cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11961402
title: 794_AMR_genes_Gibson_et_al

description: This dataset of 794 genes (and their protein-level translation) is a reference resistome that comes from contigs functionally associated with antibiotic resistance in preterm infants (Gibson et al. 2016) to overcome inconsistencies in existing AMR gene databases. 79% (n=627 out of 794) of these AMR genes had no clear homology to known ones. This reference resistome came from 401 stool samples longitudinally collected from 84 infants undergoing antibiotic treatment, and were assembled as 2,004 redundant AMR contigs experimentally tested in vitro for resistance to 16 antibiotics (Gibson et al. 2016).
DOI: 10.6084/m9.figshare.11961402.v1
title: 794_AMR_genes_Gibson_et_al

description: This dataset of 794 genes (and their protein-level translation) is a reference resistome that comes from contigs functionally associated with antibiotic resistance in preterm infants (Gibson et al. 2016) to overcome inconsistencies in existing AMR gene databases. 79% (n=627 out of 794) of these AMR genes had no clear homology to known ones. This reference resistome came from 401 stool samples longitudinally collected from 84 infants undergoing antibiotic treatment, and were assembled as 2,004 redundant AMR contigs experimentally tested in vitro for resistance to 16 antibiotics (Gibson et al. 2016).
DOI: 10.6084/m9.figshare.11961369
title: PLSDB 2020_03_04

description: PLSDB files from 2020.03.04<br>
DOI: 10.6084/m9.figshare.11961369.v1
title: PLSDB 2020_03_04

description: PLSDB files from 2020.03.04<br>
DOI: 10.6084/m9.figshare.11961345
title: Reliable Components Analysis datasets and metadata supporting the published article: Neural dynamics underlying coherent motion perception in children and adults

description: This fileset contains Reliable Components Analysis data related to the following published article: Catherine Manning, Blair Kaneshiro, Peter J. Kohler, Mihaela Duta, Gaia Scerif and Anthony M. Norcia. (2019). Neural dynamics underlying coherent motion perception in children and adults. <i>Developmental Cognitive Neuroscience, 38, </i>100670 https://doi.org/10.1016/j.dcn.2019.100670<i>.</i><i><br></i> <i> </i> Dataset <b>demographics_incl.csv</b> is in <b>.csv</b> file format and includes the age for each of 122 participants (102 children, 20 adults). DevCond refers to whether the participant has a developmental condition (1 = developmental condition, 0 = no developmental conditions; i.e., none of the participants have developmental conditions). Hands refers to the response condition that the participant was assigned to (1 = used left hand to respond up & right hand to respond down; 2 = used right hand to respond up and left hand to respond down). ID numbers beginning C are child participants and ID numbers beginning A are adult participants. <br> Data files <b>cohOut_group_1.mat, </b><b>cohOut_group_2.mat, cohOut_group_3.mat, cohOut_group_4.mat, MOVEP_datIn_group1.mat, MOVEP_datIn_group2.mat, MOVEP_datIn_group3.mat, MOVEP_datIn_group4.mat, MOVEP_datInLong_group1.mat, MOVEP_datInLong_group2.mat, MOVEP_datInLong_group3.mat, MOVEP_datInLong_group4.mat</b> are group summaries, in comparison to the 122 <b>Formatted_XXXX.3_40_preproc.mat</b> files, which are individual data files. More information about the contents of these files are provided in the document <b>Details on group summary files.docx</b>
DOI: 10.6084/m9.figshare.11961345.v1
title: Reliable Components Analysis datasets and metadata supporting the published article: Neural dynamics underlying coherent motion perception in children and adults

description: This fileset contains Reliable Components Analysis data related to the following published article: Catherine Manning, Blair Kaneshiro, Peter J. Kohler, Mihaela Duta, Gaia Scerif and Anthony M. Norcia. (2019). Neural dynamics underlying coherent motion perception in children and adults. <i>Developmental Cognitive Neuroscience, 38, </i>100670 https://doi.org/10.1016/j.dcn.2019.100670<i>.</i><i><br></i> <i> </i> Dataset <b>demographics_incl.csv</b> is in <b>.csv</b> file format and includes the age for each of 122 participants (102 children, 20 adults). DevCond refers to whether the participant has a developmental condition (1 = developmental condition, 0 = no developmental conditions; i.e., none of the participants have developmental conditions). Hands refers to the response condition that the participant was assigned to (1 = used left hand to respond up & right hand to respond down; 2 = used right hand to respond up and left hand to respond down). ID numbers beginning C are child participants and ID numbers beginning A are adult participants. <br> Data files <b>cohOut_group_1.mat, </b><b>cohOut_group_2.mat, cohOut_group_3.mat, cohOut_group_4.mat, MOVEP_datIn_group1.mat, MOVEP_datIn_group2.mat, MOVEP_datIn_group3.mat, MOVEP_datIn_group4.mat, MOVEP_datInLong_group1.mat, MOVEP_datInLong_group2.mat, MOVEP_datInLong_group3.mat, MOVEP_datInLong_group4.mat</b> are group summaries, in comparison to the 122 <b>Formatted_XXXX.3_40_preproc.mat</b> files, which are individual data files. More information about the contents of these files are provided in the document <b>Details on group summary files.docx</b>
DOI: 10.6084/m9.figshare.11961321
title: Supplementary Material for: Development and Validation of a Nomogram for Patients with Nonmetastatic BCLC Stage C Hepatocellular Carcinoma after Stereotactic Body Radiotherapy

description: <b><i>Background:</i></b> Stereotactic body radiotherapy (SBRT) is an emerging treatment modality for hepatocellular carcinoma (HCC) with promising outcome. However, appropriate survival prediction models are scarce. This study aimed to develop a simple and clinically useful prognostic nomogram for patients with nondistant metastatic Barcelona Clinic Liver Cancer (BCLC) stage C HCC undergoing SBRT. <b><i>Methods:</i></b> The data were based on a prospective multi-institutional registry enrolling 246 patients with nondistant metastatic BCLC stage C HCC treated with SBRT between January 1, 2008 and December 31, 2016. They were randomly divided into two subsets: 164 into the development cohort and 82 into the validation cohort. We identified and included prognostic factors for survival to derive a nomogram in the development cohort. The predictability of the nomogram was evaluated in the validation cohort. The area under the receiver operating characteristic curve (AUROC) and the calibration plot were used to evaluate the performance of the nomogram. <b><i>Results:</i></b> The median survival was 13.5 months, with 1- and 2-year overall survival (OS) rates of 55.0 and 32.9%, respectively. Number of tumors, largest tumor size, macrovascular invasion, Child-Turcotte-Pugh class, and biologically effective dose were significantly associated with OS (<i>p</i> &lt; 0.05). These predictors were included to develop a nomogram with an AUROC of 0.77 (0.73–0.87). The prediction model was well calibrated in the validation cohort. The OS for patients who were divided by their risk scores differed significantly (<i>p</i> &lt; 0.001). <b><i>Conclusions:</i></b> The nomogram we generated had discriminatory and satisfactory predictability for OS among nonmetastatic BCLC stage C HCC patients treated with SBRT. It demands further validations with cross-country data to confirm its worldwide usefulness.
DOI: 10.6084/m9.figshare.11961261
title: glaucoma-associated microRNA

description: glaucoma-associated microRNA
DOI: 10.6084/m9.figshare.11961243
title: Cranial anatomy of the predatory actinopterygian <i>Brazilichthys macrognathus</i> from the Permian (Cisuralian) Pedra de Fogo Formation, Parnaíba Basin, Brazil

description: <i>Brazilichthys macrognathus</i> is the only named actinopterygian from the Permian (Cisuralian) Pedra de Fogo Formation of northeastern Brazil, in which it is represented by a single three-dimensionally preserved, but incompletely described, skull of unclear systematic placement. We used X-ray micro-computed tomography (µCT) to redescribe its anatomy, in particular parts of the internal skeleton, and assess its phylogenetic affinities. We correct errors in the original description, including the number of infraorbital bones and the misidentification of the dermosphenotic as sclerotic ossifications. These reinterpretations of external anatomy are accompanied by new data on internal structure, including the palate, the parasphenoid, and the branchial and hyoid arches. A maximum parsimony analysis of anatomical data resolves <i>Brazilichthys</i> as a stem actinopterygian, crownward of all Devonian species. This placement is supported by the absence of a dermosphenotic posterior ramus and the presence of opercular process of the hyomandibula. A similar placement is suggested by a Bayesian analysis of the same data set, although relationships throughout the tree are less resolved. Our results reject previous interpretations of <i>Brazilichthys</i> as a relative of Birgeriidae, a Triassic group traditionally placed within the actinopterygian crown. Although <i>Acrolepis</i> is too poorly known to be included in our analysis, we also reject relationship between that taxon and <i>Brazilichthys</i>, because their only shared similarities appear to be broadly distributed among early actinopterygians.
DOI: 10.6084/m9.figshare.11961243.v1
title: Cranial anatomy of the predatory actinopterygian <i>Brazilichthys macrognathus</i> from the Permian (Cisuralian) Pedra de Fogo Formation, Parnaíba Basin, Brazil

description: <i>Brazilichthys macrognathus</i> is the only named actinopterygian from the Permian (Cisuralian) Pedra de Fogo Formation of northeastern Brazil, in which it is represented by a single three-dimensionally preserved, but incompletely described, skull of unclear systematic placement. We used X-ray micro-computed tomography (µCT) to redescribe its anatomy, in particular parts of the internal skeleton, and assess its phylogenetic affinities. We correct errors in the original description, including the number of infraorbital bones and the misidentification of the dermosphenotic as sclerotic ossifications. These reinterpretations of external anatomy are accompanied by new data on internal structure, including the palate, the parasphenoid, and the branchial and hyoid arches. A maximum parsimony analysis of anatomical data resolves <i>Brazilichthys</i> as a stem actinopterygian, crownward of all Devonian species. This placement is supported by the absence of a dermosphenotic posterior ramus and the presence of opercular process of the hyomandibula. A similar placement is suggested by a Bayesian analysis of the same data set, although relationships throughout the tree are less resolved. Our results reject previous interpretations of <i>Brazilichthys</i> as a relative of Birgeriidae, a Triassic group traditionally placed within the actinopterygian crown. Although <i>Acrolepis</i> is too poorly known to be included in our analysis, we also reject relationship between that taxon and <i>Brazilichthys</i>, because their only shared similarities appear to be broadly distributed among early actinopterygians.
DOI: 10.6084/m9.figshare.11961204
title: Supplementary Material for: Healthcare Costs and Utilization among Patients Hospitalized for Malignant Pleural Effusion

description: <b><i>Background:</i></b> Malignant pleural effusion (MPE) poses a considerable healthcare burden, but little is known about trends in directly attributable hospital utilization. <b><i>Objective:</i></b> We aimed to study national trends in healthcare utilization and outcomes among hospitalized MPE patients. <b><i>Methods:</i></b> We analyzed adult hospitalizations attributable to MPE using the Healthcare Cost and Utilization Project – National Inpatient Sample (HCUP-NIS) databases from 2004, 2009, and 2014. Cases were included if MPE was coded as the principal admission diagnosis or if unspecified pleural effusion was coded as the principal admission diagnosis in the setting of metastatic cancer. Annual hospitalizations were estimated for the entire US hospital population using discharge weights. Length of stay (LOS), hospital charges, and hospital mortality were also estimated. <b><i>Results:</i></b> We analyzed 92,034 hospital discharges spanning a decade (2004–2014). Yearly hospitalizations steadily decreased from 38,865 to 23,965 during this time frame, the mean LOS decreased from 7.7 to 6.3 days, and the adjusted hospital mortality decreased from 7.9 to 4.5% (<i>p</i> = 0.00 for all trend analyses). The number of pleurodesis procedures also decreased over time (<i>p</i> = 0.00). The mean inflation-adjusted charge per hospitalization rose from USD 41,252 to USD 56,951, but fewer hospitalizations drove the total annual charges down from USD 1.51 billion to USD 1.37 billion (<i>p</i> = 0.00 for both analyses). <b><i>Conclusions:</i></b> The burden of hospital-based resource utilization associated with MPE has decreased over time, with a reduction in attributable hospitalizations by one third in the span of 1 decade. Correspondingly, the number of inpatient pleurodesis procedures has decreased during this time frame.
DOI: 10.6084/m9.figshare.11961204.v1
title: Supplementary Material for: Healthcare Costs and Utilization among Patients Hospitalized for Malignant Pleural Effusion

description: <b><i>Background:</i></b> Malignant pleural effusion (MPE) poses a considerable healthcare burden, but little is known about trends in directly attributable hospital utilization. <b><i>Objective:</i></b> We aimed to study national trends in healthcare utilization and outcomes among hospitalized MPE patients. <b><i>Methods:</i></b> We analyzed adult hospitalizations attributable to MPE using the Healthcare Cost and Utilization Project – National Inpatient Sample (HCUP-NIS) databases from 2004, 2009, and 2014. Cases were included if MPE was coded as the principal admission diagnosis or if unspecified pleural effusion was coded as the principal admission diagnosis in the setting of metastatic cancer. Annual hospitalizations were estimated for the entire US hospital population using discharge weights. Length of stay (LOS), hospital charges, and hospital mortality were also estimated. <b><i>Results:</i></b> We analyzed 92,034 hospital discharges spanning a decade (2004–2014). Yearly hospitalizations steadily decreased from 38,865 to 23,965 during this time frame, the mean LOS decreased from 7.7 to 6.3 days, and the adjusted hospital mortality decreased from 7.9 to 4.5% (<i>p</i> = 0.00 for all trend analyses). The number of pleurodesis procedures also decreased over time (<i>p</i> = 0.00). The mean inflation-adjusted charge per hospitalization rose from USD 41,252 to USD 56,951, but fewer hospitalizations drove the total annual charges down from USD 1.51 billion to USD 1.37 billion (<i>p</i> = 0.00 for both analyses). <b><i>Conclusions:</i></b> The burden of hospital-based resource utilization associated with MPE has decreased over time, with a reduction in attributable hospitalizations by one third in the span of 1 decade. Correspondingly, the number of inpatient pleurodesis procedures has decreased during this time frame.
DOI: 10.6084/m9.figshare.11961159
title: Fatigue indices and perceived exertion highlight ergometer specificity for repeated sprint ability testing

description: This study aimed to compare the timecourse of measures of performance, fatigue and perceived exertion during repeated-sprint ability (RSA) testing performed on a non-motorised treadmill (NMT) and cycling ergometer (CE). Fourteen physically-active participants performed two 10x6 sec<sup>-1 </sup>RSA tests with a 1:4 work-to-rest ratio (24 s recovery) on NMT and CE. Measures of performance (peak and mean power output [PPO and MPO], cadence and the time to reach PPO [TTP]), of fatigue (fatigue index and decrement score) and ratings of perceived exertion (RPE) were collected during each session. The level of significance was set at p&lt;0.05. Participants completed the RSA test at a MPO of 1041±141 W on CE and 431±48 W on NMT, achieving PPO of 2310±339 W on CE and 1763±289 W on NMT. Participants’ weight was significantly correlated with PPO and MPO on CE (p&lt;0.001), and with MPO on NMT (p&lt;0.001). PPO on CE and NMT were significantly correlated only for absolute measures of power (p&lt;0.01). Cadence was higher and decreased throughout the RSA on NMT compared to CE, where it decreased only at the 7<sup>th</sup> bout. TTP was significantly shorter and more affected by fatigue on NMT than on CE. Fatigue indices were significantly greater on NMT compared to CE, with significant correlations between the decrement score and absolute and relative PPO on CE and NMT, between the fatigue index and absolute and relative PPO only on NMT, and no significant correlations with MPO. During RSA, RPE increased more on NMT compared to CE from bouts 3 to 7. During recovery, RPE was consistently higher on NMT at 1, 3 and 5 min postexercise compared to CE. These findings indicate that RSA performed on NMT induces greater fatigue and physiological load than CE, which originated in the lower resistive torque typically used on NMT compared to CE, resulting in a frontloaded power output profile from the greater acceleration and cadence. From these results, we discuss that despite providing highly correlated measures of power output, NMT and CE should not be used interchangeably to assess RSA as they elicit markedly different responses. We also discuss these results from the fundamental differences in active muscle mass and power application patterns between running and cycling, which could form the basis of future studies.
DOI: 10.6084/m9.figshare.11961150
title: Supplementary Material for: Treating Parental Burnout: Impact of Two Treatment Modalities on Burnout Symptoms, Emotions, Hair Cortisol, and Parental Neglect and Violence

description: Medicine
DOI: 10.6084/m9.figshare.11961150.v1
title: Supplementary Material for: Treating Parental Burnout: Impact of Two Treatment Modalities on Burnout Symptoms, Emotions, Hair Cortisol, and Parental Neglect and Violence

description: Medicine
DOI: 10.6084/m9.figshare.11961159.v1
title: Fatigue indices and perceived exertion highlight ergometer specificity for repeated sprint ability testing

description: This study aimed to compare the timecourse of measures of performance, fatigue and perceived exertion during repeated-sprint ability (RSA) testing performed on a non-motorised treadmill (NMT) and cycling ergometer (CE). Fourteen physically-active participants performed two 10x6 sec<sup>-1 </sup>RSA tests with a 1:4 work-to-rest ratio (24 s recovery) on NMT and CE. Measures of performance (peak and mean power output [PPO and MPO], cadence and the time to reach PPO [TTP]), of fatigue (fatigue index and decrement score) and ratings of perceived exertion (RPE) were collected during each session. The level of significance was set at p&lt;0.05. Participants completed the RSA test at a MPO of 1041±141 W on CE and 431±48 W on NMT, achieving PPO of 2310±339 W on CE and 1763±289 W on NMT. Participants’ weight was significantly correlated with PPO and MPO on CE (p&lt;0.001), and with MPO on NMT (p&lt;0.001). PPO on CE and NMT were significantly correlated only for absolute measures of power (p&lt;0.01). Cadence was higher and decreased throughout the RSA on NMT compared to CE, where it decreased only at the 7<sup>th</sup> bout. TTP was significantly shorter and more affected by fatigue on NMT than on CE. Fatigue indices were significantly greater on NMT compared to CE, with significant correlations between the decrement score and absolute and relative PPO on CE and NMT, between the fatigue index and absolute and relative PPO only on NMT, and no significant correlations with MPO. During RSA, RPE increased more on NMT compared to CE from bouts 3 to 7. During recovery, RPE was consistently higher on NMT at 1, 3 and 5 min postexercise compared to CE. These findings indicate that RSA performed on NMT induces greater fatigue and physiological load than CE, which originated in the lower resistive torque typically used on NMT compared to CE, resulting in a frontloaded power output profile from the greater acceleration and cadence. From these results, we discuss that despite providing highly correlated measures of power output, NMT and CE should not be used interchangeably to assess RSA as they elicit markedly different responses. We also discuss these results from the fundamental differences in active muscle mass and power application patterns between running and cycling, which could form the basis of future studies.
DOI: 10.6084/m9.figshare.11961126
title: Crane Phylosymbiosis Data Files from A bird's-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes

description: In numerous animal clades, the evolutionary history of host species drives patterns of gut microbial community structure, resulting in more divergent microbiota with increasing phylogenetic distance between hosts. This phenomenon, termed phylosymbiosis, has been observed in diverse evolutionary lineages, but has been difficult to detect in birds. Previous tests of phylosymbiosis among birds have been conducted using wild individuals, and thus interspecific differences in diet and environment may have masked a phylogenetic signal. Therefore, we tested for phylosymbiosis among all 15 species of cranes (family Gruidae) housed in the same captive environment and maintained on identical diets. 16S rRNA sequencing revealed that crane species harbour distinct gut microbiota. Overall, we detected marginally significant patterns of phylosymbiosis, the strength of which was increased when including the estimates of absolute microbial abundance (rather than relative abundance) derived from microbial densities determined by flow cytometry. Using this approach, we detected the statistically significant signatures of phylosymbiosis only after removing male cranes from our analysis, suggesting that using mixed-sex animal cohorts may prevent the detection of phylosymbiosis. Though weak compared with mammals (and especially insects), these results provide evidence of phylosymbiosis in birds. We discuss the potential differences between birds and mammals, such as transmission routes and host filtering, that may underlie the differences in the strength of phylosymbiosis.
DOI: 10.6084/m9.figshare.11961126.v1
title: Crane Phylosymbiosis Data Files from A bird's-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes

description: In numerous animal clades, the evolutionary history of host species drives patterns of gut microbial community structure, resulting in more divergent microbiota with increasing phylogenetic distance between hosts. This phenomenon, termed phylosymbiosis, has been observed in diverse evolutionary lineages, but has been difficult to detect in birds. Previous tests of phylosymbiosis among birds have been conducted using wild individuals, and thus interspecific differences in diet and environment may have masked a phylogenetic signal. Therefore, we tested for phylosymbiosis among all 15 species of cranes (family Gruidae) housed in the same captive environment and maintained on identical diets. 16S rRNA sequencing revealed that crane species harbour distinct gut microbiota. Overall, we detected marginally significant patterns of phylosymbiosis, the strength of which was increased when including the estimates of absolute microbial abundance (rather than relative abundance) derived from microbial densities determined by flow cytometry. Using this approach, we detected the statistically significant signatures of phylosymbiosis only after removing male cranes from our analysis, suggesting that using mixed-sex animal cohorts may prevent the detection of phylosymbiosis. Though weak compared with mammals (and especially insects), these results provide evidence of phylosymbiosis in birds. We discuss the potential differences between birds and mammals, such as transmission routes and host filtering, that may underlie the differences in the strength of phylosymbiosis.