A comparison of two approaches for solving unconstrained influence diagrams

AbstractInfluence diagrams and decision trees represent the two most common frameworks for specifying and solving decision problems. As modeling languages, both of these frameworks require that the decision analyst specifies all possible sequences of observations and decisions (in influence diagrams, this requirement corresponds to the constraint that the decisions should be temporarily linearly ordered). Recently, the unconstrained influence diagram was proposed to address this drawback. In this framework, we may have a partial ordering of the decisions, and a solution to the decision problem therefore consists not only of a decision policy for the various decisions, but also of a conditional specification of what to do next. Relative to the complexity of solving an influence diagram, finding a solution to an unconstrained influence diagram may be computationally very demanding w.r.t. both time and space. Hence, there is a need for efficient algorithms that can deal with (and take advantage of) the idiosyncrasies of the language. In this paper we propose two such solution algorithms. One resembles the variable elimination technique from influence diagrams, whereas the other is based on conditioning and supports any-space inference. Finally, we present an empirical comparison of the proposed methods

The European Hernia Society Prehabilitation Project: A Systematic Review of Intra-Operative Prevention Strategies for Surgical Site Occurrences in Ventral Hernia Surgery

Abdominal wall repair; Hernia; Surgical site infectionReparación de la pared abdominal; Hernia; Infección del sitio quirúrgicoReparació de la paret abdominal; Hèrnia; Infecció del lloc quirúrgicBackground: Ventral hernia repair is one of the most commonly performed surgical procedures worldwide. To reduce the risk of complications, pre- and intra-operative strategies have received increasing focus in recent years. To assess possible preventive surgical strategies, this European Hernia Society endorsed project was launched. The aim of this review was to evaluate the current literature focusing on pre- and intra-operative strategies for surgical site occurrences (SSO) and specifically surgical site infection (SSI) in ventral hernia repair. Methods: A systematic review was conducted and reported in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Databases used were Pubmed and Web of Science. Original retrospective or prospective human adult studies describing at least one intra-operative intervention to reduce SSO after ventral hernia repair were considered eligible. Results: From a total of 4775 results, a total of 18 papers were considered suitable after full text reading. Prehospital chlorhexidine gluconate (CHG) scrub appears to increase the risk of SSO in patients undergoing ventral hernia repair, while there is no association between any type of surgical hat worn and the incidence of postoperative wound events. Intraoperative measures as prophylactic negative pressure therapy, surgical drain placement and the use of quilt sutures seem beneficial for decreasing the incidence of SSO and/or SSI. No positive effect has been shown for antibiotic soaking of a synthetic mesh, nor for the use of fibrin sealants. Conclusion: This review identified a limited amount of literature describing specific preventive measures and techniques during ventral hernia repair. An advantage of prophylactic negative pressure therapy in prevention of SSI was observed, but different tools to decrease SSIs and SSOs continuously further need our full attention to improve patient outcomes and to lower overall costs

The optical afterglow of the short gamma-ray burst GRB 050709

It has long been known that there are two classes of gamma-ray bursts (GRBs), mainly distinguished by their durations. The breakthrough in our understanding of long-duration GRBs (those lasting more than ~2 s), which ultimately linked them with energetic Type Ic supernovae, came from the discovery of their long-lived X-ray and optical afterglows, when precise and rapid localizations of the sources could finally be obtained. X-ray localizations have recently become available for short (duration <2 s) GRBs, which have evaded optical detection for more than 30 years. Here we report the first discovery of transient optical emission (R-band magnitude ~23) associated with a short burst; GRB 050709. The optical afterglow was localized with subarcsecond accuracy, and lies in the outskirts of a blue dwarf galaxy. The optical and X-ray afterglow properties 34 h after the GRB are reminiscent of the afterglows of long GRBs, which are attributable to synchrotron emission from ultrarelativistic ejecta. We did not, however, detect a supernova, as found in most nearby long GRB afterglows, which suggests a different origin for the short GRBs.Comment: 11 pages, 3 figures, press material at http://www.astro.ku.dk/dark

Estimated communication range and energetic cost of bottlenose dolphin whistles in a tropical habitat

Author Posting. © Acoustical Society of America, 2012. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 131 (2012): 582-592, doi:10.1121/1.3662067.Bottlenose dolphins (Tursiops sp.) depend on frequency-modulated whistles for many aspects of their social behavior, including group cohesion and recognition of familiar individuals. Vocalization amplitude and frequency influences communication range and may be shaped by many ecological and physiological factors including energetic costs. Here, a calibrated GPS-synchronized hydrophone array was used to record the whistles of bottlenose dolphins in a tropical shallow-water environment with high ambient noise levels. Acoustic localization techniques were used to estimate the source levels and energy content of individual whistles. Bottlenose dolphins produced whistles with mean source levels of 146.7±6.2 dB re. 1 μPa(RMS). These were lower than source levels estimated for a population inhabiting the quieter Moray Firth, indicating that dolphins do not necessarily compensate for the high noise levels found in noisy tropical habitats by increasing their source level. Combined with measured transmission loss and noise levels, these source levels provided estimated median communication ranges of 750 m and maximum communication ranges up to 5740 m. Whistles contained less than 17 mJ of acoustic energy, showing that the energetic cost of whistling is small compared to the high metabolic rate of these aquatic mammals, and unlikely to limit the vocal activity of toothed whales.This study received support from the Danish Ph.D. School of Aquatic Sciences (SOAS), Aarhus University, DK, WWF Verdensnaturfonden and Aase & Ejnar Danielsens Foundation, the Siemens Foundation, the Faculty of Science at the University of Aarhus, DK, and the Danish Natural Science Foundation via a Steno scholarship and a logistics grant to PTM

Troppo - A Python framework for the reconstruction of context-specific metabolic models

The surge in high-throughput technology availability for molecular biology has enabled the development of powerful predictive tools for use in many applications, including (but not limited to) the diagnosis and treatment of human diseases such as cancer. Genome-scale metabolic models have shown some promise in clearing a path towards precise and personalized medicine, although some challenges still persist. The integration of omics data and subsequent creation of context-specific models for specific cells/tissues still poses a significant hurdle, and most current tools for this purpose have been implemented using proprietary software. Here, we present a new software tool developed in Python, troppo - Tissue-specific RecOnstruction and Phenotype Prediction using Omics data, implementing a large variety of context-specific reconstruction algorithms. Our framework and workflow are modular, which facilitates the development of newer algorithms or omics data sources.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte. The authors also thank the PhD scholarships funded by national funds through Fundacao para a Ciencia e Tecnologia, with references: SFRH/BD/133248/2017 (J.F.), SFRH/BD/118657/2016 (V.V.).info:eu-repo/semantics/publishedVersio

Evolutionary Pathways to Persistence of Highly Fit and Resistant Hepatitis C Virus Protease Inhibitor Escape Variants

Protease inhibitors (PIs) are important components of treatment regimens for patients with chronic hepatitis C virus (HCV) infection. However, emergence and persistence of antiviral resistance could reduce their efficacy. Thus, defining resistance determinants is highly relevant for efforts to control HCV. Here, we investigated patterns of PI resistance–associated substitutions (RASs) for the major HCV genotypes and viral determinants for persistence of key RASs. We identified protease position 156 as a RAS hotspot for genotype 1‐4, but not 5 and 6, escape variants by resistance profiling using PIs grazoprevir and paritaprevir in infectious cell culture systems. However, except for genotype 3, engineered 156‐RASs were not maintained. For genotypes 1 and 2, persistence of 156‐RASs depended on genome‐wide substitution networks, co‐selected under continued PI treatment and identified by next‐generation sequencing with substitution linkage and haplotype reconstruction. Persistence of A156T for genotype 1 relied on compensatory substitutions increasing replication and assembly. For genotype 2, initial selection of A156V facilitated transition to 156L, persisting without compensatory substitutions. The developed genotype 1, 2, and 3 variants with persistent 156‐RASs had exceptionally high fitness and resistance to grazoprevir, paritaprevir, glecaprevir, and voxilaprevir. A156T dominated in genotype 1 glecaprevir and voxilaprevir escape variants, and pre‐existing A156T facilitated genotype 1 escape from clinically relevant combination treatments with grazoprevir/elbasvir and glecaprevir/pibrentasvir. In genotype 1 infected patients with treatment failure and 156‐RASs, we observed genome‐wide selection of substitutions under treatment. Conclusion : Comprehensive PI resistance profiling for HCV genotypes 1‐6 revealed 156‐RASs as key determinants of high‐level resistance across clinically relevant PIs. We obtained in vitro proof of concept for persistence of highly fit genotype 1‐3 156‐variants, which might pose a threat to clinically relevant combination treatments