Software for physics of tau lepton decay in LHC experiments

Software development in high energy physics experiments offers unique experience with rapidly changing environment and variety of different standards and frameworks that software must be adapted to. As such, regular methods of software development are hard to use as they do not take into account how greatly some of these changes influence the whole structure. The following thesis summarizes development of TAUOLA C++ Interface introducing tau decays to new event record standard. Documentation of the program is already published. That is why it is not recalled here again. We focus on the development cycle and methodology used in the project, starting from the definition of the expectations through planning and designing the abstract model and concluding with the implementation. In the last part of the paper we present installation of the software within different experiments surrounding Large Hadron Collider and the problems that emerged during this process.Comment: Thesis submitted to Applied Computer Science Department in partial fulfillment of the requirements for the MSc degree. This work is partially supported by EU Marie Curie Research Training Network grant under the contract No. MRTN-CT-2006-0355505, Polish Government grant N202 06434 (2008-2011) and EU-RTN Programme: Contract No. MRTN-CT-2006-035482 'Flavianet

A co-occurrence framework conceptualized for bridging the gap between basic science, clinical research and clinical practices

The intellectual impulsiveness of man to understand the unknown and the continual need of the society to improve healthcare have encouraged extensive investigation on numerous and diverse cause-and-effect relationships. The nature of this endeavor, however, renders the inability of investigator at all levels to escape beyond the narrow conceptual boundary described by an early French philosopher as the vicious cycle. To enjoy the theoretically plausible benefits of refined labor division, data-driven healthcare management, and real-time evidence-based practices, it must first be acknowledged that co-occurrence is better than cause-and-effect in explaining how an observation takes place at a particular time. This paper details a co-occurrence framework, and discusses its implications for the global healthcare system

Search engine user behaviour: How can users be guided to quality content?

The typical behaviour of the Web search engine user is widely known: a user only types in one or a few keywords and expects the search engine to produce relevant results in an instant. Search engines not only adapt to this behaviour. On the contrary, they are often faced with criticism that they themselves created this kind of behaviour. As search engines are trendsetters for the whole information world, it is important to know how they cope with their users’ behaviour. Recent developments show that search engines try to integrate results from different collections into their results lists and to guide their users to the right results. These results should not only be relevant in general, but also be pertinent in the sense of being relevant to the user in his current situation and in accordance to his background. The article focuses on the problems of guiding the user from his initial query to these results. It shows how the general users are searching and how the intents behind their queries can be used to deliver the right results. It will be shown that search engines try to give some good results for everyone instead of focusing on complete result sets for a specific user type. If the user wishes, he can follow the paths laid out by the engines to narrow the results to a result set suitable to him

Performance Prediction of Nonbinary Forward Error Correction in Optical Transmission Experiments

In this paper, we compare different metrics to predict the error rate of optical systems based on nonbinary forward error correction (FEC). It is shown that the correct metric to predict the performance of coded modulation based on nonbinary FEC is the mutual information. The accuracy of the prediction is verified in a detailed example with multiple constellation formats, FEC overheads in both simulations and optical transmission experiments over a recirculating loop. It is shown that the employed FEC codes must be universal if performance prediction based on thresholds is used. A tutorial introduction into the computation of the threshold from optical transmission measurements is also given.Comment: submitted to IEEE/OSA Journal of Lightwave Technolog

Wolbachia and DNA barcoding insects: patterns, potential and problems

Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region

Human and Machine Speaker Recognition Based on Short Trivial Events

Trivial events are ubiquitous in human to human conversations, e.g., cough, laugh and sniff. Compared to regular speech, these trivial events are usually short and unclear, thus generally regarded as not speaker discriminative and so are largely ignored by present speaker recognition research. However, these trivial events are highly valuable in some particular circumstances such as forensic examination, as they are less subjected to intentional change, so can be used to discover the genuine speaker from disguised speech. In this paper, we collect a trivial event speech database that involves 75 speakers and 6 types of events, and report preliminary speaker recognition results on this database, by both human listeners and machines. Particularly, the deep feature learning technique recently proposed by our group is utilized to analyze and recognize the trivial events, which leads to acceptable equal error rates (EERs) despite the extremely short durations (0.2-0.5 seconds) of these events. Comparing different types of events, 'hmm' seems more speaker discriminative.Comment: ICASSP 201