Lattice QCD without topology barriers

As the continuum limit is approached, lattice QCD simulations tend to get trapped in the topological charge sectors of field space and may consequently give biased results in practice. We propose to bypass this problem by imposing open (Neumann) boundary conditions on the gauge field in the time direction. The topological charge can then flow in and out of the lattice, while many properties of the theory (the hadron spectrum, for example) are not affected. Extensive simulations of the SU(3) gauge theory, using the HMC and the closely related SMD algorithm, confirm the absence of topology barriers if these boundary conditions are chosen. Moreover, the calculated autocorrelation times are found to scale approximately like the square of the inverse lattice spacing, thus supporting the conjecture that the HMC algorithm is in the universality class of the Langevin equation.Comment: Plain TeX source, 26 pages, 4 figures include

MetAMOS: A modular and open source metagenomic assembly and analysis pipeline

© 2013 Treangen et al. We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS

Non-renormalizability of the HMC algorithm

In lattice field theory, renormalizable simulation algorithms are attractive, because their scaling behaviour as a function of the lattice spacing is predictable. Algorithms implementing the Langevin equation, for example, are known to be renormalizable if the simulated theory is. In this paper we show that the situation is different in the case of the molecular-dynamics evolution on which the HMC algorithm is based. More precisely, studying the phi^4 theory, we find that the hyperbolic character of the molecular-dynamics equations leads to non-local (and thus non-removable) ultraviolet singularities already at one-loop order of perturbation theory.Comment: Plain TeX source, 23 pages, 3 figures included; v2: typos corrected, agrees with published versio

Auditory complications among childhood cancer survivors and health-related quality of life: a PanCareLIFE study.

PURPOSE Auditory complications are potential side effects from childhood cancer treatment. Yet, limited evidence exists about the impact of auditory complications-particularly tinnitus-on health-related quality of life (HRQoL) among childhood cancer survivors (CCS). We determined the prevalence of hearing loss and tinnitus in the European PanCareLIFE cohort of CCS and examined its effect on HRQoL. METHODS We included CCS from four European countries who were diagnosed at age ≤ 18 years; survived ≥ 5 years; and aged 25-44 years at study. We assessed HRQoL (Short Form 36), hearing loss, and tinnitus using questionnaires. We used multivariable linear regression to examine associations between these two auditory complications and HRQoL adjusting for socio-demographic and clinical factors. RESULTS Our study population consisted of 6,318 CCS (53% female; median age at cancer diagnosis 9 years interquartile range [IQR] 5-13 years) with median age at survey of 31 years (IQR 28-35 years). Prevalence was 7.5% (476/6,318; confidence interval [CI]: 6.9-8.2) for hearing loss and 7.6% (127/1,668; CI: 6.4-9.0) for tinnitus. CCS with hearing loss had impaired physical (coefficient [coef.] -4.3, CI: -7.0 to -1.6) and mental (coef. -3.2, CI: -5.5 to -0.8) HRQoL when compared with CCS with normal hearing. Tinnitus was associated with impaired physical (coef. -8.2, CI: -11.8 to -4.7) and mental (coef. -5.9, CI: -8.8 to -3.1) HRQoL. CONCLUSION We observed reduced HRQoL among CCS with hearing loss and tinnitus. Our findings indicate timely treatment of hearing loss and tinnitus may contribute to quality of life of survivors. IMPLICATIONS FOR CANCER SURVIVORS CCS who experience auditory complications should be counseled about possible therapeutic and supportive measures during follow-up care

Menstrual hygiene management among women and adolescent girls in the aftermath of the earthquake in Nepal.

BACKGROUND: Menstrual hygiene management (MHM) is an essential aspect of hygiene for women and adolescent girls between menarche and menopause. Despite being an important issue concerning women and girls in the menstruating age group MHM is often overlooked in post-disaster responses. Further, there is limited evidence of menstrual hygiene management in humanitarian settings. This study aims to describe the experiences and perceptions of women and adolescent girls on menstrual hygiene management in post-earthquake Nepal. METHODS: A mixed methods study was carried out among the earthquake affected women and adolescent girls in three villages of Sindhupalchowk district of Nepal. Data was collected using a semi-structured questionnaire that captured experiences and perceptions of respondents on menstrual hygiene management in the aftermath of the Nepal earthquake. Quantitative data were triangulated with in-depth interview regarding respondent's personal experiences of menstrual hygiene management. RESULTS: Menstrual hygiene was rated as the sixth highest overall need and perceived as an immediate need by 18.8% of the respondents. There were 42.8% women & girls who menstruated within first week of the earthquake. Reusable sanitary cloth were used by about 66.7% of the respondents before the earthquake and remained a popular method (76.1%) post-earthquake. None of the respondents reported receiving menstrual adsorbents as relief materials in the first month following the earthquake. Disposable pads (77.8%) were preferred by respondents as they were perceived to be clean and convenient to use. Most respondents (73.5%) felt that reusable sanitary pads were a sustainable choice. Women who were in the age group of 15-34 years (OR = 3.14; CI = (1.07-9.20), did not go to school (OR = 9.68; CI = 2.16-43.33), married (OR = 2.99; CI = 1.22-7.31) and previously used reusable sanitary cloth (OR = 5.82; CI = 2.33-14.55) were more likely to use the reusable sanitary cloth. CONCLUSIONS: In the immediate aftermath of the earthquake, women and girls completely depended on the use of locally available resources as adsorbents during menstruation. Immediate relief activities by humanitarian agencies, lacked MHM activities. Understanding the previous practice and using local resources, the reusable sanitary cloth is a way to address the menstrual hygiene needs in the post-disaster situations in Nepal

Effects of external nutrient sources and extreme weather events on the nutrient budget of a Southern European coastal lagoon

The seasonal and annual nitrogen (N), phosphorus (P), and carbon (C) budgets of the mesotidal Ria Formosa lagoon, southern Portugal, were estimated to reveal the main inputs and outputs, the seasonal patterns, and how they may influence the ecological functioning of the system. The effects of extreme weather events such as long-lasting strong winds causing upwelling and strong rainfall were assessed. External nutrient inputs were quantified; ocean exchange was assessed in 24-h sampling campaigns, and final calculations were made using a hydrodynamic model of the lagoon. Rain and stream inputs were the main freshwater sources to the lagoon. However, wastewater treatment plant and groundwater discharges dominated nutrient input, together accounting for 98, 96, and 88 % of total C, N, and P input, respectively. Organic matter and nutrients were continuously exported to the ocean. This pattern was reversed following extreme events, such as strong winds in early summer that caused upwelling and after a period of heavy rainfall in late autumn. A principal component analysis (PCA) revealed that ammonium and organic N and C exchange were positively associated with temperature as opposed to pH and nitrate. These variables reflected mostly the benthic lagoon metabolism, whereas particulate P exchange was correlated to Chl a, indicating that this was more related to phytoplankton dynamics. The increase of stochastic events, as expected in climate change scenarios, may have strong effects on the ecological functioning of coastal lagoons, altering the C and nutrient budgets.Portuguese Science and Technology Foundation (FCT) [POCI/MAR/58427/2004, PPCDT/MAR/58427/2004]; Portuguese Science and Technology Foundation (FCT

Computational archaeology of the Pristionchus pacificus genome reveals evidence of horizontal gene transfers from insects

<p>Abstract</p> <p>Background</p> <p>The recent sequencing of nematode genomes has laid the basis for comparative genomics approaches to study the impact of horizontal gene transfer (HGT) on the adaptation to new environments and the evolution of parasitism. In the beetle associated nematode <it>Pristionchus pacificus </it>HGT events were found to involve cellulase genes of microbial origin and Diapausin genes that are known from beetles, but not from other nematodes. The insect-to-nematode horizontal transfer is of special interest given that <it>P. pacificus </it>shows a tight association with insects.</p> <p>Results</p> <p>In this study we utilized the observation that horizontally transferred genes often exhibit codon usage patterns more similar to that of the donor than that of the acceptor genome. We introduced GC-normalized relative codon frequencies as a measure to detect characteristic features of <it>P. pacificus </it>orphan genes that show no homology to other nematode genes. We found that atypical codon usage is particularly prevalent in <it>P. pacificus </it>orphans. By comparing codon usage profiles of 71 species, we detected the most significant enrichment in insect-like codon usage profiles. In cross-species comparisons, we identified 509 HGT candidates that show a significantly higher similarity to insect-like profiles than genes with nematode homologs. The most abundant gene family among these genes are non-LTR retrotransposons. Speculating that retrotransposons might have served as carriers of foreign genetic material, we found a significant local clustering tendency of orphan genes in the vicinity of retrotransposons.</p> <p>Conclusions</p> <p>Our study combined codon usage bias, phylogenetic analysis, and genomic colocalization into a general picture of the computational archaeology of the <it>P. pacificus </it>genome and suggests that a substantial fraction of the gene repertoire is of insect origin. We propose that the <it>Pristionchus</it>-beetle association has facilitated HGT and discuss potential vectors of these events.</p

The Evolution of Functionally Redundant Species; Evidence from Beetles

While species fulfill many different roles in ecosystems, it has been suggested that numerous species might actually share the same function in a near neutral way. So-far, however, it is unclear whether such functional redundancy really exists. We scrutinize this question using extensive data on the world’s 4168 species of diving beetles. We show that across the globe these animals have evolved towards a small number of regularly-spaced body sizes, and that locally co-existing species are either very similar in size or differ by at least 35%. Surprisingly, intermediate size differences (10–20%) are rare. As body-size strongly reflects functional aspects such as the food that these generalist predators can eat, these beetles thus form relatively distinct groups of functional look-a-likes. The striking global regularity of these patterns support the idea that a self-organizing process drives such species-rich groups to self-organize evolutionary into clusters where functional redundancy ensures resilience through an insurance effect

The role of the right inferior frontal gyrus in the pathogenesis of post-stroke psychosis.

Psychotic symptoms have previously been reported following right hemisphere brain injury. We sought to identify the specific neuroanatomical basis of delusions following stroke by studying a series of patients with post-stroke psychosis. Lesion overlap analysis was conducted on three individuals with delusions following right hemisphere stroke. These cases were compared with a control group of patients with similar anatomical damage. The main outcome measures were presence of delusions and presence of behavioural susceptibility. The right inferior frontal gyrus and underlying white matter, including the superior longitudinal fasciculus and anterior corona radiata, were involved in all three cases. All three had a preexisting untreated psychiatric disorder. In contrast, only one of nine control cases with equivalent lesions had evidence of previous psychiatric disorder (p = 0.0182, Fisher’s exact test), and this was being treated at the time of stroke. We provide clinical evidence from patients with structural brain lesions implicating damage to the right inferior frontal lobe in the generation of persistent psychosis following stroke. We suggest that preexisting psychiatric disease provided a behavioural susceptibility to develop delusions in these individuals. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00415-014-7242-x) contains supplementary material, which is available to authorized users