cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5387959.v1
title: <i>Araniella cucurbitina</i>: the first molecular evidence of a Palearctic species of genus <i>Araniella</i> inhabiting India

description: The present study represents first genetic record of single spider species <i>Araniella cucurbitina</i>, genus <i>Araniella</i> from Uttarakhand, India. There are 12 identified species under <i>Araniella</i> genus and they are distributed in Palearctic region. Here, we used known N = 47 (2 from present study and 45 from GenBank) cytochrome oxidase 1 (CO1) sequences of <i>A. cucurbitina</i> representing seven different geographical groups, additionally 23 sequences of eight <i>Araniella</i> species were used for phylogenetic relationship. The CO1 (561 bp) sequences of <i>A. cucurbitina</i> consisted of <i>n</i> = 14 haplotypes, where haplotype 14 (Hap 14) represents Indian species, while all 13 haplotypes (Hap1–13) shared between six <i>A. cucurbitina</i> groups. The overall ‘h’ and ‘π’ diversities among seven groups of <i>A. cucurbitina</i> were 0.85291 and 0.00888, respectively, while overall evolutionary divergence was 0.04. The Indian Hap 14, showed minimum sequence divergence (0.02) from Italy and Czech Republic haplotypes (Hap 6), it means it is the closest group compared to others. Evolutionary divergence among eight species of <i>Araniella</i> ranges from 0.003 to 0.114. The maximum likelihood (ML) topology based on 14 haplotypes of <i>A. cucurbitina</i> was divided into two major clades and further two subclades. Furthermore, ML topology between eight species of <i>Araniella</i> was divided into three major clades, where <i>A. cucurbitina</i> and <i>A. proxima</i> clustered together in clade ‘A’, while six others were present together in clade ‘B’ and ‘C’. This study helps to identify the Indian species from the rest of <i>Araniella</i> species and other <i>cucurbitina</i> population across the world. This study further needs to be on a large scale to know the exact status distribution and molecular phylogeography of this single species of genus <i>Araniella</i> from India.
DOI: 10.6084/m9.figshare.5387956.v1
title: Supplementary Material for: Chromosomal Microarray Analysis in Fetuses with Growth Restriction and Normal Karyotype: A Systematic Review and Meta-Analysis

description: <strong><em>Objective:</em></strong> To perform a systematic review of the literature and a meta-analysis to estimate the incremental yield of chromosomal microarray analysis (CMA) over karyotyping in fetal growth restriction (FGR). <b><i>Methods:</i></b> This was a systematic review conducted in accordance with the PRISMA criteria. All articles identified in PubMed, Ovid Medline, and ISI Web of Knowledge (Web of Science) from January 2009 to November 2016 describing pathogenic copy number variants (CNVs) in fetuses with growth restriction were included. Case reports were excluded. Risk differences were pooled to estimate the overall and stratified CMA incremental yield. <b><i>Results:</i></b> Ten studies with full data available met the inclusion criteria for analysis. Combined data from these studies revealed a 4% (95% confidence interval [CI] 1-6%) incremental yield of CMA over karyotyping in nonmalformed growth-restricted fetuses, and a 10% (95% CI 6-14%) incremental yield in FGR when associated with fetal malformations. The most frequently found pathogenic CNVs were 22q11.2 duplication, Xp22.3 deletion, and 7q11.23 deletion (Williams-Beuren syndrome), particularly in isolated FGR. <b><i>Conclusion:</i></b> The use of genomic CMA provides a 4% incremental yield of detecting pathogenic CNVs in fetuses with isolated growth restriction and normal karyotype.
DOI: 10.6084/m9.figshare.5387863
title: Self-reported and Pharmacy Refill Adherence in HIV+ Migrants.sav

description: In this study, we assessed two methods, self-reported adherence and pharmacy refill adherence to combination Antiretroviral Therapy (cART), in order to determine their comparative predictive value for undetectable viral load in a large group of migrants people living with HIV from different geographical origins. In addition, we examined risk factors for non-adherence based on pharmacy refill data calculation.
DOI: 10.6084/m9.figshare.5387854
title: Enhancement of anticancer activity by silibinin and paclitaxel combination on the ovarian cancer

description: <b>Background:</b> Ovarian carcinoma is the most lethal cancer among all gynaecological malignancies. One of the most chemotherapy drugs used for ovarian cancer is paclitaxel which induces apoptosis. Paclitaxel has been used for many years. Similar to the most cancers this responds to chemotherapy initially but in a long run, drug resistance happens which fails the treatment procedure. Combination of chemotherapy drugs has been suggested to deal with this issue. Silibinin, a plant extraction, has been used from ancient time in traditional medicine and identified to have powerful antioxidant activity. <b>Aim:</b> The aim of this study was to examine the effect of paclitaxel and silibinin combination on SKOV-3 cancer cell line. <b>Materials and methods:</b> The human epithelial ovarian cancer cell line, SKOV-3, was cultured and treated with paclitaxel, silibinin and paclitaxel plus silibinin for 48 hours. MTT assay was carried out to determine cell viability. For apoptotic process, we used real-time PCR to study <i>P53</i> and <i>P21</i> genes expression after drug treatment and network analysis was performed using Pathway Studio web tool (Elsevier). <b>Results:</b> Cell growth was inhibited considerably (<i>p</i> P53 and <i>P21</i> in response to combination of silibinin and paclitaxel. In addition, computational network analysis demonstrated the crosstalk between paclitaxel, silibinin and ovarian cancer. <b>Conclusions:</b> Our results showed that combination of chemotherapy drugs of silibinin and paclitaxel can be more efficient in treatment of ovarian cancer cells.
DOI: 10.6084/m9.figshare.5387863.v1
title: Self-reported and Pharmacy Refill Adherence in HIV+ Migrants.sav

description: In this study, we assessed two methods, self-reported adherence and pharmacy refill adherence to combination Antiretroviral Therapy (cART), in order to determine their comparative predictive value for undetectable viral load in a large group of migrants people living with HIV from different geographical origins. In addition, we examined risk factors for non-adherence based on pharmacy refill data calculation.
DOI: 10.6084/m9.figshare.5387854.v1
title: Enhancement of anticancer activity by silibinin and paclitaxel combination on the ovarian cancer

description: <b>Background:</b> Ovarian carcinoma is the most lethal cancer among all gynaecological malignancies. One of the most chemotherapy drugs used for ovarian cancer is paclitaxel which induces apoptosis. Paclitaxel has been used for many years. Similar to the most cancers this responds to chemotherapy initially but in a long run, drug resistance happens which fails the treatment procedure. Combination of chemotherapy drugs has been suggested to deal with this issue. Silibinin, a plant extraction, has been used from ancient time in traditional medicine and identified to have powerful antioxidant activity. <b>Aim:</b> The aim of this study was to examine the effect of paclitaxel and silibinin combination on SKOV-3 cancer cell line. <b>Materials and methods:</b> The human epithelial ovarian cancer cell line, SKOV-3, was cultured and treated with paclitaxel, silibinin and paclitaxel plus silibinin for 48 hours. MTT assay was carried out to determine cell viability. For apoptotic process, we used real-time PCR to study <i>P53</i> and <i>P21</i> genes expression after drug treatment and network analysis was performed using Pathway Studio web tool (Elsevier). <b>Results:</b> Cell growth was inhibited considerably (<i>p</i> P53 and <i>P21</i> in response to combination of silibinin and paclitaxel. In addition, computational network analysis demonstrated the crosstalk between paclitaxel, silibinin and ovarian cancer. <b>Conclusions:</b> Our results showed that combination of chemotherapy drugs of silibinin and paclitaxel can be more efficient in treatment of ovarian cancer cells.
DOI: 10.6084/m9.figshare.5387950.v3
title: Spatial rectal dose/volume metrics predict patient-reported gastro-intestinal symptoms after radiotherapy for prostate cancer

description: <b>Background:</b> Gastro-intestinal (GI) toxicity after radiotherapy (RT) for prostate cancer reduces patient’s quality of life. In this study, we explored associations between spatial rectal dose/volume metrics and patient-reported GI symptoms after RT for localized prostate cancer, and compared these with those of dose–surface/volume histogram (DSH/DVH) metrics. <b>Material and methods:</b> Dose distributions and six GI symptoms (defecation urgency/emptying difficulties/fecal leakage, ≥Grade 2, median follow-up: 3.6 y) were extracted for 200 patients treated with image-guided RT in 2005–2007. Three hundred and nine metrics assessed from 2D rectal dose maps or DSHs/DVHs were subject to 50-times iterated five-fold cross-validated univariate and multivariate logistic regression analysis (UVA, MVA). Performance of the most frequently selected MVA models was evaluated by the area under the receiving–operating characteristics curve (AUC). <b>Results:</b> The AUC increased for dose-map compared to DSH/DVH-based models (mean SD: 0.64 ± 0.03 vs. 0.61 ± 0.01), and significant relations were found for six versus four symptoms. Defecation urgency and faecal leakage were explained by high doses at the central/upper and central areas, respectively; while emptying difficulties were explained by longitudinal extensions of intermediate doses. <b>Conclusions:</b> Predictability of patient-reported GI toxicity increased using spatial metrics compared to DSH/DVH metrics. Novel associations were particularly identified for emptying difficulties using both approaches in which intermediate doses were emphasized.
DOI: 10.6084/m9.figshare.5387743
title: Insights from protein-protein interaction studies on bacterial pathogenesis

description: <b>Introduction</b>: The threat bacterial pathogens pose to human health is increasing with the number and distribution of antibiotic-resistant bacteria, while the rate of discovery of new antimicrobials dwindles. Proteomics is playing key roles in understanding the molecular mechanisms of bacterial pathogenesis, and in identifying disease outcome determinants. The physical associations identified by proteomics can provide the means to develop pathogen-specific treatment methods that reduce the spread of antibiotic resistance and alleviate the negative effects of broad-spectrum antibiotics on beneficial bacteria. <b>Areas covered</b>: This review discusses recent trends in proteomics and introduces new and developing approaches that can be applied to the study of protein-protein interactions (PPIs) underlying bacterial pathogenesis. The approaches examined encompass options for mapping proteomes as well as stable and transient interactions <i>in vivo</i> and <i>in vitro</i>. We also explored the coverage of bacterial and human-bacterial PPIs, knowledge gaps in this area, and how they can be filled. <b>Expert commentary</b>: Identifying potential antimicrobial candidates is confounded by the complex molecular biology of bacterial pathogenesis and the lack of knowledge about PPIs underlying this process. Proteomics approaches can offer new perspectives for mechanistic insights and identify essential targets for guiding the discovery of next generation antimicrobials.
DOI: 10.6084/m9.figshare.5387743.v1
title: Insights from protein-protein interaction studies on bacterial pathogenesis

description: <b>Introduction</b>: The threat bacterial pathogens pose to human health is increasing with the number and distribution of antibiotic-resistant bacteria, while the rate of discovery of new antimicrobials dwindles. Proteomics is playing key roles in understanding the molecular mechanisms of bacterial pathogenesis, and in identifying disease outcome determinants. The physical associations identified by proteomics can provide the means to develop pathogen-specific treatment methods that reduce the spread of antibiotic resistance and alleviate the negative effects of broad-spectrum antibiotics on beneficial bacteria. <b>Areas covered</b>: This review discusses recent trends in proteomics and introduces new and developing approaches that can be applied to the study of protein-protein interactions (PPIs) underlying bacterial pathogenesis. The approaches examined encompass options for mapping proteomes as well as stable and transient interactions <i>in vivo</i> and <i>in vitro</i>. We also explored the coverage of bacterial and human-bacterial PPIs, knowledge gaps in this area, and how they can be filled. <b>Expert commentary</b>: Identifying potential antimicrobial candidates is confounded by the complex molecular biology of bacterial pathogenesis and the lack of knowledge about PPIs underlying this process. Proteomics approaches can offer new perspectives for mechanistic insights and identify essential targets for guiding the discovery of next generation antimicrobials.
DOI: 10.6084/m9.figshare.5387755
title: Simulating melodic and harmonic expectations for tonal cadences using probabilistic models

description: This study examines how the mind’s predictive mechanisms contribute to the perception of cadential closure during music listening. Using the Information Dynamics of Music model (or IDyOM) to simulate the formation of schematic expectations—a finite-context (or <i>n</i>-gram) model that predicts the next event in a musical stimulus by acquiring knowledge through unsupervised statistical learning of sequential structure—we predict the terminal melodic and harmonic events from 245 exemplars of the five most common cadence categories from the classical style. Our findings demonstrate that (1) terminal events from cadential contexts are more predictable than those from non-cadential contexts; (2) models of cadential strength advanced in contemporary cadence typologies reflect the formation of schematic expectations; and (3) a significant decrease in predictability follows the terminal note and chord events of the cadential formula.
DOI: 10.6084/m9.figshare.5387719
title: Physical parameters and plasma measurements.xlsx

description: Physical parameters
DOI: 10.6084/m9.figshare.5387755.v1
title: Simulating melodic and harmonic expectations for tonal cadences using probabilistic models

description: This study examines how the mind’s predictive mechanisms contribute to the perception of cadential closure during music listening. Using the Information Dynamics of Music model (or IDyOM) to simulate the formation of schematic expectations—a finite-context (or <i>n</i>-gram) model that predicts the next event in a musical stimulus by acquiring knowledge through unsupervised statistical learning of sequential structure—we predict the terminal melodic and harmonic events from 245 exemplars of the five most common cadence categories from the classical style. Our findings demonstrate that (1) terminal events from cadential contexts are more predictable than those from non-cadential contexts; (2) models of cadential strength advanced in contemporary cadence typologies reflect the formation of schematic expectations; and (3) a significant decrease in predictability follows the terminal note and chord events of the cadential formula.
DOI: 10.6084/m9.figshare.5387713
title: MRI experiments.xlsx

description: MRI experiments
DOI: 10.6084/m9.figshare.5387707
title: Histology.xls

description: Histopathologic evaluation
DOI: 10.6084/m9.figshare.5387719.v1
title: Physical parameters and plasma measurements.xlsx

description: Physical parameters
DOI: 10.6084/m9.figshare.5387698
title: MRI experiments.xlsx

description: MRI experiments
DOI: 10.6084/m9.figshare.5387701
title: qPCR.xlsx

description: QPCR
DOI: 10.6084/m9.figshare.5387707.v1
title: Histology.xls

description: Histopathologic evaluation
DOI: 10.6084/m9.figshare.5387698.v1
title: MRI experiments.xlsx

description: MRI experiments
DOI: 10.6084/m9.figshare.5387680
title: An efficient semi-quantitative macroinvertebrate multimetric index for the assessment of water and sediment contamination in streams

description: Environmental issues and their associated legislative pressures are demanding, especially regarding costs, limited budgets, and data collection efforts. The development of effective biotic indices for monitoring generated via comprehensive data collection within human-impacted landscapes can support district- to regional-level environmental management plans. We designed a macroinvertebrate multimetric index that fulfills the requirements of the EU Water Framework Directive and measures ecological health as a deviation from a reference state, taking into consideration water and sediment contamination in streams of Central Italy. Macroinvertebrate samples were obtained by a semi-quantitative technique. The Semi-quantitative Multimetric Index (SMI) we developed has a high discrimination efficiency (reference vs. impacted sites), high stability (i.e., low coefficient of variation) at reference sites, and low specificity regarding the environmental variables reflecting contamination. The SMI is composed of 4 metrics weighted by their discrimination efficiency against reference conditions: number of families, score of the biological monitoring waters pollution index (SBWMP), Margalef’s diversity index, and relative richness of shredders. These metrics that best distinguished reference from impacted sites were selected from 71 metrics divided into 4 categories (one metric for each category): richness/abundance, tolerance, diversity, bioecological traits. The SMI exemplifies a cost-effective method that could complement supranational techniques because it is robust in terms of biological, ecological, and socioeconomic contexts used to generate it; requires little effort for the data collection; and responds to a large number of environmental stressors. To ensure comparability, however, we recommend calibrating the new SMI index against the national index currently in use.
DOI: 10.6084/m9.figshare.5387692
title: Physical parameters and plasma measurements.xlsx

description: Results of physical and plasma measurements
DOI: 10.6084/m9.figshare.5387692.v1
title: Physical parameters and plasma measurements.xlsx

description: Results of physical and plasma measurements
DOI: 10.6084/m9.figshare.5387680.v1
title: An efficient semi-quantitative macroinvertebrate multimetric index for the assessment of water and sediment contamination in streams

description: Environmental issues and their associated legislative pressures are demanding, especially regarding costs, limited budgets, and data collection efforts. The development of effective biotic indices for monitoring generated via comprehensive data collection within human-impacted landscapes can support district- to regional-level environmental management plans. We designed a macroinvertebrate multimetric index that fulfills the requirements of the EU Water Framework Directive and measures ecological health as a deviation from a reference state, taking into consideration water and sediment contamination in streams of Central Italy. Macroinvertebrate samples were obtained by a semi-quantitative technique. The Semi-quantitative Multimetric Index (SMI) we developed has a high discrimination efficiency (reference vs. impacted sites), high stability (i.e., low coefficient of variation) at reference sites, and low specificity regarding the environmental variables reflecting contamination. The SMI is composed of 4 metrics weighted by their discrimination efficiency against reference conditions: number of families, score of the biological monitoring waters pollution index (SBWMP), Margalef’s diversity index, and relative richness of shredders. These metrics that best distinguished reference from impacted sites were selected from 71 metrics divided into 4 categories (one metric for each category): richness/abundance, tolerance, diversity, bioecological traits. The SMI exemplifies a cost-effective method that could complement supranational techniques because it is robust in terms of biological, ecological, and socioeconomic contexts used to generate it; requires little effort for the data collection; and responds to a large number of environmental stressors. To ensure comparability, however, we recommend calibrating the new SMI index against the national index currently in use.
DOI: 10.6084/m9.figshare.5387590
title: Birnie-Gauvin et al. Hydrodam removal JEMA

description: Raw data on fish density estimates used to evaluate the effects of a small hydrodam removal.
DOI: 10.6084/m9.figshare.5387536
title: Matlab package for the Turnwald-1C-A3 experiment from Pedestrian motion modelled by Fokker–Planck Nash games

description: This matlab package is set up to reproduce the results of test case 2: Turnwald 1C-A3. A readme file is included to help in the simulation and to describe the main modules of the package and the location of the input.
DOI: 10.6084/m9.figshare.5387533
title: Matlab package for the Gait and Posture experiment from Pedestrian motion modelled by Fokker–Planck Nash games

description: This matlab package is set up to reproduce the results of test case 4: Gait and Posture. A readme file is included to help in the simulation and to describe the main modules of the package and the location of the input.
DOI: 10.6084/m9.figshare.5387536.v1
title: Matlab package for the Turnwald-1C-A3 experiment from Pedestrian motion modelled by Fokker–Planck Nash games

description: This matlab package is set up to reproduce the results of test case 2: Turnwald 1C-A3. A readme file is included to help in the simulation and to describe the main modules of the package and the location of the input.
DOI: 10.6084/m9.figshare.5387140
title: simulated_head_sinograms.mat

description: Simulated head sinograms<br>Mats Persson, Jonas Adler<br>Latest version 2017-09-08<br><br>These are simulated basis materials sinograms used for the proceedings paper <br>M. Persson* and J. Adler*, “Spectral CT reconstruction with anti-correlated noise model and joint prior”, in Proceedings of The 14th International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, 2017, pp. 580–585.<br><br>This is meant as an example dataset for the reconstruction code belonging to this paper, which is available online at https://github.com/adler-j/spectral_ct_examples<br><br>Contents of the .mat file:<br>multiPhantom (600x600x2)<br>This contains the two basis images for the FORBILD head phantom: multiPhantom(:,:,1) is the soft tissue image and multiPhantom(:,:,2) is the bone image.<br><br>decomposedbasisProjectionsmm (853x360x2)<br>This matrix contains the basis sinograms (soft tissue and bone in that order) estimated from measured data using basis material decomposition. The values are given as projected path lengths in mm. The first index is the detector element number, the second index is view angle and the third image is the basis material.<br><br>CRLB (853x360x2x2)<br>This is the Cramer-Rao lower bound on basis image variance estimated from the noisy projection data for each projection line. The first two indices are detector element number and view angle. CRLB(i,j,:,:) is the lower bound (and in practice also an accurate estimate) of the covariance matrix of the estimated projected thicknesses of soft tissue and bone in ray (i,j). So CRLB(i,j,1,1) is the soft tissue image variance and CRLB(i,j,2,2) is the bone variance, CRLB(i,j,1,2)=CRLB(i,j,2,1) is the covariance. <br>The unit is mm^2.
DOI: 10.6084/m9.figshare.5387041
title: F_H33NLALXX_L3_2.clean.fq.gz

description: fastq
DOI: 10.6084/m9.figshare.5387041.v1
title: F_H33NLALXX_L3_2.clean.fq.gz

description: fastq