cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6284294
title: Supplementary Material for: Parathyroid Hormone, Fibroblast Growth Factor 23, and Parameters of Phosphate Reabsorption

description: <b><i>Background:</i></b> The serum phosphorus concentration ([P]<sub>s</sub>) is the sum of E<sub>P</sub>/C<sub>cr</sub> and TR<sub>P</sub>/C<sub>cr</sub>, where C<sub>cr</sub> is creatinine clearance and E<sub>P</sub> and TR<sub>P</sub> are rates of excretion and reabsorption of phosphate. In chronic kidney disease (CKD), parathyroid hormone (PTH) and fibroblast growth factor 23 (FGF23) mediate reduction of TR<sub>P</sub>/C<sub>cr</sub>, and [PTH] and [FGF23] are linear functions of E<sub>P</sub>/C<sub>cr</sub>. If controls and patients with CKD are considered together, TR<sub>P</sub>/C<sub>cr</sub> is a hyperbolic function of E<sub>P</sub>/C<sub>cr</sub>. Given these observations, we hypothesized that hyperbolas would describe relationships of phosphate reabsorption to [PTH] and [FGF23]. <b><i>Methods:</i></b> We studied 30 patients and 28 controls with mean eGFR of 29.5 and 86.0 mL/min/1.73 m<sup>2</sup>, respectively. All analyses combined both subsets. We measured fasting [PTH] 1–84 and intact [FGF23], and determined contemporaneous E<sub>P</sub>/C<sub>cr</sub>, TR<sub>P</sub>/C<sub>cr</sub>, fractional excretion of phosphorus (FE<sub>P</sub>), and phosphate tubular maximum per volume of filtrate (Tm<sub>P</sub>/GFR). We examined linear regressions of TR<sub>P</sub>/C<sub>cr</sub> and Tm<sub>P</sub>/GFR on 100/[PTH] and 100/[FGF23]; from linear equations we derived hyperbolic equations relating reabsorptive parameters to hormone concentrations. <b><i>Results:</i></b> TR<sub>P</sub>/C<sub>cr</sub> and Tm<sub>P</sub>/GFR were linear functions of 100/[PTH] and 100/[FGF23] and hyperbolic functions of [PTH] and [FGF23]. TR<sub>P</sub>/C<sub>cr</sub> and Tm<sub>P</sub>/GFR fell minimally over the ranges of E<sub>P</sub>/C<sub>cr</sub>, [PTH], and [FGF23] seen in CKD. FE<sub>P</sub> rose with E<sub>P</sub>/C<sub>cr</sub> despite stable phosphate reabsorption. <b><i>Conclusions:</i></b> Hyperbolas describe relationships of TR<sub>P</sub>/C<sub>cr</sub> and Tm<sub>P</sub>/GFR to [PTH] and [FGF23] if subjects with normal and reduced GFR are analyzed together. Although FE<sub>P</sub> rises with [PTH] and [FGF23] as GFR falls, the simultaneous increments do not signify hormonally mediated reductions in phosphate reabsorption.
DOI: 10.6084/m9.figshare.6283115
title: Wilson Confidence Intervals for Binomial Proportions With Multiple Imputation for Missing Data

description: We present a Wilson interval for binomial proportions for use with multiple imputation for missing data. Using simulation studies, we show that it can have better repeated sampling properties than the usual confidence interval for binomial proportions based on Rubin’s combining rules. Further, in contrast to the usual multiple imputation confidence interval for proportions, the multiple imputation Wilson interval is always bounded by zero and one. Supplementary material is available online.
DOI: 10.6084/m9.figshare.6283115.v2
title: Wilson Confidence Intervals for Binomial Proportions With Multiple Imputation for Missing Data

description: We present a Wilson interval for binomial proportions for use with multiple imputation for missing data. Using simulation studies, we show that it can have better repeated sampling properties than the usual confidence interval for binomial proportions based on Rubin’s combining rules. Further, in contrast to the usual multiple imputation confidence interval for proportions, the multiple imputation Wilson interval is always bounded by zero and one. Supplementary material is available online.
DOI: 10.6084/m9.figshare.6283115.v1
title: Wilson Confidence Intervals for Binomial Proportions with Multiple Imputation for Missing Data

description: We present a Wilson interval for binomial proportions for use with multiple imputation for missing data. Using simulation studies, we show that it can have better repeated sampling properties than the usual confidence interval for binomial proportions based on Rubin's combining rules. Further, in contrast to the usual multiple imputation confidence interval for proportions, the multiple imputation Wilson interval is always bounded by zero and one. Supplementary material is available online.
DOI: 10.6084/m9.figshare.6283112
title: Safety and effectiveness of apixaban in comparison to warfarin in patients with nonvalvular atrial fibrillation: a propensity-matched analysis from Japanese administrative claims data

description: <b>Objective:</b> To investigate the risk of bleeding events and stroke/systemic embolism (SE) among Japanese patients with nonvalvular atrial fibrillation (NVAF), focusing on the initial dosage of apixaban and patient age. <b>Methods:</b> This retrospective cohort study used de-identified electronic health records based claims data from 314 acute-care hospitals in Japan. NVAF patients newly initiated on warfarin or apixaban, with no prescription during the 180-day blanking period, were eligible. Patients were allocated to receive warfarin or 5 or 2.5 mg twice daily (BID) apixaban. One-to-one propensity-score matching was used to balance patient characteristics between apixaban and warfarin. <b>Results:</b> Among 31,006 eligible patients, 11,972 matched pairs were identified for apixaban versus warfarin. Mean age ± standard deviation was 77.7 ± 10.0 and 77.6 ± 10.0 years and CHADS<sub>2</sub> score was 2.2 ± 1.4 and 2.2 ± 1.4 for warfarin and apixaban, respectively. In the apixaban cohort, 39.4% of patients received the standard dose (5 mg BID) and 60.6% received the reduced dose (2.5 mg BID). Incidence rates (events per 100 person-years) of major bleeding, any bleeding and stroke/SE were 3.7, 23.1 and 3.1, and 2.5, 18.6 and 2.0 for warfarin and apixaban cohorts, respectively. Apixaban was associated with a significantly lower risk of any bleeding (hazard ratio [HR] 0.809, 95% confidence interval [CI] 0.731–0.895; <i>p</i> p = .001) and stroke/SE (HR 0.637, 95% CI 0.478–0.850; <i>p</i> = .002). <b>Conclusions:</b> Our observational data from clinical practice broadly confirms the safety and efficacy results of pivotal randomized controlled trials of apixaban for stroke prevention among NVAF patients.
DOI: 10.6084/m9.figshare.6283112.v1
title: Safety and effectiveness of apixaban in comparison to warfarin in patients with nonvalvular atrial fibrillation: a propensity-matched analysis from Japanese administrative claims data

description: <b>Objective:</b> To investigate the risk of bleeding events and stroke/systemic embolism (SE) among Japanese patients with nonvalvular atrial fibrillation (NVAF), focusing on the initial dosage of apixaban and patient age. <b>Methods:</b> This retrospective cohort study used de-identified electronic health records based claims data from 314 acute-care hospitals in Japan. NVAF patients newly initiated on warfarin or apixaban, with no prescription during the 180-day blanking period, were eligible. Patients were allocated to receive warfarin or 5 or 2.5 mg twice daily (BID) apixaban. One-to-one propensity-score matching was used to balance patient characteristics between apixaban and warfarin. <b>Results:</b> Among 31,006 eligible patients, 11,972 matched pairs were identified for apixaban versus warfarin. Mean age ± standard deviation was 77.7 ± 10.0 and 77.6 ± 10.0 years and CHADS<sub>2</sub> score was 2.2 ± 1.4 and 2.2 ± 1.4 for warfarin and apixaban, respectively. In the apixaban cohort, 39.4% of patients received the standard dose (5 mg BID) and 60.6% received the reduced dose (2.5 mg BID). Incidence rates (events per 100 person-years) of major bleeding, any bleeding and stroke/SE were 3.7, 23.1 and 3.1, and 2.5, 18.6 and 2.0 for warfarin and apixaban cohorts, respectively. Apixaban was associated with a significantly lower risk of any bleeding (hazard ratio [HR] 0.809, 95% confidence interval [CI] 0.731–0.895; <i>p</i> p = .001) and stroke/SE (HR 0.637, 95% CI 0.478–0.850; <i>p</i> = .002). <b>Conclusions:</b> Our observational data from clinical practice broadly confirms the safety and efficacy results of pivotal randomized controlled trials of apixaban for stroke prevention among NVAF patients.
DOI: 10.6084/m9.figshare.6283103
title: PostgreSQL_TestFactExtractor_RESULTS.csv

description: Classifying the test for the ProstgressSQL parser
DOI: 10.6084/m9.figshare.6283103.v1
title: PostgreSQL_TestFactExtractor_RESULTS.csv

description: Classifying the test for the ProstgressSQL parser
DOI: 10.6084/m9.figshare.6283100
title: Dataset for: The role of PCNA as a scaffold protein in cellular signaling is functionally conserved between yeast and humans

description: Proliferating cell nuclear antigen (PCNA), a member of the highly conserved DNA sliding clamp family, is an essential protein for cellular processes including DNA replication and repair. A large number of proteins from higher eukaryotes contain one of two PCNA-interacting motifs: PIP-box (PCNA interacting protein-box) and APIM (AlkB homologue 2 PCNA-interacting motif). APIM has been shown to be especially important during cellular stress. PIP-box is known to be functionally conserved in yeast, and here we show that this is also the case for APIM. Several of the 84 APIM-containing yeast proteins are associated with cellular signaling as hub-proteins, which are able to interact with a large number of other proteins. Cellular signaling is highly conserved throughout evolution, and we recently suggested a novel role for PCNA as a scaffold protein in cellular signaling in human cells. A cell-penetrating peptide containing the APIM sequence increases the sensitivity towards the chemotherapeutic agent cisplatin in both yeast and human cells, and both yeast and human cells become hypersensitive when the Hog1/p38 MAPK pathway is blocked. These results suggest that the interactions between APIM-containing signaling proteins and PCNA during the DNA damage response is evolutionary conserved between yeast and mammals, and that PCNA has a role in cellular signaling also in yeast.
DOI: 10.6084/m9.figshare.6283100.v1
title: Dataset for: The role of PCNA as a scaffold protein in cellular signaling is functionally conserved between yeast and humans

description: Proliferating cell nuclear antigen (PCNA), a member of the highly conserved DNA sliding clamp family, is an essential protein for cellular processes including DNA replication and repair. A large number of proteins from higher eukaryotes contain one of two PCNA-interacting motifs: PIP-box (PCNA interacting protein-box) and APIM (AlkB homologue 2 PCNA-interacting motif). APIM has been shown to be especially important during cellular stress. PIP-box is known to be functionally conserved in yeast, and here we show that this is also the case for APIM. Several of the 84 APIM-containing yeast proteins are associated with cellular signaling as hub-proteins, which are able to interact with a large number of other proteins. Cellular signaling is highly conserved throughout evolution, and we recently suggested a novel role for PCNA as a scaffold protein in cellular signaling in human cells. A cell-penetrating peptide containing the APIM sequence increases the sensitivity towards the chemotherapeutic agent cisplatin in both yeast and human cells, and both yeast and human cells become hypersensitive when the Hog1/p38 MAPK pathway is blocked. These results suggest that the interactions between APIM-containing signaling proteins and PCNA during the DNA damage response is evolutionary conserved between yeast and mammals, and that PCNA has a role in cellular signaling also in yeast.
DOI: 10.6084/m9.figshare.6283094
title: Increased Circulating Proinflammatory T Lymphocytes in Children with Different Forms of Anterior Uveitis: Results from a Pilot Study

description: <i>Purpose</i>: To characterize peripheral blood T cells in juvenile idiopathic arthritis-associated uveitis (JIAU). <i>Methods</i>: Blood samples were taken from children with JIAU (n = 18), JIA without ocular involvement (n = 11), idiopathic anterior uveitis (IAU, n = 12), and healthy controls (n = 11). Cells were stained for T cell surface markers, and intracellular cytokine staining was performed after cell stimulation and analyzed by flow cytometry. <i>Results</i>: The Th1/Th2 ratio was increased in JIAU patients. Numbers of IL-13-expressing cells an level of IL-13 and IL-10 expression per cell were increased in all patient groups; whereas, percentages of IL-5-expressing T cells were decreased. Numbers of proinflammatory Th17 cells and T cells expressing CTLA-4 were increased in all patient groups; whereas, γ/δ T cell numbers were decreased. Results from JIA and IAU were similar. <i>Conclusion</i>: T cell subtypes and potential T cell function are altered in pediatric patients with uveitis and arthritis as compared to healthy children.
DOI: 10.6084/m9.figshare.6283094.v1
title: Increased Circulating Proinflammatory T Lymphocytes in Children with Different Forms of Anterior Uveitis: Results from a Pilot Study

description: <i>Purpose</i>: To characterize peripheral blood T cells in juvenile idiopathic arthritis-associated uveitis (JIAU). <i>Methods</i>: Blood samples were taken from children with JIAU (n = 18), JIA without ocular involvement (n = 11), idiopathic anterior uveitis (IAU, n = 12), and healthy controls (n = 11). Cells were stained for T cell surface markers, and intracellular cytokine staining was performed after cell stimulation and analyzed by flow cytometry. <i>Results</i>: The Th1/Th2 ratio was increased in JIAU patients. Numbers of IL-13-expressing cells an level of IL-13 and IL-10 expression per cell were increased in all patient groups; whereas, percentages of IL-5-expressing T cells were decreased. Numbers of proinflammatory Th17 cells and T cells expressing CTLA-4 were increased in all patient groups; whereas, γ/δ T cell numbers were decreased. Results from JIA and IAU were similar. <i>Conclusion</i>: T cell subtypes and potential T cell function are altered in pediatric patients with uveitis and arthritis as compared to healthy children.
DOI: 10.6084/m9.figshare.6283088
title: Rovibrational laser control targeting a dark state in acetylene. Simulation in the <i>N</i><i><sub>s</sub></i> = 1, N<i><sub>r</sub></i> = 5 polyad

description: Optimal control theory in the Liouville space is used to perform rovibrational control by means of a laser pulse in a polyad of acetylene in order to populate a dark vibrational state. The initial mixed state is a truncated Boltzmann distribution of rotational levels from <i>J</i>=27 to <i>J</i>=31 of the ground vibrational state. The target state is a rotational equidistribution of levels ranging from <i>J</i>=28 to <i>J</i>=32 of the first excited vibrational dark state including quanta of energy in each bending modes, with positive vibrational angular momenta. The simulation is performed by using a manifold of eigenstates of a full-dimensional Hamiltonian calibrated by high precision spectroscopy known as the global acetylene Hamiltonian [B. Amyay <i>et al.</i>, J. Chem. Phys. <b>131</b>, 114301 (2009)]. The control is successful as an Uhlmann's fidelity of 0.98 is reached.
DOI: 10.6084/m9.figshare.6283088.v1
title: Rovibrational laser control targeting a dark state in acetylene. Simulation in the <i>N</i><i><sub>s</sub></i> = 1, N<i><sub>r</sub></i> = 5 polyad

description: Optimal control theory in the Liouville space is used to perform rovibrational control by means of a laser pulse in a polyad of acetylene in order to populate a dark vibrational state. The initial mixed state is a truncated Boltzmann distribution of rotational levels from <i>J</i>=27 to <i>J</i>=31 of the ground vibrational state. The target state is a rotational equidistribution of levels ranging from <i>J</i>=28 to <i>J</i>=32 of the first excited vibrational dark state including quanta of energy in each bending modes, with positive vibrational angular momenta. The simulation is performed by using a manifold of eigenstates of a full-dimensional Hamiltonian calibrated by high precision spectroscopy known as the global acetylene Hamiltonian [B. Amyay <i>et al.</i>, J. Chem. Phys. <b>131</b>, 114301 (2009)]. The control is successful as an Uhlmann's fidelity of 0.98 is reached.
DOI: 10.6084/m9.figshare.6283067
title: Assessment of Multiple Membership Multilevel Models: An Application to Interviewer Effects on Nonresponse

description: Multilevel multiple membership models account for situations where lower level units are nested within multiple higher level units from the same classification. Not accounting correctly for such multiple membership structures leads to biased results. The use of a multiple membership model requires selection of weights reflecting the hypothesized contribution of each level two unit and their relationship to the level one outcome. The Deviance Information Criterion (DIC) has been proposed to identify such weights. For the case of logistic regression, this study assesses, through simulation, the model identification rates of the DIC to detect the correct multiple membership weights, and the properties of model variance estimators for different weight specifications across a range of scenarios. The study is motivated by analyzing interviewer effects across waves in a longitudinal study. Interviewers can substantially influence the behavior of sample survey respondents, including their decision to participate in the survey. In the case of a longitudinal survey several interviewers may contact sample members to participate across different waves. Multilevel multiple membership models are suitable to account for the inclusion of higher-level random effects for interviewers at various waves, and to assess, for example, the relative importance of previous and current wave interviewers on current wave nonresponse. To illustrate the application, multiple membership models are applied to the UK Family and Children Survey to identify interviewer effects in a longitudinal study. The paper takes a critical view on the substantive interpretation of the model weights and provides practical guidance to statistical modelers. The main recommendation is that it is best to specify the weights in a multiple membership model by exploring different weight specifications based on the DIC, rather than prespecifying the weights.
DOI: 10.6084/m9.figshare.6283067.v1
title: Assessment of Multiple Membership Multilevel Models: An Application to Interviewer Effects on Nonresponse

description: Multilevel multiple membership models account for situations where lower level units are nested within multiple higher level units from the same classification. Not accounting correctly for such multiple membership structures leads to biased results. The use of a multiple membership model requires selection of weights reflecting the hypothesized contribution of each level two unit and their relationship to the level one outcome. The Deviance Information Criterion (DIC) has been proposed to identify such weights. For the case of logistic regression, this study assesses, through simulation, the model identification rates of the DIC to detect the correct multiple membership weights, and the properties of model variance estimators for different weight specifications across a range of scenarios. The study is motivated by analyzing interviewer effects across waves in a longitudinal study. Interviewers can substantially influence the behavior of sample survey respondents, including their decision to participate in the survey. In the case of a longitudinal survey several interviewers may contact sample members to participate across different waves. Multilevel multiple membership models are suitable to account for the inclusion of higher-level random effects for interviewers at various waves, and to assess, for example, the relative importance of previous and current wave interviewers on current wave nonresponse. To illustrate the application, multiple membership models are applied to the UK Family and Children Survey to identify interviewer effects in a longitudinal study. The paper takes a critical view on the substantive interpretation of the model weights and provides practical guidance to statistical modelers. The main recommendation is that it is best to specify the weights in a multiple membership model by exploring different weight specifications based on the DIC, rather than prespecifying the weights.
DOI: 10.6084/m9.figshare.6283058
title: Ciliogenesis is reciprocally regulated by PPARA and NR1H4/FXR through controlling autophagy in vitro and in vivo

description: The primary cilia are evolutionarily conserved microtubule-based cellular organelles that perceive metabolic status and thus link the sensory system to cellular signaling pathways. Therefore, ciliogenesis is thought to be tightly linked to autophagy, which is also regulated by nutrient-sensing transcription factors, such as PPARA (peroxisome proliferator activated receptor alpha) and NR1H4/FXR (nuclear receptor subfamily 1, group H, member 4). However, the relationship between these factors and ciliogenesis has not been clearly demonstrated. Here, we present direct evidence for the involvement of macroautophagic/autophagic regulators in controlling ciliogenesis. We showed that activation of PPARA facilitated ciliogenesis independently of cellular nutritional states. Importantly, PPARA-induced ciliogenesis was mediated by controlling autophagy, since either pharmacological or genetic inactivation of autophagy significantly repressed ciliogenesis. Moreover, we showed that pharmacological activator of autophagy, rapamycin, recovered repressed ciliogenesis in <i>ppara<sup>−</sup><sup>/−</sup> </i> cells. Conversely, activation of NR1H4 repressed cilia formation, while knockdown of NR1H4 enhanced ciliogenesis by inducing autophagy. The reciprocal activities of PPARA and NR1H4 in regulating ciliogenesis were highlighted in a condition where de-repressed ciliogenesis by NR1H4 knockdown was further enhanced by PPARA activation. The in vivo roles of PPARA and NR1H4 in regulating ciliogenesis were examined in greater detail in <i>ppara<sup>−</sup><sup>/</sup><sup>−</sup> </i> mice. In response to starvation, ciliogenesis was facilitated in wild-type mice via enhanced autophagy in kidney, while <i>ppara<sup>−</sup><sup>/</sup><sup>−</sup> </i> mice displayed impaired autophagy and kidney damage resembling ciliopathy. Furthermore, an NR1H4 agonist exacerbated kidney damage associated with starvation in <i>ppara<sup>−</sup><sup>/</sup><sup>−</sup> </i> mice. These findings indicate a previously unknown role for PPARA and NR1H4 in regulating the autophagy-ciliogenesis axis in vivo.