cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9034166.v1
title: Cross-species transmission of poultry pathogens in backyard farms: ducks as carriers of chicken viruses

description: In backyard farms of Lao People’s Democratic Republic, mixed-species rearing of poultry is a breeding-ground for cross-species transmission. Here, the epidemiology of viruses circulating among backyard poultry in Vientiane Province was assessed to guide future control strategies. Oral/tracheal and cloacal swabs, collected from 605 poultry (308 ducks, 297 chickens) between 2011 and 2015, were screened by PCR for Newcastle disease virus (NDV), coronavirus (CoV) and chicken anaemia virus (CAV). Chicken sera were screened for anti-NDV antibodies by ELISA. Statistical and phylogenetic analyses revealed transmission patterns and relationships. Closely related strains co-circulated in chickens and ducks. While CoV RNA was detected in oral/tracheal swabs of 9.3% of the chickens and 2.4% of the ducks, rates were higher in faecal swabs of both species (27.3% and 48.2%). RNA of infectious bronchitis virus (IBV) and duck CoV was found in faecal swabs of chickens (19.7% and 7.1%) and ducks (4.1% and 44.1%). Moreover, DNA of the generally chicken-specific CAV was detected in oral/tracheal swabs of chickens (18.1%) and, sporadically, of ducks (2.4%). Despite serological evidence of NDV circulation or vaccination (86.9%), NDV RNA was not detected. We found a high prevalence and indication for cross-species transmission of different CoV strains in backyard poultry. Interestingly, ducks served as biological, or at least mechanical, carriers of viral strains closely related not only to IBV, but also to CAV. Bird containment and poultry species separation could be first steps to avoid cross-species transmission and emergence of novel strains with broad host range and enhanced pathogenicity. <b>RESEARCH HIGHLIGHTS</b>High rates of avian viruses were detected by PCR in backyard poultry from Lao PDR.Diverse coronavirus and chicken anemia virus strains co-circulated.Phylogenetic analyses suggested virus transmission between chickens and ducks.Serological evidence of Newcastle disease was found, but viral RNA was not detected. High rates of avian viruses were detected by PCR in backyard poultry from Lao PDR. Diverse coronavirus and chicken anemia virus strains co-circulated. Phylogenetic analyses suggested virus transmission between chickens and ducks. Serological evidence of Newcastle disease was found, but viral RNA was not detected.
DOI: 10.6084/m9.figshare.9034184.v2
title: Secondary structures of the training set of eukatyotic group II introns

description: Secondary structures of the training set of eukaryotic group II introns
DOI: 10.6084/m9.figshare.9034202.v2
title: Secondary structures of rfam eukaryotic group II introns

description: Structures of eukaryotic group II introns of RFAM RF00029 family
DOI: 10.6084/m9.figshare.9034232.v4
title: Supplementary Tables for "Testing the role of SOX15 in human primordial germ cell fate"

description: Oligonucleotides used in this study are listed in Supplemental Table 1. Primary antibodies used for immunofluorescence are listed in Supplemental Table 2. PGCLC fraction counts by flow cytometry are listed in Supplemental Tables 3–5. ∆∆Ct values from qPCR experiments are listed in Supplemental Tables 6–8. Raw Ct values are listed in Supplemental Table 9.
DOI: 10.6084/m9.figshare.9034145
title: Sequences identical to rfam eukaryotic group II introns

description: Sequences identical to rfam eukaryotic group II introns
DOI: 10.6084/m9.figshare.9034202.v3
title: Secondary structures of rfam eukaryotic group II introns

description: Structures of eukaryotic group II introns of RFAM RF00029 family
DOI: 10.6084/m9.figshare.9034184.v3
title: Secondary structures of the training set of eukatyotic group II introns

description: Secondary structures of the training set of eukaryotic group II introns
DOI: 10.6084/m9.figshare.9034115
title: Right bundle branch block: Prevalence, incidence, and cardiovascular morbidity and mortality in the general population

description: <b>Background:</b> Right bundle branch block (RBBB) is among the most common electrocardiographic abnormalities. <b>Objectives:</b> To establish the prevalence and incidence of RBBB in the general population without cardiovascular events (CVE) and whether RBBB increases cardiovascular morbidity and mortality compared with patients with a normal electrocardiogram (ECG). <b>Methods:</b> A historical study of two cohorts including 2981 patients from 29 primary health centres without baseline CVE. Cox (for CVE) and logistic (for cardiovascular factors) regression was used to assess their association with RBBB. <b>Results:</b> Of the patients (58% women; mean age 65.9), 92.2% had a normal ECG, 4.6% incomplete RBBB (iRBBB) and 3.2% complete RBBB (cRBBB). Mean follow-up was five years. Factors associated with appearance of cRBBB were male sex (HR = 3.8; 95%CI: 2.4–6.1) and age (HR = 1.05 per year; 95%CI: 1.03–1.08). In a univariate analysis, cRBBB was associated with an increase in all-cause mortality but only bifascicular block (BFB) was significant after adjusting for confounders. cRBBB tended to increase CVE but the results were not statistically significant. Presence of iRBBB was not associated with adverse outcomes. Patients with iRBBB who progressed to cRBBB showed a higher incidence of heart failure and chronic kidney disease. <b>Conclusion:</b> In this general population cohort with no CV disease, 8% had RBBB, with a higher prevalence among men and elderly patients. Although all-cause mortality and CVE tended to increase in the presence of cRBBB, only BFB showed a statistically significant association with cRBBB. Patients with iRBBB who progressed to cRBBB had a higher incidence of CVE. We detected no effect of iRBBB on morbidity and mortality.
DOI: 10.6084/m9.figshare.9034115.v1
title: Right bundle branch block: Prevalence, incidence, and cardiovascular morbidity and mortality in the general population

description: <b>Background:</b> Right bundle branch block (RBBB) is among the most common electrocardiographic abnormalities. <b>Objectives:</b> To establish the prevalence and incidence of RBBB in the general population without cardiovascular events (CVE) and whether RBBB increases cardiovascular morbidity and mortality compared with patients with a normal electrocardiogram (ECG). <b>Methods:</b> A historical study of two cohorts including 2981 patients from 29 primary health centres without baseline CVE. Cox (for CVE) and logistic (for cardiovascular factors) regression was used to assess their association with RBBB. <b>Results:</b> Of the patients (58% women; mean age 65.9), 92.2% had a normal ECG, 4.6% incomplete RBBB (iRBBB) and 3.2% complete RBBB (cRBBB). Mean follow-up was five years. Factors associated with appearance of cRBBB were male sex (HR = 3.8; 95%CI: 2.4–6.1) and age (HR = 1.05 per year; 95%CI: 1.03–1.08). In a univariate analysis, cRBBB was associated with an increase in all-cause mortality but only bifascicular block (BFB) was significant after adjusting for confounders. cRBBB tended to increase CVE but the results were not statistically significant. Presence of iRBBB was not associated with adverse outcomes. Patients with iRBBB who progressed to cRBBB showed a higher incidence of heart failure and chronic kidney disease. <b>Conclusion:</b> In this general population cohort with no CV disease, 8% had RBBB, with a higher prevalence among men and elderly patients. Although all-cause mortality and CVE tended to increase in the presence of cRBBB, only BFB showed a statistically significant association with cRBBB. Patients with iRBBB who progressed to cRBBB had a higher incidence of CVE. We detected no effect of iRBBB on morbidity and mortality.
DOI: 10.6084/m9.figshare.9034097
title: Interactions between TGF-β type I receptor and hypoxia-inducible factor-α mediates a synergistic crosstalk leading to poor prognosis for patients with clear cell renal cell carcinoma

description: To investigate the significance of expression of HIF-1α, HIF-2α, and SNAIL1 proteins; and TGF-β signaling pathway proteins in ccRCC, their relation with clinicopathological parameters and patient’s survival were examined. We also investigated potential crosstalk between HIF-α and TGF-β signaling pathway, including the TGF-β type 1 receptor (ALK5-FL) and the intracellular domain of ALK5 (ALK5-ICD). Tissue samples from 154 ccRCC patients and comparable adjacent kidney cortex samples from 38 patients were analyzed for HIF-1α/2α, TGF-β signaling components, and SNAIL1 proteins by immunoblot. Protein expression of HIF-1α and HIF-2α were significantly higher, while SNAIL1 had similar expression levels in ccRCC compared with the kidney cortex. HIF-2α associated with poor cancer-specific survival, while HIF-1α and SNAIL1 did not associate with survival. Moreover, HIF-2α positively correlated with ALK5-ICD, pSMAD2/3, and PAI-1; HIF-1α positively correlated with pSMAD2/3; SNAIL1 positively correlated with ALK5-FL, ALK5-ICD, pSMAD2/3, PAI-1, and HIF-2α. Intriguingly, <i>in vitro</i> experiments performed under normoxic conditions revealed that ALK5 interacts with HIF-1α and HIF-2α, and promotes their expression and the expression of their target genes GLUT1 and CA9, in a VHL dependent manner. We found that ALK5 induces expression of HIF-1α and HIF-2α, through its kinase activity. Under hypoxic conditions, HIF-α proteins correlated with the activated TGF-β signaling pathway. In conclusion, we reveal that ALK5 plays a pivotal role in synergistic crosstalk between TGF-β signaling and hypoxia pathway, and that the interaction between ALK5 and HIF-α contributes to tumor progression.
DOI: 10.6084/m9.figshare.9034184.v5
title: Secondary structures of the training set of eukatyotic group II introns

description: Secondary structures of the training set of eukaryotic group II introns
DOI: 10.6084/m9.figshare.9034184.v6
title: Secondary structures of the training set of eukatyotic group II introns

description: Secondary structures of the training set of eukaryotic group II introns
DOI: 10.6084/m9.figshare.9034097.v1
title: Interactions between TGF-β type I receptor and hypoxia-inducible factor-α mediates a synergistic crosstalk leading to poor prognosis for patients with clear cell renal cell carcinoma

description: To investigate the significance of expression of HIF-1α, HIF-2α, and SNAIL1 proteins; and TGF-β signaling pathway proteins in ccRCC, their relation with clinicopathological parameters and patient’s survival were examined. We also investigated potential crosstalk between HIF-α and TGF-β signaling pathway, including the TGF-β type 1 receptor (ALK5-FL) and the intracellular domain of ALK5 (ALK5-ICD). Tissue samples from 154 ccRCC patients and comparable adjacent kidney cortex samples from 38 patients were analyzed for HIF-1α/2α, TGF-β signaling components, and SNAIL1 proteins by immunoblot. Protein expression of HIF-1α and HIF-2α were significantly higher, while SNAIL1 had similar expression levels in ccRCC compared with the kidney cortex. HIF-2α associated with poor cancer-specific survival, while HIF-1α and SNAIL1 did not associate with survival. Moreover, HIF-2α positively correlated with ALK5-ICD, pSMAD2/3, and PAI-1; HIF-1α positively correlated with pSMAD2/3; SNAIL1 positively correlated with ALK5-FL, ALK5-ICD, pSMAD2/3, PAI-1, and HIF-2α. Intriguingly, <i>in vitro</i> experiments performed under normoxic conditions revealed that ALK5 interacts with HIF-1α and HIF-2α, and promotes their expression and the expression of their target genes GLUT1 and CA9, in a VHL dependent manner. We found that ALK5 induces expression of HIF-1α and HIF-2α, through its kinase activity. Under hypoxic conditions, HIF-α proteins correlated with the activated TGF-β signaling pathway. In conclusion, we reveal that ALK5 plays a pivotal role in synergistic crosstalk between TGF-β signaling and hypoxia pathway, and that the interaction between ALK5 and HIF-α contributes to tumor progression.
DOI: 10.6084/m9.figshare.9034097.v3
title: Interactions between TGF-β type I receptor and hypoxia-inducible factor-α mediates a synergistic crosstalk leading to poor prognosis for patients with clear cell renal cell carcinoma

description: To investigate the significance of expression of HIF-1α, HIF-2α, and SNAIL1 proteins; and TGF-β signaling pathway proteins in ccRCC, their relation with clinicopathological parameters and patient’s survival were examined. We also investigated potential crosstalk between HIF-α and TGF-β signaling pathway, including the TGF-β type 1 receptor (ALK5-FL) and the intracellular domain of ALK5 (ALK5-ICD). Tissue samples from 154 ccRCC patients and comparable adjacent kidney cortex samples from 38 patients were analyzed for HIF-1α/2α, TGF-β signaling components, and SNAIL1 proteins by immunoblot. Protein expression of HIF-1α and HIF-2α were significantly higher, while SNAIL1 had similar expression levels in ccRCC compared with the kidney cortex. HIF-2α associated with poor cancer-specific survival, while HIF-1α and SNAIL1 did not associate with survival. Moreover, HIF-2α positively correlated with ALK5-ICD, pSMAD2/3, and PAI-1; HIF-1α positively correlated with pSMAD2/3; SNAIL1 positively correlated with ALK5-FL, ALK5-ICD, pSMAD2/3, PAI-1, and HIF-2α. Intriguingly, <i>in vitro</i> experiments performed under normoxic conditions revealed that ALK5 interacts with HIF-1α and HIF-2α, and promotes their expression and the expression of their target genes GLUT1 and CA9, in a VHL dependent manner. We found that ALK5 induces expression of HIF-1α and HIF-2α, through its kinase activity. Under hypoxic conditions, HIF-α proteins correlated with the activated TGF-β signaling pathway. In conclusion, we reveal that ALK5 plays a pivotal role in synergistic crosstalk between TGF-β signaling and hypoxia pathway, and that the interaction between ALK5 and HIF-α contributes to tumor progression.
DOI: 10.6084/m9.figshare.9034184.v7
title: Secondary structures of the training set of eukatyotic group II introns

description: Secondary structures of the training set of eukaryotic group II introns
DOI: 10.6084/m9.figshare.9034097.v2
title: Interactions between TGF-β type I receptor and hypoxia-inducible factor-α mediates a synergistic crosstalk leading to poor prognosis for patients with clear cell renal cell carcinoma

description: To investigate the significance of expression of HIF-1α, HIF-2α, and SNAIL1 proteins; and TGF-β signaling pathway proteins in ccRCC, their relation with clinicopathological parameters and patient’s survival were examined. We also investigated potential crosstalk between HIF-α and TGF-β signaling pathway, including the TGF-β type 1 receptor (ALK5-FL) and the intracellular domain of ALK5 (ALK5-ICD). Tissue samples from 154 ccRCC patients and comparable adjacent kidney cortex samples from 38 patients were analyzed for HIF-1α/2α, TGF-β signaling components, and SNAIL1 proteins by immunoblot. Protein expression of HIF-1α and HIF-2α were significantly higher, while SNAIL1 had similar expression levels in ccRCC compared with the kidney cortex. HIF-2α associated with poor cancer-specific survival, while HIF-1α and SNAIL1 did not associate with survival. Moreover, HIF-2α positively correlated with ALK5-ICD, pSMAD2/3, and PAI-1; HIF-1α positively correlated with pSMAD2/3; SNAIL1 positively correlated with ALK5-FL, ALK5-ICD, pSMAD2/3, PAI-1, and HIF-2α. Intriguingly, <i>in vitro</i> experiments performed under normoxic conditions revealed that ALK5 interacts with HIF-1α and HIF-2α, and promotes their expression and the expression of their target genes GLUT1 and CA9, in a VHL dependent manner. We found that ALK5 induces expression of HIF-1α and HIF-2α, through its kinase activity. Under hypoxic conditions, HIF-α proteins correlated with the activated TGF-β signaling pathway. In conclusion, we reveal that ALK5 plays a pivotal role in synergistic crosstalk between TGF-β signaling and hypoxia pathway, and that the interaction between ALK5 and HIF-α contributes to tumor progression.
DOI: 10.6084/m9.figshare.9034067
title: Exposure to workplace bullying, microRNAs and pain; evidence of a moderating effect of miR-30c rs928508 and miR-223 rs3848900

description: Prolonged exposure to bullying behaviors may give rise to symptoms such as anxiety, depression and chronic pain. Earlier data suggest that these symptoms often are associated with stress-induced low-grade systemic inflammation. Here, using data from both animals and humans, we examined the moderating role of microRNAs (miRNAs, miRs) in this process. In the present study, a resident-intruder paradigm, blood samples, tissue harvesting and subsequent qPCR analyses were used to screen for stress-induced changes in circulating miRNAs in rats. The negative acts questionnaire (NAQ), TaqMan assays and a numeric rating scale (NRS) for pain intensity were then used to examine the associations among bullying behaviors, relevant miRNA polymorphisms and pain in a probability sample of 996 Norwegian employees. In rats, inhibited weight gain, reduced pituitary POMC expression, adrenal Nr3c1 mRNA downregulation, as well as increased miR-146a, miR-30c and miR-223 in plasma were observed following 1 week of repeated exposure to social stress. When following up the miRNA findings from the animal study in the human working population, a stronger relationship between NAQ and NRS scores was observed in subjects with the miR-30c GG genotype (rs928508) compared to other subjects. A stronger relationship between NAQ and NRS scores was also seen in men with the miR-223 G genotype (rs3848900) as compared to other men. Our findings show that social stress may induce many physiological changes including changed expression of miRNAs. We conclude that the miR-30c GG genotype in men and women, and the miR-223 G genotype in men, amplify the association between exposure to bullying behaviors and pain.Lay summaryUsing an animal model of social stress, we identified miR-146a, miR-30c and miR-223 as potentially important gene regulatory molecules that may be involved in the stress response. Interestingly, human genotypes affecting the expression of mature miR-30c and miR-223 had a moderating effect on the association between exposure to bullying and pain. Subjects with the miR-30c rs928508 GG genotype had a significantly stronger association between exposure to bullying behaviors and pain than other subjects. The same was observed in men with the miR-223 rs3848900 G genotype, as compared to other men. Using an animal model of social stress, we identified miR-146a, miR-30c and miR-223 as potentially important gene regulatory molecules that may be involved in the stress response. Interestingly, human genotypes affecting the expression of mature miR-30c and miR-223 had a moderating effect on the association between exposure to bullying and pain. Subjects with the miR-30c rs928508 GG genotype had a significantly stronger association between exposure to bullying behaviors and pain than other subjects. The same was observed in men with the miR-223 rs3848900 G genotype, as compared to other men.
DOI: 10.6084/m9.figshare.9034067.v2
title: Exposure to workplace bullying, microRNAs and pain; evidence of a moderating effect of miR-30c rs928508 and miR-223 rs3848900

description: Prolonged exposure to bullying behaviors may give rise to symptoms such as anxiety, depression and chronic pain. Earlier data suggest that these symptoms often are associated with stress-induced low-grade systemic inflammation. Here, using data from both animals and humans, we examined the moderating role of microRNAs (miRNAs, miRs) in this process. In the present study, a resident-intruder paradigm, blood samples, tissue harvesting and subsequent qPCR analyses were used to screen for stress-induced changes in circulating miRNAs in rats. The negative acts questionnaire (NAQ), TaqMan assays and a numeric rating scale (NRS) for pain intensity were then used to examine the associations among bullying behaviors, relevant miRNA polymorphisms and pain in a probability sample of 996 Norwegian employees. In rats, inhibited weight gain, reduced pituitary POMC expression, adrenal Nr3c1 mRNA downregulation, as well as increased miR-146a, miR-30c and miR-223 in plasma were observed following 1 week of repeated exposure to social stress. When following up the miRNA findings from the animal study in the human working population, a stronger relationship between NAQ and NRS scores was observed in subjects with the miR-30c GG genotype (rs928508) compared to other subjects. A stronger relationship between NAQ and NRS scores was also seen in men with the miR-223 G genotype (rs3848900) as compared to other men. Our findings show that social stress may induce many physiological changes including changed expression of miRNAs. We conclude that the miR-30c GG genotype in men and women, and the miR-223 G genotype in men, amplify the association between exposure to bullying behaviors and pain.Lay summaryUsing an animal model of social stress, we identified miR-146a, miR-30c and miR-223 as potentially important gene regulatory molecules that may be involved in the stress response. Interestingly, human genotypes affecting the expression of mature miR-30c and miR-223 had a moderating effect on the association between exposure to bullying and pain. Subjects with the miR-30c rs928508 GG genotype had a significantly stronger association between exposure to bullying behaviors and pain than other subjects. The same was observed in men with the miR-223 rs3848900 G genotype, as compared to other men. Using an animal model of social stress, we identified miR-146a, miR-30c and miR-223 as potentially important gene regulatory molecules that may be involved in the stress response. Interestingly, human genotypes affecting the expression of mature miR-30c and miR-223 had a moderating effect on the association between exposure to bullying and pain. Subjects with the miR-30c rs928508 GG genotype had a significantly stronger association between exposure to bullying behaviors and pain than other subjects. The same was observed in men with the miR-223 rs3848900 G genotype, as compared to other men.