cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4751023
title: Supplementary Material for: Making Sense of Outliers

description: Phonetic inquiry, particularly of the kind which looks at large numbers of items, frequently asks what a ‘typical’ example of a phenomenon of speech is like. For example, in describing the plosives of a language, it is common to calculate average closure durations or voice onset times in some contexts. In this paper, the focus is on examples from natural conversation where there are untypical patterns, and where the item of interest is, in statistical terms, an outlier. Outliers are generally excluded from linguistic analysis, and may be treated as e.g. production errors. The paper shows instead that at least some outliers are in fact part of a meaningful practice, and an orderly method by which speakers can create meaning. The phenomenon more precisely is that of intensifying emphasis, which has been described for German. We consider its phonetic exponents in American English, which are both ‘prosodic’ and ‘segmental’. We provide an account of function based on participants’ own use and displayed understanding of the phenomenon, and argue for a structurally rich account of the phenomenon which includes aspects of turn construction and sequential organisation.
DOI: 10.6084/m9.figshare.4751065.v1
title: Supplementary Material for: The Impact of Ovarian Stimulation on the Expression of Candidate Reprogramming Genes in Mouse Preimplantation Embryos

description: Ovarian stimulation with gonadotrophins is an integral part of assisted reproductive technologies in human subfertility/infertility treatment. Recent findings have associated ovarian stimulation with the increased incidence of imprinting disorders in humans as well as defects in genome-wide methylation reprogramming and, in particular, imprinting in mice. Here, we present the first study that determined the impact of ovarian stimulation on the expression of developmentally important reprogramming genes <i>(Apex1, Lig1, Lig3, Mbd2, Mbd3, Mbd4, </i>and<i> Polb)</i> in single early mouse morula embryos (16-cell stage). Using absolute quantification of mRNA by quantitative real-time PCR, we observed an association of ovarian stimulation with a downregulation of mRNAs encoding the base excision repair proteins APEX1 and POLB as well as the 5-methyl-CpG-binding domain protein MBD3 in individual morula embryos. Whole mount immunofluorescence staining of early and late morula embryos with an antibody against APEX1 revealed individual embryos with lower protein expression levels after ovarian stimulation and a correlation of mRNA expression with protein abundance. Our data argue for a negative impact of ovarian stimulation during female gametogenesis and/or early embryo development affecting the expression of candidate reprogramming factors.
DOI: 10.7910/dvn/pkjufn/amczu4
title: FCC2003.173.ran

description: :unav
DOI: 10.6084/m9.figshare.12904562.v1
title: R0193_20171002a_videos

description: Rat 0193, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.4751014
title: Supplementary Material for: Identification of Copy Number Variants on Human Chromosome 22 in Patients with a Variety of Clinical Findings

description: The aims of this study were to create a copy number variant (CNV) profile of human chromosome 22 and to establish a genotype-phenotype correlation for patients with genomic abnormalities on chromosome 22. Thus, 1,654 consecutive pediatric patients with a diversity of clinical findings were evaluated by high-resolution chromosomal microarray analysis (CMA). We identified 25 individuals with abnormal CNVs on chromosome 22, representing 1.5% of the cases analyzed in this cohort. Meanwhile, we detected 1,298 benign CNVs on this chromosome in these individuals. Twenty-one of the 25 abnormal CNVs and the majority of the benign CNVs occurred through involvement of the 8 unstable genomic regions enriched with low copy repeats (LCR22A–H). The highly dynamic status of LCR22s within the 22q11 region facilitates the formation of diverse genomic abnormalities. This CNV profile provides a general perspective of the spectrum of chromosome 22 genomic imbalances and subsequently improves the CNV-phenotype correlations.
DOI: 10.6084/m9.figshare.4751017
title: NCBI gene and protein identifiers

description: Download set
DOI: 10.6084/m9.figshare.4751020
title: Supplementary Material for: The Perception of Lexical Stress in German: Effects of Segmental Duration and Vowel Quality in Different Prosodic Patterns

description: Several decades of research, focusing on English, Dutch and German, have set up a hierarchy of acoustic properties for cueing lexical stress. It attributes the strongest cue to criterial-level f0 change, followed by duration, but low weight to energy and to stressed-vowel spectra. This paper re-examines the established view with new data from German. In the natural productions of the German word pair <i>Kaffee</i> ‘coffee’ – <i>Café</i> ‘locality’ (with initial vs. final stress in a North German pronunciation), vowel duration was manipulated in a complementary fashion across the two syllables in five steps, spanning the continuum from initial to final stress on each word. The two base words provided different vowel qualities as the second variable, the intervocalic fricative was varied in two values, long and short, taken from <i>Café</i> and <i>Kaffee,</i> and the generated test words were inserted in a low f0 tail and in a high f0 hat-pattern plateau, which both eliminated f0 change as a cue to lexical stress. The sentence stimuli were judged in two listening experiments by 16 listeners in each as to whether the first or the second syllable of the test word was stressed. The results show highly significant effects of vowel duration, vowel quality and fricative duration. The combined vowel-quality and fricative variable can outweigh vowel duration as a cue to lexical stress. The effect of the prosodic frame is only marginal, especially related to a rhythmic factor. The paper concludes that there is no general hierarchy with a fixed ranking of the variables traditionally adduced to signal lexical stress. Every prosodic embedding of segmental sequences defines the hierarchy afresh.
DOI: 10.6084/m9.figshare.4751026.v1
title: Supplementary Material for: Intonation Adapts to Lexical Tone: The Case of Kammu

description: In this paper, we investigate how lexical tones interact with intonation, using data from the Austroasiatic language Kammu, one of few languages with two dialects whose only major phonological difference is the presence or absence of lexical tones. Northern (and Western) Kammu have developed tones in connection with the merger of voiceless and voiced initial consonants, while the non-tonal Eastern dialect kept the segmental opposition with no tones. We found the following prosodic hierarchy: (1) lexical tones, (2) phrase-final boundary tone, (3) focus marking. The results strongly suggest that the intonational systems of the two Kammu dialects are basically identical, and that the main differences between the dialects are adaptations of intonation patterns to the lexical tones when the identities of the tones are jeopardized.
DOI: 10.6084/m9.figshare.4751017.v1
title: NCBI gene and protein identifiers

description: Download set
DOI: 10.6084/m9.figshare.4751011
title: HGNC gene_with_protein_product.xlsx

description: Download set
DOI: 10.6084/m9.figshare.4751014.v1
title: Supplementary Material for: Identification of Copy Number Variants on Human Chromosome 22 in Patients with a Variety of Clinical Findings

description: The aims of this study were to create a copy number variant (CNV) profile of human chromosome 22 and to establish a genotype-phenotype correlation for patients with genomic abnormalities on chromosome 22. Thus, 1,654 consecutive pediatric patients with a diversity of clinical findings were evaluated by high-resolution chromosomal microarray analysis (CMA). We identified 25 individuals with abnormal CNVs on chromosome 22, representing 1.5% of the cases analyzed in this cohort. Meanwhile, we detected 1,298 benign CNVs on this chromosome in these individuals. Twenty-one of the 25 abnormal CNVs and the majority of the benign CNVs occurred through involvement of the 8 unstable genomic regions enriched with low copy repeats (LCR22A–H). The highly dynamic status of LCR22s within the 22q11 region facilitates the formation of diverse genomic abnormalities. This CNV profile provides a general perspective of the spectrum of chromosome 22 genomic imbalances and subsequently improves the CNV-phenotype correlations.
DOI: 10.7910/dvn/pkjufn/6l54q5
title: FCC2003.202.ran

description: :unav
DOI: 10.6084/m9.figshare.4750999
title: Supplementary Material for: Investigating the Effect of CoCl2 Administration on Diabetic Nephropathy and Associated Aortic Dysfunction

description: <strong><em>Aim:</em></strong> Endothelial dysfunction appears to be a consistent finding in diabetic nephropathy. The study aimed to investigate the effect of cobalt chloride in the amelioration of endothelial dysfunction in uninephrectomized diabetic rats. <b><i>Methods:</i></b> We examined the effect of CoCl<sub>2</sub> (10 mg/kg, i.p., OD = once a day) treatment on contractile responses to angiotensin II (10<sup>–10</sup> to 10<sup>–6</sup>M) in an aortic preparation of control rats and uninephrectomized diabetic control rats. Blood glucose, plasma urea, creatinine, uric acid, aortic endothelial nitric oxide synthase (eNOS), nitrate/nitrite (NOx), superoxide dismutase, catalase and reduced glutathione levels were checked in the different groups. <b><i>Results:</i></b> A significant attenuation of the augmented responses to angiotensin II was observed in CoCl<sub>2</sub>-treated animals along with a fall in plasma urea, creatinine and uric acid levels. A significant reduction in blood glucose and an increase in aortic eNOS and NOx levels along with antioxidants levels were observed. <b><i>Conclusion: </i></b>Chronic hypoxia augments angiotensin II responses in the thoracic aorta of uninephrectomized diabetic control rats. CoCl<sub>2</sub> attenuates these enhanced vascular responses with a significant decrease in blood glucose signifying stabilization of the hypoxia-inducible factor in the alleviation of endothelial dysfunction in diabetic nephropathy.
DOI: 10.6084/m9.figshare.4751002
title: Supplementary Material for: Differential Effects of Prenatal Stress in Female 5-Htt-Deficient Mice: Towards Molecular Mechanisms of Resilience

description: Prenatal stress (PS) exposure is known to increase the risk of developing emotional disorders like major depression in later life. However, some individuals do not succumb to adversity following developmental stress exposure, a phenomenon referred to as resilience. To date, the molecular mechanisms explaining why some subjects are vulnerable and others more resilient to PS are far from understood. Recently, we have shown that the serotonin transporter <i>(5-HTT)</i> gene may play a modulating role in rendering individuals susceptible or resilient to PS. However, it is not clear which molecular players are mediating the interaction between PS and the <i>5-Htt</i> genotype in the context of vulnerability and resilience to PS. For this purpose, we performed a microarray study with the help of Affymetrix GeneChip® Mouse Genome 430 2.0 Array, in which we separated wild-type and heterozygous <i>5-Htt</i>-deficient <i>(5-Htt+/-)</i> PS offspring into susceptible and resilient offspring according to their performance in the forced swim test. Performance-oriented LIMMA analysis on the mRNA expression microarray data was followed by subsequent Spearman's correlation analysis linking the individual qRT-PCR mRNA expression data to various anxiety- and depression-related behavioral and neuroendocrine measures. Results indicate that, amongst others, Fos-induced growth factor <i>(Figf)</i>, galanin receptor 3 <i>(Galr3)</i>, growth hormone <i>(Gh)</i> and prolactin <i>(Prl)</i> were differentially expressed specifically in resilient offspring when compared to controls, and that the hippocampal expression of these genes showed several strong correlations with various measures of the hypothalamus-pituitary-adrenal axis (re)activity. In conclusion, there seems to be an intricate interplay between the expression of <i>Figf, Galr3, Gh</i> and <i>Prl</i> and neuroendocrine regulation, which may be critical in mediating resilience to PS exposure. More insight into the exact role of these molecular players may significantly enhance the development of new treatment strategies for stress-related emotional disorders.
DOI: 10.6084/m9.figshare.4750978
title: Supplementary Material for: Comparison of Clinical and Histological Effects between Lactobacillus-Fermented Chamaecyparis obtusa and Tea Tree Oil for the Treatment of Acne: An Eight-Week Double-Blind Randomized Controlled Split-Face Study

description: <b><i>Background:</i></b> Screening of natural compounds for the development of anti-acne therapeutic agents has been steadily required considering various side effects of acne medications. However, previous studies have mainly focused on experimental tests without clinical trials and histopathological analysis. <b><i>Objectives:</i></b> To compare the clinical efficacy, safety and histopathological changes between Lactobacillus-fermented <i>Chamaecyparis obtusa</i> (LFCO) and existing tea tree oil (TTO). <b><i>Methods:</i></b> A total of 34 patients were instructed to apply 5% LFCO to the involved areas of a randomly allocated side and 5% TTO extract to the other side for 8 weeks in a double-blind split-face clinical trial. <b><i>Results:</i></b> After 8 weeks, inflammatory acne lesions were reduced by 65.3% on the LFCO side and by 38.2% on the TTO side. LFCO was also superior to TTO in the onset time of efficacy (p &lt; 0.05). The LFCO side further demonstrated improvement for non-inflammatory lesions (52.6%, p &lt; 0.05), decreased size of sebaceous glands and sebum output reductions. Patients' subjective satisfaction was also higher without severe adverse reactions. Protein expressions of nuclear factor κB decreased earlier on the LFCO side, and those of interleukin-1a (IL-1a), IL-8, insulin-like growth factor 1 receptor and sterol regulatory element-binding protein 1 decreased subsequently. Ultra-performance liquid chromatography/high-resolution mass spectrometry further demonstrated that the contents of dihydroxybenzoic acid, taxifolin and quercetin were increased in LFCO after fermentation. <b><i>Conclusions:</i></b> LFCO treatment was rapid and effective for treating acne lesions compared to TTO. Histopathological findings correlated well with the clinical acne grade and treatment response. This novel natural compound appears to be effective and safe for acne treatment.
DOI: 10.6084/m9.figshare.4750999.v1
title: Supplementary Material for: Investigating the Effect of CoCl2 Administration on Diabetic Nephropathy and Associated Aortic Dysfunction

description: <strong><em>Aim:</em></strong> Endothelial dysfunction appears to be a consistent finding in diabetic nephropathy. The study aimed to investigate the effect of cobalt chloride in the amelioration of endothelial dysfunction in uninephrectomized diabetic rats. <b><i>Methods:</i></b> We examined the effect of CoCl<sub>2</sub> (10 mg/kg, i.p., OD = once a day) treatment on contractile responses to angiotensin II (10<sup>–10</sup> to 10<sup>–6</sup>M) in an aortic preparation of control rats and uninephrectomized diabetic control rats. Blood glucose, plasma urea, creatinine, uric acid, aortic endothelial nitric oxide synthase (eNOS), nitrate/nitrite (NOx), superoxide dismutase, catalase and reduced glutathione levels were checked in the different groups. <b><i>Results:</i></b> A significant attenuation of the augmented responses to angiotensin II was observed in CoCl<sub>2</sub>-treated animals along with a fall in plasma urea, creatinine and uric acid levels. A significant reduction in blood glucose and an increase in aortic eNOS and NOx levels along with antioxidants levels were observed. <b><i>Conclusion: </i></b>Chronic hypoxia augments angiotensin II responses in the thoracic aorta of uninephrectomized diabetic control rats. CoCl<sub>2</sub> attenuates these enhanced vascular responses with a significant decrease in blood glucose signifying stabilization of the hypoxia-inducible factor in the alleviation of endothelial dysfunction in diabetic nephropathy.
DOI: 10.6084/m9.figshare.4751002.v1
title: Supplementary Material for: Differential Effects of Prenatal Stress in Female 5-Htt-Deficient Mice: Towards Molecular Mechanisms of Resilience

description: Prenatal stress (PS) exposure is known to increase the risk of developing emotional disorders like major depression in later life. However, some individuals do not succumb to adversity following developmental stress exposure, a phenomenon referred to as resilience. To date, the molecular mechanisms explaining why some subjects are vulnerable and others more resilient to PS are far from understood. Recently, we have shown that the serotonin transporter <i>(5-HTT)</i> gene may play a modulating role in rendering individuals susceptible or resilient to PS. However, it is not clear which molecular players are mediating the interaction between PS and the <i>5-Htt</i> genotype in the context of vulnerability and resilience to PS. For this purpose, we performed a microarray study with the help of Affymetrix GeneChip® Mouse Genome 430 2.0 Array, in which we separated wild-type and heterozygous <i>5-Htt</i>-deficient <i>(5-Htt+/-)</i> PS offspring into susceptible and resilient offspring according to their performance in the forced swim test. Performance-oriented LIMMA analysis on the mRNA expression microarray data was followed by subsequent Spearman's correlation analysis linking the individual qRT-PCR mRNA expression data to various anxiety- and depression-related behavioral and neuroendocrine measures. Results indicate that, amongst others, Fos-induced growth factor <i>(Figf)</i>, galanin receptor 3 <i>(Galr3)</i>, growth hormone <i>(Gh)</i> and prolactin <i>(Prl)</i> were differentially expressed specifically in resilient offspring when compared to controls, and that the hippocampal expression of these genes showed several strong correlations with various measures of the hypothalamus-pituitary-adrenal axis (re)activity. In conclusion, there seems to be an intricate interplay between the expression of <i>Figf, Galr3, Gh</i> and <i>Prl</i> and neuroendocrine regulation, which may be critical in mediating resilience to PS exposure. More insight into the exact role of these molecular players may significantly enhance the development of new treatment strategies for stress-related emotional disorders.
DOI: 10.6084/m9.figshare.4751011.v1
title: HGNC gene_with_protein_product.xlsx

description: Download set
DOI: 10.7910/dvn/pkjufn/vlrurf
title: FCC2001.223.ran

description: :unav
DOI: 10.6084/m9.figshare.4750966
title: Supplementary Material for: Embryonic Stem Cells Facilitate the Isolation of Persistent Clonal Cardiovascular Progenitor Cell Lines and Leukemia Inhibitor Factor Maintains Their Self-Renewal and Myocardial Differentiation Potential in vitro

description: Compelling evidence for the existence of somatic stem cells in the heart of different mammalian species has been provided by numerous groups; however, so far it has not been possible to maintain these cells as self-renewing and phenotypically stable clonal cell lines in vitro. Thus, we sought to identify a surrogate stem cell niche for the isolation and persistent maintenance of stable clonal cardiovascular progenitor cell lines, enabling us to study the mechanism of self-renewal and differentiation in these cells. Using postnatal murine hearts with a selectable marker as the stem cell source and embryonic stem cells and leukemia inhibitory factor (LIF)-secreting fibroblasts as a surrogate niche, we succeeded in the isolation of stable clonal cardiovascular progenitor cell lines. These cell lines self-renew in an LIF-dependent manner. They express both stemness transcription factors Oct4, Sox2, and Nanog and early myocardial transcription factors Nkx2.5, GATA4, and Isl-1 at the same time. Upon LIF deprivation, they exclusively differentiate to functional cardiomyocytes and endothelial and smooth muscle cells, suggesting that these cells are mesodermal intermediates already committed to the cardiogenic lineage. Cardiovascular progenitor cell lines can be maintained for at least 149 passages over 7 years without phenotypic changes, in the presence of LIF-secreting fibroblasts. Isolation of wild-type cardiovascular progenitor cell lines from adolescent and old mice has finally demonstrated the general feasibility of this strategy for the isolation of phenotypically stable somatic stem cell lines.
DOI: 10.7910/dvn/pkjufn/yiof67
title: FCC2003.342.ran

description: :unav
DOI: 10.6084/m9.figshare.4750936
title: Supplementary Material for: Homomorphic Sex Chromosomes and the Intriguing Y Chromosome of Ctenomys Rodent Species (Rodentia, Ctenomyidae)

description: Unlike the X chromosome, the mammalian Y chromosome undergoes evolutionary decay resulting in small size. This sex chromosomal heteromorphism, observed in most species of the fossorial rodent <i>Ctenomys</i>, contrasts with the medium-sized, homomorphic acrocentric sex chromosomes of closely related <i>C. maulinus </i>and <i>C. </i>sp. To characterize the sequence composition of these chromosomes, fluorescent banding, self-genomic in situ hybridization, and fluorescent in situ hybridization with an X painting probe were performed on mitotic and meiotic plates. High molecular homology between the sex chromosomes was detected on mitotic material as well as on meiotic plates immunodetected with anti-SYCP3 and anti-γH2AX. The Y chromosome is euchromatic, poor in repetitive sequences and differs from the X by the loss of a block of pericentromeric chromatin. Inferred from the G-banding pattern, an inversion and the concomitant prevention of recombination in a large asynaptic region seems to be crucial for meiotic X chromosome inactivation. These peculiar findings together with the homomorphism of <i>Ctenomys</i> sex chromosomes are discussed in the light of the regular purge that counteracts Muller's ratchet and the probable mechanisms accounting for their origin and molecular homology.