Miracle-dz/UniFAR-FTUs huggingface dataset:
Melanoma and non-melanoma skin cancer in inflammatory bowel disease patients following tumor necrosis factor-α inhibitor monotherapy and in combination with thiopurines: analysis of the Food and Drug Administration Adverse Event Reporting System.

BACKGROUND AND AIMS Reports have shown an increased risk of melanoma skin cancer (MSC) with exposure to tumor necrosis factor alpha (TNF-α) inhibitors and non-melanoma skin cancer (NMSC) with thiopurine exposure in inflammatory bowel disease (IBD) patients. Using the Food and Drug Administration Adverse Event Reporting System (FAERS) we sought to evaluate the odds of developing MSC and NMSC for patients on TNF-α inhibitors as monotherapy and in combination therapy with thiopurines and/or steroids. METHODS The FAERS was queried for reports between January 2003 and June 2012. A proportional reporting ratio (PRR) metric analyses was performed on the data to determine the odds of developing MSC and NMSC. RESULTS The PRR analysis showed increased odds of developing MSC and NMSC for patients on a TNF-α inhibitor (p-value = 0.035 and p-value = 0.03, respectively) and those on a TNF-α inhibitor in combination with a thiopurine (p-value < 0.001 and p-value < 0.001). CONCLUSION TNF-α inhibitor monotherapy or use with concomitant thiopurines in patients with IBD is associated with higher odds of developing MSC and NMSC.
Screening and Identification of ssDNA Aptamer for Human GP73

As one tumor marker of HCC, Golgi Protein 73 (GP73) is given more promise in the early diagnosis of HCC, and aptamers have been developed to compete with antibodies as biorecognition probes in different detection system. In this study, we utilized GP73 to screen specific ssDNA aptamers by SELEX technique. First, GP73 proteins were expressed and purified by prokaryotic expression system and Nickle ion affinity chromatography, respectively. At the same time, the immunogenicity of purified GP73 was confirmed by Western blotting. The enriched ssDNA library with high binding capacity for GP73 was obtained after ten rounds of SELEX. Then, thirty ssDNA aptamers were sequenced, in which two ssDNA aptamers with identical DNA sequence were confirmed, based on the alignment results, and designated as A10-2. Furthermore, the specific antibody could block the binding of A10-2 to GP73, and the specific binding of A10-2 to GP73 was also supported by the observation that several tumor cell lines exhibited variable expression level of GP73. Significantly, the identified aptamer A10-2 could distinguish normal and cancerous liver tissues. So, our results indicate that the aptamer A10-2 might be developed into one molecular probe to detect HCC from normal liver specimens.
Simplification Therapy with Once-Daily Didanosine, Tenofovir and Efavirenz in HIV-1-Infected Adults with Viral Suppression Receiving a More Complex Antiretroviral Regimen: Final Results of the EFADITE Trial

Background High pill burden and side effects often impact on the long-term success of highly active anti-retroviral therapy (HAART), which has led clinicians to search for more convenient regimens. Patients and methods A prospective, multicentre, open, comparative study in which HIV-1-infected patients on HAART and with plasma HIV-1 RNA <50 copies/ml for longer than 6 months were switched to tenofovir, didanosine and efavirenz (QD arm) or remained on the same treatment regimen (control arm). Patients with grade 4 toxicities or plasma HIV-1 RNA values repeatedly >1000 copies/ml discontinued the study. Results A total of 390 patients were included in the trial (309 in the QD arm and 81 in the control arm). The main baseline characteristics were well balanced between groups. In the QD arm, 41% of patients received high (standard) didanosine doses and 59% received reduced doses. At 12 months, plasma HIV-1 RNA <400 copies/ml was attained in 66% of QD patients and 73% of controls in the intent-to-treat (ITT) analysis (P=NS). However, the number of individuals with HIV-1 RNA <400 copies/ml in the QD arm was 56% versus 71% when comparing the use of high versus low didanosine doses (P=0.007). Treatment discontinuation occurred in 87 QD cases (28%) and 17 controls (21%). Twenty QD individuals (6.5%) and 2 controls (2.5%) discontinued because of virological failure (P=NS). The median CD4+ cell count change at 12 months was -26 and +27 cells/μl in QD patients and controls, respectively (P=0.001). In individuals who attained HIV-1 RNA <400 copies/ml, CD4+ cell changes were -25 and +15 cells/μl in QD patients and controls, respectively (P=0.001). Moreover, CD4+ cell declines in the QD arm were significantly greater in patients taking high versus low didanosine doses (-59 versus -15 cells/μl; P=0.04). The lipid profile improved significantly in the QD arm, particularly in patients who were on protease inhibitors prior to simplification. Conclusions Simplification to didanosine–tenofovir–efavirenz provides a virological suppression rate at 12 months similar to that seen in patients who do not change therapy, as long as low didanosine doses are administered. Decreases in CD4+ cell levels in patients in the QD arm (especially decreases seen with high didanosine doses) and dyslipidaemias along with less convenient pill burden and schedules in controls were the main long-term concerns for each option.
Rule-based approach for enhancing the motion trajectories in human activity recognition

In this paper, we propose a rule-based system for semantically understanding and analyzing the motion of the trajectories of the human activity. The proposed system can be used as a preprocessing phase for enhancing the object detection process. Detected trajectories are classified into three categories; normal, semi-normal and abnormal trajectories according to the distances between their adjacent points. Abnormal trajectories are removed from the trajectory space. Semi-normal trajectories are broken into small normal trajectories that are linked later to form a longer normal trajectory. The proposed system does not assume a specific trajectory length and hence is more generic than similar trajectory enhancement approaches. The effectiveness of the proposed approach is demonstrated through several experimental results using known human motion datasets.
Lehrstuhl Für Informatik 10 (systemsimulation) Optimization and Profiling of the Cache Performance of Parallel Lattice Boltzmann Codes in 2d and 3d Optimization and Profiling of the Cache Performance of Parallel Lattice Boltzmann Codes in 2d and 3d *

When designing and implementing highly efficient scientific applications for parallel computers such as clusters of workstations, it is inevitable to consider and to optimize the single-CPU performance of the codes. For this purpose, it is particularly important that the codes respect the hierarchical memory designs that computer architects employ in order to hide the effects of the growing gap between CPU performance and main memory speed. In this article, we present techniques to enhance the single-CPU efficiency of lattice Boltzmann methods which are commonly used in computational fluid dynamics. We show various performance results for both 2D and 3D codes in order to emphasize the effectiveness of our optimization techniques.
Diagnostic system based on support-vector machines for board-level functional diagnosis

Fault diagnosis is critical for improving product yield and reducing manufacturing cost. However, it is very challenging to identify the root cause of failures on a complex circuit board. Ambiguous diagnosis results lead to long debug times and even wrong repair actions, which significantly increases the repair cost. We propose an automatic diagnostic system using support vector machines (SVMs). The proposed system acquires debug knowledge from empirical data; this strategy avoids the difficulties involved in knowledge acquisition in traditional fault diagnosis methods. SVMs provide an optimal separating hyperplane in classification. The optimal solution and generalization ability of SVMs lead to higher diagnostic accuracy, compared to the classical learning approaches such as artificial neural networks (ANNs). An industrial board is used to validate the effectiveness of the proposed system. Extensive simulation results demonstrate that the SVMs-based diagnostic system provides quantifiable improvement over current diagnostic software and an ANN-based diagnostic system.
Flocking in Fixed and Switching Networks

This note analyzes the stability properties of a group of mobile agents that align their velocity vectors, and stabilize their inter-agent distances, using decentralized, nearest-neighbor interaction rules, exchanging information over networks that change arbitrarily (no dwell time between consecutive switches). These changes introduce discontinuities in the agent control laws. To accommodate for arbitrary switching in the topology of the network of agent interactions we employ nonsmooth analysis. The main result is that regardless of switching, convergence to a common velocity vector and stabilization of inter-agent distances is still guaranteed as long as the network remains connected at all times
Predicting clinical outcome of nonsurgical management of blunt splenic injury: using CT to reveal abnormalities of splenic vasculature.

OBJECTIVE Using CT to grade blunt splenic injuries frequently does not predict clinical outcome. This retrospective, blinded study evaluated whether revealing a traumatic pseudoaneurysm or frank hemorrhage on an initial CT examination can be used to predict the successful clinical outcome of patients managed without surgery. MATERIALS AND METHODS The medical and CT records of all patients with blunt splenic injury during a 5-year period were independently reviewed for vascular abnormalities. Also, the grade of injury was reconfirmed. Hemodynamically stable patients with injuries of grades 1-3 were managed without surgery. Clinical failure occurred if a patient required splenectomy or splenorrhaphy after any attempt of nonsurgical management. RESULTS Two hundred sixty-three patients were treated for blunt splenic injuries. Eighty-two of these patients underwent emergent surgery on the basis of clinical and peritoneal lavage findings without CT examination. The remaining 181 (69%) patients were initially evaluated with emergent abdominal CT. Of these 181 patients, 72 (40% of those undergoing CT) were treated nonsurgically. Nonsurgical therapy failed in 11 (15%) of these 72 patients. Of these 11 patients, nine (82%) had a defined vascular abnormality of the spleen. Only eight (13%) of the remaining 61 patients who underwent CT and successful nonsurgical management had a vascular abnormality of the spleen. CONCLUSION The failure rate in patients with nonsurgically managed blunt splenic injuries may be markedly reduced if patients with traumatic pseudoaneurysm or active hemorrhage revealed on emergent CT are treated with early surgical or endovascular repair.
An Analysis of Human MicroRNA and Disease Associations

It has been reported that increasingly microRNAs are associated with diseases. However, the patterns among the microRNA-disease associations remain largely unclear. In this study, in order to dissect the patterns of microRNA-disease associations, we performed a comprehensive analysis to the human microRNA-disease association data, which is manually collected from publications. We built a human microRNA associated disease network. Interestingly, microRNAs tend to show similar or different dysfunctional evidences for the similar or different disease clusters, respectively. A negative correlation between the tissue-specificity of a microRNA and the number of diseases it associated was uncovered. Furthermore, we observed an association between microRNA conservation and disease. Finally, we uncovered that microRNAs associated with the same disease tend to emerge as predefined microRNA groups. These findings can not only provide help in understanding the associations between microRNAs and human diseases but also suggest a new way to identify novel disease-associated microRNAs.
piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis

Spreading small RNAs to protect the genome In animals, PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that protect our germ lines from the ravages of transposons. To do this, piRNAs target and cleave transposon RNAs. Synthesis of piRNA is initiated by a cut made in a long, single-stranded precursor RNA. The piRNAs can also undergo a self-perpetuating amplification cycle (see the Perspective by Siomi and Siomi). Han et al. and Mohn et al. now reveal that piRNA biogenesis can also spread in a strictly phased manner from the site of initial piRNA formation. Spreading piRNA synthesis greatly increases their sequence diversity, potentially helping them to target endogenous and novel transposons more effectively. Science, this issue p. 817, p. 812; see also p. 756 Phased synthesis of germline-protective piRNAs along precursor RNAs increases piRNA sequence diversity. [Also see Perspective by Siomi and Siomi] In animal gonads, PIWI-clade Argonaute proteins repress transposons sequence-specifically via bound Piwi-interacting RNAs (piRNAs). These are processed from single-stranded precursor RNAs by largely unknown mechanisms. Here we show that primary piRNA biogenesis is a 3′-directed and phased process that, in the Drosophila germ line, is initiated by secondary piRNA-guided transcript cleavage. Phasing results from consecutive endonucleolytic cleavages catalyzed by Zucchini, implying coupled formation of 3′ and 5′ ends of flanking piRNAs. Unexpectedly, Zucchini also participates in 3′ end formation of secondary piRNAs. Its function can, however, be bypassed by downstream piRNA-guided precursor cleavages coupled to exonucleolytic trimming. Our data uncover an evolutionarily conserved piRNA biogenesis mechanism in which Zucchini plays a central role in defining piRNA 5′ and 3′ ends.
Intelligent Manipulation and Calibration of Parameters for Hydrological Models

It would be greatly helpful to neophytes if knowledge-based system technology incorporating the existing heuristic knowledge about model manipulation can be integrated into the hydrological system. This paper delineates the development and implementation of a prototype knowledge-based system for model manipulation for hydrological processes by employing an expert system shell. The architecture and main components of the system are presented. The prototype system is verified and validated in two real watershed applications. It helps inexperienced users of hydrological models make the right choice of the appropriate model and/or direct the users throughout the calibration process.
Conformations and Dynamics of Semi-Flexible Polymers

In this dissertation, we investigate the conformations, transverse fluctuations and dynamics of two-dimensional (2D) semi-flexible polymers both in the bulk and under channel confinement. We present unified scaling relations in regard to various quantities of interest for a broad range of combinations of chain length and chain stiffness using Langevin dynamics simulation. We also present a three-dimensional (3D) heterogeneous semi-flexible chain model for a double stranded DNA (dsDNA). Our model not only confirms the established findings for homogeneous dsDNA, but also predicts new physical phenomenon for heterogeneous dsDNA. The problems studied in this dissertation are relevant to analysis of the conformations and dynamics of biopolymers (such as DNA) in living organisms, and also offer insights for developing devices which operate on the single-molecule level. In particular, we present a unified description for the dynamics of building-blocks (monomers) of a semi-flexible chain. We consider the full range of flexibility from the case where the chain is fully flexible (no stiffness at all) to the case where the chain behaves like a rod (infinite stiffness). Our theory predicts qualitatively different sub-diffusive regimes for the monomer dynamics originating from the chain stiffness by studying the mean square displacement (MSD) of the monomers before the chain dynamics become purely diffusive.
Improving defect prediction using temporal features and non linear models

Predicting the defects in the next release of a large software system is a very valuable asset for the project manger to plan her resources. In this paper we argue that temporal features (or aspects) of the data are central to prediction performance. We also argue that the use of non-linear models, as opposed to traditional regression, is necessary to uncover some of the hidden interrelationships between the features and the defects and maintain the accuracy of the prediction in some cases. Using data obtained from the CVS and Bugzilla repositories of the Eclipse project, we extract a number of temporal features, such as the number of revisions and number of reported issues within the last three months. We then use these data to predict both the location of defects (i.e., the classes in which defects will occur) as well as the number of reported bugs in the next month of the project. To that end we use standard tree-based induction algorithms in comparison with the traditional regression. Our non-linear models uncover the hidden relationships between features and defects, and present them in easy to understand form. Results also show that using the temporal features our prediction model can predict whether a source file will have a defect with an accuracy of 99% (area under ROC curve 0.9251) and the number of defects with a mean absolute error of 0.019 (Spearman's correlation of 0.96).
Fever of unknown origin.

There are 11 series that include over 1000 patients that have reported the diagnostic entities that constitute FUO. Grouping all the patients collected from 1952 until 1994 reveals that the spectrum of disease includes infections in 28% and inflammatory diseases in 21%. Malignancies account for a smaller proportion (17%). A cause is never identified in a significant proportion (19%) of patients (Fig. 1).
Ultrahigh-Q microcavities in diamond-based photonic crystal slabs

We design extremely flexible, ultrahigh-Q, diamond-based double-heterostructure photonic crystal slab cavities by modifying the refractive index of the diamond. The refractive index changes needed for ultrahigh-Q cavities with Q ∼ 107, are well within what can be achieved (Δn ∼ 0.02). The Q is around 30 times larger than previously reported designs in diamond. At the same time, the cavity volumes are still relatively small, at less than two cubic wavelengths. The range of parameters, cavity length and the index changes that enables an ultrahigh-Q is quite broad improving prospects for defect-tolerant quantum architectures.
Generalized Probabilistic LR Parsing of Natural Language (Corpora) with Unification-Based Grammars

We describe work toward the construction of a very wide-coverage probabilistic parsing system for natural language (NL), based on LR parsing techniques. The system is intended to rank the large number of syntactic analyses produced by NL grammars according to the frequency of occurrence of the individual rules deployed in each analysis. We discuss a fully automatic procedure for constructing an LR parse table from a unification-based grammar formalism, and consider the suitability of alternative LALR(1) parse table construction methods for large grammars. The parse table is used as the basis for two parsers; a user-driven interactive system that provides a computationally tractable and labor-efficient method of supervised training of the statistical information required to drive the probabilistic parser. The latter is constructed by associating probabilities with the LR parse table directly. This technique is superior to parsers based on probabilistic lexical tagging or probabilistic context-free grammar because it allows for a more context-dependent probabilistic language model, as well as use of a more linguistically adequate grammar formalism. We compare the performance of an optimized variant of Tomita's (1987) generalized LR parsing algorithm to an (efficiently indexed and optimized) chart parser. We report promising results of a pilot study training on 150 noun definitions from the Longman Dictionary of Contemporary English (LDOCE) and retesting on these plus a further 55 definitions. Finally, we discuss limitations of the current system and possible extensions to deal with lexical (syntactic and semantic) frequency of occurrence.
Energy-Optimized Image Communication on Resource-Constrained Sensor Platforms

Energy-efficient image communication is one of the most important goals for a large class of current and future sensor network applications. This paper presents a quantitative comparison between the energy costs associated with 1) direct transmission of uncompressed images and 2) sensor platform-based JPEG compression followed by transmission of the compressed image data. JPEG compression computations are mapped onto various resource-constrained sensor platforms using a design environment that allows computation using the minimum integer and fractional bit-widths needed in view of other approximations inherent in the compression process and choice of image quality parameters. Detailed experimental results examining the tradeoffs in processor resources, processing/transmission time, bandwidth utilization, image quality, and overall energy consumption are presented.
Characterization of oxalate transport by the human erythrocyte band 3 protein

This paper describes characteristics of the transport of oxalate across the human erythrocyte membrane. Treatment of cells with low concentrations of H2DIDS (4,4'-diisothiocyanatostilbene-2,2'- disulfonate) inhibits Cl(-)-Cl- and oxalate-oxalate exchange to the same extent, suggesting that band 3 is the major transport pathway for oxalate. The kinetics of oxalate and Cl- self-exchange fluxes indicate that the two ions compete for a common transport site; the apparent Cl- affinity is two to three times higher than that of oxalate. The net exchange of oxalate for Cl-, in either direction, is accompanied by a flux of H+ with oxalate, as is also true of net Cl(-)-SO4(2-) exchange. The transport of oxalate, however, is much faster than that of SO4(2-) or other divalent anions. Oxalate influx into Cl(-)-containing cells has an extracellular pH optimum of approximately 5.5 at 0 degrees C. At extracellular pH below 5.5 (neutral intracellular pH), net Cl(-)- oxalate exchange is nearly as fast as Cl(-)-Cl- exchange. The rapid Cl(- )-oxalate exchange at acid extracellular pH is not likely to be a consequence of Cl- exchange for monovalent oxalate (HOOC-COO-; pKa = 4.2) because monocarboxylates of similar structure exchange for Cl- much more slowly than does oxalate. The activation energy of Cl(-)- oxalate exchange is about 35 kCal/mol at temperatures between 0 and 15 degrees C; the rapid oxalate influx is therefore not a consequence of a low activation energy. The protein phosphatase inhibitor okadaic acid has no detectable effect on oxalate self-exchange, in contrast to a recent finding in another laboratory (Baggio, B., L. Bordin, G. Clari, G. Gambaro, and V. Moret. 1993. Biochim. Biophys. Acta. 1148:157-160.); our data provide no evidence for physiological regulation of anion exchange in red cells.