cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5121013
title: Supplementary Material for: Is Metastatic Lymph Node Ratio Superior to the Number of Metastatic Lymph Nodes to Assess Outcome and Survival of Gastric Cancer?

description: <i>Background:</i> The aim of this study was to determine the prognostic value of metastatic lymph node ratio (n ratio). <i>Patients and Methods:</i> We retrospectively analyzed 202 patients who had undergone curative gastrectomy. The prognostic factors including UICC/AJCC TNM classification and n ratio were evaluated by univariate and multivariate analysis. <i>Results:</i> The n ratio was significantly higher in patients with gastric tumors with undifferentiated histology, greater size, lymphatic vessel, blood vessel and perineural invasion (PNI), and advanced stage. Multivariate analysis indicated that n ratio and pN classification were independent prognostic factors, as were age, tumor size, Borrmann classification, PNI, and tumor differentiation. The receiver operating characteristics (ROC) analysis showed that the sensitivity and the specificity of the presence of lymph node metastasis with 16 lymph nodes resected – which was required to assess the presence of lymph node involvement – were 67.1 and 66.6%, respectively. Three-year overall survival (OS) rates and the median OS time were lower in patients with &lt;16 lymph nodes resected compared to the patients who had &gt;16 lymph nodes resected (p = 0.04). <i>Conclusions:</i> Our results showed that n ratio and pN classification were independent prognostic indicators for OS of patients with radically resected gastric cancer, but the superiority of n ratio to pN stage could not be proved.
DOI: 10.6084/m9.figshare.5121004
title: Supplementary Material for: High Prevalence of Potential Drug-Drug Interactions for Psoriasis Patients Prescribed Methotrexate or Cyclosporine for Psoriasis: Associated Clinical and Economic Outcomes in Real-World Practice

description: <i>Background:</i> Methotrexate (MTX) and cyclosporine (CYC) may adversely interact with common medications in patients with psoriasis. <i>Objective:</i> Our purpose was to investigate the prevalence and outcomes of MTX/CYC polypharmacy. <i>Methods:</i> We evaluated rates of events that may be associated with drug-related toxicity, health care resource utilization and costs for patients with psoriasis in the Ingenix® Impact National Managed Care Database (1999–2007) who were exposed or not exposed to potential drug-drug interactions. <i>Results:</i> Among 4,583 (57.6%) exposed and 3,372 (42.4%) nonexposed patients, nonsteroidal anti-inflammatory drugs and antibiotics were the most common drugs with potential interactions. The exposed patients had significantly greater risks of developing renal [adjusted odds ratio (OR): 2.58; p = 0.0145], gastrointestinal (OR: 1.36; p = 0.0197) and pulmonary events (OR: 1.20; p = 0.0470), and significantly greater health care resource utilization (e.g. OR for inpatient and emergency department visits: 1.47; p &lt; 0.0001) and costs (adjusted incremental cost: USD 1,722; p &lt; 0.0001). <i>Conclusions:</i> MTX/CYC polypharmacy is prevalent in patients with psoriasis and associated with significant risks.
DOI: 10.6084/m9.figshare.5121007.v1
title: Supplementary Material for: Genetic Variations in the Sodium Balance-Regulating Genes <i>ENaC</i>, <i>NEDD4L</i>, <i>NDFIP2</i> and <i>USP2</i> Influence Blood Pressure and Hypertension

description: <i>Background/Aims:</i> In humans, the kidneys regulate blood pressure by balancing sodium concentrations. Fine-tuning of renal sodium reabsorption and excretion depends on the epithelial sodium channel protein (ENaC: protein complex of SCNN1A, SCNN1B, and SCNN1G). The surface expression of ENaC components is directed by the ubiquitination of ENaC by NEDD4L, an ENaC-specific E3 ubiquitin ligase, and is regulated by the deubiquitination of ENaC by USP2. The activity of NEDD4L in turn is regulated by phosphorylation by SGK1 and also through interaction with NDFIP2. <i>Methods:</i> We analyzed 91 SNPs in 7 genes using the genotype data of 8,842 individuals from the Korea Association REsource subject pool for their correlation with blood pressure and hypertension. <i>Results:</i> 25 SNPs in the <i>SCNN1A</i>, <i>SCNN1B</i>, <i>SCNN1G</i>, <i>NEDD4L</i>, <i>NDFIP2, </i>and<i> USP2 </i>loci were found to be associated with blood pressure. An additional hypertension case-control study identified 13 SNPs in <i>SCNN1B</i>, <i>SCNN1G,</i> and<i> NEDD4L</i> that were linked to hypertension. <i>Conclusion:</i> These results support our hypothesis that individual variations in blood pressure are attributed to variants of the genes that regulate renal sodium reabsorption and excretion. Our data also suggest that it would be meaningful to investigate the role of NEDD4L-mediated ubiquitination in the pathogenesis of hypertension.
DOI: 10.6084/m9.figshare.5121010.v1
title: Supplementary Material for: Substrate-Dependent Regulation of Carbon Catabolism in Marine Sulfate-Reducing <i>Desulfobacterium autotrophicum</i> HRM2

description: <i>Desulfobacterium autotrophicum</i> HRM2 is a metabolically versatile sulfate-reducing bacterium, capable of heterotrophic (e.g. with organic acids and alcohols) and chemolithoautotrophic growth (with H<sub>2</sub>/CO<sub>2</sub>). It employs the Wood-Ljungdahl pathway for complete oxidation of acetyl-CoA to CO<sub>2</sub> and for CO<sub>2</sub> fixation. Here, we investigated substrate-dependent regulation at different levels of anaerobic carbon catabolism in this bacterium. (a) Whole-cell adaptation studies indicated an inducibleutilization of short-chained alcohols, agreeing with a substrate-specific abundance increase (up to 40-fold) of alcohol dehydrogenase Adh4. Simultaneous utilization of lactate and 1-propanol was paralleled by <i>adh4</i> expression and Adh4 formation, respectively. (b) Degradation of propionate generally involves methylmalonyl-CoA mutase (Sbm). Expression of <i>sbm</i> was upregulated during growth with 1-propanol, but not with a mixture of lactate and 1-propanol. Correspondingly, propionate was excreted during growth with this substrate mixture. (c) CO dehydrogenase, the key enzyme of the Wood-Ljungdahl pathway, is encoded by several genes <i>(cdhC</i>, <i>cdh1</i> and <i>cdh2)</i> located at different genomic positions. Expression of all of these genes during heterotrophic and autotrophic growth points to a reversible operation of the Wood-Ljungdahl pathway. In summary, the different regulatory patterns displayed by <i>Db. autotrophicum</i> HRM2 at the tested metabolic levels point to a multi-layered regulatory network.
DOI: 10.6084/m9.figshare.5121013.v1
title: Supplementary Material for: Is Metastatic Lymph Node Ratio Superior to the Number of Metastatic Lymph Nodes to Assess Outcome and Survival of Gastric Cancer?

description: <i>Background:</i> The aim of this study was to determine the prognostic value of metastatic lymph node ratio (n ratio). <i>Patients and Methods:</i> We retrospectively analyzed 202 patients who had undergone curative gastrectomy. The prognostic factors including UICC/AJCC TNM classification and n ratio were evaluated by univariate and multivariate analysis. <i>Results:</i> The n ratio was significantly higher in patients with gastric tumors with undifferentiated histology, greater size, lymphatic vessel, blood vessel and perineural invasion (PNI), and advanced stage. Multivariate analysis indicated that n ratio and pN classification were independent prognostic factors, as were age, tumor size, Borrmann classification, PNI, and tumor differentiation. The receiver operating characteristics (ROC) analysis showed that the sensitivity and the specificity of the presence of lymph node metastasis with 16 lymph nodes resected – which was required to assess the presence of lymph node involvement – were 67.1 and 66.6%, respectively. Three-year overall survival (OS) rates and the median OS time were lower in patients with &lt;16 lymph nodes resected compared to the patients who had &gt;16 lymph nodes resected (p = 0.04). <i>Conclusions:</i> Our results showed that n ratio and pN classification were independent prognostic indicators for OS of patients with radically resected gastric cancer, but the superiority of n ratio to pN stage could not be proved.
DOI: 10.6084/m9.figshare.5120992
title: Supplementary Material for: Differential Modulation of Sonic-Hedgehog-Induced Cerebellar Granule Cell Precursor Proliferation by the IGF Signaling Network

description: The molecular mechanisms regulating organ growth and size remain unclear. Sonic hedgehog (SHH) signaling is a major player in the regulation of cerebellar development: SHH is secreted by Purkinje neurons and acts on the proliferation of granule cell precursors (GCPs) in the external germinal layer. These then become postmitotic and form the internal granular layer but do so in the presence of SHH ligand, begging the question of how the proliferative response to SHH signaling is downregulated in differentiating GCPs. Here, we have determined the precise cellular localization of the expression of insulin-like growth factor (IGF) network components in the developing mouse cerebellum and show that this network modulates the proliferative effects of SHH signaling on GCPs. IGF1 and IGF2 are potent mitogens for GCPs and both synergize with SHH in inducing GCP proliferation. Whereas the proliferative activity of IGF1 or IGF2 on GCPs does not require intact SHH signaling, aspects of SHH activity on GCP proliferation require signaling through the IGF receptor 1. Moreover, we find that 3 of the IGF-binding proteins, IGFBP2, IGFBP3 and IGFBP5, inhibit IGF1/2-induced cell proliferation, whereas IGFBP5 also inhibits SHH-induced GCPs proliferation. This novel function of IGFBP5 that we have uncovered demonstrates the exquisite regulation of SHH signaling by different components of the IGF network.
DOI: 10.6084/m9.figshare.5121001
title: Supplementary Material for: Estimation of Short-Term Effects of Air Pollution on Stroke Hospital Admissions in Southern Sweden

description: <i>Background:</i> Short-term exposure to high levels of air pollution can increase stroke risk. In this study we investigated the short-term effects of air pollution on hospital admissions for stroke in a setting where pollutant levels are rather low. We also addressed methodological issues in evaluating the short-term effects of air pollution. <i>Methods:</i> Daily admissions of ischemic (n = 11,267) and hemorrhagic (n = 1,681) stroke were obtained from a Swedish quality register for stroke, Riks-Stroke. We used two types of exposure data: (1) daily measured background levels of ozone, temperature and particles with a diameter &lt;10 µm (PM<sub>10</sub>) and (2) modeled levels of a mixture of NO and NO<sub>2</sub> (NO<sub>x</sub>) at the residential address of each individual. <i>Results:</i> We estimated a 13% (95% confidence interval, 4–22%) increased risk for hospital admissions for ischemic stroke for levels of PM<sub>10</sub> above 30 µg/m<sup>3</sup> compared to &lt;15 µg/m<sup>3</sup>, whereas temperature above 16°C decreased the risk. No consistent associations were found for hemorrhagic stroke or for ischemic stroke and ozone or NO<sub>x</sub>. <i>Conclusion:</i> Particulate air pollution and temperature seemed to be associated with ischemic stroke hospital admissions. Individual exposure modeling facilitates a detailed exposure assessment but may also be more prone to misclassification errors. The time series and case crossover approaches yielded similar effect estimates.
DOI: 10.6084/m9.figshare.5120995
title: Supplementary Material for: Traumafolgestörungen bei Pflegekindern nach Misshandlung und Vernachlässigung

description: <i>Hintergrund: </i>Pflegekinder haben hÄufig traumatisierende Situationen erlebt, die ihre Fremdunterbringung erforderlich machten. Dennoch gibt es bislang kaum Untersuchungen zu TraumafolgestÖrungen in dieser Risikopopulation. <i>Patienten und Methoden: </i>Die traumatische Belastung bei 20 7-bis 16-jÄhrigen Pflegekindern (10 Jungen, 10 MÄdchen) aus der Inanspruchnahmepopulation einer kinder-und jugendpsychiatrischen Sprechstunde wurde mit einer hinsichtlich Alter und Geschlecht vergleichbaren klinischen Kontrollgruppe von 20 Patienten, die bei wenigstens einem biologischen Elternteil leben, verglichen. Die Diagnostik erfolgte anhand des UCLA PTSD Reaction Index fÜr DSM-IV und des semi-strukturierten Diagnostikinterviews K-SADS Present und Lifetime Version<i>. </i><i>Ergebnisse: </i>Bei den Pflegekindern liegen hÄufig multiple und chronische Traumata durch Misshandlung und/oder VernachlÄssigung vor (n = 19); die Kinder der Kontrollgrupper hingegen weisen hÄufiger einmalige, umschriebene Traumata auf (n = 9). Die PrÄvalenz posttraumatischer Stresssymptome bei Pflegekindern ist signifikant hÖher als bei den Kindern der Kontrollgruppe. <i>Schlussfolgerungen: </i>Pflegekinder entwickeln vor dem Hintergrund ihrer Misshandlungs-und VernachlÄssigungsvorgeschichte gehÄuft TraumafolgestÖrungen. Werden Pflegekinder wegen psychischer AuffÄlligkeiten zur Diagnostik vorgestellt, sollte daher eine gezielte Traumadiagnostik und bei Bedarf eine traumafokussierte Psychotherapie erfolgen.
DOI: 10.6084/m9.figshare.5120998
title: Supplementary Material for: Geographic Variation in One-Year Recurrent Ischemic Stroke Rates for Elderly Medicare Beneficiaries in the USA

description: <i>Background:</i> While geographic disparities in stroke mortality are well documented, there are no data describing geographic variation in recurrent stroke. Accordingly, we evaluated geographic variations in 1-year recurrent ischemic stroke rates in the USA with adjustment for patient characteristics. <i>Methods:</i> One-year recurrent stroke rates for ischemic stroke (International Classification of Diseases, 9th Revision codes 433, 434 and 436) following hospital discharge were calculated by county for all fee-for-service Medicare beneficiaries from 2000 to 2002. The rates were standardized and smoothed using a bayesian conditional autoregressive model that was risk-standardized for patients’ age, gender, race/ethnicity, prior hospitalizations, Deyo comorbidity score, acute myocardial infarction, congestive heart failure, diabetes, hypertension, dementia, cancer, chronic obstructive pulmonary disease and obesity. <i>Results:</i> The overall 1-year recurrent stroke rate was 9.4% among 895,916 ischemic stroke patients (mean age: 78 years; 56.6% women; 86.6% White, 9.7% Black and 1.2% Latino/Hispanic). The rates varied by geographic region and were highest in the South and in parts of the West and Midwest. Regional variation was present for all racial/ethnic subgroups and persisted after adjustment for individual patient characteristics. <i>Conclusions:</i> Almost 1 in 10 hospitalized ischemic stroke patients was readmitted for an ischemic stroke within 1 year. There was heterogeneity in recurrence patterns by geographic region. Further work is needed to understand the reasons for this regional variability.
DOI: 10.6084/m9.figshare.5121004.v1
title: Supplementary Material for: High Prevalence of Potential Drug-Drug Interactions for Psoriasis Patients Prescribed Methotrexate or Cyclosporine for Psoriasis: Associated Clinical and Economic Outcomes in Real-World Practice

description: <i>Background:</i> Methotrexate (MTX) and cyclosporine (CYC) may adversely interact with common medications in patients with psoriasis. <i>Objective:</i> Our purpose was to investigate the prevalence and outcomes of MTX/CYC polypharmacy. <i>Methods:</i> We evaluated rates of events that may be associated with drug-related toxicity, health care resource utilization and costs for patients with psoriasis in the Ingenix® Impact National Managed Care Database (1999–2007) who were exposed or not exposed to potential drug-drug interactions. <i>Results:</i> Among 4,583 (57.6%) exposed and 3,372 (42.4%) nonexposed patients, nonsteroidal anti-inflammatory drugs and antibiotics were the most common drugs with potential interactions. The exposed patients had significantly greater risks of developing renal [adjusted odds ratio (OR): 2.58; p = 0.0145], gastrointestinal (OR: 1.36; p = 0.0197) and pulmonary events (OR: 1.20; p = 0.0470), and significantly greater health care resource utilization (e.g. OR for inpatient and emergency department visits: 1.47; p &lt; 0.0001) and costs (adjusted incremental cost: USD 1,722; p &lt; 0.0001). <i>Conclusions:</i> MTX/CYC polypharmacy is prevalent in patients with psoriasis and associated with significant risks.
DOI: 10.6084/m9.figshare.5120989
title: Supplementary Material for: Bacterial and Eukaryotic Phosphoketolases: Phylogeny, Distribution and Evolution

description: Phosphoketolases (XFPs) are glycolytic enzymes present in several organisms belonging to the <i>Eukarya</i> and <i>Bacteria</i> domains. A total of 151 putative <i>xfp</i> genes were detected in 650 complete genomes available in public databases. Elimination of redundant sequences and pseudogenes rendered a final data set of 128 phosphoketolases, which was analyzed by phylogenetic methods. The distribution of <i>xfp</i> genes was uneven in most taxonomic groups, with the exception of the taxonomical division Lactobacillaceae, in which all the species studied harbored a putative <i>xfp</i> gene. Putative <i>xfp</i> genes were also present predominantly in <i>Rhizobiales</i> and <i>Actinobacteria</i> divisions, in which 23 out of 28 genomes and 23 out of 41 genomes contained at least one putative <i>xfp</i> homolog, respectively. Phylogenetic analyses showed clear discordance with the expected order of organismal descent even in groups where <i>xfp</i> is prevalent, such as <i>Lactobacillaceae.</i> The presence of putative paralogs in some organisms cannot account for these discrepancies; instead, these paralogs are most possibly xenologs. The results of the phylogenetic analyses, the distribution of <i>xfp</i> genes and the location of some <i>xfp</i> genes in plasmids are independent pieces of evidence that point to horizontal gene transfer as a major driving force in the evolution of phosphoketolases.
DOI: 10.6084/m9.figshare.5120998.v1
title: Supplementary Material for: Geographic Variation in One-Year Recurrent Ischemic Stroke Rates for Elderly Medicare Beneficiaries in the USA

description: <i>Background:</i> While geographic disparities in stroke mortality are well documented, there are no data describing geographic variation in recurrent stroke. Accordingly, we evaluated geographic variations in 1-year recurrent ischemic stroke rates in the USA with adjustment for patient characteristics. <i>Methods:</i> One-year recurrent stroke rates for ischemic stroke (International Classification of Diseases, 9th Revision codes 433, 434 and 436) following hospital discharge were calculated by county for all fee-for-service Medicare beneficiaries from 2000 to 2002. The rates were standardized and smoothed using a bayesian conditional autoregressive model that was risk-standardized for patients’ age, gender, race/ethnicity, prior hospitalizations, Deyo comorbidity score, acute myocardial infarction, congestive heart failure, diabetes, hypertension, dementia, cancer, chronic obstructive pulmonary disease and obesity. <i>Results:</i> The overall 1-year recurrent stroke rate was 9.4% among 895,916 ischemic stroke patients (mean age: 78 years; 56.6% women; 86.6% White, 9.7% Black and 1.2% Latino/Hispanic). The rates varied by geographic region and were highest in the South and in parts of the West and Midwest. Regional variation was present for all racial/ethnic subgroups and persisted after adjustment for individual patient characteristics. <i>Conclusions:</i> Almost 1 in 10 hospitalized ischemic stroke patients was readmitted for an ischemic stroke within 1 year. There was heterogeneity in recurrence patterns by geographic region. Further work is needed to understand the reasons for this regional variability.
DOI: 10.6084/m9.figshare.5121001.v1
title: Supplementary Material for: Estimation of Short-Term Effects of Air Pollution on Stroke Hospital Admissions in Southern Sweden

description: <i>Background:</i> Short-term exposure to high levels of air pollution can increase stroke risk. In this study we investigated the short-term effects of air pollution on hospital admissions for stroke in a setting where pollutant levels are rather low. We also addressed methodological issues in evaluating the short-term effects of air pollution. <i>Methods:</i> Daily admissions of ischemic (n = 11,267) and hemorrhagic (n = 1,681) stroke were obtained from a Swedish quality register for stroke, Riks-Stroke. We used two types of exposure data: (1) daily measured background levels of ozone, temperature and particles with a diameter &lt;10 µm (PM<sub>10</sub>) and (2) modeled levels of a mixture of NO and NO<sub>2</sub> (NO<sub>x</sub>) at the residential address of each individual. <i>Results:</i> We estimated a 13% (95% confidence interval, 4–22%) increased risk for hospital admissions for ischemic stroke for levels of PM<sub>10</sub> above 30 µg/m<sup>3</sup> compared to &lt;15 µg/m<sup>3</sup>, whereas temperature above 16°C decreased the risk. No consistent associations were found for hemorrhagic stroke or for ischemic stroke and ozone or NO<sub>x</sub>. <i>Conclusion:</i> Particulate air pollution and temperature seemed to be associated with ischemic stroke hospital admissions. Individual exposure modeling facilitates a detailed exposure assessment but may also be more prone to misclassification errors. The time series and case crossover approaches yielded similar effect estimates.
DOI: 10.6084/m9.figshare.5120992.v1
title: Supplementary Material for: Differential Modulation of Sonic-Hedgehog-Induced Cerebellar Granule Cell Precursor Proliferation by the IGF Signaling Network

description: The molecular mechanisms regulating organ growth and size remain unclear. Sonic hedgehog (SHH) signaling is a major player in the regulation of cerebellar development: SHH is secreted by Purkinje neurons and acts on the proliferation of granule cell precursors (GCPs) in the external germinal layer. These then become postmitotic and form the internal granular layer but do so in the presence of SHH ligand, begging the question of how the proliferative response to SHH signaling is downregulated in differentiating GCPs. Here, we have determined the precise cellular localization of the expression of insulin-like growth factor (IGF) network components in the developing mouse cerebellum and show that this network modulates the proliferative effects of SHH signaling on GCPs. IGF1 and IGF2 are potent mitogens for GCPs and both synergize with SHH in inducing GCP proliferation. Whereas the proliferative activity of IGF1 or IGF2 on GCPs does not require intact SHH signaling, aspects of SHH activity on GCP proliferation require signaling through the IGF receptor 1. Moreover, we find that 3 of the IGF-binding proteins, IGFBP2, IGFBP3 and IGFBP5, inhibit IGF1/2-induced cell proliferation, whereas IGFBP5 also inhibits SHH-induced GCPs proliferation. This novel function of IGFBP5 that we have uncovered demonstrates the exquisite regulation of SHH signaling by different components of the IGF network.