Suchergebnisse

[Background]: The identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits. So far, the majority of porcine transcriptomic studies have investigated differences in gene expression at a global scale rather than at the mRNA isoform level. In the current work, we have investigated the differential expression of mRNA isoforms in the gluteus medius (GM) muscle of 52 Duroc HIGH (increased backfat thickness, intramuscular fat and saturated and monounsaturated fatty acids contents) and LOW pigs (opposite phenotype, with an increased polyunsaturated fatty acids content). ; [Results]: Our analysis revealed that 10.9% of genes expressed in the GM muscle generate alternative mRNA isoforms, with an average of 2.9 transcripts per gene. By using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs (P-value < 0.01 and ±0.6 log2fold-change). Only five mRNA isoforms, produced by the ITGA5, SEMA4D, LITAF, TIMP1 and ANXA2 genes, remain significant after correction for multiple testing (q-value < 0.05 and ±0.6 log2fold-change), being upregulated in HIGH pigs. ; [Conclusions]: The increased levels of specific ITGA5, LITAF, TIMP1 and ANXA2 mRNA isoforms in HIGH pigs is consistent with reports indicating that the overexpression of these four genes is associated with obesity and metabolic disorders in humans. A broader knowledge about the functional attributes of these mRNA variants would be fundamental to elucidate the consequences of transcript diversity on the determinism of porcine phenotypes of economic interest. ; Part of the research presented in this publication was funded by grants AGL2013–48742-C2–1-R and AGL2013–48742-C2–2-R awarded by the Spanish Ministry of Economy and Competitivity and grant 2014 SGR 1528 from the Agency for Management of University and Research Grants of the Generalitat de Catalunya. We also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016–2019 (SEV-2015-0533) grant awarded to the Centre for Research in Agricultural Genomics (CRAG). Tainã Figueiredo Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education of the Federal Government of Brazil. Rayner Gonzalez-Prendes was funded with a FPU Ph.D. grant from the Spanish Ministry of Education (FPU12/00860). Thanks also to the CERCA Programme of the Generalitat de Catalunya. ; Peer reviewed

ABSTRACT
BackgroundFree text documents in healthcare settings contain a wealth of information not captured in electronic healthcare records (EHRs). Epilepsy clinic letters are an example of an unstructured data source containing a large amount of intricate disease information. Extracting meaningful and contextually correct clinical information from free text sources, to enhance EHRs, remains a significant challenge. SCANR (Swansea University Collaborative in the Analysis of NLP Research) was set up to use natural language processing (NLP) technology to extract structured data from unstructured sources.
IBM Watson Content Analytics software (ICA) uses NLP technology. It enables users to define annotations based on dictionaries and language characteristics to create parsing rules that highlight relevant items. These include clinical details such as symptoms and diagnoses, medication and test results, as well as personal identifiers.

ApproachTo use ICA to build a pipeline to accurately extract detailed epilepsy information from clinic letters.
MethodsWe used ICA to retrieve important epilepsy information from 41 pseudo-anonymized unstructured epilepsy clinic letters. The 41 letters consisted of 13 'new' and 28 'follow-up' letters (for 15 different patients) written by 12 different doctors in different styles. We designed dictionaries and annotators to enable ICA to extract epilepsy type (focal, generalized or unclassified), epilepsy cause, age of onset, investigation results (EEG, CT and MRI), medication, and clinic date. Epilepsy clinicians assessed the accuracy of the pipeline.
ResultsThe accuracy (sensitivity, specificity) of each concept was: epilepsy diagnosis 98% (97%, 100%), focal epilepsy 100%, generalized epilepsy 98% (93%, 100%), medication 95% (93%, 100%), age of onset 100% and clinic date 95% (95%, 100%).
Precision and recall for each concept were respectively, 98% and 97% for epilepsy diagnosis, 100% each for focal epilepsy, 100% and 93% for generalized epilepsy, 100% each for age of onset, 100% and 93% for medication, 100% and 96% for EEG results, 100% and 83% for MRI scan results, and 100% and 95% for clinic date.
Conclusions ICA is capable of extracting detailed, structured epilepsy information from unstructured clinic letters to a high degree of accuracy. This data can be used to populate relational databases and be linked to EHRs. Researchers can build in custom rules to identify concepts of interest from letters and produce structured information. We plan to extend our work to hundreds and then thousands of clinic letters, to provide phenotypically rich epilepsy data to link with other anonymised, routinely collected data.

ABSTRACTBackgroundData integration comprises methods and tools to aggregate data from disparate sources to various purposes. Heterogeneity and uncertainty are technical challenges in this field. The first involves different data representation or meaning, while the second refers to incomplete data or the expectancy that a data item exists in a data source. Our goal is to design and validate a data integration model and computing tools able to address both problems. Such model and tools will support the setup of a population-based cohort comprised by 100 million individuals and the generation of data marts (domain-specific data) to be used in epidemiological studies within an ongoing cooperation Brazil-UK. Such studies will assess the impact of a conditional cash transfer programme (PBF – Bolsa Família) on the occurrence, severity and mortality of several diseases and health problems (hospitalization, mortality, child health etc) over this cohort.
ApproachWe propose a three-dimensional data model to aggregate information on the cohort, exposition (payments received during the observed period) and health outcomes. We treat heterogeneity based on our existing probabilistic linkage pipeline that provides data quality assessment, data conditioning (standardization, cleansing, blocking, and anonymization), two methods for probabilistic record matching, and accuracy assessment. Through this pipeline, we are able to probabilistically link records from PBF, CadastroÚnico (CADU - socioeconomic information) and healthcare databases from the Unified Health System (SUS). Uncertainty is modeled through "possible worlds", which represent a data instance (record) with a corresponding probability. There exist 2^records possible worlds with the probability distribution being the product of record probabilities. We map the most probable relationships between all the databases involved and create some simulation scenarios in order to validate them. We are seeking for a good balance between the set of possible worlds, not overextending the possibilities, and their proximity to a real scenario.
ResultsThe current implementation comprises the linkage of the 2011 extraction of CADU and healthcare databases to populate the proposed model. Such linkage provides timely execution (up to 9 hours depending on the databases) with high accurate data marts (over 95% of true positive matched pairs) for samples with increasing size (from 1,447,512 to 12,036,010 records).
ConclusionOur model is able to treat heterogeneity aspects present in huge databases. Our tools provide timely execution of probabilistic linkage with high accuracy. We started to model uncertainty in order to perform simulations and decide how to incorporate it in our model.

There's a popular bumper sticker up there in Alaska that says, "Making Texans Mad Since 1959." That's loosely translated — otherwise I couldn't say it on the radio The allusion is, of course, to the fact that when Alaska became a state, Texas immediately got demoted to second biggest state. No doubt Alaska is geographically more than twice the size of Texas, but we still own the bragging rights on many fronts. Texans are still fond of pointing out that if we melted all the ice and snow up there Texas would still be bigger. Texas reigned as the biggest state in the the union for 104 years. Alaska has a long way to go to take the title from us, about 50 years yet. We are certainly bigger in population, forty times bigger. You know that famous pipeline they have up there? Guess who built it? Texans did. And Okies, too. There are no exact figures but we have proof in Alaskan folklore. An Alaskan saying back when the pipeline was being built, was this: "Happiness is 10,000 Okies pickin' up a Texan under each arm and headin' South." Don't know why they would have that attitude, we were just making them rich. Alaska is a big oil producer, sure. But Texas is still a much larger producer of oil and gas and has far greater reserves: three times as much oil as Alaska and ten times as much natural gas. Texas remains number one in oil in the U.S. and would be the sixth largest oil country in the world if she were on her own. They don't call us Saudi Texas for nothing. Final thing, and I think of this as a kind of slam dunk fact. Alaska would not be a state if Texas had not made it one. It's true. Alaska's bid for statehood had languished for years, back in the forties and fifties. And was going nowhere until Senator Lyndon Johnson and Speaker Sam Rayburn threw their weight behind Alaska's statehood ambitions. That was the tipping point. Once those two got behind it, Alaska was fast-tracked to statehood. You might say Texas was big enough to let them be bigger. Given all that we have done for Alaska, I think they could use a bumper sticker I've designed. It looks like a Texas flag and says: " Thanks Y'all."

Advancements in technologies have resulted in an explosion of data, the volume of which continues to increase at an exponential rate. The accumulating wealth of data is enabling numerous new research possibilities and is transforming the world profoundly. In genomics, new genomes are being regularly sequenced, with a growing number of individual genomes becoming available for many species. As the ability to have complete genomic information becomes the norm, the need for a reference genome that better represents the particular species population intensifies: It becomes important to utilize the newly emerged sequences to improve current references and ensure better quality for future assemblies and experiments. Additionally, the proliferation of data has necessitated the decentralization of computational resources together with the empowerment of users to a do-it-yourself system, in which users create their own assemblies, alignments, visualizations and analyses. This is because with the accelerating amount of data, it is impossible and undesirable to maintain the infrastructure model in which only a number of specialized institutions handle most if not all of the data and analyses.Joining many other on-going efforts, the works in this dissertation attempt to address some of these rising demands. First, I describe the problem of constructing a pan-genome reference for a population and demonstrate that the resulting pan-genome reference is more representative of the population than is any individual genome, using both simulated and real data. Second, I describe a comparative genomic framework that allows for easy generation of collections of web accessible UCSC genome browsers interrelated by an alignment. The pipeline, named the comparative assembly hub (CAH) pipeline, is intended to democratize UCSC comparative genomic resources and facilitate public sharing via the internet. As a demonstration, I create comparative assembly hubs for 66 Escherichia coli / Shigella genomes and highlight comparative analyses on their pan-genomic, core genomic and phylogenetic relationships. Last, I report on comprehensive assessments of the T cell receptor (TCR) repertoires of the autoimmune disease Ankylosing Spondylitis and show example comparative analyses for finding evidence of antigen selection and identifying potential disease-associated clones. In addition, I describe an open-source software package for profiling and comparing TCR sequencing data, called the "Adaptive IMmunoSequencing ToolKit", or the aimseqtk package. The aimseqtk package is comprised of four main components addressing common analyses of this type of data: clone tracking, repertoire profiling, public clone identification and publication mining.

Water is the most precious resource in the Middle East, more important even than oil, given that while the citizens represent the 5% of the total world population, the Middle East & North Africa (MENA) region contains only 0.9% of global water resources (World Bank, 1996, Allan, 1999). For this reason, almost all conflicts, in Middle East, are mainly related to shared-water resources. Historically, water was very often used as military tool or for religious purposes, Conflicts, for water management, were known from ancient years, till to the recent time. But also in our days, by 2010, the water deficit (difference between water supply and demand) is estimated to be at around 1 billion cubic meters, explaining the importance of the water to the joint futures of Palestinians, Jordanians, and Israelis. For managing the water demand, various projects were proposed or already performed related to deep aquifers pumping, brackish-groundwater reverse-osmosis desalination, sea water desalinization, water transfer using canal or pipeline systems and dam construction. Nevertheless, it is important to understand that Peace can be possible in Middle East only if a rational and fair co-management of water resources could be real. ; Water is the most precious resource in the Middle East, more important even than oil, given that while the citizens represent the 5% of the total world population, the Middle East & North Africa (MENA) region contains only 0.9% of global water resources (World Bank, 1996, Allan, 1999). For this reason, almost all conflicts, in Middle East, are mainly related to shared-water resources. Historically, water was very often used as military tool or for religious purposes, Conflicts, for water management, were known from ancient years, till to the recent time. But also in our days, by 2010, the water deficit (difference between water supply and demand) is estimated to be at around 1 billion cubic meters, explaining the importance of the water to the joint futures of Palestinians, Jordanians, and Israelis. For managing the water demand, various projects were proposed or already performed related to deep aquifers pumping, brackish-groundwater reverse-osmosis desalination, sea water desalinization, water transfer using canal or pipeline systems and dam construction. Nevertheless, it is important to understand that Peace can be possible in Middle East only if a rational and fair co-management of water resources could be real.

As a mall country among Georgia's growth factors in future might well be foreign trade. The close cooperation with the EU within the European neighborhood policy centers on improving and facilitating trade between the partners. In 2006 the EU granted Georgia the GSP+ status which allows almost duty free imports of Georgian products in the EU. The extension of these trade preferences is negotiated in the realm of a deep and com-prehensive free trade agreement between the EU and Georgia. A closer look on the trade data reveal that no trade enhancing effect of the GSP+ can be detected. The available trade data are significantly blurred by the inclusion of energy trade from Georgia which is likely only transit trade from Azerbaijan and Kazakhstan. If these export items and the movements of some raw material prices are removed from the data no export enhancing effect can be found. In addition, in the past the composi-tion of Georgian exports remained highly biased towards raw materials and simple products. Improvements in export came from the export of services, namely tourism and pipe-line transport service. Later is a significant source of income as well as the transfers of Georgian migrants working abroad? The export of pipeline service might increase in future further if envisaged additional pipelines over Georgian soil realize. Since these are mainly built with foreign capital increasing profit repatriation will result in higher capital outflows in future. At the moment the EU negotiates an deep and comprehensive free trade agreement with Georgia which foresees beyond the abolition of tariffs the removal of all types of non-tariff barriers (NTBs) . An important part of trade facilitation would be the adop-tion of EU standards and norms which hinder at the moments Georgian exporters. Al-though the EU is prepared to contribute with financial and technical help the removal of NTBs is costly for Georgian firms. The available studies forecast however significant positive effects from a comprehensive trade liberalization between the partners. Al-though not captured by the mentioned feasibility studies on a comprehensive EU-Georgian trade agreement, the strongest export enhancing effect for Georgia will only come from broadening the existing export basket. To do so best chances for Georgian firms are seen in transit services and the production of parts and components as a sup-plier for multinational firms. The existing range of export goods does not exploit effec-tively the comparative advantages of the country.

Since the early 20th century various schemes were considered for the construction of roads, trails or railways 71 to link the Yukon, northern British Columbia and Alaska to the "outside." These schemes were motivated by economic interests, including mining, lumber and tourism concerns. During the 1920s and 1930s a small but vocal group of "builders" began to campaign for a highway, either a coastal or inland route, to improve the northwest's economic base. With the impending threat of war in the late 1930s, there was an increasing awareness by the American and Canadian governments of the vulnerability of the Pacific Coast to both air and sea attacks by "unfriendly" nations. In 1939, the Northwest Staging Route (NWSR) was surveyed by the Canadian Department of Transportation with the view towards improving the existing airfields for year round use between Edmonton and Fairbanks, and meeting increasing military needs. The unexpected bombing of Pearl Harbour in December 1941 stimulated interest in the construction of the Alaska Highway by the American government. The U.S. Army Corps of Engineers selected a route based on the location of the NWSR airfields and the military needs for an alternative land route to Alaska for defence purposes. The military was not interested in developing or planning a highway for the civilian needs of the future. The chosen route ran from Edmonton to Whitehorse, then on to Fairbanks. The U.S. Army and U.S. Public Roads Administration (PRA) roughed out a "pioneer" road in eight months in 1942; the PRA then hired civilian contractors who improved the highway in 1943 and 1944. During this time the Americans grew increasingly concerned over the lack of petroleum available in the north and the submarine threat to oil tankers transporting fuel on the Pacific Ocean. Thus the Canol project was developed to ensure a continuing supply of petroleum to meet military needs. The end result of the Canol project was a pipeline and road network transporting oil from Norman Wells on the Mackenzie River, Northwest Territories, to Whitehorse, Watson Lake and Fairbanks. The military need for the Alaska Highway and Canol pipeline declined at the end of World War II. In 1946, Canada officially accepted responsibility for maintaining and developing the Yukon portion of the Alaska Highway. The Alaska Highway affected both First Nations and non-First Nations peoples immediately. The impacts included an increased awareness of the world outside of the Yukon, imported ideas and technology, improved health care, highway transportation, telecommunications, and the development of more mining and tourist-related industries.

"Local farming communities throughout the world face productivity constraints, environmental concerns, and diverse nutritional needs. Developing countries address these challenges in a number of ways. One way is public research that produces genetically modified (GM) crops and recognize biotechnology as a part of the solution. To reach these communities, GM crops, after receiving biosafety agreement, must be approved for evaluation under local conditions. However, gaps between approvals in the developed and developing world grow larger, as the process of advancing GM crops in developing countries becomes increasingly difficult. In several countries, only insect resistant cotton has successfully moved from small, confined experimental trials to larger, open trials and to farms. By far, most GM crop approvals have been for commercial products that perform well under tropical conditions. However, complete information on public GM crop research in developing countries has not been assessed. "Will policies and research institutions in the developing world stimulate the safe use of publicly funded GM food crops?" The relatively few GM crops approved from public research, coupled with growing regulatory, biosafety capacity, trade, and political concerns, argue to the contrary. To tackle this issue, we identified and analyzed public research pipelines for GM crops among 16 developing countries and transition economies. Respondents reported 209 genetic transformation events for 46 different crops at the time when the survey was conducted. The pipelines demonstrate scientific progress among publicly funded crop research institutes in participating countries. Information and findings are presented for GM crops nearing final stages of selection. Additional details are provided for the types of genes and traits used, the breadth of genetic resources documented, implications for regulation, and the type of research partnerships employed. Regulations, GM crop approvals, choice of transgene, and policy implications are discussed as they affect this research. Based on these findings, recommendations are presented that would help sustain and increase efficiency of publicly supported research while meeting biosafety requirements. To do so, the study examines results concerning investments and choices made in research, capacity, and policy development for biotechnology. These indicate the risk and potential for GM technologies in developing countries. Policy makers, those funding biotechnology, and other stakeholders can use this information to prioritize investments, consider product advancement, and assess relative magnitude of potential risks, and benefits." -- Authors' Abstract ; Non-PR ; IFPRI1; Theme 10; Subtheme 10.1; GRP1; PBS; Pro-poor science and technology policies ; EPTD; ISNAR

Ende 2012 wird der zweite Strang der Nord Stream-Gaspipeline in Betrieb gehen. Die Debatte über Erdgas aus Russland dürfte damit wieder aufflammen. Zwei Positionen konkurrieren. Die eine lautet: Erdgasbeziehungen sind kommerzielle Aktivitäten zum Nutzen von Produzent und Importeur, Abhängigkeiten sind wechselseitig. In Politik und Öffentlichkeit ist hingegen die Ansicht weit verbreitet, nur die EU sei von Russland abhängig. Nachdem der Erdgaskonflikt zwischen Russland und der Ukraine mehrfach eskaliert ist, was kurzfristig zu Liefereinstellungen geführt hat, werden Gaslieferungen aus Russland zunehmend als Sicherheitsproblem diskutiert. Das ist unhaltbar. (Osteuropa (Berlin) / SWP)