cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3860457
title: Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia, 2013-2015

description: Supplementary Table S1 as published in <i>Microbial Genomics</i> in the following article: Genomic analysis of <i>Salmonella enterica </i>serotype <i>Paratyphi A</i> during an outbreak in Cambodia, 2013-2015. DOI 10.1099/mgen.0.000092
DOI: 10.7910/dvn/v1rjpf/qcw8lm
title: snk20171012_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860430
title: Dose accuracy of the redesigned follitropin alfa pen injector for infertility treatment

description: <b>Objectives:</b> The prefilled, multi-dose follitropin alfa (GONAL-f®) pen injector was redesigned based upon user feedback, to improve pen functionality. The dose information display was altered with the intention of improving readability and the dosing mechanism hardware was modified to increase robustness. The dose accuracy of the redesigned pen injector was evaluated under different conditions and after handling processes. <b>Methods:</b> Three studies investigated the dose accuracy of the three presentations (300, 450 and 900 IU) of the redesigned pen injector according to the ISO 11608-1:2012/2014 standard. The dose accuracy was evaluated in cold, standard and warm atmospheres, and subsequent to freefall, vibration, dry-heat, cold-storage and shipping preconditioning. The total extractable volume and dispense force of the pen injector were also investigated. <b>Results:</b> All doses dispensed with all three presentations, under all the conditions examined, were within the limits for accuracy defined by the ISO standard, as was the total extractable volume. The mean ± standard deviation dispense force was 12.5 ± 0.99 and 13.8 ± 1.16 N for the 300 and 900 IU pen injectors, respectively. These are below the upper threshold of the range considered optimal for pen injectors. <b>Conclusions:</b> These studies demonstrate that the redesigned pen injector functions reliably, dispensing accurate doses under the range of conditions studied.
DOI: 10.6084/m9.figshare.3860430.v1
title: Dose accuracy of the redesigned follitropin alfa pen injector for infertility treatment

description: <b>Objectives:</b> The prefilled, multi-dose follitropin alfa (GONAL-f®) pen injector was redesigned based upon user feedback, to improve pen functionality. The dose information display was altered with the intention of improving readability and the dosing mechanism hardware was modified to increase robustness. The dose accuracy of the redesigned pen injector was evaluated under different conditions and after handling processes. <b>Methods:</b> Three studies investigated the dose accuracy of the three presentations (300, 450 and 900 IU) of the redesigned pen injector according to the ISO 11608-1:2012/2014 standard. The dose accuracy was evaluated in cold, standard and warm atmospheres, and subsequent to freefall, vibration, dry-heat, cold-storage and shipping preconditioning. The total extractable volume and dispense force of the pen injector were also investigated. <b>Results:</b> All doses dispensed with all three presentations, under all the conditions examined, were within the limits for accuracy defined by the ISO standard, as was the total extractable volume. The mean ± standard deviation dispense force was 12.5 ± 0.99 and 13.8 ± 1.16 N for the 300 and 900 IU pen injectors, respectively. These are below the upper threshold of the range considered optimal for pen injectors. <b>Conclusions:</b> These studies demonstrate that the redesigned pen injector functions reliably, dispensing accurate doses under the range of conditions studied.
DOI: 10.6084/m9.figshare.3860457.v1
title: Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia, 2013-2015

description: Supplementary Table S1 as published in <i>Microbial Genomics</i> in the following article: Genomic analysis of <i>Salmonella enterica </i>serotype <i>Paratyphi A</i> during an outbreak in Cambodia, 2013-2015. DOI 10.1099/mgen.0.000092
DOI: 10.7910/dvn/v1rjpf/umo0ss
title: snk20170705_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860367
title: Supplementary Material for: Roles of HDAC2 and HDAC8 in Cardiac Remodeling in Renovascular Hypertensive Rats and the Effects of Valproic Acid Sodium

description: Recent studies indicate that histone deacetylases (HDACs) activity is associated with the development and progression of cardiac hypertrophy. In this study, we investigated the effects of a HDACs inhibitor, valproic acid sodium (VPA), on cardiac remodeling and the differential expression of HDACs in left ventricles (LVs) of renovascular hypertensive rats. Renovascular hypertension was induced in rats by the two-kidney two-clip (2K2C) method. Cardiac remodeling, heart function and the differential expression of HDACs were examined at different weeks after 2K2C operation. The effects of VPA on cardiac remodeling, the expressions of HDACs, transforming growth factor-beta 1 (TGF-β1) and connective tissue growth factor (CTGF) in LV were investigated. The expressions of atrial natriuretic factor, β-myosin heavy chain, HDAC2 and HDAC8 increased in LV of 2K2C rats at 4, 8, 12 weeks after operation. Cardiac dysfunction, cardiac hypertrophy and fibrosis were markedly attenuated by VPA treatment in 2K2C rats. Further studies revealed that VPA inhibited the expressions of HDAC2, HDAC8, TGF-β1 and CTGF in LV of 2K2C rats. In summary, these data indicate that HDAC2 and HDAC8 play a key role in cardiac remodeling in renovascular hypertensive rats and that VPA attenuates hypertension and cardiac remodeling. The effect of VPA is possibly exerted via decreasing HDAC2, HDAC8, TGF-β1 and CTGF expressions in LV of 2K2C rats.
DOI: 10.7910/dvn/v1rjpf/tqe46x
title: snk20171128_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860355
title: A molecular dynamics strategy for CSαβ peptides disulfide-assisted model refinement

description: Many cysteine-stabilized antimicrobial peptides from a variety of living organisms could be good candidates for the development of anti-infective agents. In the absence of experimentally obtained structural data, peptide modeling is an essential tool for understanding structure–activity relationships and for optimizing the bioactive moieties. Focusing on cysteine-rich peptide structures, we reproduced the case of structure predictions in the so-called midnight zone. We developed our protocol on a training set derived by clustering the available cysteine-stabilized αβ (CSαβ) structures in nine different representative families and tested it on peptides randomly selected from each family. Starting from draft models, we tested a structure-based disulfide predictor and we used cysteine distances as constraints during molecular dynamics. Finally, we proposed an analysis for final structure selection. Accordingly, we obtained a mean root mean square deviation improvement of 21% for the test set. Our findings demonstrate that it is possible to predict the network of disulfide bridges in cysteine-stabilized peptides and to use this result to improve the accuracy of structural predictions. Finally, we applied the methods to predict the structure of royalisin, a cysteine-rich peptide with unknown structure.
DOI: 10.6084/m9.figshare.3860367.v1
title: Supplementary Material for: Roles of HDAC2 and HDAC8 in Cardiac Remodeling in Renovascular Hypertensive Rats and the Effects of Valproic Acid Sodium

description: Recent studies indicate that histone deacetylases (HDACs) activity is associated with the development and progression of cardiac hypertrophy. In this study, we investigated the effects of a HDACs inhibitor, valproic acid sodium (VPA), on cardiac remodeling and the differential expression of HDACs in left ventricles (LVs) of renovascular hypertensive rats. Renovascular hypertension was induced in rats by the two-kidney two-clip (2K2C) method. Cardiac remodeling, heart function and the differential expression of HDACs were examined at different weeks after 2K2C operation. The effects of VPA on cardiac remodeling, the expressions of HDACs, transforming growth factor-beta 1 (TGF-β1) and connective tissue growth factor (CTGF) in LV were investigated. The expressions of atrial natriuretic factor, β-myosin heavy chain, HDAC2 and HDAC8 increased in LV of 2K2C rats at 4, 8, 12 weeks after operation. Cardiac dysfunction, cardiac hypertrophy and fibrosis were markedly attenuated by VPA treatment in 2K2C rats. Further studies revealed that VPA inhibited the expressions of HDAC2, HDAC8, TGF-β1 and CTGF in LV of 2K2C rats. In summary, these data indicate that HDAC2 and HDAC8 play a key role in cardiac remodeling in renovascular hypertensive rats and that VPA attenuates hypertension and cardiac remodeling. The effect of VPA is possibly exerted via decreasing HDAC2, HDAC8, TGF-β1 and CTGF expressions in LV of 2K2C rats.
DOI: 10.6084/m9.figshare.3860355.v1
title: A molecular dynamics strategy for CSαβ peptides disulfide-assisted model refinement

description: Many cysteine-stabilized antimicrobial peptides from a variety of living organisms could be good candidates for the development of anti-infective agents. In the absence of experimentally obtained structural data, peptide modeling is an essential tool for understanding structure–activity relationships and for optimizing the bioactive moieties. Focusing on cysteine-rich peptide structures, we reproduced the case of structure predictions in the so-called midnight zone. We developed our protocol on a training set derived by clustering the available cysteine-stabilized αβ (CSαβ) structures in nine different representative families and tested it on peptides randomly selected from each family. Starting from draft models, we tested a structure-based disulfide predictor and we used cysteine distances as constraints during molecular dynamics. Finally, we proposed an analysis for final structure selection. Accordingly, we obtained a mean root mean square deviation improvement of 21% for the test set. Our findings demonstrate that it is possible to predict the network of disulfide bridges in cysteine-stabilized peptides and to use this result to improve the accuracy of structural predictions. Finally, we applied the methods to predict the structure of royalisin, a cysteine-rich peptide with unknown structure.
DOI: 10.7910/dvn/v1rjpf/vvrdiq
title: snk20170808_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860283
title: Supplementary Material for: Genotype-Phenotype Relationship in Patients and Relatives with SHOX Region Anomalies in the French Population

description: <b><i>Background:</i></b> The aim of our study was to describe a large population with anomalies involving the <i>SHOX</i> region, responsible for idiopathic short stature and Léri-Weill dyschondrosteosis (LWD), and to identify a possible genotype/phenotype correlation. <b><i>Methods:</i></b> We performed a retrospective multicenter study on French subjects with a <i>SHOX</i> region anomaly diagnosed by multiplex ligation-dependent probe amplification or Sanger sequencing. Phenotypes were collected in each of the 7 genetic laboratories practicing this technique for <i>SHOX</i> analysis. <b><i>Results:</i></b> Among 205 index cases and 100 related cases, 91.3% had LWD. For index cases, median age at evaluation was 11.7 (9.0; 15.9) years and mean height standard deviation score was -2.3 ± 1.1. A deletion of either <i>SHOX</i> or PAR1 or both was found in 74% of patients. Duplications and point mutations/indels affected 8 and 18% of the population, respectively. Genotype-phenotype correlation showed that deletions were more frequently associated with Madelung deformity and mesomelic shortening in girls, as well as with presence of radiologic anomalies, than duplications. <b><i>Conclusions:</i></b> Our results highlight genotype-phenotype relationships in the French population with a <i>SHOX</i> defect and provide new information showing that clinical expression is milder in cases of duplication compared to deletions.
DOI: 10.6084/m9.figshare.3860283.v1
title: Supplementary Material for: Genotype-Phenotype Relationship in Patients and Relatives with SHOX Region Anomalies in the French Population

description: <b><i>Background:</i></b> The aim of our study was to describe a large population with anomalies involving the <i>SHOX</i> region, responsible for idiopathic short stature and Léri-Weill dyschondrosteosis (LWD), and to identify a possible genotype/phenotype correlation. <b><i>Methods:</i></b> We performed a retrospective multicenter study on French subjects with a <i>SHOX</i> region anomaly diagnosed by multiplex ligation-dependent probe amplification or Sanger sequencing. Phenotypes were collected in each of the 7 genetic laboratories practicing this technique for <i>SHOX</i> analysis. <b><i>Results:</i></b> Among 205 index cases and 100 related cases, 91.3% had LWD. For index cases, median age at evaluation was 11.7 (9.0; 15.9) years and mean height standard deviation score was -2.3 ± 1.1. A deletion of either <i>SHOX</i> or PAR1 or both was found in 74% of patients. Duplications and point mutations/indels affected 8 and 18% of the population, respectively. Genotype-phenotype correlation showed that deletions were more frequently associated with Madelung deformity and mesomelic shortening in girls, as well as with presence of radiologic anomalies, than duplications. <b><i>Conclusions:</i></b> Our results highlight genotype-phenotype relationships in the French population with a <i>SHOX</i> defect and provide new information showing that clinical expression is milder in cases of duplication compared to deletions.
DOI: 10.6084/m9.figshare.3860289
title: Supplementary Material for: A Multi-Institutional Feasibility Study on the Use of Automated Screening Systems for Quality Control Rescreening of Cervical Cytology

description: <b><i>Objective:</i></b> To evaluate the efficacy of the automated screening system FocalPoint for cervical cytology quality control (QC) rescreening. False-negative rates (FNRs) were evaluated by a multi-institutional retrospective study. <b><i>Study Design:</i></b> Cervical cytology slides that had already been reported as negative for intraepithelial lesion or malignancy (NILM) were chosen arbitrarily for FocalPoint rescreening. Slides stratified into the highest 15% probability of being abnormal were rescreened by a cytotechnologist. The slides that were abnormal were reevaluated by a cytopathologist to be false negatives. <b><i>Results:</i></b> Rescreening of 12,000 slides, i.e. 9,000 conventional slides and 3,000 liquid-based cytology (LBC) slides, was performed; 9,826 (7,393 conventional and 2,433 LBC) were satisfactory for FocalPoint (2,174 were determined unsatisfactory) and those within the highest 15% of probability (1,496, i.e. 1,123 conventional and 373 LBC) were rescreened. As a result, 117 (96 conventional and 21 LBC) were determined as abnormal (other than NILM) and the FNR was 1.19%. Among these 117 slides, 40 (35 conventional and 5 LBC) were determined as high-grade squamous intraepithelial lesion and greater (HSIL+). <b><i>Conclusion:</i></b> Of 117 (1.19%) abnormal slides detected, 40 (0.41%) were determined to be HSIL+. This result suggests that FocalPoint is effective for QC rescreening of cervical cytology.
DOI: 10.7910/dvn/v1rjpf/pj2h12
title: snk20171003_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860250
title: Avoidance_Anxiety_Materials

description: All data, task scripts and materials for:<b><br></b><b>Modelling avoidance in pathologically anxious humans using reinforcement-learning</b> Mkrtchian A, Aylward J, Dayan P, Roiser JP and Robinson OJ<b></b>Extract the .zip file to the same file structure then run 'RecreateFiguresData.m' in matlab to recreate all the figures in the paper as well as summary data sheets. Note that this runs simulations (i.e. a posterior predictive model) so some of the figures will look slightly different to the paper each time they are run. Note also that this omnibus script was created by stitching together multiple scripts so the code is not elegant and there are clear redundancies! It should, however, work. Please let us know if you find problems/bugs (contact OJR).
DOI: 10.6084/m9.figshare.3860280
title: Biomethane potential of food waste: modeling the effects of mild thermal pretreatment and digestion temperature

description: In order to enhance anaerobic biodegradability of food waste (FW), thermal pretreatment was applied. The effectiveness in terms of biodegradability extent and process rate improvement was investigated. To this aim, Biomethane Potential tests were carried out under mesophilic and thermophilic conditions. The IWA anaerobic digestion Model 1 (ADM1), a powerful tool for modeling the anaerobic digestion (AD) of different substrates, was implemented to predict the methane production. Disintegration constant (k_dis) and maximum acetate uptake rate (km_ac) were identified as the most sensitive parameters and were calibrated over the observed methane production. Pretreatment improvement was more evident in enhancing parameters related to the process rate, such as solubilization extent (+153%) and disintegration constant (+18%), rather than increasing substrate biodegradability. Thermophilic conditions proved to be effective in speeding up the whole AD process, since all the kinetics were significantly improved (disintegration rate increased up to fivefold). Furthermore, it was demonstrated that, after k_dis and km_ac calibration, default thermophilic ADM1 parameters can be suitable to model FW digestion.
DOI: 10.6084/m9.figshare.3860280.v1
title: Biomethane potential of food waste: modeling the effects of mild thermal pretreatment and digestion temperature

description: In order to enhance anaerobic biodegradability of food waste (FW), thermal pretreatment was applied. The effectiveness in terms of biodegradability extent and process rate improvement was investigated. To this aim, Biomethane Potential tests were carried out under mesophilic and thermophilic conditions. The IWA anaerobic digestion Model 1 (ADM1), a powerful tool for modeling the anaerobic digestion (AD) of different substrates, was implemented to predict the methane production. Disintegration constant (k_dis) and maximum acetate uptake rate (km_ac) were identified as the most sensitive parameters and were calibrated over the observed methane production. Pretreatment improvement was more evident in enhancing parameters related to the process rate, such as solubilization extent (+153%) and disintegration constant (+18%), rather than increasing substrate biodegradability. Thermophilic conditions proved to be effective in speeding up the whole AD process, since all the kinetics were significantly improved (disintegration rate increased up to fivefold). Furthermore, it was demonstrated that, after k_dis and km_ac calibration, default thermophilic ADM1 parameters can be suitable to model FW digestion.
DOI: 10.7910/dvn/v1rjpf/4ofue2
title: snk20171222_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860232
title: Bioemulsifier (BE-AM1) produced by <i>Solibacillus silvestris</i> AM1 is a functional amyloid that modulates bacterial cell-surface properties

description: A novel estuarine bacterial strain, <i>Solibacillus silvestris</i> AM1, produces an extracellular, thermostable and fibrous, glycoprotein bioemulsifier (BE-AM1). The amyloid nature of the bioemulsifier (BE-AM1) was confirmed by biophysical techniques (Congo red based polarization microscopy, ThioflavinS based fluorescent microscopy, fibrous arrangement in transmission electron microscopy and secondary structure measurement by FTIR and CD spectrum analysis). Cell-bound BE-AM1 production by <i>S. silvestris</i> AM1 during the mid-logarithmic phase of growth coincided with a decrease in cell surface hydrophobicity, and an increase in cell autoaggregation and biofilm formation. It was observed that the total interfacial interaction energy () for the surface of the bioemulsifier producing <i>S. silvestris</i> AM1 and different derivatized surfaces of polystyrene (silanized and sulfonated) was found to support biofilm formation. This study has revealed that the BE-AM1, a bacterial bioemulsifier, is a functional amyloid and has a role in biofilm formation and cell surface modulation in <i>S. silvestris</i> AM1.
DOI: 10.7910/dvn/v1rjpf/euthvv
title: snk20170713_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860232.v1
title: Bioemulsifier (BE-AM1) produced by <i>Solibacillus silvestris</i> AM1 is a functional amyloid that modulates bacterial cell-surface properties

description: A novel estuarine bacterial strain, <i>Solibacillus silvestris</i> AM1, produces an extracellular, thermostable and fibrous, glycoprotein bioemulsifier (BE-AM1). The amyloid nature of the bioemulsifier (BE-AM1) was confirmed by biophysical techniques (Congo red based polarization microscopy, ThioflavinS based fluorescent microscopy, fibrous arrangement in transmission electron microscopy and secondary structure measurement by FTIR and CD spectrum analysis). Cell-bound BE-AM1 production by <i>S. silvestris</i> AM1 during the mid-logarithmic phase of growth coincided with a decrease in cell surface hydrophobicity, and an increase in cell autoaggregation and biofilm formation. It was observed that the total interfacial interaction energy () for the surface of the bioemulsifier producing <i>S. silvestris</i> AM1 and different derivatized surfaces of polystyrene (silanized and sulfonated) was found to support biofilm formation. This study has revealed that the BE-AM1, a bacterial bioemulsifier, is a functional amyloid and has a role in biofilm formation and cell surface modulation in <i>S. silvestris</i> AM1.
DOI: 10.7910/dvn/v1rjpf/sg9waa
title: snk20170810_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/o9tfl0
title: snk20170730_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/3rvmwi
title: snk20171229_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/pv3luy
title: snk20171007_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860169
title: Fault-tolerant cooperative output regulation for multi-vehicle systems with sensor faults

description: This paper presents a unified framework of fault diagnosis and fault-tolerant cooperative output regulation (FTCOR) for a linear discrete-time multi-vehicle system with sensor faults. The FTCOR control law is designed through three steps. A cooperative output regulation (COR) controller is designed based on the internal mode principle when there are no sensor faults. A sufficient condition on the existence of the COR controller is given based on the discrete-time algebraic Riccati equation (DARE). Then, a decentralised fault diagnosis scheme is designed to cope with sensor faults occurring in followers. A residual generator is developed to detect sensor faults of each follower, and a bank of fault-matching estimators are proposed to isolate and estimate sensor faults of each follower. Unlike the current distributed fault diagnosis for multi-vehicle systems, the presented decentralised fault diagnosis scheme in each vehicle reduces the communication and computation load by only using the information of the vehicle. By combing the sensor fault estimation and the COR control law, an FTCOR controller is proposed. Finally, the simulation results demonstrate the effectiveness of the FTCOR controller.
DOI: 10.7910/dvn/v1rjpf/dwvpn9
title: snk20170331_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/clbtw3
title: snk20170916_03.txt.gz

description: :unav