cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9772010
title: Impact of new-onset diabetes on clinical outcomes after ST segment-elevated myocardial infarction

description: <i>Objective.</i> Patients with diabetes have higher mortality rate than patients without diabetes after ST-segment elevated myocardial infarction (STEMI). Prognosis of patients with new onset diabetes (NOD) after STEMI remains unclear. The aim of this study was to evaluate the prognosis of patients with NOD compared to that of patients without NOD after STEMI. <i>Design.</i> This study was a retrospective observational study. We enrolled 901 STEMI patients. Patients were divided into diabetic and non-diabetic groups at index admission. Non-diabetic group was divided into NOD and non-NOD groups. Kaplan-Meier analysis and Cox's proportional hazard regression models were used to compare major adverse cardiac events (MACE) free survival rate and hazard ratio for MACE between NOD and non-NOD groups. <i>Results.</i> Mean follow-up period was 59 ± 28 months. Diabetes group had higher MACE than non-diabetes group (<i>p</i> = .038). However, MACE was not different between NOD and non-NOD groups (<i>p</i> = 1.000). After 1:2 propensity score matching, incidence of MACE was not different between the two groups. In Kaplan-Meier survival curves, MACE-free survival rates were not statistically different between NOD and non-NOD groups either (<i>p</i> = .244). Adjusted hazard ratios of NOD for MACE, all-cause of death, recurrent myocardial infarction, and target vessel revascularization were 0.697 (95% confidence interval [CI]: 0.362–1.345, <i>p =</i> .282), 0.625 (95% CI: 0.179–2.183, <i>p</i> = .461), 0.794 (95% CI: 0.223–2.835, <i>p</i> = .723), and 0.506 (95% CI: 0.196–1.303, <i>p =</i> .158), respectively. <i>Conclusion.</i> This retrospective observational study with a limited statistical power did not show a different prognosis in patients with and without NOD.
DOI: 10.6084/m9.figshare.9772034.v1
title: Table S1. Summary data for the 50 individual throat swab samples.

description: <b>Table S1. </b><b>Summary data for the 50 individual throat swab samples.</b> <br><br>from<br><b>Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples</b>Kuiama Lewandowski, Yifei Xu, Steven T. Pullan, Sheila F. Lumley, Dona Foster, Nicholas Sanderson, Alison Vaughan, Marcus Morgan, Nicole Bright, James Kavanagh, Richard Vipond, Miles Carroll, Anthony C. Marriott, Karen E Gooch, Monique Andersson, Katie Jeffery, Timothy EA Peto, Derrick W. Crook, A Sarah Walker, Philippa C. Matthews<b>bioRxiv 676155; doi: https://doi.org/10.1101/676155</b>
DOI: 10.6084/m9.figshare.9772010.v1
title: Impact of new-onset diabetes on clinical outcomes after ST segment-elevated myocardial infarction

description: <i>Objective.</i> Patients with diabetes have higher mortality rate than patients without diabetes after ST-segment elevated myocardial infarction (STEMI). Prognosis of patients with new onset diabetes (NOD) after STEMI remains unclear. The aim of this study was to evaluate the prognosis of patients with NOD compared to that of patients without NOD after STEMI. <i>Design.</i> This study was a retrospective observational study. We enrolled 901 STEMI patients. Patients were divided into diabetic and non-diabetic groups at index admission. Non-diabetic group was divided into NOD and non-NOD groups. Kaplan-Meier analysis and Cox's proportional hazard regression models were used to compare major adverse cardiac events (MACE) free survival rate and hazard ratio for MACE between NOD and non-NOD groups. <i>Results.</i> Mean follow-up period was 59 ± 28 months. Diabetes group had higher MACE than non-diabetes group (<i>p</i> = .038). However, MACE was not different between NOD and non-NOD groups (<i>p</i> = 1.000). After 1:2 propensity score matching, incidence of MACE was not different between the two groups. In Kaplan-Meier survival curves, MACE-free survival rates were not statistically different between NOD and non-NOD groups either (<i>p</i> = .244). Adjusted hazard ratios of NOD for MACE, all-cause of death, recurrent myocardial infarction, and target vessel revascularization were 0.697 (95% confidence interval [CI]: 0.362–1.345, <i>p =</i> .282), 0.625 (95% CI: 0.179–2.183, <i>p</i> = .461), 0.794 (95% CI: 0.223–2.835, <i>p</i> = .723), and 0.506 (95% CI: 0.196–1.303, <i>p =</i> .158), respectively. <i>Conclusion.</i> This retrospective observational study with a limited statistical power did not show a different prognosis in patients with and without NOD.
DOI: 10.6084/m9.figshare.9771926
title: The Relationships Between Blink Rates Before, During Perimetry and Perimetry Reliability

description: Perimetry was performed using the Humphrey Visual Field Analyzer II (model 750) with the Swedish interactive threshold algorithm (SITA) standard strategy, the 30-2 program, and a size III white stimulus on a white background (equivalent to 31.5 apostilbs). The fixation loss, false positive, and false negative rates were used to assess the reliability of perimetry.<br> (A) Data for patients with dry eye. (B) Data for normal control subjects. Group 1; eyes with decreased blink rates during perimetry in patients with dry eye; Group 2; eyes with increased or unchanged blink rates during perimetry in patients with dry eye; Group 3; eyes with decreased blink rates during perimetry in normal control subjects; Group 4; eyes with increased or unchanged blink rates during perimetry in normal control subjects.<br> Pre-perimetry blink rates in the eyes with blink rates that decreased during perimetry varied from 3 to 44/min in patients with DE (Group 1) and from 4 to 48/min in normal control subjects (Group 3). Blink rates before perimetry in the eyes with blink rates that increased or remained unchanged during perimetry were &lt; 17/min in patients with DE (Group 2) and 19/min in normal control subjects (Group 4), respectively (Fig 1). Blink rates during perimetry were significantly lower in Group 1 compared to Group 2, and in Group 3 compared to Group 4: Group 1, 4.6 (1.7-7.0 [0-21]) vs. Group 2, 13.4 (11.4-16.0 [2-39]) /min and Group 3, 2.6 (0.9-5.4 [0-12]) vs. Group 4, 20.1 (11.0-30.5 [4-36]) /min (P=0.007 and P&lt;0.001, respectively).<br> Fixation loss rate was significantly higher in eyes with decreased blink rates among patients with dry eye (P=0.002).
DOI: 10.6084/m9.figshare.9771926.v2
title: The Relationships Between Blink Rates Before, During Perimetry and Perimetry Reliability

description: Perimetry was performed using the Humphrey Visual Field Analyzer II (model 750) with the Swedish interactive threshold algorithm (SITA) standard strategy, the 30-2 program, and a size III white stimulus on a white background (equivalent to 31.5 apostilbs). The fixation loss, false positive, and false negative rates were used to assess the reliability of perimetry. (A) Data for patients with dry eye. (B) Data for normal control subjects. Group 1; eyes with decreased blink rates during perimetry in patients with dry eye; Group 2; eyes with increased or unchanged blink rates during perimetry in patients with dry eye; Group 3; eyes with decreased blink rates during perimetry in normal control subjects; Group 4; eyes with increased or unchanged blink rates during perimetry in normal control subjects. Pre-perimetry blink rates in the eyes with blink rates that decreased during perimetry varied from 3 to 44/min in patients with DE (Group 1) and from 4 to 48/min in normal control subjects (Group 3). Blink rates before perimetry in the eyes with blink rates that increased or remained unchanged during perimetry were &lt; 17/min in patients with DE (Group 2) and 19/min in normal control subjects (Group 4), respectively (Fig 1). Blink rates during perimetry were significantly lower in Group 1 compared to Group 2, and in Group 3 compared to Group 4: Group 1, 4.6 (1.7-7.0 [0-21]) vs. Group 2, 13.4 (11.4-16.0 [2-39]) /min and Group 3, 2.6 (0.9-5.4 [0-12]) vs. Group 4, 20.1 (11.0-30.5 [4-36]) /min (P=0.007 and P&lt;0.001, respectively, Fig 1). Fixation loss rate was significantly higher in eyes with decreased blink rates among patients with dry eye (P=0.002). Strip meniscometry value was directly correlated with fixation loss rate (r=0.341, P=0.025), and blink rate during perimetry was negatively was correlated with fixation loss rate (r=- 0.393, P=0.009). Dry Eye-related Quality of Life score was negatively correlated with false negative rate (r=- 0.323, P=0.035) in patients with dry eye. However, there were no apparent correlations among the perimetry reliability parameters and other parameters in normal control subjects.
DOI: 10.6084/m9.figshare.9771926.v3
title: The Relationships Between Blink Rates Before, During Perimetry and Perimetry Reliability

description: Perimetry was performed using the Humphrey Visual Field Analyzer II (model 750) with the Swedish interactive threshold algorithm (SITA) standard strategy, the 30-2 program, and a size III white stimulus on a white background (equivalent to 31.5 apostilbs). The fixation loss, false positive, and false negative rates were used to assess the reliability of perimetry. (A) Data for patients with dry eye. (B) Data for normal control subjects. Group 1; eyes with decreased blink rates during perimetry in patients with dry eye; Group 2; eyes with increased or unchanged blink rates during perimetry in patients with dry eye; Group 3; eyes with decreased blink rates during perimetry in normal control subjects; Group 4; eyes with increased or unchanged blink rates during perimetry in normal control subjects. Pre-perimetry blink rates in the eyes with blink rates that decreased during perimetry varied from 3 to 44/min in patients with DE (Group 1) and from 4 to 48/min in normal control subjects (Group 3). Blink rates before perimetry in the eyes with blink rates that increased or remained unchanged during perimetry were &lt; 17/min in patients with DE (Group 2) and 19/min in normal control subjects (Group 4), respectively (Fig 1). Blink rates during perimetry were significantly lower in Group 1 compared to Group 2, and in Group 3 compared to Group 4: Group 1, 4.6 (1.7-7.0 [0-21]) vs. Group 2, 13.4 (11.4-16.0 [2-39]) /min and Group 3, 2.6 (0.9-5.4 [0-12]) vs. Group 4, 20.1 (11.0-30.5 [4-36]) /min (P=0.007 and P&lt;0.001, respectively, Fig 1). Fixation loss rate was significantly higher in eyes with decreased blink rates among patients with dry eye (P=0.002). Strip meniscometry value was directly correlated with fixation loss rate (r=0.341, P=0.025), and blink rate during perimetry was negatively was correlated with fixation loss rate (r=- 0.393, P=0.009). Dry Eye-related Quality of Life score was negatively correlated with false negative rate (r=- 0.323, P=0.035) in patients with dry eye. However, there were no apparent correlations among the perimetry reliability parameters and other parameters in normal control subjects.
DOI: 10.6084/m9.figshare.9771791
title: All HMM states (including those &lt;100nt long)

description: All HMM states (including those &lt;100nt long).<br>As described in:Fitness Landscape of the Fission Yeast Genome.<em> Molecular Biology and Evolution</em> doi:10.1093/molbev/msz113. <br><br><br><br>All HMM state blocks are from log phase data.These are described as HMM defined elements in the article (HDEs)<br><b>Data columns are</b>chr, start, end: genome corrdinatesname: artibitrary name containing chr.start.end.state, eg: I.86889.87840.S2 counts: total insertions in this HDEmin,max,mean,median: informtion about insertion counts in the HDEs (eg: the mean insertion count for all sites in this HDE)sitespernt: total unique insertion sites/nt of HDEs lengthstate: HMM state(1-5)<br><br>
DOI: 10.6084/m9.figshare.9771743
title: Supplementary Material for: Intra-Dialytic Hemoglobin Changes and Cardiovascular Events: A Cohort Study on Dialysis Outcomes and Practice Patterns in Japan

description: <b><i>Background:</i></b> Ultrafiltration during hemodialysis (HD) causes hemoconcentration. Little is known about the relationships between intra-dialytic changes in hemoglobin concentration and cardiovascular events. Thus, this study aimed to elucidate the relationships between intra-dialytic changes in hemoglobin concentration and cardiovascular events among HD patients. <b><i>Methods:</i></b> This prospective cohort study was based on the Japanese Dialysis Outcomes and Practice Pattern Study phases 4 and 5. The predictor was the ratio of post-dialysis hemoglobin concentration to pre-dialysis hemoglobin concentration (post-Hb/pre-Hb) at baseline. The primary outcome was major adverse cardiovascular events (MACEs). Hazard ratios (HRs) were estimated using a Cox model for the association between post-Hb/pre-Hb and MACEs, adjusting for potential confounders. <b><i>Results:</i></b> A total of 865 patients were enrolled. During a median follow-up of 2.6 years, 145 (16.8%) patients developed MACEs. Patients were divided into 4 categories according to baseline post-Hb/pre-Hb (&lt;1.0, ≥1.0 to &lt;1.1, ≥1.1 to &lt;1.2, and ≥1.2). The multivariable-adjusted HRs for MACEs were 1.69 (95% CI 1.36–2.10), 1.29 (95% CI 1.10–1.51), and 1.31 (95% CI 1.02–1.68) in patients with post-Hb/pre-Hb ratios of &lt;1.0, ≥1.0 to &lt;1.1, and ≥1.2, respectively, compared with the reference post-Hb/pre-Hb ratio of ≥1.1 to &lt;1.2. Cubic spline analyses revealed a U-shaped association between post-Hb/pre-Hb and MACEs. <b><i>Conclusion:</i></b> High and low intra-dialytic changes in hemoglobin concentration are associated with a high risk of MACEs in patients undergoing HD.
DOI: 10.6084/m9.figshare.9771791.v2
title: All HMM states (including those &lt;100nt long)

description: All HMM states (including those &lt;100nt long).<br>As described in:Fitness Landscape of the Fission Yeast Genome.<em> Molecular Biology and Evolution</em> doi:10.1093/molbev/msz113. <br><br><br><br>All HMM state blocks are from log phase data.These are described as HMM defined elements in the article (HDEs)<br><b>Data columns are</b>chr, start, end: genome corrdinatesname: artibitrary name containing chr.start.end.state, eg: I.86889.87840.S2 counts: total insertions in this HDEmin,max,mean,median: informtion about insertion counts in the HDEs (eg: the mean insertion count for all sites in this HDE)sitespernt: total unique insertion sites/nt of HDEs lengthstate: HMM state(1-5)<br><br>
DOI: 10.6084/m9.figshare.9771743.v1
title: Supplementary Material for: Intra-Dialytic Hemoglobin Changes and Cardiovascular Events: A Cohort Study on Dialysis Outcomes and Practice Patterns in Japan

description: <b><i>Background:</i></b> Ultrafiltration during hemodialysis (HD) causes hemoconcentration. Little is known about the relationships between intra-dialytic changes in hemoglobin concentration and cardiovascular events. Thus, this study aimed to elucidate the relationships between intra-dialytic changes in hemoglobin concentration and cardiovascular events among HD patients. <b><i>Methods:</i></b> This prospective cohort study was based on the Japanese Dialysis Outcomes and Practice Pattern Study phases 4 and 5. The predictor was the ratio of post-dialysis hemoglobin concentration to pre-dialysis hemoglobin concentration (post-Hb/pre-Hb) at baseline. The primary outcome was major adverse cardiovascular events (MACEs). Hazard ratios (HRs) were estimated using a Cox model for the association between post-Hb/pre-Hb and MACEs, adjusting for potential confounders. <b><i>Results:</i></b> A total of 865 patients were enrolled. During a median follow-up of 2.6 years, 145 (16.8%) patients developed MACEs. Patients were divided into 4 categories according to baseline post-Hb/pre-Hb (&lt;1.0, ≥1.0 to &lt;1.1, ≥1.1 to &lt;1.2, and ≥1.2). The multivariable-adjusted HRs for MACEs were 1.69 (95% CI 1.36–2.10), 1.29 (95% CI 1.10–1.51), and 1.31 (95% CI 1.02–1.68) in patients with post-Hb/pre-Hb ratios of &lt;1.0, ≥1.0 to &lt;1.1, and ≥1.2, respectively, compared with the reference post-Hb/pre-Hb ratio of ≥1.1 to &lt;1.2. Cubic spline analyses revealed a U-shaped association between post-Hb/pre-Hb and MACEs. <b><i>Conclusion:</i></b> High and low intra-dialytic changes in hemoglobin concentration are associated with a high risk of MACEs in patients undergoing HD.
DOI: 10.6084/m9.figshare.9771791.v1
title: All HMM states (including those &lt;100nt long)

description: All HMM states (including those &lt;100nt long).<br>As described in:Fitness Landscape of the Fission Yeast Genome.<em> Molecular Biology and Evolution</em> doi:10.1093/molbev/msz113. <br><br>
DOI: 10.6084/m9.figshare.9771668
title: Supplementary Material for: Could Residents Adequately Assess the Severity of Hidradenitis Suppurativa? Interrater and Intrarater Reliability Assessment of Major Scoring Systems

description: A wide variety of assessment tools have been proposed for hidradenitis suppurativa (HS) until now, but none of them meets the criteria for an ideal score. Because there is no gold standard scoring system, the choice of the measure instrument depends on the purpose of use and even on the physician’s experience in the subject of HS. The aim of this study was to assess the intrarater and interrater reliability of 6 scoring systems commonly used for grading severity of HS: the Hurley Staging System, the Refined Hurley Staging, the Hidradenitis Suppurativa Severity Score System (IHS4), the Hidradenitis Suppurativa Severity Index (HSSI), the Sartorius Hidradenitis Suppurativa Score and the Hidradenitis Suppurativa Physician’s Global Assessment Scale (HS-PGA). On the scoring day, 9 HS patients underwent a physical examination and disease severity assessment by a group of 16 dermatology residents using all evaluated instruments. Then, intrarater reliability was calculated using intraclass correlation coefficient (ICC), and interrater variability was evaluated using the coefficient of variation (CV). In all 6 scorings the ICCs were &gt;0.75, indicating high intrarater reliability of all presented scales. The study has also demonstrated moderate agreement between raters in most of the evaluated measure instruments. The most reproducible methods, according to CVs, seem to be the Hurley staging, IHS4, and HSSI. None of the 6 evaluated scoring systems showed a significant advantage over the other when comparing ICCs, and all the instruments seem to be very reliable methods. The interrater reliability was usually good, but the most repeatable results between researchers were obtained for the easiest scales, including Hurley scoring, IHS4 and HSSI.
DOI: 10.6084/m9.figshare.9771668.v1
title: Supplementary Material for: Could Residents Adequately Assess the Severity of Hidradenitis Suppurativa? Interrater and Intrarater Reliability Assessment of Major Scoring Systems

description: A wide variety of assessment tools have been proposed for hidradenitis suppurativa (HS) until now, but none of them meets the criteria for an ideal score. Because there is no gold standard scoring system, the choice of the measure instrument depends on the purpose of use and even on the physician’s experience in the subject of HS. The aim of this study was to assess the intrarater and interrater reliability of 6 scoring systems commonly used for grading severity of HS: the Hurley Staging System, the Refined Hurley Staging, the Hidradenitis Suppurativa Severity Score System (IHS4), the Hidradenitis Suppurativa Severity Index (HSSI), the Sartorius Hidradenitis Suppurativa Score and the Hidradenitis Suppurativa Physician’s Global Assessment Scale (HS-PGA). On the scoring day, 9 HS patients underwent a physical examination and disease severity assessment by a group of 16 dermatology residents using all evaluated instruments. Then, intrarater reliability was calculated using intraclass correlation coefficient (ICC), and interrater variability was evaluated using the coefficient of variation (CV). In all 6 scorings the ICCs were &gt;0.75, indicating high intrarater reliability of all presented scales. The study has also demonstrated moderate agreement between raters in most of the evaluated measure instruments. The most reproducible methods, according to CVs, seem to be the Hurley staging, IHS4, and HSSI. None of the 6 evaluated scoring systems showed a significant advantage over the other when comparing ICCs, and all the instruments seem to be very reliable methods. The interrater reliability was usually good, but the most repeatable results between researchers were obtained for the easiest scales, including Hurley scoring, IHS4 and HSSI.
DOI: 10.6084/m9.figshare.9771620
title: Supplementary Material for: NIV NAVA versus Nasal CPAP in Premature Infants: A Randomized Clinical Trial

description: <b><i>Background:</i></b> Noninvasive ventilation is recommended for neonatal respiratory distress to avoid adverse effects of invasive ventilation. <b><i>Objective:</i></b> The aim of this study was to compare the feasibility of noninvasive neurally adjusted ventilatory assist (NIV NAVA) and continuous positive airway pressure (CPAP) in preterm newborn infants. <b><i>Methods:</i></b> Forty preterm infants (gestational age 28+0 to 36+6 weeks) requiring CPAP and supplemental oxygen (FiO<sub>2</sub> &gt;0.23) for respiratory distress at &lt;48 h of postnatal age were randomized to NIV NAVA or CPAP. The primary endpoint was the inspired oxygen concentration 12 h after study inclusion. Secondary endpoints were the duration of oxygen treatment, total duration of respiratory support, parenteral nutrition, blood gas values, patient comfort, need for invasive ventilation, and treatment complications. <b><i>Results:</i></b> The mean FiO<sub>2</sub> at the time of study inclusion was 0.29 in both groups. After 12 h of treatment, FiO<sub>2</sub> was 0.26 ± 0.07 and 0.26 ± 0.04 in the NIV NAVA and CPAP groups, respectively (difference 0.006, 95% CI –0.4 to 0.5), with no difference between the groups during the course of noninvasive ventilation (<i>p</i> = 0.80). Seven patients (35%) in the NIV NAVA group and 10 (50%) in the control group required intubation (difference 15%, 95% CI –15.5 to 4.3, <i>p</i> = 0.36). Time to intubation, gas exchange, vital parameters, pain scale, treatment complications, and neonatal outcome did not differ between the groups. <b><i>Conclusions:</i></b> In the present trial, NIV NAVA had no statistically significant effect on oxygen requirements or the need for invasive ventilation in preterm newborn infants.
DOI: 10.6084/m9.figshare.9771557
title: Experimental data

description: Experimental data sheet<br>
DOI: 10.6084/m9.figshare.9771557.v1
title: Experimental data

description: Experimental data sheet<br>
DOI: 10.6084/m9.figshare.9771506
title: A method for identifying allele-specific hydroxymethylation

description: We previously identified sequence-dependent allele-specific methylation (sd-ASM) in adult human peripheral blood leukocytes, in which ASM occurs in cis depending on adjacent polymorphic sequences. A number of groups have identified sd-ASM sites in the human and mouse genomes, illustrating the prevalence of sd-ASM in mammalian genomes. In addition, sd-ASM can lead to sequence-dependent allele-specific expression of neighbouring genes. Imprinted genes also often exhibit parent-of-origin–dependent allele-specific methylation (pd-ASM), which causes parent-of-origin–dependent allele-specific expression. However, whether most of the already known sd-ASM and pd-ASM sites are methylated or hydroxymethylated remains unclear due to technical restrictions. Accordingly, a novel method that enables examination of allelic methylation and hydroxymethylation status and also overcomes the drawbacks of conventional methods is needed. Such a method could also be used to elucidate the mechanisms underlying polymorphism-associated inter-individual differences in disease susceptibility and the mechanism of genomic imprinting. Here, we developed a simple method to determine allelic hydroxymethylation status and identified novel sequence- and parent-of-origin–dependent allele-specific hydroxymethylation sites. Correlation analyses of TF binding sequences and methylation or hydroxymethylation between three mouse strains revealed the involvement of <i>Pax5</i> in strain-specific methylation and hydroxymethylation in exon 7 of <i>Pdgfrb</i>.