cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4123230
title: Polymorphisms of the Toll-Like Receptor 2 of Goats (<i>Capra hircus</i>) may be Associated with Somatic Cell Count in Milk

description: Toll-like receptor 2 (TLR2) plays an important role in recognition by the innate immune system of Gram-positive bacteria. As Gram-positive bacteria cause mastitis, we examined variations in the region of the TLR2 gene that codes for the extracellular domain. Samples of forty goats from a single dairy herd were collected, half with low SCC (≤200,000 cells/mL), and half with higher SCC. Two synonymous single nucleotide polymorphisms (SNPs) were identified: 840G &gt; A and 1083A &gt; G. One nonsynonymous SNP 739G &gt; A was identified. This coded for valine or isoleucine, which have similar physiochemical properties, and was not in a region coding for a known functional domain. Surprisingly, the least square mean SCC of the heterozygous goats (146,220) was significantly lower than the SCC of homozygous GG goats (537,700; p = 0.004), although these two groups were similar in days in milk (p = 0.984), and there was no significant difference by breed (p = 0.941). Because factors other than mastitis can affect SCC and our sample sizes were limited, additional studies are needed to corroborate an association between TLR2 genotype and SCC or mastitis in goats.
DOI: 10.6084/m9.figshare.4123320.v2
title: Absence of Genome Reduction In Diverse, Facultative Endohyphal Bacteria

description: Supplementary material as published in <i>Microbial Genomics</i> in the following article: Absence of Genome Reduction In Diverse, Facultative Endohyphal BacteriaDOI 10.1099/mgen.0.000101
DOI: 10.6084/m9.figshare.4123230.v1
title: Polymorphisms of the Toll-Like Receptor 2 of Goats (<i>Capra hircus</i>) may be Associated with Somatic Cell Count in Milk

description: Toll-like receptor 2 (TLR2) plays an important role in recognition by the innate immune system of Gram-positive bacteria. As Gram-positive bacteria cause mastitis, we examined variations in the region of the TLR2 gene that codes for the extracellular domain. Samples of forty goats from a single dairy herd were collected, half with low SCC (≤200,000 cells/mL), and half with higher SCC. Two synonymous single nucleotide polymorphisms (SNPs) were identified: 840G &gt; A and 1083A &gt; G. One nonsynonymous SNP 739G &gt; A was identified. This coded for valine or isoleucine, which have similar physiochemical properties, and was not in a region coding for a known functional domain. Surprisingly, the least square mean SCC of the heterozygous goats (146,220) was significantly lower than the SCC of homozygous GG goats (537,700; p = 0.004), although these two groups were similar in days in milk (p = 0.984), and there was no significant difference by breed (p = 0.941). Because factors other than mastitis can affect SCC and our sample sizes were limited, additional studies are needed to corroborate an association between TLR2 genotype and SCC or mastitis in goats.
DOI: 10.7910/dvn/v1rjpf/syoux4
title: cbb20170602_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4123224
title: A Geometric Approach to Archetypal Analysis and Nonnegative Matrix Factorization

description: Archetypal analysis and nonnegative matrix factorization (NMF) are staples in a statistician's toolbox for dimension reduction and exploratory data analysis. We describe a geometric approach to both NMF and archetypal analysis by interpreting both problems as finding extreme points of the data cloud. We also develop and analyze an efficient approach to finding extreme points in high dimensions. For modern massive datasets that are too large to fit on a single machine and must be stored in a distributed setting, our approach makes only a small number of passes over the data. In fact, it is possible to obtain the NMF or perform archetypal analysis with just two passes over the data.
DOI: 10.6084/m9.figshare.4123227
title: Autophagy impairment with lysosomal and mitochondrial dysfunction is an important characteristic of oxidative stress-induced senescence

description: Macroautophagy/autophagy has profound implications for aging. However, the true features of autophagy in the progression of aging remain to be clarified. In the present study, we explored the status of autophagic flux during the development of cell senescence induced by oxidative stress. In this system, although autophagic structures increased, the degradation of SQSTM1/p62 protein, the yellow puncta of mRFP-GFP-LC3 fluorescence and the activity of lysosomal proteolytic enzymes all decreased in senescent cells, indicating impaired autophagic flux with lysosomal dysfunction. The influence of autophagy activity on senescence development was confirmed by both positive and negative autophagy modulators; and MTOR-dependent autophagy activators, rapamycin and PP242, efficiently suppressed cellular senescence through a mechanism relevant to restoring autophagic flux. By time-phased treatment of cells with the antioxidant N-acetylcysteine (NAC), the mitochondria uncoupler carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and ambroxol, a reagent with the effect of enhancing lysosomal enzyme maturation, we found that mitochondrial dysfunction plays an initiating role, while lysosomal dysfunction is more directly responsible for autophagy impairment and senescence. Interestingly, the effect of rapamycin on autophagy flux is linked to its role in functional revitalization of both mitochondrial and lysosomal functions. Together, this study demonstrates that autophagy impairment is crucial for oxidative stress-induced cell senescence, thus restoring autophagy activity could be a promising way to retard senescence.
DOI: 10.7910/dvn/v1rjpf/ryr2by
title: cbb20171228_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4123224.v2
title: A Geometric Approach to Archetypal Analysis and Nonnegative Matrix Factorization

description: Archetypal analysis and nonnegative matrix factorization (NMF) are staples in a statistician's toolbox for dimension reduction and exploratory data analysis. We describe a geometric approach to both NMF and archetypal analysis by interpreting both problems as finding extreme points of the data cloud. We also develop and analyze an efficient approach to finding extreme points in high dimensions. For modern massive datasets that are too large to fit on a single machine and must be stored in a distributed setting, our approach makes only a small number of passes over the data. In fact, it is possible to obtain the NMF or perform archetypal analysis with just two passes over the data.
DOI: 10.6084/m9.figshare.4123227.v1
title: Autophagy impairment with lysosomal and mitochondrial dysfunction is an important characteristic of oxidative stress-induced senescence

description: Macroautophagy/autophagy has profound implications for aging. However, the true features of autophagy in the progression of aging remain to be clarified. In the present study, we explored the status of autophagic flux during the development of cell senescence induced by oxidative stress. In this system, although autophagic structures increased, the degradation of SQSTM1/p62 protein, the yellow puncta of mRFP-GFP-LC3 fluorescence and the activity of lysosomal proteolytic enzymes all decreased in senescent cells, indicating impaired autophagic flux with lysosomal dysfunction. The influence of autophagy activity on senescence development was confirmed by both positive and negative autophagy modulators; and MTOR-dependent autophagy activators, rapamycin and PP242, efficiently suppressed cellular senescence through a mechanism relevant to restoring autophagic flux. By time-phased treatment of cells with the antioxidant N-acetylcysteine (NAC), the mitochondria uncoupler carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and ambroxol, a reagent with the effect of enhancing lysosomal enzyme maturation, we found that mitochondrial dysfunction plays an initiating role, while lysosomal dysfunction is more directly responsible for autophagy impairment and senescence. Interestingly, the effect of rapamycin on autophagy flux is linked to its role in functional revitalization of both mitochondrial and lysosomal functions. Together, this study demonstrates that autophagy impairment is crucial for oxidative stress-induced cell senescence, thus restoring autophagy activity could be a promising way to retard senescence.
DOI: 10.6084/m9.figshare.4123221
title: Directivities Human Tongue Clicks

description: This dataset includes the sound directivity of six different tongue clicks that are produced for human echolocation puposes. The methodology is described in the technical journal paper 'Acoustic Properties of Tongue Clicks', submitted to Acta Acustica United with Acustica, by Rick de Vos and Maarten Hornikx.
DOI: 10.6084/m9.figshare.4123224.v1
title: A geometric approach to archetypal analysis and non-negative matrix factorization

description: Archetypal analysis and non-negative matrix factorization (NMF) are staples in a statisticians toolbox for dimension reduction and exploratory data analysis. We describe a geometric approach to both NMF and archetypal analysis by interpreting both problems as finding extreme points of the data cloud. We also develop and analyze an efficient approach to finding extreme points in high dimensions. For modern massive datasets that are too large to fit on a single machine and must be stored in a distributed setting, our approach makes only a small number of passes over the data. In fact, it is possible to obtain the NMF or perform archetypal analysis with just two passes over the data.
DOI: 10.7910/dvn/v1rjpf/pi1yuv
title: cbb20170107_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4123221.v1
title: Directivities Human Tongue Clicks

description: This dataset includes the sound directivity of six different tongue clicks that are produced for human echolocation puposes. The methodology is described in the technical journal paper 'Acoustic Properties of Tongue Clicks', submitted to Acta Acustica United with Acustica, by Rick de Vos and Maarten Hornikx.
DOI: 10.6084/m9.figshare.4123197
title: Introductory Statistics Textbooks and the GAISE Recommendations

description: The six recommendations made by the Guidelines for Assessment and Instruction in Statistics Education (GAISE) committee were first communicated in 2005 and more formally in 2010. In this article, 25 introductory statistics textbooks are examined to assess how well these textbooks have incorporated the three GAISE recommendations most relevant to implementation in textbooks (statistical literacy and thinking; use of real data; stress concepts over procedures). The implementation of another recommendation (using technology) is described but not assessed. In general, most textbooks appear to be adopting the GAISE recommendations reasonably well in both exposition and exercises. The textbooks are particularly adept at using real data, using real data well, and promoting statistical literacy. Textbooks are less adept—but still rated reasonably well, in general—at explaining concepts over procedures and promoting statistical thinking. In contrast, few textbooks have easy-usable glossaries of statistical terms to assist with understanding of statistical language and literacy development. Supplementary materials for this article are available online.
DOI: 10.7910/dvn/v1rjpf/isrqac
title: cbb20170510_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4123197.v1
title: Introductory Statistics Textbooks and the GAISE Recommendations

description: The six recommendations made by the Guidelines for Assessment and Instruction in Statistics Education (GAISE) committee were first communicated in 2005 and more formally in 2010. In this article, 25 introductory statistics textbooks are examined to assess how well these textbooks have incorporated the three GAISE recommendations most relevant to implementation in textbooks (statistical literacy and thinking; use of real data; stress concepts over procedures). The implementation of another recommendation (using technology) is described but not assessed. In general, most textbooks appear to be adopting the GAISE recommendations reasonably well in both exposition and exercises. The textbooks are particularly adept at using real data, using real data well, and promoting statistical literacy. Textbooks are less adept—but still rated reasonably well, in general—at explaining concepts over procedures and promoting statistical thinking. In contrast, few textbooks have easy-usable glossaries of statistical terms to assist with understanding of statistical language and literacy development. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4123191
title: Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing

description: Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated 2 distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analyzed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the 2 exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.
DOI: 10.6084/m9.figshare.4123194
title: An Eight-Step Guide to Creating and Sustaining a Mentoring Program

description: Mentoring is an extremely valuable activity for both individuals and organizations. Mentoring within organizations can develop and integrate employees into their corporate culture. Mentoring outside the mentees’ work groups or through professional development organizations can give broader perspective and support, especially in times of transition. But mentoring programs require tremendous effort to start, organize, and maintain. Few last more than two years. This article provides a structured approach to starting and sustaining a successful program. The steps include understanding an organization’s particular needs, learning from small pilot programs, following up with mentoring pairs during a committed formal mentoring period, and evaluating results from each program’s cycle to learn and grow the program. Supplementary materials for this article are available online.
DOI: 10.7910/dvn/v1rjpf/7m73f1
title: cbb20170309_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4123194.v1
title: An Eight-Step Guide to Creating and Sustaining a Mentoring Program

description: Mentoring is an extremely valuable activity for both individuals and organizations. Mentoring within organizations can develop and integrate employees into their corporate culture. Mentoring outside the mentees’ work groups or through professional development organizations can give broader perspective and support, especially in times of transition. But mentoring programs require tremendous effort to start, organize, and maintain. Few last more than two years. This article provides a structured approach to starting and sustaining a successful program. The steps include understanding an organization’s particular needs, learning from small pilot programs, following up with mentoring pairs during a committed formal mentoring period, and evaluating results from each program’s cycle to learn and grow the program. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4123191.v2
title: Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing

description: Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated 2 distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analyzed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the 2 exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.
DOI: 10.7910/dvn/v1rjpf/beljzb
title: cbb20170828_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4123191.v1
title: Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing

description: Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.
DOI: 10.7910/dvn/v1rjpf/1uyn3y
title: cbb20170513_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4123182
title: Store-operated calcium entry-activated autophagy protects EPC proliferation via the CAMKK2-MTOR pathway in ox-LDL exposure

description: Improving biological functions of endothelial progenitor cells (EPCs) is beneficial to maintaining endothelium homeostasis and promoting vascular re-endothelialization. Because macroautophagy/autophagy has been documented as a double-edged sword in cell functions, its effects on EPCs remain to be elucidated. This study was designed to explore the role and molecular mechanisms of store-operated calcium entry (SOCE)-activated autophagy in proliferation of EPCs under hypercholesterolemia. We employed oxidized low-density lipoprotein (ox-LDL) to mimic hypercholesterolemia in bone marrow-derived EPCs from rat. Ox-LDL dose-dependently activated autophagy flux, while inhibiting EPC proliferation. Importantly, inhibition of autophagy either by silencing <i>Atg7</i> or by 3-methyladenine treatment, further aggravated proliferative inhibition by ox-LDL, suggesting the protective effects of autophagy against ox-LDL. Interestingly, ox-LDL increased STIM1 expression and intracellular Ca<sup>2+</sup> concentration. Either Ca<sup>2+</sup> chelators or deficiency in STIM1 attenuated ox-LDL-induced autophagy activation, confirming the involvement of SOCE in the process. Furthermore, CAMKK2 (calcium/calmodulin-dependent protein kinase kinase 2, β) activation and MTOR (mechanistic target of rapamycin [serine/threonine kinase]) deactivation were associated with autophagy modulation. Together, our results reveal a novel signaling pathway of SOCE-CAMKK2 in the regulation of autophagy and offer new insights into the important roles of autophagy in maintaining proliferation and promoting the survival capability of EPCs. This may be beneficial to improving EPC transplantation efficacy and enhancing vascular re-endothelialization in patients with hypercholesterolemia.