PoreFUME paper. Manuscript on bioRxiv: http://biorxiv.org/content/early/2016/08/04/067652
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PROVIDER: PRJEB14994 | ENA |
REPOSITORIES: ENA
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Project description:The COVID-19 pandemic across Chinese mainland was gradually stabilized at a low level with sporadic outbreaks, before the emergence of Omicron variant. Apart from non-pharmacological interventions (NPIs), COVID-19 vaccine has also been implemented to prevent and control the pandemic since early 2021. Although many aspects have been focused, the change of the spatiotemporal distribution of COVID-19 epidemic across Chinese mainland responding to the change of prevention and control measures were less concerned. Here, we collected the confirmed case data (including domestic cases and overseas imported cases) across Chinese mainland during both 2020/04-2020/08 and 2021/04-2021/08, and then conducted a preliminary data comparison on the spatiotemporal distribution of confirmed cases during the identical period between the two years. Distribution patterns were evaluated both qualitatively by classification method and quantitatively through employing coefficient of variation. Results revealed significant differences in the homogeneity of spatiotemporal distributions of imported or domestic cases between the two years, indicating that the important effect of the adjustment of prevention and control measures on the epidemic evolution. The findings here enriched our practical experience of COVID-19 prevention and control. And, the collected data here might be helpful for improving or verifying spatiotemporally dynamic models of infectious diseases.
| S-EPMC10363524 | biostudies-literature
Project description: Not available
| S-IHECRE00000142.1 | biostudies-other
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| S-IHECRE00000075.1 | biostudies-other
Project description:IntroductionEarly-onset Type 1 diabetes (EOT1D) is considered a disease subtype with distinctive immunological and clinical features. While both Human Leukocyte Antigen (HLA) and non-HLA variants contribute to age at T1D diagnosis, detailed analyses of EOT1D-specific genetic determinants are still lacking. This study scrutinized the involvement of the HLA class II locus in EOT1D genetic control.MethodsWe conducted genetic association and regularized logistic regression analyses to evaluate genotypic, haplotypic and allelic variants in DRB1, DQA1 and DQB1 genes in children with EOT1D (diagnosed at ≤5 years of age; n=97), individuals with later-onset disease (LaOT1D; diagnosed 8-30 years of age; n=96) and nondiabetic control subjects (n=169), in the Portuguese population.ResultsAllelic association analysis of EOT1D and LaOT1D unrelated patients in comparison with controls, revealed that the rare DRB1*04:08 allele is a distinctive EOT1D susceptibility factor (corrected p-value=7.0x10-7). Conversely, the classical T1D risk allele DRB1*04:05 was absent in EOT1D children while was associated with LaOT1D (corrected p-value=1.4x10-2). In corroboration, HLA class II haplotype analysis showed that the rare DRB1*04:08-DQ8 haplotype is specifically associated with EOT1D (corrected p-value=1.4x10-5) and represents the major HLA class II genetic driver and discriminative factor in the development of early onset disease.DiscussionThis study uncovered that EOT1D holds a distinctive spectrum of HLA class II susceptibility loci, which includes risk factors overlapping with LaOT1D and discriminative genetic configurations. These findings warrant replication studies in larger multicentric settings encompassing other ethnicities and may impact target screening strategies and follow-up of young children with high T1D genetic risk as well as personalized therapeutic approaches.
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Project description:Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
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Project description:The gut microbiome is a complex ecosystem stratified that varies along different sections of the gut. It comprises a wide array of metabolites originating from both food, host, and microbes. Microbially-derived metabolites, such as bile acids, short-chain fatty acids, and indole derivatives, are of significant interest due to their direct interactions with host physiology and regulating function. Most current studies on the gut microbiome focus on fecal samples, which do not fully represent the upper parts of the gut due to its stratification. To collect microbiome samples from the proximal gut microbiome, endoscopic methods or new non-invasive medical devices can be used. To enable comprehensive profiling of the gut metabolome and analyze key metabolites, we developed a combined approach combining untargeted and semi-targeted metabolomics using a Q-Exactive Plus Orbitrap mass spectrometer. Initially, we selected 49 metabolites of interest for the gut metabolome based on four distinct criteria. We validated these metabolites through repeatability and linearity tests and created a compound database using the software TraceFinder (ThermoFisher Scientific). For untargeted metabolomics, we established a workflow for the annotation and discovery of molecules. Finally, 37 metabolites were validated for semi-targeted metabolomics, and we conducted a proof of concept on small intestinal and fecal samples form a clinical trial (NCT05477069). Our combined approach, facilitated by molecular networking, demonstrated the potential to discover new metabolites.
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Project description:A new genome of Fraxinus excelsior (PRJNA865134) was assembled using a hybrid approach combining Nanopore and Illumina data. The gene expression of a 182 Danish tree panel (Harper et al. 2016) was assessed using the new genome as reference (BioProject PRJNA865134, SAMN30100368, genome JANJPF000000000 ).Manuscript title: Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback, G3:Genes|Genomes|Genetics
2025-03-03 | GSE214551 | GEO
Project description:E-JOURNAL LINKED ABSTRACT URL http://www.current-oncology.com/index.php/oncology/article/view/840/ Pseudocirrhosis is a rare form of liver disease that causes clinical symptoms and shows radiographic signs of cirrhosis, but that has histologic features suggesting a distinct pathologic process. In the setting of cancer, hepatic metastases and systemic chemotherapy are suspected causes of pseudocirrhosis. We present the case of a 49-year-old woman with medullary thyroid carcinoma metastatic to the liver who developed pseudocirrhosis. The patient was initially enrolled in a phase i clinical trial of 5-fluorouracil, leucovorin, and oxaliplatin (folfox) in combination with sunitinib (NCT00599924). After this patient’s liver metastases regressed measurably, she was switched to sunitinib maintenance. After 4 months of combination therapy with folfox–sunitinib and 15 months of sunitinib maintenance, she developed abdominal bloating, early satiety, and right upper quadrant pain that increased with inspiration. Computed tomography of the abdomen revealed cirrhotic morphology changes in the liver, including the appearance of a nodular surface and capsular retraction. The patient had no risk factors for cirrhosis and laboratory testing for causes of liver disease were normal or negative. Core-needle liver biopsy demonstrated sheets and nests of epithelioid and spindle cells resembling the primary tumor; septal fibrosis and regenerative nodules typical of cirrhosis were not observed. The background hepatic plate architecture was intact. Laboratory studies showed increased aminotransferases, alkaline phosphatase, and international normalized ratio, and decreased albumin. Portal hypertension, esophageal varices, portal hypertensive gastropathy, and hepatic hydrothorax developed as a result of advanced liver disease. Because of disease progression, sunitinib was discontinued, and the patient was managed with sorafenib. Pseudocirrhosis has often been attributed to chemotherapeutic agents, particularly in the context of metastatic breast cancer. The toxicity profiles of folfox and sunitinib include hepatic steatosis and other forms of hepatotoxicity, but cirrhotic-like disease has not been reported. Considering the transformation of discrete hepatic metastases into a diffuse carcinomatous infiltrate and the unrelated toxicities of folfox and sunitinib, we diagnosed this patient with carcinomatous pseudocirrhosis secondary to metastatic medullary thyroid carcinoma. We discuss the diagnosis of pseudocirrhosis in this case and review the literature regarding pseudocirrhosis in cancer.
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Project description:During the European Middle Ages, the opening of long-distance Asian trade routes introduced exotic goods, including ultramarine, a brilliant blue pigment produced from lapis lazuli stone mined only in Afghanistan. Rare and as expensive as gold, this pigment transformed the European color palette, but little is known about its early trade or use. Here, we report the discovery of lapis lazuli pigment preserved in the dental calculus of a religious woman in Germany radiocarbon-dated to the 11th or early 12th century. The early use of this pigment by a religious woman challenges widespread assumptions about its limited availability in medieval Europe and the gendered production of illuminated texts.
| S-EPMC6326749 | biostudies-literature
Project description:Rapid mapping of the E. coli antibiotic resistome
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