cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5123305.v1
title: Supplementary Material for: Excision of Nonpalpable Breast Cancer with Indocyanine Green Fluorescence-Guided Occult Lesion Localization (IFOLL)

description: <i>Background: </i>Currently employed techniques for the localization of nonpalpable breast lesions suffer from various limitations. In this paper, we report on 2 patients in order to introduce an alternative technique, indocyanine green fluorescence-guided occult lesion localization (IFOLL), and determine its applicability for the surgical removal of this type of breast lesions. <i>Case Reports: </i>Preoperatively, one of the patients had a needle biopsyproven diagnosis of breast cancer, and the other one had suspicious findings for malignancy. Lesion localization was performed within 1 h before surgery under ultrasonography control by injecting 2 ml and 0.2 ml of indocyanine green into the lesion and its subcutaneous tissue projection, respectively. During surgery, the site of skin incision and the resection margins were identified by observing the area of indocyanine-derived fluorescence under the guidance of a near-infrared-sensitive camera. In both cases, the breast lesion was correctly localized, and the area of fluorescence corresponded well to the site of the lesions. Subsequent surgical excision was successful with no complications. On histopathologic examination, the surgical margins were found to be clear. <i>Conclusion: </i>IFOLL seems to be a technically applicable and clinically acceptable procedure for the removal of nonpalpable breast cancer.
DOI: 10.6084/m9.figshare.5123293
title: Supplementary Material for: PPARγ2 Gene Pro12Ala and PPARα Gene Leu162Val Single Nucleotide Polymorphisms Interact with Dietary Intake of Fat in Determination of Plasma Lipid Concentrations

description: <i>Background/Aims:</i> The peroxisome proliferator-activated receptors (PPARs) are transcriptional regulators of lipid metabolism, activated by unsaturated fatty acids. We investigated independent and interactive effects of PPARγ2 gene <i>PPARG </i>Pro12Ala (rs1801282) andPPARαgene<i> PPARA </i>Leu162Val (rs1800206) genotypes with dietary intake of fatty acids on concentrations of plasma lipids in subjects of whom 47.5% had metabolic syndrome. <i>Methods:</i> The RISCK study is a parallel design, randomised controlled trial. Plasma lipids were quantified at baseline after a 4-week high saturated fatty acids diet and after three parallel 24-week interventions with reference (high saturated fatty acids), high monounsaturated fatty acids and low-fat diets. Single nucleotide polymorphisms were genotyped in 466 subjects. <i>Results:</i> At baseline, the<i> PPARG</i> Ala12allele was associated with increased plasma total cholesterol (n = 378; p = 0.04), LDL cholesterol (p = 0.05) and apoB (p =0.05) after adjustment for age, gender and ethnicity. At baseline, <i>PPARA</i> Leu162Val × <i>PPARG</i> Pro12Ala genotype interaction did not significantly influence plasma lipid concentrations. After dietary intervention, gene-gene interaction significantly influenced LDL cholesterol (p =0.0002) and small dense LDL as a proportion of LDL (p = 0.005) after adjustments. <i>Conclusions:</i> Interaction between <i>PPARG </i>Pro12Ala and <i>PPARA</i> Leu162Valgenotypes may influence plasma LDL cholesterol concentration and the proportion as small dense LDL after a high monounsaturated fatty acids diet.
DOI: 10.6084/m9.figshare.5123302.v1
title: Supplementary Material for: Phenotype-Genotype Correlations in Mouse Models of<b> </b>Amelogenesis Imperfecta<b> </b>Caused by<b><i> Amelx </i></b>and<b><i> Enam </i></b>Mutations

description: Mutations in human and in mouse orthologous genes <i>Amelx</i> and <i>Enam </i>result in a diverse range of enamel defects. In this study we aimed to investigate the phenotype-genotype correlation between the mutants and the wild-type controls in mouse models of amelogenesis imperfecta using novel measurement approaches. Ten hemi-mandibles and incisors were dissected from each group of <i>Amelx</i><sup>WT</sup>, <i>Amelx</i><sup>X/Y64H</sup>, <i>Amelx</i><sup>Y/Y64H</sup>, <i>Amelx</i><sup>Y64H/Y64H</sup>, and<i> Enam</i><sup>WT</sup>, <i>Enam</i><sup>Rgsc395</sup> heterozygous and <i>Enam</i><sup>Rgsc395</sup> homozygous mice. Their macro-morphology, colour and micro-topography were assessed using bespoke 2D and 3D image analysis systems and customized colour and whiteness algorithms. The novel methods identified significant differences (p ≤ 0.05) between the <i>Amelx</i> groups for mandible and incisor size and enamel colour and between the <i>Enam</i> groups for incisor size and enamel colour. The <i>Amelx</i><sup>WT</sup> mice had the largest mandibles and incisors, followed in descending order of size by the <i>Amelx</i><sup>X/Y64H</sup>, <i>Amelx</i><sup>Y/Y64H</sup> and <i>Amelx</i><sup>Y64H/Y64H</sup> mice. Within the <i>Enam</i> groups the <i>Enam</i><sup>WT</sup> incisors were largest and the <i>Enam</i><sup>Rgsc395</sup> heterozygous mice were smallest. The effect on tooth morphology was also reflected by the severity of the enamel defects in the colour and whiteness assessment. Amelogenin affected mandible morphology and incisor enamel formation, while enamelin only affected incisors, supporting the multifunctional role of amelogenin. The enamelin mutation was associated with earlier forming enamel defects. The study supported the critical involvement of amelogenin and enamelin in enamel mineralization.
DOI: 10.6084/m9.figshare.5123284
title: Supplementary Material for: High Prevalence of Major Neurological Disorders in Two Albanian Communities: Results of a Door-to-Door Survey

description: <i>Background:</i> There are few epidemiological studies on neurological disorders in Albania. <i>Methods:</i> A door-to-door survey was undertaken in two geographical areas (Tirana and Saranda) with different socioeconomic backgrounds. Two random samples of the local population underwent a structured interview to ascertain headache, epilepsy, dementia, parkinsonism, multiple sclerosis, polyneuropathy, stroke and cerebral palsy. Each diagnosis was made using standard criteria for epidemiological studies and was confirmed by history, neurological examination and, where available, the review of personal medical records. Lifetime prevalence ratios with 95% confidence intervals were calculated. <i>Results:</i> Of the 9,869 individuals screened (Tirana 4,953; Saranda 4,916), 4,867 were males aged 1–91 years (median 39 years) and 5,002 were females aged 1–96 years (median 37 years). Crude prevalence ratios (per 1,000) were: headache 241.9 (233.5–250.3), polyneuropathy 32.5 (29.0–36.0), epilepsy 14.2 (11.7–16.3), stroke 12.4 (10.2–14.6), dementia 9.6 (7.7–11.5), parkinsonism 8.0 (6.2–9.8), cerebral palsy 4.8 (3.4–6.2), and multiple sclerosis 0.3 (0.0–0.6). Prevalence varied with age and gender, with differences across diseases. Except for polyneuropathy (Tirana 39.8; Saranda 25.2), ratios were not different in the two study areas. <i>Conclusions:</i> The prevalence of selected neurological disorders in Albania is higher than in other countries. Differences may be explained by study design, population structure and/or genetic and environmental factors.
DOI: 10.6084/m9.figshare.5123290
title: Supplementary Material for: Accuracy and Sensitivity of Parkinsonian Disorder Diagnoses in Two Swedish National Health Registers

description: <i>Background:</i> Swedish population-based national health registers are widely used data sources in epidemiological research. Register-based diagnoses of Parkinson’s disease have not been validated against clinical information. <i>Methods:</i> Parkinson’s disease (PD) and other parkinsonian disorder diagnoses were ascertained in two registers, i.e. the National Patient Register (NPR) and the Cause of Death Register (CDR). Diagnoses were validated in terms of accuracy (positive predictive value) and sensitivity against data from a population-based study of PD in 1998–2004 that screened more than 35,000 persons and identified 194 cases of parkinsonian disorders including 132 PD cases (the gold standard for the purposes of this study). <i>Results:</i> Accuracy for any parkinsonian disorder diagnoses was 88.0% in the NPR and 94.4% in the CDR. Accuracy of PD diagnoses was 70.8% in the NPR and 66.7% in the CDR. Misclassification between differential parkinsonian diagnoses was common. The accuracy of PD diagnoses in the NPR improved to 83.0% by restricting the definition to primary diagnoses only. The sensitivity of PD diagnoses in the NPR and CDR combined was 83.1%, with a mean time to detection of 6.9 years. <i>Conclusions:</i> Population-based national health registers are valid data sources in epidemiological studies of PD or parkinsonian disorder etiology but are less suitable in studies of incidence or prevalence.
DOI: 10.6084/m9.figshare.5123287
title: Supplementary Material for: Downregulation of the Ubiquitin-Proteasome System in Normal Colonic Macrophages and Reinduction in Inflammatory Bowel Disease

description: <b><i>Background:</i></b> In normal mucosa, intestinal lamina propria macrophages (IMACs) maintain tolerance against food antigens and the commensal bacterial flora. Several mechanisms have been identified that mediate tolerance. The ubiquitin-proteasome system (UPS) is a large multiprotein complex that degrades cellular proteins. As the UPS may modulate immune functions of IMACs, we performed a detailed investigation of UPS expression and function under normal conditions and in cells derived from patients suffering from inflammatory bowel disease (IBD).<b><i> Methods:</i></b> IMACs were isolated from intestinal mucosa. mRNA expression of macrophages differentiated in vitro (i.v. MACs) and IMACs was compared by Affymetrix® oligonucleotide arrays. Quantitative Taqman-PCR was performed on five exemplary proteasomal and five ubiquitinylation genes each. Proteins were analyzed by immunohistochemistry and Western blotting. Proteasome function was assessed by a fluorimetric test. <b><i>Results:</i></b> Affymetrix analysis showed downregulation of mRNA expression of almost all represented proteasomal and of 22 ubiquitination-associated genes in IMACs as compared to i.v. MACs and monocytes. By quantitative PCR, up to tenfold higher mRNA expression of 10 exemplary genes of the UPS (UBE2A, UBE2D2, UBE2L6, USP14, UBB and ATPase2, β2, β5, β2i/MECL-1, β5i/LMP7) was demonstrated in i.v. MACs as compared to IMACs. Immunohistochemistry and Western blots confirmed these findings in intestinal mucosa of controls and patients suffering from diverticulitis. In contrast, a significant increase in protein amounts was found in mucosa of patients with IBD. <b><i>Conclusion:</i></b> Reduced expression of subunits of the UPS in IMACs of normal mucosa supports the concept of the presence of a nonreactive, anergic macrophage phenotype in the gut under normal conditions. Reinduction in IMACs of IBD mucosa reflects activated IMACs which can present antigenic peptides and thus support inflammation.
DOI: 10.6084/m9.figshare.5123290.v1
title: Supplementary Material for: Accuracy and Sensitivity of Parkinsonian Disorder Diagnoses in Two Swedish National Health Registers

description: <i>Background:</i> Swedish population-based national health registers are widely used data sources in epidemiological research. Register-based diagnoses of Parkinson’s disease have not been validated against clinical information. <i>Methods:</i> Parkinson’s disease (PD) and other parkinsonian disorder diagnoses were ascertained in two registers, i.e. the National Patient Register (NPR) and the Cause of Death Register (CDR). Diagnoses were validated in terms of accuracy (positive predictive value) and sensitivity against data from a population-based study of PD in 1998–2004 that screened more than 35,000 persons and identified 194 cases of parkinsonian disorders including 132 PD cases (the gold standard for the purposes of this study). <i>Results:</i> Accuracy for any parkinsonian disorder diagnoses was 88.0% in the NPR and 94.4% in the CDR. Accuracy of PD diagnoses was 70.8% in the NPR and 66.7% in the CDR. Misclassification between differential parkinsonian diagnoses was common. The accuracy of PD diagnoses in the NPR improved to 83.0% by restricting the definition to primary diagnoses only. The sensitivity of PD diagnoses in the NPR and CDR combined was 83.1%, with a mean time to detection of 6.9 years. <i>Conclusions:</i> Population-based national health registers are valid data sources in epidemiological studies of PD or parkinsonian disorder etiology but are less suitable in studies of incidence or prevalence.
DOI: 10.6084/m9.figshare.5123278
title: Supplementary Material for: The Active Site Residue V266 of Chlamydial HtrA Is Critical for Substrate Binding during both in vitro and in vivo Conditions

description: HtrA is a complex, multimeric chaperone and serine protease important for the virulence and survival of many bacteria. <i>Chlamydia trachomatis </i>is an obligate, intracellular bacterial pathogen that is responsible for severe disease pathology. <i>C. trachomatis </i>HtrA (CtHtrA) has been shown to be highly expressed in laboratory models of disease. In this study, molecular modelling of CtHtrA protein active site structure identified putative S1–S3 subsite residues I242, I265, and V266. These residues were altered by site-directed mutagenesis, and these changes were shown to considerably reduce protease activity on known substrates and resulted in a narrower and distinct range of substrates compared to wild type. Bacterial two-hybrid analysis revealed that CtHtrA is able to interact in vivo with a broad range of protein sequences with high affinity. Notably, however, the interaction was significantly altered in 35 out of 69 clones when residue V266 was mutated, indicating that this residue has an important function during substrate binding.
DOI: 10.6084/m9.figshare.5123281
title: Supplementary Material for: Corpus Callosotomy with the CO<sub>2</sub> Laser Suction Device: A Technical Note

description: <i>Introduction:</i> Patients with symptomatic generalized epilepsy who are not candidates for resections may be considered for corpus callosotomy. <i>Methods:</i> The two patients who were followed in this series underwent resection of the corpus callosum utilizing the OmniGuide CO<sub>2</sub> Laser System. <i>Surgical Technique:</i> The OmniGuide CO<sub>2</sub> Laser Systemcan be used in place of the bipolar electrocautery in a corpus callosotomy to improve midline dissection, decrease the likelihood of entering the ventricle, and improve visualization in the dissection. <i>Conclusion:</i> The OmniGuide CO<sub>2</sub> Laser System is a valuable option when performing a corpus callosotomy.
DOI: 10.6084/m9.figshare.5123284.v1
title: Supplementary Material for: High Prevalence of Major Neurological Disorders in Two Albanian Communities: Results of a Door-to-Door Survey

description: <i>Background:</i> There are few epidemiological studies on neurological disorders in Albania. <i>Methods:</i> A door-to-door survey was undertaken in two geographical areas (Tirana and Saranda) with different socioeconomic backgrounds. Two random samples of the local population underwent a structured interview to ascertain headache, epilepsy, dementia, parkinsonism, multiple sclerosis, polyneuropathy, stroke and cerebral palsy. Each diagnosis was made using standard criteria for epidemiological studies and was confirmed by history, neurological examination and, where available, the review of personal medical records. Lifetime prevalence ratios with 95% confidence intervals were calculated. <i>Results:</i> Of the 9,869 individuals screened (Tirana 4,953; Saranda 4,916), 4,867 were males aged 1–91 years (median 39 years) and 5,002 were females aged 1–96 years (median 37 years). Crude prevalence ratios (per 1,000) were: headache 241.9 (233.5–250.3), polyneuropathy 32.5 (29.0–36.0), epilepsy 14.2 (11.7–16.3), stroke 12.4 (10.2–14.6), dementia 9.6 (7.7–11.5), parkinsonism 8.0 (6.2–9.8), cerebral palsy 4.8 (3.4–6.2), and multiple sclerosis 0.3 (0.0–0.6). Prevalence varied with age and gender, with differences across diseases. Except for polyneuropathy (Tirana 39.8; Saranda 25.2), ratios were not different in the two study areas. <i>Conclusions:</i> The prevalence of selected neurological disorders in Albania is higher than in other countries. Differences may be explained by study design, population structure and/or genetic and environmental factors.
DOI: 10.6084/m9.figshare.5123287.v1
title: Supplementary Material for: Downregulation of the Ubiquitin-Proteasome System in Normal Colonic Macrophages and Reinduction in Inflammatory Bowel Disease

description: <b><i>Background:</i></b> In normal mucosa, intestinal lamina propria macrophages (IMACs) maintain tolerance against food antigens and the commensal bacterial flora. Several mechanisms have been identified that mediate tolerance. The ubiquitin-proteasome system (UPS) is a large multiprotein complex that degrades cellular proteins. As the UPS may modulate immune functions of IMACs, we performed a detailed investigation of UPS expression and function under normal conditions and in cells derived from patients suffering from inflammatory bowel disease (IBD).<b><i> Methods:</i></b> IMACs were isolated from intestinal mucosa. mRNA expression of macrophages differentiated in vitro (i.v. MACs) and IMACs was compared by Affymetrix® oligonucleotide arrays. Quantitative Taqman-PCR was performed on five exemplary proteasomal and five ubiquitinylation genes each. Proteins were analyzed by immunohistochemistry and Western blotting. Proteasome function was assessed by a fluorimetric test. <b><i>Results:</i></b> Affymetrix analysis showed downregulation of mRNA expression of almost all represented proteasomal and of 22 ubiquitination-associated genes in IMACs as compared to i.v. MACs and monocytes. By quantitative PCR, up to tenfold higher mRNA expression of 10 exemplary genes of the UPS (UBE2A, UBE2D2, UBE2L6, USP14, UBB and ATPase2, β2, β5, β2i/MECL-1, β5i/LMP7) was demonstrated in i.v. MACs as compared to IMACs. Immunohistochemistry and Western blots confirmed these findings in intestinal mucosa of controls and patients suffering from diverticulitis. In contrast, a significant increase in protein amounts was found in mucosa of patients with IBD. <b><i>Conclusion:</i></b> Reduced expression of subunits of the UPS in IMACs of normal mucosa supports the concept of the presence of a nonreactive, anergic macrophage phenotype in the gut under normal conditions. Reinduction in IMACs of IBD mucosa reflects activated IMACs which can present antigenic peptides and thus support inflammation.
DOI: 10.6084/m9.figshare.5123293.v1
title: Supplementary Material for: PPARγ2 Gene Pro12Ala and PPARα Gene Leu162Val Single Nucleotide Polymorphisms Interact with Dietary Intake of Fat in Determination of Plasma Lipid Concentrations

description: <i>Background/Aims:</i> The peroxisome proliferator-activated receptors (PPARs) are transcriptional regulators of lipid metabolism, activated by unsaturated fatty acids. We investigated independent and interactive effects of PPARγ2 gene <i>PPARG </i>Pro12Ala (rs1801282) andPPARαgene<i> PPARA </i>Leu162Val (rs1800206) genotypes with dietary intake of fatty acids on concentrations of plasma lipids in subjects of whom 47.5% had metabolic syndrome. <i>Methods:</i> The RISCK study is a parallel design, randomised controlled trial. Plasma lipids were quantified at baseline after a 4-week high saturated fatty acids diet and after three parallel 24-week interventions with reference (high saturated fatty acids), high monounsaturated fatty acids and low-fat diets. Single nucleotide polymorphisms were genotyped in 466 subjects. <i>Results:</i> At baseline, the<i> PPARG</i> Ala12allele was associated with increased plasma total cholesterol (n = 378; p = 0.04), LDL cholesterol (p = 0.05) and apoB (p =0.05) after adjustment for age, gender and ethnicity. At baseline, <i>PPARA</i> Leu162Val × <i>PPARG</i> Pro12Ala genotype interaction did not significantly influence plasma lipid concentrations. After dietary intervention, gene-gene interaction significantly influenced LDL cholesterol (p =0.0002) and small dense LDL as a proportion of LDL (p = 0.005) after adjustments. <i>Conclusions:</i> Interaction between <i>PPARG </i>Pro12Ala and <i>PPARA</i> Leu162Valgenotypes may influence plasma LDL cholesterol concentration and the proportion as small dense LDL after a high monounsaturated fatty acids diet.
DOI: 10.6084/m9.figshare.5123269
title: Supplementary Material for: Osteoporosis-Pseudoglioma Syndrome: Three Novel Mutations in the <i>LRP5 </i>Gene and Response to Bisphosphonate Treatment

description: <i>Background/Aims:</i> Osteoporosis-pseudoglioma (OPPG) syndrome is a rare disorder characterized by congenital or infancy-onset visual loss and severe juvenile osteoporosis. OPPG is caused by homozygous mutations in the low-density lipoprotein receptor-related protein 5 <i>(LRP5) </i>gene. We present three novel homozygous <i>LRP5 </i>mutations found in 3 unrelated Turkish children with consanguineous parents, along with clinical phenotypes and response to treatment with bisphosphonates (bisP). <i>Methods/Results:</i> The <i>LRP5 </i>gene was analyzed by direct sequencing after PCR amplification. Mutation screening for <i>LRP5</i> revealed homozygous nonsense R1002X mutation in the first patient and homozygous missense mutations V336M and G507S in the second and third patient, respectively. The parents were heterozygous for these mutations. The patients’ eye symptoms began during the first months of life but the OPPG diagnoses were made based on skeletal deformities and osteopenia after 4 years of age. The patients’ bone mineral density Z scores were very low and consistent with osteopenia. All patients were treated with bisP for 3.5–7 years. <i>Conclusion:</i> We report three novel <i>LRP5 </i>mutations in 3 Turkish patients with OPPG. We show that the response of bisP therapy has improved the lumbar spinal bone mineral density Z scores and the patients’ quality of life as the bone pains decreased.
DOI: 10.6084/m9.figshare.5123275
title: Supplementary Material for: Elevated Temperature Applied during Gonadal Transformation Leads to Male Bias in Zebrafish <b><i>(Danio rerio)</i></b>

description: Temperature effects on sex determination or differentiation exist in many fish species, with high temperatures predominantly producing more males. The present study aimed at elucidating the genetic background of temperature effects on sex differentiation in zebrafish. Experimental fish were generated by matings between 4 or 6 golden females and a normal or a mitotic gynogenetic male, respectively. All the larvae were reared at 28.5°C until they were divided into 3 groups per full-sib family, a control group raised at 28.5°C and 2 treatment groups reared at 35°C from 20 to 30 dpf or 25 to 35 dpf, respectively. Backcross progenies, reared at 28.5°C, were derived from F1 temperature-treated sons (35°C, 25–35 dpf) that were sired by a mitotic gynogenetic male and their corresponding mothers. No significant differences were observed regarding the survival rate between the control and treatment groups. Significant differences in the phenotypic male proportions from the controls were observed in groups treated at 35°C. The sex ratio in zebrafish was influenced by the male spawner, the female spawner, and a significant interaction of genotype by temperature. Backcross experiments point to a continuum of major genetic, minor genetic, and environmental factors in the expression of the phenotypic sex in zebrafish.