Connecting Seed Lists of Mammalian Proteins Using Steiner Trees

Multivariate experiments and genomics studies applied to mammalian cells often produce lists of genes or proteins altered under treatment/disease vs. control/normal conditions. Such lists can be identified in known protein-protein interaction networks to produce subnetworks that “connect” the genes or proteins from the lists. Such subnetworks are valuable for biologists since they can suggest regulatory mechanisms that are altered under different conditions. Often such subnetworks are overloaded with links and nodes resulting in connectivity diagrams that are illegible due to edge overlap. In this study, we attempt to address this problem by implementing an approximation to the Steiner Tree problem to connect seed lists of mammalian proteins/genes using literature-based protein-protein interaction networks. To avoid over-representation of hubs in the resultant Steiner Trees we assign a cost to Steiner Vertices based on their connectivity degree. We applied the algorithm to lists of genes commonly mutated in colorectal cancer to demonstrate the usefulness of this approach

A Comprehensive Analysis of Efficiency in the Tasmanian Salmon Industry

Food producers are under increasing pressure to provide for a growing population that is demanding good quality, nutritious foods. At the same time, they face significant supply-side constraints as the ecological support systems required to produce food are pushed to the limit and the cost of inputs reach record highs. To overcome these challenges producers will need to develop innovative solutions to improve the productive efficiency of the global food system. This research brings together three diverse yet interrelated disciplines – environment, nutrition and economics- under the universal banner of sustainability science in search of a reliable and comparable measure of eco-efficiency that will help drive the food system towards a more sustainable future. The Tasmanian salmon industry is used as a case study to identify the benefits and limitations of feed conversion ratio and the various measures of forage fish dependency that are currently used to assess the productive efficiency of aquaculture production. Life cycle assessment is identified as being a suitable compliment, wit

Systematic review of the venous thromboembolism risk assessment models used in aesthetic plastic surgery

BACKGROUND: A reliable venous thromboembolism (VTE) risk assessment model (RAM) can assist surgeons in identifying patients who would benefit from VTE prophylaxis. This systematic review was aimed at summarising the current available evidence on VTE RAMs used in aesthetic plastic surgery. METHODS: A comprehensive search was performed in the PubMed, EMBASE and Cochrane databases to include primary studies describing VTE RAMs in aesthetic plastic surgery from 1946 to February 2019. The objective was to compare the different VTE RAMs described for aesthetic plastic surgery to recommend a reliable model to stratify patients. RESULTS: Of the 557 articles identified in the PubMed, EMBASE and Cochrane databases, six articles were included in the final review. Five different RAMs were used in the included studies: Caprini 2005 RAM, Caprini 2010 RAM, Davison-Caprini 2004 RAM, the American Society of Anaesthesiologist's (ASA) physical status grading system and a tool developed by Wes et al. The difference in risk weightage amongst the tools along with the VTE incidences for different categories was compared. The Caprini 2005 RAM was the most widely reported tool and validated in plastic surgery patients. CONCLUSION: Amongst the five different tools currently used, the Caprini 2005 RAM was the most widely reported. This tool was validated in plastic surgery patients and reported to be a sensitive and reliable tool for VTE risk stratification; therefore, current data support its use until further higher quality evidence becomes available. Because of the heterogeneity of the data and low quality of the current evidence, a definitive recommendation cannot be made on the best VTE RAM for patients undergoing aesthetic plastic surgery. This paper highlights the need for randomised controlled trials evaluating the various RAMs which are essential to support future recommendations and guidelines

SOS Server Deployment for Sharing Environmental Sensor Data Through the OTALEX-C Spatial Data Infrastructure

Ponencias, comunicaciones y pósters presentados en el 17th AGILE Conference on Geographic Information Science "Connecting a Digital Europe through Location and Place", celebrado en la Universitat Jaume I del 3 al 6 de junio de 2014.OTALEX Spatial Data Infrastructure (SDI) project is funded by the INTERREG III European Programme and its main objective is to study and show the reality of the territory composed by the regions Alentejo in Portugal and Extremadura region in Spain. The current project phase is called OTALEX C and it is focused on showing the results of environmental studies through the OTALEX SDI. For that goal, it is necessary to catalogue, standardize, geoprocess and publish data from environmental sensors, as well as publish thematic contour and continuous maps derived from the interpolation of these sensors data. The first part of the project was the development of the processes to load a heterogeneous group of data from different types of sensors into a central repository using open source and self-developed Extract Transform and Load tools (ETL)

Producing lupins

The book contains detailed information on lupin establishment, weed control, disease management and harvesting. It also provides an excellent background to the history of lupins in Western Australia, the development of the plant and its adaptation to the Western Australian environmenthttps://researchlibrary.agric.wa.gov.au/bulletins/1009/thumbnail.jp

Frequency and socio-demographic correlates of eating meals out and take-away meals at home: cross-sectional analysis of the UK national diet and nutrition survey, waves 1-4 (2008-12)

Background: Food prepared out-of-home tends to be less healthful than food prepared at home, with a positive association between frequency of consumption and both fat intake and body fatness. There is little current data on who eats out-of-home food. We explored frequency and socio-demographic correlates of eating meals out and take-away meals at home, using data from a large, UK, population representative study. Methods: Data were from waves 1–4 of the UK National Diet and Nutrition Survey (2008–12). Socio-demographic variables of interest were gender, age group, and socio-economic position. Self-reported frequency of consuming meals out and take-away meals at home was categorised as: less than once per week and once per week or more. Analyses were performed separately for adults (aged 18 years or older) and children. Results: Data from 2001 adults and 1963 children were included. More than one quarter (27.1%) of adults and one fifth (19.0%) of children ate meals out once per week or more. One fifth of adults (21.1%) and children (21.0%) ate take-away meals at home once per week or more. There were no gender differences in consumption of meals out, but more boys than girls ate take-away meals at home at least weekly. The proportion of participants eating both meals out and take-away meals at home at least weekly peaked in young adults aged 19–29 years. Adults living in more affluent households were more likely to eat meals out at least once per week, but children living in less affluent households were more likely to eat take-away meals at home at least once per week. There was no relationship between socio-economic position and consumption of take-away meals at home in adults. Conclusions: One-fifth to one-quarter of individuals eat meals prepared out-of-home weekly. Interventions seeking to improve dietary intake by reducing consumption of out-of-home food may be more effective if tailored to and targeted at adults aged less than 30 years. It may also be important to develop interventions to help children and adolescents avoid becoming frequent consumers of out-of-home food

Human and murine IFIT1 proteins do not restrict infection of negative-sense RNA viruses of the Orthomyxoviridae, Bunyaviridae, and Filoviridae families

UNLABELLED: Interferon-induced protein with tetratricopeptide repeats 1 (IFIT1) is a host protein with reported cell-intrinsic antiviral activity against several RNA viruses. The proposed basis for the activity against negative-sense RNA viruses is the binding to exposed 5\u27-triphosphates (5\u27-ppp) on the genome of viral RNA. However, recent studies reported relatively low binding affinities of IFIT1 for 5\u27-ppp RNA, suggesting that IFIT1 may not interact efficiently with this moiety under physiological conditions. To evaluate the ability of IFIT1 to have an impact on negative-sense RNA viruses, we infected Ifit1(-/-) and wild-type control mice and primary cells with four negative-sense RNA viruses (influenza A virus [IAV], La Crosse virus [LACV], Oropouche virus [OROV], and Ebola virus) corresponding to three distinct families. Unexpectedly, a lack of Ifit1 gene expression did not result in increased infection by any of these viruses in cell culture. Analogously, morbidity, mortality, and viral burdens in tissues were identical between Ifit1(-/-) and control mice after infection with IAV, LACV, or OROV. Finally, deletion of the human IFIT1 protein in A549 cells did not affect IAV replication or infection, and reciprocally, ectopic expression of IFIT1 in HEK293T cells did not inhibit IAV infection. To explain the lack of antiviral activity against IAV, we measured the binding affinity of IFIT1 for RNA oligonucleotides resembling the 5\u27 ends of IAV gene segments. The affinity for 5\u27-ppp RNA was approximately 10-fold lower than that for non-2\u27-O-methylated (cap 0) RNA oligonucleotides. Based on this analysis, we conclude that IFIT1 is not a dominant restriction factor against negative-sense RNA viruses. IMPORTANCE: Negative-sense RNA viruses, including influenza virus and Ebola virus, have been responsible for some of the most deadly outbreaks in recent history. The host interferon response and induction of antiviral genes contribute to the control of infections by these viruses. IFIT1 is highly induced after virus infection and reportedly has antiviral activity against several RNA and DNA viruses. However, its role in restricting infection by negative-sense RNA viruses remains unclear. In this study, we evaluated the ability of IFIT1 to inhibit negative-sense RNA virus replication and pathogenesis both in vitro and in vivo. Detailed cell culture and animal studies demonstrated that IFIT1 is not a dominant restriction factor against three different families of negative-sense RNA viruses

La catástrofe del barranco de Arás (Biescas, Pirineo Aragonés) y su contexto espacio-temporal

[ES] Se estudian las características de la precipitación y del pico de crecida durante la catástrofe ocurrida en el barranco de Arás en la tarde del 7 de agosto de 1996. Se ha podido comprobar que aunque la tormenta fue muy intensa en toda la cuenca, su violencia alcanzó mayor magnitud en un pequeño sector de la subcuenca de Betés, en el que se ha estimado una intensidad superior a 500 mm.hr-1 y una precipitación total algo superior a 250 mm. En el tramo final del barranco de Arás debieron registrarse unos 500 m³s-1 incluyendo los sedimentos transportados, para una cuenca de 18.8 km². Las evaluaciones realizadas permiten estimar que el 75 % del caudal procedió de la subcuenca de Betés, que representa sólo el 28.7 % de la superficie total de la cuenca. Se ha evaluado el volumen de sedimentos movilizados en el sector final del barranco de Arás. Finalmente, el evento tormentoso ha sido situado en un contexto espacial y temporal más amplio. La catástofe del barranco de Arás confirma las limitaciones de los actuales sistemas de análisis probabilístico de riesgos, dada su gran irregularidad espacial y temporal.[EN] The characteristics of precipitation and peak flow during the Arás catastrophe in the evening of August, 7, 1996, are studied. The storm was very intense over the whole basin, and especially in a small area of the Betés subbasin, in which intensities greater than 500 mm.hr-1 have been estimated, with a total amount of precipitation somewhat higher than 250 mm. In the final stretch of the Arás ravine a discharge of 500 m³s-1, including the sediments, have been estimated for a basin of 18.8 km².. Seventy five per cent of the discharge carne from the Betés subbasin, which represents only 28.7 per cent of the basin. The volume of sediments mobilized in the final stretch of the Arás ravine has also been evaluated. Finally, the rainstorm event has been placed in a larger spatial and temporal context. The catastrophe of the Arás ravine confirms the lirnitations of existing systems of probabilistic analysis, due to the spatial and temporal irregularity of storm events.Peer reviewe

The contribution of vascular proteoglycans to atherothrombosis: clinical implications

The vascular extracellular matrix (ECM) produced by endothelial and smooth muscle cells is composed of collagens and glycoproteins and plays an integral role in regulating the structure and function of the vascular wall. Alteration in the expression of these proteins is associated with endothelial dysfunction and has been implicated in the development and progression of atherosclerosis. The ECM composition of atherosclerotic plaques varies depending on plaque phenotype and vulnerability, with distinct differences observed between ruptured and erodes plaques. Moreover, the thrombi on the exposed ECM are diverse in structure and composition, suggesting that the best antithrombotic approach may differ depending on plaque phenotype. This review provides a comprehensive overview of the role of proteoglycans in atherogenesis and thrombosis. It discusses the differential expression of the proteoglycans in different plaque phenotypes and the potential impact on platelet function and thrombosis. Finally, the review highlights the importance of this concept in developing a targeted approach to antithrombotic treatments to improve clinical outcomes in cardiovascular disease