cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30498437
title: Supplementary Material for: Coexistence of mosaic marker chromosome and isodisomy 1 in reproductive failure: A cytogenomic case report and review of the literature

description: IAbstract
Introduction:
Reproductive failure has been associated with various chromosomal abnormalities, including small supernumerary marker chromosomes (sSMCs). In rare cases, uniparental disomy (UPD) may also contribute to reproductive problems, particularly when invoving imprinted regions or in cases of isodisomy where autosomal recessive disorders may manifest. UPD involving chromosome 1 (UPD1) is rare and has not been linked to a consistent phenotype.
Case Presentation:
We present a 27-year-old woman with a five-year history of reproductive difficulty, including one biochemical pregnancy loss and one clinically recognized miscarriage at 8 weeks of gestation. Cytogenetic analysis revealed mosaicism for a small supernumerary marker chromosome derived from chromosome 1. SNP microarray identified complete UPD1 without copy number changes. Fluorescence in situ hybridization (FISH) confirmed centromeric material of chromosome 1 in the marker chromosome.
Conclusion:
To the best of our knowledge, this is the first reported case combining mosaic sSMC(1) and complete UPD1 in a phenotypically healthy woman with reproductive failure. The coexistence of these abnormalities likely reflects a postzygotic chromosomal rescue mechanism. These findings underscore the diagnostic value of integrated cytogenomic analyses in unexplained reproductive failure and subfertility.
Keywords: reproductive failure, supernumerary marker chromosome, isodisomy, uniparental disomy, cytogenetics, case report
DOI: 10.6084/m9.figshare.30498437.v1
title: Supplementary Material for: Coexistence of mosaic marker chromosome and isodisomy 1 in reproductive failure: A cytogenomic case report and review of the literature

description: IAbstract
Introduction:
Reproductive failure has been associated with various chromosomal abnormalities, including small supernumerary marker chromosomes (sSMCs). In rare cases, uniparental disomy (UPD) may also contribute to reproductive problems, particularly when invoving imprinted regions or in cases of isodisomy where autosomal recessive disorders may manifest. UPD involving chromosome 1 (UPD1) is rare and has not been linked to a consistent phenotype.
Case Presentation:
We present a 27-year-old woman with a five-year history of reproductive difficulty, including one biochemical pregnancy loss and one clinically recognized miscarriage at 8 weeks of gestation. Cytogenetic analysis revealed mosaicism for a small supernumerary marker chromosome derived from chromosome 1. SNP microarray identified complete UPD1 without copy number changes. Fluorescence in situ hybridization (FISH) confirmed centromeric material of chromosome 1 in the marker chromosome.
Conclusion:
To the best of our knowledge, this is the first reported case combining mosaic sSMC(1) and complete UPD1 in a phenotypically healthy woman with reproductive failure. The coexistence of these abnormalities likely reflects a postzygotic chromosomal rescue mechanism. These findings underscore the diagnostic value of integrated cytogenomic analyses in unexplained reproductive failure and subfertility.
Keywords: reproductive failure, supernumerary marker chromosome, isodisomy, uniparental disomy, cytogenetics, case report
DOI: 10.6075/j02v2f0t
title: CIL:25377, Maize mosaic virus, Peregrinus maidis, secretory cell. In Cell Image Library

description: Electron micrograph of Maize mosaic virus (MMV, Rhabdoviridae) in secretory cells from the principal salivary gland of the insect vector Peregrinus maidis (planthopper, Hemiptera, Delphacidae). MMV virions are bullet-shaped or bacilliform, 186-213 nm long and ca. 61 nm in diameter. In the principal salivary glands, MMV (arrows) buds through cytoplasmic membranes. Abbreviations: ics, intercellular space; SV, secretory vesicles. The accompanying image in this image group is unlabeled. 
 
Methods: Dissected insect organs were processed for TEM by fixation in glutaraldehyde and osmium tetroxide and embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM.

Associated references: 
Ammar, E.-D. and S. A. Hogenhout, S.A. (2008). A neurotropic route for Maize mosaic virus (Rhabdoviridae) in its planthopper vector Peregrinus maidis. Virus Research 131: 77-85.
Ammar, E.-D. and Nault, L.R. (1985). Assembly and accumulation sites of Maize mosaic virus in its planthopper vector. Intervirology 24: 33-41.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: detection of electrons; illumination by electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt
Processing history: recorded image
Data qualification: Raw;spatialmeasurements
DOI: 10.6084/m9.figshare.30498440
title: Supplementary Material for: Prenatal Diagnosis of Tubulinopathy: Case Report of Neurosonographic Features and a Novel TUBA1A Variant

description: Introduction: Tubulinopathies are a heterogeneous group of rare disorders which are primarily characterized by brain malformations caused by pathogenic variants in the genes that encode tubulin. Although scarce, prenatal diagnosis has been recently reported through expert neurosonography and magnetic resonance imaging (MRI), most commonly at 28-34 weeks’ gestation, followed by identification of pathogenic variant in TUBA1A, TUBB, TUBB2A, TUBB2B, TUBB3, or TUBG1 using gene sequencing.
Case Presentation: We present detailed ultrasound findings of 21-week fetus with brain abnormalities including low normal head circumference (HC), cerebellar hypoplasia, dysmorphic cavum vellum pellucidum (CSP), partial agenesis and dysgenesis of the corpus callosum, distortion with interdigitation of the interhemispheric fissure, ventricular asymmetry with dysmorphic and/or dilated frontal horns, as well as asymmetry in the basal ganglia.
Amniocentesis with trio genome sequencing (GS) detected a novel, de novo heterozygous c.799T&gt;C variant in TUBA1A that has not been previously reported.
Conclusions: This case offers a detailed characterization of the subtle neurosonographic phenotype in this fetus with early manifestation of malformations of cortical development
(MCD) related to tubulinopathy and provides information regarding the novel variant in the TUBA1A gene. It further underscores the importance of neurosonography and genetic analysis in identifying tubulinopathies and informing clinical decision-making during pregnancy.
DOI: 10.6084/m9.figshare.30498440.v1
title: Supplementary Material for: Prenatal Diagnosis of Tubulinopathy: Case Report of Neurosonographic Features and a Novel TUBA1A Variant

description: Introduction: Tubulinopathies are a heterogeneous group of rare disorders which are primarily characterized by brain malformations caused by pathogenic variants in the genes that encode tubulin. Although scarce, prenatal diagnosis has been recently reported through expert neurosonography and magnetic resonance imaging (MRI), most commonly at 28-34 weeks’ gestation, followed by identification of pathogenic variant in TUBA1A, TUBB, TUBB2A, TUBB2B, TUBB3, or TUBG1 using gene sequencing.
Case Presentation: We present detailed ultrasound findings of 21-week fetus with brain abnormalities including low normal head circumference (HC), cerebellar hypoplasia, dysmorphic cavum vellum pellucidum (CSP), partial agenesis and dysgenesis of the corpus callosum, distortion with interdigitation of the interhemispheric fissure, ventricular asymmetry with dysmorphic and/or dilated frontal horns, as well as asymmetry in the basal ganglia.
Amniocentesis with trio genome sequencing (GS) detected a novel, de novo heterozygous c.799T&gt;C variant in TUBA1A that has not been previously reported.
Conclusions: This case offers a detailed characterization of the subtle neurosonographic phenotype in this fetus with early manifestation of malformations of cortical development
(MCD) related to tubulinopathy and provides information regarding the novel variant in the TUBA1A gene. It further underscores the importance of neurosonography and genetic analysis in identifying tubulinopathies and informing clinical decision-making during pregnancy.
DOI: 10.6075/j0222sp0
title: CIL:25393, Drosophila melanogaster, Salivary gland. In Cell Image Library

description: Salivary glands from 3rd instar larvae of Drosophila melanogaster were dissected, fixed with formalin-acetic acid containing 0.1% Triton-X 100, and squashed on a glass slide. After freezing in liquid nitrogen, the cover slips removed, and the slide thawed and stained with 1% uranyl acetate, rinsed in 50% ethanol, dehydrated and transferred to amyl acetate, and covered with 2% parlodion in amyl acetate. Selected areas of the parlodion film, are transferred to formvar coated EM grids, and the parlodion removed by immersion in amyl acetate (see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV. 

Image shows a series of bands and interbands in a polytene chromosome. This image was taken with a tilt angle of 55 degrees. The accompanying grouped image, taken at 45 degrees forms a stereo pair, providing an oblique 3D view of the chromosome.
description: Preparation: formaldehyde fixed tissue; acetic acid treatment
Relation to intact cell: squashed preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6084/m9.figshare.30498443
title: Supplementary Material for: Long-term trends in incidence, attack rates, and early case-fatality of spontaneous intracerebral hemorrhage. Dijon Stroke Registry (1985-2022)

description: Background: Spontaneous intracerebral hemorrhage (ICH) is a leading cause of disability and death worldwide. Understanding temporal trends in the burden of the disease is critical to evaluate the effectiveness of preventive strategies and identify targets for action. This study aimed to assess long-term temporal trends in incidence, attack rates, and early case-fatality of ICH. 
Methods: All cases of ICH among residents of Dijon, France, were prospectively recorded between 1985 and 2022 using a population-based registry. Annual incidence and attack rates were assessed, and temporal trends were analysed by calculating incidence (IRR) and attack rate ratios (ARR). Case-fatality was measured at 30 days. 
Results: 1,015 ICH cases (mean age 73.5 ±16.4 years old, 52.7% women) were recorded including 815 patients with a first-ever ICH and 200 cases of ICH as stroke recurrences. Age-standardized incidence increased progressively from 12.6/100,000/year in 1985-1991 to 20.8/100,000/year in 2011-2016 (IRR: 1.96, p&lt;0.001). A slight decrease was observed during period 2017-2022 (18.9/100,000/year, IRR: 0.81; 95% CI: 0.61-1.06, p=0.11). A similar trend was noted in attack rates, with a peak during 2011-2016 (27.9/100,000/year; ARR: 1.79 95% CI: 1.47-2.20, p&lt;0.001) and a decrease in the most recent period (23.2/100,000/year; ARR: 0.83; 95% CI: 0.69-0.99, p=0.04). In men, a significant increase in incidence and attack rates was observed from 1985-1991 to 2011-2016, followed by a slight decline. In contrast, women showed a delayed increase in rates, with no decline in the most recent period. The 30-day case-fatality rate declined between 1985 and 2010 (from 40.3% to 26.3%), followed by an increase thereafter, reaching 38.8% during the last study period
Conclusion: Our study revealed an overall increase in incidence and attack rates of ICH followed by a slight decline in recent years. Sex-differences in trends warrant further investigation into the contributing factors, and emphasizes the continued need for prevention strategies to further reduce the burden of ICH. The recent increase in early case-fatality rates highlights the need for specific acute-phase treatments of ICH.
DOI: 10.6084/m9.figshare.30498443.v1
title: Supplementary Material for: Long-term trends in incidence, attack rates, and early case-fatality of spontaneous intracerebral hemorrhage. Dijon Stroke Registry (1985-2022)

description: Background: Spontaneous intracerebral hemorrhage (ICH) is a leading cause of disability and death worldwide. Understanding temporal trends in the burden of the disease is critical to evaluate the effectiveness of preventive strategies and identify targets for action. This study aimed to assess long-term temporal trends in incidence, attack rates, and early case-fatality of ICH. 
Methods: All cases of ICH among residents of Dijon, France, were prospectively recorded between 1985 and 2022 using a population-based registry. Annual incidence and attack rates were assessed, and temporal trends were analysed by calculating incidence (IRR) and attack rate ratios (ARR). Case-fatality was measured at 30 days. 
Results: 1,015 ICH cases (mean age 73.5 ±16.4 years old, 52.7% women) were recorded including 815 patients with a first-ever ICH and 200 cases of ICH as stroke recurrences. Age-standardized incidence increased progressively from 12.6/100,000/year in 1985-1991 to 20.8/100,000/year in 2011-2016 (IRR: 1.96, p&lt;0.001). A slight decrease was observed during period 2017-2022 (18.9/100,000/year, IRR: 0.81; 95% CI: 0.61-1.06, p=0.11). A similar trend was noted in attack rates, with a peak during 2011-2016 (27.9/100,000/year; ARR: 1.79 95% CI: 1.47-2.20, p&lt;0.001) and a decrease in the most recent period (23.2/100,000/year; ARR: 0.83; 95% CI: 0.69-0.99, p=0.04). In men, a significant increase in incidence and attack rates was observed from 1985-1991 to 2011-2016, followed by a slight decline. In contrast, women showed a delayed increase in rates, with no decline in the most recent period. The 30-day case-fatality rate declined between 1985 and 2010 (from 40.3% to 26.3%), followed by an increase thereafter, reaching 38.8% during the last study period
Conclusion: Our study revealed an overall increase in incidence and attack rates of ICH followed by a slight decline in recent years. Sex-differences in trends warrant further investigation into the contributing factors, and emphasizes the continued need for prevention strategies to further reduce the burden of ICH. The recent increase in early case-fatality rates highlights the need for specific acute-phase treatments of ICH.
DOI: 10.6075/j09w0dc3
title: CIL:25386, Drosophila melanogaster, Intestinal. In Cell Image Library

description: Intestines from 3rd instar larvae of Drosophila melanogaster were dissected, fixed with formalin-acetic acid containing 0.1% Triton-X 100, and squashed on a glass slide. After freezing in liquid nitrogen, the cover slips removed, and the slide thawed and stained with 1% uranyl acetate, rinsed in 50% ethanol, dehydrated and critical point dried (see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV. 

Image shows a series of bands and interbands in a polytene chromosome. This image was taken with a tilt angle of 60 degrees. The accompanying grouped image, taken at 45 degrees forms a stereo pair, providing an oblique 3D view of the chromosome.
description: Preparation: formaldehyde fixed tissue; acetic acid treatment
Relation to intact cell: squashed preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0pc31bg
title: CIL:25385, Drosophila melanogaster, Intestinal. In Cell Image Library

description: Intestines from 3rd instar larvae of Drosophila melanogaster were dissected, fixed with formalin-acetic acid containing 0.1% Triton-X 100, and squashed on a glass slide. After freezing in liquid nitrogen, the cover slips removed, and the slide thawed and stained with 1% uranyl acetate, rinsed in 50% ethanol, dehydrated and critical point dried (see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV. 

Image shows a series of bands and interbands in a polytene chromosome. This image was taken with a tilt angle of 45 degrees. The accompanying grouped image, taken at 60 degrees forms a stereo pair, providing an oblique 3D view of the chromosome.
description: Preparation: formaldehyde fixed tissue; acetic acid treatment
Relation to intact cell: squashed preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6084/m9.figshare.30498446
title: Supplementary Material for: Molecular Characterization and Phenotype-Genotype Correlation of Childhood Thyroid Nodules and Cancers: A study of 62 patients

description: Introduction: Pediatric thyroid nodules and cancer are uncommon but have significant challenges in clinical management due to potential malignancy. Understanding the genotype-phenotype correlation helps in enhancing patient care and personalized treatment strategies.
Methods: Our study aimed to determine the molecular characterization of thyroid nodules and cancer in childhood and investigate the genotype-phenotype relationship. The Bethesda Category (BC) is a standardized framework for classifying thyroid fine-needle aspiration (FNA) results. We conducted a retrospective analysis of clinical data, including next-generation sequencing (NGS), from pediatric thyroid nodule and cancer patients. Analysis was conducted using samples from a pathology archive and follow-up clinical data from a tertiary care center.
Results: A cohort of 62 pediatric patients (50 female, 12 male) aged 2.67-19.61 years (mean 14.18 ± 3.45 years), evaluated over a mean follow-up period of 5.06 ± 3.99 years. NGS analysis of 34 genes for DNA variants and RNA sequencing for gene fusions in BC II-VI samples. Of 62 patients, 37 (59.7%) had differentiated thyroid cancer (DTC), 14 (22.6%) had benign findings, and 9 (14.5%) were categorized as other. Pathogenic variants were found in 80% of DTC patients, with BRAFV600E being the most common (37%). RET, NTRK, and ALK fusions were present in 32% of DTC patients. In the benign group, variants in DICER1, TSHR, and PTEN were noted. Pathogenic variants were also identified in BC-II to BC-IV patients that later developed DTC. High-risk DTC patients included those with BRAFV600E and NCOA4-RET fusions.
Conclusions: BRAFV600E and gene fusions involving RET, NTRK, and ALK were the most frequent pathogenic findings in pediatric DTC, with implications for risk stratification and tailored management. Early molecular analysis can guide prognosis and treatment in patients with initial benign or indeterminate diagnoses.
DOI: 10.6084/m9.figshare.30498446.v1
title: Supplementary Material for: Molecular Characterization and Phenotype-Genotype Correlation of Childhood Thyroid Nodules and Cancers: A study of 62 patients

description: Introduction: Pediatric thyroid nodules and cancer are uncommon but have significant challenges in clinical management due to potential malignancy. Understanding the genotype-phenotype correlation helps in enhancing patient care and personalized treatment strategies.
Methods: Our study aimed to determine the molecular characterization of thyroid nodules and cancer in childhood and investigate the genotype-phenotype relationship. The Bethesda Category (BC) is a standardized framework for classifying thyroid fine-needle aspiration (FNA) results. We conducted a retrospective analysis of clinical data, including next-generation sequencing (NGS), from pediatric thyroid nodule and cancer patients. Analysis was conducted using samples from a pathology archive and follow-up clinical data from a tertiary care center.
Results: A cohort of 62 pediatric patients (50 female, 12 male) aged 2.67-19.61 years (mean 14.18 ± 3.45 years), evaluated over a mean follow-up period of 5.06 ± 3.99 years. NGS analysis of 34 genes for DNA variants and RNA sequencing for gene fusions in BC II-VI samples. Of 62 patients, 37 (59.7%) had differentiated thyroid cancer (DTC), 14 (22.6%) had benign findings, and 9 (14.5%) were categorized as other. Pathogenic variants were found in 80% of DTC patients, with BRAFV600E being the most common (37%). RET, NTRK, and ALK fusions were present in 32% of DTC patients. In the benign group, variants in DICER1, TSHR, and PTEN were noted. Pathogenic variants were also identified in BC-II to BC-IV patients that later developed DTC. High-risk DTC patients included those with BRAFV600E and NCOA4-RET fusions.
Conclusions: BRAFV600E and gene fusions involving RET, NTRK, and ALK were the most frequent pathogenic findings in pediatric DTC, with implications for risk stratification and tailored management. Early molecular analysis can guide prognosis and treatment in patients with initial benign or indeterminate diagnoses.
DOI: 10.6075/j05q4ttf
title: CIL:25384, Maize mosaic virus, Peregrinus maidis, peripheral neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain; distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; propidium iodide
Processing history: recorded image
Data qualification: Raw;spatialmeasurements
description: Aggregates of Maize mosaic virus (MMV, Rhabdoviridae) in nerves of the insect vector Peregrinus maidis (planthopper, Hemiptera, Delphacidae). Antibodies to MMV identify aggregates (green/yellow fluorescence). Nuclei are stained red. The accompanying image in the image group contains a scale bar.

Dissected insect organs were fixed in paraformaldehyde, labeled with primary antibodies to MMV, and with secondary antibodies: Alexa Fluor-488 (green), and later stained with the nuclear stain propidium iodide (red). Whole mounts were examined with confocal laser- scanning microscope (Leica TCS SP).

Associated references: 
Ammar, E.-D. and S. A. Hogenhout, S.A. (2008). A neurotropic route for Maize mosaic virus (Rhabdoviridae) in its planthopper vector Peregrinus maidis. Virus Research 131: 77-85.
Ammar, E.-D. and Nault, L.R. (1985). Assembly and accumulation sites of Maize mosaic virus in its planthopper vector. Intervirology 24: 33-41.