VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data.

RNA viruses exist as large heterogeneous populations within their host. The structure and diversity of virus populations affects disease progression and treatment outcomes. Next-generation sequencing allows detailed viral population analysis, but inferring diversity from error-prone reads is challenging.

V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.

The large amount and diversity of viral genomic datasets generated by next-generation sequencing technologies poses a set of challenges for computational data analysis workflows, including rigorous quality control, scaling to large sample sizes, and tailored steps for specific applications. Here, we present V-pipe 3.0, a computational pipeline designed for analyzing next-generation sequencing data of short viral genomes.

Pan-cancer evaluation of tumor-infiltrating lymphocytes and programmed cell death protein ligand-1 in metastatic biopsies and matched primary tumors.

Tumor immunological characterization includes evaluation of tumor-infiltrating lymphocytes (TILs) and programmed cell death protein ligand-1 (PD-L1) expression. This study investigated TIL distribution, its prognostic value, and PD-L1 expression in metastatic and matched primary tumors (PTs). Specimens from 550 pan-cancer patients of the SHIVA01 trial (NCT01771458) with available metastatic biopsy and 111 matched PTs were evaluated for TILs and PD-L1.

E-Cadherin Mutational Landscape and Outcomes in Breast Invasive Lobular Carcinoma.

Invasive lobular carcinomas (ILC) are characterized by the loss of E-cadherin expression and CDH1 gene inactivation. Diagnostic reproducibility for this tumor type is currently suboptimal and could be improved by a better understanding of its histomolecular and clinical heterogeneity. We have analyzed the relationship between the presence, type, or position of CDH1 mutations, E-cadherin expression, and clinicopathological features (including outcome) in a retrospective series of 251 primary ILC with a long follow-up (median: 9.

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity, which can be used to identify viral lineages (including variants of concern) that are circulating in a local population.

Support after return to alcohol use: a mixed-methods study on how abstinence motivation and app use change after return to alcohol use in an app-based aftercare intervention for individuals with alcohol use disorder.

Background: As the return to alcohol use in individuals with alcohol use disorder (AUD) is common during treatment and recovery, it is important that abstinence motivation is maintained after such critical incidences. Our study aims to explore how individuals with AUD participating in an app-based intervention with telephone coaching after inpatient treatment perceived their abstinence motivation after the return to alcohol use, whether their app use behavior was affected and to identify helpful factors to maintain abstinence motivation.

Methods: Using a mixed-methods approach, ten participants from the intervention group of the randomized controlled trial SmartAssistEntz who returned to alcohol use and recorded this in the app Appstinence, a smartphone application with telephone coaching designed for individuals with AUD, were interviewed about their experiences.

Automatic inference of ICD-10 codes from German ophthalmologic physicians' letters using natural language processing.

Physicians' letters are the optimal source of diagnoses for registries. However, most registries demand for diagnosis codes such as ICD-10. We herein describe an algorithm that infers ICD-10 codes from German ophthalmologic physicians' letters.

Molecular and Clinical Portrait of HER2-low Invasive Lobular Carcinomas.

Invasive lobular carcinomas (ILCs) have a low frequency of ERBB2 amplification, therefore restricting the use of conventional anti-HER2 therapies for this histologic special type. Conversely, ILCs with low HER2 overexpression may represent a broader target for the use of emerging antibody drug conjugate therapies targeting HER2, since these treatments have proven effective in HER2-low breast cancers. Very scarce data about HER2-low ILCs have been so far published, although these tumors could have different prevalence and histomolecular specificities compared with invasive breast carcinoma of no special type (IBC-NST).

Additive effects of adjunctive app-based interventions for mental disorders - A systematic review and meta-analysis of randomised controlled trials.

Background: It is uncertain whether app-based interventions add value to existing mental health care.

Objective: To examine the incremental effects of app-based interventions when used as adjunct to mental health interventions.

Methods: We searched PubMed, PsycINFO, Scopus, Web of Science, and Cochrane Library databases on September 15th, 2023, for randomised controlled trials (RCTs) on mental health interventions with an adjunct app-based intervention compared to the same intervention-only arm for adults with mental disorders or respective clinically relevant symptomatology.

Parallel evolution and enhanced virulence upon passage of an RNA virus in .

Virus evolution is strongly affected by antagonistic co-evolution of virus and host. Host immunity positively selects for viruses that evade the immune response, which in turn may drive counter-adaptations in host immune genes. We investigated how host immune pressure shapes virus populations, using the fruit fly and its natural pathogen Drosophila C virus (DCV), as a model.

National survey of user-reported usability of electronic medical record software in ophthalmology in Germany.

Purpose: A nationwide, comparative survey of the physician-reported usability of electronic medical record (EMR) software used by ophthalmologists in Germany using the System Usability Scale (SUS) as a standardized metric.

Methods: A cross-sectional survey of members of the German Ophthalmological Society (DOG) and professional association of ophthalmologists (BVA) was conducted in May 2022. All 7788 physician members of both societies were invited to participate in an anonymous online-survey by individualized links.

MDM4 amplification in atypical lipomatous tumors/well-differentiated liposarcoma: Private event or alternative oncogenic mechanism?

Adipocytic tumors are the most common mesenchymal tumors in soft tissues. Among them, a diagnostic challenge relies in the distinction between lipoma and atypical lipomatous tumor (ALT)/well differentiated liposarcoma (WDLPS), as both entities are often undistinguishable not only from a radiological point of view, but also at the microscopic level and particularly when dealing with small tumor specimen. Thus, detection of recurrent MDM2 amplifications may be the only criteria to discriminate malignant tumors from lipomas.

Effects of a Specific Pre- and Probiotic Combination and Parent Stock Vaccination on Performance and Bacterial Communities in Broilers Challenged with a Multidrug-Resistant .

Antibiotic resistance poses a risk for human and animal health, leading to a growing demand for effective alternatives. Combining nutritional tools and parent stock vaccination could be an approach to achieve sufficient protection against bacterial infections in poultry. In an O1/O18 challenge trial, we investigated the protective effects of feeding diets containing DSM 7134 and fructooligosaccharides (FOS) combined with specific parent stock vaccination in 225 ROSS 308 broilers.

Influence of short-term face mask wear on semiautomatically measured tear film parameters in dry eye patients and healthy volunteers.

Purpose: The use of face masks has been proposed to cause or exacerbate the symptoms of dry eye disease (DED), which has been widely discussed under the term mask-associated dry eye (MADE). However, no studies have systematically investigated tear film parameters during the use of different face masks. Therefore, the objective of the present study was to investigate clinically relevant parameters of the tear film before and during the short-time use of face masks in dry and normal eyes.

Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC.

The continuing emergence of SARS-CoV-2 variants of concern and variants of interest emphasizes the need for early detection and epidemiological surveillance of novel variants. We used genomic sequencing of 122 wastewater samples from three locations in Switzerland to monitor the local spread of B.1.

Breast carcinomas with osteoclast-like giant cells: a comprehensive clinico-pathological and molecular portrait and evidence of RANK-L expression.

Breast carcinomas (BC) with osteoclast-like giant cells (OGC) are rare. Despite their distinct stromal features, their molecular characteristics remain unknown. Here, we report comprehensive clinico-pathological and molecular findings for 27 patients diagnosed with BC-OGC at Institut Curie between 2000 and 2021.

[Current situation of electronic medical records in ophthalmological departments in Germany].

Background: Electronic medical records are required in ophthalmology clinics to be integrated into digital care networks and efficient clinical registry databases.

Aim Of The Work: To assess the prevalence and methods of electronic medical recordkeeping in inpatient ophthalmological care in Germany.

Material And Methods: An online questionnaire was sent to all German university eye hospitals and ophthalmology departments in June 2021.

App-based maintenance treatment for alcohol use disorder after acute inpatient treatment: Study protocol for a multicentre randomized controlled trial.

Background: Alcohol use disorder, a prevalent and disabling mental health problem, is often characterized by a chronic disease course. While effective inpatient and aftercare treatment options exist, the transferal of treatment success into everyday life is challenging and many patients remain without further assistance. App-based interventions with human guidance have great potential to support individuals after inpatient treatment, yet evidence on their efficacy remains scarce.

Lower Emotion Regulation Competencies Mediate the Association between Impulsivity and Craving during Alcohol Withdrawal Treatment.

There is evidence that craving mediates the relationship between Impulsive Personality Traits (IPTs) and relapse during the treatment of an Alcohol Use Disorder (AUD). To provide tailored interventions, a deeper understanding of the relation between IPTs and craving, namely mediating processes, is important. Based on previous literature, we proposed that lower emotion regulation competencies mediate the relation between attentional as well as non-planning IPTs and craving.

The Impact of Pre- and Probiotic Product Combinations on Ex vivo Growth of Avian Pathogenic and Enteritidis.

Due to the global spread of antibiotic resistance, there is a strong demand to replace antimicrobial growth promotors in livestock. To identify suitable additives that inhibit the growth of avian pathogenic O1/O18 and serotype Enteritidis strains, an ex vivo screening was performed. Inulin and fructooligosaccharides (FOS) were investigated as prebiotics.

Assessment of the Molecular Heterogeneity of E-Cadherin Expression in Invasive Lobular Breast Cancer.

Mutations and loss of E-cadherin protein expression define the vast majority of invasive lobular carcinomas. In a subset of these cases, the heterogeneous expression of E-cadherin is observed either as wild-type (strong membranous) expression or aberrant expression (cytoplasmic expression). However, it is unclear as to whether the two components would be driven by distinct genetic or epigenetic alterations.

Association of impulsivity with quality of life and well-being after alcohol withdrawal treatment.

Objectives: Impulsivity is related to a higher risk of relapse in alcohol use disorders. However, besides drinking behavior, other recovery outcomes like physical and mental health-related quality of life are at least as important. The present study aimed to fill a research gap regarding the association of different impulsivity facets with health-related quality of life and well-being in alcohol use disorder.