cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8174297.v1
title: Preliminary report on the genetic structure of <i>Glyphoglossus molossus</i> (Anura: Microhylidae) from the Khorat Plateau, north-eastern Thailand

description: <i>Glyphoglossus molossus</i>, is one of the most economically important amphibians in the Khorat Plateau, north-eastern Thailand. It is categorised as a near-threatened species by IUCN due to over-exploitation. Here, we examined the genetic structure of <i>G. molossus</i> using partial mitochondrial cytochrome-b gene sequences from specimens collected at 11 localities. The sequence analysis revealed the presence of 15 haplotypes, 5 of which are shared by 2 or more populations, and 10 haplotypes that are confined to a single population. The relatively low haplotype (<i>h</i>) and nucleotide (<i>π</i>) diversities suggest that the Phu Phan Mountain Range is not high enough to act as an effective dispersal barrier between the Sakon Nakhon and Khorat Basins. However, AMOVA and phylogenetic analyses based on Maximum likelihood (ML) and Bayesian inference (BI) strongly supported the presence of two genetically divergent clades, Sakon Nakhon Basin and the northern part of the Khorat Basin (clade A) and the southern part of the Khorat Basin (clade B). These two lineages are separated by substantial geographical distance, which has putatively resulted in a reduction of gene flow. Further studies, with more extensive genetic sampling, especially from throughout the species range will aid in better interpreting our results.
DOI: 10.6084/m9.figshare.8174558.v1
title: A simple and versatile authenticity assay of coffee products by single-nucleotide polymorphism genotyping

description: Interspecific single-nucleotide polymorphisms (SNPs) in the <i>rbcL</i> DNA barcode have been strictly validated and adopted as a designed SNP genotyping maker to discriminate between two major coffee species, <i>Coffea arabica</i> and <i>C. canephora</i>, and to estimate the mixing ratio of DNA from <i>C. arabica</i>/<i>C. canephora</i> in this study. The SNP genotyping is applicable to not only green (unroasted) coffee beans, but also processed coffee products (roasted coffee beans and instant coffee powder), in which genomic DNA is degraded, because the genotyping developed in this study requires only 10 copies of 63-bp-long DNA fragments of <i>rbcL</i> gene. The authenticity assay established in this study has several advantages: a high versatility to DNA sample conditions; simple and rapid procedures (only two steps; DNA extraction and SNP genotyping); the feasibility in coffee business for practical use to prevent false advertising and provide quality control. <b>Abbreviations:</b> SNP: single-nucleotide polymorphism; SBS: single base substitution; ISR: intergenic spacer region; INDEL: insertion-deletion. SNP Genotyping: Required only 10 copies of 63-bp-long DNA fragment of rbcL gene.
DOI: 10.6084/m9.figshare.8174588
title: Design and development of novel therapeutics for brucellosis treatment based on carbonic anhydrase inhibition

description: Carbonic anhydrase is a metalloprotein, an enzyme with strong inhibition in antibacterial treatment. This study presents QSAR modeling for a series of 41 chemical compounds, 40 sulfonamides and one sulfamate, including 13 clinically tested drugs as carbonic anhydrase inhibitors based on the Monte Carlo optimization with molecular descriptors based on the SMILES notation and local invariants of the molecular graph, and field 3D based methods. Conformation independent QSAR models were developed for three random splits and a 3D QSAR model for one random split into the training and test sets. The statistical quality of the developed models, including robustness and predictability, was tested using various statistical approaches and the results that were obtained were very good. An excellent correlation between the results from the conformation independent and the 3D QSAR model was obtained. A novel statistical metric known as <i>the index of ideality of correlation</i> was used for the final assessment of the model, and the obtained results were good. Molecular fragments responsible for the increases and decreases of a studied activity were defined and further used for the computer-aided design of new compounds as potential carbonic anhydrase inhibitors. Molecular docking was applied for the final assessment of the developed QSAR model and designed inhibitors, and an excellent correlation between the results from QSAR modeling and molecular docking studies was obtained. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8174588.v1
title: Design and development of novel therapeutics for brucellosis treatment based on carbonic anhydrase inhibition

description: Carbonic anhydrase is a metalloprotein, an enzyme with strong inhibition in antibacterial treatment. This study presents QSAR modeling for a series of 41 chemical compounds, 40 sulfonamides and one sulfamate, including 13 clinically tested drugs as carbonic anhydrase inhibitors based on the Monte Carlo optimization with molecular descriptors based on the SMILES notation and local invariants of the molecular graph, and field 3D based methods. Conformation independent QSAR models were developed for three random splits and a 3D QSAR model for one random split into the training and test sets. The statistical quality of the developed models, including robustness and predictability, was tested using various statistical approaches and the results that were obtained were very good. An excellent correlation between the results from the conformation independent and the 3D QSAR model was obtained. A novel statistical metric known as <i>the index of ideality of correlation</i> was used for the final assessment of the model, and the obtained results were good. Molecular fragments responsible for the increases and decreases of a studied activity were defined and further used for the computer-aided design of new compounds as potential carbonic anhydrase inhibitors. Molecular docking was applied for the final assessment of the developed QSAR model and designed inhibitors, and an excellent correlation between the results from QSAR modeling and molecular docking studies was obtained. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8174591
title: Nectar robbing does not affect female reproductive success of an endangered <i>Antirrhinum</i> species, Plantaginaceae

description: <b>Background:</b> Nectar robbers in many plant species affect female reproductive success, usually decreasing the amount of seed produced by plants, which can affect populations persistence. <b>Aims:</b> To evaluate the impact of nectar robbers on the viability of the populations, we investigated the effects of nectar robbing on the female reproductive success of a threatened snapdragon species in four populations over 2 years. <b>Methods:</b> We observed insect visitors and their behaviour and quantified the percentage of robbed and non-robbed flowers and the production of fruits and seeds. <b>Results:</b> The results showed the degree of variation in nectar robbing among the populations and between years within the populations. Nectar robbers were detected in only two populations, and all were <i>Bombus terrestris</i>. Differences in flower size among populations were not related to the nectar robbing behaviour of <i>B. terrestris</i>. A comparison of the percentage of fructification and seed production between flowers that were and were not robbed showed no evidence of a negative effect of nectar robbing. <b>Conclusions:</b> Our study reports for the first time on nectar robbing in <i>Antirrhinum</i> species and concludes that this does not affect the female reproductive success of individuals or the viability of <i>A. valentinum</i> populations.
DOI: 10.6084/m9.figshare.8174687
title: Transthyretin stabilization activity of the catechol-<i>O</i>-methyltransferase inhibitor tolcapone (SOM0226) in hereditary ATTR amyloidosis patients and asymptomatic carriers: proof-of-concept study<sup>#</sup>

description: <b>Objective:</b> To assess the transthyretin (TTR) stabilization activity of tolcapone (SOM0226) in patients with hereditary ATTR amyloidosis, asymptomatic carriers and healthy volunteers. <b>Methods:</b> A phase IIa proof-of-concept trial included two phases separated by a 6-week washout period. Phase A: single 200 mg dose of tolcapone; phase B: three 100 mg doses taken at 4 h intervals. The primary efficacy variable was TTR stabilization. <b>Results:</b> Seventeen subjects were included (wild type, <i>n</i> = 6; mutation TTR Val30Met, <i>n</i> = 11). TTR stabilization was observed in all participants. Two hours after dosing, 82% of participants in phase A and 93% of those in phase B reached a TTR stabilization value of at least 20%. In phase A, there was an increase of 52% in TTR stabilization vs baseline values 2 h after dosing, which decreased to 22.9% at 8 h. In phase B, there was a significant increase of 38.8% in TTR stabilization 2 h after the first 100 mg dose. This difference was maintained after 10 h and decreased after 24 h. No serious adverse events were observed. <b>Conclusions:</b> The ability of tolcapone for stabilizing TTR supports further development and repositioning of the drug for the treatment of ATTR amyloidosis. <b>Trial registration:</b> EudraCT identifier: 2014-001586-27 <b>Trial registration:</b>ClinicalTrials.gov identifier: NCT02191826.
DOI: 10.6084/m9.figshare.8175158
title: DataTrachemysScripta.csv

description: Data that includes the native and non-native (alien) ocurrence records for Trachemys scripta used in the study, our generated random points (bg), and all corresponding climatic variables values. BIO1: annual mean temperature, BIO10: mean temperature of the warmest quarter, BIO11: mean temperature of the coldest quarter, BIO12: annual precipitation, BIO14: precipitation of driest month, RAD: annual mean radiation, NearDist: Euclidian distance to the nearest freshwater body.
DOI: 10.6084/m9.figshare.8179136
title: Rocky shore community composition in Southern Chile.xls

description: The dataset describe the abundance of rocky-intertidal seaweeds and invertebrates measured between June and August 2012. The sites surveyed where Cheuque (39° 24' S, 73° 13' W), Calfuco (39° 47' S, 73° 23' W), and Pucatrihue (40° 32' S, 73° 42' W), on the Pacific coast in Chile. At each of the three sites, we randomly surveyed 50 cm x 50 cm quadrat spaced a few tens of cm from one another following the shoreline at both the low and high intertidal zones. For each quadrat, species abundance was quantified as percent cover for sessile taxa and density (individuals/m<sup>2</sup>) for mobile taxa.
DOI: 10.6084/m9.figshare.8179136.v1
title: Rocky shore community composition in Southern Chile.xls

description: The dataset describe the abundance of rocky-intertidal seaweeds and invertebrates measured between June and August 2012. The sites surveyed where Cheuque (39° 24' S, 73° 13' W), Calfuco (39° 47' S, 73° 23' W), and Pucatrihue (40° 32' S, 73° 42' W), on the Pacific coast in Chile. At each of the three sites, we randomly surveyed 50 cm x 50 cm quadrat spaced a few tens of cm from one another following the shoreline at both the low and high intertidal zones. For each quadrat, species abundance was quantified as percent cover for sessile taxa and density (individuals/m<sup>2</sup>) for mobile taxa.
DOI: 10.6084/m9.figshare.8179664
title: Additional file 2 of The effectiveness of spawning habitat creation or enhancement for substrate-spawning temperate fish: a systematic review

description: Additional file 2. List of articles excluded on the basis of full-text assessment and reasons for exclusion.
DOI: 10.6084/m9.figshare.8179664.v1
title: MOESM2 of The effectiveness of spawning habitat creation or enhancement for substrate-spawning temperate fish: a systematic review

description: Additional file 2. List of articles excluded on the basis of full-text assessment and reasons for exclusion.
DOI: 10.6084/m9.figshare.8179670
title: Additional file 3 of The effectiveness of spawning habitat creation or enhancement for substrate-spawning temperate fish: a systematic review

description: Additional file 3. Data-extraction sheet.
DOI: 10.6084/m9.figshare.8179676
title: Additional file 4 of The effectiveness of spawning habitat creation or enhancement for substrate-spawning temperate fish: a systematic review

description: Additional file 4. List of supplementary articles.
DOI: 10.6084/m9.figshare.8179694.v1
title: MOESM6 of The effectiveness of spawning habitat creation or enhancement for substrate-spawning temperate fish: a systematic review

description: Additional file 6. Meta-analysis database.
DOI: 10.6084/m9.figshare.8179709
title: Additional file 8 of The effectiveness of spawning habitat creation or enhancement for substrate-spawning temperate fish: a systematic review

description: Additional file 8. ROSES systematic review checklist.
DOI: 10.6084/m9.figshare.8179709.v1
title: MOESM8 of The effectiveness of spawning habitat creation or enhancement for substrate-spawning temperate fish: a systematic review

description: Additional file 8. ROSES systematic review checklist.
DOI: 10.6084/m9.figshare.8179670.v1
title: MOESM3 of The effectiveness of spawning habitat creation or enhancement for substrate-spawning temperate fish: a systematic review

description: Additional file 3. Data-extraction sheet.
DOI: 10.6084/m9.figshare.8179676.v1
title: MOESM4 of The effectiveness of spawning habitat creation or enhancement for substrate-spawning temperate fish: a systematic review

description: Additional file 4. List of supplementary articles.
DOI: 10.6084/m9.figshare.8179694
title: Additional file 6 of The effectiveness of spawning habitat creation or enhancement for substrate-spawning temperate fish: a systematic review

description: Additional file 6. Meta-analysis database.
DOI: 10.6084/m9.figshare.8180912.v1
title: Experimental and computational investigation of the influence of stoichiometric mixture fraction on structure and extinction of laminar, nonpremixed dimethyl ether flames

description: Experimental and computational investigation is carried out to elucidate the influence of stoichiometric mixture fraction, ξst, on the structure and critical conditions of extinction of nonpremixed dimethyl ether (DME) flames. The stoichiometric mixture fraction represents the location of a thin reaction zone in terms of a conserved scalar quantity. The counterflow configuration is employed, wherein two reactant streams flow towards a stagnation plane. One stream is made up of DME and nitrogen (N2) and the other stream is oxygen and N2. Previous studies have shown that critical conditions of extinction depend on ξst and the adiabatic temperature Tst. Therefore, the present investigation is carried out with the composition of the reactants in the counterflowing streams so chosen that the adiabatic temperature is the same for different values of ξst. The strain rate at extinction, aq, is measured for values of ξst up to 0.8. Computations are performed using detailed kinetic mechanisms and critical conditions of extinction and flame structures are predicted. The measurements and predictions show that, with increasing ξst, the strain rate at extinction first decreases and then increases. The predictions agree with measurements for ξst&lt;0.4, but significant deviations between measurements and predictions are observed at higher values of ξst. The scalar dissipation rate at extinction, χst,q is calculated using measured and predicted values of aq. With increasing ξst, the measured and predicted values of χst,q first increase and then decrease. It is noteworthy that changes in values of χst,q with ξst for dimethyl ether flames are similar to those for methane flames, while the changes in values of aq with ξst are remarkably different. Flame structures are predicted and they are found to be qualitatively similar to those for hydrocarbon fuels.
DOI: 10.6084/m9.figshare.8181587.v1
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.8175254
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.8181917
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.8180378
title: Eucalypt response to crown fire regimes

description: Data used in Collins, L (xxxx) Eucalypt forests dominated by epicormic resprouters are resilient to
repeated canopy fires, Journal of Ecology, xxx: xxx - xxx
DOI: 10.6084/m9.figshare.8180765
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.