cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5120653.v1
title: Supplementary Material for: Prenatal Diagnosis of a Spontaneous Monochorionic Five-Amniotic Quintuplet Pregnancy

description: <i>Objectives:</i> It is the aim of this study to report on the prenatal diagnosis and course of a spontaneous monochorionic (MC) 5-amniotic (5A) quintuplet pregnancy which is such a rare event that it has up to now never been described antenatally. <i>Case Report:</i> A spontaneous MC 5A quintuplet pregnancy was diagnosed at 12 weeks by 2D ultrasound. Video tapes (2D and 4D) were made showing that 2D ultrasound still better documented simultaneous visualization of all quintuplets including their activities compared with 4D ultrasound, which, however, adds the information of space location. Variances of crown-rump length, nuchal translucency and nasal bone were evaluated. After informed consent and a second opinion of 2 centers performing invasive laser coagulation or occlusion of the umbilical cord, the parents decided to interrupt pregnancy. Pathologic evaluation confirmed MC 5A quintuplet pregnancy. <i>Conclusion:</i> The case demonstrates that splitting of 1 zygote into 5 embryos might even occur spontaneously. In view of the poor outcome and limited success of fetal reduction, pregnancy termination was finally part of the counseling.
DOI: 10.6084/m9.figshare.5120662.v1
title: Supplementary Material for: Analysis of Allele and Haplotype Diversity Across 25 Genomic Regions in Three Eastern European Populations

description: <i>Objective:</i> Individual population history is the main reason for the variability of linkage disequilibrium (LD) patterns and haplotype frequencies among populations. Such diversity may influence the transferability of tag SNPs from one population to another. Our goal was to compare patterns of pairwise LD and allele and haplotype frequencies in Estonian and Russian populations, to estimate the genetic variation between populations and assess the potential transferability of tag SNPs. <i>Methods:</i> 452 SNPs from 25 unlinked genomic regions on 12 chromosomes were genotyped in 140 Estonians and 207 Russians from Northern and Western regions of the European area of Russia. <i>Results:</i> The allele frequency distributions were highly consistent between populations (<i>R</i> &gt; 0.90 for all pairwise comparisons). The overall frequency variation among populations was low (F<sub>ST</sub> = 0.0054). The number of SNPs with high-range F<sub>ST</sub> values (0.02–0.09) was most prominent for the <i>MC5R</i> genomic region. Haplotype heterogeneity among populations was low (F<sub>ST</sub> values ranged within 0.00–0.01, with the exception of haploblocks in the <i>ADIPOR2</i> and <i>MC5R</i> regions). The interpopulation proximity was also evaluated using haplotype diversity. <i>Conclusion:</i> Our data showed a high concordance between the populations studied, which may be considered as the result of their historical formation on a cognate genetic basis.
DOI: 10.6084/m9.figshare.5120647
title: Supplementary Material for: Evaluation of a Novel Anti-Mucin 1 (MUC1) Antibody (PankoMab) as a Potential Diagnostic Tool in Human Ductal Breast Cancer; Comparison with Two Established Antibodies

description: <i>Aim: </i>PankoMab is a novel antibody that recognizes a tumor-specific epitope of Mucin 1 (MUC1). The aim of this study was the evaluation of PankoMab as a potential diagnostic tool and its comparison with two established antibodies against MUC1 in human ductal breast cancer. <i>Materials and Methods: </i>Breast carcinomas were obtained from 82 patients. MUC1 expression and hormone receptor status were determined by immunohistochemistry of paraffin-embedded material. <i>Results: </i>PankoMab revealed strong correlation to hormone receptor expression. DF3 showed no correlation with grading, lymph node involvement and/or estrogen receptor (ER) expression. In the subgroup of lymph node-positive and ER-negative tumors, we saw a significantly reduced DF3 staining in G3 tumors compared to G2 tumors. VU-4-H5 showed increased staining intensity in correlation with increased grading. In addition, we also identified a significantly higher expression of the VU-4-H5 epitope in lymph node-positive carcinomas compared to carcinomas without lymph node involvement. <i>Conclusion: </i>PankoMab revealed strong correlation to hormone receptor expression in ductal carcinoma of the breast. VU-4-H5 showed increased staining intensity in correlation with increased grading and lymph node involvement. PankoMab and VU-4-H5 staining could be a useful combination in ductal breast cancer prognosis by immunohistochemistry.
DOI: 10.6084/m9.figshare.5120656.v1
title: Supplementary Material for: ADAR1 and ADAR2 Expression and Editing Activity during Forebrain Development

description: The conversion of adenosine to inosine within RNA transcripts is regulated by a family of double-stranded RNA-specific adenosine deaminases referred to as adenosine deaminases that act on RNA (ADARs). Little is known regarding the developmental expression of ADAR family members or the mechanisms responsible for the specific patterns of editing observed for ADAR substrates. We have examined the spatiotemporal expression patterns for ADAR1 and ADAR2 in mouse forebrain. ADAR1 and ADAR2 are broadly distributed in most regions of the mouse forebrain by P0, including the cerebral cortex, hippocampus, and diencephalon. High expression levels were maintained into adulthood. Colocalization studies demonstrated ADAR1 and ADAR2 expression in neurons but not astrocytes. Editing for specific ADAR mRNA targets precedes high expression of ADAR proteins, suggesting that region-specific differences in editing patterns may not be mediated solely by ADAR expression levels.
DOI: 10.6084/m9.figshare.5120635
title: Supplementary Material for: Telomeric associations correlate with telomere length reduction and clonal chromosome aberrations in giant cell tumor of bone

description: Giant cell tumor of bone (GCTB) is characterized cytogenetically by frequent telomeric associations (tas). To explore the mechanisms behind the formation of tas in GCTB and to investigate their karyotypic consequences, the frequencies of tas and clonal aberrations other than tas in 20 GCTBs were compared to telomere length and status, as assessed by quantitative PCR, fluorescence in situ hybridization (FISH), and expression levels of four genes involved in telomere maintenance. Based on the G-banding results, the tumors were divided into two groups, one with a high frequency of tas and one with a low frequency. Clonal aberrations were found to be restricted to the group with a high level of tas, and the same group showed a significantly larger reduction in telomere length in tumor cells compared to peripheral blood cells. Furthermore, 65 out of 66 tas analyzed by FISH were negative for telomeric sequences. The expression levels of <i>TERT, TERF1, TERF2, </i>and <i>POT1 </i>did not correlate with telomere length or the frequency of tas. Thus, the present findings provide strong support for the notion that decreased telomere length is a prerequisite for tas in GCTBs and that the clonal changes occurring in GCTBs are derived from tas.
DOI: 10.6084/m9.figshare.5120638
title: Supplementary Material for: Interstitial telomeric sequences (ITSs) are not located at the exact evolutionary breakpoints in primates

description: Although their function has not yet been clearly elucidated, interstitial telomeric sequences (ITSs) have been cytogenetically associated with chromosomal reorganizations, fragile sites, and recombination hotspots. In this paper, we show that ITSs are not located at the exact evolutionary breakpoints of the inversions between human and chimpanzee and between human and rhesus macaque chromosomes. We proved that ITSs are not signs of repair in the breakpoints of the chromosome reorganizations analyzed. We found ITSs in the region (0.7–2.7 Mb) flanking one of the two breakpoints in all the inversions assessed. The presence of ITSs in those locations is not by chance. They are short (up to 7.83 repeats) and almost perfect (82.5–97.1% matches). The ITSs are conserved in the species compared, showing that they were present before the reorganizations occurred.
DOI: 10.6084/m9.figshare.5120641
title: Supplementary Material for: Studies on the short range spreading of the male specific lethal (MSL) complex on the X chromosome in <i>Drosophila</i>

description: A series of autosomal insertions of chromosomal fragments derived from around the X linked white eye color locus have been examined for male specific lethal (MSL) complex binding using both immunostaining and fluorescence in situ hybridization (FISH) techniques. The results show that the transposing elements (TEs) composed of several genes in the white region (3C2-3C5) do not recruit the MSL complex when inserted into an autosome. The same result is found for the Tp(1:3)wzh insertion, a fragment of the X chromosome inserted into the third chromosome. Two other insertions, Dp(1:2)w70h (3A7-3C2-3) and Dp(1:2)51b (3C2-3D6), which extend more distally or proximally beyond the TE insertion, respectively, display a binding pattern of the MSL complex at the autosomal location. These insertions were also examined in females ectopically expressing MSL-2 and show similar binding activity. In addition, the Tp(3:1)O5 transposition strain containing an autosomal segment in the X chromosome was examined for spreading of the MSL complex. Limited spreading of the MSL complex into autosomal regions was indicated by immunostaining and FISH. This spreading was further confirmed by chromatin immunoprecipitation of the MSL complex covering the autosomal sequences.
DOI: 10.6084/m9.figshare.5120644
title: Supplementary Material for: Rhythm in Speech and Language

description: Like any other aspect of spoken language, rhythm needs to be, and has been, studied from four different perspectives for a comprehensive and insightful account of its nature and functioning in speech communication: symbolic representation, production, perception, communicative function. The paper first gives an overview of the milestones in the analysis of rhythm under the headings of these four approaches over the past 70 years. This survey of the development of scientific ideas in rhythm research prepares the ground for the integration of the four strands in an interrelated framework of linguistic and speech signal analysis. On the basis of a definition of rhythm derived from the theoretical and methodological discussion, a new paradigm is outlined for future research, centred on the listener and on communicative function.
DOI: 10.6084/m9.figshare.5120638.v1
title: Supplementary Material for: Interstitial telomeric sequences (ITSs) are not located at the exact evolutionary breakpoints in primates

description: Although their function has not yet been clearly elucidated, interstitial telomeric sequences (ITSs) have been cytogenetically associated with chromosomal reorganizations, fragile sites, and recombination hotspots. In this paper, we show that ITSs are not located at the exact evolutionary breakpoints of the inversions between human and chimpanzee and between human and rhesus macaque chromosomes. We proved that ITSs are not signs of repair in the breakpoints of the chromosome reorganizations analyzed. We found ITSs in the region (0.7–2.7 Mb) flanking one of the two breakpoints in all the inversions assessed. The presence of ITSs in those locations is not by chance. They are short (up to 7.83 repeats) and almost perfect (82.5–97.1% matches). The ITSs are conserved in the species compared, showing that they were present before the reorganizations occurred.
DOI: 10.6084/m9.figshare.5120629
title: Supplementary Material for: The Effects of Dairy Components on Energy Partitioning and Metabolic Risk in Mice: A Microarray Study

description: <i>Background/Aim:</i> High-calcium diets modulate energy metabolism and suppress inflammatory stress. These effects are primarily mediated by calcium suppression of calcitriol. We have now investigated the effect of additional components in dairy products [branched-chain amino acids (BCAA) and angiotensin-converting enzyme inhibitors (ACEi)] on adipocyte and muscle metabolism in an animal model of diet-induced obesity. <i>Methods:</i> aP2-agouti mice were fed four different 70% restricted diets for 6 weeks: basal-restricted diet (0.4% Ca), nonfat dry milk (1.2% Ca), calcium-depleted milk (0.4% Ca), or basal-restricted diet (0.4% Ca) with supplemented BCAA/ACEi. A high-density oligonucleotide microarray approach was used to compare the effects on energy metabolism. <i>Results:</i> Lipogenic genes in adipose tissue were downregulated in the milk group while in muscle protein synthetic pathways were stimulated by the Ca-depleted and low Ca/BCAA/ACEi diets. Pathways involved in inflammation were altered in adipose tissue and muscle by all three diet treatment groups. <i>Conclusions:</i> The results support our previous findings that calcium and BCAA contribute to the alteration of energy partitioning between adipose tissue and muscle. They provide further evidence for a calcium-independent effect of BCAA and ACEi in energy metabolism and inflammation.
DOI: 10.6084/m9.figshare.5120632
title: Supplementary Material for: Establishment of a Predominantly African-American Cohort for the Study of Alzheimer’s Disease

description: <i>Background/Aims:</i> The recruitment of culturally diverse subject populations into research studies, particularly African-Americans (AA), has been the focus of intense interest by many groups. <i>Methods:</i> In this paper, we present the methodology utilized to create a predominantly AA cohort for the longitudinal study of risk factors in Alzheimer’s disease (AD). The underlying strategy was that of identifying geographically diverse clinical venues within South Carolina (SC) where large numbers of AA patients already come to seek medical care. <i>Results:</i> This strategy was successful, although recruitment rates for AA subjects (43.4%) still fell below those for white subjects (70.3%; p = 0.0025). Subject characteristics of AA subjects that chose to enroll were not substantially different from those that declined to participate. The demographic characteristics of this cohort were largely similar to those of the SC Alzheimer Disease Registry, a population-based database. The problems of standardization of subject recruitment and assessment across diverse clinical venues are also addressed. <i>Conclusion:</i> The utilization of geographically diverse sites for research recruitment where minorities already receive medical care is one practical solution to the problem of minority participation in research. Multi-site recruitment to improve minority recruitment can be accomplished with acceptable standardization and inter-rater reliability.
DOI: 10.6084/m9.figshare.5120635.v1
title: Supplementary Material for: Telomeric associations correlate with telomere length reduction and clonal chromosome aberrations in giant cell tumor of bone

description: Giant cell tumor of bone (GCTB) is characterized cytogenetically by frequent telomeric associations (tas). To explore the mechanisms behind the formation of tas in GCTB and to investigate their karyotypic consequences, the frequencies of tas and clonal aberrations other than tas in 20 GCTBs were compared to telomere length and status, as assessed by quantitative PCR, fluorescence in situ hybridization (FISH), and expression levels of four genes involved in telomere maintenance. Based on the G-banding results, the tumors were divided into two groups, one with a high frequency of tas and one with a low frequency. Clonal aberrations were found to be restricted to the group with a high level of tas, and the same group showed a significantly larger reduction in telomere length in tumor cells compared to peripheral blood cells. Furthermore, 65 out of 66 tas analyzed by FISH were negative for telomeric sequences. The expression levels of <i>TERT, TERF1, TERF2, </i>and <i>POT1 </i>did not correlate with telomere length or the frequency of tas. Thus, the present findings provide strong support for the notion that decreased telomere length is a prerequisite for tas in GCTBs and that the clonal changes occurring in GCTBs are derived from tas.
DOI: 10.6084/m9.figshare.5120641.v1
title: Supplementary Material for: Studies on the short range spreading of the male specific lethal (MSL) complex on the X chromosome in <i>Drosophila</i>

description: A series of autosomal insertions of chromosomal fragments derived from around the X linked white eye color locus have been examined for male specific lethal (MSL) complex binding using both immunostaining and fluorescence in situ hybridization (FISH) techniques. The results show that the transposing elements (TEs) composed of several genes in the white region (3C2-3C5) do not recruit the MSL complex when inserted into an autosome. The same result is found for the Tp(1:3)wzh insertion, a fragment of the X chromosome inserted into the third chromosome. Two other insertions, Dp(1:2)w70h (3A7-3C2-3) and Dp(1:2)51b (3C2-3D6), which extend more distally or proximally beyond the TE insertion, respectively, display a binding pattern of the MSL complex at the autosomal location. These insertions were also examined in females ectopically expressing MSL-2 and show similar binding activity. In addition, the Tp(3:1)O5 transposition strain containing an autosomal segment in the X chromosome was examined for spreading of the MSL complex. Limited spreading of the MSL complex into autosomal regions was indicated by immunostaining and FISH. This spreading was further confirmed by chromatin immunoprecipitation of the MSL complex covering the autosomal sequences.
DOI: 10.6084/m9.figshare.5120626
title: Supplementary Material for: Mouse Neutrophil Extracellular Traps in Microbial Infections

description: Neutrophil extracellular traps (NETs) play an important role in innate immunity to microbial infections. NETs have been described in several species, but the molecular details of NET formation and their role in infection has not been addressed, partly because we lack optimal experimental models. Here we describe tools to investigate NET formation in neutrophils isolated from mice. Upon in vitro stimulation of wild-type mouse neutrophils with PMA, we analyzed 3 important steps in the process of NET formation: reactive oxygen species (ROS) production, NET cell death and NET release. As expected, neutrophils from NADPH oxidase-deficient mice failed to produce ROS and did not die nor release NETs upon stimulation. We found that neutrophils from several mouse strains produced NETs with different efficiency and that NET formation correlated with the amount of ROS produced. Activation with <i>Candida albicans</i> also resulted in ROS production and NET cell death. The hyphal form of this fungus induced NETs more effectively than the yeast form. With this work, we provide tools to study in vitro NET assembly in the mouse system.
DOI: 10.6084/m9.figshare.5120629.v1
title: Supplementary Material for: The Effects of Dairy Components on Energy Partitioning and Metabolic Risk in Mice: A Microarray Study

description: <i>Background/Aim:</i> High-calcium diets modulate energy metabolism and suppress inflammatory stress. These effects are primarily mediated by calcium suppression of calcitriol. We have now investigated the effect of additional components in dairy products [branched-chain amino acids (BCAA) and angiotensin-converting enzyme inhibitors (ACEi)] on adipocyte and muscle metabolism in an animal model of diet-induced obesity. <i>Methods:</i> aP2-agouti mice were fed four different 70% restricted diets for 6 weeks: basal-restricted diet (0.4% Ca), nonfat dry milk (1.2% Ca), calcium-depleted milk (0.4% Ca), or basal-restricted diet (0.4% Ca) with supplemented BCAA/ACEi. A high-density oligonucleotide microarray approach was used to compare the effects on energy metabolism. <i>Results:</i> Lipogenic genes in adipose tissue were downregulated in the milk group while in muscle protein synthetic pathways were stimulated by the Ca-depleted and low Ca/BCAA/ACEi diets. Pathways involved in inflammation were altered in adipose tissue and muscle by all three diet treatment groups. <i>Conclusions:</i> The results support our previous findings that calcium and BCAA contribute to the alteration of energy partitioning between adipose tissue and muscle. They provide further evidence for a calcium-independent effect of BCAA and ACEi in energy metabolism and inflammation.
DOI: 10.6084/m9.figshare.5120617
title: Supplementary Material for: Pivotal Role of Bedside Doppler Echocardiography in the Assessment of Patients with Acute Heart Failure and Mitral Regurgitation

description: Patients presenting with mitral regurgitation and acute heart failure remain a challenge for the clinicians. Bedside echocardiography ascertains the functional or primary nature of mitral regurgitation, thereby allowing to focus therapy on the left ventricle and mitral valve apparatus in patients with functional mitral regurgitation and to hasten mitral valve repair or replacement when acute heart failure results from primary mitral regurgitation. This short article reviews the evaluation by bedside echocardiography to guide management of these patients.
DOI: 10.6084/m9.figshare.5120623
title: Supplementary Material for: Isolation, Culture and Characterization of Cardiac Progenitor Cells Derived from Human Embryonic Heart Tubes

description: A variety of studies have reported on the isolation and expansion of cardiac stem cells from adult hearts. However, there is little information concerning cardiac stem/progenitor cells derived from embryonic hearts/heart tubes. To provide more evidence for embryonic heart-derived stem/progenitor cells, Nkx2.5+ human cardiac progenitorcells (hCPCs) were isolated and cloned from human heart tubes. The cells stained positive for Nkx2.5 and Oct-4, and negative for α-smooth muscle actin (α-SMA), cytokeratin, factor-VIII, α-sarcomeric actin and c-Kit. GATA-4 expression of Nkx2.5+ hCPCs was higher than that of embryonic limb bud mesenchymal cells of the control group (p &lt; 0.05). These cells were passaged continuously for &gt;3 months (23 passages) and proliferated actively in vitro. After being treated with 5-azacytidine, Nkx2.5+ hCPCs underwent cardiomyogenic differentiation. Ultrastructural observation confirmed that the longitudinal section of these cardiomyogenic differentiation cells clearly revealed typical sarcomeres and intercalated discs. α-MHC, α-sarcomeric actin and GATA-4 levels were increased in Nkx2.5+ hCPCs treated with 5-azacytidine compared to untreated cells. Nkx2.5+ hCPCs exhibited positive staining and had a higher expression for α-SMA when cocultured with canine vascular endothelial cells. After Nkx2.5+ hCPCs were treated with endothelin-1, all cells displayed spontaneous electrical activity and spontaneous beating. Connexin-40 and -45 were stained positive in the treated cells. In conclusion, Nkx2.5+ hCPCs derived from heart tubes have been isolated and cloned in vitro. These cells are capable of long-term self-renewal and possess a potential to differentiate into cardiac muscle-like cells, cardiac pacemaking cells and smooth muscle-like cells. They could have a significant impact on cardiac regeneration medicine and developmental biology.