Finding 2-Edge and 2-Vertex Strongly Connected Components in Quadratic Time

We present faster algorithms for computing the 2-edge and 2-vertex strongly connected components of a directed graph, which are straightforward generalizations of strongly connected components. While in undirected graphs the 2-edge and 2-vertex connected components can be found in linear time, in directed graphs only rather simple $O(m n)$-time algorithms were known. We use a hierarchical sparsification technique to obtain algorithms that run in time $O(n^2)$. For 2-edge strongly connected components our algorithm gives the first running time improvement in 20 years. Additionally we present an $O(m^2 / \log{n})$-time algorithm for 2-edge strongly connected components, and thus improve over the $O(m n)$ running time also when $m = O(n)$. Our approach extends to k-edge and k-vertex strongly connected components for any constant k with a running time of $O(n^2 \log^2 n)$ for edges and $O(n^3)$ for vertices

Traditional birth attendants lack basic information on HIV and safe delivery practices in rural Mysore, India

<p>Abstract</p> <p>Background</p> <p>There is little research on HIV awareness and practices of traditional birth attendants (TBA) in India. This study investigated knowledge and attitudes among rural TBA in Karnataka as part of a project examining how traditional birth attendants could be integrated into prevention-of-mother-to-child transmission of HIV (PMTCT) programs in India.</p> <p>Methods</p> <p>A cross-sectional survey was conducted between March 2008 and January 2009 among TBA in 144 villages in Mysore <it>Taluk</it>, Karnataka. Following informed consent, TBA underwent an interviewer-administered questionnaire in the local language of <it>Kannada </it>on practices and knowledge around birthing and HIV/PMTCT.</p> <p>Results</p> <p>Of the 417 TBA surveyed, the median age was 52 years and 96% were Hindus. A majority (324, 77.7%) had no formal schooling, 88 (21.1%) had up to 7 years and 5 (1%) had more than 7 yrs of education. Only 51 of the 417 TBA (12%) reported hearing about HIV/AIDS. Of those who had heard about HIV/AIDS, only 36 (72%) correctly reported that the virus could be spread from mother to child; 37 (74%) identified unprotected sex as a mode of transmission; and 26 (51%) correctly said healthy looking people could spread HIV. Just 22 (44%) knew that infected mothers could lower the risk of transmitting the virus to their infants. An overwhelming majority of TBA (401, 96.2%) did not provide antenatal care to their clients. Over half (254, 61%) said they would refer the woman to a hospital if she bled before delivery, and only 53 (13%) felt referral was necessary if excessive bleeding occurred after birth.</p> <p>Conclusions</p> <p>Traditional birth attendants will continue to play an important role in maternal child health in India for the foreseeable future. This study demonstrates that a majority of TBA lack basic information about HIV/AIDS and safe delivery practices. Given the ongoing shortage of skilled birth attendance in rural areas, more studies are needed to examine whether TBA should be trained and integrated into PMTCT and maternal child health programs in India.</p

The Cell Shape-determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of L,D-Carboxypeptidase

Helicobacter pylori causes gastrointestinal diseases, including gastric cancer. Its high motility in the viscous gastric mucosa facilitates colonization of the human stomach and depends on the helical cell shape and the flagella. In H. pylori, Csd6 is one of the cell shape-determining proteins that play key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. Csd6 is also involved in deglycosylation of the flagellar protein FlaA. To better understand its function, biochemical, biophysical, and structural characterizations were carried out. We show that Csd6 has a three-domain architecture and exists as a dimer in solution. The N-terminal domain plays a key role in dimerization. The middle catalytic domain resembles those of L,D-transpeptidases, but its pocket-shaped active site is uniquely defined by the four loops I to IV, among which loops I and III show the most distinct variations from the known L,D-transpeptidases. Mass analyses confirm that Csd6 functions only as an L,D-carboxypeptidase and not as an L,D-transpeptidase. The D-Ala-complexed structure suggests possible binding modes of both the substrate and product to the catalytic domain. The C-terminal nuclear transport factor 2-like domain possesses a deep pocket for possible binding of pseudaminic acid, and in silico docking supports its role in deglycosylation of flagellin. On the basis of these findings, it is proposed that H. pylori Csd6 and its homologs constitute a new family of L,D-carboxypeptidase. This work provides insights into the function of Csd6 in regulating the helical cell shape and motility of H. pylori.1165Ysciescopu

Micro-manufacturing : research, technology outcomes and development issues

Besides continuing effort in developing MEMS-based manufacturing techniques, latest effort in Micro-manufacturing is also in Non-MEMS-based manufacturing. Research and technological development (RTD) in this field is encouraged by the increased demand on micro-components as well as promised development in the scaling down of the traditional macro-manufacturing processes for micro-length-scale manufacturing. This paper highlights some EU funded research activities in micro/nano-manufacturing, and gives examples of the latest development in micro-manufacturing methods/techniques, process chains, hybrid-processes, manufacturing equipment and supporting technologies/device, etc., which is followed by a summary of the achievements of the EU MASMICRO project. Finally, concluding remarks are given, which raise several issues concerning further development in micro-manufacturing

An integrated approach to a combinatorial optimisation problem

Funding: MRC grant MR/S003819/1 and Health Data Research UK, an initiative funded by UK Research and Innovation, Department of Health and Social Care (England) and the devolved administrations, and leading medical research charities.We take inspiration from a problem from the healthcare domain, where patients with several chronic conditions follow different guidelines designed for the individual conditions, and where the aim is to find the best treatment plan for a patient that avoids adverse drug reactions, respects patient’s preferences and prioritises drug efficacy. Each chronic condition guideline can be abstractly described by a directed graph, where each node indicates a treatment step (e.g., a choice in medications or resources) and has a certain duration. The search for the best treatment path is seen as a combinatorial optimisation problem and we show how to select a path across the graphs constrained by a notion of resource compatibility. This notion takes into account interactions between any finite number of resources, and makes it possible to express non-monotonic interactions. Our formalisation also introduces a discrete temporal metric, so as to consider only simultaneous nodes in the optimisation process. We express the formal problem as an SMT problem and provide a correctness proof of the SMT code by exploiting the interplay between SMT solvers and the proof assistant Isabelle/HOL. The problem we consider combines aspects of optimal graph execution and resource allocation, showing how an SMT solver can be an alternative to other approaches which are well-researched in the corresponding domains.Postprin

The cytochrome bd-I respiratory oxidase augments survival of multidrug-resistant Escherichia coli during infection

Nitric oxide (NO) is a toxic free radical produced by neutrophils and macrophages in response to infection. Uropathogenic Escherichia coli (UPEC) induces a variety of defence mechanisms in response to NO, including direct NO detoxification (Hmp, NorVW, NrfA), iron-sulphur cluster repair (YtfE), and the expression of the NO-tolerant cytochrome bd-I respiratory oxidase (CydAB). The current study quantifies the relative contribution of these systems to UPEC growth and survival during infection. Loss of the flavohemoglobin Hmp and cytochrome bd-I elicit the greatest sensitivity to NO-mediated growth inhibition, whereas all but the periplasmic nitrite reductase NrfA provide protection against neutrophil killing and promote survival within activated macrophages. Intriguingly, the cytochrome bd-I respiratory oxidase was the only system that augmented UPEC survival in a mouse model after 2 days, suggesting that maintaining aerobic respiration under conditions of nitrosative stress is a key factor for host colonisation. These findings suggest that while UPEC have acquired a host of specialized mechanisms to evade nitrosative stresses, the cytochrome bd-I respiratory oxidase is the main contributor to NO tolerance and host colonisation under microaerobic conditions. This respiratory complex is therefore of major importance for the accumulation of high bacterial loads during infection of the urinary tract

Assortative Mating in Fallow Deer Reduces the Strength of Sexual Selection

Background: Assortative mating can help explain how genetic variation for male quality is maintained even in highly polygynous species. Here, we present a longitudinal study examining how female and male ages, as well as male social dominance, affect assortative mating in fallow deer (Dama dama) over 10 years. Assortative mating could help explain the substantial proportion of females that do not mate with prime-aged, high ranking males, despite very high mating skew. We investigated the temporal pattern of female and male matings, and the relationship between female age and the age and dominance of their mates. Results: The peak of yearling female matings was four days later than the peak for older females. Younger females, and especially yearlings, mated with younger and lower-ranking males than older females. Similarly, young males and lowerranking males mated with younger females than older males and higher-ranking males. Furthermore, the timing of matings by young males coincided with the peak of yearling female matings, whereas the timing of older male matings (irrespective of rank) coincided with the peak of older female matings. Conclusions: Assortative mating, through a combination of indirect and/or direct female mate choice, can help explain th

Fast and flexible analysis of direct dark matter search data with machine learning

We present the results from combining machine learning with the profile likelihood fit procedure, using data from the Large Underground Xenon (LUX) dark matter experiment. This approach demonstrates reduction in computation time by a factor of 30 when compared with the previous approach, without loss of performance on real data. We establish its flexibility to capture nonlinear correlations between variables (such as smearing in light and charge signals due to position variation) by achieving equal performance using pulse areas with and without position-corrections applied. Its efficiency and scalability furthermore enables searching for dark matter using additional variables without significant computational burden. We demonstrate this by including a light signal pulse shape variable alongside more traditional inputs, such as light and charge signal strengths. This technique can be exploited by future dark matter experiments to make use of additional information, reduce computational resources needed for signal searches and simulations, and make inclusion of physical nuisance parameters in fits tractable

Nutraceutical therapies for atherosclerosis

Atherosclerosis is a chronic inflammatory disease affecting large and medium arteries and is considered to be a major underlying cause of cardiovascular disease (CVD). Although the development of pharmacotherapies to treat CVD has contributed to a decline in cardiac mortality in the past few decades, CVD is estimated to be the cause of one-third of deaths globally. Nutraceuticals are natural nutritional compounds that are beneficial for the prevention or treatment of disease and, therefore, are a possible therapeutic avenue for the treatment of atherosclerosis. The purpose of this Review is to highlight potential nutraceuticals for use as antiatherogenic therapies with evidence from in vitro and in vivo studies. Furthermore, the current evidence from observational and randomized clinical studies into the role of nutraceuticals in preventing atherosclerosis in humans will also be discussed