Recent studies exploring the impact of methylation in tumor evolution suggest that while the methylation status of many of the CpG sites are preserved across distinct lineages, others are altered as the cancer progresses. Since changes in methylation status of a CpG site may be retained in mitosis, they could be used to infer the progression history of a tumor via single-cell lineage tree reconstruction. In this work, we introduce the first principled distance-based computational method, Sgootr, for inferring a tumor’s single-cell methylation lineage tree and jointly identifying lineage-informative CpG sites which harbor changes in methylation status that are retained along the lineage. We apply Sgootr on the single-cell bisulfite-treated whole genome sequencing data of multiregionally-sampled tumor cells from 9 metastatic colorectal cancer patients made available by Bian et al., as well as multiregionally-sampled single-cell reduced-representation bisulfite sequencing data from a glioblastoma patient made available by Chaligne et al.. We demonstrate that the tumor lineages constructed reveal a simple model underlying colorectal tumor progression and metastatic seeding. A comparison of Sgootr against alternative approaches shows that Sgootr can construct lineage trees with fewer migration events and more in concordance with the sequential-progression model of tumor evolution, in time a fraction of that used in prior studies. Interestingly, lineage-informative CpG sites identified by Sgootr are in inter-CpG island (CGI) regions, as opposed to CGI’s, which have been the main regions of interest in genomic methylation-related analyses. Sgootr is implemented as a Snakemake workflow, available at https://github.com/algo-cancer/Sgootr.

Food contaminated with bacterial pathogens is a great threat to human health and food spoilage, having an impact on public health and the food industry. Research in food safety seeks to develop a practical, rapid, and sensitive detection technique for food-borne pathogens. In the past few decades, real-time quantitative polymerase chain reaction (qPCR) has been developed, and multiplex qPCR is a preferred feature. Multiplex qPCR enables the simultaneous amplification of many targets of interest in one reaction by using more than one pair of primers. In this study, we have developed and evaluated a hydrolysis (TaqMan) probe-based system for simultaneous detection of eight of the most common food-borne pathogens in a single-step procedure by multiplex qPCR. A multicolor combinational probe coding (MCPC) strategy was utilized that allows multiple fluorophores to label different probes in combinatorial manner. This strategy enabled simultaneous detection, identification, and quantification of targeted genes. The efficiency of the individual qPCR reactions for each target gene had values comparable to those established for multiplex qPCR, with detection limits of approximately < 10 copies of DNA per reaction. Pathogen load helps to predict bacteriological quality status in food products and serves to validate the efficiency of procedures to minimize or eliminate their presence, so newly developed multiplex qPCR was quantitative for each pathogen. During sample preparation, a step to concentrate the target organism from a relatively large sample size, remove all potential PCR inhibitors, and yield samples in a volume suitable for qPCR was incorporated.

<p>The participation of deaf and hard of hearing people in sports activities contributes to the improvement of the quality of life in all its domains, and compared to people with some other types of disabilities, deaf and hard of hearing people achieve higher scores in sports activities. Practicing sports activities improves physical health, mental state, degree of independence and social relationships. Sports activities have a positive effect on building and strengthening the self-esteem of individuals. Subjective experience and individual perception have a great influence on the quality of an individual&rsquo;s life, therefore, self-esteem is a very important factor that contributes to this. The aim of this paper is to review the literature from the period 2000&ndash;2021 on the impact of sports activities on the psychophysical health of deaf and hard of hearing people. The subject of interest was: to determine the role of sports activities in the quality of life of deaf and hard of hearing people, as well as how they affect their level of self-esteem. The following search engines were used for the literature search: Ebscohost, ScienceDirect, Wiley Inter Science and SpringerLink, KoBSON, Google Scholar. The results of the literature review showed that sports activities contributed to the preservation and development of the overall psychophysical health of deaf and hard of hearing people. Participation in sports activities, whether recreational or professional in nature, has proven to be a significant factor in raising the level of self-esteem, alleviating symptoms of anxiety and stress. Participation in sports activities leads to better social functioning among peers and building an inclusive society.</p>

Secure multiparty computation (MPC) is a cryptographic tool that allows computation on top of sensitive biomedical data without revealing private information to the involved entities. Here, we introduce Sequre, an easy-to-use, high-performance framework for developing performant MPC applications. Sequre offers a set of automatic compile-time optimizations that significantly improve the performance of MPC applications and incorporates the syntax of Python programming language to facilitate rapid application development. We demonstrate its usability and performance on various bioinformatics tasks showing up to 3–4 times increased speed over the existing pipelines with 7-fold reductions in codebase sizes.

As sessile organisms, plants have evolved different strategies to defend themselves against various biotic stressors. An important aspect of the complex response of plants to biotic stress is the emission of volatile compounds (VOCs), which are involved in direct and indirect plant defence mechanisms. Indirect plant defences include a range of plant traits that mediate defence against herbivores and play an important ecological role by not only utilising plants-' own capabilities but also signalling and attracting natural enemies of herbivores. Often the combination of volatiles emitted is specific to herbivores; they are consequently recognised by parasites and other predators, providing a clear link between the volatile signature and the prey. In this review, we focus on indirect plant defence and summarise current knowledge and perspectives on relationships between plants, aphids, and parasitic wasps.

The purpose of this work is to show the development and evaluation of behavioural intentions of students by using mobile banking. The research goal is to explain determinants of students’ intentions towards the use of mobile banking. PLS SEM (partial least squares structural equation modeling) analysis was used for the model evaluation. The sample consists of 83 students from four higher education institutions operating in Bosnia and Herzegovina (B&H). Research results confirmed that subjective norm and attitude are significant predictors of the user’s attitude towards mobile banking acceptance, while the influence of self-efficacy was not determined. Attitudes related to mobile banking acceptance are primarily determined by perception of usefulness and self-efficacy, and to a lower degree by perception of privacy and security risk. Perception of mobile banking usefulness appeared to be the most significant predictor of attitudes, while simultaneously it influenced positively on acceptance of behavioral intention, including intervening effect of attitude variable. Digital literacy was proved to be a significant predictor for self-efficacy. From the perspective of banks, it is very important to see how a generation that a high potential for the use of modern technologies has perceives mobile banking, and what affects it to accept mobile banking. The results of this research are useful for banks to attract new younger users of mobile banking and increase their own benefits.

This corrigendum corrects the authorship information to: Yipeng Xu, Gabriela Pachnikova, He Wang, Yaoyao Wu, Dorothea Przybilla, Zihao Chen, Shaoxing Zhu, Ulrich Keilholz. At the request of Dr. Reinhold Schäfer and with the agreement of all authors, Dr. Reinhold Schäfer is excluded from the list of authors. Dr. Schäfer expresses no doubts about the article's results and conclusion but was erroneously included on the list of authors. The authors sincerely apologize for the error and confirm that this correction does not change the conclusion of the article.

Introduction This study aims to examine can sport protect children against loneliness and, if yes, whether this relationship depends on gender and/or sports-related variables. Methods The sample includes 762 10-year-old children (414 boys). The total score of The Children's Loneliness Scale is a dependent variable in the study, while sports participation (sports active—individual or team sports, or non-active) and level/duration of sports participation are independent variables. Results Obtained results indicate that the degree of loneliness differs depending on gender and whether the children are in sports activities or not. Unlike the level of sports participation, the duration of sports participation is relevant to the loneliness degree in both boys and girls. Discussion This research results could represent the right direction for educators and/or parents in their endeavor to preserve and develop school-age children's mental health.

Tomato powder is produced by dehydrating tomatoes. The powder consists of only one ingredient, it represents the specificity of this product, namely dehydrated natural tomatoes. Among other things, drying as a preservation process is considered one of the best methods, because it ensures ease of use, transportation and storage. As part of the canning and processing of fruits and especially vegetables, tomato products have always occupied a very important place due to the organoleptic and culinary properties of these products, and the nutritional value of tomatoes as a raw material. Compared to other types of vegetables, tomatoes have a high yield, with some varieties even over 90%.The most important factor in tomato dehydration is the dehydration temperature as well as the time interval during which the dehydration process is carried out. In the dehydration process, two varieties of fresh tomatoes from the local market were used, which were dehydrated at temperatures of 50 and 75 °C. In parallel, a comparative physicochemical analysis of fresh tomato samples with dehydrated ground samples of tomato powder was performed. All analyzes in this research work were edited three times, and the mean value was used to display the graphical results.

Coevolution of microbiome and immunity at mucosal sites is essential for our health. Whether the oral microbiome, the second largest community after the gut, contributes to the immunogenicity of COVID-19 vaccines is not known. We investigated the baseline oral microbiome in individuals in the COVAXID clinical trial receiving the BNT162b2 mRNA vaccine. Participants (n=115) included healthy controls (HC; n=57) and people living with HIV (PLHIV; n=58) who met the study selection criteria. Vaccine-induced Spike antibodies in saliva and serum from 0 to 6 months were assessed and comparative analyses were performed against the individual salivary 16S ASV microbiome diversity. High- versus low vaccine responders were assessed on general, immunological, and oral microbiome features. Our analyses identified oral microbiome features enriched in high- vs. low-responders among healthy and PLHIV participants. In low-responders, an enrichment of Gram-negative, anaerobic species with proteolytic activity were found including Campylobacter, Butyrivibrio, Selenomonas, Lachnoanaerobaculum, Leptotrichia, Megasphaera, Prevotella and Stomatobaculum. In high-responders, enriched species were mainly Gram-positive and saccharolytic facultative anaerobes: Abiotrophia, Corynebacterium, Gemella, Granulicatella, Rothia, and Haemophilus. Combining identified microbial features in a classifier using the area under the receiver operating characteristic curve (ROC AUC) yielded scores of 0.879 (healthy controls) to 0.82 (PLHIV), supporting the oral microbiome contribution in the long-term vaccination outcome. The present study is the first to suggest that the oral microbiome has an impact on the durability of mucosal immunity after Covid-19 vaccination. Microbiome-targeted interventions to enhance long-term duration of mucosal vaccine immunity may be exploited.

Background Retinal degeneration leading to optical coherence tomography (OCT) changes is frequent in patients with multiple sclerosis (PwMS). Objective To investigate associations among OCT changes, MRI measurements of global and regional brain volume loss, and physical and cognitive impairment in PwMS. Methods 95 PwMS and 52 healthy controls underwent OCT and MRI examinations. Mean peripapillary retinal nerve fiber layer (pRNFL) thickness and ganglion cell/inner plexiform layer (GCIPL) volume were measured. In PwMS disability was quantified with the Expanded Disability Status Scale (EDSS) and Symbol Digit Modalities Test (SDMT). Associations between OCT, MRI, and clinical measures were investigated with multivariable regression models. Results In PwMS, pRNFL and GCIPL were associated with the volume of whole brain ( p  < 0.04), total gray matter ( p  < 0.002), thalamus ( p  ≤ 0.04), and cerebral cortex ( p  ≤ 0.003) –both globally and regionally–, but not white matter. pRNFL and GCIPL were also inversely associated with T2-lesion volume (T2LV), especially in the optic radiations ( p  < 0.0001). The brain volumes associated with EDSS and SDMT significantly overlapped with those correlating with pRNFL and GCIPL. Conclusions In PwMS, pRNFL and GCIPL reflect the integrity of clinically-relevant gray matter structures, underling the value of OCT measures as markers of neurodegeneration and disability in multiple sclerosis.

ABSTRACT Background Large international differences exist in kidney transplantation (KT) rates. We aimed to investigate which factors may explain the total, deceased donor and living donor KT rates over the last decade. Methods KT experts from 39 European countries completed the Kidney Transplantation Rate Survey on measures and barriers and their potential effect on the KT rate in their country. In the analyses, countries were divided into low, middle and high KT rate countries based on the KT rate at the start of study period in 2010. Results Experts from low KT rate countries reported more frequently that they had taken measures regarding staff, equipment and facilities to increase the total KT rate compared with middle and high KT rate countries. For donor type–specific KT, the largest international differences in measures taken were reported for deceased donor KT, with middle and high KT rate countries taking more measures, such as the use of expanded criteria donor kidneys, the presence of transplantation coordinators and (inter)national exchange of donor kidneys. Once a measure was taken, experts’ opinion on its success was similar across the low, middle and high KT rate countries. Experts from low KT rate countries more often reported potential barriers, such as patients’ lack of knowledge and distrust in the healthcare system. Conclusions Particularly in low KT rate countries, the KT rate might be stimulated by optimizing staff, equipment and facilities. In addition, all countries may benefit from measures specific to deceased and living donors.

Objectives Application of ‘treat-to-target’ (T2T) in childhood-onset systemic lupus erythematosus (cSLE) may improve care and health outcomes. This initiative aimed to harmonise existing evidence and expert opinion regarding T2T for cSLE. Methods An international T2T Task Force was formed of specialists in paediatric rheumatology, paediatric nephrology, adult rheumatology, patient and parent representatives. A steering committee formulated a set of draft overarching principles and points-to-consider, based on evidence from systematic literature review. Two on-line preconsensus meeting Delphi surveys explored healthcare professionals’ views on these provisional overarching principles and points-to-consider. A virtual consensus meeting employed a modified nominal group technique to discuss, modify and vote on each overarching principle/point-to-consider. Agreement of >80% of Task Force members was considered consensus. Results The Task Force agreed on four overarching principles and fourteen points-to-consider. It was agreed that both treatment targets and therapeutic strategies should be subject to shared decision making with the patient/caregivers, with full remission the preferred target, and low disease activity acceptable where remission cannot be achieved. Important elements of the points-to-consider included: aiming for prevention of flare and organ damage; glucocorticoid sparing; proactively addressing factors that impact health-related quality of life (fatigue, pain, mental health, educational challenges, medication side effects); and aiming for maintenance of the target over the long-term. An extensive research agenda was also formulated. Conclusions These international, consensus agreed overarching principles and points-to-consider for T2T in cSLE lay the foundation for future T2T approaches in cSLE, endorsed by the Paediatric Rheumatology European Society.