cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5426710
title: PathTrace Demo (Query)

description: This is a FASTA-formated file containing 86 enzymes that participate in the nine metabolic pathways in the Case Study of the PathTrace tool (https://github.com/CGU-CERTH/PathTrace).<br>The nine pathways are the following:- Leucine Biosynthesis I- TCA cycle I (prokaryotic)- Methionine Biosynthesis I- Isoleucine Biosynthesis I (from threonine)- Lysine Biosynthesis I- Biotin Biosynthesis I- Glycolysis V (Pyrococcus)- Lysine Biosynthesis II- Biotin biosynthesis II<br>The file contains the enzymes of each pathway as a block, starting with the character '#'. You can remove all these lines for a ready-to-use FASTA file, using the following command:<br>sed '/^#/ d' &lt; PathTrace-Demo-Query.fasta &gt; PathTrace-Demo-Query-clean.fasta
DOI: 10.6084/m9.figshare.5426713.v1
title: Humber NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426698
title: Hounslow and Richmond Community Healthcare NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426704
title: Hull and East Yorkshire Hospitals NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426710.v1
title: PathTrace Demo (Query)

description: This is a FASTA-formated file containing 86 enzymes that participate in the nine metabolic pathways in the Case Study of the PathTrace tool (https://github.com/CGU-CERTH/PathTrace).<br>The nine pathways are the following:- Leucine Biosynthesis I- TCA cycle I (prokaryotic)- Methionine Biosynthesis I- Isoleucine Biosynthesis I (from threonine)- Lysine Biosynthesis I- Biotin Biosynthesis I- Glycolysis V (Pyrococcus)- Lysine Biosynthesis II- Biotin biosynthesis II<br>The file contains the enzymes of each pathway as a block, starting with the character '#'. You can remove all these lines for a ready-to-use FASTA file, using the following command:<br>sed '/^#/ d' &lt; PathTrace-Demo-Query.fasta &gt; PathTrace-Demo-Query-clean.fasta
DOI: 10.6084/m9.figshare.5426689
title: Homerton University Hospital NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426698.v1
title: Hounslow and Richmond Community Healthcare NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426704.v1
title: Hull and East Yorkshire Hospitals NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426689.v1
title: Homerton University Hospital NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426680
title: Healthcare utilization and direct costs of non-infectious comorbidities in HIV-infected patients in the USA

description: <b>Objective:</b> To estimate the incremental healthcare utilization and costs associated with common non-infectious comorbid conditions among commercially and Medicaid-insured HIV-infected patients in the US. <b>Methods:</b> US administrative claims were used to select adult HIV patients with chronic kidney disease (CKD), cardiovascular disease (CVD) events, or fracture/osteoporosis, three common comorbidities that have been associated with HIV and HIV treatment, between 1 January 2004 and 30 June 2013. Propensity score matched controls with no CKD, no CVD events, and no fracture/osteoporosis were identified for comparison. All-cause healthcare utilization and costs were reported as per patient per month (PPPM). <b>Results:</b> The commercial cohort comprised 381 CKD patients, 624 patients with CVD events, and 774 fracture/osteoporosis patients, and 1013, 1710, and 2081 matched controls, respectively; while the Medicaid HIV cohort comprised 207 CKD and 271 CVD cases, and 516 and 735 matched controls, respectively. There was insufficient Medicaid data for fracture analyses. Across both payers, HIV patients with CKD or CVD events had significantly higher healthcare utilization and costs than controls. The average incremental PPPM costs in HIV patients with CKD were $1403 in the commercial cohort and $3051 in the Medicaid cohort. In those with CVD events, the incremental costs were $2655 (commercial) and $4959 (Medicaid) for HIV patients compared to controls (<i>p</i> <b>Conclusions:</b> The results suggested a considerable increase in healthcare utilization and costs associated with CKD, CVD and fracture/osteoporosis comorbidities among HIV patients in the past decade. Because these conditions have been associated with treatment, it is critical to consider their impact on costs and outcomes when optimizing patient care.
DOI: 10.6084/m9.figshare.5426680.v1
title: Healthcare utilization and direct costs of non-infectious comorbidities in HIV-infected patients in the USA

description: <b>Objective:</b> To estimate the incremental healthcare utilization and costs associated with common non-infectious comorbid conditions among commercially and Medicaid-insured HIV-infected patients in the US. <b>Methods:</b> US administrative claims were used to select adult HIV patients with chronic kidney disease (CKD), cardiovascular disease (CVD) events, or fracture/osteoporosis, three common comorbidities that have been associated with HIV and HIV treatment, between 1 January 2004 and 30 June 2013. Propensity score matched controls with no CKD, no CVD events, and no fracture/osteoporosis were identified for comparison. All-cause healthcare utilization and costs were reported as per patient per month (PPPM). <b>Results:</b> The commercial cohort comprised 381 CKD patients, 624 patients with CVD events, and 774 fracture/osteoporosis patients, and 1013, 1710, and 2081 matched controls, respectively; while the Medicaid HIV cohort comprised 207 CKD and 271 CVD cases, and 516 and 735 matched controls, respectively. There was insufficient Medicaid data for fracture analyses. Across both payers, HIV patients with CKD or CVD events had significantly higher healthcare utilization and costs than controls. The average incremental PPPM costs in HIV patients with CKD were $1403 in the commercial cohort and $3051 in the Medicaid cohort. In those with CVD events, the incremental costs were $2655 (commercial) and $4959 (Medicaid) for HIV patients compared to controls (<i>p</i> <b>Conclusions:</b> The results suggested a considerable increase in healthcare utilization and costs associated with CKD, CVD and fracture/osteoporosis comorbidities among HIV patients in the past decade. Because these conditions have been associated with treatment, it is critical to consider their impact on costs and outcomes when optimizing patient care.
DOI: 10.6084/m9.figshare.5426626
title: Dataset for: Muscle oxygenation profiles between active and inactive muscles with nitrate supplementation under hypoxic exercise

description: Whether dietary nitrate supplementation improves exercise performance or not is still controversial. While redistribution of sufficient oxygen from inactive to active muscles is essential for optimal exercise performance, no studies was investigated effects of nitrate supplementation on muscle oxygenation profiles between active and inactive muscles. Nine healthy males performed 25 minutes of submaximal (heart rate ~ 140 bpm; EXsub) and incremental cycling (EXmax) until exhaustion under three conditions: (a) normoxia without drink; (b) hypoxia (FiO2 = 13.95%) with placebo (PL); and (c) hypoxia with beetroot juice (BR). PL and BR were provided for four days. Oxygenated and deoxygenated hemoglobin (HbO2 and HHb) were measured in vastus lateralis (active) and biceps brachii (inactive) muscles, and the oxygen saturation of skeletal muscle (StO2; HbO2/total Hb) were calculated. During EXsub, BR suppressed the HHb increases in active muscles during the last 5 min of exercise. During EXmax, time to exhaustion with BR (513 ± 24 s) was significantly longer than with PL (490 ± 39 s, P &lt; 0.05). In active muscles, BR suppressed the HHb increases at moderate work rates during EXmax compared to PL (P &lt; 0.05). Additionally, BR supplementation was associated with greater reductions in HbO2 and StO2 at higher work rates in inactive muscles during EXmax. Collectively, these findings indicate that short-term dietary nitrate supplementation improved hypoxic exercise tolerance, perhaps due to suppressed increases in HHb in active muscles at moderate work rates. Moreover, nitrate supplementation caused greater reductions in oxygenation in inactive muscle at higher work rates during hypoxic exercise.
DOI: 10.6084/m9.figshare.5426626.v1
title: Dataset for: Muscle oxygenation profiles between active and inactive muscles with nitrate supplementation under hypoxic exercise

description: Whether dietary nitrate supplementation improves exercise performance or not is still controversial. While redistribution of sufficient oxygen from inactive to active muscles is essential for optimal exercise performance, no studies was investigated effects of nitrate supplementation on muscle oxygenation profiles between active and inactive muscles. Nine healthy males performed 25 minutes of submaximal (heart rate ~ 140 bpm; EXsub) and incremental cycling (EXmax) until exhaustion under three conditions: (a) normoxia without drink; (b) hypoxia (FiO2 = 13.95%) with placebo (PL); and (c) hypoxia with beetroot juice (BR). PL and BR were provided for four days. Oxygenated and deoxygenated hemoglobin (HbO2 and HHb) were measured in vastus lateralis (active) and biceps brachii (inactive) muscles, and the oxygen saturation of skeletal muscle (StO2; HbO2/total Hb) were calculated. During EXsub, BR suppressed the HHb increases in active muscles during the last 5 min of exercise. During EXmax, time to exhaustion with BR (513 ± 24 s) was significantly longer than with PL (490 ± 39 s, P &lt; 0.05). In active muscles, BR suppressed the HHb increases at moderate work rates during EXmax compared to PL (P &lt; 0.05). Additionally, BR supplementation was associated with greater reductions in HbO2 and StO2 at higher work rates in inactive muscles during EXmax. Collectively, these findings indicate that short-term dietary nitrate supplementation improved hypoxic exercise tolerance, perhaps due to suppressed increases in HHb in active muscles at moderate work rates. Moreover, nitrate supplementation caused greater reductions in oxygenation in inactive muscle at higher work rates during hypoxic exercise.
DOI: 10.6084/m9.figshare.5426599
title: Dataset for: CEREBELLAR DIRECT CURRENT STIMULATION MODULATES HAND BLINK REFLEX: IMPLICATIONS FOR DEFENSIVE BEHAVIOR IN HUMANS

description: The cerebellum is involved in a wide number of integrative functions. We evaluated the role of cerebellum in peripersonal defensive behavior, as assessed by the so-called hand blink reflex (HBR), modulating cerebellar activity with transcranial direct current stimulation (tDCS). Healthy subjects underwent to cerebellar (sham, anodal and cathodal tcDCS) and motor cortex tDCS (anodal or cathodal; 20’, 2 mA). For the recording of HBR, electrical stimuli were delivered using a surface bipolar electrode placed on the median nerve at the wrist and EMG activity recorded from the orbicularis oculi muscle bilaterally. Depending on the hand position respective to the face, HBR was assessed in four different conditions: “hand far”, “hand near” (eyes open), “side hand” and “hand-patched” (eyes closed). While sham and cathodal cerebellar stimulation had no significant effect, anodal tcDCS dramatically dampened the magnitude of the HBR, as measured by the area under the curve (AUC), in the “hand-patched” and “side hand” conditions only, for ipsilateral (F(4,171) = 15.08, p &lt; 0.0001; F(4,171) = 8.95, p &lt; 0.0001) as well as contralateral recordings (F(4,171) = 17.96, p &lt; 0.0001); F4,171) = 5.35, p = 0.0004). Cerebellar polarization did not modify AUC in the “hand far” and “hand near” sessions. tDCS applied over the motor area did not affect HBR. These results seem to support a role of the cerebellum in the defensive responses within the peripersonal space surrounding the face, thus suggesting a possible cerebellar involvement in visual-independent defensive behavior.
DOI: 10.6084/m9.figshare.5426599.v1
title: Dataset for: CEREBELLAR DIRECT CURRENT STIMULATION MODULATES HAND BLINK REFLEX: IMPLICATIONS FOR DEFENSIVE BEHAVIOR IN HUMANS

description: The cerebellum is involved in a wide number of integrative functions. We evaluated the role of cerebellum in peripersonal defensive behavior, as assessed by the so-called hand blink reflex (HBR), modulating cerebellar activity with transcranial direct current stimulation (tDCS). Healthy subjects underwent to cerebellar (sham, anodal and cathodal tcDCS) and motor cortex tDCS (anodal or cathodal; 20’, 2 mA). For the recording of HBR, electrical stimuli were delivered using a surface bipolar electrode placed on the median nerve at the wrist and EMG activity recorded from the orbicularis oculi muscle bilaterally. Depending on the hand position respective to the face, HBR was assessed in four different conditions: “hand far”, “hand near” (eyes open), “side hand” and “hand-patched” (eyes closed). While sham and cathodal cerebellar stimulation had no significant effect, anodal tcDCS dramatically dampened the magnitude of the HBR, as measured by the area under the curve (AUC), in the “hand-patched” and “side hand” conditions only, for ipsilateral (F(4,171) = 15.08, p &lt; 0.0001; F(4,171) = 8.95, p &lt; 0.0001) as well as contralateral recordings (F(4,171) = 17.96, p &lt; 0.0001); F4,171) = 5.35, p = 0.0004). Cerebellar polarization did not modify AUC in the “hand far” and “hand near” sessions. tDCS applied over the motor area did not affect HBR. These results seem to support a role of the cerebellum in the defensive responses within the peripersonal space surrounding the face, thus suggesting a possible cerebellar involvement in visual-independent defensive behavior.
DOI: 10.6084/m9.figshare.5426593
title: Junior Farmer Field Schools, Agricultural Knowledge and Spillover Effects: Quasi-Experimental Evidence from Northern Uganda

description: We analyse the impact of a junior farmer field school project in Northern Uganda on students’ agricultural knowledge and practices. We also test for the presence of intergenerational learning spillover within households. We use differences-in-differences estimators with ex-ante matching and find evidence that the programme had positive effects on students’ agricultural knowledge and adoption of good practices. The project also produced spillover effects in terms of improvements of household agricultural knowledge and food security. Overall, our results point to the importance of adapting the basic principles of farmer field schools to children.
DOI: 10.6084/m9.figshare.5426572
title: Dataset for the manuscript entitled "Decision making measured by the Iowa Gambling Task in alcohol use disorder and gambling disorder: a systematic review and meta-analysis".

description: Data file for the manuscript entitled "Decision making measured by the Iowa Gambling Task in alcohol<br>use disorder and gambling disorder: a systematic review and meta-analysis".
DOI: 10.6084/m9.figshare.5426593.v1
title: Junior Farmer Field Schools, Agricultural Knowledge and Spillover Effects: Quasi-Experimental Evidence from Northern Uganda

description: We analyse the impact of a junior farmer field school project in Northern Uganda on students’ agricultural knowledge and practices. We also test for the presence of intergenerational learning spillover within households. We use differences-in-differences estimators with ex-ante matching and find evidence that the programme had positive effects on students’ agricultural knowledge and adoption of good practices. The project also produced spillover effects in terms of improvements of household agricultural knowledge and food security. Overall, our results point to the importance of adapting the basic principles of farmer field schools to children.
DOI: 10.6084/m9.figshare.5426542
title: BMC BIO

description: Data from the equipment CM400
DOI: 10.6084/m9.figshare.5426572.v1
title: Dataset for the manuscript entitled "Decision making measured by the Iowa Gambling Task in alcohol use disorder and gambling disorder: a systematic review and meta-analysis".

description: Data file for the manuscript entitled "Decision making measured by the Iowa Gambling Task in alcohol<br>use disorder and gambling disorder: a systematic review and meta-analysis".
DOI: 10.6084/m9.figshare.5426512
title: Supplementary Figures to manuscript "Relamination styles in collisional orogens" by P. Maierova, K. Schulmann and T. Gerya.

description: Material distribution (left), viscosity and isotherms (right) in representative timesteps. Color coding of materials shown in Fig. 1 in the manuscript. Labels of isotherms are in degrees Celsius.<br>
DOI: 10.6084/m9.figshare.5426503
title: Supplementary Material for: Association of Serum Amyloid A with Kidney Outcomes and All-Cause Mortality in American Indians with Type 2 Diabetes

description: <b><i>Background:</i></b> Serum amyloid A (SAA) induces inflammation and apoptosis in kidney cells and is found to be causing the pathologic changes that are associated with diabetic kidney disease (DKD). Higher serum SAA concentrations were previously associated with increased risk of end-stage renal disease (ESRD) and death in persons with type 2 diabetes and advanced DKD. We explored the prognostic value of SAA in American Indians with type 2 diabetes without DKD or with early DKD. <b><i>Methods:</i></b> SAA concentration was measured in serum samples obtained at the start of follow-up. Multivariate proportional hazards models were employed to examine the magnitude of the risk of ESRD or death across tertiles of SAA concentration after adjustment for traditional risk factors. The C statistic was used to assess the additional predictive value of SAA relative to traditional risk factors. <b><i>Results:</i></b> Of 256 participants (mean ± SD glomerular filtration rate [iothalamate] = 148 ± 45 mL/min, and median [interquartile range] urine albumin/creatinine = 39 [14-221] mg/g), 76 developed ESRD and 125 died during a median follow-up period of 15.2 and 15.7 years, respectively. After multivariable proportional hazards regression, participants in the 2 highest SAA tertiles together exhibited a 53% lower risk of ESRD (hazard ratio [HR] 0.47, 95% CI 0.29-0.78), and a 30% lower risk of death (HR 0.70, 95% CI 0.48-1.02), compared with participants in the lowest SAA tertile, although the lower risk of death was not statistically significant. Addition of SAA to the ESRD model increased the C statistic from 0.814 to 0.815 (<i>p </i>= 0.005). <b><i>Conclusions:</i></b> Higher circulating SAA concentration is associated with a reduced risk of ESRD in American Indians with type 2 diabetes.
DOI: 10.6084/m9.figshare.5426506
title: Genome - Pirum gemmata

description: Genome assembly and annotation of Pirum gemmata<i> </i><br>- XXXX_gDNA.fasta: "Genome assembly (fasta format)" <br>- XXXX_long.annot.gff: "Gene annotation (GFF)"<br>- XXXX_long.cds.fasta: "Predicted transcripts (CDS only, fasta format)"<br>- XXXX_long.pep.fasta: "Predicted peptides (fasta format)"<br>If you use this data, please cite: Dynamics of genomic innovation in the unicellular ancestry of animals, Grau-Bové <i>et al., </i>eLife 2017 https://elifesciences.org/articles/26036/<br>​WARNING: highly fragmented genome assembly. See ​paper for further details<br>​
DOI: 10.6084/m9.figshare.5426512.v1
title: Supplementary Figures to manuscript "Relamination styles in collisional orogens" by P. Maierova, K. Schulmann and T. Gerya.

description: Material distribution (left), viscosity and isotherms (right) in representative timesteps. Color coding of materials shown in Fig. 1 in the manuscript. Labels of isotherms are in degrees Celsius.<br>
DOI: 10.6084/m9.figshare.5426488
title: Genome - Ichthyophonus hoferi

description: Genome assembly and annotation of Ichthyophonus hoferi:<i> </i><br>- XXXX_gDNA.fasta: "Genome assembly (fasta format)" <br>- XXXX_long.annot.gff: "Gene annotation (GFF)"<br>- XXXX_long.cds.fasta: "Predicted transcripts (CDS only, fasta format)"<br>- XXXX_long.pep.fasta: "Predicted peptides (fasta format)"<br>If you use this data, please cite: Dynamics of genomic innovation in the unicellular ancestry of animals, Grau-Bové <i>et al., </i>eLife 2017 <br>Genome assembly courtesy of Krista M. Nichols (NOAA Fisheries) and Chris Whipps (SUNY-ESF).<br><br>www.multicellgenome.com
DOI: 10.6084/m9.figshare.5426494
title: Genome - Chromosphaera perkinsii

description: Genome assembly and annotation of Chromosphaera perkinsii:<i> </i><br>- XXXX_gDNA.fasta: "Genome assembly (fasta format)" <br>- XXXX_long.annot.gff: "Gene annotation (GFF)"<br>- XXXX_long.cds.fasta: "Predicted transcripts (CDS only, fasta format)"<br>- XXXX_long.pep.fasta: "Predicted peptides (fasta format)"<br>If you use this data, please cite: Dynamics of genomic innovation in the unicellular ancestry of animals, Grau-Bové <i>et al., </i>eLife 2017 <br>https://elifesciences.org/articles/26036/<br>​
DOI: 10.6084/m9.figshare.5426470
title: Genome - Corallochytrium limacisporum

description: Genome assembly and annotation of Corallochytrium limacisporum<i> </i><br>- XXXX_gDNA.fasta: "Genome assembly (fasta format)"<br>- XXXX_long.annot.gff: "Gene annotation (GFF)"<br>- XXXX_long.cds.fasta: "Predicted transcripts (CDS only, fasta format)"<br>- XXXX_long.pep.fasta: "Predicted peptides (fasta format)"<br>If you use this data, please cite: Dynamics of genomic innovation in the unicellular ancestry of animals, Grau-Bové <i>et al., </i>eLife 2017<br>www.multicellgenome.com
DOI: 10.6084/m9.figshare.5426506.v1
title: Genome - Pirum gemmata

description: Genome assembly and annotation of Pirum gemmata<i> </i><br>- XXXX_gDNA.fasta: "Genome assembly (fasta format)" <br>- XXXX_long.annot.gff: "Gene annotation (GFF)"<br>- XXXX_long.cds.fasta: "Predicted transcripts (CDS only, fasta format)"<br>- XXXX_long.pep.fasta: "Predicted peptides (fasta format)"<br>If you use this data, please cite: Dynamics of genomic innovation in the unicellular ancestry of animals, Grau-Bové <i>et al., </i>eLife 2017 https://elifesciences.org/articles/26036/<br>​WARNING: highly fragmented genome assembly. See ​​​paper for further details<br>​
DOI: 10.6084/m9.figshare.5426458
title: Genome - Abeoforma whisleri​

description: Genome assembly and annotation of Abeoforma whisleri:<br>- XXXX_gDNA.fasta: "Genome assembly (fasta format)" <br>- XXXX_long.annot.gff: "Gene annotation (GFF)"<br>- XXXX_long.cds.fasta: "Predicted transcripts (CDS only, fasta format)"<br>- XXXX_long.pep.fasta: "Predicted peptides (fasta format)"<br>If you use this data, please cite: Dynamics of genomic innovation in the unicellular ancestry of animals, Grau-Bové <i>et al., </i>eLife 2017 <br>WARNING: highly fragmented genome assembly. See ​paper for further details.<br><br>www.multicellgenome.com