cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5128954.v1
title: Supplementary Material for: Impact of Socioeconomic Status and Ethnicity on Melanoma Presentation and Recurrence in Caucasian Patients

description: <b><i>Objectives:</i></b> The impact of ethnicity and the socioeconomic status (SES) among Caucasians is not well studied. Here, we examine the impact of income on melanoma presentation and prognosis within a Caucasian cohort, accounting for ethnicity, as some reports suggest increased melanoma incidence in Ashkenazi Jewish (AJ) <i>BRCA</i> mutation carriers. <b><i>Methods:</i></b> We studied prospectively enrolled primary melanoma patients at New York University. SES data were estimated using United States' Census Bureau data and patient zip codes. We evaluated associations between ethnicity, SES, and baseline characteristics using the χ<sup>2</sup> test and multivariate logistic regression. We compared survival distributions using Kaplan-Meier curves, log-rank tests, and Cox proportional hazard ratios. <b><i>Results:</i></b> Of the 1,339 enrolled patients, AJ represented 32% (n = 423). Apart from AJ being older at presentation (p &lt; 0.001), no significant differences were observed in baseline characteristics between ethnic groups. Patients with a median household income (MHI) lower than the median of the cohort were significantly more likely to present with advanced stages (p &lt; 0.001) compared to patients with a higher MHI. Shorter overall (p = 0.016) and post-recurrence survival (p = 0.042) was also observed in patients from lower-income households. <b><i>Conclusion:</i></b> Data suggest that disparities in melanoma presentation in Caucasians stratify according to income independent of ethnic background.
DOI: 10.6084/m9.figshare.5128936
title: Supplementary Material for: Effect of Antecolic versus Retrocolic Gastroenteric Reconstruction after Pancreaticoduodenectomy on Delayed Gastric Emptying: A Meta-Analysis of Six Randomized Controlled Trials

description: <b><i>Background:</i></b> One of the most frequent complications of pancreaticoduodenectomy (PD) is delayed gastric emptying (DGE). The study aim was to evaluate the impact of the type of gastro/duodenojejunal reconstruction (antecolic vs. retrocolic) after PD on DGE incidence. <b><i>Methods:</i></b> A systematic review was made according to the PRISMA guidelines. Randomized controlled trials (RCTs) comparing antecolic vs. retrocolic reconstruction were included irrespective of the PD techniques. A meta-analysis was then performed. <b><i>Results:</i></b> Six RCTs were included for a total of 588 patients. The overall quality was good. General risk of bias was low. DGE was not statistically significantly different between the antecolic and retrocolic group (OR 0.6, 95% CI 0.31-1.16, p = 0.13). The other main surgery-related complications (pancreatic fistula, hemorrhage, intra-abdominal abscess, bile leak and wound infection) were not dependent on the reconstruction route (OR 0.84, 95% CI 0.41-1.70, p = 0.63). No statistically significant difference in terms of length of hospital stay was found between the 2 groups. There was also no difference of DGE incidence if only pylorus-preserving PD was considered and between the DGE grades A, B or C. <b><i>Conclusion:</i></b> This meta-analysis shows that antecolic reconstruction after PD is not superior to retrocolic reconstruction in terms of DGE.
DOI: 10.6084/m9.figshare.5128948.v1
title: Supplementary Material for: Subpubic Arch Angle and Mode of Delivery in Low-Risk Nulliparous Women

description: <b><i>Objective:</i></b> To assess whether subpubic arch angle (SPA) measurement before labor onset can predict labor outcome among low-risk pregnant women. <b><i>Methods:</i></b> 3D ultrasound volume was transperineally acquired from a series of nulliparous women with uncomplicated pregnancy at term before the onset of labor. SPA was measured offline using Oblique View Extended Imaging (OVIX) on each volume performed by an investigator not involved in the clinical management. Labor outcome was prospectively investigated in the whole study group. <b><i>Results:</i></b> Overall, 145 women were enrolled in the study. Of these, 83 underwent spontaneous vaginal delivery, whereas obstetric intervention was performed in 62 cases (Cesarean section in 40 and vacuum extraction in 22). The SPA appeared to be significantly narrower in the women submitted to obstetric intervention compared with those undergoing spontaneous vaginal delivery (116.8 ± 10.3° vs. 123.7 ± 9.6°, p &lt; 0.01). At multivariate analysis SPA and maternal age were identified as independent predictors of the mode of delivery. On the other hand, the duration of labor did not show a significant relationship with SPA. <b><i>Conclusions:</i></b> In low-risk nulliparous women at term gestation, SPA measurement obtained by 3D ultrasound before the onset of labor seems to predict the likelihood of an obstetric intervention but not the duration of labor.
DOI: 10.6084/m9.figshare.5128933
title: Supplementary Material for: High Innate Immune Specificity through Diversified C-Type Lectin-Like Domain Proteins in Invertebrates

description: A key question in current immunity research is how the innate immune system can generate high levels of specificity. Evidence is accumulating that invertebrates, which exclusively rely on innate defense mechanisms, can differentiate between pathogens on the species and even strain level. In this review, we identify and discuss the particular potential of C-type lectin-like domain (CTLD) proteins to generate high immune specificity. Whilst several CTLD proteins are known to act as pattern recognition receptors in the vertebrate innate immune system, the exact role of CTLD proteins in invertebrate immunity is much less understood. We show that CTLD genes are highly abundant in most metazoan genomes and summarize the current state of knowledge on CTLD protein function in insect, crustacean and nematode immune systems. We then demonstrate extreme CTLD gene diversification in the genomes of <i>Caenorhabditis </i>nematodes and provide an update of data from CTLD gene function studies in <i>C. elegans</i>, which indicate that the diversity of CTLD genes could contribute to immune specificity. In spite of recent achievements, the exact functions of the diversified invertebrate CTLD genes are still largely unknown. Our review therefore specifically discusses promising research approaches to rectify this knowledge gap.
DOI: 10.6084/m9.figshare.5128939
title: Supplementary Material for: The Subjective Health Horizon Questionnaire (SHH-Q): Assessing Future Time Perspectives for Facets of an Active Lifestyle

description: <b><i>Background:</i></b> A wider subjective time horizon is assumed to be positively associated with longevity and vitality. In particular, a lifestyle with exposure to novel and varied information is considered beneficial for healthy cognitive aging. At present, measures that specifically assess individuals' perceived temporal extension to engage in active lifestyles in the future are not available. <b><i>Objectives:</i></b> We introduce and validate a new self-report measure, the Subjective Health Horizon Questionnaire (SHH-Q). The SHH-Q assesses individuals' future time perspectives in relation to four interrelated but distinct lifestyle dimensions: (1) novelty-oriented exploration (Novelty), (2) bodily fitness (Body), (3) work goals (Work), and (4) goals in life (Life Goals). The present study aims at: (a) validating the hypothesized factor structure of the SHH-Q, according to which the SHH-Q consists of four interrelated but distinct subscales, and (b) testing the hypothesis that the Novelty and Body subscales of the SHH-Q show positive and selective associations with markers of cognition and somatic health, respectively. <b><i>Methods:</i></b> Using structural equation modeling, we analyzed data from 1,371 healthy individuals (51% women) with a mean age of 70.1 years (SD = 3.6) who participated in the Berlin Aging Study II (BASE-II) and completed the SHH-Q. <b><i>Results:</i></b> As predicted, the SHH-Q formed four correlated but distinct subscales: (1) Novelty, (2) Body, (3) Work, and (4) Life Goals. Greater self-reported future novelty orientation was associated with higher current memory performance, and greater future expectations regarding bodily fitness with better current metabolic status. <b><i>Conclusion:</i></b> The SHH-Q reliably assesses individual differences in four distinct dimensions of future time perspective. Two of these dimensions, Novelty and Body, show differential associations with cognitive status and somatic health. The SHH-Q may serve as a tool to assess how different facets of future time perspective relate to somatic health, cognition, motivation, and affect, and may help to identify the socioeconomic and individual antecedents, correlates, and consequences of an active lifestyle.
DOI: 10.6084/m9.figshare.5128945.v1
title: Supplementary Material for: A Case of Wiedemann-Steiner Syndrome Associated with a 46,XY Disorder of Sexual Development and Gonadal Dysgenesis

description: We report the case of a female patient suffering from a 46,XY disorder of sexual development (DSD) with complete gonadal dysgenesis and Wiedemann-Steiner Syndrome (WDSTS). The coexistence of these 2 conditions has not yet been reported. Using whole exome sequencing and comparative genome hybridization array, we identified a de novo <i>MLL/KMT2A</i> gene nonsense mutation which explains the WDSTS phenotype. In addition, we discovered novel genetic variants, which could explain the testicular dysgenesis observed in the patient, a maternally inherited 167-kb duplication of <i>DAAM2</i> and <i>MOCS1</i> genes and a de novo<i> LRRC33/NRROS</i> gene mutation. These genes, some of which are expressed during mouse gonadal development, could be considered as potentially new candidate genes for DSD.
DOI: 10.6084/m9.figshare.5128927
title: Supplementary Material for: Bias in Peripheral Depression Biomarkers

description: <b><i>Background:</i></b> To aid in the differentiation of individuals with major depressive disorder (MDD) from healthy controls, numerous peripheral biomarkers have been proposed. To date, no comprehensive evaluation of the existence of bias favoring the publication of significant results or inflating effect sizes has been conducted. <b><i>Methods:</i></b> Here, we performed a comprehensive review of meta-analyses of peripheral nongenetic biomarkers that could discriminate individuals with MDD from nondepressed controls. PubMed/MEDLINE, EMBASE, and PsycINFO databases were searched through April 10, 2015. <b><i>Results:</i></b> From 15 references, we obtained 31 eligible meta-analyses evaluating biomarkers in MDD (21,201 cases and 78,363 controls). Twenty meta-analyses reported statistically significant effect size estimates. Heterogeneity was high (<i>I</i><sup><i>2</i></sup> ≥50%) in 29 meta-analyses. We plausibly assumed that the true effect size for a meta-analysis would equal the one of its largest study. A significant summary effect size estimate was observed for 20 biomarkers. We observed an excess of statistically significant studies in 21 meta-analyses. The summary effect size of the meta-analysis was higher than the effect of its largest study in 25 meta-analyses, while 11 meta-analyses had evidence of small-study effects. <b><i>Conclusions:</i></b> Our findings suggest that there is an excess of studies with statistically significant results in the literature of peripheral biomarkers for MDD. The selective publication of ‘positive studies' and the selective reporting of outcomes are possible mechanisms. Effect size estimates of meta-analyses may be inflated in this literature.
DOI: 10.6084/m9.figshare.5128930
title: Supplementary Material for: <b><i>NUP214-RAC1</i></b> and <b><i>RAC1-COL12A1</i></b> Fusion in Complex Variant Translocations Involving Chromosomes 6, 7 and 9 in an Acute Myeloid Leukemia Case with <b><i>DEK-NUP214</i></b>

description: <i>DEK-NUP214</i> gene fusion in acute myeloid leukemia (AML) is associated with poor prognosis. It is most often a sole translocation and more rarely observed as complex chromosomal forms. We describe an AML case with complex karyotype abnormalities involving chromosome bands 6p23, 6q13, 7p22, and 9q34. RNA sequencing analysis revealed that exon 17 of <i>NUP214 </i>(9q34) was fused to exon 2 of <i>RAC1</i> (7p22). We also detected that the 5′-end of intron 1 of <i>RAC1</i> was fused with the antisense strand of intron 5 of <i>COL12A1</i> (6q13). RT-PCR analysis confirmed the expression of <i>DEK-NUP214</i>, <i>NUP214-RAC1</i>, <i>RAC1-COL12A1</i>, <i>NUP214</i>, and <i>RAC1</i>. These results suggest that the 5′- and 3′-ends of <i>NUP214 </i>from the breakpoint in the same locus were fused to <i>RAC1</i> and <i>DEK</i>, respectively, and the 5′-end of <i>RAC1</i> was fused to <i>COL12A1</i>. The reading frame of <i>NUP214</i> was not matched with <i>RAC1</i>; however, high expression of the RAC1 protein was detected by Western blotting. This study identifies the variant complex fusion gene<i>s</i><i>NUP214-RAC1</i> and <i>RAC1- COL12A1</i> in a case of AML.
DOI: 10.6084/m9.figshare.5128939.v1
title: Supplementary Material for: The Subjective Health Horizon Questionnaire (SHH-Q): Assessing Future Time Perspectives for Facets of an Active Lifestyle

description: <b><i>Background:</i></b> A wider subjective time horizon is assumed to be positively associated with longevity and vitality. In particular, a lifestyle with exposure to novel and varied information is considered beneficial for healthy cognitive aging. At present, measures that specifically assess individuals' perceived temporal extension to engage in active lifestyles in the future are not available. <b><i>Objectives:</i></b> We introduce and validate a new self-report measure, the Subjective Health Horizon Questionnaire (SHH-Q). The SHH-Q assesses individuals' future time perspectives in relation to four interrelated but distinct lifestyle dimensions: (1) novelty-oriented exploration (Novelty), (2) bodily fitness (Body), (3) work goals (Work), and (4) goals in life (Life Goals). The present study aims at: (a) validating the hypothesized factor structure of the SHH-Q, according to which the SHH-Q consists of four interrelated but distinct subscales, and (b) testing the hypothesis that the Novelty and Body subscales of the SHH-Q show positive and selective associations with markers of cognition and somatic health, respectively. <b><i>Methods:</i></b> Using structural equation modeling, we analyzed data from 1,371 healthy individuals (51% women) with a mean age of 70.1 years (SD = 3.6) who participated in the Berlin Aging Study II (BASE-II) and completed the SHH-Q. <b><i>Results:</i></b> As predicted, the SHH-Q formed four correlated but distinct subscales: (1) Novelty, (2) Body, (3) Work, and (4) Life Goals. Greater self-reported future novelty orientation was associated with higher current memory performance, and greater future expectations regarding bodily fitness with better current metabolic status. <b><i>Conclusion:</i></b> The SHH-Q reliably assesses individual differences in four distinct dimensions of future time perspective. Two of these dimensions, Novelty and Body, show differential associations with cognitive status and somatic health. The SHH-Q may serve as a tool to assess how different facets of future time perspective relate to somatic health, cognition, motivation, and affect, and may help to identify the socioeconomic and individual antecedents, correlates, and consequences of an active lifestyle.
DOI: 10.6084/m9.figshare.5128921
title: Supplementary Material for: Adequacy of Using Consensus Guidelines for Diagnosis of Dementia with Lewy Bodies in Clinical Trials for Drug Development

description: <b><i>Background/Aims:</i></b> To evaluate the adequacy of using the consensus diagnostic criteria for dementia with Lewy bodies (DLB) to recruit patients with homogeneous characteristics in future clinical trials, where multiple departments of multinational centres are expected to participate with a long enrolment period, and additionally, to contribute to the possible future criteria revision. <b><i>Methods:</i></b> Using data from 2 trials of donepezil for DLB, conducted 3 years apart, characteristics in patients with probable DLB were analysed and compared between studies and between psychiatric and neurological centres. <b><i>Results:</i></b> In 273 patients (phase II: 135, phase III: 138; psychiatric: 73, neurological: 184), clinical characteristics overall were very similar between studies, and between specialty centres, excluding distinctive parkinsonism in the neurological versus psychiatric centres: incidence of parkinsonism (91.8 vs. 71.2%, p &lt; 0.001), Hoehn and Yahr stage (III: 55.0 vs. 21.2%, p &lt; 0.001), and concomitant anti-Parkinson medication (24.5 vs. 11.0%, p = 0.017). Rapid eye movement sleep behaviour disorder, depression, and delusion, suggestive or supportive features, were observed in 35-40%. Additionally, a high prevalence (55.3%) of anxiety was observed. <b><i>Conclusion:</i></b> Employing the consensus criteria is adequate to enrol homogeneous DLB patients into future clinical trials regardless of the specialty of centres and time. Further discussion could involve adding anxiety to future criteria.
DOI: 10.6084/m9.figshare.5128927.v1
title: Supplementary Material for: Bias in Peripheral Depression Biomarkers

description: <b><i>Background:</i></b> To aid in the differentiation of individuals with major depressive disorder (MDD) from healthy controls, numerous peripheral biomarkers have been proposed. To date, no comprehensive evaluation of the existence of bias favoring the publication of significant results or inflating effect sizes has been conducted. <b><i>Methods:</i></b> Here, we performed a comprehensive review of meta-analyses of peripheral nongenetic biomarkers that could discriminate individuals with MDD from nondepressed controls. PubMed/MEDLINE, EMBASE, and PsycINFO databases were searched through April 10, 2015. <b><i>Results:</i></b> From 15 references, we obtained 31 eligible meta-analyses evaluating biomarkers in MDD (21,201 cases and 78,363 controls). Twenty meta-analyses reported statistically significant effect size estimates. Heterogeneity was high (<i>I</i><sup><i>2</i></sup> ≥50%) in 29 meta-analyses. We plausibly assumed that the true effect size for a meta-analysis would equal the one of its largest study. A significant summary effect size estimate was observed for 20 biomarkers. We observed an excess of statistically significant studies in 21 meta-analyses. The summary effect size of the meta-analysis was higher than the effect of its largest study in 25 meta-analyses, while 11 meta-analyses had evidence of small-study effects. <b><i>Conclusions:</i></b> Our findings suggest that there is an excess of studies with statistically significant results in the literature of peripheral biomarkers for MDD. The selective publication of ‘positive studies' and the selective reporting of outcomes are possible mechanisms. Effect size estimates of meta-analyses may be inflated in this literature.
DOI: 10.6084/m9.figshare.5128930.v1
title: Supplementary Material for: <b><i>NUP214-RAC1</i></b> and <b><i>RAC1-COL12A1</i></b> Fusion in Complex Variant Translocations Involving Chromosomes 6, 7 and 9 in an Acute Myeloid Leukemia Case with <b><i>DEK-NUP214</i></b>

description: <i>DEK-NUP214</i> gene fusion in acute myeloid leukemia (AML) is associated with poor prognosis. It is most often a sole translocation and more rarely observed as complex chromosomal forms. We describe an AML case with complex karyotype abnormalities involving chromosome bands 6p23, 6q13, 7p22, and 9q34. RNA sequencing analysis revealed that exon 17 of <i>NUP214 </i>(9q34) was fused to exon 2 of <i>RAC1</i> (7p22). We also detected that the 5′-end of intron 1 of <i>RAC1</i> was fused with the antisense strand of intron 5 of <i>COL12A1</i> (6q13). RT-PCR analysis confirmed the expression of <i>DEK-NUP214</i>, <i>NUP214-RAC1</i>, <i>RAC1-COL12A1</i>, <i>NUP214</i>, and <i>RAC1</i>. These results suggest that the 5′- and 3′-ends of <i>NUP214 </i>from the breakpoint in the same locus were fused to <i>RAC1</i> and <i>DEK</i>, respectively, and the 5′-end of <i>RAC1</i> was fused to <i>COL12A1</i>. The reading frame of <i>NUP214</i> was not matched with <i>RAC1</i>; however, high expression of the RAC1 protein was detected by Western blotting. This study identifies the variant complex fusion gene<i>s</i><i>NUP214-RAC1</i> and <i>RAC1- COL12A1</i> in a case of AML.
DOI: 10.6084/m9.figshare.5128918
title: Supplementary Material for: Comparison between Fondaparinux and Low-Molecular-Weight Heparin in Patients with Acute Coronary Syndrome: A Meta-Analysis

description: <b><i>Objective:</i></b> A number of studies have evaluated the efficacy and safety of fondaparinux versus low-molecular-weight heparin (LMWH) in patients with acute coronary syndrome (ACS), but the findings were not consistent across these studies.<b><i> Methods:</i></b> Electronic databases and article references were searched for studies that assessed fondaparinux versus LMWH in ACS patients. <b><i>Results:</i></b> Six studies met the inclusion criteria. There was a lower risk of major adverse cardiac events (MACE) with fondaparinux-based regimens both in randomized controlled trials (RCT; risk ratio, RR: 0.91, p = 0.04) and observational studies (RR: 0.85, p &lt; 0.0001). Mortality decreased in fondaparinux-treated patients in RCT (RR: 0.84, p = 0.02), but not in observational studies (RR: 1.44, p = 0.64). For the analysis of myocardial infarction (MI), recurrent ischemia and stroke, none of the studies showed significant results. In addition, fondaparinux lowered the risk of major bleeding in RCT (RR: 0.62, p &lt; 0.0001) and observational studies (RR: 0.65, p &lt; 0.0001). The net clinical outcome also favored fondaparinux over LMWH in RCT (RR: 0.82, p &lt; 0.0001) and observational studies (RR: 0.84, p &lt; 0.0001). <b><i>Conclusions:</i></b> Among ACS patients, a fondaparinux-based regimen presented advantages regarding MACE and major bleeding, and a net clinical benefit compared with LMWH, although the benefit is minimal regarding MACE. For death, MI, recurrent ischemia and stroke, fondaparinux has not shown significant benefits.
DOI: 10.6084/m9.figshare.5128924
title: Supplementary Material for: Expression and Purification of Recombinant Human Basic Fibroblast Growth Factor Fusion Proteins and Their Uses in Human Stem Cell Culture

description: To reduce the cost of cytokines and growth factors in stem cell research, a simple method for the production of soluble and biological active human basic fibroblast growth factor (hbFGF) fusion protein in <i>Escherichia coli</i> was established. Under optimal conditions, approximately 60-80 mg of &gt;95% pure hbFGF fusion proteins (Trx-6xHis-hbFGF and 6xHis-hbFGF) were obtained from 1 liter of culture broth. The purified hbFGF proteins, both with and without the fusion tags, were biologically active, which was confirmed by their ability to stimulate proliferation of NIH3T3 cells. The fusion proteins also have the ability to support several culture passages of undifferentiated human embryonic stem cells and induce pluripotent stem cells. This paper describes a low-cost and uncomplicated method for the production and purification of biologically active hbFGF fusion proteins.