Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of the Rockall risk scoring system in upper gastrointestinal bleeding

BACKGROUND Several scoring systems have been developed to predict the risk of rebleeding or death in patients with upper gastrointestinal bleeding (UGIB). These risk scoring systems have not been validated in a new patient population outside the clinical context of the original study. AIMS To assess internal and external validity of a simple risk scoring system recently developed by Rockall and coworkers. METHODS Calibration and discrimination were assessed as measures of validity of the scoring system. Internal validity was assessed using an independent, but similar patient sample studied by Rockall and coworkers, after developing the scoring system (Rockall’s validation sample). External validity was assessed using patients admitted to several hospitals in Amsterdam (Vreeburg’s validation sample). Calibration was evaluated by a χ2 goodness of fit test, and discrimination was evaluated by calculating the area under the receiver operating characteristic (ROC) curve. RESULTS Calibration indicated a poor fit in both validation samples for the prediction of rebleeding (p<0.0001, Vreeburg; p=0.007, Rockall), but a better fit for the prediction of mortality in both validation samples (p=0.2, Vreeburg; p=0.3, Rockall). The areas under the ROC curves were rather low in both validation samples for the prediction of rebleeding (0.61, Vreeburg; 0.70, Rockall), but higher for the prediction of mortality (0.73, Vreeburg; 0.81, Rockall). CONCLUSIONS The risk scoring system developed by Rockall and coworkers is a clinically useful scoring system for stratifying patients with acute UGIB into high and low risk categories for mortality. For the prediction of rebleeding, however, the performance of this scoring system was unsatisfactory.
Combined treatment of alendronate and low-intensity pulsed ultrasound (LIPUS) increases bone mineral density at the cancellous bone osteotomy site in aged rats: a preliminary study.

INTRODUCTION During fracture healing, alendronate encourages callus volume by inhibiting bone resorption, whereas low-intensity pulsed ultrasound (LIPUS) enhances bone regeneration by promoting an anabolic response. METHODS In the present study, 9-month-old Sprague-Dawley rats, with a unilateral proximal tibial osteotomy, were treated with alendronate (daily, 1 µg/kg) plus sham-LIPUS (n = 14), saline plus LIPUS (20 min/day) (n = 18), alendronate plus LIPUS (n = 16), or saline plus sham-LIPUS as a control (n = 13) for 4 weeks. The rats were then examined for changes in bone mineral density (BMD) during metaphyseal bone repair. RESULTS The combined therapy significantly increased BMD at the osteotomy site at 4 weeks (p < 0.001) compared with the control, without affecting the contralateral, non-osteotomized tibia. Both alendronate and LIPUS alone also exerted a positive, albeit less, effect on BMD in the affected limb (p < 0.001 and p = 0.006, respectively). CONCLUSION Alendronate and LIPUS cooperate to enhance BMD during metaphyseal bone healing.
Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

Genetic association studies, in particular the genome-wide association study (GWAS) design, have provided a wealth of novel insights into the aetiology of a wide range of human diseases and traits, in particular cardiovascular diseases and lipid biomarkers. The next challenge consists of understanding the molecular basis of these associations. The integration of multiple association datasets, including gene expression datasets, can contribute to this goal. We have developed a novel statistical methodology to assess whether two association signals are consistent with a shared causal variant. An application is the integration of disease scans with expression quantitative trait locus (eQTL) studies, but any pair of GWAS datasets can be integrated in this framework. We demonstrate the value of the approach by re-analysing a gene expression dataset in 966 liver samples with a published meta-analysis of lipid traits including >100,000 individuals of European ancestry. Combining all lipid biomarkers, our re-analysis supported 26 out of 38 reported colocalisation results with eQTLs and identified 14 new colocalisation results, hence highlighting the value of a formal statistical test. In three cases of reported eQTL-lipid pairs (SYPL2, IFT172, TBKBP1) for which our analysis suggests that the eQTL pattern is not consistent with the lipid association, we identify alternative colocalisation results with SORT1, GCKR, and KPNB1, indicating that these genes are more likely to be causal in these genomic intervals. A key feature of the method is the ability to derive the output statistics from single SNP summary statistics, hence making it possible to perform systematic meta-analysis type comparisons across multiple GWAS datasets (implemented online at http://coloc.cs.ucl.ac.uk/coloc/). Our methodology provides information about candidate causal genes in associated intervals and has direct implications for the understanding of complex diseases as well as the design of drugs to target disease pathways.
Lexical validation of answers in Question Answering

Question answering (QA) aims at retrieving precise information from a large collection of documents, typically the Web. Different techniques can be used to find relevant information, and to compare these techniques, it is important to evaluate question answering systems. The objective of an Answer Validation task is to estimate the correctness of an answer returned by a QA system for a question, according to the text snippet given to support it. In this article, we present a lexical strategy for deciding if the snippets justify the answers, based on our own question answering system. We discuss our results, and show the possible extensions of our strategy.
Dual Spin-Cast Thermally Interdiffused Polymeric Photovoltaic Devices

An in depth study of the performance of thermally interdiffused concentration gradient polymer photovoltaic devices is carried out with particular attention to the effect of the thickness and the thermal treatments on the power conversion efficiency, short circuit current, open circuit voltage and other key electrical properties. Bilayer films of sequentially spin-cast donor and acceptor materials are exposed to various heat treatments in order to induce the interdiffusion. The depth profiles show concentration gradients in the donor and acceptor as a result of interdiffusion and these devices show an order of magnitude increase in the device performance compared to the bilayer devices. Dual spin-cast poly (3-octylthiophene-2,5-diyl) (P3OT)[6,6] phenyl C61 butyric acid methyl ester (PCBM) and poly (3-hexylthiophene-2,5-diyl) (P3HT)PCBM interdiffused devices are studied in detail by varying the thickness of the donor and acceptor layers as well as the annealing conditions for initial polymer layer and the time and temperature of the interdiffusion process. Auger spectroscopy and X-ray photoelectron spectroscopy along with ion beam milling are used to investigate the concentration gradient formed as a result of the interdiffusion. The sulfur signal present in the P3OT and P3HT backbone is detected to identify the concentration profiles in the P3OT-PCBM and P3HT-PCBM devices. The interdiffusion conditions and thickness of the active layers have been optimized to obtain the highest power conversion efficiency. The best device performance of the P3OT-PCBM interdiffused devices is achieved when the interdiffusion is carried out at 150 °C for 20 minutes and the P3OT thickness is
Microfilament-organizing centers in areas of cell contact: cytoskeletal interactions during cell attachment and locomotion

In this article we discuss three aspects of cell contact formation: (a) the molecular architecture of the cytomatrix in cell-to-substrate focal contacts, (b) the dynamic properties of membrane- and microfilament-associated proteins in the contact areas, and (c) the involvement of microtubules in the coordinated and directed formation of new substrate contacts during cell locomotion. We show that different microfilament-associated proteins exhibit distinct patterns of association with focal contacts: some proteins are specifically associated with focal contacts (vinculin and talin); alpha-actinin is enriched in the contact areas but also is present along the stress fibers and in the lamellipodium; actin and filamin are detected throughout the contact areas but in apparently reduced amounts compared with the associated stress fibers; and tropomyosin, myosin, and spectrin are either absent from the endofacial surfaces of contact areas or are present in only very small amounts. Fluorescence photobleaching recovery analyses performed with living cells microinjected with fluorescently labeled actin, vinculin, and alpha-actinin indicate that each of these proteins maintains a dynamic equilibrium between a soluble cytoplasmic pool and a membrane-bound fraction. Correlation of the distribution of vinculin and tubulin in motile fibroblasts to local movements of the leading edge of the same cells indicates that free-end microtubules extend into actively ruffling areas along the lamellipodium and that new vinculin-containing contacts are preferentially formed in these protruding regions.
Integrated analysis of the genome and the transcriptome by FANTOM

The key to reliable annotation of a mammalian genome is broad characterisation of the transcriptional output, the transcriptome. FANTOM, the functional annotation of mouse cDNA, is a large-scale analysis of both the genome and the transcriptome of the mouse. In the early days of this work, the transcripts were characterised using our sophisticated methods. After the timely release of the first draft of mouse genome sequences, interesting information was obtained by its integration with these one-by-one annotations. Moreover, each transcript included its expression profile. Here, the two integrated annotation methods used by FANTOM are reviewed: one-by-one and categorised. One-by-one annotation refers to naming carried out based on well-known transcripts or its fragments using the top-down-style pipeline developed mostly by the FANTOM project. Categorised annotation, which refers to transcript grouping, not only helps naming of unknown transcripts, but will be the most utilised method for integration of the genome and the transcriptome from now on.
Automatic annotation of head velocity and acceleration in Anvil

We describe an automatic face tracker plugin for the ANVIL annotation tool. The face tracker produces data for velocity and for acceleration in two dimensions. We compare annotations generated by the face tracking algorithm with independently made manual annotations for head movements. The annotations are a useful supplement to manual annotations and may help human annotators to quickly and reliably determine onset of head movements and to suggest which kind of head movement is taking place.
International Supplier Selection : : A Multi-attribute Utility Approach

For Authors: If you would like to write for this, or any other Emerald publication, then please use our Emerald for Authors service. Information about how to choose which publication to write for and submission guidelines are available for all. Please visit About Emerald www.emeraldinsight. com With over forty years' experience, Emerald Group Publishing is a leading independent publisher of global research with impact in business, society, public policy and education. In total, Emerald publishes over 275 journals and more than 130 book series, as well as an extensive range of online products and services. Emerald is both COUNTER 3 and TRANSFER compliant. The organization is a partner of the Committee on Publication Ethics (COPE) and also works with Portico and the LOCKSS initiative for digital archive preservation. Introduction Over the last few years, the world business community has witnessed a series of revolutionary changes overseas that are exemplified by three historical events: (1) the official formation of the European Community (EC) 1992 under the auspices of the Single European Act; (2) the demise of Communism in the Eastern bloc countries; and (3) the pending ratification of the North American Free Trade Agreement. These changes contributed to the globalization of the world economy. As the market becomes globalized, an increasing number of firms that once concentrated on domestic sourcing are now seeking their supply bases around the world. Globalization of a firm's sourcing activity means the establishment of long-term business relationships with often unfamiliar and unproven foreign suppliers. Owing to unfamiliarity and uncertainty involved in global sourcing, international supplier selection is risky and complicated. Besides, many factors influencing international supplier selection decisions are in conflict with one another. For instance, the low price of purchased materials from a certain foreign supplier can be offset by the firm's loose quality standards or chronic financial instability. On the other hand, the availability of more advanced technology from a foreign source can be undermined by the sourcing firm's high purchasing costs and excessive tariffs. These illustrate only a few examples of obstacles that the firm has to face when sourcing overseas. It is obvious therefore that effective international supplier selection must deal with a host of quantitative and qualitative factors that are in conflict with one another. As a useful tool for such selection, this article proposes multiple attribute utility theory (MAUT) that can effectively deal with both qualitative and quantitative factors in multiple …
High‐throughput detection of nuclear factor‐kappaB activity using a sensitive oligo‐based chemiluminescent enzyme‐linked immunosorbent assay

Contemporary research on cellular signaling has undergone a shift of focus from qualitative measurements of single signaling pathways to high‐throughput quantitation of comprehensive signaling networks. Notably, nuclear factor‐kappaB (NFκB) is a family of transcription factors involved in immune and inflammatory responses, developmental processes, cellular growth and apoptosis and is deregulated in a number of disease states. We have established a chemiluminescent oligonucleotide‐based enzyme‐linked immunosorbent assay (co‐ELISA) that is simple and quantitative. In contrast to currently used assays, it allows quantitation of all NFκB components (i.e., RelA, p50, p52, RelB and c‐Rel). In addition, it can make use of whole extract and does not require cumbersome nuclear/cytosolic fractionation, saving time and resources. Co‐ELISA has a 3.5‐ to 43‐fold higher signal‐over‐noise ratio than currently available assays, whereas the percent relative standard deviation is 3‐ to 6‐fold lower. Furthermore, the novel method is faster than electrophoretic mobility shift assay, not restricted to transfectable cells as is the case for luciferase reporter assays and 10 times more cost efficient than commercially available ELISA assays. Co‐ELISA is a sensitive, fast and cost‐efficient quantitation method for all DNA‐binding NFκB proteins that can be used in high‐throughput experimentation.
GReAT Model: A Model for the Automatic Generation of Semantic Relations between Text Summaries based on the Relevant Information to the User.

The large available amount of non-structured texts that be- long to different domains such as healthcare (e.g. medical records), justice (e.g. laws, declarations), insurance (e.g. declarations), etc. increases the effort required for the analysis of information in a decision making pro- cess. Different projects and tools have proposed strategies to reduce this complexity by classifying, summarizing or annotating the texts. Partic- ularly, text summary strategies have proven to be very useful to provide a compact view of an original text. However, the available strategies to generate these summaries do not fit very well within the domains that require take into consideration the temporal dimension of the text (e.g. a recent piece of text in a medical record is more important than a pre- vious one) and the profile of the person who requires the summary (e.g the medical specialization). To cope with these limitations this paper presents ”GReAT” a model for automatic summary generation that re- lies on natural language processing and text mining techniques to extract the most relevant information from narrative texts and discover new in- formation from the detection of related information. GReAT Model was implemented on software to be validated in a health institution where it has shown to be very useful to display a preview of the information about medical health records and discover new facts and hypotheses within the information. Several tests were executed such as Functional- ity, Usability and Performance regarding to the implemented software. In addition, precision and recall measures were applied on the results ob- tained through the implemented tool, as well as on the loss of information obtained by providing a text more shorter than the original.
Active Clustering with Model-Based Uncertainty Reduction

Semi-supervised clustering seeks to augment traditional clustering methods by incorporating side information provided via human expertise in order to increase the semantic meaningfulness of the resulting clusters. However, most current methods are passive in the sense that the side information is provided beforehand and selected randomly. This may require a large number of constraints, some of which could be redundant, unnecessary, or even detrimental to the clustering results. Thus in order to scale such semi-supervised algorithms to larger problems it is desirable to pursue an active clustering method- i.e. an algorithm that maximizes the effectiveness of the available human labor by only requesting human input where it will have the greatest impact. Here, we propose a novel online framework for active semi-supervised spectral clustering that selects pairwise constraints as clustering proceeds, based on the principle of uncertainty reduction. Using a first-order Taylor expansion, we decompose the expected uncertainty reduction problem into a gradient and a step-scale, computed via an application of matrix perturbation theory and cluster-assignment entropy, respectively. The resulting model is used to estimate the uncertainty reduction potential of each sample in the dataset. We then present the human user with pairwise queries with respect to only the best candidate sample. We evaluate our method using three different image datasets (faces, leaves and dogs), a set of common UCI machine learning datasets and a gene dataset. The results validate our decomposition formulation and show that our method is consistently superior to existing state-of-the-art techniques, as well as being robust to noise and to unknown numbers of clusters.
Validity of the phase approximation for coupled nonlinear oscillators: A case study

Motivated by neuroscience applications, we rigorously derive the phase dynamics of an ensemble of interconnected nonlinear oscillators under the effect of a proportional feedback. We individuate the critical parameters determining the validity of the phase approximation and derive bounds on the accuracy of the latter in reproducing the behavior of the original system. We use these results to study the existence of oscillating phase-locked solutions in the original oscillator model.
Underpowering NAND flash: Profits and perils

MLC Flash memory is getting more popular in computer systems ranging from sensor networks and embedded systems to large-scale server systems. However, MLC flash has many reliability concerns, including the potential for corruption due to supply voltage fluctuations. This paper characterizes MLC flash when the chip is underpowered (i.e., power fading and voltage droops). We demonstrate that underpowering flash can cause serious errors, but also help saving up to 45% of operation energy without incurring failure.
There is high potential for the formation of common mycorrhizal networks between understorey and canopy trees in a mixed evergreen forest

1 The patterns of ectomycorrhizal (ECM) host specificity between understorey and canopy trees were investigated in three mixed evergreen forest stands in northern coastal California. ECM root tips from the dominant canopy (Pseudotsuga menziesii) and understorey (Lithocarpus densiflora) trees were sampled from 18 soil cores (six per stand) and identified using molecular techniques (PCR, RFLP, and DNA sequencing of the rDNA ITS region). 2 We found 56 ECM taxa; 17 on both hosts, 27 solely on Pseudotsuga and 12 on Lithocarpus. There were no significant differences in ECM taxon richness or diversity across stands, although ECM taxon richness was significantly higher on Pseudotsuga than Lithocarpus. ECM taxa similarity across stands was low. 3 Multiple‐host ECM taxa had significantly higher abundance than single‐host ECM taxa and 13 of the 17 multiple‐host ECM taxa were present on both hosts within at least one core. Twelve of the 14 cores had at least one ECM taxon that was present on both hosts, although the specific taxon varied between cores and stands. In addition, shared ECM taxa often had unequal relative abundances on the two hosts. 4 Taken together, our results suggest that there is high potential for common mycorrhizal networks to form between Lithocarpus understories and Pseudotsuga canopies in mixed evergreen forests.