cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5122510
title: Supplementary Material for: Evaluating the Influence of Quality Control Decisions and Software Algorithms on SNP Calling for the Affymetrix 6.0 SNP Array Platform

description: <i>Objective:</i> Our goal was to evaluate the influence of quality control (QC) decisions using two genotype calling algorithms, CRLMM and Birdseed, designed for the Affymetrix SNP Array 6.0. <i>Methods:</i> Various QC options were tried using the two algorithms and comparisons were made on subject and call rate and on association results using two data sets. <i>Results:</i> For Birdseed, we recommend using the contrast QC instead of QC call rate for sample QC. For CRLMM, we recommend using the signal-to-noise rate ≧4 for sample QC and a posterior probability of 90% for genotype accuracy. For both algorithms, we recommend calling the genotype separately for each plate, and dropping SNPs with a lower call rate (&lt;95%) before evaluating samples with lower call rates. To investigate whether the genotype calls from the two algorithms impacted the genome-wide association results, we performed association analysis using data from the GENOA cohort; we observed that the number of significant SNPs were similar using either CRLMM or Birdseed. <i>Conclusions:</i> Using our suggested workflow both algorithms performed similarly; however, fewer samples were removed and CRLMM took half the time to run our 854 study samples (4.2 h) compared to Birdseed (8.4 h).
DOI: 10.6084/m9.figshare.5122501
title: Supplementary Material for: An Autoradiographic Study on the Pathogenesis of Levodopa-Induced Dyskinesia: Regulation of Dopamine Transporter by Levodopa in a Rat Model of Parkinson’s Disease

description: <i>Background:</i> The development of abnormal involuntary movements or dyskinesia is a serious complication of <i>L</i>-3,4-dihydroxyphenylalanine (L-DOPA) therapy for Parkinson’s disease (PD). <i>Objective:</i> To evaluate the correlation between dopamine transporter (DAT) regulated by L-DOPA and the pathogenesis of dyskinesia in PD rats. <i>Methods:</i> Thirty rats were used to establish the PD model by injecting 6-hydroxydopamine into the right medial forebrain bundle. The sham surgery rats (n = 4) received 4 µl of physiological saline. Then, 19 rats in which PD has been successfully induced were randomly assigned to the L-DOPA (20 mg/kg/day; n = 15) or model (saline; n = 4) group. After 4 weeks of treatment, <sup>131</sup>I-N-(3-fluoropropyl)-2β-carbomethoxy-3 β-(4-iodophenyl)nortropane was injected into the rats, and images of DAT in the brain were acquired using a storage phosphor plate. The levels of DAT-specific radioactivity uptake in the bilateral corpora striata (left/right) were compared. <i>Results:</i> There was no difference in DAT-specific radioactivity uptake between the bilateral corpora striata in the sham surgery rats. The images were clear and symmetrically distributed in the corpora striata. In PD model rats, the DAT-specific radioactivity uptake decreased on the lesioned side and the ratios of uptake between the corpora striata were increased. Accumulation of the radioligand on the lesioned side was sparse. In the L-DOPA group, the average ratio values were significantly increased in dyskinetic rats and reduced in nondyskinetic rats. In addition, the differences between the bilateral corpora striata were reduced in nondyskinetic rats. <i>Conclusion:</i> L-DOPA was shown to downregulate DAT in some PD model rats. That process may be involved in the pathogenesis of dyskinesia.
DOI: 10.6084/m9.figshare.5122510.v1
title: Supplementary Material for: Evaluating the Influence of Quality Control Decisions and Software Algorithms on SNP Calling for the Affymetrix 6.0 SNP Array Platform

description: <i>Objective:</i> Our goal was to evaluate the influence of quality control (QC) decisions using two genotype calling algorithms, CRLMM and Birdseed, designed for the Affymetrix SNP Array 6.0. <i>Methods:</i> Various QC options were tried using the two algorithms and comparisons were made on subject and call rate and on association results using two data sets. <i>Results:</i> For Birdseed, we recommend using the contrast QC instead of QC call rate for sample QC. For CRLMM, we recommend using the signal-to-noise rate ≧4 for sample QC and a posterior probability of 90% for genotype accuracy. For both algorithms, we recommend calling the genotype separately for each plate, and dropping SNPs with a lower call rate (&lt;95%) before evaluating samples with lower call rates. To investigate whether the genotype calls from the two algorithms impacted the genome-wide association results, we performed association analysis using data from the GENOA cohort; we observed that the number of significant SNPs were similar using either CRLMM or Birdseed. <i>Conclusions:</i> Using our suggested workflow both algorithms performed similarly; however, fewer samples were removed and CRLMM took half the time to run our 854 study samples (4.2 h) compared to Birdseed (8.4 h).
DOI: 10.6084/m9.figshare.5122507.v1
title: Supplementary Material for: Behandlungsintegrität: Implementierung, Messung, Evaluation und Zusammenhänge zum Therapieerfolg

description: Die Sicherung und Überprüfung der Behandlungsintegrität stellt eine essenzielle Voraussetzung für Wirksamkeitsanalysen in der Psychotherapieforschung dar. Die Behandlungsintegrität liefert wichtige Hinweise darüber, ob eine Behandlung so durchgeführt wurde, wie es intendiert war. Es lassen sich 3 unterschiedliche Aspekte der Behandlungsintegrität unterscheiden. Diese sind Adhärenz, Differenzierbarkeit und Kompetenz. Die vorliegende Arbeit gibt Empfehlungen zur Implementierung, Messung und Evaluation der Behandlungsintegrität. Zudem wird eine Übersicht über empirische Befunde gegeben, die einen Bezug zwischen Behandlungsintegrität und Behandlungserfolg herstellen. Es wird deutlich, dass das methodische Vorgehen, insbesondere bei Messung und Evaluation, heterogen und somit die Vergleichbarkeit der Ergebnisse erschwert ist. Dennoch findet sich für viele Studien ein direkter oder indirekter Zusammenhang zwischen Behandlungsintegrität und Behandlungserfolg. Bei nachfolgenden Studien sollten die vorliegenden Empfehlungen zur Implementierung, Messung und Evaluation der Behandlungsintegrität stärker berücksichtigt werden, um eine bessere Vergleichbarkeit der Studien zu ermöglichen.
DOI: 10.6084/m9.figshare.5122513.v1
title: Supplementary Material for: Functional Genomics of Tick Thioester-Containing Proteins Reveal the Ancient Origin of the Complement System

description: Ticks are important ectoparasites and vectors of multiple human and animal diseases. The obligatory hemophagy of ticks provides a formidable route for parasite transmission from one host to another. Parasite survival inside the tick relies on the ability of a pathogen to escape or inhibit tick immune defenses, but the molecular interactions between the tick and its pathogens remain poorly understood. Here we report that tick genomes are unique in that they contain all known classes of the α<sub>2</sub>-macroglobulin family (α<sub>2</sub>M-F) proteins: α<sub>2</sub>-macroglobulin pan-protease inhibitors, C3 complement components, and insect thioester-containing and macroglobulin-related proteins. By using RNA interference-mediated gene silencing in the hard tick <i>Ixodes ricinus</i> we demonstrated the central role of a C3-like molecule in the phagocytosis of bacteria and revealed nonredundant functions for α<sub>2</sub>M-F proteins. Assessment of α<sub>2</sub>M-F functions in a single organism should significantly contribute to the general knowledge on the evolution and function of the complement system. Importantly, understanding the tick immune mechanisms should provide new concepts for efficient transmission blocking of tick-borne diseases.
DOI: 10.6084/m9.figshare.5122498
title: Supplementary Material for: The Effect of HMGB1, a Damage-Associated Molecular Pattern Molecule, on Polymorphonuclear Neutrophil Migration Depends on Its Concentration

description: Polymorphonuclear neutrophils (PMN) play a key role in host defenses against invading microorganisms but also potentiate inflammatory reactions in case of excessive or misdirected responses. Release of the alarmin high-mobility group box 1 (HMGB1) by cells that die at an inflammatory site may act as an alert signal for the immune system. We studied the effect of HMGB1 on human PMN migration, using whole-blood samples to avoid cell activation associated with isolation procedures. HMGB1 50–100 ng/ml reduced baseline PMN migration as well as formyl-methionyl-leucyl-phenylalanine- and IL-8-induced PMN chemotaxis. This inhibitory effect was mediated by the RAGE receptor. In contrast, a higher HMGB1 concentration (5,000 ng/ml) had a chemoattractant effect on PMN through IL-8 production. This effect required the engagement of Toll-like receptors 2 and 4 in addition to the RAGE receptor. The A box component of HMGB1, which antagonizes the endogenous protein, reduced chemotaxis and also strongly inhibited the enhancement of PMN migration observed with the highest HMGB1 concentration. In contrast, the B box, reported to be the active form of HMGB1, exerted a chemoattractant effect. These results strongly point to a key regulatory role of HMGB1 in PMN recruitment to inflammatory tissues. The A box component could potentially serve to inhibit inappropriate PMN recruitment during chronic inflammatory disorders associated with excessive HMGB1 release.
DOI: 10.6084/m9.figshare.5122489
title: Supplementary Material for: Blood Biomarkers for the Diagnosis of Acute Cerebrovascular Diseases: A Prospective Cohort Study

description: <i>Background:</i> The diagnosis of stroke or TIA in the emergency department is difficult, though important for early treatment. Circulating biomarkers might improve upon clinical assessment at admission. <i>Methods:</i> We recruited symptomatic patients with suspected stroke or TIA and drew blood soon after admission. Each patient was assessed with the Face Arm Speech Test (FAST). We measured a panel of 15 circulating inflammatory, thrombotic, cardiac, and cerebral tissue damage biomarkers. Improvement in diagnostic performance was assessed by adding biomarkers to the FAST in logistic regression models to predict a final diagnosis of stroke or TIA (verified by expert review and imaging). <i>Results:</i> 405 patients had suspected stroke: 285 with TIA or stroke (230 definite or probable ischemic stroke, 40 TIA, 15 hemorrhagic stroke) and 120 with other diagnoses. Only the markers t-PA and NT-proBNP were associated positively and significantly (p &lt; 0.01) with a diagnosis of TIA or stroke. The FAST had a sensitivity of 82% (95% CI 78–87) and specificity of 38% (95% CI 29–46) for the diagnosis of TIA or stroke. No biomarker individually improved the sensitivity or specificity of the FAST. A model containing the FAST, age, systolic blood pressure, NT-proBNP and t-PA had a better sensitivity (88%, p &lt; 0.006) and a better specificity (48%, p = 0.04) than the FAST test alone. <i>Conclusions:</i> No single blood marker improved the diagnostic performance of a validated clinical stroke scale. Panels of biomarkers may marginally improve diagnosis, but their practicability is uncertain, and requires further study.
DOI: 10.6084/m9.figshare.5122492
title: Supplementary Material for: Aortic Regurgitation and Coronary Microfistulae: Double Jeopardy Causing Myonecrosis

description: We describe a 3-case series of patients with a rare combination of mild-to-moderate aortic regurgitation and coronary microfistulae but nonobstructed epicardial coronary arteries who presented with symptoms of unstable angina and had confirmed myonecrosis. A plausible pathophysiological mechanism for this phenomenon and its clinical implication are discussed.
DOI: 10.6084/m9.figshare.5122495
title: Supplementary Material for: Predictive Value of F-18 FDG PET/CT for Malignant Pleural Effusion in Non-Small Cell Lung Cancer Patients

description: <i>Background:</i> The purpose of this study was to evaluate the accuracy of F-18 fluorodeoxyglucose positron emission tomography/computed tomography (F-18 FDG PET/CT) imaging in the detection of malignant pleural effusion and pleural metastasis in patients with non-small cell lung cancer (NSCLC). <i>Materials and Methods:</i> We analyzed F-18 FDG PET/CT images of 33 lung cancer patients with pleural effusion. We used 2 categorical parameters to differentiate malignant from benign pleural effusion: i) quantitative parameters using maximum standardized uptake value (SUVmax of effusion and pleura, and the following ratios: lesion to aorta (L/Ao), to cerebellum (L/Cbl), to liver (L/Liv), to nonlesion (L/NL), and to primary lung cancer (L/Prim)) and ii) various parameters determined by PET and CT scans (uptake at the pleural region, Hounsfield unit, size, and morphology of any solid abnormality). <i>Results:</i> Malignant pleural effusions showed significantly higher L/Prim values than benign pleural effusions. The presence of pleural abnormality on CT and pleural region uptake on PET images were found to be significantly more frequent in cases of malignant pleural disease. These parameters could differentiate malignant and benign pleural effusion according to receiver operating characteristic (ROC) analyses. There were no statistical differences between L/Prim, pleural abnormality on CT, and pleural region uptake on PET images. Abnormal pleural region uptake on PET images was the most accurate parameter identifying malignant pleural effusion by logistic regression analysis. <i>Conclusions:</i> Our results suggest that F-18 FDG PET/CT can be used as a reliable and noninvasive method for the differentiation of malignant and benign pleural disease in patients with NSCLC.
DOI: 10.6084/m9.figshare.5122486
title: Supplementary Material for: Anti-Infective Properties of <i>Lactobacillus fermentum</i> against <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i>

description: Surgical wounds and implant-associated <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa </i>infections are often difficult to treat because of limited susceptibility of several of these strains to conventional antibiotics. As a result, there is a constant need for new alternative drugs. The aim of this study was to investigate the antimicrobial properties of <i>Lactobacillus fermentum, </i>a probiotic bacterium, which we have isolated from colonic biopsies. The inhibition of <i>S. aureus</i> and <i>P. aeruginosa</i> growth was evaluated by coincubating with <i>L. fermentum</i> strains. Growth inhibition was tested for several of their clinical isolates using agar well diffusion assays. For biofilm assay <i>S. aureus</i> and <i>P. aeruginosa</i> were grown on the glass slides and in 96-well plates in presence of 2.5 µg/ml culture filtrate of <i>L. fermentum</i>. Biofilms were photographed using confocal microscope or stained with 0.1% crystal violet. Reduction in the cytotoxicity of <i>S. aureus</i> and <i>P. aeruginosa </i>was observed in presence of 2.5 µg/ml <i>L. fermentum</i>-spent media. Using in vitroexperiments, we showed that <i>L. fermentum</i>-secreted compound(s) inhibits the growth, cytotoxicity and biofilm formation of several <i>S. aureus</i> and <i>P. aeruginosa</i> strains. Compound(s) present in the culture supernatant of <i>L. fermentum</i> may have promising applications in treating hospital-acquired infections.
DOI: 10.6084/m9.figshare.5122495.v1
title: Supplementary Material for: Predictive Value of F-18 FDG PET/CT for Malignant Pleural Effusion in Non-Small Cell Lung Cancer Patients

description: <i>Background:</i> The purpose of this study was to evaluate the accuracy of F-18 fluorodeoxyglucose positron emission tomography/computed tomography (F-18 FDG PET/CT) imaging in the detection of malignant pleural effusion and pleural metastasis in patients with non-small cell lung cancer (NSCLC). <i>Materials and Methods:</i> We analyzed F-18 FDG PET/CT images of 33 lung cancer patients with pleural effusion. We used 2 categorical parameters to differentiate malignant from benign pleural effusion: i) quantitative parameters using maximum standardized uptake value (SUVmax of effusion and pleura, and the following ratios: lesion to aorta (L/Ao), to cerebellum (L/Cbl), to liver (L/Liv), to nonlesion (L/NL), and to primary lung cancer (L/Prim)) and ii) various parameters determined by PET and CT scans (uptake at the pleural region, Hounsfield unit, size, and morphology of any solid abnormality). <i>Results:</i> Malignant pleural effusions showed significantly higher L/Prim values than benign pleural effusions. The presence of pleural abnormality on CT and pleural region uptake on PET images were found to be significantly more frequent in cases of malignant pleural disease. These parameters could differentiate malignant and benign pleural effusion according to receiver operating characteristic (ROC) analyses. There were no statistical differences between L/Prim, pleural abnormality on CT, and pleural region uptake on PET images. Abnormal pleural region uptake on PET images was the most accurate parameter identifying malignant pleural effusion by logistic regression analysis. <i>Conclusions:</i> Our results suggest that F-18 FDG PET/CT can be used as a reliable and noninvasive method for the differentiation of malignant and benign pleural disease in patients with NSCLC.
DOI: 10.6084/m9.figshare.5122483
title: Supplementary Material for: Expression of Keratin 19 Is Related to High Recurrence of Hepatocellular Carcinoma after Radiofrequency Ablation

description: <i>Objective:</i> Keratin (K) 19 positivity has been reported to be a useful predictive marker for recurrence in patients with hepatocellular carcinoma (HCC) who have undergone hepatic resection. We investigated the clinical usefulness of K19 positivity in patients who had received curative radiofrequency ablation (RFA). <i>Methods:</i> We retrospectively evaluated the clinicopathological features, including imaging and K19 expression, in 246 patients with HCC who were within the Milan criteria and had received curative RFA. Using a two-step insertion method, tumor biopsies were obtained just prior to RFA and were evaluated histologically. <i>Results:</i> Tumor seeding due to liver biopsy and RFA was not observed. Ten patients (4.1%) had K19-positive HCC. Imaging findings were similar between K19-positive and -negative HCC (p = 0.187). Nine out of 10 patients (90%) who had K19-positive HCC had recurrence of HCC after RFA, and intrahepatic recurrences were observed within 12 months in 6 out of 10 (60.0%). K19 positivity was a significant risk factor for recurrence (p &lt; 0.0001) and early recurrence (&lt;1 year after RFA; p =0.012). K19 expression (p = 0.016) was an independent risk factor for tumor status exceeding the Milan criteria after RFA. <i>Conclusion:</i> Expression of K19 is related to high recurrence of HCC after curative RFA.
DOI: 10.6084/m9.figshare.5122480
title: Supplementary Material for: Evolution of Leptin Structure and Function

description: Leptin, the protein product of the <i>obese</i><i>(ob</i> or <i>Lep)</i> gene, is a hormone synthesized by adipocytes that signals available energy reserves to the brain, and thereby influences development, growth, metabolism and reproduction. In mammals, leptin functions as an adiposity signal: circulating leptin fluctuates in proportion to fat mass, and it acts on the hypothalamus to suppress food intake. Orthologs of mammalian <i>Lep </i>genes were recently isolated from several fish and two amphibian species, and here we report the identification of two <i>Lep</i> genes in a reptile, the lizard <i>Anolis carolinensis</i>. While vertebrate leptins show large divergence in their primary amino acid sequence, they form similar tertiary structures, and may have similar potencies when tested in vitro on heterologous leptin receptors (LepRs). Leptin binds to LepRs on the plasma membrane, activating several intracellular signaling pathways. Vertebrate LepRs signal via the Janus kinase (Jak) and signal transducer and activator of transcription (STAT) pathway. Three tyrosine residues located within the LepR cytoplasmic domain are phosphorylated by Jak2 and are required for activation of SH2-containing tyrosine phosphatase-2, STAT5 and STAT3 signaling. These tyrosines are conserved from fishes to mammals, demonstrating their critical role in signaling by the LepR. Leptin is anorexigenic in representatives of all vertebrate classes, suggesting that its role in energy balance is ancient and has been evolutionarily conserved. In addition to its integral role as a regulator of appetite and energy balance, leptin exerts pleiotropic actions in development, physiology and behavior.
DOI: 10.6084/m9.figshare.5122483.v1
title: Supplementary Material for: Expression of Keratin 19 Is Related to High Recurrence of Hepatocellular Carcinoma after Radiofrequency Ablation

description: <i>Objective:</i> Keratin (K) 19 positivity has been reported to be a useful predictive marker for recurrence in patients with hepatocellular carcinoma (HCC) who have undergone hepatic resection. We investigated the clinical usefulness of K19 positivity in patients who had received curative radiofrequency ablation (RFA). <i>Methods:</i> We retrospectively evaluated the clinicopathological features, including imaging and K19 expression, in 246 patients with HCC who were within the Milan criteria and had received curative RFA. Using a two-step insertion method, tumor biopsies were obtained just prior to RFA and were evaluated histologically. <i>Results:</i> Tumor seeding due to liver biopsy and RFA was not observed. Ten patients (4.1%) had K19-positive HCC. Imaging findings were similar between K19-positive and -negative HCC (p = 0.187). Nine out of 10 patients (90%) who had K19-positive HCC had recurrence of HCC after RFA, and intrahepatic recurrences were observed within 12 months in 6 out of 10 (60.0%). K19 positivity was a significant risk factor for recurrence (p &lt; 0.0001) and early recurrence (&lt;1 year after RFA; p =0.012). K19 expression (p = 0.016) was an independent risk factor for tumor status exceeding the Milan criteria after RFA. <i>Conclusion:</i> Expression of K19 is related to high recurrence of HCC after curative RFA.
DOI: 10.6084/m9.figshare.5122471
title: Supplementary Material for: Regimen Complexity and Prescription Adherence in Dialysis Patients

description: <i>Objectives:</i> Poor medication adherence is common in end-stage renal disease and may cause suboptimal outcomes and increased healthcare costs. We assessed the association between regimen complexity, perceived burden of oral therapy (BOT) and medication adherence in a large sample of hemodialysis (HD) patients. <i>Methods:</i> 1,238 HD patients in 54 Italian centers participated. Data were collected on patients’ socio-demographic characteristics, perceived BOT, quality of life, healthcare satisfaction, social support and medication adherence with a self-administered questionnaire. Data on medication regimen, comorbidities, hospitalizations, and transplant listing status were provided by the nursing staff. We estimated the adjusted association of regimen complexity, BOT and medication adherence with logistic regression. <i>Results:</i> There were 789 (64%) men and the median age was 67 years. Mean daily burden was 9.7 tablets and 48% of patients were adherent to medication prescriptions. The number of tablets prescribed in the medication regimen was associated to adherence likelihood after adjustment for possible confounders. Perceived BOT moderated the association between tablet count and self-reported adherence. <i>Conclusion:</i> Poor adherence was very common in our sample. Reducing tablet burden might help patients be adherent. However, our results suggest that modulating regimen complexity might be ineffective if patients’ negative attitudes toward medications are not addressed concurrently.