Abstract Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide information for the complex task of phylogenetic inference. We present MEDICC2, a method for inferring evolutionary trees and WGD using haplotype-specific somatic copy-number alterations from single-cell or bulk data. MEDICC2 eschews simplifications such as the infinite sites assumption, allowing multiple mutations and parallel evolution, and does not treat adjacent loci as independent, allowing overlapping copy-number events....

Am 12. Mai 2022 veranstaltete das Helmholtz Open Science Office ein Helmholtz Open Science Forum zum Thema Open Science und Transfer. Die virtuelle, Helmholtz-interne Veranstaltung widmete sich verschiedenen Aspekten und Fragestellungen rund um das Zusammenspiel von Open Science, Technologietransfer sowie Wissenstransfer in der Helmholtz-Gemeinschaft. Gemeinsam mit den Referent:innen und Teilnehmenden wurden Kooperationsmöglichkeiten, Handlungsnotwendigkeiten und Perspektiven thematisiert. Ein zentrales Resümee der Vorträge und Diskussionen war, dass in Helmholtz ein Konsens darüber besteht, dass Open Science und...

Additional file 1. Supplementary material regarding (i) the definition of cancer cases for HCC, GBC, Adv.PrC and Loc.PrC; (ii) the definition and implementation of the data-shared lasso; (iii) the models used to derive point estimates and confidence intervals from the model selected by the data-shared lasso; and (iv) the univariate analysis conducted for comparison.

Abstract Background Epidemiological studies of associations between metabolites and cancer risk have typically focused on specific cancer types separately. Here, we designed a multivariate pan-cancer analysis to identify metabolites potentially associated with multiple cancer types, while also allowing the investigation of cancer type-specific associations. Methods We analysed targeted metabolomics data available for 5828 matched case-control pairs from cancer-specific case-control studies on breast, colorectal, endometrial, gallbladder, kidney, localized and advanced prostate cancer, and hepatocellular carcinoma nested...

Additional file 2: Supplementary tables and figures. Figure S1. Pearson correlation between the 117 original metabolites. Figure S2. Sensitivity analyses of mutually adjusted ORs for the overall associations and cancer type-specific deviations. Figure S3. Sensitivity analysis of mutually adjusted ORs for the overall associations and cancer type-specific deviations with or without excluding hormone users. Figure S4. p-values of tests for departure from linearity and effect modification by BMI. Figure S5. ORs for the overall associations...

Additional file 4: Fig. S2. T-SNE analysis displaying Prague samples (large red dots) among reference cohort samples.

Additional file 1. Appendix: Figures of Quantile regression and DEA Results.

Additional file 10: Table S5. The summary of lncRNAs exhibiting allele-specific expression in cultivated sunflower lines for edible fruit and oil identified in 12 DAP sunflower endosperm.

Additional file 12: Table S7. GO Gene Ontology analysis of co-expressed protein-coding genes with lncRNAs of allelic bias toward cultivated lines for oil.

Additional file 2: Table S2. The genomic information of lncRNAs in sunflower endosperm at 12DAP.

Additional file 11: Table S6. GO Gene Ontology analysis of co-expressed protein-coding genes with lncRNAs of allelic bias toward cultivated lines for edible fruit.

Additional file 1: Figure S1. Shows the respective molecular tumor board workflows of Heidelberg (HDB) and Berlin (BLN). Corresponding steps are indicated by their respective colors.

Verify the applicability of three-level simulation to BDFA through experiments

The factors that influence survival during severe infection are unclear. Extracellular chromatin drives pathology, but the mechanisms enabling its accumulation remain elusive. Here, we show that in murine sepsis models, splenocyte death interferes with chromatin clearance through the release of the DNase I inhibitor actin. Actin-mediated inhibition was compensated by upregulation of DNase I or the actin scavenger gelsolin. Splenocyte death and neutrophil extracellular trap (NET) clearance deficiencies were prevalent in individuals with severe COVID-19...

Supplemental material, sj-pdf-1-smm-10.1177_09622802221139233 for Standard error estimation in meta-analysis of studies reporting medians by Sean McGrath, Stephan Katzenschlager, Alexandra J Zimmer, Alexander Seitel, Russell Steele and Andrea Benedetti in Statistical Methods in Medical Research

The structural instability of inactivated Foot-and-mouth disease virus antigen hinders the development of vaccine industry. The use of an inexpensive, biocompatible formulation to slow down the degradation of antigen would address the problem. Here, phosphate-buffered saline (PBS) was showed to be effective in stabilizing 146S and hence determined as basic solution buffer. Excipients such as trehalose, sucrose, arginine, cysteine, calcium chloride, BSA and ascorbic acid were found to protect 146S from massive structural breakdown. Using...

Additional file 1.

Abstract Background Many researchers have noticed that there is an increasing trend of Bielschowsky acquired comitant esotropia (ACE) in recent years related to excessive near work, but the exact pathogenesis and treatment methods have not been reported yet. Therefore, we aimed to characterize the clinical features of this ACE in adults and to evaluate the efficacy of botulinum toxin (BTX) injections in these patients. Methods This was a prospective consecutive case series of 47 patients...

Abstract Background Many researchers have noticed that there is an increasing trend of Bielschowsky acquired comitant esotropia (ACE) in recent years related to excessive near work, but the exact pathogenesis and treatment methods have not been reported yet. Therefore, we aimed to characterize the clinical features of this ACE in adults and to evaluate the efficacy of botulinum toxin (BTX) injections in these patients. Methods This was a prospective consecutive case series of 47 patients...

Additional file 2: Supplementary Figure 2. Distribution of EVI1 continuous expression in breast cancer: A: Histogram of EVI1 continuous expression in the entire cohort (N=993); B: Boxplots of EVI1 continuous expression within breast cancer subtypes. Note, 882/993 patients with available BC subtype information were included in this analysis. Horizontal bold lines present EVI1 median values of 116.65 in HR+/HER2-, 98.67 in HR+/HER2+, 114.77in HR-/HER2+, and 115.64 in TNBC; boxes present the interquartile range between first...

Abstract Background Overexpression of the EVI1 (ecotropic viral integration site 1) oncogene has recently been implicated as a prognostic factor in breast cancer (BC), particularly in triple-negative BC (TNBC). In this study we aimed to investigate frequency and clinical relevance of EVI1 expression in newly diagnosed BC treated with neoadjuvant chemotherapy. Methods EVI1 expression was determined by immunohistochemistry using H-score as a cumulative measurement of protein expression in pretherapeutic biopsies of BC patients treated with...

Additional file 1: Figure S1. Expression of mRNA of ribosomal proteins in MDA-MB-231 cells. qPCR of the depicted genes in KLF7 transfected MDA-MB-231 cells reveal downregulation of RPL34 and RPL27 mRNA.

Additional file 1: Figure S1. Expression of mRNA of ribosomal proteins in MDA-MB-231 cells. qPCR of the depicted genes in KLF7 transfected MDA-MB-231 cells reveal downregulation of RPL34 and RPL27 mRNA.

Additional file 2: Figure S2. KLF7 expression in MCF7 cells. A. mRNA in KLF7 transfected MCF7 cells was strongly enhanced compared to control cells B. western blot of MCF7 protein lysate demonstrated increased protein level in KLF7OE cells. C. Densitometric quantification of western blots showed significantly higher KLF7 levels (n = 4). D. Nuclear localization of KLF7 in MCF7 cell spheres.

Additional file 2: Figure S2. KLF7 expression in MCF7 cells. A. mRNA in KLF7 transfected MCF7 cells was strongly enhanced compared to control cells B. western blot of MCF7 protein lysate demonstrated increased protein level in KLF7OE cells. C. Densitometric quantification of western blots showed significantly higher KLF7 levels (n = 4). D. Nuclear localization of KLF7 in MCF7 cell spheres.