Miracle-dz/UniFAR-FTUs huggingface dataset:
Variation in the 13C-urea breath test value by nationality in Helicobacter pylori-infected children.

BACKGROUND The 13C-urea breath (13C-UBT) test value is (semi-)quantitatively related to Helicobacter pylori density in the gastric antrum, and the value correlates with the grade of gastritis. The aim of this study was to assess variation of the 13C-urea breath test value by sociodemographic factors in H. pylori-positive children. METHODS The analysis was performed on 127 asymptomatic children (aged 5-7 years) who were identified as H. pylori-positive with the 13C-UBT test in a large population-based epidemiologic study in the city of Ulm (southern Germany). The parents of the children were asked to fill out a standardized questionnaire about sociodemographic data. RESULTS Forty-two infected children (33.1%) were of German nationality, 47 children (37.0%) were of Turkish and 38 children (29.9%) were of another nationality. Turkish children had a significantly higher 13C-UBT value (geometric mean = 27.2%) than German children (16.7%) or children with another nationality (19.3%) (P < 0.001). Girls had a trend towards higher values than boys (P = 0.058 after adjustment for nationality). Body mass index, education of the parents, and prior use of antibiotics were unrelated to the extent of the 13C-UBT. CONCLUSIONS This study identified significant variation in the extent of the 13C value by nationality among H. pylori-infected children. Further studies are needed to elucidate the causes and potential consequences of these variations.
Strong Natural Pausing by RNA Polymerase II within 10 Bases of Transcription Start May Result in Repeated Slippage and Reextension of the Nascent RNA

ABSTRACT We find that immediately following transcript initiation, RNA polymerase II pauses at several locations even in the presence of relatively high (200 μM) levels of nucleoside triphosphates. Strong pauses with half-lives of >30 s were observed at +7, +18/19, and about +25 on the template used in these experiments. We show that the strong pause at +7, after the synthesis of 5′-ACUCUCU, leads to repeated cycles of upstream slippage of the RNA-DNA hybrid followed by re-pairing with the DNA and continued RNA synthesis. The resulting transcripts are 2, 4, and 6 bases longer than predicted by the template sequence. Slippage is efficient when transcription is primed with the +1/+2 (ApC) dinucleotide, and it occurs at even higher levels with the +2/+3 primer (CpU). Slippage can occur at high levels with ATP initiation, but priming with CpA (−1/+1) supports very little slippage. This latter result is not simply an effect of transcript length at the point of pausing. Slippage can also occur with a second template on which the polymerase can be paused after synthesizing ACUCU. Slippage is not reduced by an ATP analog that blocks promoter escape, but it is inhibited by substitution of 5Br-U for U in the RNA. Our results reveal an unexpected flexibility of RNA polymerase II ternary complexes during the very early stage of transcription, and they suggest that initiation at different locations within the same promoter gives rise to transcription complexes with different properties.
Atomic Layer Etching: What Can We Learn from Atomic Layer Deposition?

Current trends in semiconductor device manufacturing impose extremely stringent requirements on nanoscale processing techniques, both in terms of accurately controlling material properties and in terms of precisely controlling nanometer dimensions. To take nanostructuring by dry etching to the next level, there is a fast growing interest in so-called atomic layer etching processes, which are considered the etching counterpart of atomic layer deposition processes. In this article, past research efforts are reviewed and the key defining characteristics of atomic layer etching are identified, such as cyclic step-wise processing, self-limiting surface chemistry, and repeated removal of atomic layers (not necessarily a full monolayer) of the material. Subsequently, further parallels are drawn with the more mature and mainstream technology of atomic layer deposition from which lessons and concepts are extracted that can be beneficial for advancing the field of atomic layer etching.
Frequent compartmentalization of hepatitis C virus variants in circulating B cells and monocytes

Differences in the composition of the hepatitis C virus (HCV) quasispecies between plasma and blood mononuclear cells (BMC) strongly suggest that BMCs support viral replication. We examined the frequency of such compartmentalization, the cell types involved, the constraints exerted on the different variants, and the role of immunoglobulin‐complexed variants. We screened the hypervariable region (HVR1) of HCV isolates from 14 HBsAg‐ and HIV‐seronegative patients with chronic HCV infection. HCV RNA was amplified and cloned from plasma, the immunoglobulin G (IgG)‐bound fraction, and total and sorted BMCs (CD19+, CD8+, CD4+, and CD14+ cells). Compartmentalization was estimated using a matrix correlation test. The ratio of nonsynonymous/synonymous substitutions (dN/dS ratio) was calculated for each compartment. HCV RNA was detected in 3/3 BMC, 11/11 CD19+, 10/11 CD14+, 4/11 CD8+ and 0/11 CD4+ cell samples. HVR1 sequences were significantly different between plasma and at least one cellular compartment in all nine cases analyzed, and between B cells (CD19+) and monocytes (CD14+) in all five available cases. IgG‐bound variants were distinct from cellular variants. DN/dS ratios were similar (n = 3) or lower (n = 6) in cellular compartments compared with plasma and the IgG‐bound fraction. In conclusion, HCV compartmentalization is a common phenomenon. B cells and monocytes harbor HCV variants showing a low rate of nonsynonymous mutations, a feature that might contribute to the persistence of HCV infection. (HEPATOLOGY 2004;39:817–825.)
Vocational Training and Gender: Wages and Occupational Mobility Among Young Workers

This paper investigates the relationship between the gender wage gap, the choice of training occupation, and occupational mobility. We use longitudinal data for young workers with apprenticeship training in West Germany. Workers make occupational career choices early during their careers and women and men pursue very different occupational careers. We reconsider whether through occupational segregation women are locked in low wage careers (Kunze, 2005) or whether they can move up to higher wage paths through mobility. We furthermore investigate whether patterns have changed across cohorts during the period 1975 and 2001 and whether effects vary across the distribution. The main results are: First, while there exists a persistent gender wage gap over experience, the gap has decreased over time. Second, in the lower part of the wage distribution, the gap is highest and it increases with experience. Third, occupational mobility is lower for women than for men and the wage gains due to occupational mobility are higher for men than for women, especially in the lower part of the wage distribution. We conclude that occupational mobility has reduced the gender wage gap, but lock-in effects are still stronger for women compared to men.
Speeding up Genetic Programming

One of the major drawbacks of Evolutionary Computation is the need for great computational power. The set of problems that can be solved, in practice, by evolutionary approaches is highly connected with the efficiency of the algorithm. In most Genetic Programming applications the majority of time is spent on the evaluation of the individuals. Accordingly, it is desirable to optimise this step of the process. In this paper we present two approaches through which significant speed improvements can be achieved. The first approach, T-functions, is effective in tasks, such as symbolic regression, that require repeated evaluation of the individuals. The second approach, caching, resorts to the storage of the execution results of individuals’ sub-trees, thus avoiding the recalculation of these sub-programs. Caching finds its application when the function set includes complex, time-consuming functions.
Phase transition and landscape statistics of the number partitioning problem.

The phase transition in the number partitioning problem (NPP), i.e., the transition from a region in the space of control parameters in which almost all instances have many solutions to a region in which almost all instances have no solution, is investigated by examining the energy landscape of this classic optimization problem. This is achieved by coding the information about the minimum energy paths connecting pairs of minima into a tree structure, termed a barrier tree, the leaves and internal nodes of which represent, respectively, the minima and the lowest energy saddles connecting those minima. Here we apply several measures of shape (balance and symmetry) as well as of branch lengths (barrier heights) to the barrier trees that result from the landscape of the NPP, aiming at identifying traces of the easy-hard transition. We find that it is not possible to tell the easy regime from the hard one by visual inspection of the trees or by measuring the barrier heights. Only the difficulty measure, given by the maximum value of the ratio between the barrier height and the energy surplus of local minima, succeeded in detecting traces of the phase transition in the tree. In addition, we show that the barrier trees associated with the NPP are very similar to random trees, contrasting dramatically with trees associated with the p spin-glass and random energy models. We also examine critically a recent conjecture on the equivalence between the NPP and a truncated random energy model.
Introduction to Wireless Sensor Networks

Description: Explores real–world wireless sensor network development, deployment, and applications The book begins with an introduction to wireless sensor networks and their fundamental concepts. Hardware components, operating systems, protocols, and algorithms that make up the anatomy of a sensor node are described in chapter two. Properties of wireless communications, medium access protocols, wireless links, and link estimation protocols are described in chapter three and chapter four. Routing basics and metrics, clustering techniques, time synchronization and localization protocols, as well as sensing techniques are introduced in chapter five to nine. The concluding chapter summarizes the learnt methods and shows how to use them to deploy real–world sensor networks in a structured way. -Presents state–of–the–art protocols and algorithms-Includes end–of–chapter summaries, exercises, and references-For students, there are hardware overviews, reading links, programming examples, and tests available at [website to follow]-For Instructors, there are PowerPoint slides and solutions available at [website to follow] This book is intended for graduate and undergraduate students interested in learning about wireless sensor networks. Only minimal experience with programming and an understanding of basic computer science concepts is necessary to understand the material included in the book. Her main research interests lie in the area of sustainable communication networks and their applications to sustainability. Her passion is teaching these topics, both to students and the general public.
Robust integer optimization and scheduling problems for large electricity consumers

With the advent of the liberalization of the electricity sector new markets have emerged, including markets for network ancillary services. Large electricity consumers' interest in participating in these markets is growing as they see an opportunity to make profits by selling flexibility of consumption. Time margins for shifting part of the scheduled consumption often exist, and they can be used to provide said flexibility. But if the schedule is not designed to support these shifts, delaying the execution of a job may cause infeasibility problems (e.g. related to safety constraints). In this paper, the problem of calculating flexible schedules is tackled with a robust optimization based approach. For this purpose a new explicit robust counterpart is developed. The proposed method is also demonstrated with an example involving the scheduling of two cement milling machines.
Effects of Genital Response Measurement Device and Stimulus Characteristics on Sexual Concordance in Women

Investigations of sexual concordance suggest that, on average, women exhibit a low, positive correlation between their subjective sexual arousal and genital response. However, this relationship appears to be stronger, on average, when genital response is measured via the external tissues of the vulva than within the vagina walls. Given the methodological variations, such as stimulus content and duration, in studies of vulvar and vaginal concordance, direct comparisons between individual studies are limited. In the current study, sexual concordance was examined using concurrent measures of vulvar blood flow (using laser Doppler imaging) and vaginal vasocongestion (using vaginal photoplethysmography) to investigate potential differences in vulvar and vaginal concordance. Twenty-five women viewed two erotic films that differed in sexual activity content (foreplay and intercourse) while their subjective sexual arousal and genital response was measured. In support of previous meta-analytic findings, results suggest that subjective sexual arousal is more strongly correlated with vulvar blood flow than with vaginal vasocongestion. Likewise, perceived genital response and actual vulvar blood flow are more strongly related than are vaginal vasocongestion and self-reported genital sensations. Practical implications for the study of women’s sexual concordance as well as broader implications for the understanding of female sexuality are considered.
A Modified Joint Source-Channel Model for Transliteration

Most machine transliteration systems transliterate out of vocabulary (OOV) words through intermediate phonemic mapping. A framework has been presented that allows direct orthographical mapping between two languages that are of different origins employing different alphabet sets. A modified joint source-channel model along with a number of alternatives have been proposed. Aligned transliteration units along with their context are automatically derived from a bilingual training corpus to generate the collocational statistics. The transliteration units in Bengali words take the pattern C+M where C represents a vowel or a consonant or a conjunct and M represents the vowel modifier or matra. The English transliteration units are of the form C*V* where C represents a consonant and V represents a vowel. A Bengali-English machine transliteration system has been developed based on the proposed models. The system has been trained to transliterate person names from Bengali to English. It uses the linguistic knowledge of possible conjuncts and diphthongs in Bengali and their equivalents in English. The system has been evaluated and it has been observed that the modified joint source-channel model performs best with a Word Agreement Ratio of 69.3% and a Transliteration Unit Agreement Ratio of 89.8%.
Drawing a Line between Literal and Idiomatic Meanings Based on Supervised WSD

Hashimoto, Chikara and Kawahara, Daisuke. 2008. Drawing a Line between Literal and Idiomatic Meanings Based on Supervised WSD. Linguistic Research 25(2), 105-123. Some phrases can be interpreted either idiomatically (figuratively) or literally in context, and the precise identification of idioms is indispensable for full-fledged natural language processing (NLP). To this end, we have constructed an idiom corpus for Japanese. This paper reports on the corpus and the results of an idiom identification experiment using the corpus. The corpus targets 146 ambiguous idioms, and consists of 102,846 sentences, each of which is annotated with a literal / idiom label. For idiom identification, we targeted 90 out of the 146 idioms and adopted a word sense disambiguation (WSD) method using both common WSD features and idiom-specific features. The corpus and the experiment are the largest of their kind, as far as we know. As a result, we found that a standard supervised WSD method works well for the idiom identification and achieved an accuracy of 89.25% and 88.86% with / without idiom-specific features.
“See and Treat” or “See” and “Treat” in an emergency department

"See and Treat" in an Emergency Department combines the process of patient assessment with treatment in the expectation that it will increase patient throughput and decrease queuing. This paper describes an evaluation of the flow of minor emergencies in an Emergency Department in the UK that had partially implemented "See and Treat" and was planning to reorganize the department yet again to re- separate the activities of assessment and treatment. A discrete event simulation indicated that the proposed system in which "See" and "Treat" were separated improved patient throughput and was likely to be more cost-effective. There were difficulties in obtaining credible data for the analysis, though this was mitigated by using the same distributions, for the analysis of both of the systems. With increasing pressure to introduce industrial concepts, such as Lean, to the health sector, simulation provides a means of assessing expensive and disruptive changes before implementation.
Efficient Parallel Video Processing Techniques on GPU: From Framework to Implementation

Through reorganizing the execution order and optimizing the data structure, we proposed an efficient parallel framework for H.264/AVC encoder based on massively parallel architecture. We implemented the proposed framework by CUDA on NVIDIA's GPU. Not only the compute intensive components of the H.264 encoder are parallelized but also the control intensive components are realized effectively, such as CAVLC and deblocking filter. In addition, we proposed serial optimization methods, including the multiresolution multiwindow for motion estimation, multilevel parallel strategy to enhance the parallelism of intracoding as much as possible, component-based parallel CAVLC, and direction-priority deblocking filter. More than 96% of workload of H.264 encoder is offloaded to GPU. Experimental results show that the parallel implementation outperforms the serial program by 20 times of speedup ratio and satisfies the requirement of the real-time HD encoding of 30 fps. The loss of PSNR is from 0.14 dB to 0.77 dB, when keeping the same bitrate. Through the analysis to the kernels, we found that speedup ratios of the compute intensive algorithms are proportional with the computation power of the GPU. However, the performance of the control intensive parts (CAVLC) is much related to the memory bandwidth, which gives an insight for new architecture design.
A pooling-LiNGAM algorithm for effective connectivity analysis of fMRI data

The Independent Component Analysis (ICA)—linear non-Gaussian acyclic model (LiNGAM), an algorithm that can be used to estimate the causal relationship among non-Gaussian distributed data, has the potential value to detect the effective connectivity of human brain areas. Under the assumptions that (a): the data generating process is linear, (b) there are no unobserved confounders, and (c) data have non-Gaussian distributions, LiNGAM can be used to discover the complete causal structure of data. Previous studies reveal that the algorithm could perform well when the data points being analyzed is relatively long. However, there are too few data points in most neuroimaging recordings, especially functional magnetic resonance imaging (fMRI), to allow the algorithm to converge. Smith's study speculates a method by pooling data points across subjects may be useful to address this issue (Smith et al., 2011). Thus, this study focus on validating Smith's proposal of pooling data points across subjects for the use of LiNGAM, and this method is named as pooling-LiNGAM (pLiNGAM). Using both simulated and real fMRI data, our current study demonstrates the feasibility and efficiency of the pLiNGAM on the effective connectivity estimation.
A Topic Similarity Model for Hierarchical Phrase-based Translation

Previous work using topic model for statistical machine translation (SMT) explore topic information at the word level. However, SMT has been advanced from word-based paradigm to phrase/rule-based paradigm. We therefore propose a topic similarity model to exploit topic information at the synchronous rule level for hierarchical phrase-based translation. We associate each synchronous rule with a topic distribution, and select desirable rules according to the similarity of their topic distributions with given documents. We show that our model significantly improves the translation performance over the baseline on NIST Chinese-to-English translation experiments. Our model also achieves a better performance and a faster speed than previous approaches that work at the word level.
MAMView: a visual tool for exploring and understanding metric access methods

The MAMView framework is a data exploration tool that allows developers and users of Metric Access Methods (MAMs) to explore and share dynamic and interactive 3D presentations of a MAM, making the understanding of those structures easier. It is able to create visual representations of metric datasets, including high-dimensional and non-dimensional information. This is achieved by using an extension of the FastMap algorithm. This framework was developed as a practical tool that has been successfully applied to study existing MAMs, helping both new and experienced users to better understand them. The MAMView was also applied to a new under development MAM. With MAMView in hands, the development team of this MAM was able to drill-down its algorithms, quickly finding problems and also potential points for improvement and optimizations. Our focus on this work is on proposing an intuitive yet powerful visualization framework that can be easily employed to build intuitive visual presentations that can bypass the drawback of MAMs dealing with datasets with no spatial representation. Besides MAMView being a powerful visualization tool, its greatest strengths are the ability to interactively explore a visual presentation of a MAM at any level of detail, and the ability to seamlessly query and produce graphical representations in XML format that can be straightforward executed. This paper presents the MAMView framework and its main techniques, describes the current tool, and reports on our experiences in applying it to real applications.
Investigating Freehand Pan and Zoom

The availability of low-cost and flexible tracking systems for hand and body movements is increasing. With this, more thorough investigations for more natural and efficient physical interaction styles are required which take particular limitations of such systems into account, such as the limited ability to track individual fingers. To contribute to this, we describe an investigation of basic hand gestures for the exploration of large information spaces. A set of four pan-and-zoom alternatives using two-handed gestural controls have been implemented and compared using Google Earth as an example. For this we conducted a small-scaled formative user study with nine participants to fundamentally assess users' acceptance and the qualification of these freehand gestures for pan-and-zoom operations. As a result, a simple forward and backward hand movement for zooming and a joystick metaphor for panning yielded in the best overall results. Especially the seamless integration of continuous pan and zoom was positively highlighted by participants.