cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3824070.v1
title: Supplementary Material for: Cl-Amidine Prevents Histone 3 Citrullination and Neutrophil Extracellular Trap Formation, and Improves Survival in a Murine Sepsis Model

description: Sepsis refers to the presence of a serious infection that correlates with systemic and uncontrolled immune activation. Posttranslational histone modification plays an important role in chromatin decondensation, which is regulated by citrullination. Citrullinated histone H3 (H3cit) has been identified as a component of neutrophil extracellular traps (NETs), which are released into the extracellular space as part of the neutrophil response to infection. The conversion of arginine to citrulline residues on histones is catalyzed by peptidylarginine deiminase 4 (PAD4). This study's goals were to characterize the presence of PAD4-catalyzed H3cit and NET formation during the onset of sepsis and elucidate the effects on the immune response when this mechanism of action is blocked. Adult C57BL/6 male mice were treated with Cl-amidine, an inhibitor of PAD4, 1 h prior to sepsis induced by cecal ligation and puncture (CLP). Twenty-four hours after CLP, cytokine levels, H3cit protein expression, neutrophil counts, and NET production were evaluated in the peritoneal cavity. Survival studies were also performed. Here we demonstrate that Cl-amidine treatment prior to CLP improves overall survival in sepsis and the abrogation of PAD4 has minimal effects on the proinflammatory immune response to sepsis, while it has no effect on overall neutrophil migration to the peritoneum.
DOI: 10.7910/dvn/v1rjpf/kavzpc
title: iqa20151012_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ft2oth
title: iqa20161010_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/7vfuir
title: iqa20151006_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/oam4ij
title: iqa20150101_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3824046
title: Supplementary Material for: Impact of Alzheimer's Disease, Lewy Body and Vascular Co-Pathologies on Clinical Transition to Dementia in a National Autopsy Cohort

description: <b><i>Aims:</i></b> We examined the effect of vascular or Lewy body co-pathologies in subjects with autopsy-confirmed Alzheimer's disease (AD) on the rate of cognitive and functional decline and transition to dementia. <b><i>Methods:</i></b> In an autopsy sample of prospectively characterized subjects from the National Alzheimer's Coordinating Center database, neuropathology diagnosis was used to define the groups of pure AD (pAD, n = 84), mixed vascular and AD (ADV, n = 54), and mixed Lewy body disease and AD (ADLBD, n = 31). Subjects had an initial Clinical Dementia Rating-Global (CDR-G) score &lt;1, Mini-Mental State Examination ≥15, a final visit CDR-G &gt;1, ≥3 evaluations, and Braak tangle stage ≥III. We compared the rate of cognitive and functional decline between the groups. <b><i>Results:</i></b> The rate of functional and cognitive decline was lower for ADV, and ADV patients had less severe deficits on CDR-G and the CDR-Sum of Boxes scores at the last visit than pAD and ADLBD patients. No significant differences were noted between ADLBD and pAD patients. After controlling for age at death, the odds of reaching CDR ≥1 at the last visit were lower in the ADV subjects compared to the pAD subjects. <b><i>Conclusions:</i></b> The mean rate of functional and cognitive decline among ADV subjects was slower than among either pAD or ADLBD patients. Vascular pathology did not increase the odds of attaining CDR ≥1 when occurring with AD in this national cohort.
DOI: 10.7910/dvn/v1rjpf/h06wvd
title: iqa20150310_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3824046.v1
title: Supplementary Material for: Impact of Alzheimer's Disease, Lewy Body and Vascular Co-Pathologies on Clinical Transition to Dementia in a National Autopsy Cohort

description: <b><i>Aims:</i></b> We examined the effect of vascular or Lewy body co-pathologies in subjects with autopsy-confirmed Alzheimer's disease (AD) on the rate of cognitive and functional decline and transition to dementia. <b><i>Methods:</i></b> In an autopsy sample of prospectively characterized subjects from the National Alzheimer's Coordinating Center database, neuropathology diagnosis was used to define the groups of pure AD (pAD, n = 84), mixed vascular and AD (ADV, n = 54), and mixed Lewy body disease and AD (ADLBD, n = 31). Subjects had an initial Clinical Dementia Rating-Global (CDR-G) score &lt;1, Mini-Mental State Examination ≥15, a final visit CDR-G &gt;1, ≥3 evaluations, and Braak tangle stage ≥III. We compared the rate of cognitive and functional decline between the groups. <b><i>Results:</i></b> The rate of functional and cognitive decline was lower for ADV, and ADV patients had less severe deficits on CDR-G and the CDR-Sum of Boxes scores at the last visit than pAD and ADLBD patients. No significant differences were noted between ADLBD and pAD patients. After controlling for age at death, the odds of reaching CDR ≥1 at the last visit were lower in the ADV subjects compared to the pAD subjects. <b><i>Conclusions:</i></b> The mean rate of functional and cognitive decline among ADV subjects was slower than among either pAD or ADLBD patients. Vascular pathology did not increase the odds of attaining CDR ≥1 when occurring with AD in this national cohort.
DOI: 10.7910/dvn/v1rjpf/a4mler
title: iqa20150406_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/iqtyzb
title: iqa20151211_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ku1gj2
title: iqa20151215_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/8luamb
title: iqa20151213_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qkrdsq
title: iqa20161128_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823959
title: Temporal trends of temperate coprophilous beetles and flies

description: Data for dung-inhabiting beetles and flies temporal patterns from Czech Republic and United Kingdom<br><br>Data are currently used in article "Temporal segregation between dung-inhabiting beetle and fly species." which is under review in PLOS ONE <br><br>More details are provided in the attached read-me file. <br>
DOI: 10.6084/m9.figshare.3823959.v1
title: Temporal trends of temperate coprophilous beetles and flies

description: Data for dung-inhabiting beetles and flies temporal patterns from Czech Republic and United Kingdom<br><br>Data are currently used in article "Temporal segregation between dung-inhabiting beetle and fly species." which is under review in PLOS ONE <br><br>More details are provided in the attached read-me file. <br>
DOI: 10.7910/dvn/v1rjpf/k8lsfh
title: iqa20161127_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823953
title: Supplementary Material for: Predictive Parameters Identifying Men Eligible for a Sole MRI/Ultrasound Fusion-Guided Targeted Biopsy without an Additional Systematic Biopsy

description: <br><strong><em>Objective:</em></strong> Evaluating the predictive factors that enable identifying men in which a sole MRI/ultrasound (MRI/US) fusion-guided targeted biopsy (TB) detects the maximal prostate cancer (PCa) risk group. <b><i>Patients and Methods:</i></b> Retrospective analysis of 251 consecutive patients who received a sensor-based, real-time MRI/US TB in combination with a 10-core systematic biopsy (SB) between August 2013 and July 2015. Univariate and multivariate binary regression analyses were performed to evaluate the predictors for equal/superior detection of the PCa risk group by TB compared to SB. <b><i>Results:</i></b> TB detected PCa in 63% (157/251); SB detected PCa in 70% (176/251); a combination of TB and SB detected PCa in 77% (193/251) of cancer patients. Fifty percent (291/584) of TB cores and 22% (539/2,486) of SB cores showed PCa. Predictors for equal/superior performance of a sole TB were lesion size (maximal diameter; OR 1.050, 95% CI 1.002-1.101, p = 0.043), suspicious digital rectal examination (DRE; OR 2.448, 95% CI 1.062-5.645, p = 0.036) and free/total prostate-specific antigen (PSA) ratio (f/t PSA ratio) ≤0.15 (OR 0.916, 95% CI 0.867-0.967, p = 0.002) on univariate regression analysis and f/t PSA ratio ≤0.15 (OR 0.916, 95% CI 0.867-0.967, p = 0.002) on multivariate regression analysis. <b><i>Conclusion:</i></b> The maximal axial diameter of the Prostate Imaging Reporting and Data System-lesion and f/t PSA ratio and a suspicious DRE are possible selection criteria for men eligible for a sole MRI/US fusion-guided targeted prostate biopsy.
DOI: 10.7910/dvn/v1rjpf/h4xfmz
title: iqa20150109_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823953.v1
title: Supplementary Material for: Predictive Parameters Identifying Men Eligible for a Sole MRI/Ultrasound Fusion-Guided Targeted Biopsy without an Additional Systematic Biopsy

description: <br><strong><em>Objective:</em></strong> Evaluating the predictive factors that enable identifying men in which a sole MRI/ultrasound (MRI/US) fusion-guided targeted biopsy (TB) detects the maximal prostate cancer (PCa) risk group. <b><i>Patients and Methods:</i></b> Retrospective analysis of 251 consecutive patients who received a sensor-based, real-time MRI/US TB in combination with a 10-core systematic biopsy (SB) between August 2013 and July 2015. Univariate and multivariate binary regression analyses were performed to evaluate the predictors for equal/superior detection of the PCa risk group by TB compared to SB. <b><i>Results:</i></b> TB detected PCa in 63% (157/251); SB detected PCa in 70% (176/251); a combination of TB and SB detected PCa in 77% (193/251) of cancer patients. Fifty percent (291/584) of TB cores and 22% (539/2,486) of SB cores showed PCa. Predictors for equal/superior performance of a sole TB were lesion size (maximal diameter; OR 1.050, 95% CI 1.002-1.101, p = 0.043), suspicious digital rectal examination (DRE; OR 2.448, 95% CI 1.062-5.645, p = 0.036) and free/total prostate-specific antigen (PSA) ratio (f/t PSA ratio) ≤0.15 (OR 0.916, 95% CI 0.867-0.967, p = 0.002) on univariate regression analysis and f/t PSA ratio ≤0.15 (OR 0.916, 95% CI 0.867-0.967, p = 0.002) on multivariate regression analysis. <b><i>Conclusion:</i></b> The maximal axial diameter of the Prostate Imaging Reporting and Data System-lesion and f/t PSA ratio and a suspicious DRE are possible selection criteria for men eligible for a sole MRI/US fusion-guided targeted prostate biopsy.
DOI: 10.7910/dvn/v1rjpf/ivzrta
title: iqa20150830_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823932
title: PowerPoint Slides for: Parathyroidectomy Increases Heart Rate Variability and Leptin Levels in Patients with Stage 5 Chronic Kidney Disease

description: <strong><em>Background:</em></strong> In chronic kidney disease (CKD) patients, decreased heart rate variability (HRV) reflects impaired cardiac automatic nervous function and high risk of cardiovascular disease (CVD). Lower HRV in patients with severe secondary hyperparathyroidism (SHPT), a clinical manifestation of CKD-mineral and bone disorder (CKD-MBD), could be reversed by parathyroidectomy (PTX). It has been proved that leptin interacts with the autonomic nervous function. However, the associations between leptin and HRV in CKD patients and their longitudinal changes in SHPT patients after PTX are still unknown. <b><i>Methods:</i></b> This was a cross-sectional study including 141 stage 5 CKD patients, and a prospective study in 36 severe SHPT patients with PTX. HRV was measured by Holter and serum leptin was measured by ELISA. Serum leptin levels were adjusted for body mass index (BMI) and transformed using natural logarithm (lnleptin/BMI). <b><i>Results:</i></b> With a gradient of lnleptin/BMI across quartiles from Q1 to Q4 in CKD patients, HRV indices showed no differences among quartiles. Patients in Q1 group had higher mean 24 h heart rates, and lower ln(very low frequency) (lnVLF) than other quartiles, although there were no statistically significant difference. In multivariate stepwise regression, serum leptin/BMI was an independent predictor for low frequency/high frequency. HRV indices and lnleptin/BMI levels were increased in severe SHPT patients after PTX. Compared to other quartiles, SHPT patients in Q1 group had larger improvement of lnVLF after PTX. <b><i>Conclusion:</i></b> Circulating leptin levels may be a novel treatment target to reduce CVD risk in advanced CKD-MBD patients.
DOI: 10.7910/dvn/v1rjpf/vhyasm
title: iqa20150520_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zp1gzx
title: iqa20160806_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823920
title: PowerPoint Slides for: Prognostic Utility of a Self-Reported Depression Questionnaire versus Clinician-Based Assessment on Renal Outcomes

description: <br><strong><em>Background:</em></strong> The prognostic utility of self-administered depression scales in chronic kidney disease (CKD) independent of a clinician-based major depressive disorder (MDD) diagnosis is neither clearly established nor are the optimal cutoff scores for predicting outcomes. The overlap between symptoms of depression and chronic disease raises the question of whether a cutoff score on a depression scale can be substituted for a time-consuming diagnostic interview to prognosticate risk. <b><i>Methods:</i></b> The 16-item Quick Inventory of Depression Symptomatology-Self Report scale (QIDS-SR<sub>16</sub>) was administered to 266 consecutive outpatients with non-dialysis CKD, followed prospectively for 12 months for an apriori composite outcome of death or dialysis or hospitalization. Association of QIDS-SR<sub>16</sub> best cutoff score, determined by receiver/responder operating characteristics curves, with outcomes was investigated using survival analysis. The effect modification of an interview-based clinician MDD diagnosis on this association was ascertained. <b><i>Results:</i></b> There were 126 composite events. A QIDS-SR<sub>16</sub> cutoff ≥8 had the best prognostic accuracy, hazards ratio (HR) = 1.77, 95% CI 1.24-2.53, p = 0.002. This cutoff remained significantly associated with outcomes even after controlling for comorbidities, estimated glomerular filtration rate, hemoglobin and serum albumin, adjusted HR (aHR) = 1.80, 95% CI 1.23-2.62, p = 0.002, and performed similarly to a clinician-based MDD diagnosis (aHR = 1.72, 95% CI 1.14-2.68). Adjustment for MDD conferred the association of QIDS-SR<sub>16</sub> with outcomes no longer significant. <b><i>Conclusions:</i></b> QIDS-SR<sub>16</sub> cutoff ≥8 adds to the prognostic information available to practicing nephrologists during routine clinic visits from comorbidities and laboratory data. This cutoff score performs similar to a clinician diagnosis of MDD and provides a feasible and time-saving alternative to an interview-based MDD diagnosis for determining prognosis in CKD patients.
DOI: 10.6084/m9.figshare.3823932.v1
title: PowerPoint Slides for: Parathyroidectomy Increases Heart Rate Variability and Leptin Levels in Patients with Stage 5 Chronic Kidney Disease

description: <strong><em>Background:</em></strong> In chronic kidney disease (CKD) patients, decreased heart rate variability (HRV) reflects impaired cardiac automatic nervous function and high risk of cardiovascular disease (CVD). Lower HRV in patients with severe secondary hyperparathyroidism (SHPT), a clinical manifestation of CKD-mineral and bone disorder (CKD-MBD), could be reversed by parathyroidectomy (PTX). It has been proved that leptin interacts with the autonomic nervous function. However, the associations between leptin and HRV in CKD patients and their longitudinal changes in SHPT patients after PTX are still unknown. <b><i>Methods:</i></b> This was a cross-sectional study including 141 stage 5 CKD patients, and a prospective study in 36 severe SHPT patients with PTX. HRV was measured by Holter and serum leptin was measured by ELISA. Serum leptin levels were adjusted for body mass index (BMI) and transformed using natural logarithm (lnleptin/BMI). <b><i>Results:</i></b> With a gradient of lnleptin/BMI across quartiles from Q1 to Q4 in CKD patients, HRV indices showed no differences among quartiles. Patients in Q1 group had higher mean 24 h heart rates, and lower ln(very low frequency) (lnVLF) than other quartiles, although there were no statistically significant difference. In multivariate stepwise regression, serum leptin/BMI was an independent predictor for low frequency/high frequency. HRV indices and lnleptin/BMI levels were increased in severe SHPT patients after PTX. Compared to other quartiles, SHPT patients in Q1 group had larger improvement of lnVLF after PTX. <b><i>Conclusion:</i></b> Circulating leptin levels may be a novel treatment target to reduce CVD risk in advanced CKD-MBD patients.
DOI: 10.7910/dvn/v1rjpf/d4g429
title: iqa20150717_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823920.v1
title: PowerPoint Slides for: Prognostic Utility of a Self-Reported Depression Questionnaire versus Clinician-Based Assessment on Renal Outcomes

description: <br><strong><em>Background:</em></strong> The prognostic utility of self-administered depression scales in chronic kidney disease (CKD) independent of a clinician-based major depressive disorder (MDD) diagnosis is neither clearly established nor are the optimal cutoff scores for predicting outcomes. The overlap between symptoms of depression and chronic disease raises the question of whether a cutoff score on a depression scale can be substituted for a time-consuming diagnostic interview to prognosticate risk. <b><i>Methods:</i></b> The 16-item Quick Inventory of Depression Symptomatology-Self Report scale (QIDS-SR<sub>16</sub>) was administered to 266 consecutive outpatients with non-dialysis CKD, followed prospectively for 12 months for an apriori composite outcome of death or dialysis or hospitalization. Association of QIDS-SR<sub>16</sub> best cutoff score, determined by receiver/responder operating characteristics curves, with outcomes was investigated using survival analysis. The effect modification of an interview-based clinician MDD diagnosis on this association was ascertained. <b><i>Results:</i></b> There were 126 composite events. A QIDS-SR<sub>16</sub> cutoff ≥8 had the best prognostic accuracy, hazards ratio (HR) = 1.77, 95% CI 1.24-2.53, p = 0.002. This cutoff remained significantly associated with outcomes even after controlling for comorbidities, estimated glomerular filtration rate, hemoglobin and serum albumin, adjusted HR (aHR) = 1.80, 95% CI 1.23-2.62, p = 0.002, and performed similarly to a clinician-based MDD diagnosis (aHR = 1.72, 95% CI 1.14-2.68). Adjustment for MDD conferred the association of QIDS-SR<sub>16</sub> with outcomes no longer significant. <b><i>Conclusions:</i></b> QIDS-SR<sub>16</sub> cutoff ≥8 adds to the prognostic information available to practicing nephrologists during routine clinic visits from comorbidities and laboratory data. This cutoff score performs similar to a clinician diagnosis of MDD and provides a feasible and time-saving alternative to an interview-based MDD diagnosis for determining prognosis in CKD patients.
DOI: 10.7910/dvn/v1rjpf/ksuxid
title: iqa20150315_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823908
title: PowerPoint Slides for: Patients' Characteristics Affect the Survival Benefit of Warfarin Treatment for Hemodialysis Patients with Atrial Fibrillation. A Historical Cohort Study

description: <br><strong><em>Background:</em></strong> Stroke prevention in dialysis-dependent patients with atrial fibrillation (AF) is an unresolved clinical dilemma. Indeed, no randomized controlled trial evaluating the efficacy and safety of oral anticoagulants in this population, has been conducted so far. Observational research on the use of warfarin in patients on dialysis has shown conflicting results. This uncertainty is mirrored by the wide variations in warfarin prescription patterns across centers. We sought to evaluate the association between the use of vitamin K antagonists (VKAs) and mortality among hemodialysis patient with AF and to assess potential factors affecting the risk-benefit profile of warfarin in this population. <b><i>Methods:</i></b> A total of 91,987 patients registered in the European Clinical Dialysis Database® system from January 2004 to January 2015. Of which, 9,238 patients were identified with a diagnosis of AF. After excluding ineligible patients, a 1:1 propensity score matched cohort of 1,324 warfarin users and non-users were assembled. <b><i>Results:</i></b> VKA use was associated with both increased 90-day survival (hazard ratio, HR 0.47, p &lt; 0.01) and 6-year survival (HR 0.76, p &lt; 0.01); however, a trend indicated a stronger early benefit (p for time-interaction &lt;0.01). Moderation analysis showed that patients' age and clinical history of stroke strongly influenced warfarin-related benefits on survival. <b><i>Conclusion:</i></b> VKA may provide an early survival benefit; however, this is partially offset later during the follow-up. In addition, heterogeneous risk-benefit profiles were observed among subgroups of dialysis-dependent patients with AF, further emphasizing the complexities of tailoring stroke prevention strategies in this population.
DOI: 10.7910/dvn/v1rjpf/jemtv6
title: iqa20160612_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823908.v1
title: PowerPoint Slides for: Patients' Characteristics Affect the Survival Benefit of Warfarin Treatment for Hemodialysis Patients with Atrial Fibrillation. A Historical Cohort Study

description: <br><strong><em>Background:</em></strong> Stroke prevention in dialysis-dependent patients with atrial fibrillation (AF) is an unresolved clinical dilemma. Indeed, no randomized controlled trial evaluating the efficacy and safety of oral anticoagulants in this population, has been conducted so far. Observational research on the use of warfarin in patients on dialysis has shown conflicting results. This uncertainty is mirrored by the wide variations in warfarin prescription patterns across centers. We sought to evaluate the association between the use of vitamin K antagonists (VKAs) and mortality among hemodialysis patient with AF and to assess potential factors affecting the risk-benefit profile of warfarin in this population. <b><i>Methods:</i></b> A total of 91,987 patients registered in the European Clinical Dialysis Database® system from January 2004 to January 2015. Of which, 9,238 patients were identified with a diagnosis of AF. After excluding ineligible patients, a 1:1 propensity score matched cohort of 1,324 warfarin users and non-users were assembled. <b><i>Results:</i></b> VKA use was associated with both increased 90-day survival (hazard ratio, HR 0.47, p &lt; 0.01) and 6-year survival (HR 0.76, p &lt; 0.01); however, a trend indicated a stronger early benefit (p for time-interaction &lt;0.01). Moderation analysis showed that patients' age and clinical history of stroke strongly influenced warfarin-related benefits on survival. <b><i>Conclusion:</i></b> VKA may provide an early survival benefit; however, this is partially offset later during the follow-up. In addition, heterogeneous risk-benefit profiles were observed among subgroups of dialysis-dependent patients with AF, further emphasizing the complexities of tailoring stroke prevention strategies in this population.
DOI: 10.7910/dvn/v1rjpf/rn75g1
title: iqa20150111_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ybgwyb
title: iqa20161022_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zujnex
title: iqa20150524_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823902
title: Minimal Tool Set for a Prokaryotic Circadian Clock Raw Data

description: Raw Data from the reciprocal BLAST of circadian clock factors from <i>Synechococcus elongatus</i> PCC 7942 and <i>Synechocystis</i> sp. PCC 6803.<br>
DOI: 10.7910/dvn/v1rjpf/3ztfg3
title: iqa20150331_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823902.v1
title: Raw Data

description: Raw Data from the reciprocal BLAST of circadian clock factors from <i>Synechococcus elongatus</i> PCC 7942 and <i>Synechocystis</i> sp. PCC 6803.<br>
DOI: 10.7910/dvn/v1rjpf/exl6x3
title: iqa20150104_03.txt.gz

description: :unav