PCA and K-Means decipher genome

In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of genetic text of a bacterial genome and analyze its structure. By means of principal component analysis they ``discover'' that the information in the genome is encoded by non-overlapping triplets. Next, they learn how to find gene positions. This exercise on PCA and K-Means clustering enables active study of the basic bioinformatics notions. Appendix 1 contains program listings that go along with this exercise. Appendix 2 includes 2D PCA plots of triplet usage in moving frame for a series of bacterial genomes from GC-poor to GC-rich ones. Animated 3D PCA plots are attached as separate gif files. Topology (cluster structure) and geometry (mutual positions of clusters) of these plots depends clearly on GC-content.Comment: 18 pages, with program listings for MatLab, PCA analysis of genomes and additional animated 3D PCA plot

Network-wide Configuration Synthesis

Computer networks are hard to manage. Given a set of high-level requirements (e.g., reachability, security), operators have to manually figure out the individual configuration of potentially hundreds of devices running complex distributed protocols so that they, collectively, compute a compatible forwarding state. Not surprisingly, operators often make mistakes which lead to downtimes. To address this problem, we present a novel synthesis approach that automatically computes correct network configurations that comply with the operator's requirements. We capture the behavior of existing routers along with the distributed protocols they run in stratified Datalog. Our key insight is to reduce the problem of finding correct input configurations to the task of synthesizing inputs for a stratified Datalog program. To solve this synthesis task, we introduce a new algorithm that synthesizes inputs for stratified Datalog programs. This algorithm is applicable beyond the domain of networks. We leverage our synthesis algorithm to construct the first network-wide configuration synthesis system, called SyNET, that support multiple interacting routing protocols (OSPF and BGP) and static routes. We show that our system is practical and can infer correct input configurations, in a reasonable amount time, for networks of realistic size (> 50 routers) that forward packets for multiple traffic classes.Comment: 24 Pages, short version published in CAV 201

Awareness and willingness to use HIV pre-exposure prophylaxis amongst gay and bisexual men in Scotland: implications for biomedical HIV prevention

Objectives:<p></p> To investigate the awareness of, and willingness to use, HIV Pre-Exposure Prophylaxis (PrEP), and willingness to take part in a PrEP study among gay and bisexual men in Scotland.<p></p> Methods:<p></p> Cross-sectional survey of 17 gay commercial venues in Glasgow and Edinburgh in May 2011 (N = 1515, 65.2% response rate); 1393 are included in the analyses.<p></p> Results:<p></p> Just under one-third of participants had heard of PrEP (n = 434; 31.2%), with awareness associated with being aged older than 35 years, talking to UAI partners about HIV, and with having had an HIV or STI test in the previous 12 months. Around half were willing to take part in a PrEP study (n = 695; 49.9%) or to take PrEP on a daily basis (n = 756; 54.3%). In multivariate analysis, willingness to take PrEP was associated with lower levels of education, regular gay scene attendance, ‘high-risk’ unprotected anal intercourse (UAI) and testing for HIV or STI in the previous 12 months. Reasons for not wanting to participate in a PrEP study or take PrEP included perceptions of low personal risk of HIV and concerns with using medication as an HIV prevention method.<p></p> Conclusions:<p></p> There is a willingness to engage in new forms of HIV prevention and research amongst a significant number of gay and bisexual men in Scotland. Future biomedical HIV interventions need to consider the links between sexual risk behaviour, testing, and potential PrEP use

Dental Findings in Cornelia De Lange Syndrome

Cornelia de Lange syndrome is a congenital disease, basically characterized by psychomotor retardation associated with a series of malformations, including mainly skeletal, craniofacial deformities together with gastrointestinal and cardiac malformations. There is no definitive biochemical or chromosomal marker for the prenatal diagnosis of this syndrome. We actually want to present the case of a 10-year-old patient, who was admitted to our clinic for dental pain. The patient had the symptoms of Cornelia de Lange syndrome. During the oral examination of this patient, the patient was found to have the typical symptoms of Cornelia de Lange syndrome, such as micrognathia and delayed eruption in conjunction with the symptoms of the Hutchinson's syndrome, which had never been reported before

Spatial and topological organization of DNA chains induced by gene co-localization

Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated. Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close-by. This is motivated by recurrent evidence that there exists physical interactions between genes that operate together. Three important results come out of this simple framework. First, the resulting formation of transcription foci can be viewed as a micro-phase separation of the interacting sites from the rest of the DNA. In this respect, a thermodynamic analysis suggests transcription factors to be appropriate candidates for mediating the physical interactions between genes. Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting sites. Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization of multiple families of genes particularly efficient.Comment: Figures and Supplementary Material freely available on http://dx.doi.org/10.1371/journal.pcbi.100067

Mums Alone: Exploring the Role of Isolation and Loneliness in the Narratives of Women Diagnosed with Perinatal Depression.

In this study, we explore the role that isolation and loneliness play in the narratives of women diagnosed with perinatal depression. Isolation and loneliness are increasingly seen as risk factors for depression, including in the perinatal period, but little is known about whether, and in what ways, women themselves associate isolation or loneliness with perinatal distress. Based on the thematic analysis of semi-structured interviews with fourteen mothers in England, we found that women often connected feelings of depression during and after pregnancy to feeling dislocated from their previous identities and relationships. Women felt lost, confined to their homes, and often unsupported by their partners and families. However, fears of being judged to be inadequate mothers made it difficult for women to make authentic connections with others or to express negative feelings, increasing isolation and depression. We drew on the intersectionality theory to illustrate how the intersect between motherhood and other aspects of women's identities (being young, single, deprived and/or from an ethnic minority) could leave some women particularly isolated and marginalised. Our conclusions emphasise the need to challenge social constructions of the good/bad mother, advocate for social change to lessen pressures on mothers, and develop support that addresses women's interpersonal contexts and social networks

Seeing the baby, doing family: commercial ultrasound as family practice?

Medical sociologists and anthropologists have studied the social significance of obstetric ultrasound for families but little is known about how women and families make use of commercially available ultrasound scans. This article draws on interviews with women who booked a scan with a commercial company in the UK. For some women, commercial ultrasound can be understood as a family practice. We investigate this theme by examining who accompanies women to commercial scan appointments, how scan images are shared and how sonograms are used as prompts to resemblance talk. We argue that commercial scans are more than an additional opportunity to acquire ‘baby’s first picture’ and offer a flexible resource to do family, creating and affirming family relationships and rehearsing roles as parents, siblings and grandparents. Our findings confirm the importance of imagination in doing family and raise questions about the role of technology and commercial interests in shaping family practices

Combustion in thermonuclear supernova explosions

Type Ia supernovae are associated with thermonuclear explosions of white dwarf stars. Combustion processes convert material in nuclear reactions and release the energy required to explode the stars. At the same time, they produce the radioactive species that power radiation and give rise to the formation of the observables. Therefore, the physical mechanism of the combustion processes, as reviewed here, is the key to understand these astrophysical events. Theory establishes two distinct modes of propagation for combustion fronts: subsonic deflagrations and supersonic detonations. Both are assumed to play an important role in thermonuclear supernovae. The physical nature and theoretical models of deflagrations and detonations are discussed together with numerical implementations. A particular challenge arises due to the wide range of spatial scales involved in these phenomena. Neither the combustion waves nor their interaction with fluid flow and instabilities can be directly resolved in simulations. Substantial modeling effort is required to consistently capture such effects and the corresponding techniques are discussed in detail. They form the basis of modern multidimensional hydrodynamical simulations of thermonuclear supernova explosions. The problem of deflagration-to-detonation transitions in thermonuclear supernova explosions is briefly mentioned.Comment: Author version of chapter for 'Handbook of Supernovae,' edited by A. Alsabti and P. Murdin, Springer. 24 pages, 4 figure