cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5122591
title: Supplementary Material for: A Simultaneous Iris Angiography Technique in Pigmented Rabbits

description: <i>Purpose:</i> To report a simultaneous iris angiography (IA) technique combined with the use of indocyanine green (ICG) and fluorescein sodium (FS) in pigmented rabbits. <i>Methods:</i> 15 rabbits were randomly divided into 3 groups according to the dye doses: the dose of the lower-volume group was 2 mg FS and 2 mg ICG; the dose of the moderate-volume group was 5 mg FS and 5 mg ICG, and the dose of the higher-volume group was 8 mg FS and 8 mg ICG. Fifteen IAs were performed by a confocal scanning laser ophthalmoscope and a rapid localization technique giving a flat-on image. <i>Results:</i> Simultaneous digital angiography provided two kinds of a fully dynamic video of iris vessels fluorescein in all pigmented rabbits, which is the same in pigmented and albino rabbits and no vascular pattern was hidden by the iris stromal pigment. Furthermore, dye doses influenced the IA effect in rabbits. The lower-volume dye can demonstrate iris vessels, without obvious leakage, which, however, extinguish rapidly after 10–15 s. In the higher-volume group, vascular imaging lasted longer, but subsequently significant FS and ICG leakage appeared as streams on the surface of the iris until the dye disappeared from the iris vessels; the diffuse and intense aqueous fluid lasted 1 day. The moderate-volume dye displayed vessels clearly by ICG for 300 s, without leakage; FS clear vessels were maintained for about 15–20 s and the structure of the iris became fuzzy due to quick leakage. <i>Conclusions:</i> Simultaneous IA with a rapid localization technique allows high-quality imaging of the pigmented rabbits and the moderate dosage of 5 mg FS and 5 mg ICG is preferred for best visualization.
DOI: 10.6084/m9.figshare.5122582
title: Supplementary Material for: Importance of Toll-Like Receptor 9 in Host Defense against M1T1 Group A <i>Streptococcus </i>Infections

description: Timely recognition and elimination of invasive group A <i>Streptococcus</i> (GAS) by innate immunity is crucial to control infection. The intracellular pattern recognition receptor Toll-like receptor 9 (TLR9) promotes macrophage hypoxia-inducible factor-1α levels, oxidative burst and nitric oxide production in response to GAS. TLR9 contributes to GAS clearance in vivo in both localized cutaneous and systemic infection models.
DOI: 10.6084/m9.figshare.5122588
title: Supplementary Material for: Her-2/neu Overexpression Due to Polysomy 17 in Breast Cancer: Molecular Testing to Guide Therapeutic Options

description: <i>Background:</i> Fluorescent in situ hybridization (FISH) equivocal results for Her-2/neu still pose a diagnostic dilemma in oncology practice. In this study, we evaluate if Her-2/neu mRNA expression is an alternative to FISH for detecting Her-2/neu positivity. <i>Patients and Methods:</i> Archival paraffin blocks of 54 breast cancer patients were analyzed for Her-2/neu status using immunohistochemistry (IHC), FISH, and Her-2/neu gene expression using mRNA. <i>Results:</i> There was a 100% positive agreement and 64.7% negative agreement of Her-2/neu mRNA expression with respect to the reference standard (FISH), with the kappa value for agreement being 0.36. mRNA levels correlated positively and strongly with FISH ratio and IHC positivity. For Her-2/neu mRNA expression, Her-2/neu copy number was a significant predictor indicating that mRNA expression is independent of polysomy status. <i>Conclusions:</i> Her-2/neu mRNA expression may help tide over ambiguity posed by polysomy and FISH equivocal samples.
DOI: 10.6084/m9.figshare.5122576
title: Supplementary Material for: Macroscopic Analysis of Human Masseter Compartments Assessed by Magnetic Resonance Imaging

description: The human masseter is divided into compartments by aponeuroses. So far, the qualitative and quantitative features of these compartments and their aponeuroses have been scarcely investigated. This study investigated the three-dimensional compartmentalization of the masseter muscle and tested the hypothesis that aponeurosis content varies systematically across different masseter subportions as well as between genders. The right masseter of 14 healthy participants was scanned by magnetic resonance, and the outlines of muscle and aponeuroses were segmented and rendered in three dimensions by AMIRA software. The internal architecture of the masseter muscle varied markedly across individuals, with respect to the number, shape and location of the compartments delimited by aponeuroses. Aponeuroses were widely represented inside the masseter, amounting to 7.1 ± 2.1% of its volume. The aponeurosis content varied systematically across masseter subvolumes and did not differ between genders after adjusting for body height and weight.
DOI: 10.6084/m9.figshare.5122585
title: Supplementary Material for: Genetic Variations in the Dopamine System and Facial Expression Recognition in Healthy Chinese College Students

description: <i>Objective:</i> This study investigated the relation between genetic variations in the dopamine system and facial expression recognition. <i>Methods:</i> A sample of Chinese college students (n = 478) was given a facial expression recognition task. Subjects were genotyped for 98 loci [96 single-nucleotide polymorphisms (SNPs) and 2 variable number tandem repeats] in 16 genes involved in the dopamine neurotransmitter system, including its 4 subsystems: synthesis<i> (TH, DDC,</i> and <i>DBH)</i>, degradation/transport <i>(COMT,</i><i>MAOA,</i><i>MAOB,</i> and <i>SLC6A3)</i>, receptors<i> (DRD1,</i><i>DRD2,</i><i>DRD3,</i><i>DRD4,</i> and <i>DRD5)</i>, and modulation <i>(NTS,</i><i>NTSR1,</i><i>NTSR2,</i> and <i>NLN)</i>. To quantify the total contributions of the dopamine system to emotion recognition, we used a series of multiple regression models. Permutation analyses were performed to assess the posterior probabilities of obtaining such results. <i>Results:</i> Among the 78 loci that were included in the final analyses (after excluding 12 SNPs that were in high linkage disequilibrium and 8 that were not in Hardy-Weinberg equilibrium), 1 (for fear), 3 (for sadness), 5 (for anger), 13 (for surprise), and 15 (for disgust) loci exhibited main effects on the recognition of facial expressions. Genetic variations in the dopamine system accounted for 3% for fear, 6% for sadness, 7% for anger, 10% for surprise, and 18% for disgust, with the latter surviving a stringent permutation test. <i>Conclusions:</i> Genetic variations in the dopamine system (especially the dopamine synthesis and modulation subsystems) made significant contributions to individual differences in the recognition of disgust faces.
DOI: 10.6084/m9.figshare.5122579
title: Supplementary Material for: Interaction Studies of an Anticancer Alkaloid, (+)-(13aS)-Deoxytylophorinine, with Calf Thymus DNA and Four Repeated Double-Helical DNAs

description: <i>Background:</i> Phenanthroindolizidine alkaloids are a family of plant-derived compounds with significant antineoplastic activity. The specific biomolecular targets of these alkaloids have not yet been clearly identified. (+)-(13aS)-deoxytylophorinine is a new phenanthroindolizidine alkaloid originally extracted from the roots of <i>Tylophora atrofolliculat</i>a and <i>Tylophora ovata</i> in our institute. (+)-(13aS)-deoxytylophorinine exerts both in vitro and in vivoanticancer activities. <i>Methods:</i> The in vivo anticancer effects and toxicity of this compound were investigated in mice, and interactions between this compound and double-helical DNA sequences were studied in detail with circular dichroic spectroscopy and fluorescence spectroscopy. Viscosity measurements were applied to check the interactive mode between this compound and DNA. <i>Results:</i> Potent anticancer effects were observed in vivo. Also, concentration-dependent interactions were observed and this compound seemed to interact in a sequence-specific manner with AT-repeated sequences of double-helical DNA. Such interactions were proved to be intercalating by viscosity measurements. <i>Conclusions:</i> Anticancer alkaloid (+)-(13aS)-deoxytylophorinine can have sequence-specific interactions with DNA in an intercalating manner.
DOI: 10.6084/m9.figshare.5122579.v1
title: Supplementary Material for: Interaction Studies of an Anticancer Alkaloid, (+)-(13aS)-Deoxytylophorinine, with Calf Thymus DNA and Four Repeated Double-Helical DNAs

description: <i>Background:</i> Phenanthroindolizidine alkaloids are a family of plant-derived compounds with significant antineoplastic activity. The specific biomolecular targets of these alkaloids have not yet been clearly identified. (+)-(13aS)-deoxytylophorinine is a new phenanthroindolizidine alkaloid originally extracted from the roots of <i>Tylophora atrofolliculat</i>a and <i>Tylophora ovata</i> in our institute. (+)-(13aS)-deoxytylophorinine exerts both in vitro and in vivoanticancer activities. <i>Methods:</i> The in vivo anticancer effects and toxicity of this compound were investigated in mice, and interactions between this compound and double-helical DNA sequences were studied in detail with circular dichroic spectroscopy and fluorescence spectroscopy. Viscosity measurements were applied to check the interactive mode between this compound and DNA. <i>Results:</i> Potent anticancer effects were observed in vivo. Also, concentration-dependent interactions were observed and this compound seemed to interact in a sequence-specific manner with AT-repeated sequences of double-helical DNA. Such interactions were proved to be intercalating by viscosity measurements. <i>Conclusions:</i> Anticancer alkaloid (+)-(13aS)-deoxytylophorinine can have sequence-specific interactions with DNA in an intercalating manner.
DOI: 10.6084/m9.figshare.5122582.v1
title: Supplementary Material for: Importance of Toll-Like Receptor 9 in Host Defense against M1T1 Group A <i>Streptococcus </i>Infections

description: Timely recognition and elimination of invasive group A <i>Streptococcus</i> (GAS) by innate immunity is crucial to control infection. The intracellular pattern recognition receptor Toll-like receptor 9 (TLR9) promotes macrophage hypoxia-inducible factor-1α levels, oxidative burst and nitric oxide production in response to GAS. TLR9 contributes to GAS clearance in vivo in both localized cutaneous and systemic infection models.
DOI: 10.6084/m9.figshare.5122585.v1
title: Supplementary Material for: Genetic Variations in the Dopamine System and Facial Expression Recognition in Healthy Chinese College Students

description: <i>Objective:</i> This study investigated the relation between genetic variations in the dopamine system and facial expression recognition. <i>Methods:</i> A sample of Chinese college students (n = 478) was given a facial expression recognition task. Subjects were genotyped for 98 loci [96 single-nucleotide polymorphisms (SNPs) and 2 variable number tandem repeats] in 16 genes involved in the dopamine neurotransmitter system, including its 4 subsystems: synthesis<i> (TH, DDC,</i> and <i>DBH)</i>, degradation/transport <i>(COMT,</i><i>MAOA,</i><i>MAOB,</i> and <i>SLC6A3)</i>, receptors<i> (DRD1,</i><i>DRD2,</i><i>DRD3,</i><i>DRD4,</i> and <i>DRD5)</i>, and modulation <i>(NTS,</i><i>NTSR1,</i><i>NTSR2,</i> and <i>NLN)</i>. To quantify the total contributions of the dopamine system to emotion recognition, we used a series of multiple regression models. Permutation analyses were performed to assess the posterior probabilities of obtaining such results. <i>Results:</i> Among the 78 loci that were included in the final analyses (after excluding 12 SNPs that were in high linkage disequilibrium and 8 that were not in Hardy-Weinberg equilibrium), 1 (for fear), 3 (for sadness), 5 (for anger), 13 (for surprise), and 15 (for disgust) loci exhibited main effects on the recognition of facial expressions. Genetic variations in the dopamine system accounted for 3% for fear, 6% for sadness, 7% for anger, 10% for surprise, and 18% for disgust, with the latter surviving a stringent permutation test. <i>Conclusions:</i> Genetic variations in the dopamine system (especially the dopamine synthesis and modulation subsystems) made significant contributions to individual differences in the recognition of disgust faces.
DOI: 10.6084/m9.figshare.5122564
title: Supplementary Material for: Circulating Sex Hormones Modulate Vascular Contractions and Acute Response to 17β-Estradiol in Rat Mesenteric Arteries

description: <i>Aims:</i> We investigated how modification of levels of the sex hormones 17β-estradiol and testosterone affects vascular contraction and nongenomic vascular effects of 17β-estradiol. <i>Methods:</i> Male and female rats were treated with vehicle, 17β-estradiol (25 µg/kg/day) or testosterone (1 mg/kg/day) for 14 consecutive days after sham gonadectomy or gonadectomy was performed. Isometric tensions were then measured from mesenteric arteries of each group of rats. <i>Results:</i> Contraction to phenylephrine was increased in mesenteric arteries from rats with or without gonadectomy treated with testosterone for 14 days compared to their intact controls. Contraction to phenylephrine was reduced in mesenteric arteries of rats with or without gonadectomy treated with 17β-estradiol for 14 days compared to their intact controls. Incubation of mesenteric arteries with 17β-estradiol (1 nmol/l) for 30 min reduced contraction to phenylephrine in mesenteric arteries of rats that were treated with testosterone for 14 days. This acute incubation of 17β-estradiol had no effect on arteries from rats that were treated with 17β-estradiol for 14 days. The acute effect of 17β-estradiol (1 nmol/l) is preserved in arteries without endothelium. <i>Conclusion:</i> Our results suggest that 14 days’ testosterone treatment enhances while 14 days’ 17β-estradiol treatment suppresses contraction as well as the nongenomic effects of 17β-estradiol in the vascular smooth muscles.
DOI: 10.6084/m9.figshare.5122567
title: Supplementary Material for: Genome-Wide Analysis of <i>Sox</i> Genes in Medaka <i>(Oryzias latipes)</i> and Their Expression Pattern in Embryonic Development

description: Genes of the Sox family encode evolutionarily conserved high-mobility group box containing transcription factors, which play key roles in various events of developmental contexts. In this study, we identified 15 <i>sox</i> genes by searching for the high-mobility group domain in the medaka genome and by polymerase chain reaction using primers designed from the results obtained from homology protein alignment. All medaka <i>sox</i> genes except a novel <i>sox</i> gene, <i>Olsox32</i>, are encoded in 5 groups as follows: 4 <i>sox</i> genes in group B; 3 <i>sox</i> genes in group D and F, respectively; 2 <i>sox</i> genes in group C and E, respectively, while no <i>sox</i> genes were found in groups A, G, H, I, and J. The medaka <i>Olsox32</i> does not fall within any of the previously defined groups A–J. Here we have assigned it to a new group K. Together with the Sox protein sequences of other species, the phylogenetic relationship was analyzed and compared. Our findings point to recent <i>sox</i> gene loss, duplication and divergence occurring during the evolution of tetrapod and teleost lineages. The expression pattern shows that <i>sox</i> genes play a variety of roles in the early embryonic development of medaka.
DOI: 10.6084/m9.figshare.5122570
title: Supplementary Material for: Overexpression of <i>Lis1</i> in Different Stages of Spermatogenesis Does Not Result in an Aberrant Phenotype

description: Previous studies showed that in the mouse mutant <i>Lis1</i><sup>GT/GT</sup> gene trap integration in intron 2 of <i>Lis1</i> gene leads to male infertility in homozygous <i>Lis1</i><sup>GT/GT</sup> mice. We further analyzed this line and could confirm the suggested downregulation of a testis-specific <i>Lis1</i> transcript in mutant animals in a quantitative manner. Moreover, we analyzed the gene trap mutation on different genetic backgrounds in incipient congenic animals and could exclude a genetic background effect. To gain further insights into the role and requirement of LIS1 in spermatogenesis, 3 transgenic lines were generated, that overexpress <i>Lis1</i> under control of the testis-specific promoters <i>hEF-1</i>α, which is exclusively active in spermatogonial cells, <i>PGK2</i>, which is active in pachytene spermatocytes and following stages of spermatogenesis, and <i>Tnp2</i> which is active in round spermatids and following stages of spermatogenesis, respectively. All 3 transgenic lines remained fertile and testis sections displayed no abnormalities. To overcome the infertility of <i>Lis1</i><sup>GT/GT</sup> males, these transgenic <i>Lis1</i>-overexpressing animals were mated with <i>Lis1</i><sup>GT/GT</sup> mice to generate ‘rescued’ <i>Lis1</i><sup>GT/GT</sup><i>/Lis1</i><sup>Tpos</sup> males. ‘Rescued’ animals from all transgenic lines remained infertile, thus overexpression of <i>Lis1</i> in different stages of spermatogenesis could not rescue the infertility phenotype of homozygous gene trap males.
DOI: 10.6084/m9.figshare.5122573
title: Supplementary Material for: The Evolutionary History of TLR4 Polymorphisms in Europe

description: Infections exert important evolutionary pressures shaping the human genome, especially on genes involved in host defense. A crucial step for host defense is recognition of pathogens by pattern recognition receptors on innate immune cells, among which Toll-like receptor 4 (<i>TLR4)</i> is one of the best known. Genetic variation in <i>TLR4</i> (Asp299Gly, Thr399Ile) has been recently described. Haplotype frequencies of these polymorphisms differ among African, Asian and European populations, suggesting evolutionary pressures exerted by local infections. The <i>TLR4</i> 299Gly/399Ile haplotype, characteristic mainly of European populations, has relatively high frequency in the Iberian peninsula. This region is also described as refuge area during the last glacial maximum 20,000 years ago, from which repopulation of Europe took place. We speculate that a genetic bottleneck in the Iberian peninsula could have promoted the increased frequency of this haplotype by genetic drift. This hypothesis is supported by three arguments: (1) the West-East gradient of prevalence in the haplotype among European populations; (2) ancient DNA from Neolithic burials in the Iberian peninsula, dated 6,600–4,500 years before present, confirmed the relatively high frequency of this haplotype in the region, and (3) no functional differences between this haplotype and wild-type <i>TLR4</i> have been found. In contrast, the disappearance of the 299Gly/399Thr haplotype in Europe is most likely due to negative selection due to sepsis. In conclusion, differences in distribution of <i>TLR4</i> polymorphisms Asp299Gly and Thr399Ile in European populations are most likely due to a combination of population migration events combined with selection due to sepsis.
DOI: 10.6084/m9.figshare.5122564.v1
title: Supplementary Material for: Circulating Sex Hormones Modulate Vascular Contractions and Acute Response to 17β-Estradiol in Rat Mesenteric Arteries

description: <i>Aims:</i> We investigated how modification of levels of the sex hormones 17β-estradiol and testosterone affects vascular contraction and nongenomic vascular effects of 17β-estradiol. <i>Methods:</i> Male and female rats were treated with vehicle, 17β-estradiol (25 µg/kg/day) or testosterone (1 mg/kg/day) for 14 consecutive days after sham gonadectomy or gonadectomy was performed. Isometric tensions were then measured from mesenteric arteries of each group of rats. <i>Results:</i> Contraction to phenylephrine was increased in mesenteric arteries from rats with or without gonadectomy treated with testosterone for 14 days compared to their intact controls. Contraction to phenylephrine was reduced in mesenteric arteries of rats with or without gonadectomy treated with 17β-estradiol for 14 days compared to their intact controls. Incubation of mesenteric arteries with 17β-estradiol (1 nmol/l) for 30 min reduced contraction to phenylephrine in mesenteric arteries of rats that were treated with testosterone for 14 days. This acute incubation of 17β-estradiol had no effect on arteries from rats that were treated with 17β-estradiol for 14 days. The acute effect of 17β-estradiol (1 nmol/l) is preserved in arteries without endothelium. <i>Conclusion:</i> Our results suggest that 14 days’ testosterone treatment enhances while 14 days’ 17β-estradiol treatment suppresses contraction as well as the nongenomic effects of 17β-estradiol in the vascular smooth muscles.
DOI: 10.6084/m9.figshare.5122567.v1
title: Supplementary Material for: Genome-Wide Analysis of <i>Sox</i> Genes in Medaka <i>(Oryzias latipes)</i> and Their Expression Pattern in Embryonic Development

description: Genes of the Sox family encode evolutionarily conserved high-mobility group box containing transcription factors, which play key roles in various events of developmental contexts. In this study, we identified 15 <i>sox</i> genes by searching for the high-mobility group domain in the medaka genome and by polymerase chain reaction using primers designed from the results obtained from homology protein alignment. All medaka <i>sox</i> genes except a novel <i>sox</i> gene, <i>Olsox32</i>, are encoded in 5 groups as follows: 4 <i>sox</i> genes in group B; 3 <i>sox</i> genes in group D and F, respectively; 2 <i>sox</i> genes in group C and E, respectively, while no <i>sox</i> genes were found in groups A, G, H, I, and J. The medaka <i>Olsox32</i> does not fall within any of the previously defined groups A–J. Here we have assigned it to a new group K. Together with the Sox protein sequences of other species, the phylogenetic relationship was analyzed and compared. Our findings point to recent <i>sox</i> gene loss, duplication and divergence occurring during the evolution of tetrapod and teleost lineages. The expression pattern shows that <i>sox</i> genes play a variety of roles in the early embryonic development of medaka.
DOI: 10.6084/m9.figshare.5122558
title: Supplementary Material for: Use of Online Conductivity Monitoring to Study Sodium Mass Balance in Chronic Haemodialysis Patients: Prospects for Treatment Individualisation

description: <i>Background:</i> Failure to achieve isonatric haemodialysis (HD) drives an expansion of extracellular volume leading to increased interdialytic weight gain (IDWG). This may be a causative factor in the development of HD-induced cardiac injury. We examined total and diffusive sodium mass balance during HD. <i>Methods:</i> 24 chronic HD patients using a fixed 140 mmol/l sodium concentration were studied over 4 weeks. Dialysate and plasma conductivity and ionic mass balance (IMB) were recorded. IMB estimates total ionic transfer across the HD membrane. <i>Results:</i> Mean total IMB was 338 mmol indicating net sodium removal. Intrapatient variability was less than interpatient variability (coefficient of variation = 42 vs. 26%, respectively). The diffusive component of ionic mass balance (IMB<sub>diff</sub>) was 97 ± 18 mmol approximating 29% (±22–36) of total sodium removal. IMB<sub>diff</sub> also correlated with both plasma conductivity and predialysis plasma sodium (r<sup>2</sup> = 0.82 and 0.6, respectively; p &lt; 0.0001) as well as the reduction in plasma conductivity and plasma sodium during HD (r<sup>2</sup> = 0.7 and 0.5, respectively; p &lt; 0.0001). <i>Conclusion:</i> HD against a fixed dialysate sodium concentration of 140 mmol/l results in a wide range of sodium removal with a mean of 29% removed by diffusion. Online conductivity monitoring can be utilized as part of a variety of strategies to enable the delivery of individualised and isonatric HD. Further study is required to explore the utility of such strategies which may be crucial in reducing IDWG and HD-induced cardiac injury.