cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5121208
title: Supplementary Material for: Quantitative mRNA Analysis of Serotonin 5-HT<sub>4</sub> and Adrenergic β<sub>2</sub> Receptors in the Mouse Embryonic Telencephalon

description: The adrenergic β<sub>2</sub> receptor (β<sub>2</sub>-AR) gene is embedded (nested) within the serotonin 5-HT<sub>4</sub> receptor (5-HT<sub>4</sub>-R) gene and these two receptors can interact at the transcriptional and post-transcriptional levels. The mouse 5-HT<sub>4</sub>-R gene contains a number of exons and codes at least four mRNA splice variants (5-HT<sub>4(a)</sub>-R, 5-HT<sub>4(b)</sub>-R, 5-HT<sub>4(e)</sub>-R, 5-HT<sub>4(f)</sub>-R), whereas the β<sub>2</sub>-AR gene is intronless. Since 5-HT<sub>4</sub>-Rs and β<sub>2</sub>-ARs can form homodimers and heterodimers and they increase intracellular cAMP levels, these receptors may be important for integrating serotonergic and noradrenergic signals at the single-neuron level. Both 5-HT<sub>4</sub>-R and β<sub>2</sub>-AR have been implicated in autism spectrum disorders, depression, and Alzheimer’s disease. In the fetal brain, these receptors may mediate the effects of stress on neurodevelopmental processes. We used quantitative reverse-transcription PCR (qRT-PCR) to investigate the developmental expression of 5-HT<sub>4</sub>-R and β<sub>2</sub>-AR in the mouse telencephalon at embryonic days (E) 13–18. At E13–E14, the mRNA levels of all 5-HT<sub>4</sub>-R splice variants were very low, but by E17–E18 they increased 7-fold (5- HT<sub>4(a)</sub>-R), 5-fold (5-HT<sub>4(b)</sub>-R), 9-fold (5-HT<sub>4(e)</sub>-R), and 11-fold (5-HT<sub>4(f)</sub>-R). The expression of 5-HT<sub>4(a)</sub>-R and 5-HT<sub>4(b)</sub>-R was rapidly upregulated between E14 and E15, at the time when the thalamocortical projections arrive in the telencephalon. This pattern was not observed in the expression of 5-HT<sub>4(e)</sub>-R and 5-HT<sub>4(f)</sub>-R, the mRNA levels of which showed a steady, gradual increase from E13 to E18. The β<sub>2</sub>-AR mRNA levels were relatively high throughout the studied period of development and increased only by 70% from E13–E14 to E17–E18. These findings suggest that 5-HT<sub>4</sub>-R splice variants and β<sub>2</sub>-ARs are differentially regulated in the embryonic telencephalon and that their relative amounts may carry developmentally important information.
DOI: 10.6084/m9.figshare.5121211
title: Supplementary Material for: Elevated Levels of Methylmalonate and Homocysteine in Parkinson’s Disease, Progressive Supranuclear Palsy and Amyotrophic Lateral Sclerosis

description: <i>Background/Aims:</i> Increasing evidence suggests that elevated levels of homocysteine (Hcy) and methylmalonate (MMA) may be involved in the pathogenesis of neurodegenerative diseases. <i>Methods:</i> The urine levels of MMA and serum levels of Hcy as well as folic acid and vitamin B<sub>12</sub> were measured in patients suffering from the distinct neurodegenerative diseases progressive supranuclear palsy (PSP), amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD), and compared to age- and gender-matched control subjects. <i>Results:</i> We found significantly elevated concentrations of Hcy (PD 15.1, PSP 15.8, ALS 13.9, control 11.2 µmol/l) and MMA (PD 3.7, PSP 3.1, ALS 3.7, control 1.8 mg/g) in all patient groups in comparison with controls. Levels of Hcy and MMA did not differ significantly between the neurodegenerative diseases. <i>Conclusion:</i> Our findings might imply that Hcy and MMA are released as a consequence of neurodegeneration regardless of the underlying cause and serve as surrogate markers of neurodegeneration. Alternatively they might be directly implicated in the pathogenesis of these diseases. Since elevated levels of both Hcy and MMA are neurotoxic, further studies might investigate the effect of vitamin therapy on disease progression.
DOI: 10.6084/m9.figshare.5121223.v1
title: Supplementary Material for: An Analysis of Histone Modifications in Relation to Sex-Specific Chromatin Organization in the Mealybug <i>Maconellicoccus hirsutus</i>

description: The male-specific heterochromatization of the paternal genome, observed in coccids, is an example of both genomic imprinting and differential regulation of homologous chromosomes. We observed a highly nuclease-resistant chromatin (NRC) organization of a part of the paternal genome in males of <i>Maconellicoccus hirsutus</i> as reported earlier in <i>Planococcus lilacinus</i>. The nuclease resistance of NRC is correlated with nuclear matrix association and is lost when NRC is dissociated from the matrix. We carried out a comparative analysis of epigenetic modifications of histones in matrix associated chromatin of male and female mealybugs by ELISA. We detected H3K27me3, H4K20me3, H3K9me2 and H3K4me3 in both males and females and observed significant enrichment of H3K27me3 in the nuclear matrix of males compared to that of females. To further examine the presence of NRC in the germ line, nuclei were sorted based on chromatin compaction. The analysis of sorted nuclei indicates the presence of NRC in nuclei with different DNA content including the haploid nuclei from males. We discuss these results in the light of the presence of NRC exclusively in male nuclei and the retention of the maternal genome in sperm nuclei of mealybugs.
DOI: 10.6084/m9.figshare.5121205
title: Supplementary Material for: Predictors of Very-Low-Energy Diet Outcome in Obese Women and Men

description: <i>Objective:</i> The aim of this study was to explore baseline outcome predictors of a 12-week very-low-energy diet (VLED) treatment. <i>Methods:</i> Obese patients (177 women and 90 men) started treatment. Multivariate linear and logistic regressions were used to predict weight loss (%), successful outcome (≧ 10% weight loss) and attrition. Potential predictors were anthropometry, socioeconomic variables, established questionnaires on health-related quality of life, and eating behavior, and additional questions related to dieting. <i>Results:</i> Mean weight loss was 13.5% (standard deviation (SD) 5.6) in women and 15.1% (6.1) in men (p = 0.054). Greater weight loss in women was predicted by having more children, lower education, and better perceived physical health (R-square (R<sup>2</sup>) = 12.7%), and in men by better ambulation capacity, living with a partner/children, and snacking on ice-cream more often (R<sup>2</sup> = 39.4%). Successful outcome in women was predicted by less obesity-related psychosocial dysfunction, and in men by better functioning in social interaction and ambulation capacity. Attrition was predicted by lower age and larger hip circumference in women, and in men by lower perceived general health. Two-week weight loss was independently associated with all outcomes except attrition in women. <i>Conclusion:</i> Factors related to perceived physical health, social interaction, socio-economic factors, and obesity-related psychosocial problems predicted VLED outcome. The predictors differed by gender.
DOI: 10.6084/m9.figshare.5121214.v1
title: Supplementary Material for: Global Transcriptional Analysis of <i>Bacillus licheniformis</i> Reveals an Overlap between Heat Shock and Iron Limitation Stimulon

description: In this study, we characterized the heat shock stimulon of the important industrial microorganism <i>Bacillus licheniformis</i> using DNA microarrays. While sharing a high degree of homology with the closely related model organism <i>Bacillus subtilis</i>, the heat shock stimulon of <i>B. licheniformis</i> exhibited several novel and unexpected features. Most notably, heat shock in <i>B. licheniformis</i> resulted in decreased amounts of mRNA from the <i>ytrABCEF</i> operon, encoding a putative acetoin uptake system, and stimulated the transcription of purine biosynthesis and iron uptake genes. Unexpectedly, deletion of the <i>ytrEF</i> genes did not affect acetoin uptake, but increased heat sensitivity. To investigate the connection between heat stress and iron uptake further, we analyzed the iron limitation response of <i>B. licheniformis</i> by DNA microarrays and concluded that the response mostly involves the genes related to iron uptake and metabolism, while the only heat shock gene affected by iron limitation was <i>clpE</i>. We also attempted to delete the <i>fur </i>gene (encoding the ferric uptake repressor), but unexpectedly found it to be essential in <i>B. licheniformis</i>. Using the fluorescent protein-encoding reporter gene under control of the <i>dhb </i>promoter, which responded to both heat shock and iron-starvation, we confirmed the overlap between these responses.
DOI: 10.6084/m9.figshare.5121199
title: Supplementary Material for: Constructing Defined Chromosome Segmental Duplications in Maize

description: We describe the production of chromosome segmental duplications and deletions of defined length in maize. The method utilizes a collection of previously isolated transposon-induced reciprocal translocations with sequence-defined breakpoints. These balanced translocations involve a first common breakpoint at the site of transposon <i>Ac/fAc </i>insertions on chromosome 1S, and a second variable endpoint elsewhere in the genome. Stocks containing translocations with different endpoints on the same chromosome arms were crossed together to generate heterozygous combinations. Subsequent meiotic segregation generates gametes that contain the original balanced translocations, or pairs of translocation chromosomes that are genetically unbalanced; i.e., they contain a duplication or deletion of the affected segment. Self-pollination produces progeny plants that are genetically balanced, or that contain 0 to 4 copies of the affected segment. The chromosome constitution of progeny plants can be determined using PCR primers flanking the translocation breakpoints. In addition, plants segregating genetically unbalanced gametes exhibit significant pollen grain abnormalities and thus can be easily detected in the field. In this way, we constructed 4 different segmental tetrasomic stocks involving genomic regions of approximately 7.8, 18.7, 21, and 42.6 Mb on chromosomes 5S, 5L, 5L, and 4L, respectively. FISH analysis using specific probes located within the affected segments confirms their aneuploid composition. These and similar lines containing precisely defined segmental duplications and deletions may be useful to study the genetic impact of gene dosage.
DOI: 10.6084/m9.figshare.5121205.v1
title: Supplementary Material for: Predictors of Very-Low-Energy Diet Outcome in Obese Women and Men

description: <i>Objective:</i> The aim of this study was to explore baseline outcome predictors of a 12-week very-low-energy diet (VLED) treatment. <i>Methods:</i> Obese patients (177 women and 90 men) started treatment. Multivariate linear and logistic regressions were used to predict weight loss (%), successful outcome (≧ 10% weight loss) and attrition. Potential predictors were anthropometry, socioeconomic variables, established questionnaires on health-related quality of life, and eating behavior, and additional questions related to dieting. <i>Results:</i> Mean weight loss was 13.5% (standard deviation (SD) 5.6) in women and 15.1% (6.1) in men (p = 0.054). Greater weight loss in women was predicted by having more children, lower education, and better perceived physical health (R-square (R<sup>2</sup>) = 12.7%), and in men by better ambulation capacity, living with a partner/children, and snacking on ice-cream more often (R<sup>2</sup> = 39.4%). Successful outcome in women was predicted by less obesity-related psychosocial dysfunction, and in men by better functioning in social interaction and ambulation capacity. Attrition was predicted by lower age and larger hip circumference in women, and in men by lower perceived general health. Two-week weight loss was independently associated with all outcomes except attrition in women. <i>Conclusion:</i> Factors related to perceived physical health, social interaction, socio-economic factors, and obesity-related psychosocial problems predicted VLED outcome. The predictors differed by gender.
DOI: 10.6084/m9.figshare.5121211.v1
title: Supplementary Material for: Elevated Levels of Methylmalonate and Homocysteine in Parkinson’s Disease, Progressive Supranuclear Palsy and Amyotrophic Lateral Sclerosis

description: <i>Background/Aims:</i> Increasing evidence suggests that elevated levels of homocysteine (Hcy) and methylmalonate (MMA) may be involved in the pathogenesis of neurodegenerative diseases. <i>Methods:</i> The urine levels of MMA and serum levels of Hcy as well as folic acid and vitamin B<sub>12</sub> were measured in patients suffering from the distinct neurodegenerative diseases progressive supranuclear palsy (PSP), amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD), and compared to age- and gender-matched control subjects. <i>Results:</i> We found significantly elevated concentrations of Hcy (PD 15.1, PSP 15.8, ALS 13.9, control 11.2 µmol/l) and MMA (PD 3.7, PSP 3.1, ALS 3.7, control 1.8 mg/g) in all patient groups in comparison with controls. Levels of Hcy and MMA did not differ significantly between the neurodegenerative diseases. <i>Conclusion:</i> Our findings might imply that Hcy and MMA are released as a consequence of neurodegeneration regardless of the underlying cause and serve as surrogate markers of neurodegeneration. Alternatively they might be directly implicated in the pathogenesis of these diseases. Since elevated levels of both Hcy and MMA are neurotoxic, further studies might investigate the effect of vitamin therapy on disease progression.
DOI: 10.6084/m9.figshare.5121190
title: Supplementary Material for: The FOUR Score: A Reliable Instrument to Assess the Comatose Stroke Patient

description: Medicine
DOI: 10.6084/m9.figshare.5121196
title: Supplementary Material for: Data Management System in a Movement Disorder Center: Technical Report

description: <i>Objective:</i> We designed a specialized monitoring unit and data management system with systematic storage and easy access for a deep brain stimulation program of patients with movement disorders. <i>Methods:</i> All patients were monitored and evaluated in a specialized 24-hour monitoring system whenever it was needed, postoperatively as well as preoperatively. We digitized all the data and developed a data management system that allowed for systematic storage and easy access to the data on demand by users in the offices and outpatient clinics. <i>Conclusion:</i> We describe our data management system and how it provides benefit to patients in order that others may use it as a template for designing their own data management system.
DOI: 10.6084/m9.figshare.5121202
title: Supplementary Material for: Association of Serum Adipocytokines with Hepatic Steatosis and Fibrosis in Patients with Chronic Hepatitis C

description: <i>Background:</i> The pathogenic mechanisms of hepatic steatosis in hepatitis C (HCV) remain unclear. <i>Aim:</i> To assess the potential role of cytokines and adipokines in HCV-related steatosis and fibrosis. <i>Methods:</i> We profiled several adipokines, cytokines, and related soluble molecules in 99 HCV patients and analyzed their potential associations with hepatic steatosis and fibrosis. <i>Results:</i> Serum leptin and IL-1RA were significantly higher in HCV genotype 1 as compared to genotype 3. On the other hand, serum resistin, IL-8, IL-1B and sIL-6R, were significantly higher in HCV genotype 3. No differences were observed for adiponectin, visfatin, IL-6 and TNF-α. Regardless of HCV genotype, steatosis could be predicted by a combination of IL-8, IL-6, and sIL-6R/IL-6. When analysis was repeated for each of the genotypes, the reliability of models improved. Regardless of HCV genotype, moderate to severe fibrosis (Metavir score &gt;F2), was predicted by IL-8 and resistin levels. <i>Conclusions:</i> Analysis of adipocytokines associated with steatosis supports the hypothesis that steatogenic pathways differ in HCV genotype 3 from those infected with non-genotype 3 infections.
DOI: 10.6084/m9.figshare.5121193
title: Supplementary Material for: Diversity of Chromosomal Karyotypes in Maize and Its Relatives

description: Maize is a highly diverse species on the gene sequence level. With the recent development of methods to distinguish each of the 10 pairs of homologues in somatic root tip spreads, a wide collection of maize lines was subjected to karyotype analysis to serve as a reference for the community and to examine the spectrum of chromosomal features in the species. The core nested association mapping progenitor collection and additional selections of diversity lines were examined. Commonly used inbred lines were included in the analysis. The centromere 4 specific repeat and ribosomal RNA loci were invariant. The CentC centromere repeat exhibited extensive differences in quantity on any particular chromosome across lines. Knob heterochromatin was highly variable with locations at many sites in the genome. Lastly, representative examples from other species in the genus <i>Zea</i> (teosintes) were examined, which provide information on the evolution of chromosomal features.
DOI: 10.6084/m9.figshare.5121196.v1
title: Supplementary Material for: Data Management System in a Movement Disorder Center: Technical Report

description: <i>Objective:</i> We designed a specialized monitoring unit and data management system with systematic storage and easy access for a deep brain stimulation program of patients with movement disorders. <i>Methods:</i> All patients were monitored and evaluated in a specialized 24-hour monitoring system whenever it was needed, postoperatively as well as preoperatively. We digitized all the data and developed a data management system that allowed for systematic storage and easy access to the data on demand by users in the offices and outpatient clinics. <i>Conclusion:</i> We describe our data management system and how it provides benefit to patients in order that others may use it as a template for designing their own data management system.
DOI: 10.6084/m9.figshare.5121193.v1
title: Supplementary Material for: Diversity of Chromosomal Karyotypes in Maize and Its Relatives

description: Maize is a highly diverse species on the gene sequence level. With the recent development of methods to distinguish each of the 10 pairs of homologues in somatic root tip spreads, a wide collection of maize lines was subjected to karyotype analysis to serve as a reference for the community and to examine the spectrum of chromosomal features in the species. The core nested association mapping progenitor collection and additional selections of diversity lines were examined. Commonly used inbred lines were included in the analysis. The centromere 4 specific repeat and ribosomal RNA loci were invariant. The CentC centromere repeat exhibited extensive differences in quantity on any particular chromosome across lines. Knob heterochromatin was highly variable with locations at many sites in the genome. Lastly, representative examples from other species in the genus <i>Zea</i> (teosintes) were examined, which provide information on the evolution of chromosomal features.
DOI: 10.6084/m9.figshare.5121202.v1
title: Supplementary Material for: Association of Serum Adipocytokines with Hepatic Steatosis and Fibrosis in Patients with Chronic Hepatitis C

description: <i>Background:</i> The pathogenic mechanisms of hepatic steatosis in hepatitis C (HCV) remain unclear. <i>Aim:</i> To assess the potential role of cytokines and adipokines in HCV-related steatosis and fibrosis. <i>Methods:</i> We profiled several adipokines, cytokines, and related soluble molecules in 99 HCV patients and analyzed their potential associations with hepatic steatosis and fibrosis. <i>Results:</i> Serum leptin and IL-1RA were significantly higher in HCV genotype 1 as compared to genotype 3. On the other hand, serum resistin, IL-8, IL-1B and sIL-6R, were significantly higher in HCV genotype 3. No differences were observed for adiponectin, visfatin, IL-6 and TNF-α. Regardless of HCV genotype, steatosis could be predicted by a combination of IL-8, IL-6, and sIL-6R/IL-6. When analysis was repeated for each of the genotypes, the reliability of models improved. Regardless of HCV genotype, moderate to severe fibrosis (Metavir score &gt;F2), was predicted by IL-8 and resistin levels. <i>Conclusions:</i> Analysis of adipocytokines associated with steatosis supports the hypothesis that steatogenic pathways differ in HCV genotype 3 from those infected with non-genotype 3 infections.
DOI: 10.6084/m9.figshare.5121175
title: Supplementary Material for: Interspecific Hybrids of <i>Hordeum marinum </i>ssp. <i>marinum </i>×<i> H. bulbosum </i>Are Mitotically Stable and Reveal No Gross Alterations in Chromatin Properties

description: Interspecific hybrids between the related wild barley species <i>Hordeum marinum</i> and <i>H. bulbosum</i> were generated and tested regarding their chromosomal stability and chromatin properties. Unlike in <i>H. vulgare</i> × <i>H. bulbosum</i> hybrid embryos, there was no effect of temperature on uniparental chromosome elimination or retention during hybrid seed development and 7 chromosomes from each parent were detected according to genomic in situ hybridization analyses. The centromere-specific histone H3 gene <i>(CENH3)</i> of both parental genomes is active in hybrid plants. Indirect immunostaining of flow-sorted 2C nuclei indicated that no major reorganization of histone H3 methylation (K4, K9 and K27), H3K9 acetylation and histone H2A ubiquitination marks or location of active RNA polymerase II sites occurred after interspecific hybridization.
DOI: 10.6084/m9.figshare.5121184
title: Supplementary Material for: An Effective Way to Solve Equivocal Mammography Findings: The Rolled Views

description: <i>Background:</i> The aim of this study was to investigate the efficacy of the rolled views taken in craniocaudal (CC) and mediolateral oblique (MLO) projections in solving equivocal mammography findings. <i>Patients and Methods:</i> The rolled views were taken by changing the positioning of the breast but not the obliquity of the X-ray beams. The breast was rolled medially or laterally in the rolled CC view, and inferiorly or superiorly in the rolled MLO view to separate overlapping structures from each other. <i>Results:</i> We evaluated equivocal findings in 87 asymptomatic women undergoing either CC (n = 48, 55%) or MLO (n = 39, 45%) rolled views between 2001 and 2008. The rolled views were helpful in solving equivocal mammographic findings and making proper decisions on management in 85 of the 87 (97.7%) women. This technique was used for breast asymmetries in 55 of the 87 (63.2%) women, and was sufficient to directly show summation artifacts in 59 of 79 (74.6%) women. The rolled views revealed 4 intramammary lymph nodes, 2 circumscribed masses out of 6 obscured masses, 7 summation artifacts, and 2 circumscribed masses out of 9 questionable masses. <i>Conclusions:</i> The rolled view is an effective method of differentiating summation artifacts from real lesions on mammography in both the CC and the MLO view.