Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of molecularly targeted therapies in biliary tract cancers: Reassessing the challenges and opportunities

Biliary tract cancers (BTCs), which encompass intra‐ and extrahepatic cholangiocarcinomas as well as gallbladder carcinomas, are a genetically diverse collection of cancers. Most patients with BTC will present with unresectable or metastatic disease. Although the standard systemic chemotherapy approaches are emerging, the prognosis remains poor. Development of molecularly targeted therapies in advanced BTC remains challenging. Recent early‐stage clinical trials with targeted therapies appear promising, although the relationships between subsets of patients with positive responses to therapy and tumor genetics remain unexplored. Here we summarize the relevant molecular pathogenesis, recent and ongoing clinical trials with targeted agents, and the key issues in clinical trial design in BTC. (HEPATOLOGY 2011;53:695‐704)
Parallel-perspective stereo mosaics

In this paper we present a novel method for automatically and efficiently generating stereoscopic mosaics by seamless registration of optical data collected by a video camera mounted on an airborne platform that undergoes dominant translational motion. There are four critical points discussed in this paper: (1) Using a parallel-perspective representation, a pair of geometrically registered stereo mosaics can be constructed before we explicitly recover any 3D information under rather general motion. (2) A PRISM (parallel ray interpolation for stereo mosaicing) technique is proposed to make stereo mosaics seamless in the presence of motion parallax and for rather arbitrary scenes. A fast PRISM algorithm is presented and issues on stitching point selection and occlusion handling are discussed. (3) The epipolar geometry of parallel-perspective stereo mosaics generated under constrained 6 DOF motion is formulated, which shows optimal baselines, easy search for correspondence and constant depth resolution. (4) The proposed methods for the generation of stereo mosaics and then the reconstruction of a 3D map are efficient in both computation and storage. Experimental results on long video sequences are given.
Mimic: computing models for opaque code

Opaque code, which is executable but whose source is unavailable or hard to process, can be problematic in a number of scenarios, such as program analysis. Manual construction of models is often used to handle opaque code, but this process is tedious and error-prone. (In this paper, we use model to mean a representation of a piece of code suitable for program analysis.) We present a novel technique for automatic generation of models for opaque code, based on program synthesis. The technique intercepts memory accesses from the opaque code to client objects, and uses this information to construct partial execution traces. Then, it performs a heuristic search inspired by Markov Chain Monte Carlo techniques to discover an executable code model whose behavior matches the opaque code. Native execution, parallelization, and a carefully-designed fitness function are leveraged to increase the effectiveness of the search. We have implemented our technique in a tool Mimic for discovering models of opaque JavaScript functions, and used Mimic to synthesize correct models for a variety of array-manipulating routines.
The COMT rs4680 Met allele contributes to long‐lasting low back pain, sciatica and disability after lumbar disc herniation

The COMT enzyme metabolizes catecholamines and thus modulates adrenergic, noradrenergic and dopaminergic signaling. A functional polymorphism in the gene encoding this enzyme, i.e. the COMT Val158Met SNP that reduces enzyme activity, has previously been linked to pain sensitivity.
Using Node Centrality and Optimal Control to Maximize Information Diffusion in Social Networks

We model information dissemination as a susceptible-infected epidemic process and formulate a problem to jointly optimize seeds for the epidemic and time varying resource allocation over the period of a fixed duration campaign running on a social network with a given adjacency matrix. Individuals in the network are grouped according to their centrality measure and each group is influenced by an external control function—implemented through advertisements—during the campaign duration. The aim is to maximize an objective function which is a linear combination of the reward due to the fraction of informed individuals at the deadline, and the aggregated cost of applying controls (advertising) over the campaign duration. We also study a problem variant with a fixed budget constraint. We set up the optimality system using Pontryagin’s maximum principle from optimal control theory and solve it numerically using the forward–backward sweep technique. Our formulation allows us to compare the performance of various centrality measures (pagerank, degree, closeness, and betweenness) in maximizing the spread of a message in the optimal control framework. We find that degree—a simple and local measure—performs well on the three social networks used to demonstrate results: 1) scientific collaboration; 2) Slashdot; and 3) Facebook. The optimal strategy targets central nodes when the resource is scarce, but noncentral nodes are targeted when the resource is in abundance. Our framework is general and can be used in similar studies for other disease or information spread models—that can be modeled using a system of ordinary differential equations—for a network with a known adjacency matrix.
Transductive learning with EM algorithm to classify proteins based on phylogenetic profiles

We proposed a novel method for protein classification based on phylogenetic profiles. Each protein's profile was extended with extra bits encoding the phylogenetic tree structure and the likelihood, in the form of weights on profile indices, of the protein's functional family membership in each of the reference genomes. The extended profiles were then integrated as part of a kernel of a support vector machine, which was trained in a transductive learning scheme using the EM algorithm to update the weights. Classification accuracy was greatly increased when tested on the proteome of Saccharomyces cerevisiae using the MIPS classification as a benchmark.
A multi-dimensional model for search intent

The interaction of users with search engines is part of goal driven behaviour involving an underlying information need. Information needs range from simple lookups to complex long-term desk studies. This paper proposes a new multidimensional model for search intent, which can be used for the description of search sessions. Using examples from a search engine log we show that our model allows a more comprehensive description of information need than existing categorizations.
Electrical Properties of Polyesters

Polyesters occupy an important place in the group of polymers as engineering materials to be used in electrotechnology and electronics. These polymers are characterized by excellent electro-insulating properties, showing mechanical strength, thermal resistance, and easiness in processing at the same time. The chapter presents the behavior analysis of the following polyesters in electric field: poly(ethylene terephthalate), poly(lactic acid), and polycarbonate. The effect of polymer microstructure on electric properties is presented, including its susceptibility to polarization that makes it possible to use polyesters as electrets materials. The second trend of the study presents the possibilities of transforming the electro-insulating properties of polyester fabrics to conductive properties with the use of modern processing methods such as PVD, CVD, and digital print. The functionalization of polyester fabrics extends their application range, for example, in e-textiles and reduces the fabric susceptibility to static electricity, increasing the safety of use.
Impact of severity of renal dysfunction on determinants of in‐hospital mortality among patients undergoing percutaneous coronary intervention

Background: Chronic kidney disease (CKD) is a known prognostic indicator of poor outcomes following percutaneous coronary intervention (PCI) for coronary artery disease. However, it is unclear whether other predictors of mortality differ among patients with varying degrees of renal impairment. Thus, we aimed to identify determinants of in‐hospital mortality which are specific to patients with preserved renal function, moderate CKD, or end stage renal disease (ESRD) on dialysis, undergoing PCI. Methods: The study population included 25,018 patients who underwent PCI between January 1, 2004, and December 31, 2007, at four New York State hospitals. The primary endpoint of the study was in‐hospital mortality. Results: A total of 474 (1.9%) patients had ESRD on dialysis, 6,596 (26.4%) had moderate CKD (GFR<60 ml/min/1.73m2), and 17,948 (71.7%) had preserved renal function (GFR>60 ml/min/1.73m2). Patients with ESRD and moderate CKD were older, more often male, and had higher rates of prior coronary revascularization, peripheral vascular disease, congestive heart failure, prior stroke, and diabetes than those with preserved function. All‐cause in‐hospital mortality rates were significantly higher in patients with ESRD and moderate CKD compared to patients with GFR >60ml/min/1.73m2 (2.1% and 1.3%, respectively vs. 0.3%, p < 0.001). In multivariable analysis, ESRD (OR: 3.68, 95% CI 1.62–8.36) and moderate CKD (OR: 2.92, 95% CI 1.91–4.46) were independently associated with higher rates of in‐hospital mortality. Independent predictors of mortality were markedly distinct in each group and included female gender and myocardial infarction within the past 72 hr in the ESRD group, versus left ventricular ejection fraction, peripheral vascular disease, congestive heart failure, emergency PCI, and absence of prior PCI in the moderate CKD group and age, prior bypass graft surgery, congestive heart failure, emergency PCI, and absence of prior myocardial infarction in patients with preserved renal function Conclusions: Patients with moderate CKD or ESRD undergoing PCI have an approximately threefold increase in the risk of in‐hospital mortality compared with patients with preserved renal function, with radically different mortality predictors existing for varying levels of renal function. © 2012 Wiley Periodicals, Inc.
Performance Overhead of ERP Systems in Paravirtualized Environments

Virtualization is a big trend in current IT world and is used intensively in today’s computing centres. But little is known about what happens to the performance of computer systems when running in virtual environments. This work focuses on the performance aspect especially in the field of Enterprise Resource Planning systems (ERP). Therefore, this work utilizes a quantitative approach by using laboratory experiments to measure the performance differences between a virtualized and non-virtualized ERP system. First, on basis of a literature review a performance measurement framework will be developed to provide a comprehensive guideline how to measure the performance of an ERP system in a virtualized environment. Second, the performance measurement focuses on the overhead in CPU, memory and I/O intensive situations. Third, the focus lays on a root cause analysis. Gained results will be analyzed and interpreted to give recommendations for further development of both ERP system and virtualization solution. The outcome may be useful for further computing centre design when introducing new ERP systems and service delivery concepts like Software as a Service (SaaS) in a virtualized or non-virtualized environment.
An analysis of road accidents involving child pedestrians.

In order to obtain absolute measures of accident risk to children of different ages and sex when crossing different types of road, measures of exposure, which can be related to the accident statistics, are required. We have devised a suitable framework to achieve this which is presented here in detail. Measures of exposure were obtained from interviews with children and from traffic density counts on the roads they crossed in the previous 24 hours. The estimates of risk showed that the raw accident figures greatly underestimate the relative risk to children aged 5, 6 and 7 years, that the greater number of accidents to boys of this age is not due to their greater exposure to traffic, and that by the age of 8, boys, given their greater exposure, are no more at risk than girls.
The exokernel operating system architecture

On traditional operating systems only trusted software such as privileged servers or the kernel can manage resources. This thesis proposes a new approach, the exokernel architecture, which makes resource management unprivileged but safe by separating management from protection: an exokernel protects resources, while untrusted application-level software manages them. As a result, in an exokernel system, untrusted software (e.g., library operating systems) can implement abstractions such as virtual memory, file systems, and networking. The main thrusts of this thesis are: (1) how to build an exokernel system; (2) whether it is possible to build a real one; and (3) whether doing so is a good idea. Our results, drawn from two exokernel systems [25, 48], show that the approach yields dramatic benefits. For example, Xok, an exokernel, runs a web server an order of magnitude faster than the closest equivalent on the same hardware, common unaltered Unix applications up to three times faster, and improves global system performance up to a factor of five. The thesis also discusses some of the new techniques we have used to remove the overhead of protection. The most unusual technique, untrusted deterministic functions, enables an exokernel to verify that applications correctly track the resources they own, eliminating the need for it to do so. Additionally, the thesis reflects on the subtle issues in using downloaded code for extensibility and the sometimes painful lessons learned in building three exokernel-based systems. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Source and the HLA : I Swear it ' s Here Somewhere

The benefits of vibrant and active open source communities have been enjoyed in both commercial and non-commercial activities within many and varied domains. Previously the domain of altruists and enthusiasts, recent times have seen the uptake of free software grow at a significant pace. As commercial enterprises have come to accept open source software as potentially delivering numerous and substantial benefits to the products and services they provide, the number and momentum of open source efforts continues to build. While many commercial options fill the development, infrastructure and support needs that surround the HLA, the prevalence of open source software is minimal at best. Although commercial products can satisfy many needs, licensing costs remain prohibitive for small-to-medium enterprises and academic institutions. Of particular importance is the impact this can have on research activities within the domain. Where a vibrant open source community would provide a pool of resources on which research efforts could build, the current situation often requires significant effort be expended developing an environment in which the primary research can be conducted. This lack of such a resource has been conspicuous to many, and discussions surrounding community support for initiatives such as open source HLA Run-Time Infrastructures have been witnessed. Not totally devoid of any open source influence, those projects that do exist in the domain have as yet failed to reach the prevalence such endeavours often aspire to. This paper is a discussion of the current circumstances, the effect they can have and some of the efforts underway to begin addressing the problems, presented from the point of view of a research student within an academic institution.
Monitoring of intracellular calcium in Saccharomyces cerevisiae with an apoaequorin cDNA expression system.

A method is described for measuring cytosolic free Ca2+ and its time-dependent changes in the yeast Saccharomyces cerevisiae by using the luminescent protein aequorin as a Ca(2+)-specific indicator. This method with intact yeast cells is labeled "in vivo" to distinguish it from methods with cell extracts, labeled "in vitro. " A plasmid in which the apoaequorin cDNA was joined downstream from the glyceraldehyde-3-phosphate dehydrogenase gene promoter was constructed and introduced into yeast cells. The intracellular concentration of apoaequorin expressed by the cDNA was approximately 1 microM, which was high enough to detect the cytosolic Ca2+. Growth of the transformed cells was normal. In the in vitro method, apoaequorin in crude cell extracts was regenerated into aequorin by mixing with coelenterazine, the substrate for the luminescence reaction, whereas in the in vivo method, aequorin was regenerated by incubating intact cells with coelenterazine. Simultaneous addition of 10 mM CaCl2 and 10 microM A23187, a Ca2+ ionophore, to coelenterazine-incorporated cells generated luminescence. Coelenterazine-incorporated cells also responded to native extracellular stimuli. A mating pheromone, alpha-factor, added to cells of mating type a or alpha, generated extracellular Ca(2+)-dependent luminescence specifically in a mating type cells, with maximal intensity occurring 45-50 min after addition of alpha-factor. Glucose added to glucose-starved G0/G1 cells stimulated an increase in extracellular Ca(2+)-dependent luminescence with maximal intensity occurring 2 min after addition. These results show the usefulness of the aequorin system in monitoring [Ca2+]i response to extracellular stimuli in yeast cells.
Software Verification and System Assurance

Littlewood introduced the idea that software may be possibly perfect and that we can contemplate its probability of (im)perfection. We review this idea and show how it provides a bridge between correctness, which is the goal of software verification (and especially formal verification), and the probabilistic properties such as reliability that are the targets for system-level assurance. We enumerate the hazards to formal verification, consider how each of these may be countered, and propose relative weightings that an assessor may employ in assigning a probability of perfection.
Association of TNFSF4 polymorphisms with systemic lupus erythematosus: a meta-analysis

IntroductionTo more precisely estimate the association between the tumor necrosis factor ligand superfamily member 4 (TNFSF4) gene polymorphisms and systemic lupus erythematosus (SLE) risk, we surveyed studies on the association of the TNFSF4 rs2205960, rs1234315, rs844644, and rs844648 polymorphisms with SLE.Methods A literature-based search was conducted to identify all relevant studies. A total of eight independent studies were identified and subsequently reviewed in the meta-analysis.ResultsThe meta-analysis showed an association between the TNFSF4 rs2205960 polymorphism and SLE in all subjects [ odds ratio (OR) 1.327, 95 % confidence interval (CI) 1.227–1.436, P < 0.001]. In a subgroup analysis by ethnicity, a significantly increased risk for SLE was associated with TNFSF4 rs2205960 T allele among patients of European (OR 1.254, 95 % CI 1.185–1.328, P < 0.001) and Asian ethnicity (OR 1.425, 95 % CI 1.352–1.501, P < 0.001). The meta-analysis of the rs1234315 polymorphism revealed no association between SLE and the rs1234315 T allele in all subjects (OR 1.167, 95 % CI 0.874–1.558, P = 0.296), but the results of the subgroup analysis revealed significant association in subjects of Asian ethnicity (OR 1.386, 95 % CI 1.318–1.458, P < 0.001). No association was found between the rs844644 and rs844648 polymorphisms and SLE.ConclusionThe results of our meta-analysis suggest that the TNFSF4 rs2205960 polymorphism may confer susceptibility to SLE in different populations and that the TNFSF4 rs1234315 polymorphism is associated with susceptibility to SLE in Asians.
Real-time eye detection and tracking under various light conditions

Non-intrusive methods based on active remote IR illumination for eye tracking are important for many applications of vision-based man-machine interaction. One problem that has plagued those methods is their sensitivity to lighting condition change. This tends to significantly limit their scope of application. In this paper, we present a new real-time eye detection and tracking methodology that works under variable and realistic lighting conditions. Based on combining the bright-pupil effect resulted from IR light and the conventional appearance-based object recognition technique, our method can robustly track eyes when the pupils are not very bright due to significant external illumination interferences. The appearance model is incorporated in both eyes detection and tracking via the use of support vector machine and the mean shift tracking. Additional improvement is achieved from modifying the image acquisition apparatus including the illuminator and the camera.
Human mobility prediction from region functions with taxi trajectories

People in cities nowadays suffer from increasingly severe traffic jams due to less awareness of how collective human mobility is affected by urban planning. Besides, understanding how region functions shape human mobility is critical for business planning but remains unsolved so far. This study aims to discover the association between region functions and resulting human mobility. We establish a linear regression model to predict the traffic flows of Beijing based on the input referred to as bag of POIs. By solving the predictor in the sense of sparse representation, we find that the average prediction precision is over 74% and each type of POI contributes differently in the predictor, which accounts for what factors and how such region functions attract people visiting. Based on these findings, predictive human mobility could be taken into account when planning new regions and region functions.