Miracle-dz/UniFAR-FTUs huggingface dataset:
Entry of Hepatitis B Virus into Immortalized Human Primary Hepatocytes by Clathrin-Dependent Endocytosis

ABSTRACT The lack of a suitable in vitro hepatitis B virus (HBV) infectivity model has limited examination of the early stages of the virus-cell interaction. In this study, we used an immortalized cell line derived from human primary hepatocytes, HuS-E/2, to study the mechanism of HBV infection. HBV infection efficiency was markedly increased after dimethyl sulfoxide (DMSO)-induced differentiation of the cells. Transmission electron microscopy demonstrated the presence of intact HBV particles in DMSO-treated HBV-infected HuS-E/2 cells, which could be infected with HBV for up to at least 50 passages. The pre-S1 domain of the large HBsAg (LHBsAg) protein specifically interacted with clathrin heavy chain (CHC) and clathrin adaptor protein AP-2. Short hairpin RNA knockdown of CHC or AP-2 in HuS-E/2 cells significantly reduced their susceptibility to HBV, indicating that both are necessary for HBV infection. Furthermore, HBV entry was inhibited by chlorpromazine, an inhibitor of clathrin-mediated endocytosis. LHBsAg also interfered with the clathrin-mediated endocytosis of transferrin by human hepatocytes. This infection system using an immortalized human primary hepatocyte cell line will facilitate investigations into HBV entry and in devising therapeutic strategies for manipulating HBV-associated liver disorders.
On the absorbance changes in the photocycle of the photoactive yellow protein: A quantum-chemical analysis

Spectral changes in the photocycle of the photoactive yellow protein (PYP) are investigated by using ab initio multiconfigurational second-order perturbation theory at the available structures experimentally determined. Using the dark ground-state crystal structure [Genick, U. K. , Soltis, S. M. , Kuhn, P., Canestrelli, I. L. & Getzoff, E. D. (1998) Nature (London) 392, 206–209], the ππ* transition to the lowest excited state is related to the typical blue-light absorption observed at 446 nm. The different nature of the second excited state (nπ*) is consistent with the alternative route detected at 395-nm excitation. The results suggest the low-temperature photoproduct PYPHL as the most plausible candidate for the assignment of the cryogenically trapped early intermediate (Genick et al.). We cannot establish, however, a successful correspondence between the theoretical spectrum for the nanosecond time-resolved x-ray structure [Perman, B. , Šrajer, V. , Ren, Z. , Teng, T. , Pradervand, C. , et al. (1998) Science 279, 1946–1950] and any of the spectroscopic photoproducts known up to date. It is fully confirmed that the colorless light-activated intermediate recorded by millisecond time-resolved crystallography [Genick, U. K. , Borgstahl, G. E. O. , Ng, K. , Ren, Z. , Pradervand, C. , et al. (1997) Science 275, 1471–1475] is protonated, nicely matching the spectroscopic features of the photoproduct PYPM. The overall contribution demonstrates that a combined analysis of high-level theoretical results and experimental data can be of great value to perform assignments of detected intermediates in a photocycle.
Decreased risk of aortic valve surgery.

SINCE FEBRUARY 1963, when the Starr-Edwards aortic ball-valve prosthesis1was introduced into our practice, 100 consecutive operations for the replacement of the aortic valve have been accomplished without any hospital mortality. A detailed analysis of this experience may be of value in defining the reasons for this decrease in risk. Operative Series This consecutive series of 100 operations included all operations for replacement of the aortic valve except those in which another valve was also replaced. However, in seven of the operations of this series, repair of associated mitral valve disease short of valve replacement was also performed. The series of 100 operations was completed by December 1964. No patient was denied operation for aortic valve disease because of disability and failure which were too far advanced. Thus, several patients included in this experience were in advanced failure which had responded only partially to prolonged medical treatment. This is
Exploring Cross-cultural Crowd Sentiments on Twitter

Twitter is frequently used to express personal opinions and sentiments. This work presents a novel crowd sentiment analysis of Twitter for exploring cross-cultural differences. We aim to find similar meanings but different sentiments between Twitter data collected over diverse geographic places. For this, we detect sentiments and topics of each tweet and assign sentiments to each topic based on the sentiments of the corresponding tweets. This permits finding interesting cross-cultural patterns. We demonstrate a visualization system that supports the interactive analysis of two countries: France and Italy.
The Beam Radiance Estimate for Volumetric Photon Mapping

We present a new method for efficiently simulating the scattering of light within participating media. Using a theoretical reformulation of volumetric photon mapping, we develop a novel photon gathering technique for participating media. Traditional volumetric photon mapping samples the in‐scattered radiance at numerous points along the length of a single ray by performing costly range queries within the photon map. Our technique replaces these multiple point‐queries with a single beam‐query, which explicitly gathers all photons along the length of an entire ray. These photons are used to estimate the accumulated in‐scattered radiance arriving from a particular direction and need to be gathered only once per ray. Our method handles both fixed and adaptive kernels, is faster than regular volumetric photon mapping, and produces images with less noise.
Involvement of phosphatidylinositol 3'-kinase in stem-cell-factor-induced phospholipase D activation and arachidonic acid release.

We have shown previously that the stem cell factor (SCF) receptor undergoes phosphorylation on serine residues following ligand stimulation, and that this phopshorylation is dependent mainly on the activity of protein kinase C (PKC). In the present study, we have further investigated the molecular mechanisms behind SCF-stimulated activation of PKC, and found that SCF does not activate phosphatidylinositol-specific phospholipase C. In contrast, phospholipase D (PLD) is activated in response to SCF in a dose-dependent manner. Activation of PLD was not inhibited by calphostin C, an inhibitor of PKC. On the other hand, inhibitors of phosphatidylinositol PtdIns 3'-kinase (PtdIns 3'-kinase), i.e. wortmannin and LY294002, inhibited SCF-induced PLD activation. Moreover, a mutant SCF receptor in which Tyr721, which is responsible for activation of PtdIns 3'-kinase, is mutated to a phenylalanine residue was unable to mediate activation of PLD. Thus, PtdIns 3'-kinase appears to be essential for SCF-induced PLD activation. Furthermore, we demonstrate that phosphatidic acid (PtdH), generated through the action of PLD in response to SCF, is metabolized to diacylglycerol by dephosphorylation. Diacylglycerol can then activate PKC, and, moreover, after deacylation by a diacylglycerol lipase, yield arachidonic acid, an important second messenger in cell signaling.
A flexible model for the mean and variance functions, with application to medical cost data

Medical cost data are often skewed to the right and heteroscedastic, having a nonlinear relation with covariates. To tackle these issues, we consider an extension to generalized linear models by assuming nonlinear associations of covariates in the mean function and allowing the variance to be an unknown but smooth function of the mean. We make no further assumption on the distributional form. The unknown functions are described by penalized splines, and the estimation is carried out using nonparametric quasi‐likelihood. Simulation studies show the flexibility and advantages of our approach. We apply the model to the annual medical costs of heart failure patients in the clinical data repository at the University of Virginia Hospital System. Copyright © 2013 John Wiley & Sons, Ltd.
Efficient Key Management and Distribution for MANET

Ad hoc networks are being used in applications ranging from disaster recovery to distributed collaborative entertainment applications. Ad hoc networks have become one of the most attractive solution for rapid deployment of interconnecting large number of mobile personal devices. The user community of mobile personal devices are demanding a variety of value added multimedia entertainment services. The popularity of peer group is increasing and one or some members of the peer group need to send data to some or all members of the peer group. The increasing demand for group oriented value added services is driving for efficient multicast service over ad hoc networks. Access control mechanisms need to be deployed to provide guarantee that the unauthorized users cannot access the multicast content. In this paper, we present a topology aware key management and distribution scheme for secure overlay multicast over MANET to address node mobility related issues for multicast key management. We use overlay approach for key distribution and our objective is to keep communication overhead low for key management and distribution. We also incorporate reliability using explicit acknowledgments with the key distribution scheme. Through simulations we show that the proposed key management scheme has low communication overhead for rekeying and improves the reliability of key distribution.
Characteristic Analysis from Excessive to Deficient Syndromes in Hepatocarcinoma Underlying miRNA Array Data

Traditional Chinese medicine (TCM) treatment is regarded as a safe and effective method for many diseases. In this study, the characteristics among excessive, excessive-deficient, and deficient syndromes of Hepatocellular carcinoma (HCC) were studied using miRNA array data. We first calculated the differentially expressed miRNAs based on random module t-test and classified three TCM syndromes of HCC using SVM method. Then, the weighted miRNA-target networks were constructed for different TCM syndromes using predicted miRNA targets. Subsequently, the prioritized target genes of upexpression network of TCM syndromes were analyzed using DAVID online analysis. The results showed that there are distinctly different hierarchical cluster and network structure of TCM syndromes in HCC, but the excessive-deficient combination syndrome is extrinsically close to deficient syndrome. GO and pathway analysis revealed that the molecular mechanisms of excessive-deficient and deficient syndromes of HCC are more complex than excessive syndrome. Furthermore, although excessive-deficient and deficient syndromes have similar complex mechanisms, excessive-deficient syndrome is more involved than deficient syndrome in development of cancer process. This study suggested that miRNAs might be important mediators involved in the changing process from excessive to deficient syndromes and could be potential molecular markers for the diagnosis of TCM syndromes in HCC.
Test-Retest Reliability of an Automated Infrared-Assisted Trunk Accelerometer-Based Gait Analysis System

The aim of this study was to determine the test-retest reliability of an automated infrared-assisted, trunk accelerometer-based gait analysis system for measuring gait parameters of healthy subjects in a hospital. Thirty-five participants (28 of them females; age range, 23–79 years) performed a 5-m walk twice using an accelerometer-based gait analysis system with infrared assist. Measurements of spatiotemporal gait parameters (walking speed, step length, and cadence) and trunk control (gait symmetry, gait regularity, acceleration root mean square (RMS), and acceleration root mean square ratio (RMSR)) were recorded in two separate walking tests conducted 1 week apart. Relative and absolute test-retest reliability was determined by calculating the intra-class correlation coefficient (ICC3,1) and smallest detectable difference (SDD), respectively. The test-retest reliability was excellent for walking speed (ICC = 0.87, 95% confidence interval = 0.74–0.93, SDD = 13.4%), step length (ICC = 0.81, 95% confidence interval = 0.63–0.91, SDD = 12.2%), cadence (ICC = 0.81, 95% confidence interval = 0.63–0.91, SDD = 10.8%), and trunk control (step and stride regularity in anterior-posterior direction, acceleration RMS and acceleration RMSR in medial-lateral direction, and acceleration RMS and stride regularity in vertical direction). An automated infrared-assisted, trunk accelerometer-based gait analysis system is a reliable tool for measuring gait parameters in the hospital environment.
Double threshold energy detection using sequential cooperative spectrum sensing in Rayleigh fading

Spectrum sensing is the primary essentiality to monitor the presence of primary user in cognitive radios. Among all the spectrum sensing techniques energy detection is preferable because it is simple and prior knowledge of primary user is not required, but conventional energy detection is not preferable in low SNR regions. In this paper we discuss a cooperative double threshold method with two thresholds which are decided by an uncertainty parameter. In the confusion region we use a weighted sequential energy detection (WSED) method which considers a fixed number of past observations. For making a decision in confusion region, both the current and past observations are weighted and aggregated. Equations for probability of detection and probability of false alarm in Rayleigh channel are derived for the discussed scheme. Numerical results shows that the scheme gives better performance as compared to the conventional method.
A Nonlinear System Model of Isometric Force

The analysis of isometric force may provide early detection of certain types of neuropathology such as Parkinson's disease. Our long term goal is to determine if there are detectable differences between model parameters of healthy and unhealthy individuals. In this study we used system identification techniques to estimate the parameters of dynamic system models of the isometric force exerted by the index finger and focused on a single category of subjects, healthy young adults. The experiments involved subjects exerting isometric force over a range from 5% to 95% of maximal voluntary contraction. The coefficients of the differential equation models depended on the target force level. This finding suggests that a nonlinear dynamic system model provides the best fit for isometric force experiments
Optimal participation of a microgrid to the energy market with an intelligent EMS

The interconnection of large amounts of nontraditional generation causes problems in a network designed for 'conventional' operation. A microgrid consists of a combination of generation sources, loads and energy storage interfaced through fast acting power electronics. The aim of operating microgrid sub-systems is to move away from considering DG as badly behaved system components, of which a limited amount can be tolerated in an area, to 'good citizens'. The paper is focused on the development of a novel energy management system (EMS) based on the application of neural networks (NN). The EMS is able to autonomously make decisions and determine hour by hour the correct dispatch of generators with the final goal of minimising the global energy costs. The application of the EMS to a small test case has showed significant saves in the global energy bill by using typical Italian energy and fuel price data
Formalizing the Problem of Music Description

The lack of a formalism for “the problem of music description” results in, among other things: ambiguity in what problem a music description system must address, how it should be evaluated, what criteria define its success, and the paradox that a music description system can reproduce the “ground truth” of a music dataset without attending to the music it contains. To address these issues, we formalize the problem of music description such that all elements of an instance of it are made explicit. This can thus inform the building of a system, and how it should be evaluated in a meaningful way. We provide illustrations of this formalism applied to three examples drawn from the literature.
Modules in the metabolic network of E.coli with regulatory interactions

We examine the modular structure of the metabolic network when combined with the regulatory network representing direct regulation of enzymes by small metabolites in E. coli. We introduce novel clustering algorithm and compare it with mainstream module detection method based on simulated annealing. Both methods identify the similar modular core. Slight but significant increase in modularity is observed after regulatory interactions addition. We also identify new functional modules in the combined network, which cannot be detected in the metabolic network only. Regulatory loops in the modules are the source of their autonomy, and allow us to hypothesise about module function.
MAC/FAC: A Model of Similarity-Based Retrieval

We present a model of similarity-based retrieval that attempts to capture three seemingly contradictory psychological phenomena: (a) structural commonalities are weighed more heavily than surface commonalities in similarity judgments for items in working memory; (b) in retrieval, superficial similarity is more important than structural similarity; and yet (c) purely structural (analogical) remindings e sometimes experienced. Our model, MAC/FAC, explains these phenomena in terms of a two-stage process. The first stage uses a computationally cheap, non-structural matcher to filter candidate long-term memory items. It uses content vectors, a redundant encoding of structured representations whose dot product estimates how well the corresponding structural representations will match. The second stage uses SME (structure-mapping engine) to compute structural matches on the handful of items found by the first stage. We show the utility of the MAC/FAC model through a series of computational experiments: (a) We demonstrate that MAC/FAC can model patterns of access found in psychological data; (b) we argue via sensitivity analyses that these simulation results rely on the theory; and (c) we compare the performance of MAC/FAC with ARCS, an alternate model of similarity-based retrieval, and demonstrate that MAC/FAC explains the data better than ARCS. Finally, we discuss limitations and possible extensions of the model, relationships with other recent retrieval models, and place MAC/FAC in the context of other recent work on the nature of similarity.
Context-based adaptive image resolution upconversion

We propose a practical context-based adaptive image resolution upconversion algorithm. The basic idea is to use a low- resolution (LR) image patch as a context in which the missing high- resolution (HR) pixels are estimated. The context is quantized into classes and for each class an adaptive linear filter is designed using a training set. The training set incorporates the prior knowledge of the point spread function, edges, textures, smooth shades, etc. into the upconversion filter design. For low complexity, two 1-D context- based adaptive interpolators are used to generate the estimates of the missing pixels in two perpendicular directions. The two direc- tional estimates are fused by linear minimum mean-squares weight- ing to obtain a more robust estimate. Upon the recovery of the miss- ing HR pixels, an efficient spatial deconvolution is proposed to deblur the observed LR image. Also, an iterative upconversion step is performed to further improve the upconverted image. Experimen- tal results show that the proposed context-based adaptive resolution upconverter performs better than the existing methods in both peak SNR and visual quality. © 2010 SPIE and IS&T.
Fundamental analysis of a car to car visible light communication system

This paper presents a mathematical model for car-to-car (C2C) visible light communications (VLC) that aims to predict the system performance under different communication geometries. A market-weighted headlamp beam pattern model is employed. We consider both the line-of-sight (LOS) and non-line-of-sight (NLOS) links, and outline the relationship between the communication distance, the system bit error rate (BER) performance and the BER distribution on a vertical plane. Results show that by placing a photodetector (PD) at a height of 0.2-0.4 m above road surface in the car, the communications coverage range can be extended up to 20 m at a data rate of 2Mbps.
Impaired Function of Dendritic Cells Deficient in Angiotensin II Type 1 Receptors

Dendritic cells (DC) are highly specialized antigen-presenting cells with a unique ability to activate resting T lymphocytes and initiate primary immune responses. Angiotensin II (AII) is involved in key events of the inflammatory response. Because our previous work implicated an effect of AII on differentiation and function of murine and human DC, we investigated the impact of AII type 1 receptor (AT1) deficiency on the phenotypical and functional properties of mouse DC in vitro and in vivo. Bone marrow (BM) cells isolated from mice lacking AII subtype 1a receptor (AT1a), AII subtype 1b receptor (AT1b), or both receptor isoforms and control littermates [wild type (WT)] were cultured for 7 days in the presence of recombinant mouse granulocyte/macrophage colony-stimulating factor to generate myeloid DC in vitro. Generation of CD11c+ cells was less efficient in both AT1a- and AT1b-deficient BM cells than in WT BM cell cultures. Moreover, DC generated from AT1-deficient progenitors showed lower levels of expression of major histocompatibility complex II (MHC-II) and CD11c (p < 0.01) and a marked reduction in their allostimulatory activity (p < 0.01 or 0.001). Although AT1-deficient DC released comparable levels of interleukin (IL)-10 and IL-12p70 to WT DC, they produced significantly lower levels of tumor necrosis factor α (TNF-α) (p < 0.05). Remarkably, CD11c+ cells isolated from the spleen of AT1 knockout mice challenged with lipopolysaccharide in vivo up-regulated MHC-II, CD40, and CD80 as did WT, but released significantly lower levels of TNF-α (p < 0.01). These data provide clear evidence that AT1 controls differentiation and functionality of DC and thus may have a crucial impact on inflammatory processes where local angiotensinergic systems are known to be activated.
Open Information Extraction for SOV Language Based on Entity-Predicate Pair Detection

Open IE usually has been studied for English which of one of subject-verb-object(SVO) languages where a relation between two entities tends to occur in order of entity-relational phrase-entity within a sentence. However, in SOV languages, two entities occur before the relational phrase so that the subject and the relation have a long distance. The conventional methods for Open IE mostly dealing with SVO languages have difficulties of extracting relations from SOV style sentences. In this paper, we propose a new method of extracting relations from SOV languages. Our approach tries to solve long distance problems by identifying an entity-predicate pair and recognizing a relation within a predicate. Furthermore, we propose a post-processing approach using a language model, so that the system can detect more fluent and precise relations. Experimental results on Korean corpus show that the proposed approach is effective in improving the performance of relation extraction.