The IBMAP approach for Markov networks structure learning

In this work we consider the problem of learning the structure of Markov networks from data. We present an approach for tackling this problem called IBMAP, together with an efficient instantiation of the approach: the IBMAP-HC algorithm, designed for avoiding important limitations of existing independence-based algorithms. These algorithms proceed by performing statistical independence tests on data, trusting completely the outcome of each test. In practice tests may be incorrect, resulting in potential cascading errors and the consequent reduction in the quality of the structures learned. IBMAP contemplates this uncertainty in the outcome of the tests through a probabilistic maximum-a-posteriori approach. The approach is instantiated in the IBMAP-HC algorithm, a structure selection strategy that performs a polynomial heuristic local search in the space of possible structures. We present an extensive empirical evaluation on synthetic and real data, showing that our algorithm outperforms significantly the current independence-based algorithms, in terms of data efficiency and quality of learned structures, with equivalent computational complexities. We also show the performance of IBMAP-HC in a real-world application of knowledge discovery: EDAs, which are evolutionary algorithms that use structure learning on each generation for modeling the distribution of populations. The experiments show that when IBMAP-HC is used to learn the structure, EDAs improve the convergence to the optimum

Renormalization Group and Universality

It is argued that universality is severely limited for models with multiple fixed points. As a demonstration the renormalization group equations are presented for the potential and the wave function renormalization constants in the $O(N)$ scalar field theory. Our equations are superior compared with the usual approach which retains only the contributions that are non-vanishing in the ultraviolet regime. We find an indication for the existence of relevant operators at the infrared fixed point, contrary to common expectations. This result makes the sufficiency of using only renormalizable coupling constants in parametrizing the long distance phenomena questionable.Comment: 32pp in plain tex; revised version to appear in PR

Lectures on the functional renormalization group method

These introductory notes are about functional renormalization group equations and some of their applications. It is emphasised that the applicability of this method extends well beyond critical systems, it actually provides us a general purpose algorithm to solve strongly coupled quantum field theories. The renormalization group equation of F. Wegner and A. Houghton is shown to resum the loop-expansion. Another version, due to J. Polchinski, is obtained by the method of collective coordinates and can be used for the resummation of the perturbation series. The genuinely non-perturbative evolution equation is obtained in a manner reminiscent of the Schwinger-Dyson equations. Two variants of this scheme are presented where the scale which determines the order of the successive elimination of the modes is extracted from external and internal spaces. The renormalization of composite operators is discussed briefly as an alternative way to arrive at the renormalization group equation. The scaling laws and fixed points are considered from local and global points of view. Instability induced renormalization and new scaling laws are shown to occur in the symmetry broken phase of the scalar theory. The flattening of the effective potential of a compact variable is demonstrated in case of the sine-Gordon model. Finally, a manifestly gauge invariant evolution equation is given for QED.Comment: 47 pages, 11 figures, final versio

An experimental investigation of the composting process in an innovative home composting System: The influence of additives

Data availability: Data will be made available on request.Food-waste out of household consumption ends up in landfills resulting into huge waste of materials and energy enhancing greenhouse effect and threatening water supplies. Composting is common solution for solid organic waste management and can safely and effectively be employed in each household to produce quality compost materials. This study palpates the average composition of the Mediterranean dietary pattern food-wastes and investigates the efficiency of a novel home-composter in managing organic wastes from dish to composter to quality compost. Four different additives, low cost and easily found in the market, are addressed, (1) woodchip, (2) woodchips & zeolite, (3) woodchips & vermiculite and (4) perlite. C/N≈20 substrate’s composition is investigated. Results indicate that the composting process effectively converts food-wastes to compost within 21 days. The monitored parameters show good aeration and humidity levels of the substrate and an aerobic process. The product exhibits minor alkalinity and requires further maturing. Mineral additives help reducing TOC with vermiculite and perlite be the most promising. Zeolite and vermiculite result in higher TKN values of the product with zeolite exhibiting better performance. All minerals enchance C/N reduction when woodchips is proven inadequate as an additive if employed alone. The product can safely be used in domestic applications

A mRNA landscape of bovine embryos after standard and MAPK-inhibited culture conditions: a comparative analysis.

BACKGROUND: Genes and signalling pathways involved in pluripotency have been studied extensively in mouse and human pre-implantation embryos and embryonic stem (ES) cells. The unsuccessful attempts to generate ES cell lines from other species including cattle suggests that other genes and pathways are involved in maintaining pluripotency in these species. To investigate which genes are involved in bovine pluripotency, expression profiles were generated from morula, blastocyst, trophectoderm and inner cell mass (ICM) samples using microarray analysis. As MAPK inhibition can increase the NANOG/GATA6 ratio in the inner cell mass, additionally blastocysts were cultured in the presence of a MAPK inhibitor and changes in gene expression in the inner cell mass were analysed. RESULTS: Between morula and blastocyst 3,774 genes were differentially expressed and the largest differences were found in blastocyst up-regulated genes. Gene ontology (GO) analysis shows lipid metabolic process as the term most enriched with genes expressed at higher levels in blastocysts. Genes with higher expression levels in morulae were enriched in the RNA processing GO term. Of the 497 differentially expressed genes comparing ICM and TE, the expression of NANOG, SOX2 and POU5F1 was increased in the ICM confirming their evolutionary preserved role in pluripotency. Several genes implicated to be involved in differentiation or fate determination were also expressed at higher levels in the ICM. Genes expressed at higher levels in the ICM were enriched in the RNA splicing and regulation of gene expression GO term. Although NANOG expression was elevated upon MAPK inhibition, SOX2 and POU5F1 expression showed little increase. Expression of other genes in the MAPK pathway including DUSP4 and SPRY4, or influenced by MAPK inhibition such as IFNT, was down-regulated. CONCLUSION: The data obtained from the microarray studies provide further insight in gene expression during bovine embryonic development. They show an expression profile in pluripotent cells that indicates a pluripotent, epiblast-like state. The inability to culture ICM cells as stem cells in the presence of an inhibitor of MAPK activity together with the reported data indicates that MAPK inhibition alone is not sufficient to maintain a pluripotent character in bovine cells

Characterization of bovine embryos cultured under conditions appropriate for sustaining human naïve pluripotency.

In mammalian preimplantation development, pluripotent cells are set aside from cells that contribute to extra-embryonic tissues. Although the pluripotent cell population of mouse and human embryos can be cultured as embryonic stem cells, little is known about the pathways involved in formation of a bovine pluripotent cell population, nor how to maintain these cells in vitro. The objective of this study was to determine the transcriptomic profile related to bovine pluripotency. Therefore, in vitro derived embryos were cultured in various culture media that recently have been reported capable of maintaining the naïve pluripotent state of human embryonic cells. Gene expression profiles of embryos cultured in these media were compared using microarray analysis and quantitative RT-PCR. Compared to standard culture conditions, embryo culture in 'naïve' media reduced mRNA expression levels of the key pluripotency markers NANOG and POU5F1. A relatively high percentage of genes with differential expression levels were located on the X-chromosome. In addition, reduced XIST expression was detected in embryos cultured in naïve media and female embryos contained fewer cells with H3K27me3 foci, indicating a delay in X-chromosome inactivation. Whole embryos cultured in one of the media, 5iLA, could be maintained until 23 days post fertilization. Together these data indicate that 'naïve' conditions do not lead to altered expression of known genes involved in pluripotency. Interestingly, X-chromosome inactivation and development of bovine embryos were dependent on the culture conditions

A preliminary analysis of in-depth accident data for powered two-wheelers and bicycles in Europe

Despite progress from scientific and technological advancements, road safety remains a major issue worldwide. Road accident impacts such as fatalities, injuries and property damage consist considerable costs borne not only by involved people but society as well. This study aims to present preliminary findings of in-depth accident analysis for two-wheelers (bicycles and powered two wheelers – PTWs) across six countries in Europe. Data regarding the conditions underlying accident occurrence are presented, including time and date, weather, vehicle and road conditions and rider-related parameters such as age, intoxication and use of protective equipment. In addition, a Two Step Cluster Analysis is implemented in order to explore any possible classification of the analysed cases. It appears that two clusters are formed: the first includes more favourable conditions (“no wind, no drugs, good lighting”) while the second consists of less favourable conditions for road safety (“windy, lighting, unknown DUI condition”). This hints at a meaningful separation of the examination of two-wheeler accidents when the influence of outside factors is considerable. The inclusion of different but representative areas across Europe offers robustness and transferability to the data and respective results

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

SaferWheels study on powered two-wheeler and bicycle accidents in the EU - Annex 6 case summaries

SaferWheels study on powered two-wheeler and bicycle accidents in the EU - Annex 6 case summarie