Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of the tat and nef gene products of human immunodeficiency virus type 1 (HIV-1) on transcription controlled by the HIV-1 long terminal repeat and on cell growth in macrophages

The RAW264 murine macrophage cell line was used as a model to examine the role of the tat and nef gene products in the transcription regulation of the human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) in macrophages. Contrary to claims that the activity of the HIV-1 LTR responds poorly in rodent cells to trans activation by the viral tat gene product, cotransfection of RAW264 cells with a tat expression plasmid in transient transfection assays caused a > 20-fold increase in reporter gene expression that was inhibited by mutations in the TAR region. RAW264 cells stably transfected with the tat plasmid displayed similarly elevated HIV-1 LTR-driven reporter gene activity. By contrast to previous reports indicating a negative role for nef in HIV transcription, cotransfection of RAW264 cells with a nef expression plasmid trans activated the HIV-1 LTR driving either a chloramphenicol acetyltransferase or a luciferase reporter gene. The action of nef was specific to the LTR, as expression of nef had no effect on the activity of the simian virus 40, c-fms, urokinase plasminogen activator, or type 5 acid phosphatase promoter. trans-activating activity was also manifested by a frameshift mutant expressing only the first 35 amino acids of the protein. The effects of nef were multiplicative with those of tat gene product and occurred even in the presence of bacterial lipopolysaccharide, which itself activated LTR-directed transcription. Examination of the effects of selected mutations in the LTR revealed that neither the kappa B sites in the direct repeat enhancer nor the TAR region was required as a cis-acting element in nef action. The action of nef was not species restricted; it was able to trans activate in the human monocyte-like cell line Mono Mac 6. The presence of a nef expression cassette in a neomycin phosphotransferase gene expression plasmid greatly reduced the number of G418-resistant colonies generated in stable transfection of RAW264 cells, and many of the colonies that were formed exhibited very slow growth. The frameshift mutant was also active in reducing colony generation. Given the absence of any effect of the frameshift mutation on nef function, its actions on macrophage growth and HIV transcription are discussed in terms of the role of the N-terminal 30 amino acids and of stable secondary structures in the mRNA.
Residual stresses in forged IN718 turbine discs

Abstract Residual stresses play an important role in the production of forged components like turbine discs. Variations in the processing parameters can lead to different residual stress states, which complicate subsequent processing steps, e. g. turning to the final shape. Therefore, a deeper understanding of the residual stress evolution during thermo-mechanical processing and the resulting distortions during machining is essential in order to optimize the manufacturing process with respect to cost efficiency and quality of the product. Consequently, the development of residual stresses in a forged turbine disc made of nickel-based superalloy IN718 was simulated using a finite element (FE) model. The experimental verification of the model was done by independently performed neutron strain scanning. For the studied forged and subsequently water-quenched disc the obtained residual stresses agree well with the stresses predicted by the used FE.
Lyrics, Music, and Emotions

In this paper, we explore the classification of emotions in songs, using the music and the lyrics representation of the songs. We introduce a novel corpus of music and lyrics, consisting of 100 songs annotated for emotions. We show that textual and musical features can both be successfully used for emotion recognition in songs. Moreover, through comparative experiments, we show that the joint use of lyrics and music brings significant improvements over each of the individual textual and musical classifiers, with error rate reductions of up to 31%.
FcγRIIb Inhibits Allergic Lung Inflammation in a Murine Model of Allergic Asthma

Allergic asthma is characterized by airway eosinophilia, increased mucin production and allergen-specific IgE. Fc gamma receptor IIb (FcγRIIb), an inhibitory IgG receptor, has recently emerged as a negative regulator of allergic diseases like anaphylaxis and allergic rhinitis. However, no studies to date have evaluated its role in allergic asthma. Our main objective was to study the role of FcγRIIb in allergic lung inflammation. We used a murine model of allergic airway inflammation. Inflammation was quantified by BAL inflammatory cells and airway mucin production. FcγRIIb expression was measured by qPCR and flow cytometry and the cytokines were quantified by ELISA. Compared to wild type animals, FcγRIIb deficient mice mount a vigorous allergic lung inflammation characterized by increased bronchoalveolar lavage fluid cellularity, eosinophilia and mucin content upon ragweed extract (RWE) challenge. RWE challenge in sensitized mice upregulated FcγRIIb in the lungs. Disruption of IFN-γ gene abrogated this upregulation. Treatment of naïve mice with the Th1-inducing agent CpG DNA increased FcγRIIb expression in the lungs. Furthermore, treatment of sensitized mice with CpG DNA prior to RWE challenge induced greater upregulation of FcγRIIb than RWE challenge alone. These observations indicated that RWE challenge upregulated FcγRIIb in the lungs by IFN-γ- and Th1-dependent mechanisms. RWE challenge upregulated FcγRIIb on pulmonary CD14+/MHC II+ mononuclear cells and CD11c+ cells. FcγRIIb deficient mice also exhibited an exaggerated RWE-specific IgE response upon sensitization when compared to wild type mice. We propose that FcγRIIb physiologically regulates allergic airway inflammation by two mechanisms: 1) allergen challenge mediates upregulation of FcγRIIb on pulmonary CD14+/MHC II+ mononuclear cells and CD11c+ cells by an IFN-γ dependent mechanism; and 2) by attenuating the allergen specific IgE response during sensitization. Thus, stimulating FcγRIIb may be a therapeutic strategy in allergic airway disorders.
Spectral Methods Meet EM: A Provably Optimal Algorithm for Crowdsourcing

The Dawid-Skene estimator has been widely used for inferring the true labels from the noisy labels provided by non-expert crowdsourcing workers. However, since the estimator maximizes a non-convex log-likelihood function, it is hard to theoretically justify its performance. In this paper, we propose a two-stage efficient algorithm for multi-class crowd labeling problems. The first stage uses the spectral method to obtain an initial estimate of parameters. Then the second stage refines the estimation by optimizing the objective function of the Dawid-Skene estimator via the EM algorithm. We show that our algorithm achieves the optimal convergence rate up to a logarithmic factor. We conduct extensive experiments on synthetic and real datasets. Experimental results demonstrate that the proposed algorithm is comparable to the most accurate empirical approach, while outperforming several other recently proposed methods.
Source Code Retrieval using Conceptual Similarity

We propose a method for retrieving segments of source code from a large repository. The method is based on conceptual modeling of the code, combining information extracted from the structure of the code and standard information-distance measures. Our results show an improvement over traditional retrieval models, indicating that, for this type of highly-structured documents, usage of structure is indeed beneficial for retrieval.
Polyimide Electronic Structural and Optical Properties from First Principles Calculations

The electronic structural and optical properties of Polyimide (PI) are studied by first principle method of density theory. It is shown that molecules orbit contribution of PI is derived from carbon 2p orbital and oxygen 2p orbital, respectively,and the band gap from the energy band structure is much smaller than that of the experimental value. It is also found that the band gap calculated from the absorption edge of absorption spectra is in agreement with the result of the energy band structure. Furthermore, the relationship between the formation of dielectric function peaks and other spectral characteristics is interpreted.
The price of anarchy of finite congestion games

We consider the price of anarchy of pure Nash equilibria in congestion games with linear latency functions. For asymmetric games, the price of anarchy of maximum social cost is Θ(√N), where N is the number of players. For all other cases of symmetric or asymmetric games and for both maximum and average social cost, the price of anarchy is 5/2. We extend the results to latency functions that are polynomials of bounded degree. We also extend some of the results to mixed Nash equilibria.
An embedded smart surveillance system for target tracking using a PTZ camera

Video surveillance systems have become relatively cheap consumer products employed in the most diverse scenarios. Digital IP cameras can deliver very high quality images and can be directly connected to the Internet. As digital circuits become smaller and faster, video surveillance sensors can be equipped with general processors and DSPs. Smart video analytics algorithms can thus be embedded in the surveillance sensors, for fast at-camera processing. In this paper we present an embedded smart surveillance system for object and people tracking, using an IP PTZ camera, which can pan and tilt to follow the target. The system is implemented on the DM6437 Evaluation Module based on the TMS320DM6437 processor from Texas Instruments. The PTZ camera is driven by our proposed tracking algorithm via HTTP-based commands, to keep the target always in the field of view. The system runs in real-time and a quantitative performance evaluation is provided in the paper.
Visual memory as a potential cognitive endophenotype of attention deficit hyperactivity disorder

Background Executive functions have been proposed as endophenotypes for attention deficit hyperactivity disorder (ADHD); however, data regarding visual memory are lacking. We therefore assessed visual memory in adolescents with ADHD and their unaffected siblings compared with controls. Method The participants included 279 adolescents with ADHD, 108 unaffected siblings, and 173 unaffected school controls. They were assessed by using the visual memory tasks of the Cambridge Neuropsychological Test Automated Battery (CANTAB): Delayed Matching to Sample (DMS), Spatial Recognition Memory (SRM), Paired Associates Learning (PAL), and Pattern Recognition Memory (PRM). Results Compared with the controls, probands with ADHD had a significantly lower number of correct responses, a higher probability of an error following a correct response and following an error response in the DMS, and a lower percentage of correct responses in the SRM. Their unaffected siblings occupied an intermediate position between ADHD probands and controls in the probability of an error following a correct response and following an error response in the DMS, and in the percentage of correct responses in the SRM. In general, lower IQ and current use of and duration of treatment with methylphenidate were associated with more severe visual memory deficits. Conclusions The present results suggest that ADHD is associated with poorer visual memory function. Visual memory assessed by the DMS and SRM tasks in the CANTAB may be a useful endophenotype for ADHD.
Access Control for Home Data Sharing: Attitudes, Needs and Practices

As digital content becomes more prevalent in the home, non-technical users are increasingly interested in sharing that content with others and accessing it from multiple devices. Not much is known about how these users think about controlling access to this data. To better understand this, we conducted semi-structured, in-situ interviews with 33 users in 15 households. We found that users create ad-hoc access-control mechanisms that do not always work; that their ideal policies are complex and multi-dimensional; that a priori policy specification is often insufficient; and that people's mental models of access control and security are often misaligned with current systems. We detail these findings and present a set of associated guidelines for designing usable access-control systems for the home environment.
Efficiency Based Feedback Reduction

Most of up-to-date wireless data systems are based on the OFDM technology and employ the opportunistic scheduling to exploit channel itself fully. Thus, feedback reduction in multiuser multi-carrier systems becomes more of an issue due to the large amount of feedback required to pass to the base station. In this paper, we propose a novel feedback reduction scheme preserving the essential of multi-user diversity. In our proposed scheme, active users determine their feedback amount based on the feedback efficiency factor in a distributed manner. The objective is to reduce the feedback load remarkably while achieving almost the same performance to the full feedback condition. Our proposed scheme offers several advantages over existing ones. First, it does not distort the property of the scheduling policies. Second, total feedback load can be explicitly controlled to a target level regardless of the number of users in a system by adjusting each user's feedback load adaptively.
Bitcoin meets strong consistency

The Bitcoin system only provides eventual consistency. For everyday life, the time to confirm a Bitcoin transaction is prohibitively slow. In this paper we propose a new system, built on the Bitcoin blockchain, which enables strong consistency. Our system, PeerCensus, acts as a certification authority, manages peer identities in a peer-to-peer network, and ultimately enhances Bitcoin and similar systems with strong consistency. Our extensive analysis shows that PeerCensus is in a secure state with high probability. We also show how Discoin, a Bitcoin variant that decouples block creation and transaction confirmation, can be built on top of PeerCensus, enabling real-time payments. Unlike Bitcoin, once transactions in Discoin are committed, they stay committed.
Identifying the factors that influence task allocation in global software development: preliminary results

Over the last decade, an increasing number of organizations have started software development in a globally distributed environment. One of the major challenges is that many organizations endorse the process of global software development without testing their management readiness for the globally distributed development activity. This includes work distribution through task allocation in the globally distributed development environment. The objective of this research paper is to identify factors that influence task allocation in global software development through carrying out a systematic literature review. We used customized search terms, derived from our research question, to identify literature on work distribution and task allocation in a global context. We identified criteria such as site technical expertise, time zone difference, resource cost, task dependency, vendor reliability, task size and vendor maturity level as key task allocation factors in globally distributed software projects. Based on the systematic literature review results, we suggest that there is a need to develop work distribution strategies and standards through global task allocation to help software development organizations in achieving the true potential of global software development at lower development costs and shorter time-to-market.
BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model

With the rapid development of biomedical sciences, a great number of documents have been published to report new scientific findings and advance the process of knowledge discovery. By the end of 2013, the largest biomedical literature database, MEDLINE, has indexed over 23 million abstracts. It is thus not easy for scientific professionals to find experts on a certain topic in the biomedical domain. In contrast to the existing services that use some ad hoc approaches, we developed a novel solution to biomedical expert finding, BMExpert, based on the language model. For finding biomedical experts, who are the most relevant to a specific topic query, BMExpert mines MEDLINE documents by considering three important factors: relevance of documents to the query topic, importance of documents, and associations between documents and experts. The performance of BMExpert was evaluated on a benchmark dataset, which was built by collecting the program committee members of ISMB in the past three years (2012-2014) on 14 different topics. Experimental results show that BMExpert outperformed three existing biomedical expert finding services: JANE, GoPubMed, and eTBLAST, with respect to both MAP (mean average precision) and P@50 (Precision). BMExpert is freely accessed at http://datamining-iip.fudan. edu.cn/service/BMExpert/.
Tracking players and a ball in video image sequence and estimating camera parameters for 3D interpretation of soccer games

To recognize and retrieve soccer game scenes, the movement of the players and the ball must be analyzed. This paper describes a method of tracking the players and the ball and estimating their 3D positions from video images recorded from TV broadcasting. Our system detects the players and tracks them by predicting their motions. Our system determines the ball from among ball candidates by considering the motion continuity of the ball. The camera parameters (Pan, tilt, and zoom) are estimated by defecting line regions on the field in every frame and by matching them to the model. Because our method uses not only straight lines but also circular ones for the matching, it can be applied to the whole area of the field. Our system also estimates the 3D position of the ball by fitting a 3D physical model to the observed ball trajectory. The effectiveness of the method is shown by experiments with actual image sequences.
Identifying novel genetic determinants of hemostatic balance

Summary. Incomplete penetrance and variable expressivity confound the diagnosis and therapy of most inherited thrombotic and hemorrhagic disorders. For many of these diseases, some or most of this variability is determined by genetic modifiers distinct from the primary disease gene itself. Clues toward identifying such modifier genes may come from studying rare Mendelian disorders of hemostasis. Examples include identification of the cause of combined factor V and VIII deficiency as mutations in the ER Golgi intermediate compartment proteins LMAN1 and MCFD2. These proteins form a cargo receptor that facilitates the transport of factors V and VIII, and presumably other proteins, from the ER to the Golgi. A similar positional cloning approach identified ADAMTS‐13 as the gene responsible for familial TTP. Along with the work of many other groups, these findings identified VWF proteolysis by ADAMTS‐13 as a key regulatory pathway for hemostasis. Recent advances in mouse genetics also provide powerful tools for the identification of novel genes contributing to hemostatic balance. Genetic studies of inbred mouse lines with unusually high and unusually low plasma VWF levels identified polymorphic variation in the expression of a glycosyltransferase gene, Galgt2, as an important determinant of plasma VWF levels in the mouse. Ongoing studies in mice genetically engineered to carry the factor V Leiden mutation may similarly identify novel genes contributing to thrombosis risk in humans.
A common data model to assess cardiovascular hospitalization and mortality in atrial fibrillation patients using administrative claims and medical records

Purpose Atrial fibrillation/flutter (AF) is frequently associated with cardiovascular comorbidities. Observational health care databases are commonly used for research purposes in studies of quality of care, health economics, outcomes research, drug safety, and epidemiology. This retrospective cohort study applied a common data model to administrative claims data (Truven Health Analytics MarketScan® claims databases [MS-Claims]) and electronic medical records data (Geisinger Health System’s MedMining electronic medical record database [MG-EMR]) to examine the risk of cardiovascular hospitalization and all-cause mortality in relation to clinical risk factors in recent-onset AF and to assess the consistency of analyses for each data source. Methods Cohorts of patients with newly diagnosed AF (n=105,262 [MS-Claims] and n=3,919 [MG-EMR]) and demographically similar patients without AF (n=105,262 [MS-Claims] and n=3,872 [MG-EMR]) were followed from the qualifying AF diagnosis until cardiovascular hospitalization, death, database disenrollment, or study completion. A common data model standardized the data in structure, format, content, and nomenclature to allow for systematic assessment and comparison of outcomes from two disparate data sets. Results In both databases, AF patients had greater overall baseline comorbidity and higher incidence rates of cardiovascular hospitalization (threefold higher) and all-cause mortality (46% higher) than non-AF patients. For AF patients, incidence rates of cardiovascular hospitalization and all-cause mortality were increased by the concomitant presence of coronary disease, chronic obstructive pulmonary disease, and stroke at baseline. Overall, the pattern of cardiovascular hospitalization in the MS-Claims database was similar to that in the MG-EMR database. Compared with the MS-Claims database, the use of cardiovascular medications and the capture of certain comorbidities among AF patients appeared to be higher in the MG-EMR data set. Conclusion Similar standardized analyses across EMR and Claims databases were consistent in the association of AF with acute morbidity and an increased risk of all-cause mortality. Areas of inconsistency were due to differences in underlying population demographics and cardiovascular risks and completeness of certain data fields.
Modulation of the UGT 2 B 7 Enzyme Activity by C-Terminally Truncated Proteins Derived from Alternative Splicing s

The enzyme UGT2B7 is one of the most active UDP-glucuronosyltransferases (UGTs) involved in drug metabolism and in maintaining homeostasis of endogenous compounds. We recently reported the existence of 22 UGT2B7 mRNAs, two with a classic 59 region but alternative 39 ends namely UGT2B7_v5 (containing a novel terminal exon 6b) and _v7 (exon 5 excluded) that encode enzymatically inactive isoforms 2 and 4 (i2 and i4), respectively. The v1 mRNA encoding the UGT2B7 enzyme (renamed isoform 1 or i1) is coexpressed with the splice variants v5 and v7 in human liver, kidney, and small intestine and the hepatic cell lines HepG2 and C3A. The presence of alternate v5 and v7 transcripts in isolated polysomes from these hepatic cells further supports endogenous protein translation. Cellular fractionation of clonal HEK293 cell lines overexpressing UGT2B7 isoforms demonstrates that i1, i2, and i4 proteins colocalize in the microsomal/Golgi fraction, whereas i2 and i4 can also be found in the cytosol; a finding sustained by immunofluorescence experiments using tagged proteins. By modifying splice variant abundance in overexpression in HEK293 and HepG2 cells as well as RNA interference experiments in HepG2 and C3A cells, we observe drug glucuronidation phenotypes compatible with variant-mediated repression of UGT2B7 activity without consequent alteration of the apparent enzyme affinity (Km). Finally, coimmunoprecipitation experiments support a direct protein– protein interaction of i2 and i4 proteins with the functional UGT2B7 enzyme as a potential causative mechanism. These findings point toward a novel autoregulatory mechanism of the UGT2B7 glucuronidation pathway by naturally occurring alternative i2 and i4