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Search Results: 1 - 10 of 428986 matches for " B. S?rensen "
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Replication of Prostate Cancer Risk Variants in a Danish Case-Control Association Study  [PDF]
Diem Nguyen Bentzon, Mette Nyegaard, Anders B?rglum, Torben ?rntoft, Michael Borre, Karina Dalsgaard Srensen
Open Journal of Urology (OJU) , 2012, DOI: 10.4236/oju.2012.22009
Abstract: Background: Prostate cancer is one of the main causes for cancer morbidity and mortality in Western countries. Recently, several single nucleotide polymorphisms (SNPs) associated with prostate cancer have been identified in genome-wide association studies and multiple variant models have been developed to predict prostate cancer risk. The association between genetic markers and clinico-pathological tumor variables has, however, been inconsistent. Methods and Materials: A total of 32 previously identified prostate cancer-associated risk SNPs were genotyped in 648 prostate cancer cases and 526 age-matched controls. Family history was obtained by questionnaire. Age at diagnosis, clinical tumor variables including pre- and postoperative PSA, Gleason score, and T stage were obtained from prospectively collected clinical data (Aarhus Prostate Cancer Study). The SNPs were genotyped using Sequenom and Taqman assays and associations between SNPs, prostate cancer risk, and clinico-pathological variables were assessed. Results: Seventeen SNPs were successfully replicated in our case-control study and the association estimates were consistent with previous reports. Four markers were excluded from further analysis due to linkage disequilibrium. The cumulative effect of having the disease-associated genotype at five SNPs (rs4430796, rs6983267, rs1859962, rs1447295 and rs16901979) increased the prostate cancer risk with odds ratio 6.02 (95% CI: 2.21 - 16.38; P = 1.0 × 10–4) in patients with any combination of ≥4 markers compared with patients without any of the five SNPs (P for trend = 1.0 × 10–4). Six markers were significantly associated with clinico-pathological variables: SNP rs2735839 (GG) at locus 19q13, which is in the KLK3 gene encoding PSA, was associated with high preoperative PSA (P = 0.04), low Gleason score (P = 0.01) and low T stage (P = 0.02). Variants rs5759167 (GG/GT) (22q13) and rs7679673 (CC/CA) (4q24) were correlated with low risk for biochemical relapse (P = 0.015 and P = 0.009, respectively), whereas rs6983267 (GG) (8q24) was significantly associated with biochemical recurrence (P = 0.045). In addition, variants rs6983267 (GG) and rs5759167 (GG/GT) were significantly associated with negative family history (P = 0.04 and P = 0.02, respectively). Conclusion: We replicated 17 previously identified prostate cancer-associated risk SNPs in a Danish case-control study and found a cumulative and significant association between five SNPs and prostate cancer. Overall, we
Die Archivierung von L ngsschnittdaten für künftige Forschungsarbeiten. Warum qualitative Daten zur Nützlichkeit wissenschaftlicher Untersuchungen beitragen Archiving Longitudinal Data for Future Research. Why Qualitative Data Add to a Study's Usefulness El almacenamiento de datos longitudinales para la investigación futura: Por qué los datos cualitativos incrementan la utilidad de los estudios
Jacquelyn B. James,Annemette Srensen
Forum : Qualitative Social Research , 2000,
Abstract: In dem vorliegenden Beitrag diskutieren wir die besonderen Herausforderungen, denen Archive begegnen müssen, wenn sie L ngsschnittdaten mit breiten qualitativen Datenanteilen für künftige Forschungsarbeiten bereitstellen wollen. Wir berühren dabei Fragen des Datenschutzes, einer optimalen Aufbereitung der Daten für Re-Analysen (und m glicher Wege für Follow-Ups ohne Verletzungen des Datenschutzes) sowie M glichkeiten, Forschende bei der (Planung der) Archivierung von Daten für L ngsschnittuntersuchungen zu unterstützen. Das Kernstück unseres Beitrages besch ftigt sich mit dem besonderen Nutzen von qualitativen Daten für künftige Forschungsarbeiten. Dabei ist unser Hauptargument, dass qualitatives Material in einem weitaus gr eren Ausma als quantitative Daten sp teren Forscher(inne)n neue/zus tzliche Perspektiven und Deutungsm glichkeiten er ffnet. Wir verdeutlichen dies an Re-Analysen von Daten, die im Murray Research Center archiviert wurden. URN: urn:nbn:de:0114-fqs0003235 In this paper we discuss the special challenges that data archives face when archiving and preparing for new research longitudinal studies with a large qualitative component. We discuss issues of confidentiality, how best to organize longitudinal data for future use, including ways in which to permit future follow-ups without compromising confidentiality, and ways to teach investigators how to plan for the archiving of their longitudinal research. The core of the paper, however, is an examination of the strengths that qualitative data lend to longitudinal studies for future researchers. Our main argument is that qualitative data to a much greater extent permit new investigators to look at the data in new ways than do quantitative data. We present examples of this based on re-analyses of data archived at the Murray Research Center. URN: urn:nbn:de:0114-fqs0003235 En este trabajo discutimos los retos especiales que enfrenta el archivo de los datos, cuando se almacenan y se preparan para nuevas investigaciones longitudinales que tienen un notable componente cualitativo. Discutimos los temas de la confidencialidad y las procedimientos preferibles para la organización de datos longitudinales para uso futuro, incluyendo técnicas que permiten el uso posterior de los datos sin comprometer la confidencialidad de éstos. También consideramos cómo ense ar a los investigadores a planificar el almacenamiento de sus datos longitudinales. El punto central de este trabajo, sin embargo, consiste en examinar los beneficios que tienen los datos cualitativos para los estudios longitudinales de futuros
NORMA-Gene: A simple and robust method for qPCR normalization based on target gene data
Lars-Henrik Heckmann, Peter B Srensen, Paul Krogh, Jesper G Srensen
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-250
Abstract: We developed a data driven normalization algorithm (NORMA-Gene). An analysis of the performance of NORMA-Gene compared to reference gene normalization on artificially generated data-sets showed that the NORMA-Gene normalization yielded more precise results under a large range of parameters tested. Furthermore, when tested on three very different real qPCR data-sets NORMA-Gene was shown to be best at reducing variance due to experimental bias in all three data-sets compared to normalization based on the use of reference gene(s).Here we present the NORMA-Gene algorithm that is applicable to all biological and biomedical qPCR studies, especially those that are based on a limited number of assayed genes. The method is based on a data-driven normalization and is useful for as little as five target genes comprising the data-set. NORMA-Gene does not require the identification and validation of reference genes allowing researchers to focus their efforts on studying target genes of biological relevance.Real-time quantitative PCR (qPCR) represents the current state-of-the-art approach for measuring gene expression; and the method has numerous applications in both biology and biomedicine. Although qPCR is a robust technique results can vary depending on factors such as RNA integrity, reverse transcriptase (RT) efficiencies, sample-to-sample variations in amplification efficiency, and variation in cDNA sample loading. Using equal sample sizes, assessing RNA integrity and equalizing RNA concentrations prior to RT are fundamental normalization steps in qPCR [1]. Still, normalization to some internal control is essential for accurate qPCR in order to balance sample-to-sample variations within the RT and PCR reactions. Currently, the preferred internal control is achieved by using reference genes (also referred to as housekeeping genes) or better a normalization factor based on several reference genes calculated using e.g. geNorm [2]. However, the use of reference genes suffer from
From Sociocultural Disintegration to Community Connectedness Dimensions of Local Community Concepts and Their Effects on Psychological Health of Its Residents
Tom Srensen,Robert Kleiner,Paul Ngo,Andreas Srensen,Nils B?e
Psychiatry Journal , 2013, DOI: 10.1155/2013/872146
Abstract: In a series of community mental health promotion studies in Lofoten, Norway, the concept of sociocultural integration is used to describe properties of a local community that are related to people's psychological health. Starting with Durkheim's description of a cohesive society, we compare different concepts that are related to sociocultural integration, for example, sense of community, social capital, and social cohesion. We then examine the relationship of various individual oriented social psychological concepts to sociocultural integration. These concepts often share theoretical and operational definitions. The concept of sociocultural integration in the Lofoten studies was proved to be very valuable in understanding how the properties of a community can affect people's mental health and their social psychological properties. It has also shown its value in the planning of mental health services and demonstrating its success in concrete community-based mental health promotion projects. Thus they could make important contributions to further studies and actions in local communities where the intersection between the individual, their social network, and their local community occurs. 1. Introduction The seminal Stirling County study [1] took social psychiatry to a position where mental health promotion could be translated into concrete community involvement. From a social psychiatry that linked social stratification and social class to prevalence of psychiatric disorders [2, 3], Leighton amplified the ecological approach to include concrete community processes and to operational measures of the phenomena, thereby linking the context of geographic areas to specific characteristics, that is, the sociocultural integration of a local community to the occurrence and distribution of mental disorders. A main finding from the Stirling County studies was the stronger effects on mental health of higher levels of sociocultural integration of a local community than higher social class within those same communities [4, 5]. Taking off from Leighton’s Stirling County study, Dalgard et al. [6, 7] and S?rensen [8] combined a psychiatric service perspective with an analytical focus on the local community that itself contributed to the mental health of a population. The major thrust of our basic and applied research project has been to contribute effective and sustainable strategies for treatment, intervention, prevention, and promotion of mental health and well-being, especially at the local community level. Unfortunately, the definition of “community” can vary from
Regional analysis of groundwater nitrate concentrations and trends in Denmark in regard to agricultural influence
B. Hansen,T. Dalgaard,L. Thorling,B. Srensen
Biogeosciences Discussions , 2012, DOI: 10.5194/bgd-9-5321-2012
Abstract: The act of balancing between an intensive agriculture with a high potential for nitrate pollution and a~drinking water supply almost entirely based on groundwater is a challenge faced by Denmark and similar regions around the globe. Since the 1980s, regulations implemented by Danish farmers have succeeded in optimizing the N (nitrogen) management at farm level. As a result, the upward agricultural N surplus trend has been reversed, and the N surplus has reduced by 30–55 % from 1980 to 2007 depending on region. The reduction in the N surplus served to reduce the losses of N from agriculture, with documented positive effects on nature and the environment in Denmark. In groundwater, the upward trend in nitrate concentration was reversed around 1980, and a larger number of downward nitrate trends were seen in the youngest groundwater compared with the oldest groundwater. However, on average, approximately 48 % of the oxic monitored groundwater has nitrate concentrations above the groundwater and drinking water standards of 50 mg l 1. Furthermore, trend analyses show that 33 % of all the monitored groundwater has upward nitrate trends, while only 18 % of the youngest groundwater has upward nitrate trends according to data sampled from 1988–2009. A regional analysis shows a correlation between a high level of N surplus in agriculture, high concentrations of nitrate in groundwater and the largest number of downward nitrate trends in groundwater in the livestock-dense northern and western parts of Denmark compared with the south-eastern regions with lower livestock densities. These results indicate that the livestock farms dominating in northern and western parts of Denmark have achieved the largest reductions in N surpluses. Groundwater recharge age determinations allow comparison of long-term changes in N surplus in agriculture with changes in oxic groundwater quality. The presented data analysis is based on groundwater recharged from 1952–2003, but sampled from 1988–2009. Repetition of the nitrate trend analyses at five-year intervals using dating of the groundwater recharged in the coming years and a longer time series of the nitrate analyses can reveal the evolution in nitrate leaching from Danish agriculture during the past 10 yr. Similar analyses can be carried out to compare with other regions internationally.
A mass conserving and multi-tracer efficient transport scheme in the online integrated Enviro-HIRLAM model
B. Srensen,E. Kaas,U. S. Korsholm
Geoscientific Model Development Discussions , 2012, DOI: 10.5194/gmdd-5-3733-2012
Abstract: In this paper a new advection scheme for the online coupled chemical-weather prediction model Enviro-HIRLAM is presented. The new scheme is based on the locally mass conserving semi-Lagrangian method (LMCSL), where the original two-dimensional scheme has been extended to a fully three-dimensional version. This means that the three-dimensional semi-implicit semi-Lagrangian scheme which is currently used in Enviro-HIRLAM, is largely unchanged. The HIRLAM model is a computationally efficient hydrostatic operational short term numerical weather prediction model, which is used as the base for the online integrated Enviro-HIRLAM. The new scheme is shown to be efficient, mass conserving, and shape-preserving while only requiring minor alterations to the original code. It still retains the stability at long time steps, which the semi-Lagrangian schemes are known for, while handling the emissions of chemical species accurately. Several mass conserving filters have been tested to assess the optimal balance of accuracy vs. efficiency.
An improved PCR strategy for fast screening of specific and random integrations in rAAV-mediated gene targeted cell clones
Yonglun Luo, Lars Bolund, Charlotte B Srensen
BMC Research Notes , 2011, DOI: 10.1186/1756-0500-4-246
Abstract: In this study, we have developed an improved PCR screening method, which can be used for fast screening of clones with unwanted random integration (RI) of the rAAV genome. This improved screening method includes four PCRs: a PCR for the selection gene (e.g. Neo-PCR), a PCR for targeted gene knockout (e.g. BRCA1-KO-PCR), and two generalized PCRs for random integration of the rAAV genome (5'-AAV-RI-PCR, and 3'-AAV-RI-PCR). We have shown that this screening method greatly facilitates the procedure of screening for BRCA1 (BReast CAncer susceptibility gene 1) targeted cell clones, eliminating cell clones with both BRCA1 knockout and random integration of the rAAV genome.This screening method has facilitated the screening of correct gene-targeted cells. As the AAV-RI-PCRs are generalized PCRs, this method can also be applied for screening of rAAV-mediated targeting of other genes.We have been using recombinant adeno-associated virus (rAAV)-mediated gene targeting to generate cloned pigs with specific gene knockout (KO) as models of human diseases [1]. However, screening for the pure gene knockout cell clones among the selection-positive cell clones can be difficult and hampers the applications of this technology. Primary fibroblasts are commonly used as target cells for gene targeting prior to cloning by somatic cell nuclear transfer. Unlike stem cells, these cells have a limited proliferation capacity rendering fast screening for knockout clones necessary. The standard screening strategy is based on PCR on cell lysates from cell clones (Figure 1A), and Southern blot analysis that requires long-term cultivation to obtain sufficient amounts of genomic DNA [1-3]. We have experienced that less than 50% of the selection-positive cell clones can be expanded sufficient for Southern blot screening when cultured in a normal growth medium (DMEM, +15%FCS, +P/S, +glutamine).In this study, we have developed an improved PCR screening method, which can be used for screening of clones w
Kinetics and mechanism of the uptake of N2O5 on mineral dust at 298 K
S. Seisel, C. B rensen, R. Vogt,R. Zellner
Atmospheric Chemistry and Physics (ACP) & Discussions (ACPD) , 2005,
Abstract: The heterogeneous reaction of N2O5 with mineral (Saharan) dust has been studied at T=298 K using a combination of Knudsen and DRIFTS cells for kinetic and product investigations, respectively. The initial uptake coefficient has been determined to be γ=(8.0±0.3)·10 2. This uptake slowly saturates into a steady state uptake of γ=(1.3±0.3)·10 2 suggesting that reaction of N2O5 with the mineral dust surface and hydrolysis of N2O5 on the surface take place simultaneously. Both uptake coefficients have been calculated on the basis of the geometric (projected) surface area of the sample and must therefore be regarded as upper limits. In addition, the product investigations show that N2O5 is irreversibly taken up to form nitrate on the surface. Recent model calculations suggest that the uptake rates of N2O5 on Saharan dust which we measured may be large enough to influence the photo-oxidant budget of the atmosphere.
Review of Survey activities 2012: Evaluation of total groundwater abstraction from public waterworks in Denmark using principal component analysis
Srensen B.L.,M?ller, R.R.
Geological Survey of Denmark and Greenland Bulletin , 2013,
Timeability of Extensive-Form Games
Sune K. Jakobsen,Troels B. Srensen,Vincent Conitzer
Computer Science , 2015,
Abstract: Extensive-form games constitute the standard representation scheme for games with a temporal component. But do all extensive-form games correspond to protocols that we can implement in the real world? We often rule out games with imperfect recall, which prescribe that an agent forget something that she knew before. In this paper, we show that even some games with perfect recall can be problematic to implement. Specifically, we show that if the agents have a sense of time passing (say, access to a clock), then some extensive-form games can no longer be implemented; no matter how we attempt to time the game, some information will leak to the agents that they are not supposed to have. We say such a game is not exactly timeable. We provide easy-to-check necessary and sufficient conditions for a game to be exactly timeable. Most of the technical depth of the paper concerns how to approximately time games, which we show can always be done, though it may require large amounts of time. Specifically, we show that for some games the time required to approximately implement the game grows as a power tower of height proportional to the number of players and with a parameter that measures the precision of the approximation at the top of the power tower. In practice, that makes the games untimeable. Besides the conceptual contribution to game theory, we believe our methodology can have applications to preventing information leakage in security protocols.
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