cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5124484
title: Supplementary Material for: Genetic Variation in <b><i>MAOA</i></b> Modulates Prefrontal Cortical Regulation of Approach-Avoidance Reactions

description: <b><i>Background:</i></b> Regulation of automatic approach and avoidance behavior requires affective and cognitive control, which are both influenced by a genetic variation in the gene encoding Monoamine Oxidase A (termed <i>MAOA</i>-uVNTR). <b><i>Methods:</i></b> The current study investigated <i>MAOA</i> genotype as a moderator of prefrontal cortical activation measured with functional near-infrared spectroscopy (fNIRS) in 37 healthy young adults during performance of the approach-avoidance task with positive and negative pictures. <b><i>Results:</i></b> Carriers of the low- compared to the high-expressing genetic variant <i>(MAOA-L</i> vs. <i>MAOA-H)</i> showed increasing regulatory activity in the right dorsolateral prefrontal cortex (DLPFC) during incompatible conditions (approach negative, avoid positive). This might have been a compensatory mechanism for stronger emotional reactions as shown in previous studies and might have prevented any influence of incompatibility on behavior. In contrast, fewer errors but also lower activity in the right DLPFC during processing of negative compared to positive stimuli indicated <i>MAOA-H</i> carriers to have used other regulatory areas. This resulted in slower reaction times in incompatible conditions, but - in line with the known better cognitive regulation efficiency - allowed them to perform incompatible reactions without activating the DLPFC as the highest control instance. Carriers of one low- and one high-expressing allele lay as an intermediate group between the reactions of the low- and high-expressing groups. <b><i>Conclusions:</i></b> The relatively small sample size and restriction to fNIRS for assessment of cortical activity limit our findings. Nevertheless, these first results suggest monoam-inergic mechanisms to contribute to interindividual differences in the two basic behavioral principles of approach and avoidance and their neuronal correlates.
DOI: 10.6084/m9.figshare.5124481
title: Supplementary Material for: Identification of Rare Variants from Exome Sequence in a Large Pedigree with Autism

description: We carried out analyses with the goal of identifying rare variants in exome sequence data that contribute to disease risk for a complex trait. We analyzed a large, 47-member, multigenerational pedigree with 11 cases of autism spectrum disorder, using genotypes from 3 technologies representing increasing resolution: a multiallelic linkage marker panel, a dense diallelic marker panel, and variants from exome sequencing. Genome-scan marker genotypes were available on most subjects, and exome sequence data was available on 5 subjects. We used genome-scan linkage analysis to identify and prioritize the chromosome 22 region of interest, and to select subjects for exome sequencing. Inheritance vectors (IVs) generated by Markov chain Monte Carlo analysis of multilocus marker data were the foundation of most analyses. Genotype imputation used IVs to determine which sequence variants reside on the haplotype that co-segregates with the autism diagnosis. Together with a rare-allele frequency filter, we identified only one rare variant on the risk haplotype, illustrating the potential of this approach to prioritize variants. The associated gene, MYH9, is biologically unlikely, and we speculate that for this complex trait, the key variants may lie outside the exome.
DOI: 10.6084/m9.figshare.5124487.v1
title: Supplementary Material for: Quantitative Profiling and Identification of Plasma Proteins of Spinocerebellar Ataxia Type 2 Patients

description: <b><i>Background:</i></b> Spinocerebellar ataxia type 2 (SCA2) is an autosomal-dominant hereditary ataxia characterized by progressive gait and limb ataxia, dysarthria, slow saccades, neuropathy and dementia. The expansion of trinucleotide CAG repeats in the coding region of the <i>ATXN-2</i> gene leads to expanded polyglutamine stretch in the mutated protein which causes neuronal death. <b><i>Objective:</i></b> In this study, we investigated the blood plasma of SCA2 patients to find protein biomarkers. <b><i>Methods:</i></b> Thirty-two ataxia patients clinically suspected for SCA2 were evaluated by the International Co-operative Ataxia Rating Scale followed by genetic analysis using PCR. Plasma proteomics of SCA2 patients and age- and gender-matched healthy controls was done using 2D-difference in-gel electrophoresis, LC-MS/MS and Western blot. <b><i>Results:</i></b> Genetic analysis confirmed 10 of 32 suspected SCA2 patients. Proteomic data revealed nine differentially expressed proteins in SCA2. These proteins find good association with oxidative stress, calcium-dependent apoptosis, neuropathy, and cognitive impairment in SCA2 patients. Interestingly, the elevated levels of the voltage-dependent calcium channel γ-3 subunit showed a direct correlation with calcium-generated apoptosis of Purkinje cells. The cognitive deficit, a common symptom in SCA2 patients, seems to correlate with decreased levels of transthyretin and retinol-binding protein-4. <b><i>Conclusions:</i></b> Some of these identified proteins in SCA2 can be useful for therapeutic, diagnostic and prognostic purposes.
DOI: 10.6084/m9.figshare.5124496.v1
title: Supplementary Material for: White Matter Hyperintensities and Functional Outcomes at 2 Weeks and 1 Year after Stroke

description: <b><i>Background:</i></b> Many stroke survivors remain at a functionally disabled state. Early prediction of functional outcome is an important step in the treatment and care of stroke patients. Brain imaging measures have received particular attention as one of the predictors of stroke outcomes. However, the associations between white matter hyperintensities (WMHs) and post-stroke recovery have been controversial. This study aimed to investigate whether deep and periventricular WMHs (DWMHs and PVWMHs, respectively) were associated with functional outcomes at 2 weeks and 1 year after stroke separately and interactively. <b><i>Methods:</i></b> A total of 408 patients were evaluated at the time of admission and 2 weeks after stroke, and 284 (78%) were followed 1 year later in order to evaluate consequences of stroke at both acute and chronic stages. Stroke outcomes were dichotomized into good and poor by applying a modified Rankin Scale (mRS) score cutoff of 1 (no significant disability)/2 (slight disability). Measures of stroke severity (National Institutes of Health Stroke Scale: NIHSS), physical disability (Barthel Index: BI), and cognitive function (Mini-Mental State Examination: MMSE) were administered. Brain magnetic resonance imaging (MRI) was performed at admission. DWMHs and PVWMHs were rated visually on axial FLAIR images using the 4-point modified Fazeka’s scale and categorized into mild (grades 0 and 1) or severe (grades 2 and 3). The demographic and clinical covariates of age, gender, years of education, previous history of stroke, depression, stroke location, and vascular risk factors were obtained. Associations of WMHs with stroke outcomes (mRS) and other measures (NIHSS, BI, and MMSE) at 2 weeks and at 1 year after stroke were investigated using logistic regression and repeated measures ANOVA after adjustment for the potential covariates. <b><i>Results:</i></b> Severe PVWMHs, but not severe DWMHs, were significantly associated with worse outcomes both at 2 weeks and at 1 year after stroke. Furthermore, significant interactive effects of PVWMHs and DWMHs on poor outcomes were found. Significant PVWMH group by time interactions on NIHSS and BI scores, and significant group effects of both DWMHs and PVWMHs on MMSE score were found. <b><i>Conclusions:</i></b> PVWMHs predicted poorer functional outcomes after stroke both in the acute and chronic phases, independently and interactively with DWMHs. In addition, PVWMHs were independently associated with worsening of stroke severity and physical disability. More careful evaluation and management of stroke patients with a high risk of functional dependence are indicated. Overall, PVWMH might be a prognostic marker of short- and long-term stroke outcomes.
DOI: 10.6084/m9.figshare.5124472
title: Supplementary Material for: Gene Polymorphisms of Interleukin-10 and Tumor Necrosis Factor-α Are Associated with Contrast-Induced Nephropathy

description: <b><i>Background/Aims:</i></b> Contrast-induced nephropathy (CIN) is the third most common cause of hospital-acquired acute renal failure. However, the pathogenesis of CIN remains unclear. This study evaluated the role of anti-inflammatory cytokine interleukin-10 (IL-10) and pro-inflammatory cytokine tumor necrosis factor-α (TNF-α) gene polymorphisms as CIN susceptibility markers after percutaneous coronary intervention (PCI). <b><i>Methods:</i></b> Four IL-10 tag SNPs (rs1554286, rs3021094, rs3790622, rs1800896) and three TNF-α tag SNPs (rs1799964, rs1800630, rs1800629) were analyzed by MALDI-TOF mass spectrometry in 53 CIN patients and 455 control subjects. Serum IL-10 and TNF-α were detected using ELISA. <b><i>Results:</i></b> When compared to controls, the CIN patients showed increased frequencies of CC (rs1554286) and AG+GG (rs1800896) genotypes in IL-10 and GA+AA (rs1800629) genotype in TNF-α (OR = 2.24 (1.13–4.44), p = 0.018; OR = 2.61 (1.30–5.26), p = 0.005, and OR = 2.11 (1.08–4.09), p = 0.025, respectively). Baseline serum IL-10 levels in CIN patients were significantly lower (1.02 ± 1.14 vs. 2.78 ± 4.73 pg/ml, p = 0.008). Patients with CIN had a higher rate of decline in renal function than those without CIN (0.89 ± 1.67 vs. 0.30 ± 0.95 ml/min/1.73 m<sup>2</sup> per month, p = 0.002). Significantly higher rates of decline in creatinine clearance were noted in patients with TNF-α (rs1800629) GA+AA than GG genotype (0.88 ± 1.83 vs. 0.36 ± 0.70, p = 0.03), and with IL-10 (rs1800896) AG+GG than AA genotype (1.28 ± 2.14 vs. 0.33 ± 0.90, p &lt; 0.001). <b><i>Conclusions:</i></b> Gene polymorphisms of IL-10 and TNF-α are associated with CIN risk and long-term renal outcome after PCI. More prospective studies are needed to confirm our results.
DOI: 10.6084/m9.figshare.5124475
title: Supplementary Material for: Mediterranean Diet Adherence in Individuals with Prediabetes and Unknown Diabetes: The Di@bet.es Study

description: <b><i>Background and Aims:</i></b> Mediterranean diet (MedDiet) is causally related to diabetes and is a dietary pattern recommended to individuals with diabetes. We investigated MedDiet adherence in individuals with prediabetes and unknown (PREDM/UKDM) or known diabetes (KDM) compared to those with normal glucose metabolism (NORMAL). <b><i>Methods:</i></b> This was a national, population-based, cross-sectional, cluster-sampling study. MedDiet adherence was scored (MedScore, mean ± SD 24 ± 5) using a qualitative food frequency questionnaire. Logistic regression was used to examine the association between MedScore and PREDM/UKDM or KDM versus control subjects. <b><i>Results:</i></b> We evaluated 5,076 individuals. Mean age was 50 years, 57% were female, 826 (582/244) were PREDM/UKDM, 478 were KDM and 3,772 were NORMAL. Mean age increased across MedScore tertiles (46, 51 and 56 years, p &lt; 0.0001). Higher age-adjusted adherence to MedDiet (5-unit increment in the MedScore) was associated with lower and nondifferent odds (OR, 95% CI) of prevalent PREDM/UKDM (0.88, 0.81-0.96, p = 0.001) and KDM (0.97, 0.87-1.07, p = 0.279), respectively, compared to individuals in the NORMAL group. <b><i>Conclusions:</i></b> In a representative sample of the whole Spanish population, MedDiet adherence is independently associated with PREDM/UKDM. Therapeutic intervention may be, in part, responsible for the lack of differences in adherence observed between the KDM and NORMAL groups. However, reverse causation bias cannot be ruled out in cross-sectional studies.
DOI: 10.6084/m9.figshare.5124484.v1
title: Supplementary Material for: Genetic Variation in <b><i>MAOA</i></b> Modulates Prefrontal Cortical Regulation of Approach-Avoidance Reactions

description: <b><i>Background:</i></b> Regulation of automatic approach and avoidance behavior requires affective and cognitive control, which are both influenced by a genetic variation in the gene encoding Monoamine Oxidase A (termed <i>MAOA</i>-uVNTR). <b><i>Methods:</i></b> The current study investigated <i>MAOA</i> genotype as a moderator of prefrontal cortical activation measured with functional near-infrared spectroscopy (fNIRS) in 37 healthy young adults during performance of the approach-avoidance task with positive and negative pictures. <b><i>Results:</i></b> Carriers of the low- compared to the high-expressing genetic variant <i>(MAOA-L</i> vs. <i>MAOA-H)</i> showed increasing regulatory activity in the right dorsolateral prefrontal cortex (DLPFC) during incompatible conditions (approach negative, avoid positive). This might have been a compensatory mechanism for stronger emotional reactions as shown in previous studies and might have prevented any influence of incompatibility on behavior. In contrast, fewer errors but also lower activity in the right DLPFC during processing of negative compared to positive stimuli indicated <i>MAOA-H</i> carriers to have used other regulatory areas. This resulted in slower reaction times in incompatible conditions, but - in line with the known better cognitive regulation efficiency - allowed them to perform incompatible reactions without activating the DLPFC as the highest control instance. Carriers of one low- and one high-expressing allele lay as an intermediate group between the reactions of the low- and high-expressing groups. <b><i>Conclusions:</i></b> The relatively small sample size and restriction to fNIRS for assessment of cortical activity limit our findings. Nevertheless, these first results suggest monoam-inergic mechanisms to contribute to interindividual differences in the two basic behavioral principles of approach and avoidance and their neuronal correlates.
DOI: 10.6084/m9.figshare.5124472.v1
title: Supplementary Material for: Gene Polymorphisms of Interleukin-10 and Tumor Necrosis Factor-α Are Associated with Contrast-Induced Nephropathy

description: <b><i>Background/Aims:</i></b> Contrast-induced nephropathy (CIN) is the third most common cause of hospital-acquired acute renal failure. However, the pathogenesis of CIN remains unclear. This study evaluated the role of anti-inflammatory cytokine interleukin-10 (IL-10) and pro-inflammatory cytokine tumor necrosis factor-α (TNF-α) gene polymorphisms as CIN susceptibility markers after percutaneous coronary intervention (PCI). <b><i>Methods:</i></b> Four IL-10 tag SNPs (rs1554286, rs3021094, rs3790622, rs1800896) and three TNF-α tag SNPs (rs1799964, rs1800630, rs1800629) were analyzed by MALDI-TOF mass spectrometry in 53 CIN patients and 455 control subjects. Serum IL-10 and TNF-α were detected using ELISA. <b><i>Results:</i></b> When compared to controls, the CIN patients showed increased frequencies of CC (rs1554286) and AG+GG (rs1800896) genotypes in IL-10 and GA+AA (rs1800629) genotype in TNF-α (OR = 2.24 (1.13–4.44), p = 0.018; OR = 2.61 (1.30–5.26), p = 0.005, and OR = 2.11 (1.08–4.09), p = 0.025, respectively). Baseline serum IL-10 levels in CIN patients were significantly lower (1.02 ± 1.14 vs. 2.78 ± 4.73 pg/ml, p = 0.008). Patients with CIN had a higher rate of decline in renal function than those without CIN (0.89 ± 1.67 vs. 0.30 ± 0.95 ml/min/1.73 m<sup>2</sup> per month, p = 0.002). Significantly higher rates of decline in creatinine clearance were noted in patients with TNF-α (rs1800629) GA+AA than GG genotype (0.88 ± 1.83 vs. 0.36 ± 0.70, p = 0.03), and with IL-10 (rs1800896) AG+GG than AA genotype (1.28 ± 2.14 vs. 0.33 ± 0.90, p &lt; 0.001). <b><i>Conclusions:</i></b> Gene polymorphisms of IL-10 and TNF-α are associated with CIN risk and long-term renal outcome after PCI. More prospective studies are needed to confirm our results.
DOI: 10.6084/m9.figshare.5124481.v1
title: Supplementary Material for: Identification of Rare Variants from Exome Sequence in a Large Pedigree with Autism

description: We carried out analyses with the goal of identifying rare variants in exome sequence data that contribute to disease risk for a complex trait. We analyzed a large, 47-member, multigenerational pedigree with 11 cases of autism spectrum disorder, using genotypes from 3 technologies representing increasing resolution: a multiallelic linkage marker panel, a dense diallelic marker panel, and variants from exome sequencing. Genome-scan marker genotypes were available on most subjects, and exome sequence data was available on 5 subjects. We used genome-scan linkage analysis to identify and prioritize the chromosome 22 region of interest, and to select subjects for exome sequencing. Inheritance vectors (IVs) generated by Markov chain Monte Carlo analysis of multilocus marker data were the foundation of most analyses. Genotype imputation used IVs to determine which sequence variants reside on the haplotype that co-segregates with the autism diagnosis. Together with a rare-allele frequency filter, we identified only one rare variant on the risk haplotype, illustrating the potential of this approach to prioritize variants. The associated gene, MYH9, is biologically unlikely, and we speculate that for this complex trait, the key variants may lie outside the exome.
DOI: 10.6084/m9.figshare.5124460
title: Supplementary Material for: Continuous Positive Airway Pressure Failure in Preterm Infants: Incidence, Predictors and Consequences

description: <b><i>Background:</i></b> Preterm infants ≤32 weeks' gestation are increasingly being managed on continuous positive airway pressure (CPAP), without prior intubation and surfactant therapy. Some infants treated in this way ultimately fail on CPAP and require intubation and ventilation. <b><i>Objectives:</i></b> To define the incidence, predictors and consequences of CPAP failure in preterm infants managed with CPAP from the outset. <b><i>Methods:</i></b> Preterm infants 25-32 weeks' gestation were included in the study if inborn and managed with CPAP as the initial respiratory support, with division into two gestation ranges and grouping according to whether they were successfully managed on CPAP (CPAP-S) or failed on CPAP and required intubation &lt;72 h (CPAP-F). Predictors of CPAP failure were sought, and outcomes compared between the groups. <b><i>Results:</i></b> 297 infants received CPAP, of which 65 (22%) failed, with CPAP failure being more likely at lower gestational age. Most infants failing CPAP had moderate or severe respiratory distress syndrome radiologically. In multivariate analysis, CPAP failure was found to be predicted by the highest FiO<sub>2</sub> in the first hours of life. CPAP-F infants had a prolonged need for respiratory support and oxygen therapy, and a higher risk of death or bronchopulmonary dysplasia at 25-28 weeks' gestation (CPAP-F 53% vs. CPAP-S 14%, relative risk 3.8, 95% CI 1.6, 9.3) and a substantially higher risk of pneumothorax at 29-32 weeks. <b><i>Conclusion:</i></b> CPAP failure in preterm infants usually occurs because of unremitting respiratory distress syndrome, is predicted by an FiO<sub>2</sub> ≥0.3 in the first hours of life, and is associated with adverse outcomes.
DOI: 10.6084/m9.figshare.5124463
title: Supplementary Material for: Home Artificial Nutrition in Switzerland: An Epidemiological Survey from 2005 to 2009

description: <b><i>Background and Aims:</i></b> Home artificial nutrition (HAN), including oral nutritional supplements (ONS) and enteral (HEN) and parenteral (HPN) nutrition, is an established, important treatment for malnourished patients. The aim of this study was to analyze the epidemiological data of patients on HAN in Switzerland. <b><i>Methods:</i></b> This retrospective study recorded all new cases of HAN in Switzerland from January 2005 to December 2009. <b><i>Results:</i></b> A total of 12,917 cases were recorded: 6,731 (52%) males and 6,186 (48%) females, with a mean age of 65.0 ± 17.6 years. The number of patients on ONS was 7,827 (57.4%), on HEN 3,966 (39.4%) and on HPN 433 (3.2%). The most common underlying disease category was neoplasms (6,519, 50.7%). The number of patients on ONS increased from 57.0% (n = 1,252) to 60.8% (n = 2,039), and on HPN from 2.1% (n = 45) to 4.0% (n = 134) between 2005 and 2009. <b><i>Conclusions:</i></b> This first analysis of the large-scale Swiss registry of HAN shows that approximately half of the patients received ONS, whereas HPN was rarely delivered. The frequency of ONS and HPN increased from the year 2005 to 2009. In accordance with previous European studies, malignant tumors were by far the most frequent indication for HAN.
DOI: 10.6084/m9.figshare.5124466
title: Supplementary Material for: Lamination of the Lateral Geniculate Nucleus of Catarrhine Primates

description: The lateral geniculate nucleus (LGN) of catarrhine primates - with the exception of gibbons - is typically described as a 6-layered structure, comprised of 2 ventral magnocellular layers, and 4 dorsal parvocellular layers. The parvocellular layers of the LGN are involved in color vision. Therefore, it is hypothesized that a 6-layered LGN is a shared-derived trait among catarrhines. This might suggest that in gibbons the lack of further subdivisions of the parvocellular layers is a recent change, and could be related to specializations of visual information processing in this taxon. To address these hypotheses, the lamination of the LGN was investigated in a range of catarrhine species, including several taxa not previously described, and the evolution of the LGN was reconstructed using phylogenetic information. The findings indicate that while all catarrhine species have 4 parvocellular leaflets, two main patterns of LGN parvocellular lamination occur: 2 undivided parvocellular layers in some species, and 4 parvocellular leaflets (with occasional subleaflets) in other species. LGN size was not found to be related to lamination pattern. Both patterns were found to occur in divergent clades, which is suggestive of homoplasy within the catarrhines in LGN morphology.
DOI: 10.6084/m9.figshare.5124475.v1
title: Supplementary Material for: Mediterranean Diet Adherence in Individuals with Prediabetes and Unknown Diabetes: The Di@bet.es Study

description: <b><i>Background and Aims:</i></b> Mediterranean diet (MedDiet) is causally related to diabetes and is a dietary pattern recommended to individuals with diabetes. We investigated MedDiet adherence in individuals with prediabetes and unknown (PREDM/UKDM) or known diabetes (KDM) compared to those with normal glucose metabolism (NORMAL). <b><i>Methods:</i></b> This was a national, population-based, cross-sectional, cluster-sampling study. MedDiet adherence was scored (MedScore, mean ± SD 24 ± 5) using a qualitative food frequency questionnaire. Logistic regression was used to examine the association between MedScore and PREDM/UKDM or KDM versus control subjects. <b><i>Results:</i></b> We evaluated 5,076 individuals. Mean age was 50 years, 57% were female, 826 (582/244) were PREDM/UKDM, 478 were KDM and 3,772 were NORMAL. Mean age increased across MedScore tertiles (46, 51 and 56 years, p &lt; 0.0001). Higher age-adjusted adherence to MedDiet (5-unit increment in the MedScore) was associated with lower and nondifferent odds (OR, 95% CI) of prevalent PREDM/UKDM (0.88, 0.81-0.96, p = 0.001) and KDM (0.97, 0.87-1.07, p = 0.279), respectively, compared to individuals in the NORMAL group. <b><i>Conclusions:</i></b> In a representative sample of the whole Spanish population, MedDiet adherence is independently associated with PREDM/UKDM. Therapeutic intervention may be, in part, responsible for the lack of differences in adherence observed between the KDM and NORMAL groups. However, reverse causation bias cannot be ruled out in cross-sectional studies.