were collected from the literature and docked inside the receptor cavity of DNA Gyrase B (PDB ID: 5L3J). The best 10 docked complexes were used to identify novel antibacterial chemical agents through a <i>de novo</i> design approach. Out of initial 300 chemical analogues, the best six analogues were identified using screening with a set of criteria followed by pharmacokinetic analysis. The binding interactions of the best six analogues revealed that all molecules formed a number of critical interactions with catalytic amino residues of DNA Gyrase B with high binding energy. The predicted inhibitory constant biological activity based on binding energy supported the potential of the molecules as DNA Gyrase B ligands. The RMSD, RMSF, and radius of gyration parameters obtained from the 100 ns molecular dynamics simulation study clearly demonstrated that all six analogues were efficient enough to form stable complexes with DNA Gyrase B. High negative binding energy of all ligands obtained from MM-GBSA approach undoubtedly explained the strong affinity toward the DNA Gyrase B. Therefore, the proposed <i>de novo</i> designed molecules can be considered as promising antibacterial chemical agents subject to experimental validation, <i>in vitro</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8181701
title: Nematode 18S Alignment (Fig. 2A)

description: This is a multiple sequence alignment of 18S sequences.
DOI: 10.6084/m9.figshare.8175254.v1
title: Microclimatic variables influence the temporal dynamics of an anuran metacommunity in a non-stationary way

description: Understanding the temporal dynamics of communities is crucial to elucidate how communities respond to climate change. The activities of ectothermic vertebrates are sensitive to climatic variations due to their sensibility to temperature and humidity. However, the factors that affect the temporal dynamics of communities of terrestrial ectothermic vertebrate remain poorly known. Here, we tested how microclimatic variables influence anuran species composition and if species abundances are stable through time in a metacommunity in the Atlantic Forest of southern Brazil. Using a multivariate method, called STATICO, we described the stable patterns and the spatio-temporal changes of the relationship between species composition and the microclimatic variables. We found that species turnover showed an asynchronous spatial pattern, while species composition exhibited a non-stationary response to climate, which was mainly related to temperature, rainfall, and humidity during the spring and summer. These results suggest storage effect as the main coexistence mechanism at play in the metacommunity, in which the asynchronous fluctuations promote species coexistence under a scenario of environmental variability.<br><br>
DOI: 10.6084/m9.figshare.8186984
title: Differential requirements of protein geranylgeranylation for the virulence of human pathogenic fungi

description: Protein prenylation is a crucial post-translational modification largely mediated by two heterodimeric enzyme complexes, farnesyltransferase and geranylgeranyltransferase type-I (GGTase-I), each composed of a shared α-subunit and a unique β-subunit. GGTase-I enzymes are validated drug targets that contribute to virulence in <i>Cryptococcus neoformans</i> and to the yeast-to-hyphal transition in <i>Candida albicans</i>. Therefore, we sought to investigate the importance of the α-subunit, RamB, and the β-subunit, Cdc43, of the <i>A. fumigatus</i> GGTase-I complex to hyphal growth and virulence. Deletion of <i>cdc43</i> resulted in impaired hyphal morphogenesis and thermo-sensitivity, which was exacerbated during growth in rich media. The Δ<i>cdc43</i> mutant also displayed hypersensitivity to cell wall stress agents and to cell wall synthesis inhibitors, suggesting alterations of cell wall biosynthesis or stress signaling. In support of this, analyses of cell wall content revealed decreased amounts of β-glucan in the Δ<i>cdc43</i> strain. Despite strong <i>in vitro</i> phenotypes, the Δ<i>cdc43</i> mutant was fully virulent in two models of murine invasive aspergillosis, similar to the control strain. We further found that a strain expressing the α-subunit gene, <i>ramB</i>, from a tetracycline-inducible promoter was inviable under non-inducing <i>in vitro</i> growth conditions and was virtually avirulent in both mouse models. Lastly, virulence studies using <i>C. albicans</i> strains with tetracycline-repressible <i>RAM2</i> or <i>CDC43</i> expression revealed reduced pathogenicity associated with downregulation of either gene in a murine model of disseminated infection. Together, these findings indicate a differential requirement for protein geranylgeranylation for fungal virulence, and further inform the selection of specific prenyltransferases as promising antifungal drug targets for each pathogen.
DOI: 10.6084/m9.figshare.8186843.v1
title: Antimicrobial treatment of <i>Stenotrophomonas maltophilia</i> invasive infections: Systematic review

description: <i>Stenotrophomonas maltophilia</i> can cause serious infections in immunocompromised patients. The aim of this systematic review was to establish what invasive infections in humans are caused by <i>S. maltophilia</i> and to evaluate the optimal choice of antibiotics for their treatment. MEDLINE, EBSCO, SCOPUS, SCINDEKS and GOOGLE SCHOLAR were systematically searched for clinical trials, observational studies, case reports or case series describing invasive infections with <i>S. maltophilia</i> in patients of any age. <i>S. maltophilia</i> may cause invasive infections of various tissues in hospitalized patients. In the great majority of cases it was susceptible to co-trimoxazole, levofloxacin and ceftazidime. In about three fourths of the cases, the treatment was successful, while less than 20% of the patients died. <i>S. maltophilia</i> is increasingly associated with serious invasive infections in hospitalized patients and due to growing trend of resistance to almost all antibiotics requires a careful approach to patients who is harboring this bacterium.
DOI: 10.6084/m9.figshare.8187143.v1
title: The alignment and tree files of chloroplost genome

description: The alignment and tree files of supportting the  plastid genome phylogenetic analysis for the genus Camellia
DOI: 10.6084/m9.figshare.8186843
title: Antimicrobial treatment of <i>Stenotrophomonas maltophilia</i> invasive infections: Systematic review

description: <i>Stenotrophomonas maltophilia</i> can cause serious infections in immunocompromised patients. The aim of this systematic review was to establish what invasive infections in humans are caused by <i>S. maltophilia</i> and to evaluate the optimal choice of antibiotics for their treatment. MEDLINE, EBSCO, SCOPUS, SCINDEKS and GOOGLE SCHOLAR were systematically searched for clinical trials, observational studies, case reports or case series describing invasive infections with <i>S. maltophilia</i> in patients of any age. <i>S. maltophilia</i> may cause invasive infections of various tissues in hospitalized patients. In the great majority of cases it was susceptible to co-trimoxazole, levofloxacin and ceftazidime. In about three fourths of the cases, the treatment was successful, while less than 20% of the patients died. <i>S. maltophilia</i> is increasingly associated with serious invasive infections in hospitalized patients and due to growing trend of resistance to almost all antibiotics requires a careful approach to patients who is harboring this bacterium.
DOI: 10.6084/m9.figshare.8186978.v1
title: Phosphoproteomic and proteomic profiling of serine/threonine protein kinase PkaE of <i>Streptomyces coelicolor</i> A3(2) and its role in secondary metabolism and morphogenesis

description: This study aimed to investigate the role of serine/threonine kinase PkaE in <i>Streptomyces coelicolor</i> A3(2). Liquid chromatography tandem mass spectrometry was performed for comparative phosphoproteome and proteome analyses of <i>S. coelicolor</i> A3(2), followed by an <i>in vitro</i> phosphorylation assay. Actinorhodin production in the <i>pkaE</i> deletion mutant was lower than that in wild-type <i>S. coelicolor</i> A3(2), and the spores of the <i>pkaE</i> deletion mutant were damaged. Furthermore, phosphoproteome analysis revealed that 6 proteins were significantly differentially hypophosphorylated in <i>pkaE</i> deletion mutant (<i>p</i> in vitro phosphorylation assay revealed that PkaE phosphorylated FtsZ. Comparative proteome analysis revealed 362 differentially expressed proteins (<i>p</i> pkaE deletion mutant involved in actinorhodin biosynthesis. Gene ontology enrichment analysis revealed that PkaE participates in various biological and cellular processes. Hence, <i>S. coelicolor</i> PkaE participates in actinorhodin biosynthesis and morphogenesis. Liquid chromatography tandem mass spectrometry was performed for comparative phosphoproteome and proteome analyses of <i>S. coelicolor</i> A3(2) wild-type and <i>pkaE</i> deletion mutant, followed by an <i>in vitro</i> phosphorylation assay.
DOI: 10.6084/m9.figshare.8187035.v1
title: Differences in the fast muscle methylome provide insight into sex-specific epigenetic regulation of growth in Nile tilapia during early stages of domestication

description: Growth is a complex trait whose variability within a population cannot be explained solely by genetic variation. Epigenetic regulation is often suggested as an important factor shaping the phenotype, but its association with growth can be highly context- and species-dependent. Nevertheless, the mechanisms involved in epigenetic regulation of growth in fish are poorly understood. We have used reduced representation bisulphite sequencing to determine the genome-wide CpG methylation patterns in male and female Nile tilapia of different sizes but at the same early stage of domestication. The average CpG methylation level in the reduced genome representation was 63% across groups but many sites displayed group-specific methylation patterns. The number of differentially methylated (DM) CpGs was much higher when the interaction between sex and weight was included rather than when these factors were considered separately. There were 1128 DM CpGs between large and small females and 970 DM CpGs between large and small males. We have found many growth-related genes associated with DM CpGs, namely <i>map3k5</i> and <i>akt3</i> in females and <i>gadd45g</i> and <i>ppargc1a</i> in males. Only 5% of CpG locations associated with growth were common to both sexes. In particular, the autophagy-related gene <i>atg14</i> displayed a high association of methylation with growth exclusively in males. The sexually dimorphic association between <i>atg14</i> methylation and growth may uncover novel metabolic mechanisms at play during mouth brooding in Nile tilapia females. Taken together, our data suggest that epigenetic regulation of growth in Nile tilapia involves different gene networks in males and females.
DOI: 10.6084/m9.figshare.8187143
title: The alignment and tree files of chloroplost genome

description: The alignment and tree files of supportting the  plastid genome phylogenetic analysis for the genus Camellia
DOI: 10.6084/m9.figshare.8186978
title: Phosphoproteomic and proteomic profiling of serine/threonine protein kinase PkaE of <i>Streptomyces coelicolor</i> A3(2) and its role in secondary metabolism and morphogenesis

description: This study aimed to investigate the role of serine/threonine kinase PkaE in <i>Streptomyces coelicolor</i> A3(2). Liquid chromatography tandem mass spectrometry was performed for comparative phosphoproteome and proteome analyses of <i>S. coelicolor</i> A3(2), followed by an <i>in vitro</i> phosphorylation assay. Actinorhodin production in the <i>pkaE</i> deletion mutant was lower than that in wild-type <i>S. coelicolor</i> A3(2), and the spores of the <i>pkaE</i> deletion mutant were damaged. Furthermore, phosphoproteome analysis revealed that 6 proteins were significantly differentially hypophosphorylated in <i>pkaE</i> deletion mutant (<i>p</i> in vitro phosphorylation assay revealed that PkaE phosphorylated FtsZ. Comparative proteome analysis revealed 362 differentially expressed proteins (<i>p</i> pkaE deletion mutant involved in actinorhodin biosynthesis. Gene ontology enrichment analysis revealed that PkaE participates in various biological and cellular processes. Hence, <i>S. coelicolor</i> PkaE participates in actinorhodin biosynthesis and morphogenesis. Liquid chromatography tandem mass spectrometry was performed for comparative phosphoproteome and proteome analyses of <i>S. coelicolor</i> A3(2) wild-type and <i>pkaE</i> deletion mutant, followed by an <i>in vitro</i> phosphorylation assay.
DOI: 10.6084/m9.figshare.8186984.v1
title: Differential requirements of protein geranylgeranylation for the virulence of human pathogenic fungi

description: Protein prenylation is a crucial post-translational modification largely mediated by two heterodimeric enzyme complexes, farnesyltransferase and geranylgeranyltransferase type-I (GGTase-I), each composed of a shared α-subunit and a unique β-subunit. GGTase-I enzymes are validated drug targets that contribute to virulence in <i>Cryptococcus neoformans</i> and to the yeast-to-hyphal transition in <i>Candida albicans</i>. Therefore, we sought to investigate the importance of the α-subunit, RamB, and the β-subunit, Cdc43, of the <i>A. fumigatus</i> GGTase-I complex to hyphal growth and virulence. Deletion of <i>cdc43</i> resulted in impaired hyphal morphogenesis and thermo-sensitivity, which was exacerbated during growth in rich media. The Δ<i>cdc43</i> mutant also displayed hypersensitivity to cell wall stress agents and to cell wall synthesis inhibitors, suggesting alterations of cell wall biosynthesis or stress signaling. In support of this, analyses of cell wall content revealed decreased amounts of β-glucan in the Δ<i>cdc43</i> strain. Despite strong <i>in vitro</i> phenotypes, the Δ<i>cdc43</i> mutant was fully virulent in two models of murine invasive aspergillosis, similar to the control strain. We further found that a strain expressing the α-subunit gene, <i>ramB</i>, from a tetracycline-inducible promoter was inviable under non-inducing <i>in vitro</i> growth conditions and was virtually avirulent in both mouse models. Lastly, virulence studies using <i>C. albicans</i> strains with tetracycline-repressible <i>RAM2</i> or <i>CDC43</i> expression revealed reduced pathogenicity associated with downregulation of either gene in a murine model of disseminated infection. Together, these findings indicate a differential requirement for protein geranylgeranylation for fungal virulence, and further inform the selection of specific prenyltransferases as promising antifungal drug targets for each pathogen.
DOI: 10.6084/m9.figshare.8187035
title: Differences in the fast muscle methylome provide insight into sex-specific epigenetic regulation of growth in Nile tilapia during early stages of domestication

description: Growth is a complex trait whose variability within a population cannot be explained solely by genetic variation. Epigenetic regulation is often suggested as an important factor shaping the phenotype, but its association with growth can be highly context- and species-dependent. Nevertheless, the mechanisms involved in epigenetic regulation of growth in fish are poorly understood. We have used reduced representation bisulphite sequencing to determine the genome-wide CpG methylation patterns in male and female Nile tilapia of different sizes but at the same early stage of domestication. The average CpG methylation level in the reduced genome representation was 63% across groups but many sites displayed group-specific methylation patterns. The number of differentially methylated (DM) CpGs was much higher when the interaction between sex and weight was included rather than when these factors were considered separately. There were 1128 DM CpGs between large and small females and 970 DM CpGs between large and small males. We have found many growth-related genes associated with DM CpGs, namely <i>map3k5</i> and <i>akt3</i> in females and <i>gadd45g</i> and <i>ppargc1a</i> in males. Only 5% of CpG locations associated with growth were common to both sexes. In particular, the autophagy-related gene <i>atg14</i> displayed a high association of methylation with growth exclusively in males. The sexually dimorphic association between <i>atg14</i> methylation and growth may uncover novel metabolic mechanisms at play during mouth brooding in Nile tilapia females. Taken together, our data suggest that epigenetic regulation of growth in Nile tilapia involves different gene networks in males and females.
DOI: 10.6084/m9.figshare.8187047
title: Banerjee_Survey Dataset.zip

description: There were two separate surveys link for discrete collection of data from UK and non-UK registered healthcare professionals using Snap Surveys database (WebHost). Data were downloaded in .csv file format and imported in Microsoft Excel software for analysis, and then pooled together to calculate descriptive statistics.
DOI: 10.6084/m9.figshare.8187047.v1
title: Banerjee_Survey Dataset.zip

description: There were two separate surveys link for discrete collection of data from UK and non-UK registered healthcare professionals using Snap Surveys database (WebHost). Data were downloaded in .csv file format and imported in Microsoft Excel software for analysis, and then pooled together to calculate descriptive statistics.
DOI: 10.6084/m9.figshare.8187206
title: Alignment and tree files of the mitochondria genome

description: Alignment and tree files of the  Camellia genus mitochondria genome
DOI: 10.6084/m9.figshare.8187206.v1
title: Alignment and tree files of the mitochondria genome

description: Alignment and tree files of the  Camellia genus mitochondria genome