cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5123695.v1
title: Supplementary Material for: Correlation of Cognition and SPECT Perfusion: Easy Z Score and SPM Analysis of a Pilot Sample with Cerebral Small Vessel Disease

description: <b><i>Background/Aims:</i></b> To associate neuropsychology test performance with perfusion on single-photon emission computed tomography (SPECT) among 12 patients with cerebral small vessel disease. <b><i>Methods:</i></b> The easy Z score imaging system (eZIS) was used to compare patient images to those of normal controls. Scores from neuropsychological tests commonly used to screen for dementia were associated with SPECT resting perfusion image values using the statistical parametric mapping (SPM) program. <b><i>Results:</i></b> Immediate Memory and Delayed Memory index scores, as well as memory subtests of the Repeatable Battery for Assessment of Neuropsychological Status showed cluster- and voxelwise positive correlations with hypoperfusion in frontal, temporal and cerebellar regions. Negative correlations, primarily in frontal regions, were interpreted as compensatory hyperperfusion. <b><i>Conclusion:</i></b> eZIS and SPM analyses of SPECT images showed perfusion correlations with neuropsychological tests with small vessel disease.
DOI: 10.6084/m9.figshare.5123689.v1
title: Supplementary Material for: Analysis of Four Genes Involved in the Neurodevelopment Shows Association of rs4307059 Polymorphism in the Cadherin 9/10 Region with Completed Suicide

description: <b><i>Background:</i></b> We hypothesized that DNA variants affecting neurodevelopment such as rs4307059 <i>(CDH10/CDH9)</i>, rs930752 <i>(NRXN1)</i>, rs6265 <i>(BDNF)</i> or rs10868235 <i>(NTRK2)</i> may predispose to completed suicide. <b><i>Methodology:</i></b> We used a case-control two-stage approach based on a discovery cohort (557 cases and ∼550 controls) and replication cohort (159 cases and 186 controls). The suicides were ascertained as consecutive cases autopsied at the Department of Forensic Medicine, Medical University of Warsaw, Poland. <b><i>Results:</i></b> In the discovery cohort we found an association between suicide and the CC genotype in the rs4307059 polymorphism (OR 1.64, p = 0.012). The trend for an overrepresentation of the CC homozygotes among suicides was replicated in the second cohort (OR 1.97, p = 0.056). Analysis in the pooled cohorts showed that rs4307059 CC was associated with completed suicide (OR 1.71, p = 0.002) also after Bonferroni correction (p<sub>cor.</sub> = 0.024). In an exploratory search for genotype-phenotype correlation we found that males with the rs4307059 CC genotype committed suicide earlier than those with CT/TT genotypes (p = 0.049). <b><i>Conclusions:</i></b> The CC genotype of rs4307059 located in the region between <i>CDH9</i> and <i>CDH10</i> is associated with completed suicide in a Polish cohort.
DOI: 10.6084/m9.figshare.5123674
title: Supplementary Material for: Increased Shedding of Microvesicles from Intimal Smooth Muscle Cells in Athero-Prone Areas of the Human Aorta: Implications for Understanding of the Predisease Stage

description: <b><i>Objective:</i></b> This study evaluated whether a change in the content of matrix microvesicles might occur at the preatherosclerotic stage. <b><i>Methods:</i></b> Applying quantitative electron microscopic and immunohistochemical analyses, two areas of grossly normal segments of the thoracic aorta were compared: atherosclerosis-prone (AP) areas, situated at the dorsal aspect of the aorta along the rows of intercostal branch origins, and atherosclerosis-resistant (AR) areas, situated at the corresponding sites of the ventral aspect of the aorta. <b><i>Results:</i></b> The electron microscopic analysis showed that there were 1.4 times more microvesicles in AP areas than AR areas (p = 0.019). It was found that matrix microvesicles originated as a result of blebbing and shedding of surface membranes of smooth muscle cells. A quantitative analysis of the expression of ADP-ribosylation factor 6 (ARF6), which is known to be involved in membrane trafficking and microvesicle formation, showed that ARF6 expression was 1.3 times higher in AP areas than that in AR areas (p = 0.006). There was a positive correlation between the content of matrix microparticles and the expression of ARF6 by intimal smooth muscle cells (r = 0.61; p &lt; 0.0001). <b><i>Conclusion:</i></b> The present study supports the concept that alterations of the arterial intima occur at the predisease stage.
DOI: 10.6084/m9.figshare.5123677
title: Supplementary Material for: Expression Profiling of Breast Tumors Based on Human Epidermal Growth Factor Receptor 2 Status Defines Migration-Related Genes

description: <b><i>Objective:</i></b> Breast cancer is a heterogeneous neoplasm. Distinct subtypes of breast cancer have been defined, suggesting the existence of molecular differences contributing to their clinical outcomes. However, the molecular differences between human epidermal growth factor receptor 2 (HER2)-positive and HER2-negative breast cancer tumors remain unclear. The aim of this study was to identify a gene expression profile for breast tumors based on their HER2 status. <b><i>Methods:</i></b> The HER2 status was determined by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) in 54 breast tumor samples. Using Affymetrix microarray data from these breast tumors, we established the expression profiling of breast cancer based on HER2 IHC and FISH results. To validate microarray experiment data, real-time quantitative reverse transcription-PCR was performed. <b><i>Results:</i></b> We found significant differences between the HER2-positive and HER2-negative breast tumor samples, which included overexpression of HER2, other genes located on 17q12 and genes functionally related to migration. <b><i>Conclusion:</i></b> Our study shows the potential of integrated genomic profiling to shed light on the molecular knowledge of HER2-positive breast tumors.
DOI: 10.6084/m9.figshare.5123680
title: Supplementary Material for: Childhood Stiff-Person Syndrome Improved with Rituximab

description: <b><i>Introduction:</i></b> Stiff-person syndrome (SPS) is manifested by fluctuating rigidity of axial musculature with painful episodic spasms due to simultaneous co-contraction of agonist and antagonist muscles. We present a case report and video illustrating response to treatment with rituximab. <b><i>Materials and Methods:</i></b> Case description and video are provided. A literature search for other reports of treatment with rituximab was performed. <b><i>Results:</i></b> Nine cases in addition to our case were described. Substantial clinical benefit was reported in 7/9 (78%) cases. Four out of 9 (44%) cases displayed persistent anti-glutamic acid decarboxylase (GAD) antibody positivity. <b><i>Conclusion:</i></b> Rituximab is an important treatment strategy in SPS. The persistence of anti-GAD antibody positivity even with clinical remission remains to be elucidated.
DOI: 10.6084/m9.figshare.5123683.v1
title: Supplementary Material for: Cloning and Characterization of Chromosomal Markers from a Cot-1 Library of Peanut (<b><i>Arachis hypogaea</i></b> L.)

description: The cultivated peanut, <i>Arachis hypogaea</i> (AABB, 2n = 40), is an allotetraploid which was probably originated from a hybridization event between 2 ancestors, <i>A. duranensis</i> (A genome) and <i>A. ipaensis</i> (B genome) followed by chromosome doubling. The wild species in the <i>Arachis</i> section are useful genetic resources for genes that confer biotic and abiotic stress resistance for peanut breeding. However, the resource is not well exploited because little information on the genetic, cytogenetic, and phylogenetic relationships between cultivated peanut and its wild relatives is known. Characterization of its chromosome components will benefit the understanding of these issues. But the paucity of information on the DNA sequence and the presence of morphologically similar chromosomes impede the construction of a detailed karyotype for peanut chromosome identification. In our study, a peanut Cot-1 library was constructed to isolate highly and moderately repetitive sequences from the cultivated peanut, and the chromosomal distributions of these repeats were investigated. Both genome and chromosome specific markers were identified that allowed the distinguishing of A and B genomes in tetraploid peanut and a possible karyotyping of peanut chromosomes by FISH. In particular, a 115-bp tandem repetitive sequence was identified to be a possible centromere repetitive DNA, mainly localized in the centromeres of B chromosomes, and a partial retrotransposable element was also identified in the centromeres of B chromosomes. The cloning and characterization of various chromosomal markers is a major step for FISH-based karyotyping of peanut. The FISH markers are expected to provide a reference tool for sequence assembly, phylogenetic studies of peanut and its wild species, and breeding.
DOI: 10.6084/m9.figshare.5123668
title: Supplementary Material for: Yamaguchi Facial Expression-Making Task in Alzheimer’s Disease: A Novel and Enjoyable Make-a-Face Game

description: <b><i>Background:</i></b> To assess the ability to make emotional facial expressions, we newly developed the Yamaguchi facial expression-making task (Y-FEMT). <b><i>Method:</i></b> We recruited 20 normal controls and 61 outpatients: 10 with amnestic mild cognitive impairment (aMCI), 34 with mild Alzheimer’s disease (AD), and 17 with moderate AD. In the Y-FEMT, smile and anger expressions were made by arranging face parts. We examined the relationship between each Y-FEMT score and the Mini-Mental State Examination (MMSE) score or overlapping figure identification test (Fig-test). <b><i>Results:</i></b> The Total score (0–20) was nearly achieved in controls (18.9 ± 1.4) and declined with AD progression (aMCI 17.2 ± 2.4, mild AD 15.7 ± 2.6, moderate AD 12.3 ± 2.7). The Anger score (0–10) was significantly lower than the Smile score (0–10) in mild and moderate AD (p = 0.007 and p = 0.006, respectively). The Structure score (0–6 each) correlated well with both the MMSE score (r = 0.44, p &lt; 0.001) and Fig-test (r = 0.45, p &lt; 0.001), whereas the Expression score (0–4 each) correlated only with the MMSE score (r = 0.33, p = 0.01). The Subjective scores (0–4), evaluated by 10 therapists, highly correlated with the Total score. Additionally, the Y-FEMT promoted laughter and a convivial atmosphere. <b><i>Conclusion:</i></b> The Y-FEMT pleasantly assessed the ability to make emotional facial expressions without special equipment. Furthermore, the Y-FEMT may provide helpful clues for caregivers to achieve good communication with AD patients for better care.
DOI: 10.6084/m9.figshare.5123671
title: Supplementary Material for: Role of the MicroRNA-17–92 Cluster in the Endothelial Differentiation of Stem Cells

description: MicroRNAs (miRs) are small non-coding RNAs that recently emerged as potent regulators of gene expression. The members of the miR-17–92 cluster have been shown to control endothelial cell functions and neovascularization; however, the regulation and function of the cluster in endothelial cell lineage commitment has not been explored. This project aimed to test the role of the miR-17–92 cluster during endothelial differentiation. We demonstrate that miR-17, miR-18, miR-19 and miR-20 are increased upon the induction of endothelial cell differentiation of murine embryonic stem cells or induced pluripotent stem cells. In contrast, miR-92a and the primary miR-17–92 transcript were downregulated. The inhibition of each individual miR of the cluster by cholesterol-modified antagomirs did not affect endothelial marker gene expression. Moreover, the combination of all antagomirs had no effect. These findings illustrate that although the miR-17–92 cluster regulates vascular integrity and angiogenesis, none of the members has a significant impact on the endothelial differentiation of pluripotent stem cells.
DOI: 10.6084/m9.figshare.5123665
title: Supplementary Material for: A High-Resolution 15,000<sub>Rad</sub> Radiation Hybrid Panel for the Domestic Cat

description: The current genetic and recombination maps of the cat have fewer than 3,000 markers and a resolution limit greater than 1 Mb. To complement the first-generation domestic cat maps, support higher resolution mapping studies, and aid genome assembly in specific areas as well as in the whole genome, a 15,000<sub>Rad</sub> radiation hybrid (RH) panel for the domestic cat was generated. Fibroblasts from the female Abyssinian cat that was used to generate the cat genomic sequence were fused to a Chinese hamster cell line (A23), producing 150 hybrid lines. The clones were initially characterized using 39 short tandem repeats (STRs) and 1,536 SNP markers. The utility of whole-genome amplification in preserving and extending RH panel DNA was also tested using 10 STR markers; no significant difference in retention was observed. The resolution of the 15,000<sub>Rad</sub> RH panel was established by constructing framework maps across 10 different 1-Mb regions on different feline chromosomes. In these regions, 2-point analysis was used to estimate RH distances, which compared favorably with the estimation of physical distances. The study demonstrates that the 15,000<sub>Rad</sub> RH panel constitutes a powerful tool for constructing high-resolution maps, having an average resolution of 40.1 kb per marker across the ten 1-Mb regions. In addition, the RH panel will complement existing genomic resources for the domestic cat, aid in the accurate re-assemblies of the forthcoming cat genomic sequence, and support cross-species genomic comparisons.
DOI: 10.6084/m9.figshare.5123671.v1
title: Supplementary Material for: Role of the MicroRNA-17–92 Cluster in the Endothelial Differentiation of Stem Cells

description: MicroRNAs (miRs) are small non-coding RNAs that recently emerged as potent regulators of gene expression. The members of the miR-17–92 cluster have been shown to control endothelial cell functions and neovascularization; however, the regulation and function of the cluster in endothelial cell lineage commitment has not been explored. This project aimed to test the role of the miR-17–92 cluster during endothelial differentiation. We demonstrate that miR-17, miR-18, miR-19 and miR-20 are increased upon the induction of endothelial cell differentiation of murine embryonic stem cells or induced pluripotent stem cells. In contrast, miR-92a and the primary miR-17–92 transcript were downregulated. The inhibition of each individual miR of the cluster by cholesterol-modified antagomirs did not affect endothelial marker gene expression. Moreover, the combination of all antagomirs had no effect. These findings illustrate that although the miR-17–92 cluster regulates vascular integrity and angiogenesis, none of the members has a significant impact on the endothelial differentiation of pluripotent stem cells.
DOI: 10.6084/m9.figshare.5123674.v1
title: Supplementary Material for: Increased Shedding of Microvesicles from Intimal Smooth Muscle Cells in Athero-Prone Areas of the Human Aorta: Implications for Understanding of the Predisease Stage

description: <b><i>Objective:</i></b> This study evaluated whether a change in the content of matrix microvesicles might occur at the preatherosclerotic stage. <b><i>Methods:</i></b> Applying quantitative electron microscopic and immunohistochemical analyses, two areas of grossly normal segments of the thoracic aorta were compared: atherosclerosis-prone (AP) areas, situated at the dorsal aspect of the aorta along the rows of intercostal branch origins, and atherosclerosis-resistant (AR) areas, situated at the corresponding sites of the ventral aspect of the aorta. <b><i>Results:</i></b> The electron microscopic analysis showed that there were 1.4 times more microvesicles in AP areas than AR areas (p = 0.019). It was found that matrix microvesicles originated as a result of blebbing and shedding of surface membranes of smooth muscle cells. A quantitative analysis of the expression of ADP-ribosylation factor 6 (ARF6), which is known to be involved in membrane trafficking and microvesicle formation, showed that ARF6 expression was 1.3 times higher in AP areas than that in AR areas (p = 0.006). There was a positive correlation between the content of matrix microparticles and the expression of ARF6 by intimal smooth muscle cells (r = 0.61; p &lt; 0.0001). <b><i>Conclusion:</i></b> The present study supports the concept that alterations of the arterial intima occur at the predisease stage.
DOI: 10.6084/m9.figshare.5123656
title: Supplementary Material for: Mood and the Menstrual Cycle

description: <b><i>Background:</i></b> Premenstrual mood symptoms are considered common in women, but such prevailing attitudes are shaped by social expectations about gender, emotionality and hormonal influences. There are few prospective, community studies of women reporting mood data from all phases of the menstrual cycle (MC). We aimed (i) to analyze daily mood data over 6 months for MC phase cyclicity and (ii) to compare MC phase influences on a woman’s daily mood with that attributable to key alternate explanatory variables (physical health, perceived stress and social support). <b><i>Method:</i></b> A random sample of Canadian women aged 18–40 years collected mood and health data daily over 6 months, using telemetry, producing 395 complete MCs for analysis. <b><i>Results:</i></b> Only half the individual mood items showed any MC phase association; these links were either with the menses phase alone or the menses plus the premenstrual phase. With one exception, the association was not solely premenstrual. The menses-follicular-luteal MC division gave similar results. Less than 0.5% of the women’s individual periodogram records for each mood item showed MC entrainment. Physical health, perceived stress and social support were much stronger predictors of mood (p &lt; 0.0001 in each case) than MC phase. <b><i>Conclusions: </i></b>The results of this study do not support the widespread idea of specific premenstrual dysphoria in women. Daily physical health status, perceived stress and social support explain daily mood better than MC phase.
DOI: 10.6084/m9.figshare.5123662
title: Supplementary Material for: Evolutionary Molecular Cytogenetics of Catarrhine Primates: Past, Present and Future

description: The catarrhine primates were the first group of species studied with comparative molecular cytogenetics. Many of the fundamental techniques and principles of analysis were initially applied to comparisons in these primates, including interspecific chromosome painting, reciprocal chromosome painting and the extensive use of cloned DNA probes for evolutionary analysis. The definition and importance of chromosome syntenies and associations for a correct cladistics analysis of phylogenomic relationships were first applied to catarrhines. These early chromosome painting studies vividly illustrated a striking conservation of the genome between humans and macaques. Contemporarily, it also revealed profound differences between humans and gibbons, a group of species more closely related to humans, making it clear that chromosome evolution did not follow a molecular clock. Chromosome painting has now been applied to more that 60 primate species and the translocation history has been mapped onto the major taxonomic divisions in the tree of primate evolution. In situ hybridization of cloned DNA probes, primarily BAC-FISH, also made it possible to more precisely map breakpoints with spanning and flanking BACs. These studies established marker order and disclosed intrachromosomal rearrangements. When applied comparatively to a range of primate species, they led to the discovery of evolutionary new centromeres as an important new category of chromosome evolution. BAC-FISH studies are intimately connected to genome sequencing, and probes can usually be assigned to a precise location in the genome assembly. This connection ties molecular cytogenetics securely to genome sequencing, assuring that molecular cytogenetics will continue to have a productive future in the multidisciplinary science of phylogenomics.
DOI: 10.6084/m9.figshare.5123665.v1
title: Supplementary Material for: A High-Resolution 15,000<sub>Rad</sub> Radiation Hybrid Panel for the Domestic Cat

description: The current genetic and recombination maps of the cat have fewer than 3,000 markers and a resolution limit greater than 1 Mb. To complement the first-generation domestic cat maps, support higher resolution mapping studies, and aid genome assembly in specific areas as well as in the whole genome, a 15,000<sub>Rad</sub> radiation hybrid (RH) panel for the domestic cat was generated. Fibroblasts from the female Abyssinian cat that was used to generate the cat genomic sequence were fused to a Chinese hamster cell line (A23), producing 150 hybrid lines. The clones were initially characterized using 39 short tandem repeats (STRs) and 1,536 SNP markers. The utility of whole-genome amplification in preserving and extending RH panel DNA was also tested using 10 STR markers; no significant difference in retention was observed. The resolution of the 15,000<sub>Rad</sub> RH panel was established by constructing framework maps across 10 different 1-Mb regions on different feline chromosomes. In these regions, 2-point analysis was used to estimate RH distances, which compared favorably with the estimation of physical distances. The study demonstrates that the 15,000<sub>Rad</sub> RH panel constitutes a powerful tool for constructing high-resolution maps, having an average resolution of 40.1 kb per marker across the ten 1-Mb regions. In addition, the RH panel will complement existing genomic resources for the domestic cat, aid in the accurate re-assemblies of the forthcoming cat genomic sequence, and support cross-species genomic comparisons.
DOI: 10.6084/m9.figshare.5123653
title: Supplementary Material for: Combining Structural Brain Changes Improves the Prediction of Alzheimer’s Disease and Mild Cognitive Impairment

description: <b><i>Background: </i></b>Several structural brain changes have been associated with Alzheimer’s disease (AD). This study investigated the prediction of AD by combining multiple brain changes with the hallmark medial temporal lobe atrophy (MTA). <b><i>Methods: </i></b>High-resolution magnetic resonance imaging (MRI) data of people with mild AD (n = 39), mild cognitive impairment (MCI; n = 82), and of healthy controls (HC; n = 58) were obtained at baseline. Among these people, 26 AD, 53 MCI, and 46 HC subjects had 24-month follow-up MRI scans. Bilateral MTA was evaluated using a medial temporal lobe atrophy scale (MTAS). Common changes in the aging brain were summarized using a brain atrophy and lesion index (BALI). The performance of the MTAS, BALI, and a score combining both, using a logistic regression model, were assessed. <b><i>Results: </i></b>The MTAS and BALI scores were closely correlated (r<sup>2</sup> &gt; 0.56); each differed between the diagnostic groups. Having an unfavorable MTAS score was associated with an increased risk of MCI-AD conversion (OR = 3.71, p = 0.039), adjusted for age, sex, and education; having an unfavorable BALI score marginally contributed to such risks (OR = 4.08, p = 0.080). Combining MTAS and BALI components resulted in a greater OR (8.99, p = 0.007) and an improved predictive accuracy (75.9%, p = 0.002). <b><i>Conclusion: </i></b>Multiple structural changes have an additive effect on AD. The data support potential future roles of combining multiple coexisting structural changes to benefit AD diagnosis, progression monitoring, and/or treatment effect evaluation.