cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5124199
title: Supplementary Material for: Differential Effects of High-Temperature Stress on Nuclear Topology and Transcription of Repetitive Noncoding and Coding Rye Sequences

description: The plant stress response has been extensively characterized at the biochemical and physiological levels. However, knowledge concerning repetitive sequence genome fraction modulation during extreme temperature conditions is scarce. We studied high-temperature effects on subtelomeric repetitive sequences (pSc200) and 45S rDNA in rye seedlings submitted to 40°C during 4 h. Chromatin organization patterns were evaluated through fluorescent in situ hybridization and transcription levels were assessed using quantitative real-time PCR. Additionally, the nucleolar dynamics were evaluated through fibrillarin immunodetection in interphase nuclei. The results obtained clearly demonstrated that the pSc200 sequence organization is not affected by high-temperature stress (HTS) and proved for the first time that this noncoding subtelomeric sequence is stably transcribed. Conversely, it was demonstrated that HTS treatment induces marked rDNA chromatin decondensation along with nucleolar enlargement and a significant increase in ribosomal gene transcription. The role of noncoding and coding repetitive rye sequences in the plant stress response that are suggested by their clearly distinct behaviors is discussed. While the heterochromatic conformation of pSc200 sequences seems to be involved in the stabilization of the interphase chromatin architecture under stress conditions, the dynamic modulation of nucleolar and rDNA topology and transcription suggest their role in plant stress response pathways.
DOI: 10.6084/m9.figshare.5124202
title: Supplementary Material for: Characterization of Sociodemographic and Clinicopathological Features in Brazilian Patients with Vulvar Squamous Cell Carcinoma

description: <b><i>Aim:</i></b> To investigate sociodemographic and clinical-epidemiological profiles of patients with vulvar carcinoma in São Paulo, the largest city of Brazil, to establish a more consistent profile of these features once the incidence of vulvar carcinoma has risen considerably. Data regarding the epidemiological aspects of this tumor are scarce. <b><i>Methods:</i></b> A retrospective study was performed using 300 medical records from patients diagnosed with squamous cell carcinoma of the vulva and surgically treated at A.C. Camargo Hospital in São Paulo, Brazil, from 1978 to 2009. <b><i>Results:</i></b> The median age of onset was 70 years, ranging from 15 to 98 years, and most women were white (88.51%). Most patients (83.54%) had little or no schooling and had the lowest survival curve. Many patients were diagnosed in the early stages of the disease (57.09% FIGO IB), 59% had complications due to surgery and 43.71% had disease recurrence, of which about 70% died. <b><i>Conclusions:</i></b> Our study adds 300 Brazilian cases of vulvar carcinoma to the world literature. Given the high rate of disease recurrence and mortality in Brazil, we conclude that regular gynecologic evaluation and educational policies should be reinforced in order to raise awareness for vulvar cancer.
DOI: 10.6084/m9.figshare.5124205
title: Supplementary Material for: The p.G146A and p.P125P Polymorphisms in the Steroidogenic Factor-1 <b><i>(SF-1)</i></b> Gene Do Not Affect the Risk for Hypospadias in Caucasians

description: Hypospadias is a frequent congenital malformation in boys and is characterized by incomplete fusion of the urethral folds. The steroidogenic factor-1 <i>(SF-1, NR5A1)</i> gene plays a key role in hypothalamic-pituitary-steroidogenic organ development, and has previously been reported to be mutated in individuals with 46,XY disorder of sex development. Here, we investigated the role of <i>SF-1</i> in hypospadias, a milder form of 46,XY disorder of sex development. We performed direct sequencing analysis of the <i>SF-1</i> gene in 2 male Caucasian twins exhibiting very severe hypospadias, and in 95 Caucasian boys with mild and severe hypospadias. We further extended the analysis by investigating 332 mild and severe hypospadias cases and 422 male controls using TaqMan assays. Our sequencing revealed a novel heterozygous p.R313H (c.938G&gt;A) missense mutation in each twin, and no mutations in the 95 Caucasian cases. Instead, a missense p.G146A (c.437G&gt;C), and a silent known p.P125P (c.375C&gt;T) polymorphism, respectively, was found in several of the latter cases. Further investigation of the 2 polymorphisms in the larger material of cases and controls showed no significant genotypic or allelic association. In conclusion, the <i>SF-1</i> gene may not play a significant role in the development of hypospadias in Caucasians.
DOI: 10.6084/m9.figshare.5124208.v1
title: Supplementary Material for: Sexing Frogs by Real-Time PCR: Using Aromatase <b><i>(cyp19) </i></b>as an Early Ovarian Differentiation Marker

description: Most anurans have no identified sex-markers; therefore, alternative methods for identification of early changes in sex ratios are required. In this study, <i>Lithobates sylvaticus</i> and <i>Silurana tropicalis</i> tadpoles were sampled at different developmental stages covering the entire process of sex differentiation. Three candidate genes known to be involved in sex differentiation in other vertebrate species were selected to develop a method to identify phenotypic sex in frogs: cytochrome p450 aromatase <i>(cyp19)</i>, forkhead box L2 <i>(foxl2)</i> and the cytochrome 17-alpha-hydroxylase/17,20 lyase <i>(cyp17)</i>. Cloning of these genes revealed nucleotide identity values ranging between 75–97% when compared to other amphibian species. Gene expression of <i>cyp17,</i><i>cyp19</i> and <i>foxl2</i> in <i>L. sylvaticus</i> adult gonads and gonad-mesonephros complex (GMC) of tadpoles was analyzed by real-time RT-PCR. Results showed clear sexually dimorphic patterns in the expression of the 3 genes. Our analysis reveals that GMC gene expression levels of <i>cyp19</i> alone can be used as a robust predictor of phenotypic sex in<i> L. sylvaticus </i>tadpoles. In addition, we validated this method measuring <i>cyp19</i> mRNA levels in <i>S. tropicalis </i>GMCs. We propose measuring <i>cyp19</i> as a tool to study the effects of chemical contaminants (including endocrine disrupting compounds) on amphibian gonadal development and sex ratios in the future.
DOI: 10.6084/m9.figshare.5124193
title: Supplementary Material for: Analysis of Differentiation Potentials and Gene Expression Profiles of Mesenchymal Stem Cells Derived from Periodontal Ligament and Wharton’s Jelly of the Umbilical Cord

description: PDLSC-mediated periodontal tissue regeneration is considered a promising method for periodontitis treatment, but the supply of PDLSCs is limited. As a potential alternative, WJCMSCs are readily available; however, there is a lack of evidence proving that WJCMSCs are suitable for periodontal tissue regeneration. In this study, we investigated the characteristics of WJCMSCs and PDLSCs. We found the osteo-/dentinogenic, adipogenic and chondrogenic differentiation potentials of PDLSCs were more powerful than those of WJCMSCs. Microarray analysis discovered that 903 genes were significantly down-regulated and 726 genes up-regulated in WJCMSCs compared with PDLSCs. Based on the microarray data, we found that several genes may be associated with MSCs characteristics. Further bioinformatic analysis identified that TGF-β and WNT signaling pathways, and several genes, including <i>STAT5B </i>and<i> ITGA4</i>, may play key roles in MSCs. Our results indicate that the differentiation potentials of WJCMSCs are far less than those of PDLSCs, and that unmodified WJCMSCs may not be good seeding cells for periodontal tissue regeneration. Our results also help to elucidate the differentiation mechanisms in MSCs and to find the key factors to prompt WJCMSC-mediated periodontal tissue regeneration.
DOI: 10.6084/m9.figshare.5124196
title: Supplementary Material for: Molecular Analysis of Desmoid Tumors with a High-Density Single-Nucleotide Polymorphism Array Identifies New Molecular Candidate Lesions

description: <b><i>Background: </i></b>Desmoid tumors are neoplastic proliferations of connective tissues. The mutation status of the gene coding for catenin (cadherin-associated protein) beta 1 (CTNNB1) and trisomy 8 on the chromosomal level have been described to have prognostic relevance. <b><i>Patients and Methods: </i></b>In order to elucidate new molecular mechanisms underlying these tumors, we carried out a molecular analysis with a genome-wide human high-density single-nucleotide polymorphism (SNP) array, in 9 patients. <b><i>Results: </i></b>Single samples showed numerical aberrations on chromosomes (Chrs) 20 and 6 with either trisomy 20 or monosomy 6. No trisomy 8 could be detected. Recurrent heterozygous deletions were found in Chr 5q (including the <i>APC </i>gene locus, n = 3) and Chr 8p23 (n = 4, containing coding regions for the potential tumor suppressor gene <i>CSMD1</i>). This novel deletion in 8p23 showed an association with local recurrence. In addition, structural chromosomal changes (gain of Chrs 8 and 20) were found in a minority of cases. <b><i>Conclusion: </i></b>The genomic alteration affecting the candidate gene <i>CSMD1 </i>could be important in the development of desmoid tumors.
DOI: 10.6084/m9.figshare.5124193.v1
title: Supplementary Material for: Analysis of Differentiation Potentials and Gene Expression Profiles of Mesenchymal Stem Cells Derived from Periodontal Ligament and Wharton’s Jelly of the Umbilical Cord

description: PDLSC-mediated periodontal tissue regeneration is considered a promising method for periodontitis treatment, but the supply of PDLSCs is limited. As a potential alternative, WJCMSCs are readily available; however, there is a lack of evidence proving that WJCMSCs are suitable for periodontal tissue regeneration. In this study, we investigated the characteristics of WJCMSCs and PDLSCs. We found the osteo-/dentinogenic, adipogenic and chondrogenic differentiation potentials of PDLSCs were more powerful than those of WJCMSCs. Microarray analysis discovered that 903 genes were significantly down-regulated and 726 genes up-regulated in WJCMSCs compared with PDLSCs. Based on the microarray data, we found that several genes may be associated with MSCs characteristics. Further bioinformatic analysis identified that TGF-β and WNT signaling pathways, and several genes, including <i>STAT5B </i>and<i> ITGA4</i>, may play key roles in MSCs. Our results indicate that the differentiation potentials of WJCMSCs are far less than those of PDLSCs, and that unmodified WJCMSCs may not be good seeding cells for periodontal tissue regeneration. Our results also help to elucidate the differentiation mechanisms in MSCs and to find the key factors to prompt WJCMSC-mediated periodontal tissue regeneration.
DOI: 10.6084/m9.figshare.5124196.v1
title: Supplementary Material for: Molecular Analysis of Desmoid Tumors with a High-Density Single-Nucleotide Polymorphism Array Identifies New Molecular Candidate Lesions

description: <b><i>Background: </i></b>Desmoid tumors are neoplastic proliferations of connective tissues. The mutation status of the gene coding for catenin (cadherin-associated protein) beta 1 (CTNNB1) and trisomy 8 on the chromosomal level have been described to have prognostic relevance. <b><i>Patients and Methods: </i></b>In order to elucidate new molecular mechanisms underlying these tumors, we carried out a molecular analysis with a genome-wide human high-density single-nucleotide polymorphism (SNP) array, in 9 patients. <b><i>Results: </i></b>Single samples showed numerical aberrations on chromosomes (Chrs) 20 and 6 with either trisomy 20 or monosomy 6. No trisomy 8 could be detected. Recurrent heterozygous deletions were found in Chr 5q (including the <i>APC </i>gene locus, n = 3) and Chr 8p23 (n = 4, containing coding regions for the potential tumor suppressor gene <i>CSMD1</i>). This novel deletion in 8p23 showed an association with local recurrence. In addition, structural chromosomal changes (gain of Chrs 8 and 20) were found in a minority of cases. <b><i>Conclusion: </i></b>The genomic alteration affecting the candidate gene <i>CSMD1 </i>could be important in the development of desmoid tumors.
DOI: 10.6084/m9.figshare.5124199.v1
title: Supplementary Material for: Differential Effects of High-Temperature Stress on Nuclear Topology and Transcription of Repetitive Noncoding and Coding Rye Sequences

description: The plant stress response has been extensively characterized at the biochemical and physiological levels. However, knowledge concerning repetitive sequence genome fraction modulation during extreme temperature conditions is scarce. We studied high-temperature effects on subtelomeric repetitive sequences (pSc200) and 45S rDNA in rye seedlings submitted to 40°C during 4 h. Chromatin organization patterns were evaluated through fluorescent in situ hybridization and transcription levels were assessed using quantitative real-time PCR. Additionally, the nucleolar dynamics were evaluated through fibrillarin immunodetection in interphase nuclei. The results obtained clearly demonstrated that the pSc200 sequence organization is not affected by high-temperature stress (HTS) and proved for the first time that this noncoding subtelomeric sequence is stably transcribed. Conversely, it was demonstrated that HTS treatment induces marked rDNA chromatin decondensation along with nucleolar enlargement and a significant increase in ribosomal gene transcription. The role of noncoding and coding repetitive rye sequences in the plant stress response that are suggested by their clearly distinct behaviors is discussed. While the heterochromatic conformation of pSc200 sequences seems to be involved in the stabilization of the interphase chromatin architecture under stress conditions, the dynamic modulation of nucleolar and rDNA topology and transcription suggest their role in plant stress response pathways.
DOI: 10.6084/m9.figshare.5124202.v1
title: Supplementary Material for: Characterization of Sociodemographic and Clinicopathological Features in Brazilian Patients with Vulvar Squamous Cell Carcinoma

description: <b><i>Aim:</i></b> To investigate sociodemographic and clinical-epidemiological profiles of patients with vulvar carcinoma in São Paulo, the largest city of Brazil, to establish a more consistent profile of these features once the incidence of vulvar carcinoma has risen considerably. Data regarding the epidemiological aspects of this tumor are scarce. <b><i>Methods:</i></b> A retrospective study was performed using 300 medical records from patients diagnosed with squamous cell carcinoma of the vulva and surgically treated at A.C. Camargo Hospital in São Paulo, Brazil, from 1978 to 2009. <b><i>Results:</i></b> The median age of onset was 70 years, ranging from 15 to 98 years, and most women were white (88.51%). Most patients (83.54%) had little or no schooling and had the lowest survival curve. Many patients were diagnosed in the early stages of the disease (57.09% FIGO IB), 59% had complications due to surgery and 43.71% had disease recurrence, of which about 70% died. <b><i>Conclusions:</i></b> Our study adds 300 Brazilian cases of vulvar carcinoma to the world literature. Given the high rate of disease recurrence and mortality in Brazil, we conclude that regular gynecologic evaluation and educational policies should be reinforced in order to raise awareness for vulvar cancer.
DOI: 10.6084/m9.figshare.5124205.v1
title: Supplementary Material for: The p.G146A and p.P125P Polymorphisms in the Steroidogenic Factor-1 <b><i>(SF-1)</i></b> Gene Do Not Affect the Risk for Hypospadias in Caucasians

description: Hypospadias is a frequent congenital malformation in boys and is characterized by incomplete fusion of the urethral folds. The steroidogenic factor-1 <i>(SF-1, NR5A1)</i> gene plays a key role in hypothalamic-pituitary-steroidogenic organ development, and has previously been reported to be mutated in individuals with 46,XY disorder of sex development. Here, we investigated the role of <i>SF-1</i> in hypospadias, a milder form of 46,XY disorder of sex development. We performed direct sequencing analysis of the <i>SF-1</i> gene in 2 male Caucasian twins exhibiting very severe hypospadias, and in 95 Caucasian boys with mild and severe hypospadias. We further extended the analysis by investigating 332 mild and severe hypospadias cases and 422 male controls using TaqMan assays. Our sequencing revealed a novel heterozygous p.R313H (c.938G&gt;A) missense mutation in each twin, and no mutations in the 95 Caucasian cases. Instead, a missense p.G146A (c.437G&gt;C), and a silent known p.P125P (c.375C&gt;T) polymorphism, respectively, was found in several of the latter cases. Further investigation of the 2 polymorphisms in the larger material of cases and controls showed no significant genotypic or allelic association. In conclusion, the <i>SF-1</i> gene may not play a significant role in the development of hypospadias in Caucasians.
DOI: 10.6084/m9.figshare.5124184
title: Supplementary Material for: Specific Collaborative Group Intervention for Patients with Medically Unexplained Symptoms in General Practice: A Cluster Randomized Controlled Trial

description: <b><i>Background:</i></b> Patients with medically unexplained symptoms (MUS) are frequent in primary care and substantially impaired in their quality of life (QoL). Specific training of general practitioners (GPs) alone did not demonstrate sustained improvement at later follow-up in current reviews. We evaluated a collaborative group intervention. <b><i>Methods:</i></b> We conducted a cluster randomized controlled trial. Thirty-five GPs recruited 304 MUS patients (intervention group: 170; control group: 134). All GPs were trained in diagnosis and management of MUS (control condition). Eighteen randomly selected intervention GPs participated in training for a specific collaborative group intervention. They conducted 10 weekly group sessions and 2 booster meetings in their practices, together with a psychosomatic specialist. Six and 12 months after baseline, QoL was assessed with the Short-Form 36. The primary outcome was the physical composite score (PCS), and the secondary outcome was the mental composite score (MCS). <b><i>Results:</i></b> At 12 months, intention-to-treat analyses showed a significant between-group effect for the MCS (p = 0.023) but not for the PCS (p = 0.674). This effect was preceded by a significant reduction of somatic symptom severity (15-item somatic symptom severity scale of the Patient Health Questionnaire, PHQ-15) at 6 months (p = 0.008) that lacked significance at 12 months (p = 0.078). As additional between-group effects at 12 months, per-protocol analyses showed less health anxiety (Whiteley-7; p = 0.038) and less psychosocial distress (PHQ; p = 0.024); GP visits were significantly (p = 0.042) reduced in the intervention group. <b><i>Conclusions:</i></b> Compared to pure GP training, collaborative group intervention achieved a progressive, clinically meaningful improvement in mental but not physical QoL. It could bridge gaps between general practice and mental health care.
DOI: 10.6084/m9.figshare.5124187
title: Supplementary Material for: Brain-Site-Specific Proteome Changes Induced by Neuronal P60TRP Expression

description: p60 transcription regulator protein (p60TRP) facilitates the processing of the amyloid precursor protein towards the non-amyloidogenic pathway by inhibiting the β-secretase action. This protein was initially identified to be downregulated in the temporal lobe of brains from Alzheimer's disease patients. p60TRP is one of the G-protein-coupled receptor (GPCR)-associated proteins which directly influences the signalling capacity of GPCRs. In the present study, we investigated the brain-region-specific proteome profile of transgenic p60TRP mice to gain an insight into the molecular events mediated by the long-term effect of neuronal p60TRP overexpression on brain proteome changes and its potential implication for neuronal functions in the central nervous system. Using a proteomics research approach based on isobaric tags for relative and absolute quantitation, we identified 2,025 proteins, whereby 1,735 proteins were quantified, out of which 56 were found to be significantly altered in the cortex and/or hippocampus of neuronal transgenic neuronal p60TRP mice. Our data suggests that in vivo overexpression of neuronal p60TRP significantly affects cognitive and neuroprotective capacities.
DOI: 10.6084/m9.figshare.5124190
title: Supplementary Material for: Developmental Changes in Voltage-Gated Calcium Channel α<sub>2</sub>δ-Subunit Expression in the Canine Dorsal Root Ganglion

description: The voltage-gated calcium channel subunit α<sub>2</sub>δ plays a fundamental role in propagation of excitatory signals associated with release of glutamate and neuropeptides substance P (SP) and calcitonin gene-related protein (CGRP). It can be selectively inhibited by gabapentinoids. Hence, investigation of the α<sub>2</sub>δ subunit may predict the efficacy of gabapentinoid therapy in neuropathic pain. Since sensory processing underlies significant age-related changes, this study was conducted in order to elucidate the role of the α<sub>2</sub>δ subunit in the sensory transmission during canine development. Dorsal root ganglia (DRG) were harvested from four spinal segments of 16 puppies and 10 adult dogs without a history of neurological signs, pain, spinal disease or orthopedic disorders. α<sub>2</sub>δ-Subunit expression and coexpression with SP and CGRP was evaluated immunohistochemically regarding the number of immunopositive ganglion cells, staining intensity and subcellular distribution. All tested ganglia were immunopositive for α<sub>2</sub>δ. Cell counts and expression levels were significantly lower in pups than in adult dogs (p &lt; 0.05). In the cervical segments of both groups, the number and percentage of immunopositive neurons was significantly higher than in lumbar DRG (p &lt; 0.05). Multilabeling studies in all tested animals confirmed the coexpression of α<sub>2</sub>δ and pain peptides SP and CGRP. This anatomical study for the first time documents the involvement of α<sub>2</sub>δ subunits in sensory signal processing in dogs. The proportion of positive neurons and the intracellular expression levels show a net increase from early postnatal life to adulthood. A significant portion of α<sub>2</sub>δ-positive cells in the dogs exhibited C- and Aδ-phenotypes compatible with nociceptive neurons. The coexpression of α<sub>2</sub>δ, SP and CGRP imply that these neurons are involved with peptidergic nociception. The cervicolumbar gradient of α<sub>2</sub>δ expression in adults reflects functional differences in between forelimbs and hind limbs. These data will facilitate translational studies on neuropathic pain states in this species such as common canine nerve entrapment syndromes.