RepViz: A replicate-driven R tool for visualizing genomic regions

Objective: Visualization of sequencing data is an integral part of genomic data analysis. Although there are several tools to visualize sequencing data on genomic regions, they do not ofer user-friendly ways to view simultaneously diferent groups of replicates. To address this need, we developed a tool that allows efcient viewing of both intraand intergroup variation of sequencing counts on a genomic region, as well as their comparison to the output of user selected analysis methods, such as peak calling. Results: We present an R package RepViz for replicate-driven visualization of genomic regions. With ChIP-seq and ATAC-seq data we demonstrate its potential to aid visual inspection involved in the evaluation of normalization, outlier behavior, detected features from diferential peak calling analysis, and combined analysis of multiple data types. RepViz is readily available on Bioconductor (https://www.bioconductor.org/packages/devel/bioc/html/RepViz.html) and on Github (https://github.com/elolab/RepViz).</p

Ectodysplasin target gene Fgf20 regulates mammary bud growth and ductal invasion and branching during puberty

Mammary gland development begins with the appearance of epithelial placodes that invaginate, sprout, and branch to form small arborized trees by birth. The second phase of ductal growth and branching is driven by the highly invasive structures called terminal end buds (TEBs) that form at ductal tips at the onset of puberty. Ectodysplasin (Eda), a tumor necrosis factor-like ligand, is essential for the development of skin appendages including the breast. In mice, Eda regulates mammary placode formation and branching morphogenesis, but the underlying molecular mechanisms are poorly understood. Fibroblast growth factor (Fgf) receptors have a recognized role in mammary ductal development and stem cell maintenance, but the ligands involved are ill-defined. Here we report that Fgf20 is expressed in embryonic mammary glands and is regulated by the Eda pathway. Fgf20 deficiency does not impede mammary gland induction, but compromises mammary bud growth, as well as TEB formation, ductal outgrowth and branching during puberty. We further show that loss of Fgf20 delays formation of Eda-induced supernumerary mammary buds and normalizes the embryonic and postnatal hyperbranching phenotype of Eda overexpressing mice. These findings identify a hitherto unknown function for Fgf20 in mammary budding and branching morphogenesis.Peer reviewe

A carbohydrate-active enzyme (CAZy) profile links successful metabolic specialization of Prevotella to its abundance in gut microbiota

Gut microbiota participates in diverse metabolic and homeostatic functions related to health and well-being. Its composition varies between individuals, and depends on factors related to host and microbial communities, which need to adapt to utilize various nutrients present in gut environment. We profiled fecal microbiota in 63 healthy adult individuals using metaproteomics, and focused on microbial CAZy (carbohydrate-active) enzymes involved in glycan foraging. We identified two distinct CAZy profiles, one with many Bacteroides-derived CAZy in more than one-third of subjects (n = 25), and it associated with high abundance of Bacteroides in most subjects. In a smaller subset of donors (n = 8) with dietary parameters similar to others, microbiota showed intense expression of Prevotella-derived CAZy including exo-beta-(1,4)-xylanase, xylan-1,4-beta-xylosidase, alpha-L-arabinofuranosidase and several other CAZy belonging to glycosyl hydrolase families involved in digestion of complex plant-derived polysaccharides. This associated invariably with high abundance of Prevotella in gut microbiota, while in subjects with lower abundance of Prevotella, microbiota showed no Prevotella-derived CAZy. Identification of Bacteroides- and Prevotella-derived CAZy in microbiota proteome and their association with differences in microbiota composition are in evidence of individual variation in metabolic specialization of gut microbes affecting their colonizing competence

Effects of age, gender and soil-transmitted helminth infection on prevalence of Plasmodium infection among population living in bata district, equatorial Guinea

INTRODUCTION: Malaria and soil-transmitted helminth (STH) co-infection is an important parasitic infection affecting populations in co-endemic countries including Equatorial Guinea. To date, the health impact of STH and malaria co-infection is inconclusive. The current study aimed to report the malaria and STH infection epidemiology in the continental region of Equatorial Guinea. METHODS: We performed a cross-sectional study between October 2020 and January 2021 in the Bata district of Equatorial Guinea. Participants aged 1-9 years, 10-17 years and above 18 were recruited. Fresh venous blood was collected for malaria testing via mRDTs and light microscopy. Stool specimens were collected, and the Kato-Katz technique was used to detect the presence of Ascaris lumbricoides, Trichuris trichiura, hookworm spp. and intestinal Schistosoma eggs. RESULTS: A total of 402 participants were included in this study. An amount of 44.3% of them lived in urban areas, and only 51.9% of them reported having bed nets. Malaria infections were detected in 34.8% of the participants, while 50% of malaria infections were reported in children aged 10-17 years. Females had a lower prevalence of malaria (28.8%) compared with males (41.7%). Children of 1-9 years carried more gametocytes compared with other age groups. An amount of 49.3% of the participants infected with T. trichiura had malaria parasites compared with those infected with A. lumbricoides (39.6%) or both (46.8%). CONCLUSIONS: The overlapping problem of STH and malaria is neglected in Bata. The current study forces the government and other stakeholders involved in the fight against malaria and STH to consider a combined control program strategy for both parasitic infections in Equatorial Guinea

Learned helplessness in chess players: The importance of task similarity and the role of skill

The effects of noncontingency between subjects' responses and outcomes were examined with respect to treatment/posttest similarity and skill in the task. The experimental design consisted of three groups. The first group had to solve chess problems with objective solutions and received veridical feedback; each member of the second group faced problems with no objective solutions, and received the same feedback as the member of the first group he was yoked with, but without any control on it; the control group received a waiting task. It was found that the group with unsolvable problems was more depressed than the two other groups at the end of the experiment. The mid-strength players were the most sensitive to the manipulation, and the weakest players showed little effect of learned helplessness. It was also found that the effects were proportional to the degree of similarity between the treatment and the posttest. The results limit the domain of applicability of the learned helplessness model

Exploring local knowledge and perceptions on zoonoses among pastoralists in northern and eastern Tanzania

Background: Zoonoses account for the most commonly reported emerging and re-emerging infectious diseases in Sub-Saharan Africa. However, there is limited knowledge on how pastoral communities perceive zoonoses in relation to their livelihoods, culture and their wider ecology. This study was carried out to explore local knowledge and perceptions on zoonoses among pastoralists in Tanzania. Methodology and principal findings: This study involved pastoralists in Ngorongoro district in northern Tanzania and Kibaha and Bagamoyo districts in eastern Tanzania. Qualitative methods of focus group discussions, participatory epidemiology and interviews were used. A total of 223 people were involved in the study. Among the pastoralists, there was no specific term in their local language that describes zoonosis. Pastoralists from northern Tanzania possessed a higher understanding on the existence of a number of zoonoses than their eastern districts' counterparts. Understanding of zoonoses could be categorized into two broad groups: a local syndromic framework, whereby specific symptoms of a particular illness in humans concurred with symptoms in animals, and the biomedical framework, where a case definition is supported by diagnostic tests. Some pastoralists understand the possibility of some infections that could cross over to humans from animals but harm from these are generally tolerated and are not considered as threats. A number of social and cultural practices aimed at maintaining specific cultural functions including social cohesion and rites of passage involve animal products, which present zoonotic risk. Conclusions: These findings show how zoonoses are locally understood, and how epidemiology and biomedicine are shaping pastoralists perceptions to zoonoses. Evidence is needed to understand better the true burden and impact of zoonoses in these communities. More studies are needed that seek to clarify the common understanding of zoonoses that could be used to guide effective and locally relevant interventions. Such studies should consider in their approaches the pastoralists' wider social, cultural and economic set up

Drama as a pedagogical tool for practicing death notification-experiences from Swedish medical students

<p>Abstract</p> <p>Background</p> <p>One of the toughest tasks in any profession is the deliverance of death notification. Marathon Death is an exercise conducted during the fourth year of medical school in northern Sweden to prepare students for this responsibility. The exercise is designed to enable students to gain insight into the emotional and formal procedure of delivering death notifications. The exercise is inspired by Augusto Boal's work around Forum Theatre and is analyzed using video playback. The aim of the study was to explore reflections, attitudes and ideas toward training in delivering death notifications among medical students who participate in the Marathon Death exercise based on forum play.</p> <p>Methods</p> <p>After participation in the Marathon Death exercise, students completed semi-structured interviews. The transcribed interviews were analyzed using the principles of qualitative content analysis including a deductive content analysis approach with a structured matrix based on Bloom's taxonomy domains.</p> <p>Results</p> <p>The Marathon Death exercise was perceived as emotionally loaded, realistic and valuable for the future professional role as a physician. The deliverance of a death notification to the next of kin that a loved one has died was perceived as difficult. The exercise conjured emotions such as positive expectations and sheer anxiety. Students perceived participation in the exercise as an important learning experience, discovering that they had the capacity to manage such a difficult situation. The feedback from the video playback of the exercise and the feedback from fellow students and teachers enhanced the learning experience.</p> <p>Conclusions</p> <p>The exercise, Marathon Death, based on forum play with video playback is a useful pedagogical tool that enables students to practice delivering death notification. The ability to practice under realistic conditions contributes to reinforce students in preparation for their future professional role.</p

Experiences of dementia in a foreign country: qualitative content analysis of interviews with people with dementia

Background: Dementia is a worldwide health concern of epidemic proportions. Research in the field of subjective experience of dementia suffers from a lack of diversity of their participants including immigrants. Different portraits of life with dementia could help us understand how people with dementia conceptualise their experiences of dementia and how they live. Our study aimed to explore the subjective experiences of living with dementia among Iranian immigrants in Sweden. Methods: Qualitative content analysis of interviews with fifteen people with dementia from Iranian immigrant backgrounds were conducted (8 females and 7 males). Results: Three themes and seven associated sub-themes were revealed. The themes included: Being a person with dementia means living with forgetfulness (personal sphere), living with forgetfulness in the private sphere means feeling incompetent but still loved, living with forgetfulness in the public sphere means feeling confident and secure but also isolated. Conclusions: Living with dementia for the participants meant living with forgetfulness. They experienced feeling incompetent but still loved within their families and feeling confident and secure but also isolated in the society. Educating people with dementia and their families about the course and process of dementia may help them understand the changes better and adjust their expectations. Our study can provide a basis for healthcare workers to understand the experiences of living with dementia from this specific perspective