cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5120533
title: Supplementary Material for: Proteome Patterns in Uremic Plasma

description: In patients with chronic kidney disease (CKD), peptides and proteins circulate at altered concentrations versus in healthy individuals. We have characterized proteome samples from 7 pooled CKD stage 5 patients not yet on dialysis and with no known co-morbidities. We also analyzed pooled plasma samples from 7 healthy age- and sex-matched controls. After immunodepletion of the 6 most abundant plasma proteins, HPLC and SDS-PAGE patterns differed between the healthy and disease groups. The differing proteins were identified by peptide mass fingerprinting using MALDI mass spectrometry and verified with electrospray tandem mass spectrometry sequence analysis. Multiple differences in at least 19 HPLC fractions were observed, from which we identified 29 proteins, 25 in greater yield and 4 in lower yield than in the healthy controls, adding at least 6 protein components to those that were previously known to be altered in CKD.
DOI: 10.6084/m9.figshare.5120536
title: Supplementary Material for: Deviations from Hardy-Weinberg Equilibrium in Parental and Unaffected Sibling Genotype Data

description: <i>Background:</i> Genotyping error can increase both type I and II errors. In order to elucidate potential genotyping errors, data quality control often includes testing genotype data for deviations from Hardy-Weinberg Equilibrium (HWE). <i>Methods:</i> The Hardy-Weinberg Disequilibrium (HWD) coefficient and the ability to reject the null hypothesis of HWE were calculated analytically for genotype data from parents and unaffected siblings of affected probands. <i>Results:</i> Genotype data from parents and unaffected siblings display deviations from HWE when functional or markers in LD with functional locus are tested. For the parental genotype data all deviations from HWE are negative, indicating an excess of heterozygous genotypes with the strongest deviations from HWE observed for the multiplicative model. In contrast, for affected proband genotype data, there is no deviation from HWE under the multiplicative model and the deviations from HWE for the recessive model are positive. For the unaffected sibling data, patterns of deviation from HWE are similar to those observed in the proband data with the exception of the multiplicative model where the HWD coefficient although close to 0 can be either positive or negative depending on the allele frequency. <i>Conclusion:</i> Deviations from HWE in parental and unaffected sibling genotype data could be due to an association with the functional locus. However these deviations for genotypic relative risk ≤2.0 are not large and therefore the power to detect them is usually low. Testing for deviations from HWE in parental and unaffected sibling genotype data is still beneficial for quality control even though functional loci, in parental and unaffected sibling genotype data, can produce an association signal.
DOI: 10.6084/m9.figshare.5120545.v1
title: Supplementary Material for: High Molecular Weight Gingipains from <i>Porphyromonas gingivalis</i> Induce Cytokine Responses from Human Macrophage-Like Cells via a Nonproteolytic Mechanism

description: Periodontal disease is an oral inflammatory disease affecting the supporting structures of teeth. <i>Porphyromonas gingivalis</i>, a major pathogenic agent for the disease, expresses a number of virulence factors, including cysteine proteases called the gingipains. The arginine- and lysine-specific gingipains, HRgpA and Kgp, respectively, are expressed as high molecular weight forms containing both catalytic and adhesin subunits. We examined the expression pattern of cytokines and their receptors in differentiated macrophages following exposure to active and inactive forms of the gingipains, using a cDNA array, quantitative PCR and ELISA analysis. Amongst other pro-inflammatory cytokines, results from the cDNA array suggested that interleukin-1β, granulocyte-macrophage colony stimulatory factor and interferon-γ were upregulated after exposure of the macrophages to the gingipains. Quantitative PCR analysis substantiated these observations and indicated that active or inactive forms of the high molecular weight gingipains were able to upregulate expression of transcripts for these cytokines. The strongly enhanced production of interleukin-1β and granulocyte-macrophage colony stimulatory factor by differentiated macrophages in response to active or inactive forms of the high molecular weight gingipains was confirmed at the protein level by ELISA analysis. The results indicate that the adhesin subunits of the gingipains mediate strong upregulation of the expression of pro-inflammatory cytokines in macrophages.
DOI: 10.6084/m9.figshare.5120527
title: Supplementary Material for: The Central Kink Region of Fowlicidin-2, an α-Helical Host Defense Peptide, Is Critically Involved in Bacterial Killing and Endotoxin Neutralization

description: Fowlicidins are a group of newly identified chicken cathelicidin host defense peptides. We have shown that the putatively mature fowlicidin-2 of 31 amino acid residues possesses potent antibacterial and lipopolysaccharide (LPS)- neutralizing activities, but with a noticeable toxicity to mammalian cells. As a first step in exploring the structure-activity relationships of fowlicidin-2, in this study we determined its tertiary structure by nuclear magnetic resonance spectroscopy. Unlike the majority of cathelicidins, which are composed of a predominant α-helix with a short hinge sequence near the center, fowlicidin-2 consists of 2 well-defined α-helical segments (residues 6–12 and 23–27) connected by a long extensive kink (residues 13–20) induced by proline. To further investigate the functional significance of each of these structural components, several N- and C-terminal deletion analogs of fowlicidin-2 were synthesized and analyzed for their antibacterial, cytotoxic and LPS-neutralizing activities. Our results indicated that neither the N- nor C-terminal α-helix alone is sufficient to confer any function. Rather, fowlicidin-2(1–18) and fowlicidin-2(15–31), 2 α-helical segments with inclusion of the central cationic kink region, retained substantial capacities to kill bacteria and neutralize the LPS-induced proinflammatory response, relative to the parent peptide. More desirably, these 2 peptide analogs showed substantially reduced toxicity to human erythrocytes and epithelial cells, indicative of improved potential as antibacterial and antisepsis agents. To our knowledge, fowlicidin-2 is the first α-helical cathelicidin, with the central kink region shown to be critically important in killing bacteria and neutralizing LPS.
DOI: 10.6084/m9.figshare.5120530
title: Supplementary Material for: Health-Related Direct-to-Consumer Genetic Tests: A Public Health Assessment and Analysis of Practices Related to Internet-Based Tests for Risk of Thrombosis

description: <i>Background:</i> Recent years have seen increased concern about direct-to-consumer (DTC) genetic testing (i.e., the sale and use of genetic tests without involving a health care provider). Numerous professional organizations have developed policies in this area. However, little systematic evidence exists to inform public policy about these tests. <i>Methods:</i> We conducted a systematic search to identify genetic tests that are sold DTC without involving a health care provider. We evaluated the practices of companies offering DTC genetic tests for risk of thrombosis using criteria from multiple sources and a minimal set of key practices. <i>Results:</i> We identified 84 instances of currently available health-related DTC genetic tests sold on 27 Web sites; the most common were for pharmacogenomics (12), risk of thrombosis (10), and nutrigenomics (10). For the DTC genetic tests for risk of thrombosis, we found low adherence to recommendations. Online information was frequently incomplete and had low agreement with professional recommendations. <i>Conclusion:</i> Our findings document the rapid growth in the availability of health-related DTC genetic tests and highlight the need to improve the delivery of DTC genetic tests. A major implication of this study is the need for the scientific and medical community to develop consistent recommendations to increase their impact.
DOI: 10.6084/m9.figshare.5120536.v1
title: Supplementary Material for: Deviations from Hardy-Weinberg Equilibrium in Parental and Unaffected Sibling Genotype Data

description: <i>Background:</i> Genotyping error can increase both type I and II errors. In order to elucidate potential genotyping errors, data quality control often includes testing genotype data for deviations from Hardy-Weinberg Equilibrium (HWE). <i>Methods:</i> The Hardy-Weinberg Disequilibrium (HWD) coefficient and the ability to reject the null hypothesis of HWE were calculated analytically for genotype data from parents and unaffected siblings of affected probands. <i>Results:</i> Genotype data from parents and unaffected siblings display deviations from HWE when functional or markers in LD with functional locus are tested. For the parental genotype data all deviations from HWE are negative, indicating an excess of heterozygous genotypes with the strongest deviations from HWE observed for the multiplicative model. In contrast, for affected proband genotype data, there is no deviation from HWE under the multiplicative model and the deviations from HWE for the recessive model are positive. For the unaffected sibling data, patterns of deviation from HWE are similar to those observed in the proband data with the exception of the multiplicative model where the HWD coefficient although close to 0 can be either positive or negative depending on the allele frequency. <i>Conclusion:</i> Deviations from HWE in parental and unaffected sibling genotype data could be due to an association with the functional locus. However these deviations for genotypic relative risk ≤2.0 are not large and therefore the power to detect them is usually low. Testing for deviations from HWE in parental and unaffected sibling genotype data is still beneficial for quality control even though functional loci, in parental and unaffected sibling genotype data, can produce an association signal.
DOI: 10.6084/m9.figshare.5120539.v1
title: Supplementary Material for: Treating Histiocytic Necrotizing Lymphadenitis with Chinese Herbs: A Case Report

description: We present the case of a young woman who suffered from right cervical lymphadenopathy with associated malaise for 8 weeks. The sonography showed multiple, enlarged lymph nodes in the cervical, submaxillary, and subclavicular chains on the right side. The biopsy of a right cervical lymph node disclosed necrosis, histiocytic accumulation, infiltration with lymphocytes and immunoblasts, and cellular debris, demonstrating histiocytic necrotizing lymphadenitis (HNL). Although the patient had received treatment with dexamethasone for 5 weeks and antibiotic drugs for 6 weeks, the lymphadenopathy and the associated malaise had not improved. For fear of the side-effects caused by dexamethasone and the antibiotic drugs, the patient and her parents asked for treatment with Chinese herbs instead of dexamethasone and antibiotics. With the patient’s and her parents’ consent, the dose of dexamethasone was tapered according to its specifications and Chinese herbs were applied to treat her disease. After 6 weeks of orally administered Chinese herbs both the lymphadenopathy and the associated malaise disappeared. Follow-up by phone 6 months later showed no abnormality. Chinese medicinal herbs, as a natural treatment, can be used as an alternative in treating HNL.
DOI: 10.6084/m9.figshare.5120524
title: Supplementary Material for: Actin and Phosphoinositide Recruitment to Fully Formed <i>Candida albicans </i>Phagosomes in Mouse Macrophages

description: <i>Candida albicans</i> is a dimorphic yeast that enters macrophages (Mφ) via the β-glucan receptor dectin-1. Phagocytosis of <i>C. albicans</i> is characterized by actin polymerization, Syk kinase activation and rapid acquisition of phagolysosomal markers. In mice, <i>C. albicans</i> are able to resist the harsh environment of the phagosome and form pseudohyphae inside the phagolysosomal compartment, eventually extending from the Mφ. In this study, we investigated these unique <i>C. albicans </i>phagosomes and found that actin localized dynamically around the phagosomes, before disintegrating. Membrane phosphoinositides, PI(4,5)P<sub>2</sub>, PI(3,4,5)P<sub>3</sub>, PI(3,4)P<sub>2</sub>, and PI(3)P also localized to the phagosomes. Localization was not related to actin polymerization, and inhibitor studies showed that polymerization of actin on the <i>C. albicans</i> phagosome was independent of PI3K. The ability of mature <i>C. albicans</i> phagosomes to stimulate actin polymerization could facilitate the escape of the growing yeast from the Mφ.
DOI: 10.6084/m9.figshare.5120521
title: Supplementary Material for: Age-Distinct Predictors of Symptomatic Cervicocephalic Atherosclerosis

description: <i>Background:</i> Little is known about whether vascular risk factors predispose to atherosclerotic stroke depending on age. We evaluated predictors of large vessel atherosclerotic stroke (LVAS) stratified by age in two geographically and racially distinct study populations. <i>Methods:</i> Data collected over a 4-year period in prospectively maintained registries on 3,053 subjects with ischemic cerebrovascular events were analyzed: 1,982 patients from a hospital in South Korea and 1,071 patients admitted to a hospital in Los Angeles, Calif., USA. Independent vascular risk factor associations with LVAS mechanism were evaluated in three groups stratified by age (years) at symptom onset: young (≤50 years), older (51–75 years), and oldest (&gt;75 years). <i>Results:</i> Altogether at both study sites, 972 (31.8%) patients had LVAS mechanism, of whom 391 (40.2%) were female. Risk factor profiles were not significantly different between LVAS versus other stroke mechanisms. Among young patients, after adjusting for covariates, current smoking was the only predictor of atherosclerotic stroke at both Korean (OR 2.04; 95% CI: 1.13–3.69) and Californian sites (OR 4.78, 95% CI 1.54–14.89), while the metabolic syndrome was the only predictor of atherosclerotic stroke among the older patients (OR 1.58, 95% CI 1.17–2.12 for Korean; OR 1.75, 95% CI 1.07–2.84 for Californian), but not in the young or oldest groups. <i>Conclusions:</i> Across race and region, the estimated impact of vascular risk factors for LVAS varies by age, and this is most prominently seen among persons of less than 76 years of age. Some risk factors have an early effect (smoking) and others an effect that plays out over time.
DOI: 10.6084/m9.figshare.5120515
title: Supplementary Material for: Atresia of Proximal Coronary Arteries in Pulmonary Atresia with Intact Ventricular Septum – Fetal and Neonatal Findings

description: Pulmonary atresia with intact ventricular septum (PA+IVS) is a rare congenital cardiac malformation which is associated with ventriculocoronary arterial communications from the right ventricle. We present a case of PA+IVS with a bilateral atresia of the coronary ostia, and thus, a completely right ventricular-dependent coronary circulation followed up by fetal echocardiography. Eventually the infant died of myocardial infarction at 2 days of age.
DOI: 10.6084/m9.figshare.5120509
title: Supplementary Material for: Two faces of Solanaceae telomeres: a comparison between <i>Nicotiana</i> and <i>Cestrum</i> telomeres and telomere-binding proteins

description: While most Solanaceae genera (e.g.<i>Solanum, Nicotiana</i>) possess <i>Arabidopsis</i>-type telomeres of (TTTAGGG)n maintained by telomerase, the genera <i>Cestrum, Vestia</i> and <i>Sessea</i> (<i>Cestrum </i>group) lack these telomeres. Here we show that in the <i>Cestrum</i>-group the activity of telomerase has been lost. Nevertheless, proteins binding the single-stranded G-rich strand of the <i>Arabidopsis</i>-type and related human-type (TTAGGG)n telomeric sequences are present in nuclear extracts of both <i>Nicotiana</i> and <i>Cestrum </i>species. These proteins may have a role in telomere function or other cellular activities. In addition to characterizing DNA binding specificity and molecular weights of these proteins, we searched in both <i>N. tabacum </i>(tobacco) and <i>C. parqui </i>for the presence of POT1-like proteins, involved in telomere capping and telomerase regulation. Analysis of POT1-like proteins available on public databases and cloned by us from <i>C. parqui, </i>revealed the N-terminal OB folds typical for this protein family and a novel, plant-specific conserved C-terminal OB-fold domain (CTOB). We propose that CTOB is involved in protein-protein interactions.
DOI: 10.6084/m9.figshare.5120512
title: Supplementary Material for: Gene Expression Profiles in Murine Influenza Pneumonia

description: <i>Background:</i> Many in vitro studies have focused on gene expression in influenza-infected leukocytes, lung tissue or cell lines. However, knowledge of in vivo gene expression in these compartments is limited. <i>Methods:</i> To obtain insight into gene expression profiles during influenza infection, we determined the expression of multiple genes by using a newly developed mouse-specific multiplex ligation-dependent probe amplification assay. <i>Results:</i> The genes involved in inflammation, Toll-like receptor signaling, coagulation, fibrinolysis, cell adhesion, tissue repair and homeostasis were measured in lung tissue, leukocytes in bronchoalveolar lavage fluid and tracheal epithelial cells in mice, before and after intranasal infection with influenza A. Most of the genes investigated were differentially expressed during the course of infection and returned to baseline levels when mice had recovered from the infection. However, expression of several genes remained altered even though mice had completely cleared the virus. <i>Conclusion:</i> These data provide the first information on compartmentalized gene expression profiles in the respiratory tract during influenza.
DOI: 10.6084/m9.figshare.5120515.v1
title: Supplementary Material for: Atresia of Proximal Coronary Arteries in Pulmonary Atresia with Intact Ventricular Septum – Fetal and Neonatal Findings

description: Pulmonary atresia with intact ventricular septum (PA+IVS) is a rare congenital cardiac malformation which is associated with ventriculocoronary arterial communications from the right ventricle. We present a case of PA+IVS with a bilateral atresia of the coronary ostia, and thus, a completely right ventricular-dependent coronary circulation followed up by fetal echocardiography. Eventually the infant died of myocardial infarction at 2 days of age.
DOI: 10.6084/m9.figshare.5120518
title: Supplementary Material for: Singing and Science

description: Starting out from Manuel Garcia, attention is paid to the work of outstanding personalities having excelled both in performing arts as singers as well as in scientific elaborations. The main focus will be on two aspects: the controversies about the principles of voice production as provoked by Raoul Husson and his revolutionary ideas, and the influence of the vocal tract on the formation of the sound of the voice. Both of these topics offer the opportunity of referring to the basic contributions of the Groningen voice research pioneers Janwillem van den Berg and his scholar Harm Schutte. For the online edition, supplementary material in the form of video and audio clips contributes to a kaleidoscopic compilation of a series of selected fragments representing the fascinating field of the human voice.
DOI: 10.6084/m9.figshare.5120506
title: Supplementary Material for: Telomeres, histone code, and DNA damage response

description: Genomic stability is maintained by telomeres, the end terminal structures that protect chromosomes from fusion or degradation. Shortening or loss of telomeric repeats or altered telomere chromatin structure is correlated with telomere dysfunction such as chromosome end-to-end associations that could lead to genomic instability and gene amplification. The structure at the end of telomeres is such that its DNA differs from DNA double strand breaks (DSBs) to avoid nonhomologous end-joining (NHEJ), which is accomplished by forming a unique higher order nucleoprotein structure. Telomeres are attached to the nuclear matrix and have a unique chromatin structure. Whether this special structure is maintained by specific chromatin changes is yet to be thoroughly investigated. Chromatin modifications implicated in transcriptional regulation are thought to be the result of a code on the histone proteins (histone code). This code, involving phosphorylation, acetylation, methylation, ubiquitylation, and sumoylation of histones, is believed to regulate chromatin accessibility either by disrupting chromatin contacts or by recruiting non-histone proteins to chromatin. The histone code in which distinct histone tail-protein interactions promote engagement may be the deciding factor for choosing specific DSB repair pathways. Recent evidence suggests that such mechanisms are involved in DNA damage detection and repair. Altered telomere chromatin structure has been linked to defective DNA damage response (DDR), and eukaryotic cells have evolved DDR mechanisms utilizing proficient DNA repair and cell cycle checkpoints in order to maintain genomic stability. Recent studies suggest that chromatin modifying factors play a critical role in the maintenance of genomic stability. This review will summarize the role of DNA damage repair proteins specifically ataxia-telangiectasia mutated (ATM) and its effectors and the telomere complex in maintaining genome stability.
DOI: 10.6084/m9.figshare.5120512.v1
title: Supplementary Material for: Gene Expression Profiles in Murine Influenza Pneumonia

description: <i>Background:</i> Many in vitro studies have focused on gene expression in influenza-infected leukocytes, lung tissue or cell lines. However, knowledge of in vivo gene expression in these compartments is limited. <i>Methods:</i> To obtain insight into gene expression profiles during influenza infection, we determined the expression of multiple genes by using a newly developed mouse-specific multiplex ligation-dependent probe amplification assay. <i>Results:</i> The genes involved in inflammation, Toll-like receptor signaling, coagulation, fibrinolysis, cell adhesion, tissue repair and homeostasis were measured in lung tissue, leukocytes in bronchoalveolar lavage fluid and tracheal epithelial cells in mice, before and after intranasal infection with influenza A. Most of the genes investigated were differentially expressed during the course of infection and returned to baseline levels when mice had recovered from the infection. However, expression of several genes remained altered even though mice had completely cleared the virus. <i>Conclusion:</i> These data provide the first information on compartmentalized gene expression profiles in the respiratory tract during influenza.