A new population of terrestrial gamma-ray flashes in the RHESSI data

Terrestrial gamma-ray flashes (TGFs) are the most energetic photon phenomenon occurring naturally on Earth. An outstanding question is as follows: Are these flashes just a rare exotic phenomenon or are they an intrinsic part of lightning discharges and therefore occurring more frequently than previously thought? All measurements of TGFs so far have been limited by the dynamic range and sensitivity of spaceborne instruments. In this paper we show that there is a new population of weak TGFs that has not been identified by search algorithms. We use the World Wide Lightning Location Network (WWLLN) to identify lightning that occurred in 2006 and 2012 within the 800 km field of view of Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI). By superposing 740,210 100 ms RHESSI data intervals, centered at the time of the WWLLN detected lightning, we identify at least 141 and probably as many as 191 weak TGFs that were not part of the second RHESSI data catalogue. This supports the suggestion that the global TGF production rate is larger than previously reported

Efficient approaches for large-scale GWAS with genotype uncertainty

Association studies using genetic data from SNP-chip-based imputation or low-depth sequencing data provide a cost-efficient design for large-scale association studies. We explore methods for performing association studies applicable to such genetic data and investigate how using different priors when estimating genotype probabilities affects the association results. Our proposed method, ANGSD-asso’s latent model, models the unobserved genotype as a latent variable in a generalized linear model framework. The software is implemented in C/C++ and can be run multi-threaded. ANGSD-asso is based on genotype probabilities, which can be estimated using either the sample allele frequency or the individual allele frequencies as a prior. We explore through simulations how genotype probability-based methods compare with using genetic dosages. Our simulations show that in a structured population using the individual allele frequency prior has better power than the sample allele frequency. In scenarios with sequencing depth and phenotype correlation ANGSD-asso’s latent model has higher statistical power and less bias than using dosages. Adding additional covariates to the linear model of ANGSD-asso’s latent model has higher statistical power and less bias than other methods that accommodate genotype uncertainty, while also being much faster. This is shown with imputed data from UK Biobank and simulations

Detection of Legionella by quantitative-polymerase chain reaction (qPCR) for monitoring and risk assessment

<p>Abstract</p> <p>Background</p> <p>Culture and quantitative polymerase chain reaction (qPCR) assays for the detection of <it>Legionella </it>were compared on samples from a residential area before and after two interventions. A total of 84 samples were collected from shower hoses and taps as first flush samples and at constant temperature. Samples were grouped according to the origin of the sample, a) circulation water b) water from empty apartments c) water from shower hoses. The aims were to investigate the usefulness of qPCR compared to culture for monitoring remedial actions for elimination of <it>Legionella </it>bacteria and as a tool for risk assessment.</p> <p>Results</p> <p>In water collected from the apartments <it>Legionella </it>spp were detected by qPCR in the concentration range from LOQ to 9.6*10⁵GU/L while <it>L. pneumophila </it>were detected in a range from LOQ to 6.8*10⁵GU/L. By culturing, the legionellae were detected in the range from below detection limit (> 10 CFU/L) to 1.6*10⁶CFU/L. In circulating water and in first flush water from shower hoses, culture and qPCR showed the same tendencies. The overall correlation between the bacteria number detected by culture and the two developed qPCR assays (<it>L</it>. spp and <it>L. pneumophila</it>) was relatively poor (r²= 0.31 for culture and <it>Legionella </it>spp. assay, r²= 0.20 for culture and <it>L. pneumophila </it>assay).</p> <p>Conclusion</p> <p>Detection by qPCR was suitable for monitoring changes in the concentration of <it>Legionella </it>but the precise determination of bacteria is difficult. Risk assessment by qPCR only on samples without any background information regarding treatment, timing, etc is dubious. However, the rapid detection by qPCR of high concentrations of <it>Legionella </it>- especially <it>Legionella pneumophila </it>- is valuable as an indicator of risk, although it may be false positive compared to culture results. On the other hand, the detection of a low number of bacteria by qPCR is a strong indication for the absence of risk.</p

A Web-based multimedia collaboratory. Empirical work studies in film archives

This report represents the latest study in the activity on Ecological Information Systems conducted in the Center for Human Machine Interaction situated at Ris National Laboratory and the University of Aarhus. The purpose of this activity is to give a description of the characteristics of work domains that will serve to outline the general context of concern to design of collaboratories. In addition, a set of preliminary implications for the design of a collaboratory are derived from the cognitive work analysis. To anticipate, further research on this approach to the design of collaboratories will show how the preceding analysis is likely to lead to a novel theoretical framework, called Ecological Collaborative Information Systems (ECIS), required for the design of collaboratories. The intention is to illustrate how the general principles of ECIS can be instantiated to develop a concrete design product: A crossdisciplinary and cross-cultural collaboratory to support customer service and professional research in archives. A web based Collaboratory Numerous valuable historic and cultural films and their sources are scattered in various national archives. Knowledge and usage of the multinational film material are severely impeded by access problems. To fully exploit the cultural film heritage internationally, a high degree of cross-disciplinary and international collaboration among professionals working with the film media is required. The Collaboratory for Annotation, Indexing and Retrieval of Digitized Historical Archive Material (Collate) is intended to foster and support collaboration on research, cultural mediation and preservation of films through a distributed multimedia repository. The collaboratory will provide webbased tools and interfac..

The Validation and Assessment of Machine Learning: A Game of Prediction from High-Dimensional Data

In applied statistics, tools from machine learning are popular for analyzing complex and high-dimensional data. However, few theoretical results are available that could guide to the appropriate machine learning tool in a new application. Initial development of an overall strategy thus often implies that multiple methods are tested and compared on the same set of data. This is particularly difficult in situations that are prone to over-fitting where the number of subjects is low compared to the number of potential predictors. The article presents a game which provides some grounds for conducting a fair model comparison. Each player selects a modeling strategy for predicting individual response from potential predictors. A strictly proper scoring rule, bootstrap cross-validation, and a set of rules are used to make the results obtained with different strategies comparable. To illustrate the ideas, the game is applied to data from the Nugenob Study where the aim is to predict the fat oxidation capacity based on conventional factors and high-dimensional metabolomics data. Three players have chosen to use support vector machines, LASSO, and random forests, respectively

FoxK1 and FoxK2 in insulin regulation of cellular and mitochondrial metabolism

A major target of insulin signaling is the FoxO family of Forkhead transcription factors, which translocate from the nucleus to the cytoplasm following insulin-stimulated phosphorylation. Here we show that the Forkhead transcription factors FoxK1 and FoxK2 are also downstream targets of insulin action, but that following insulin stimulation, they translocate from the cytoplasm to nucleus, reciprocal to the translocation of FoxO1. FoxK1/FoxK2 translocation to the nucleus is dependent on the Akt-mTOR pathway, while its localization to the cytoplasm in the basal state is dependent on GSK3. Knockdown of FoxK1 and FoxK2 in liver cells results in upregulation of genes related to apoptosis and down-regulation of genes involved in cell cycle and lipid metabolism. This is associated with decreased cell proliferation and altered mitochondrial fatty acid metabolism. Thus, FoxK1/K2 are reciprocally regulated to FoxO1 following insulin stimulation and play a critical role in the control of apoptosis, metabolism and mitochondrial function

Archaic adaptive introgression in TBX15/WARS2

A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using SNP chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15