The COVID-19 pandemic has demonstrated the need for massively-parallel, cost-effective tests monitoring viral spread. Here we present SARSeq, saliva analysis by RNA sequencing , a method to detect SARS-CoV-2 and other respiratory viruses on tens of thousands of samples in parallel. SARSeq relies on next generation sequencing of multiple amplicons generated in a multiplexed RT-PCR reaction. Two-dimensional, unique dual indexing, using four indices per sample, enables unambiguous and scalable assignment of reads to individual samples. We calibrate SARSeq on SARS-CoV-2 synthetic RNA, virions, and hundreds of human samples of various types. Robustness and sensitivity were virtually identical to quantitative RT-PCR. Double-blinded benchmarking to gold standard quantitative-RT-PCR performed by human diagnostics laboratories confirms this high sensitivity. SARSeq can be used to detect Influenza A and B viruses and human rhinovirus in parallel, and can be expanded for detection of other pathogens. Thus, SARSeq is ideally suited for differential diagnostic of infections during a pandemic. Massively parallel but cost-effective testing is essential to monitor the spread of pathogenic agents. Here the authors present SARSseq, which uses a dual indexing strategy in a multiplexed RT-PCR reaction to diagnose SARS-CoV-2 at scale.

Purpose The acute scrotum (AS) in the pediatric population is a medical emergency. The most common causes of AS include testicular torsion (TT) and torsion of the appendix testis (TAT). Their distinction may be clinically challenging. The purpose of our study was to compare demographic and clinical characteristics of the pediatric cases of TT and TAT and thus provide clinical evidence for distinguishing these two conditions. Methods We retrospectively analyzed all children ≤ 16 years who underwent surgical exploration for AS. The patients were divided into Group 1 or TT and Group 2 or TAT groups. Results Ninety patients were included in the study (24 with TT and 66 with TAT). Patients with TT were significantly older than those with TAT (p < 0.001). The peak incidence of TT was in the age of 12–16 years (p < 0.001), whereas the peak of TAT was in the age group of 7–11 years (p < 0.001). Scrotal pain was more prevalent in patients with TAT (p = 0.02), whereas systemic signs (nausea/vomiting and abdominal pain) affected more frequently the TT patients (p = 0.003 and p < 0.001, respectively). The mean duration of symptoms was significantly longer in the TAT group than in the TT group (p < 0.001). Color-Doppler Ultrasound (CDUS) findings of absent or decreased testicular blood flow in the affected testis strongly favored the diagnosis of TT (p < 0.001). Conclusion Our data indicate that the older age, shorter duration of symptoms, systemic signs (nausea/vomiting and abdominal pain), and characteristics CDUS findings can help distinguish between the two most common acute scrotum causes.

Background: Pandemic caused by the COVID-19 virus brought tremendous changes in the lifestyle of adolescents, about which numerous studies have been published. Due to extended restrictions, long term impact should be investigated.Methods: This cross-sectional study enrolled 953 voluntary participants aged 14 to 21, from different regions of B&H. Participants were asked to complete an online 37-item survey, regarding socio-demographics, geographic, social characteristics, dietary and lifestyle habits, physical activity, including their consumption of dietary, vitamin and mineral supplements. They also needed to provide information about their weight, height and weight change during the entire period of the COVID-19 pandemic from March 2020 until the end of November when the study was completed. For data entry and analysis, SPSS (version 25) and Microsoft Excel were used.Results: At the time of completing the survey, a slightly lower BMI of participants was noticed compared to the time before the pandemic. A statistically significant difference was determined between males and females BMI, boys BMI was slightly higher. Females gained and men lost BW. Increased intake of unhealthy types of food was associated with weight change. Increased mental stress during the pandemic was associated with dietary changes, respectively with decreased as also increased food amount. High percent of participants (40.4%) who increased their physical activity did not alter their eating in the form of the food amount. This study reported use of some dietary supplements which have not been used before the pandemic by 63.5% participants.Conclusions: This paper presents a unique insight into the changing lifestyle and eating habits of adolescents in B&H during lockdown and post-lockdown period of research. Considering that pandemic is still ongoing, data from study like this may be useful to create further steps in battling the pandemic.

The application of electronic findings to biology and medicine has significantly impacted health and wellbeing [...]

Deoxyribonuclease 1 like 3 (DNASE1L3) is a secreted enzyme that has been shown to digest the extracellular chromatin derived from apoptotic bodies, and DNASE1L3 pathogenic variants have been associated to a lupus phenotype. It is unclear whether interferon signaling is sustained in DNASE1L3 deficiency in humans. Here we report four new patients carrying biallelic DNASE1L3 pathogenic variations, including two previously unreported mutations. Disease in one patient was characterized by lupus nephritis and skin lesions, while two others exhibited hypocomplementemic urticarial vasculitis syndrome. The fourth patient presented with early-onset inflammatory bowel disease. To explore whether or not the interferon cascade was strongly and sustainably induced, Interferon stimulated genes (ISGs) expression was assessed for each patient. Contrary to canonical type-I interferonopathies, we noticed a transient increase of ISGs in blood, which reverted to normal with disease remission. Reviewing previous reports, DNASE1L3-related disease appears to carry a significant risk of lupus nephritis and a poor outcome together with the presence of anti-neutrophil cytoplasmic antibodies (ANCA). DNASE1L3 deficiency may share the pathogenesis with C1q deficiency by affecting efferocytosis, and this report suggests that interferon production is not directly driven by DNASE1L3 pathogenic variants.

Advances in single-cell RNA sequencing (scRNAseq) technologies uncovered an unexpected complexity in tumors, underlining the relevance of intratumor heterogeneity to cancer progression and therapeutic resistance. Heterogeneity in the mutational composition of cancer cells is a result of distinct (sub)clonal expansions, each with a distinct metastatic potential and resistance to specific treatments. Unfortunately, due to their low read coverage per cell, scRNAseq datasets are too sparse and noisy to be used for detecting expressed mutations in single cells. Additionally, the large number of cells and mutations present in typical scRNAseq datasets are too large for available computational tools to, e.g., infer distinct subclones, lineages or trajectories in a tumor. Finally, there are no principled methods to assess distinct subclones inferred through single-cell sequencing data and the genomic alterations that seed and potentially cause them. Here we present Trisicell, a computational toolkit for scalable mutational intratumor heterogeneity inference and assessment from scRNAseq as well as single-cell genome or exome sequencing data. Trisicell allows reliable identification of distinct clonal lineages of a tumor, offering the ability to focus on the most important subclones and the genomic alterations that are associated with tumor proliferation. We comprehensively assessed Trisicell on a melanoma model by comparing distinct lineages and subclones it identifies on scRNAseq data, to those inferred using matching bulk whole exome (bWES) and transcriptome (bWTS) sequencing data from clonal sublines derived from single cells. Our results demonstrate that distinct lineages and subclones of a tumor can be reliably inferred and evaluated based on mutation calls from scRNAseq data through the use of Trisicell. Additionally, they reveal a strong correlation between aggressiveness and mutational composition, both across the inferred subclones, and among human melanomas. We also applied Trisicell to infer and evaluate distinct subclonal expansion patterns of the same mouse melanoma model after treatment with immune checkpoint blockade (ICB). After integratively analyzing our cell-specific mutation calls with their expression profiles, we observed that each subclone with a distinct set of novel somatic mutations is strongly associated with a specific developmental status. Moreover, each subclone had developed a unique ICB-resistance mechanism. These results demonstrate that Trisicell can robustly utilize scRNAseq data to delineate intratumor heterogeneity and help understand biological mechanisms underlying tumor progression and resistance to therapy.

This paper presents a new method of steganography based on a combination of Catalan objects and Voronoi–Delaunay triangulation. Two segments are described within the proposed method. The first segment describes the process of embedding data and generating a complex stego key. The second segment explains the extraction of a hidden message. The main goal of this paper is to transfer a message via the Internet (or some other medium) using an image so that the image remains absolutely unchanged. In this way, we prevented the potential attacker from noticing some secret message hidden in that picture. Additionally, the complex stego key consists of three completely different parts (the image, the encrypted Delaunay triangulation, and the array Rk in Base64 code), which are very difficult to relate with each other. Finally, a few security analyses of the proposed method are conducted, as well as the corresponding steganalysis.

Abstract Clinopodium alpinum subsp. orontium (K.Malý) Govaerts and Thymus bracteosus Vis. ex Benth. are endemic Lamiaceae species in Bosnia and Herzegovina with rather limited data about their cytotoxic and genotoxic effects. This study aimed to analyse phenolic compounds composition of C. alpinum subsp. orontium and T. bracteosus aqueous and dimethyl sulphoxide (DMSO) extracts and their cytotoxic and genotoxic potential in human peripheral blood lymphocyte cultures. Among 33 analytes, 17 were identified and quantified in the examined extracts with the rosmarinic and chlorogenic acids as main constituents. Genotoxic effects of extracts from both species are proven at the highest applied dose. T. bracteosus extracts and DMSO as a solvent exhibited stronger genotoxic potential that should be further investigated in tumour cell lines. Nevertheless, non-endemic species with similar phenolic composition and bioactivity should be the first choice for medicinal purposes. Graphical Abstract

The present study was designed to determine the efficacy of a novel multicomponent mycotoxin detoxifying agent (MMDA) containing modified zeolite (Clinoptilolite), Bacillus subtilis, B. licheniformis, Saccharomyces cerevisiae cell walls and silymarin against the deleterious effects of Aflatoxin B1 (AFB1) and Ochratoxin A (OTA) in broiler chicks. A total of 160 one-day-old Ross 308® broiler chicks were randomly allocated in four treatment groups, with four replicates, according to the following experimental design for 42 days. Group A received a basal diet; Group B received a basal diet contaminated with AFB1 and OTA at 0.1 mg/kg and 1 mg/kg, respectively; Group C received a basal diet contaminated with AFB1 and OTA and MMDA at 1 g/kg feed, and Group D received a basal diet contaminated with AFB1 and OTA and MMDA at 3 g/kg feed. Results showed that ingested mycotoxins led to significant (p ≤ 0.05) reduction in body weight and feed conversion from 25 days of age, induced histopathological changes, increased the pH of the intestinal content, and altered the biochemical profile of birds with significantly (p ≤ 0.05) increased aspartate aminotransferase (AST) values (p ≤ 0.05). On the other hand, the supplementation of MMDA significantly (p ≤ 0.05) improved the feed conversion ratio (FCR) during the second part of the study, diminished biochemical alterations, reduced pH in jejunal and ileal content, and E. coli counts in the caeca of birds (p ≤ 0.05). It may be concluded that the dietary supplementation of the MMDA partially ameliorated the adverse effects of AFB1 and OTA in broilers and could be an efficient tool in a mycotoxin control program.