RNF: a general framework to evaluate NGS read mappers

Aligning reads to a reference sequence is a fundamental step in numerous bioinformatics pipelines. As a consequence, the sensitivity and precision of the mapping tool, applied with certain parameters to certain data, can critically affect the accuracy of produced results (e.g., in variant calling applications). Therefore, there has been an increasing demand of methods for comparing mappers and for measuring effects of their parameters. Read simulators combined with alignment evaluation tools provide the most straightforward way to evaluate and compare mappers. Simulation of reads is accompanied by information about their positions in the source genome. This information is then used to evaluate alignments produced by the mapper. Finally, reports containing statistics of successful read alignments are created. In default of standards for encoding read origins, every evaluation tool has to be made explicitly compatible with the simulator used to generate reads. In order to solve this obstacle, we have created a generic format RNF (Read Naming Format) for assigning read names with encoded information about original positions. Futhermore, we have developed an associated software package RNF containing two principal components. MIShmash applies one of popular read simulating tools (among DwgSim, Art, Mason, CuReSim etc.) and transforms the generated reads into RNF format. LAVEnder evaluates then a given read mapper using simulated reads in RNF format. A special attention is payed to mapping qualities that serve for parametrization of ROC curves, and to evaluation of the effect of read sample contamination

FCA as a means for consolidation of clustering results derived from multiple experiments

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Book review: disrupt this! MOOCs and the promise of technology by Karen Head

In Disrupt This! MOOCs and the Promise of Technology, Karen Head draws on a 'view from inside' of developing and teaching a first-year writing massive open online course (MOOC) to critically interrogate the claim that such technology will fundamentally ‘disrupt’ educational structures. This is an eloquent and intricate analysis that shows how personal experience and practice can add nuance to questions regarding the egalitarian potential of MOOCs, writes Yana Boeva

Book review: unreal objects: digital materialities, technoscientific projects and political realities by Kate O'Riordan

In Unreal Objects: Digital Materialities, Technoscientific Projects and Political Realities, Kate O’Riordan explores how emerging and future technologies such as in vitro meat and fitness trackers are ‘unreal objects’ that are shaped and brought into being through the media and often hidden networks of financial investment. In inviting readers to think critically about the discourses and material structures behind technological hype, this book is an excellent analysis of the role of mediation in constructing visions of technoscience, recommends Yana Boeva. Unreal Objects: Digital Materialities, Technoscientific Projects and Political Realities. Kate O’Riordan. Pluto Press. 2017

Break, Make, Retake: Interrogating the Social and Historical Dimensions of Making as a Design Practice

Making and digital fabrication technologies are the focus of bold promises. Among the most tempting are that these activities and processes require little initial skill, knowledge, and expertise. Instead, they enable their acquisition, opening them up to everyone. Makerspaces and fab labs would blur the identities between professional and amateur, designer and engineer, maker and hacker, ushering in a broad-based de-professionalization. Prototyping and digital fabrication would unite design and manufacturing in ways that resemble and revive traditional craftwork. These activities and processes promise the reindustrialization of places where manufacturing has disappeared. These promises deploy historical categories and conditionsexpertise, design, craft production, manufacturing, post- industrial urbanismwhile claiming to transform them. This dissertation demonstrates how these proposals and narratives rely on imaginaries in which countercultural practices become mainstream by presenting a threefold argument. First, making and digital fabrication sustain supportive environments that reconfigure contemporary design practice. Second, making and digital fabrication simultaneously reshape the categories of professional, amateur, work, leisure, and expertise; but not always in the ways its proponents suggest. Third, as making and digital fabrication propagate, they reproduce traditional practices and values, negating much of their countercultural and alternative capacities. The dissertation supports these claims through a multi-sited and multinational ethnographic investigation of the historical and social effects of making and digital fabrication on design practice and the people and places enacting. The study lies at the intersection of science and technology studies, human-computer interaction, and design research. In addressing the argument throughout this scholarship, it explores three central themes: (1) the idea that making and digital fabrication lead to instant materialization of design while re-uniting design with manufacturing; (2) the amount of skill and expertise expected for participation in these practices and how these are encoded in rhetoric and in practice; and (3) the material and social infrastructures that configure making as a design practice. The dissertation demonstrates that that the perceived marginality of making, maker cultures, digital fabrication allows for its bolder promises to thrive invisibly by concealing other social issues, while the societal contributions of this technoculture say something different on the surface

Factors influencing on the decision for abortion and not using contraception

The problems of the reproductive health and sexual behavior provoke an increasing scholarly interest and study in Bulgaria. Research made on various aspects of sexual behavior say, that abortion is still practiced as a means of regulating number of children in family and contraception are not known enough. The larger choice of contraceptive methods is associated with lower fertility and a smaller percentage of abortions

Opinion of Midwives on the Introduction of Post-Birth Patronage

The postpartum period is very stressful for every woman. This is the time for the mother to get to know and adapt to the newborn. The scale of the worries depends on the family's financial resources, the preliminary preparation for this moment, the age of the woman, and the presence or absence of help at home. (5). Home obstetric visits after childbirth are the natural continuation of the support and care for the woman who has just given birth (4). The aim of the present study is to determine the attitudes of midwives in hospital and outpatient care towards conducting home postpartum visits. It was carried out between 2020 and 2022 among 94 midwives from northeastern Bulgaria working in the Department/Sector Pathology of Pregnancy and Maternity Ward and 21 midwives working in the outpatient care field in Varna. Documentary, sociological, and statistical methods were used. According to the data analysis, 94.7% of those working in hospital care and 71% of those working in outpatient care optimize obstetric treatment during the puerperium. The proportion of midwives in hospital care who support the introduction of obstetric care is exceptionally high (97.9%), while 80.9% of outpatient care is responding positively. More than 2/3 (68.1%) of the working midwives in hospital care would work as patronage midwives, and the same desire is expressed by 52.4% of the respondents in outpatient care. The conclusion we draw from the data obtained is that hospital midwives are more supportive of the introduction of home postpartum patronage.