cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4047492
title: Supplementary Material for: BRCA Mutation-Related and Claudin-Low Breast Cancer: Blood Relatives or Stepsisters?

description: <br><strong><em>Background:</em></strong> BRCA mutation-associated (BRCAmut) breast cancer represents a heterogeneous group displaying certain molecular features. Claudin-low breast cancers (CLBC) overlap with characteristics of BRCAmut tumors; therefore, we have investigated whether these are identical subtypes. <b><i>Methods:</i></b> Using public gene expression data, CLDN, CDH1, 9-cell line claudin-low predictor (9CLCLP) and PAM50 expression was evaluated in BRCAmut and BRCA wild-type (BRCAwt) breast cancer cases focusing on their possible overlap with the CLBC subtype. A separate formalin-fixed, paraffin-embedded (FFPE) cohort of 22 BRCAmut and 19 BRCAwt tumor tissues was used for immunohistochemical examination of AR, CD24, CD44, CK5/6, claudin-1, -3, -4 and -7, E-cadherin, EGFR, estrogen receptor (ER), EZH2, HER2, Ki67, p53, progesterone receptor (PgR) and vimentin expression. <b><i>Results:</i></b> In the data sets, CLDN1 (ROC = 0.785, p &lt; 0.001), CDH1 (ROC = 0.785, p &lt; 0.001), CLDN7 (ROC = 0.723, p &lt; 0.001), CLDN3 (ROC = 0.696, p = 0.020) and CLDN4 (ROC = 0.685, p = 0.027) were expressed at higher level in BRCAmut than BRCAwt tumor tissue. The PAM50 subtype differed from the assigned immunohistochemistry (IHC)-based subtype in 30%. Based on accessible 9CLCLP predictor genes, BRCAmut breast cancer does not display the claudin-low phenotype. Utilizing FFPE samples, claudins were evidently expressed in both BRCAmut and BRCAwt cases. However, at the protein level, only claudin-3 expression was higher in BRCAmut tumors, while claudin-1, -4 and -7 and E-cadherin expression was lower compared to BRCAwt cases. A CD24<sup>low</sup>/CD44<sup>high</sup> phenotype was found in BRCAmut tumors upon comparison with BRCAwt cases (p &lt; 0.001 and p = 0.001, respectively). <b><i>Conclusions:</i></b> There is a prominent correlation between the genes under focus herein and BRCA mutation status. BRCAmut tumors bear stem cell characteristics displaying a distinct cell adhesion molecule profile characterized by high expression of CDH1 and CLDN4 according to public gene expression data set analysis, and higher claudin-3 expression as detected by IHC; thus, BRCAmut breast carcinomas are not identical with the previously identified claudin-low subtype of breast cancer.
DOI: 10.7910/dvn/v1rjpf/dbmhin
title: blc20161011_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4047489
title: Supplementary Material for: Demineralized Dentin Matrix Induces Odontoblastic Differentiation of Dental Pulp Stem Cells

description: <br>The aim of this study was to investigate the effect of demineralized dentin matrix (DDM) on dental pulp stem cells (DPSCs) and the potential of complexes with DPSCs and DDM for mineralized tissue formation. Stem cells derived from the dental pulp of healthy pigs aged 18 months were isolated and cultured. DPSCs were incubated with alpha-minimum essential medium treated with DDM extract at 1 mg/ml (DDM1) or 10 mg/ml (DDM10). The concentrations of 3 growth factors in DDM extract was measured by enzyme-linked immunosorbent assay. Adhesion of DPSCs on DDM and hydroxyapatite-tricalcium phosphate (HA-TCP) surfaces was observed using scanning electron microscopy. Cell proliferation was evaluated with cell counting kit-8 and migration by Transwell migration assays. Odontoblastic differentiation was assessed by alkaline phosphatase (ALP) and alizarin red staining, ALP activity and real-time polymerase chain reaction analysis of markers of ALP, runt-related transcription factor 2, type I collagen, dentin matrix acidic phosphoprotein-1, osteonectin and dentin sialophosphoprotein (DSPP). Finally, DPSCs were combined with DDM and placed subcutaneously in nude mice for 12 weeks; DPSCs combined with HA-TCP and DDM alone served as controls. DDM could promote DPSC adhesion, migration and odontoblastic differentiation. Mineralized tissue formation was observed with the DPSC and DDM combination and the DPSC and HA-TCP combination. The mineralized tissue of the DPSC + DDM combination stained positive for DSPP, similar to the dentin tissue. These results indicate that DDM induces DPSC odontoblastic differentiation, suggesting applications for dentin regeneration.
DOI: 10.6084/m9.figshare.4047492.v1
title: Supplementary Material for: BRCA Mutation-Related and Claudin-Low Breast Cancer: Blood Relatives or Stepsisters?

description: <br><strong><em>Background:</em></strong> BRCA mutation-associated (BRCAmut) breast cancer represents a heterogeneous group displaying certain molecular features. Claudin-low breast cancers (CLBC) overlap with characteristics of BRCAmut tumors; therefore, we have investigated whether these are identical subtypes. <b><i>Methods:</i></b> Using public gene expression data, CLDN, CDH1, 9-cell line claudin-low predictor (9CLCLP) and PAM50 expression was evaluated in BRCAmut and BRCA wild-type (BRCAwt) breast cancer cases focusing on their possible overlap with the CLBC subtype. A separate formalin-fixed, paraffin-embedded (FFPE) cohort of 22 BRCAmut and 19 BRCAwt tumor tissues was used for immunohistochemical examination of AR, CD24, CD44, CK5/6, claudin-1, -3, -4 and -7, E-cadherin, EGFR, estrogen receptor (ER), EZH2, HER2, Ki67, p53, progesterone receptor (PgR) and vimentin expression. <b><i>Results:</i></b> In the data sets, CLDN1 (ROC = 0.785, p &lt; 0.001), CDH1 (ROC = 0.785, p &lt; 0.001), CLDN7 (ROC = 0.723, p &lt; 0.001), CLDN3 (ROC = 0.696, p = 0.020) and CLDN4 (ROC = 0.685, p = 0.027) were expressed at higher level in BRCAmut than BRCAwt tumor tissue. The PAM50 subtype differed from the assigned immunohistochemistry (IHC)-based subtype in 30%. Based on accessible 9CLCLP predictor genes, BRCAmut breast cancer does not display the claudin-low phenotype. Utilizing FFPE samples, claudins were evidently expressed in both BRCAmut and BRCAwt cases. However, at the protein level, only claudin-3 expression was higher in BRCAmut tumors, while claudin-1, -4 and -7 and E-cadherin expression was lower compared to BRCAwt cases. A CD24<sup>low</sup>/CD44<sup>high</sup> phenotype was found in BRCAmut tumors upon comparison with BRCAwt cases (p &lt; 0.001 and p = 0.001, respectively). <b><i>Conclusions:</i></b> There is a prominent correlation between the genes under focus herein and BRCA mutation status. BRCAmut tumors bear stem cell characteristics displaying a distinct cell adhesion molecule profile characterized by high expression of CDH1 and CLDN4 according to public gene expression data set analysis, and higher claudin-3 expression as detected by IHC; thus, BRCAmut breast carcinomas are not identical with the previously identified claudin-low subtype of breast cancer.
DOI: 10.7910/dvn/v1rjpf/cobxwu
title: blc20160313_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/okumef
title: blc20160415_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4047468
title: Supplementary Material for: GABAergic Neurotransmission in the Premammillary Nucleus of the Turkey Hypothalamus Regulates Reproductive Seasonality and the Onset of Photorefractoriness

description: <br><strong><em>Background/Aims:</em></strong> Photoperiod is a major environmental cue in temperate-zone birds which synchronizes breeding with the time of year that offers the optimal environment for offspring survival. Despite continued long photoperiods, these birds eventually become refractory to the stimulating photoperiod and their reproductive systems regress. In this study, we characterized the role of γ-aminobutyric acid (GABA)ergic neurotransmission in modulating the response of the premammillary nucleus (PMM) to a gonad stimulatory photoperiod and the onset of photorefractoriness. <b><i>Methods and Results:</i></b> Bilateral ablation of the PMM blocked the light-induced neuroendocrine response from occurring in photosensitive turkeys. Microarray analyses revealed an increase in GABAergic activity in the PMM of photorefractory birds as opposed to photosensitive ones, and this enhanced GABAergic activity appeared to inhibit the photoperiodic signal. Additionally, GABA<sub>A</sub> and GABA<sub>B</sub> receptors were expressed by dopamine-melatonin neurons in the PMM, and the administration of the GABA receptor agonist baclofen blocked the photoperiodic reproductive neuroendocrine responses. <b><i>Conclusions:</i></b> Consistent with the present findings, we propose that the long-sought-after mechanism underlying photorefractoriness is linked to the inhibitory actions of GABA. We suggest that (1) GABAergic interference with photoperiodic entrainment in the PMM initiates the photorefractory state and terminates the annual breeding season in temperate-zone birds, and (2) the PMM is a site of photoreception and photorefractoriness that controls the initiation and termination of avian reproductive seasonality.
DOI: 10.6084/m9.figshare.4047462
title: Micro-structured materials: inhomogeneities and imperfect interfaces in plane micropolar elasticity, a boundary element approach. Supporting material.

description: Supporting FEniCS-based finite element method solver and Docker image used to generate the FEM results in the paper:<br>Micro-structured materials: inhomogeneities and imperfect interfaces in plane micropolar elasticity, a boundary element approach. Elena Atroshchenko , Jack S. Hale, Javier A. Videla, Stanislav Potapenko, and Stéphane P.A. Bordas.<br>This is a permanent archival and DOI citation for the material in the repositories below. It is easiest to use the Bitbucket repository and the Dockerhub to get the supporting materials.
DOI: 10.6084/m9.figshare.4047468.v1
title: Supplementary Material for: GABAergic Neurotransmission in the Premammillary Nucleus of the Turkey Hypothalamus Regulates Reproductive Seasonality and the Onset of Photorefractoriness

description: <br><strong><em>Background/Aims:</em></strong> Photoperiod is a major environmental cue in temperate-zone birds which synchronizes breeding with the time of year that offers the optimal environment for offspring survival. Despite continued long photoperiods, these birds eventually become refractory to the stimulating photoperiod and their reproductive systems regress. In this study, we characterized the role of γ-aminobutyric acid (GABA)ergic neurotransmission in modulating the response of the premammillary nucleus (PMM) to a gonad stimulatory photoperiod and the onset of photorefractoriness. <b><i>Methods and Results:</i></b> Bilateral ablation of the PMM blocked the light-induced neuroendocrine response from occurring in photosensitive turkeys. Microarray analyses revealed an increase in GABAergic activity in the PMM of photorefractory birds as opposed to photosensitive ones, and this enhanced GABAergic activity appeared to inhibit the photoperiodic signal. Additionally, GABA<sub>A</sub> and GABA<sub>B</sub> receptors were expressed by dopamine-melatonin neurons in the PMM, and the administration of the GABA receptor agonist baclofen blocked the photoperiodic reproductive neuroendocrine responses. <b><i>Conclusions:</i></b> Consistent with the present findings, we propose that the long-sought-after mechanism underlying photorefractoriness is linked to the inhibitory actions of GABA. We suggest that (1) GABAergic interference with photoperiodic entrainment in the PMM initiates the photorefractory state and terminates the annual breeding season in temperate-zone birds, and (2) the PMM is a site of photoreception and photorefractoriness that controls the initiation and termination of avian reproductive seasonality.
DOI: 10.7910/dvn/v1rjpf/somfo8
title: blc20160617_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4047462.v2
title: Micro-structured materials: inhomogeneities and imperfect interfaces in plane micropolar elasticity, a boundary element approach. Supporting material.

description: Supporting FEniCS-based finite element method solver and Docker image used to generate the FEM results in the paper:<br>Micro-structured materials: inhomogeneities and imperfect interfaces in plane micropolar elasticity, a boundary element approach. Elena Atroshchenko , Jack S. Hale, Javier A. Videla, Stanislav Potapenko, and Stéphane P.A. Bordas.<br>This is a permanent archival and DOI citation for the material in the repositories below. It is easiest to use the Bitbucket repository and the Dockerhub to get the supporting materials.
DOI: 10.7910/dvn/v1rjpf/1qezec
title: blc20160428_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4047453
title: Supplementary Material for: Oxidative Balance Score and Chronic Kidney Disease

description: <br><strong><em>Background:</em></strong> The oxidative balance score (OBS) is a composite estimate of the overall pro- and antioxidant exposure status in an individual. The aim of this study was to determine the association between OBS and renal disease. <b><i>Methods:</i></b> Using the Reasons for Geographic and Racial Differences in Stroke cohort study, OBS was calculated by combining 13 a priori-defined pro- and antioxidant factors by using baseline dietary and lifestyle assessment. OBS was divided into quartiles (Q1-Q4) with the lowest quartile, Q1 (predominance of pro-oxidants), as the reference. Multivariable logistic regression and Cox proportional hazards models were used to estimate adjusted ORs for albuminuria defined as urine albumin/creatinine ratio (ACR) &gt;30 mg/g, macroalbuminuria defined as ACR &gt;300 mg/g and chronic kidney disease (CKD) defined as estimated glomerular filtration rate &lt;60 ml/min/1.73 m<sup>2</sup> according to the Chronic Kidney Disease Epidemiology Collaboration and hazards ratios for end-stage renal disease (ESRD), respectively. <b><i>Results:</i></b> Of the 19,461 participants analyzed, 12.9% had albuminuria and 10.1% had CKD at baseline; over a median follow-up of 3.5 years (range 2.14-4.32 years), 0.46% developed ESRD. Higher OBS quartiles were associated with lower prevalence of CKD (OR vs. Q1: Q2 = 0.93 [95% CI 0.80-1.08]; Q3 = 0.90 [95% CI 0.77-1.04] and Q4 = 0.79 [95% CI 0.67-0.92], p for trend &lt;0.01). The associations between OBS and albuminuria (p for trend 0.31) and incident ESRD (p for trend 0.56) were not significant in the fully adjusted models. <b><i>Conclusions:</i></b> These findings suggest that higher OBS is associated with lower prevalence of CKD. Lack of association with ESRD incidence in the multivariable analyses indicates that temporal relation between OBS and renal damage remains unclear.
DOI: 10.6084/m9.figshare.4047462.v1
title: Nano-structured materials: inhomogeneities and imperfect interfaces in plane micropolar elasticity, a boundary element approach. Supporting material.

description: Supporting FEniCS-based finite element method solver and Docker image used to generate the FEM results in the paper:<br>Nano-structured materials: inhomogeneities and imperfect interfaces in plane micropolar elasticity, a boundary element approach. Elena Atroshchenko , Jack S. Hale, Javier A. Videla, Stanislav Potapenko, and Stéphane P.A. Bordas.<br>This is a permanent archival and DOI citation for the material in the repositories below.
DOI: 10.7910/dvn/v1rjpf/u4vvdr
title: blc20160911_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gyshox
title: blc20160317_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/dpdxq5
title: blc20160411_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4047441
title: Supplementary Material for: Angelman Syndrome Caused by Chromosomal Rearrangements: A Case Report of 46,XX,+der(13)t(13;15)(q14.1;q12)mat,-15 with an Atypical Phenotype and Review of the Literature

description: <br>Less than 1% of the cases with Angelman syndrome (AS) are caused by chromosomal rearrangements. This category of AS is not well defined and may manifest atypical phenotypes. Here, we report a girl with AS due to der(13)t(13;15)(q14.1;q12)mat. SNP array detected the precise deletion/duplication points and the parental origin of the 15q deletion. Multicolor FISH confirmed a balanced translocation t(13;15)(q14.1;q12) in her mother. Her facial appearance showed some features of dup(13)(pter→q14). Also, she lacked the most characteristic and unique behavioral symptoms of AS, i.e., frequent laughter, happy demeanor, and easy excitability. A review of the literature indicated that AS cases caused by chromosomal rearrangements can be classified into 2 major categories and 4 groups. The first category is paternal uniparental disomy 15, which is subdivided into isodisomy by de novo rob(15;15) and heterodisomy caused by paternal translocation. The second category is the deletion of the AS locus due to maternal reciprocal translocation, which is subdivided into 2 groups associated with partial monosomy by 3:1 segregation and partial trisomy by adjacent-2 segregation. Classification into these categories facilitates the understanding of the mechanisms of chromosomal rearrangements and helps in accurate diagnosis and genetic counseling of these rare forms of AS.
DOI: 10.6084/m9.figshare.4047441.v1
title: Supplementary Material for: Angelman Syndrome Caused by Chromosomal Rearrangements: A Case Report of 46,XX,+der(13)t(13;15)(q14.1;q12)mat,-15 with an Atypical Phenotype and Review of the Literature

description: <br>Less than 1% of the cases with Angelman syndrome (AS) are caused by chromosomal rearrangements. This category of AS is not well defined and may manifest atypical phenotypes. Here, we report a girl with AS due to der(13)t(13;15)(q14.1;q12)mat. SNP array detected the precise deletion/duplication points and the parental origin of the 15q deletion. Multicolor FISH confirmed a balanced translocation t(13;15)(q14.1;q12) in her mother. Her facial appearance showed some features of dup(13)(pter→q14). Also, she lacked the most characteristic and unique behavioral symptoms of AS, i.e., frequent laughter, happy demeanor, and easy excitability. A review of the literature indicated that AS cases caused by chromosomal rearrangements can be classified into 2 major categories and 4 groups. The first category is paternal uniparental disomy 15, which is subdivided into isodisomy by de novo rob(15;15) and heterodisomy caused by paternal translocation. The second category is the deletion of the AS locus due to maternal reciprocal translocation, which is subdivided into 2 groups associated with partial monosomy by 3:1 segregation and partial trisomy by adjacent-2 segregation. Classification into these categories facilitates the understanding of the mechanisms of chromosomal rearrangements and helps in accurate diagnosis and genetic counseling of these rare forms of AS.
DOI: 10.7910/dvn/v1rjpf/c96mzq
title: blc20160922_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/i50sz1
title: blc20160816_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/u0jhky
title: blc20161008_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4047414
title: Supplementary Material for: Inhibition of Pathogenic Mutant SOD1 Aggregation in Cultured Motor Neuronal Cells by Prevention of Its SUMOylation on Lysine 75

description: <br>Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the selective death of motor neurons. Mutations in the <i>SOD1 </i>gene encoding the superoxide dismutase 1 are present in 15% of familial ALS cases and in 2% of sporadic cases. These mutations are associated with the formation of SOD1-positive aggregates. The mechanisms of aggregation remain unknown, but posttranslational modifications of SOD1 may be involved. Here, we report that NSC-34 motor neuronal cells expressing mutant SOD1 contained aggregates positive for small ubiquitin modifier-1 (SUMO-1), and in parallel a reduced level of free SUMO-1. CLEM (correlative light and electron microscopy) analysis showed nonorganized cytosolic aggregates for all mutations tested (SOD1<sup>A4V</sup>, SOD1<sup>V31A</sup>, and SOD1<sup>G93C</sup>). We next show that preventing the SUMOylation of mutant SOD1 by the substitution of lysine 75, the SUMOylation site of SOD1, significantly reduces the number of motor neuronal cells with aggregates. These results support the need for further research on the SUMOylation pathways, which may be a potential therapeutic target in ALS.
DOI: 10.7910/dvn/v1rjpf/vqxl0v
title: blc20160511_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4047411
title: Supplementary Material for: Impact of Collateral Status on Successful Revascularization in Endovascular Treatment: A Systematic Review and Meta-Analysis

description: <br><strong><em>Background:</em></strong> Pre-treatment collateral status may be associated with the rates of successful revascularization in acute ischemic stroke patients receiving endovascular treatment (EVT). We conducted a systematic review and meta-analysis to synthesize relevant evidence currently available. <b><i>Methods:</i></b> Relevant full-text articles published in English since January 1, 2000, reporting associations between collateral status and successful reperfusion and/or recanalization in acute ischemic stroke patients receiving EVT in cohort or case-control studies, or randomized clinical trials, were retrieved through search of PubMed. Study selection, data extraction and study quality assessment were carried out by 2 investigators. Risk ratios (RR) were pooled for good vs. poor collaterals for the outcomes of successful reperfusion and recanalization, based on random-effects models. Subgroup analyses were conducted to explore for potential factors that might interfere with the effects of pre-treatment collateral status on reperfusion by EVT. <b><i>Results:</i></b> In total, 27 studies (2,366 subjects) were included in qualitative analysis, among which 24 studies (2,239 subjects) were quantitatively analyzed. Overall, good pre-treatment collaterals significantly increased the rate of both successful reperfusion (RR 1.28, 95% CI 1.17-1.40; p &lt; 0.001) and recanalization (RR 1.23, 95% CI 1.06-1.42; p = 0.006), as compared with poor collaterals. Subgroup analyses revealed that the effects of collateral status on successful reperfusion by EVT might be different between populations with different ethnicities. <b><i>Conclusions:</i></b> Good pre-treatment collaterals may enhance the rates of successful reperfusion and recanalization in EVT for acute ischemic stroke. This may partly explain the favorable effects of good pre-treatment collaterals on clinical outcomes of stroke patients receiving EVT. Thus, it would be valuable to assess the collateral status prior to EVT in acute ischemic stroke. But studies are needed to further verify if the positive effects of good collaterals on revascularization by EVT are restricted to certain subgroups of patients.
DOI: 10.6084/m9.figshare.4047408
title: subcostal diameter.xlsx

description: The data describes right ventricular diameters in mm during resuscitation form cardiac arrest caused by hypovolemia, hyperkalemia, and primary arrhythmia.
DOI: 10.7910/dvn/v1rjpf/tennqc
title: blc20160508_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ithvvq
title: blc20160907_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hapbur
title: blc20160102_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4047399
title: Data from "testing the environmental filtering concept in global drylands"

description: Sheets contains all predictors and response variables used in the paper.<br>
DOI: 10.7910/dvn/v1rjpf/hnpmcl
title: blc20160502_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4047399.v1
title: Data from "testing the environmental filtering concept in global drylands"

description: Sheets contains all predictors and response variables used in the paper.<br>
DOI: 10.7910/dvn/v1rjpf/0p3d8t
title: blc20160810_03.txt.gz

description: :unav