cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5692930
title: Mikado compare analyses

description: This dataset contains the results of Mikado compare results for all the assemblers and combiners. For details on the file formats, please consult the online documentation for Mikado:<br><br>https://mikado.readthedocs.io/en/latest/Usage/Compare.html<br><br>- Comparisons_real_and_simulated: comparisons for the real and simulated datasets. <br>- Multiple_Isoform_Fractions_comparisons.zip: comparisons for Stringtie/CLASS and derived Mikados obtained by varying the MIF parameter.<br>- Comparisons_multiple_samples.zip: Comparisons for the assemblies and combinations obtained by analysing multiple samples of A. thaliana.<br>- Comparisons_pacbio.zip: Comparisons for the analysis on human and Illumina and PacBio data (raw assemblies/alignments, EvidentialGene, and Mikado).<br>
DOI: 10.6084/m9.figshare.5692930.v1
title: Mikado compare analyses

description: This dataset contains the results of Mikado compare results for all the assemblers and combiners. For details on the file formats, please consult the online documentation for Mikado:<br><br>https://mikado.readthedocs.io/en/latest/Usage/Compare.html<br><br>- Comparisons_real_and_simulated: comparisons for the real and simulated datasets. <br>- Multiple_Isoform_Fractions_comparisons.zip: comparisons for Stringtie/CLASS and derived Mikados obtained by varying the MIF parameter.<br>- Comparisons_multiple_samples.zip: Comparisons for the assemblies and combinations obtained by analysing multiple samples of A. thaliana.<br>- Comparisons_pacbio.zip: Comparisons for the analysis on human and Illumina and PacBio data (raw assemblies/alignments, EvidentialGene, and Mikado).<br>
DOI: 10.6084/m9.figshare.5692852
title: Intrinsic ankle stiffness during standing increases with ankle torque and passive stretch of the Achilles tendon _ Study 2 dataset

description: Dataset used for study 2 (dorsiflexion). <br><br>pXX_normal / dorsi = trials recorded with perturbations to measure stiffness<br><br>pXX_topplingtorque = trials recorded for toppling torque per unit angle estimation, in which participants were swaying backwards/forwards very gently<br><br>Data recordings are distributed as:<br> <br>pos=calibrate(Dataset(:,2),potCF); % footplate angular rotation<br>LTq=calibrate(Dataset(:,4),ltqCF); % left torque<br>acc=Dataset(:,3); acc=calibrate(acc,accCF); % acceleration<br>laser1=calibrate(Dataset(:,6),laser1CF); <br>shinpos=atan(laser1./laserH1); % calculate angular rotation with atan of tan=linear displacement/laser height <br>anklepos=pos+shinpos; % ankle angular rotation<br>laser2=calibrate(Dataset(:,7),laser2CF); boardpos=atan(laser2./laserH2); <br>bodypos=pos+boardpos; % body angular rotation <br>EMG1=abs(Dataset(:,8)); % channel 7 EMG1 (left tibialis anterior)<br>EMG2=abs(Dataset(:,9)); % channel 8 EMG2 (left medial gastrocnemius)<br>EMG3=abs(Dataset(:,10)); % channel 9 EMG3 (right tibialis anterior)<br>EMG4=abs(Dataset(:,11)); % channel 10 EMG4 (right medial gastrocnemius)<br><br>Calibration: <br> Motor 0,6 <br> Potentiometer (rad) 0,0253 <br>Potentiometer (deg) 1,45 <br>Left load cell -9,88 <br>Right load cell -20,6 <br>Accelerometer -127,681 <br>Laser #1 0,01 <br>Laser #2 0,02
DOI: 10.6084/m9.figshare.5692852.v1
title: Intrinsic ankle stiffness during standing increases with ankle torque and passive stretch of the Achilles tendon _ Study 2 dataset

description: Dataset used for study 2 (dorsiflexion). <br><br>pXX_normal / dorsi = trials recorded with perturbations to measure stiffness<br><br>pXX_topplingtorque = trials recorded for toppling torque per unit angle estimation, in which participants were swaying backwards/forwards very gently<br><br>Data recordings are distributed as:<br> <br>pos=calibrate(Dataset(:,2),potCF); % footplate angular rotation<br>LTq=calibrate(Dataset(:,4),ltqCF); % left torque<br>acc=Dataset(:,3); acc=calibrate(acc,accCF); % acceleration<br>laser1=calibrate(Dataset(:,6),laser1CF); <br>shinpos=atan(laser1./laserH1); % calculate angular rotation with atan of tan=linear displacement/laser height <br>anklepos=pos+shinpos; % ankle angular rotation<br>laser2=calibrate(Dataset(:,7),laser2CF); boardpos=atan(laser2./laserH2); <br>bodypos=pos+boardpos; % body angular rotation <br>EMG1=abs(Dataset(:,8)); % channel 7 EMG1 (left tibialis anterior)<br>EMG2=abs(Dataset(:,9)); % channel 8 EMG2 (left medial gastrocnemius)<br>EMG3=abs(Dataset(:,10)); % channel 9 EMG3 (right tibialis anterior)<br>EMG4=abs(Dataset(:,11)); % channel 10 EMG4 (right medial gastrocnemius)<br><br>Calibration: <br> Motor 0,6 <br> Potentiometer (rad) 0,0253 <br>Potentiometer (deg) 1,45 <br>Left load cell -9,88 <br>Right load cell -20,6 <br>Accelerometer -127,681 <br>Laser #1 0,01 <br>Laser #2 0,02
DOI: 10.6084/m9.figshare.5692834
title: Allen Human Brain Atlas H0351.2002

description: The dataset is a zip archive. It contains normalised gene expression values in brain regions available from Allen Brain Atlas http://human.brain-map.org.This archive contains normalized microarray expression values as well as probe and sample metadata necessary for analysis, altogether there are four files.<br>The details about normalization procedure are provided in the technical white paper http://help.brain-map.org/display/humanbrain/Documentation
DOI: 10.6084/m9.figshare.5692834.v1
title: Allen Human Brain Atlas H0351.2002

description: The dataset is a zip archive. It contains normalised gene expression values in brain regions available from Allen Brain Atlas http://human.brain-map.org.This archive contains normalized microarray expression values as well as probe and sample metadata necessary for analysis, altogether there are four files.<br>The details about normalization procedure are provided in the technical white paper http://help.brain-map.org/display/humanbrain/Documentation
DOI: 10.6084/m9.figshare.5692831
title: Allen Human Brain Atlas H0351.2001

description: The dataset is a zip archive. It contains normalised gene expression values in brain regions available from Allen Brain Atlas http://human.brain-map.org.This archive contains normalized microarray expression values as well as probe and sample metadata necessary for analysis, altogether there are four files.<br>The details about normalization procedure are provided in the technical white paper http://help.brain-map.org/display/humanbrain/Documentation
DOI: 10.6084/m9.figshare.5692831.v1
title: Allen Human Brain Atlas H0351.2001

description: The dataset is a zip archive. It contains normalised gene expression values in brain regions available from Allen Brain Atlas http://human.brain-map.org.This archive contains normalized microarray expression values as well as probe and sample metadata necessary for analysis, altogether there are four files.<br>The details about normalization procedure are provided in the technical white paper http://help.brain-map.org/display/humanbrain/Documentation
DOI: 10.6084/m9.figshare.5692804
title: Genome wide selection for the economic value of forage yield in tetraploid perennial ryegrass.

description: Poster presented at Plant and Animal Genome (PAG) January 2018 on using genomic variants to predict forage yield in perennial ryegrass.
DOI: 10.6084/m9.figshare.5692804.v2
title: Genome wide selection for the economic value of forage yield in tetraploid perennial ryegrass.

description: Poster presented at Plant and Animal Genome (PAG) January 2018 on using genomic variants to predict forage yield in perennial ryegrass.
DOI: 10.6084/m9.figshare.5692741
title: Food consumption in ground beetles is limited under hypoxic conditions when feeding on large but not on small meals

description: Habitats on land with low oxygen availability provide unique niches inhabited by numerous species. The occupation of such hypoxic niches by animals is hypothesized to come at a cost linked to the limitations of aerobic metabolism and thus energy budget but may also provide benefits through physical protection from predators and parasitoids or reduced competition for food. We investigated the effects of hypoxic conditions on standard metabolic rate (SMR) and specific dynamic action (SDA) in male <i>Carabus nemoralis</i>. SMR and SDA were determined under three manipulated oxygen availabilities: 7, 14 and 21% O<sub>2</sub> and two feeding regimes: limited or <i>ad libitum</i> food consumption. In both hypoxic conditions, <i>C. nemoralis</i> was able to maintain SMR at levels similar to those in normoxia. When the meal size was limited, SDA duration did not differ among the oxygen availability conditions, but SDA was smaller under hypoxic conditions than at normoxic levels. The relative cost of digestion was significantly higher in normoxia than in hypoxia, but it did not affect net energy intake. In contrast, when offered a large meal to simulate <i>ad libitum</i> food conditions, beetles reduced their food consumption and net energy gain by 30% under hypoxia. Oxygen availability may influence the consumed prey size: the hypoxic condition did not limit net energy gain when the beetles fed on a small meal but did when they fed on a large meal. The results indicate that meal size is an important variable in determining differences in physiological costs and whole animal energy budgets at different concentrations of environmental oxygen levels.
DOI: 10.6084/m9.figshare.5692741.v1
title: Food consumption in ground beetles is limited under hypoxic conditions when feeding on large but not on small meals

description: Habitats on land with low oxygen availability provide unique niches inhabited by numerous species. The occupation of such hypoxic niches by animals is hypothesized to come at a cost linked to the limitations of aerobic metabolism and thus energy budget but may also provide benefits through physical protection from predators and parasitoids or reduced competition for food. We investigated the effects of hypoxic conditions on standard metabolic rate (SMR) and specific dynamic action (SDA) in male <i>Carabus nemoralis</i>. SMR and SDA were determined under three manipulated oxygen availabilities: 7, 14 and 21% O<sub>2</sub> and two feeding regimes: limited or <i>ad libitum</i> food consumption. In both hypoxic conditions, <i>C. nemoralis</i> was able to maintain SMR at levels similar to those in normoxia. When the meal size was limited, SDA duration did not differ among the oxygen availability conditions, but SDA was smaller under hypoxic conditions than at normoxic levels. The relative cost of digestion was significantly higher in normoxia than in hypoxia, but it did not affect net energy intake. In contrast, when offered a large meal to simulate <i>ad libitum</i> food conditions, beetles reduced their food consumption and net energy gain by 30% under hypoxia. Oxygen availability may influence the consumed prey size: the hypoxic condition did not limit net energy gain when the beetles fed on a small meal but did when they fed on a large meal. The results indicate that meal size is an important variable in determining differences in physiological costs and whole animal energy budgets at different concentrations of environmental oxygen levels.
DOI: 10.6084/m9.figshare.5692723
title: Image dataset

description: 1,000 original images with no transformation (only resized).<br>3,000 rotated images (the original one with rotations of 90, 180 and 270 degrees).4,000 images with a frame (applied to the original one and its possible rotations).4,000 images with a color mask (applied to the original one and its possible rotations).4,000 images with a watermark (applied to the original one and its possible rotations).4,000 images with a watermark and a frame (applied to the original one and its possible rotations).4,000 images with a watermark and a color mask (applied to the original one and its possible rotations).4,000 images with a frame and a color mask (applied to the original one and its possible rotations).4,000 images with a frame, a watermark and a color mask (applied to the original one and its possible rotations).
DOI: 10.6084/m9.figshare.5692117
title: Clinicopathological and prognostic significance of platelet count in patients with ovarian cancer

description: <b>Aim:</b> Increasing evidence indicates that platelet count is a useful biomarker of long-term outcomes in patients with ovarian cancer. However, the prognostic value of platelet count in patients with ovarian cancer remains controversial. We therefore conducted a meta-analysis aimed to investigate the prognostic role of the platelet count in patients with ovarian cancer. <b>Method:</b> A comprehensive search was performed from the databases of PubMed, Embase and the Cochrane Library until June 20, 2017. A total of 18 studies with 6754 patients were included. Hazard ratios (HRs) and the corresponding 95% confidence intervals (CIs) and odds ratios and 95% CIs from each study were pooled. <b>Results:</b> The results demonstrated that elevated pretreatment platelet count was significantly related to poor survival from ovarian cancer; the pooled HRs for overall, progression-free and disease-free survival were 1.81 (95% CI 1.52–2.15), 1.48 (95% CI 1.24–1.75) and 1.39 (95% CI 1.19–1.61), respectively. Subgroup analyses were divided by ethnicity, sample size, FIGO stage, cut-off value of the platelet count, analysis method and Newcastle Ottawa Scale score, but the results did not show any significant change in the main results. Increased platelet count was also significantly associated with the FIGO stage, tumor differentiation, ascites, residual tumor mass, CA125 level, recurrence and metastasis. <b>Conclusion:</b> This meta-analysis revealed that an elevated platelet count pretreatment denotes a predictive factor of poor prognosis and unfavorable clinicopathological parameters for ovarian cancer patients.
DOI: 10.6084/m9.figshare.5692117.v1
title: Clinicopathological and prognostic significance of platelet count in patients with ovarian cancer

description: <b>Aim:</b> Increasing evidence indicates that platelet count is a useful biomarker of long-term outcomes in patients with ovarian cancer. However, the prognostic value of platelet count in patients with ovarian cancer remains controversial. We therefore conducted a meta-analysis aimed to investigate the prognostic role of the platelet count in patients with ovarian cancer. <b>Method:</b> A comprehensive search was performed from the databases of PubMed, Embase and the Cochrane Library until June 20, 2017. A total of 18 studies with 6754 patients were included. Hazard ratios (HRs) and the corresponding 95% confidence intervals (CIs) and odds ratios and 95% CIs from each study were pooled. <b>Results:</b> The results demonstrated that elevated pretreatment platelet count was significantly related to poor survival from ovarian cancer; the pooled HRs for overall, progression-free and disease-free survival were 1.81 (95% CI 1.52–2.15), 1.48 (95% CI 1.24–1.75) and 1.39 (95% CI 1.19–1.61), respectively. Subgroup analyses were divided by ethnicity, sample size, FIGO stage, cut-off value of the platelet count, analysis method and Newcastle Ottawa Scale score, but the results did not show any significant change in the main results. Increased platelet count was also significantly associated with the FIGO stage, tumor differentiation, ascites, residual tumor mass, CA125 level, recurrence and metastasis. <b>Conclusion:</b> This meta-analysis revealed that an elevated platelet count pretreatment denotes a predictive factor of poor prognosis and unfavorable clinicopathological parameters for ovarian cancer patients.
DOI: 10.6084/m9.figshare.5692006
title: Posture alteration as a measure to accommodate uneven ground in able-bodied gait

description: Data-set collected from 12 participants contains: The ensemble average of following parameters of interest, in addition to their angular trajectories throughout stance phase of each individual step, were determined in the sagittal plane: 1) hip, knee and ankle joint angles at the instants of TD and TO (ankle: dorsiflexion and plantarflexion); 2) effective leg length, defined as the length between the hip and CoP; 3) vertical position of the CoM relative to the ground determined by the body segmental analysis method relative to the laboratory coordinate system throughout the stance phase; 4) leg angle, angle between effective leg and ground was calculated with respect to the negative x-axis. The effective leg length and CoM were both normalized to the distance between the greater trochanter marker and the lateral malleoli marker at the instant of TD. Backward rotation during step-down was calculated as the difference of the maximum of the trunk angle in the pre-perturbation step and the minimal trunk angle in perturbation step (step-down). Each column lists the mean value of variable of interest pertaining 12 participants. The dataset is arranged for the performance of a two-way repeated measures ANOVA to examine the effects of the posture (regular erect, 30° and 50° of trunk flexion from the vertical) and step (level step, pre-perturbation step, step-down, step-up).Zero values within the Exel file represent NaN. For understanding the names (i.e., abbrev./codes) given to the variable, please refer to 'read me' file. <br>
DOI: 10.6084/m9.figshare.5691982
title: Dataset for: Subgroup identification in dose-finding trials via model-based recursive partitioning

description: An important task in early phase drug development is to identify patients, which respond better or worse to an experimental treatment. While a variety of different subgroup identification methods have been developed for the situation of trials that study an experimental treatment and control, much less work has been done in the situation when patients are randomized to different dose groups. In this article we propose new strategies to perform subgroup analyses in dose-finding trials and discuss the challenges, which arise in this new setting. We consider model-based recursive partitioning, which has recently been applied to subgroup identification in two arm trials, as a promising method to tackle these challenges and assess its viability using a real trial example and simulations.Our results show that model-based recursive partitioning can be used to identify subgroups of patients with different dose-response curves and improves estimation of treatment effects and minimum effective doses, when heterogeneity among patients is present.
DOI: 10.6084/m9.figshare.5691982.v1
title: Dataset for: Subgroup identification in dose-finding trials via model-based recursive partitioning

description: An important task in early phase drug development is to identify patients, which respond better or worse to an experimental treatment. While a variety of different subgroup identification methods have been developed for the situation of trials that study an experimental treatment and control, much less work has been done in the situation when patients are randomized to different dose groups. In this article we propose new strategies to perform subgroup analyses in dose-finding trials and discuss the challenges, which arise in this new setting. We consider model-based recursive partitioning, which has recently been applied to subgroup identification in two arm trials, as a promising method to tackle these challenges and assess its viability using a real trial example and simulations.Our results show that model-based recursive partitioning can be used to identify subgroups of patients with different dose-response curves and improves estimation of treatment effects and minimum effective doses, when heterogeneity among patients is present.
DOI: 10.6084/m9.figshare.5691934
title: Dataset for: Broadband homonuclear decoupled HSQMBC methods

description: Long-range heteronuclear coupling constants convey invaluable information for stereochemical and conformational analysis of molecules from synthetic and natural origin. Here we report a real-time Zangger-Sterk CPMG-HSQMBC method for the precise and direct measurement of multiple-bond heteronuclear couplings. It is demonstrated that the real-time acquisition strategy combined with multiple slice selective excitation can provide substantial improvement in sensitivity (or reduction of experimental time) as compared to other variants of broadband homonuclear decoupled HSQMBC methods published previously. Scope and limitations of the different strategies applied for decoupling are reviewed. Moreover, practical guidelines for the choice of the most appropriate method are also presented. Applications are given on a metal complex incorporating P-heterocycles and two diglycosyl-selenides for the extraction of <sup>n</sup><i>J</i>(<sup>1</sup>H, <sup>31</sup>P) and <sup>n</sup><i>J</i>(<sup>1</sup>H, <sup>77</sup>Se), respectively.
DOI: 10.6084/m9.figshare.5691934.v1
title: Dataset for: Broadband homonuclear decoupled HSQMBC methods

description: Long-range heteronuclear coupling constants convey invaluable information for stereochemical and conformational analysis of molecules from synthetic and natural origin. Here we report a real-time Zangger-Sterk CPMG-HSQMBC method for the precise and direct measurement of multiple-bond heteronuclear couplings. It is demonstrated that the real-time acquisition strategy combined with multiple slice selective excitation can provide substantial improvement in sensitivity (or reduction of experimental time) as compared to other variants of broadband homonuclear decoupled HSQMBC methods published previously. Scope and limitations of the different strategies applied for decoupling are reviewed. Moreover, practical guidelines for the choice of the most appropriate method are also presented. Applications are given on a metal complex incorporating P-heterocycles and two diglycosyl-selenides for the extraction of <sup>n</sup><i>J</i>(<sup>1</sup>H, <sup>31</sup>P) and <sup>n</sup><i>J</i>(<sup>1</sup>H, <sup>77</sup>Se), respectively.
DOI: 10.6084/m9.figshare.5691865
title: MOESM6 of Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis

description: Additional file 6. BLAST against B. glabrata: A reciprocal BLAST search against the recently published transcriptome of twelve pooled Biomphalaria glabrata tissues [3].
DOI: 10.6084/m9.figshare.5691865.v1
title: MOESM6 of Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis

description: Additional file 6. BLAST against B. glabrata: A reciprocal BLAST search against the recently published transcriptome of twelve pooled Biomphalaria glabrata tissues [3].
DOI: 10.6084/m9.figshare.5691844
title: MOESM5 of Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis

description: Additional file 5. Hi-Express transcripts: Highly expressed transcripts annotated by the BLAST results against the comprehensive NCBI Non-Redundant (NR) database.
DOI: 10.6084/m9.figshare.5691844.v1
title: MOESM5 of Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis

description: Additional file 5. Hi-Express transcripts: Highly expressed transcripts annotated by the BLAST results against the comprehensive NCBI Non-Redundant (NR) database.
DOI: 10.6084/m9.figshare.5691838
title: Additional file 2: of Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii

description: Dataset. A) Average DESeq2 normalized RNA-seq and Ribo-seq read counts for all the transcripts tested for differential expression and ribosome occupancy. B) Genes exhibiting low ribosome occupancy but above background mRNA abundance. C) Genes exhibiting low mRNA abundance but above background ribosome occupancy. D) Genes that are differentially regulated both at the level of mRNA abundance and ribosome occupancy (RNAâ +â RIBO). E) Genes that are differentially regulated only at the level of mRNA abundance (RNA-Only). F) Genes that are differentially regulated only at the level of ribosome occupancy (RIBO-Only). G) Genes that exhibit significant differences in translation efficiency between in intercellular and extracellular parasites. (XLS 4356Â kb)