cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5121121.v1
title: Supplementary Material for: Cytogenetic Characterization and Fluorescence in situ Hybridization of (GATA)<sub>10</sub> Repeats on Established Primary Cell Cultures from Indian Water Snake <i>(Natrix piscator)</i> and Indian Mugger <i>(Crocodylus palustris)</i> Embryos

description: Sex determination among reptiles has continued to draw the attention of geneticists and the mechanisms involved have been extensively studied and documented in the past 3 decades. The setting up of primary cell lines of reptilian tissues is an important tool in the present study which is a unique aspect not applied in earlier studies. Establishing the cell lines from various species of reptiles would help in our understanding of the mechanisms of evolution and differentiation of sex chromosomes. Therefore, in the present study, we have established for the first time primary cell cultures from Indian water snake <i>(Natrix piscator)</i> and Indian mugger <i>(Crocodylus palustris)</i> embryos. In the preliminary growth stage, 2 types of cells, fibroblast- and epithelial-like, were found to be attached and proliferating in vitro. These fibroblast-like cell cultures were later overtaken by epithelial cells. The cell lines were grown in minimal essential medium supplemented with fetal bovine serum and subcultured for a period of 8–10 months. The morphology of cell types was kept under constant observation microscopically. Interestingly, at a subsequent passage of the cells sporadically scattered neuronal-like and beating cells were observed. The suitable temperature for growth of these cell cultures was 28–30°C. Chromosome analysis was performed from the actively proliferating cells, which revealed 5 pairs of macrochromosomes and 15 pairs of microchromosomes in <i>Natrix piscator,</i> and 15 pairs of only macrochromosomes in <i>Crocodylus palustris</i>. (GATA)<sub>n</sub> repeats are well known to be associated with sex chromosomes. Fluorescence in situ hybridization performed with (GATA)<sub>10</sub> repeats delineated the W chromosome in the cells of <i>Natrix piscator</i> which has so far not been reported. This cell culture method has presently only been applied to water snakes and crocodile embryos in the current study, but it will be employed in other reptilian species and could go a long way to being a sustainable source of primary cells. This would eventually serve as an important tool for molecular studies in reptiles and other species in the future.
DOI: 10.6084/m9.figshare.5121127
title: Supplementary Material for: Central Precocious Puberty due to Hypothalamic Hamartomas Correlates with Anatomic Features but Not with Expression of GnRH, TGFα, or <i>KISS1</i>

description: <i>Background/Aims:</i> Hypothalamic hamartomas are the most common identifiable cause of central precocious puberty (CPP). Hamartoma characteristics proposed to be associated with CPP include specific anatomic features and expression of molecules such as gonadotropin-releasing hormone (GnRH), transforming growth factor α (TGFα), and <i>GRM1A</i>, which encodes the type 1 metabotropic glutamate receptor α isoform. We sought to determine whether hamartomas that cause CPP could be distinguished by anatomic features, expression of these molecules, or expression of <i>KISS1</i>, whose products signal through the receptor GPR54 to stimulate GnRH release. <i>Methods:</i> Clinical records and radiologic images were reviewed for 18 patients who underwent hamartoma resection for intractable seizures; 7 had precocious puberty. Resected tissue was examined for expression of GnRH, GnRH receptor (GnRHR), TGFα, <i>KISS1</i>, <i>GPR54</i>, and <i>GRM1A</i>. <i>Results:</i> Hypothalamic hamartomas associated with CPP were more likely to contact the infundibulum or tuber cinereum and were larger than hamartomas not associated with CPP. GnRH, TGFα, and GnRHR were expressed by all hamartomas studied. Expression of <i>KISS1</i>, <i>GPR54</i>, and <i>GRM1A</i> did not differ significantly between hamartomas associated and not associated with CPP. <i>Conclusion:</i> Anatomic features rather than expression patterns of candidate molecules distinguish hypothalamic hamartomas that are associated with CPP from those that are not.
DOI: 10.6084/m9.figshare.5121115
title: Supplementary Material for: Cross-Talk between Human Dendritic Cell Subsets Influences Expression of RNA Sensors and Inhibits Picornavirus Infection

description: Dendritic cells (DCs) are professional antigen-presenting cells that provide a link between innate and adaptive immunity. Multiple DC subsets exist and their activation by microorganisms occurs through binding of conserved pathogen-derived structures to so-called pattern recognition receptors (PRRs). In this study we analyzed the expression of PRRs responding to viral RNA in human monocyte-derived DCs (moDCs) under steady-state or pro-inflammatory conditions. We found that mRNA and protein levels for most PRRs were increased under pro-inflammatory conditions, with the most pronounced increases in the RIG-like helicase (RLH) family. Additionally, freshly isolated human plasmacytoid DCs (pDCs) displayed significantly higher levels of TLR7, RIG-I, MDA5 and PKR as compared to myeloid DCs and moDCs. Finally, we demonstrate for the first time that cross-talk between TLR-matured or virus-stimulated pDCs and moDCs leads to a type I interferon-dependent antiviral state in moDCs. This antiviral state was characterized by enhanced RLH expression and protection against picornavirus infection. These findings might represent a novel mechanism by which pDCs can preserve the function and viability of myeloid DCs that are attracted to a site with ongoing infection, thereby optimizing the antiviral immune response.
DOI: 10.6084/m9.figshare.5121118.v1
title: Supplementary Material for: Synaptonemal Complex Protein SYCP3 Exists in Two Isoforms Showing Different Conservation in Mammalian Evolution

description: Meiosis-specific protein SYCP3 is a major structural component of synaptonemal complex (SC) lateral elements. SYCP3 is rather well conserved in vertebrates. However, some differences in SYCP3 expression have been shown among mammals. To clarifiy these differences, we have investigated SYCP3 expression with the aid of bioinformatic, biochemical and cell biological methods. Here we show that, in contrast to other vertebrates, rat and mouse SYCP3 exist in 2 isoforms. The short isoform is conserved among vertebrates. However, the longer isoform, which represents an N-terminal extension of the shorter one, most likely appeared about 15 million years ago in a common ancestor of rat and mouse and after separation from the hamster branch.
DOI: 10.6084/m9.figshare.5121106
title: Supplementary Material for: Stroke and Action Slowing: Mechanisms, Determinants and Prognosis Value

description: <i>Aim:</i> The present study aimed to determine the mechanisms and determinants of stroke-related action slowing. <i>Methods:</i> Thirty-six stroke patients not presenting any clinical motor deficit of the preferred hand (mean post-stroke delay 11 months) were compared to matched controls on Finger Tapping test (motor speed), Visual Inspection Time test (visual perceptual speed) and Simple and Choice Reaction Time tests. <i>Results:</i> Patients were slower on all tests except Choice Reaction Time: Visual Inspection (p = 0.003), Finger Tapping test (p = 0.001), Simple Reaction Time (p = 0.002) tests were impaired including performance measured with the ipsi-lesional hand. This pattern and the uniform lengthening across the entire reaction time distribution both suggest that psychomotor slowing was due to slowing of perceptual and motor processes. The main determinant of action slowing was lesion location: (1) Visual Inspection Time = right inferior parietal lobulus (OR 18, 95% CI 2.9–108); (2) Finger Tapping = left frontal middle gyrus (OR 18, 95% CI 2.9–108) and lenticular nucleus (OR 59, 95% CI 1.9–1,775), and (3) Simple Reaction Time = right lenticular nucleus (OR 110, 95% CI 8–1,490) and posterior fossa (OR 55, 95% CI 3.4–890). Finally poor outcome depended on Tapping Frequency measured with the contra-lesional index (OR 0.1, 95% CI 0.02–0.5; p = 0.0005) and impairment on the Token test (OR 151, 95% CI 2.24–1136; p = 0.02). <i>Conclusions:</i> This study shows that stroke-related action slowing is mainly due to slowing of perceptual and motor processes. Action slowing was related to lesions of the large network. Finally Tapping Frequency is an independent predictor of outcome. This supports that action slowing is an important consequence of stroke and that it is a promising prognosis index.
DOI: 10.6084/m9.figshare.5121109
title: Supplementary Material for: Nuclear Bud Formation: A Novel Manifestation of Zidovudine Genotoxicity

description: Normal diploid somatic mammalian cell division generates 2 daughter cells as a result of a strict and well-controlled mitotic process. However, some defects during the progression of that process could generate an unbalanced distribution of chromosomes, aneuploidy and eventually, a malignant phenotype. Previous observations using a transgenic mouse model with diminished DNA repair capacity revealed the presence of nuclear buds (NBs) induced in vitro by the nucleoside analog zidovudine (Retrovir®, 3′-azido-3′-deoxythymidine, AZT). Here we used bone marrow mesenchymal cells, taken from mice with the <i>Xpa</i><sup>–/–</sup><i>Trp53</i><sup>+/–</sup> genotype, that were cultured and exposed to 0 and 100 µ<i>M</i> AZT for 24 hours. Fixed and denatured cells were processed by fluorescence in situ hybridization (FISH) with whole chromosome painting probes used to identify chromosomes in cells growing on glass chamber slides (2 probes/slide). A variety of sizes and shapes of NBs were observed. Some NBs had a large connection with the main nucleus (&gt;¼ of the NB diameter), others hada smaller connection (
DOI: 10.6084/m9.figshare.5121115.v1
title: Supplementary Material for: Cross-Talk between Human Dendritic Cell Subsets Influences Expression of RNA Sensors and Inhibits Picornavirus Infection

description: Dendritic cells (DCs) are professional antigen-presenting cells that provide a link between innate and adaptive immunity. Multiple DC subsets exist and their activation by microorganisms occurs through binding of conserved pathogen-derived structures to so-called pattern recognition receptors (PRRs). In this study we analyzed the expression of PRRs responding to viral RNA in human monocyte-derived DCs (moDCs) under steady-state or pro-inflammatory conditions. We found that mRNA and protein levels for most PRRs were increased under pro-inflammatory conditions, with the most pronounced increases in the RIG-like helicase (RLH) family. Additionally, freshly isolated human plasmacytoid DCs (pDCs) displayed significantly higher levels of TLR7, RIG-I, MDA5 and PKR as compared to myeloid DCs and moDCs. Finally, we demonstrate for the first time that cross-talk between TLR-matured or virus-stimulated pDCs and moDCs leads to a type I interferon-dependent antiviral state in moDCs. This antiviral state was characterized by enhanced RLH expression and protection against picornavirus infection. These findings might represent a novel mechanism by which pDCs can preserve the function and viability of myeloid DCs that are attracted to a site with ongoing infection, thereby optimizing the antiviral immune response.
DOI: 10.6084/m9.figshare.5121127.v1
title: Supplementary Material for: Central Precocious Puberty due to Hypothalamic Hamartomas Correlates with Anatomic Features but Not with Expression of GnRH, TGFα, or <i>KISS1</i>

description: <i>Background/Aims:</i> Hypothalamic hamartomas are the most common identifiable cause of central precocious puberty (CPP). Hamartoma characteristics proposed to be associated with CPP include specific anatomic features and expression of molecules such as gonadotropin-releasing hormone (GnRH), transforming growth factor α (TGFα), and <i>GRM1A</i>, which encodes the type 1 metabotropic glutamate receptor α isoform. We sought to determine whether hamartomas that cause CPP could be distinguished by anatomic features, expression of these molecules, or expression of <i>KISS1</i>, whose products signal through the receptor GPR54 to stimulate GnRH release. <i>Methods:</i> Clinical records and radiologic images were reviewed for 18 patients who underwent hamartoma resection for intractable seizures; 7 had precocious puberty. Resected tissue was examined for expression of GnRH, GnRH receptor (GnRHR), TGFα, <i>KISS1</i>, <i>GPR54</i>, and <i>GRM1A</i>. <i>Results:</i> Hypothalamic hamartomas associated with CPP were more likely to contact the infundibulum or tuber cinereum and were larger than hamartomas not associated with CPP. GnRH, TGFα, and GnRHR were expressed by all hamartomas studied. Expression of <i>KISS1</i>, <i>GPR54</i>, and <i>GRM1A</i> did not differ significantly between hamartomas associated and not associated with CPP. <i>Conclusion:</i> Anatomic features rather than expression patterns of candidate molecules distinguish hypothalamic hamartomas that are associated with CPP from those that are not.
DOI: 10.6084/m9.figshare.5121100
title: Supplementary Material for: Expression of a Hypoxia-Associated Protein, Carbonic Anhydrase-9, Correlates with Malignant Phenotypes of Gastric Carcinoma

description: <i>Background/Aims:</i> Gastric cancers are characterized by a heterogeneously hypoxic environment. Hypoxia might stimulate the malignant potential of cancer cells. The purpose of our study was to clarify the significance of hypoxia in gastric carcinoma by evaluating the expression of a hypoxic marker, namely carbonic anhydrase-9 (CA-9). <i>Methods:</i> A total of 265 patients who had undergone a resection of the primary tumor and were confirmed histologically to have sporadic gastric cancer were enrolled in this study. We evaluated the immunohistochemical expression of CA-9 in the paraffin-embedded specimens of 265 gastric adenocarcinomas. <i>Results:</i> The CA-9 expression was positive in 88 (33%) of 265 gastric carcinomas. The CA-9 expression level was significantly high in cases of type 4 carcinoma (60%, p &lt; 0.001) and diffuse type carcinoma (41%, p &lt; 0.001), and significantly correlated with the invasion depth (p &lt; 0.001), lymph node metastasis (p &lt; 0.001) and lymphatic invasion p = 0.002). The prognosis for CA-9-positive patients was significantly poorer than that of CA-9-negative patients (p = 0.003, log-rank). <i>Conclusion:</i> Hypoxia might be associated with aggressive tumor phenotypes of gastric carcinomas. The hypoxic marker CA-9 may be a useful prognostic indicator.
DOI: 10.6084/m9.figshare.5121103
title: Supplementary Material for: Development and Validation of a Self-Administered Questionnaire for Myasthenia Gravis Patients

description: <i>Background:</i> To date, the investigation of the epidemiological profile of myasthenia gravis (MG) is sparse, and the influence of environmental and lifestyle factors on the occurrence of the disease remains thus unknown. The main aim of this study, which is part of a European collaborative project (EuroMyasthenia), was to develop a self-administered questionnaire to investigate these potential predisposing factors for MG. No instrument for investigating these particular factors has previously been designed for MG patients. <i>Material and Methods:</i> The questionnaire was developed in 3 stages: (1) devising a draft questionnaire based on questions derived from previously validated questionnaires and self-designed questions on MG characteristics; (2) testing the questionnaire on Norwegian MG patients (n = 57), and (3) assessing the content and criterion validity, and test-retest reliability, of the final questionnaire. <i>Results:</i> The questionnaire was easy to use and showed good feasibility for MG patients. Psychometric evaluation established the validity and reliability of the self-designed questions on MG characteristics. <i>Conclusion:</i> This is the first validated instrument developed to identify self-assessed environmental factors and potential predisposing factors for MG, and suitable for use in large-scale epidemiological studies.
DOI: 10.6084/m9.figshare.5121109.v1
title: Supplementary Material for: Nuclear Bud Formation: A Novel Manifestation of Zidovudine Genotoxicity

description: Normal diploid somatic mammalian cell division generates 2 daughter cells as a result of a strict and well-controlled mitotic process. However, some defects during the progression of that process could generate an unbalanced distribution of chromosomes, aneuploidy and eventually, a malignant phenotype. Previous observations using a transgenic mouse model with diminished DNA repair capacity revealed the presence of nuclear buds (NBs) induced in vitro by the nucleoside analog zidovudine (Retrovir®, 3′-azido-3′-deoxythymidine, AZT). Here we used bone marrow mesenchymal cells, taken from mice with the <i>Xpa</i><sup>–/–</sup><i>Trp53</i><sup>+/–</sup> genotype, that were cultured and exposed to 0 and 100 µ<i>M</i> AZT for 24 hours. Fixed and denatured cells were processed by fluorescence in situ hybridization (FISH) with whole chromosome painting probes used to identify chromosomes in cells growing on glass chamber slides (2 probes/slide). A variety of sizes and shapes of NBs were observed. Some NBs had a large connection with the main nucleus (&gt;¼ of the NB diameter), others hada smaller connection (
DOI: 10.6084/m9.figshare.5121097
title: Supplementary Material for: Macrophage Response to Apoptotic Cells Varies with the Apoptotic Trigger and Is Not Altered by a Deficiency in LRP Expression

description: Rapid engulfment of apoptotic cells in the absence of inflammation is required for maintenance of normal tissue homeostasis. The low-density lipoprotein receptor-related protein-1 (LRP/CD91) is a receptor mediating interactions between macrophages and apoptotic cells, but recent reports have challenged the requirement of this surface protein in this process. To explore the role of LRP in the recognition of apoptotic cells, target cells were generated with two distinct inducers of apoptotic cell death, etoposide and actinomycin-D. Jurkat T cells rendered apoptotic with etoposide exposed phosphatidylserine (PtdSer) and triggered engulfment by murine bone marrow-derived macrophages (BMDM), however they failed to suppress lipopolysaccharide-driven inflammatory cytokine secretion or, correspondingly, NFĸB-dependent or TNFα promoter-driven transcriptional activity in transfected RAW264.7 macrophages. In contrast, induction of apoptosis in either Jurkat cells or HeLa epithelial cells with actinomycin-D resulted in diminution of proinflammatory signaling from RAW264.7 cells and BMDM. Treatment of actinomycin-treated Jurkat cells with Q-VD-OPh, an irreversible inhibitor of caspase activity, blocked apoptosis, as assessed by the inhibition of PtdSer exposure; however, the cells maintained anti-inflammatory activity. Anti-inflammatory signaling mediated by actinomycin-treated cells was not affected by a macrophage-specific deletion in LRP. Moreover, the presence of LRP on macrophages did not alter the efficiency of engulfment of apoptotic cells in vitro or in vivo. These data demonstrate that the method of induction of apoptosis of target cells influences subsequent macrophage responsiveness, and that LRP is not required for engulfment of apoptotic cells regardless of the method of induction.
DOI: 10.6084/m9.figshare.5121106.v1
title: Supplementary Material for: Stroke and Action Slowing: Mechanisms, Determinants and Prognosis Value

description: <i>Aim:</i> The present study aimed to determine the mechanisms and determinants of stroke-related action slowing. <i>Methods:</i> Thirty-six stroke patients not presenting any clinical motor deficit of the preferred hand (mean post-stroke delay 11 months) were compared to matched controls on Finger Tapping test (motor speed), Visual Inspection Time test (visual perceptual speed) and Simple and Choice Reaction Time tests. <i>Results:</i> Patients were slower on all tests except Choice Reaction Time: Visual Inspection (p = 0.003), Finger Tapping test (p = 0.001), Simple Reaction Time (p = 0.002) tests were impaired including performance measured with the ipsi-lesional hand. This pattern and the uniform lengthening across the entire reaction time distribution both suggest that psychomotor slowing was due to slowing of perceptual and motor processes. The main determinant of action slowing was lesion location: (1) Visual Inspection Time = right inferior parietal lobulus (OR 18, 95% CI 2.9–108); (2) Finger Tapping = left frontal middle gyrus (OR 18, 95% CI 2.9–108) and lenticular nucleus (OR 59, 95% CI 1.9–1,775), and (3) Simple Reaction Time = right lenticular nucleus (OR 110, 95% CI 8–1,490) and posterior fossa (OR 55, 95% CI 3.4–890). Finally poor outcome depended on Tapping Frequency measured with the contra-lesional index (OR 0.1, 95% CI 0.02–0.5; p = 0.0005) and impairment on the Token test (OR 151, 95% CI 2.24–1136; p = 0.02). <i>Conclusions:</i> This study shows that stroke-related action slowing is mainly due to slowing of perceptual and motor processes. Action slowing was related to lesions of the large network. Finally Tapping Frequency is an independent predictor of outcome. This supports that action slowing is an important consequence of stroke and that it is a promising prognosis index.
DOI: 10.6084/m9.figshare.5121103.v1
title: Supplementary Material for: Development and Validation of a Self-Administered Questionnaire for Myasthenia Gravis Patients

description: <i>Background:</i> To date, the investigation of the epidemiological profile of myasthenia gravis (MG) is sparse, and the influence of environmental and lifestyle factors on the occurrence of the disease remains thus unknown. The main aim of this study, which is part of a European collaborative project (EuroMyasthenia), was to develop a self-administered questionnaire to investigate these potential predisposing factors for MG. No instrument for investigating these particular factors has previously been designed for MG patients. <i>Material and Methods:</i> The questionnaire was developed in 3 stages: (1) devising a draft questionnaire based on questions derived from previously validated questionnaires and self-designed questions on MG characteristics; (2) testing the questionnaire on Norwegian MG patients (n = 57), and (3) assessing the content and criterion validity, and test-retest reliability, of the final questionnaire. <i>Results:</i> The questionnaire was easy to use and showed good feasibility for MG patients. Psychometric evaluation established the validity and reliability of the self-designed questions on MG characteristics. <i>Conclusion:</i> This is the first validated instrument developed to identify self-assessed environmental factors and potential predisposing factors for MG, and suitable for use in large-scale epidemiological studies.