Miracle-dz/UniFAR-FTUs huggingface dataset:
Pretreatment serum HBsAg-to-HBV DNA ratio predicts a virologic response to entecavir in chronic hepatitis B

Background/Aims Decay of hepatitis B surface antigen (HBsAg) titers has previously been shown to be predictive of a virologic response (VR), especially during peginterferon-alpha therapy. However, the role of HBsAg levels in predicting a VR to nucleos(t)ide analog therapy has not yet been established. In this study we sought to determine whether the VR can be predicted from HBsAg titers in nucleos(t)ide-naïve chronic hepatitis B (CHB) patients treated with entecavir. Methods CHB patients who started entecavir as an initial antiviral therapy were enrolled in this study. Serum hepatitis B virus (HBV) DNA, HBsAg, and alanine aminotransferase levels were measured every 3 months during treatment. A VR was defined as undetectable serum HBV DNA titer by real-time PCR assay (<60 IU/mL). Results Fifty-two patients were enrolled, and the median duration of treatment was 26 months (range 7-35 months). Forty-five patients achieved a VR; the cumulative VR rates at 3, 6, 12, and 24 months were 40%, 71.2%, 81.5%, and 88%, respectively. Baseline HBV DNA levels were significantly lower in patients with VR, whereas the HBsAg levels did not differ significantly between patients with or without VR. In a univariate analysis the cumulative VR rate was significantly higher in HBeAg negative patients and patients with an HBsAg/HBV DNA ratio above 0.56. However, in a multivariate analysis only an HBsAg/HBV DNA ratio above 0.56 was an independent predictor of VR (P=0.003). The area under the receiver operating characteristic curve was larger for the HBsAg/HBV DNA ratio than for either HBV DNA or HBsAg. Conclusions Pretreatment HBsAg/HBV DNA ratio can predict a long-term VR to entecavir therapy in nucleos(t)ide-naïve CHB patients.
On filtering the noise from the random parameters in Monte Carlo rendering

Monte Carlo (MC) rendering systems can produce spectacular images but are plagued with noise at low sampling rates. In this work, we observe that this noise occurs in regions of the image where the sample values are a direct function of the random parameters used in the Monte Carlo system. Therefore, we propose a way to identify MC noise by estimating this functional relationship from a small number of input samples. To do this, we treat the rendering system as a black box and calculate the statistical dependency between the outputs and inputs of the system. We then use this information to reduce the importance of the sample values affected by MC noise when applying an image-space, cross-bilateral filter, which removes only the noise caused by the random parameters but preserves important scene detail. The process of using the functional relationships between sample values and the random parameter inputs to filter MC noise is called Random Parameter Filtering (RPF), and we demonstrate that it can produce images in a few minutes that are comparable to those rendered with a thousand times more samples. Furthermore, our algorithm is general because we do not assign any physical meaning to the random parameters, so it works for a wide range of Monte Carlo effects, including depth of field, area light sources, motion blur, and path-tracing. We present results for still images and animated sequences at low sampling rates that have higher quality than those produced with previous approaches.
A New Data Model: Persistent Attribute-Centric Objects

Trying to nd information on the Web is like trying to nd something at a jumble sale it s fun and you can make serendipitous discoveries but for directed search it s better to go to a department store there someone has already done most of the arranging for you Unfortunately the Web s continuing explosion in size its enormous diversity of topics and its great volatility make unaided human indexing impossible This problem is just a special case of the general problem of organizing information to create knowledge A similar problem arises on the desktop when dealing with le systems where users must search by name and often they do not remember the le s name or location File names are artifacts of current operating systems but human understanding neither requires objects to be named nor does it have problems with multiple objects sharing properties names for instance The limitations mentioned above result because today s computer systems do not analyze the les they are asked to store Instead they note only simple attributes like creation date and le type and leave the bulk of organizing naming annotating and nding those les to their users This may have made sense in the s when computers were slow and expensive but it makes no sense today We argue for a new data model to information representation based on the use of persis tent objects with dynamic attributes and search operations over them This representation is The work of the rst author was supported by Chile Fondecyt Grant and the second author by DARPA Contract N C and by a grant from Intel organization neutral thereby giving a exible substrate for anyone to build multiple simultane ous organizations In addition it is uniform allows easy sharing of objects and can be simply extended to the Web We present an initial prototype of this idea AVS and to show its po tential two system prototypes that have as their main goal to organize personal information DomainView and KnownSpace
Neural integrators for decision making: A favorable tradeoff between robustness and sensitivity

A key step in many perceptual decision tasks is the integration of sensory inputs over time, but fundamental questions remain about how this is accomplished in neural circuits. One possibility is to balance decay modes of membranes and synapses with recurrent excitation. To allow integration over long timescales, however, this balance must be precise; this is known as the fine tuning problem. The need for fine tuning can be overcome via a ratchet-like mechanism, in which momentary inputs must be above a preset limit to be registered by the circuit. The degree of this ratcheting embodies a tradeoff between sensitivity to the input stream and robustness against parameter mistuning. The goal of our study is to analyze the consequences of this tradeoff for decision making performance. For concreteness, we focus on the well-studied random dot motion discrimination task. For stimulus parameters constrained by experimental data, we find that loss of sensitivity to inputs has surprisingly little cost for decision performance. This leads robust integrators to performance gains when feedback becomes mistuned. Moreover, we find that substantially robust and mistuned integrator models remain consistent with chronometric and accuracy functions found in experiments. We explain our findings via sequential analysis of the momentary and integrated signals, and discuss their implication: robust integrators may be surprisingly well-suited to subserve the basic function of evidence integration in many cognitive tasks.
Airline Tra ± c and Urban Economic Development

This paper provides new evidence on the link between airline tra±c and employment in a metro area. The evidence con ̄rms the common view that good airline service is an important factor in urban economic development. Frequent service to a variety of destinations, re°ected in a high level of passenger enplanements, facilitates easy face-to-face contact with businesses in other cities, attracting new ̄rms to the metro area and stimulating employment at established enterprises. The empirical results show that a 10 percent increase in passenger enplanements in a metro area leads approximately to a 1 percent increase in employment in service-related industries. However, airline tra±c has no e®ect on manufacturing and other goods-related employment, suggesting that air travel is less important for such ̄rms than for service-related businesses. These estimates are generated controlling for reverse causality between employment and tra±c. The results imply that expansion of Chicago's O'Hare airport would raise servicerelated employment in the Chicago metro area by 185,000 jobs (this impact assumes that expansion raises tra±c by 50 percent). Thus, the expansion of O'Hare airport represents a powerful economic development tool, as argued by its proponents. Airline Tra±c and Urban Economic Development
Learner instruction, attitudes during class and academic achievement of junior high school students in Korea: a panel analysis

Abstract This study examined changes in the structural relationship among learner-centred classes perceived by Korean junior high school students, attitudes during class and academic achievement. A linear change model was identified as optimal, showing a steady increase over time for each parameter. The higher the initial value for learner-centred classes, the higher both the initial value and rate of change was for attitudes during class and academic achievement. The initial values for attitudes during class also had a significant effect on initial values of academic achievement, suggesting that attitudes are important in increasing academic achievement. The rate of change of both learner-centred classes and attitudes during class significantly influenced the rate of change of academic achievement.
A Novel Metric for ACLR of Output Signals of Power Amplifier in Multicarrier Systems

One of the main drawbacks of multi-carrier signals is the large envelope fluctuations. When multi-carrier signals with large envelopes pass through a power amplifier (PA), a degradation of adjacent channel leakage ratio (ACLR) happens. There exist two metrics commonly utilized to describe the envelope fluctuations of multi-carrier signals, i.e., peak-to-average power ratio (PAPR) and cubic metric (CM). However, our research shows that these two metrics cannot indicate the degradation of ACLR sufficiently accurately. In this paper, we study the Volterra-series-based PA model and sufficiently analyze the distortion caused by the nonlinearity and memory effect of PA. Base on this analysis, a novel metric of signal envelope fluctuations is proposed. The simulation results demonstrate that, compared with PAPR and CM, the new metric is more accurate to indicate the ACLR of output signals of PA.
A Rapid Tree Pattern Matching Algorithm for XML Query

Finding all distinct matching’s of the query tree pattern is the main operation of XML query evaluation. The existing methods we research a large set of XML tree pattern, called extended XML tree pattern, which may include P-C, A-D relationships, negation functions, wildcards and order restriction. We establish a theoretical framework about "matching cross" which demonstrates the intrinsic reason in the proof of optimality on holistic algorithms for tree pattern matching are decomposition matching-merging processes, which may produce large useless intermediate result or require repeated matching of some sub-patterns. We propose a fast tree pattern matching algorithm called TreeMatch to directly find all distinct matchings of a query tree pattern. The only requirement for the data source is that the matching elements of the non-leaf pattern nodes do not contain subelements with the same tag. The TreeMatch does not produce any intermediate results and the final results are compactly encoded in stacks, from which the explicit representation can be produced efficiently. It can effectively control the size of intermediate results during query processing. Keywords— leaf pattern, Query processing, XML, algorithms, tree pattern , Query patterns.
Prompt Shocks in the Gas Disk around a Recoiling Supermassive Black Hole Binary

Supermassive black hole binaries (BHBs) produced in galaxy mergers recoil at the time of their coalescence due to the emission of gravitational waves (GWs). We simulate the response of a thin, 2D disk of collisionless particles, initially on circular orbits around a 106 M☉ BHB, to kicks that are either parallel or perpendicular to the initial orbital plane. Typical kick velocities (vkick) can exceed the sound speed in a circumbinary gas disk. While the inner disk is strongly bound to the recoiling binary, the outer disk is only weakly bound or unbound. This leads to differential motions in the disturbed disk that increase with radius and can become supersonic at ≳700 Schwarzschild radii for vkick = 500 km s-1 implying that shocks form beyond this radius. We indeed find that kicks in the disk plane lead to immediate strong density enhancements (within weeks) in a tightly wound spiral caustic, propagating outward at the speed ~vkick. Concentric density enhancements are also observed for kicks perpendicular to the disk, but are weaker and develop into caustics only after a long delay (>1 yr). Unless both BH spins are low or precisely aligned with the orbital angular momentum, a significant fraction (≳ several %) of kicks are sufficiently large and well aligned with the orbital plane for strong shocks to be produced. The shocks could result in an afterglow whose luminosity and characteristic photon energy increases with time, helping to identify the EM counterparts of GW sources discovered by LISA.
Unsupervised Detection of Suspicious Tissue Using Data Modeling and PCA

Breast cancer is a major cause of death and morbidity among women all over the world, and it is a fact that early detection is a key in improving outcomes. Therefore development of algorithms that aids radiologists in identifying changes in breast tissue early on is essential. In this work an algorithm that investigates the use of principal components analysis (PCA) is developed to identify suspicious regions on mammograms. The algorithm employs linear structure and curvelinear modeling prior to PCA implementations. Evaluation of the algorithm is based on the percentage of correct classification, false positive (FP) and false negative (FN) in all experimental work using real data. Over 90% accuracy in block classification is achieved using mammograms from MIAS database.
.1 Protein Trafficking 1.1.2 the Endocytic Pathway

Introduction A prerequisite for normal synapse formation is precise coordination of trafficking of synaptic proteins and the structural assembly of the presynaptic exocytic machinery and the postsynaptic neurotransmitter units. One of the key players in the formation and functioning of synapses is the protein Neurobeachin. Nbea is an A-kinase anchoring protein (AKAP) that has been implicated in membrane trafficking and belongs to the BEACH family of proteins. In order to understand what this means, this chapter presents a short review of these theoretical concepts, which will accompany us throughout this thesis. The first section is dedicated to protein traffic in general, which is followed by a description of the family of BEACH (beige and Chediak-Higashi) proteins. Then the structure and function of AKAPs as dynamic organizers of cellular events is explained. The aim and outline of the thesis comprise the end of this chapter. Eukaryotic cells have compartmentalized the cytoplasm into distinct membrane-bound organelles, which enable them to regulate delivery of newly synthesized proteins, carbohydrates , and lipids to the cell exterior and to take up macromolecules by the process of endocytosis (Alberts et al., 2002; Derby and Gleeson, 2007). The initial definition of the outward-bound membrane transport pathway as the secretory pathway and the inward-bound membrane transport pathway as the endocytic pathway, has lost its sharp distinction when it became clear that the two pathways converge at a variety of locations (Derby and Gleeson, 2007). The components of the secretory and endocytic pathway include the endoplasmic Chapter1 reticulum (ER), the ER-Golgi intermediate compartment (ERGIC), the Golgi apparatus , the trans-Golgi network (TGN), a heterogenous set of endosomes, lysosomes, the plasma membrane, and secretory granules in regulated secretory cells (Condon and Ehlers, 2007; Derby and Gleeson, 2007). These membrane-bound organelles must selectively allow the movement of proteins and membrane in a vectorial fashion by a carefully coordinated series of vesicle budding and fusion events and at the same time maintain a unique set of resident proteins that define their structural and functional 1.1. 1 The early biosynthetic-secretory pathway The endoplasmic reticulum The ER, the first organelle in the secretory pathway, is a polygonal meshwork of membrane tubules and sheet-like cisternae (Palade, 1956) that are connected with the continuous membrane of the outer nuclear envelope (Prinz et al., 2000). It can be divided into the ribosome-bound rough ER (RER) that is constituted primarily by sheets or cisternae, and the ribosome-free smooth ER …
Disulfide Connectivity Prediction with Normalized Bond Vector

The prediction of the location of disulfide bridges helps towards the solution of protein folding problem. Most of previous works on disulfide connectivity pattern prediction use the prior knowledge of the bonding state of cysteines. In this study an effective method is proposed to predict disulfide connectivity pattern for proteins that have at least two disulfide bonds but without the prior knowledge of cysteins (cid:2) bonding state. The method is based on template matching and only a global feature called the normalized bond vector is used. This method can also be applied and achieves a better accuracy if the bonding state of cysteines is known. In previous research works reported in the literature, to the best of our knowledge, without the prior knowledge of the bonding state of cysteines, the best accuracy of disulfide connectivity pattern prediction is 51%. With the prior knowledge of the bonding state of cysteines, the best accuracy is 70%. Testing our method on the same test dataset SwissProt39 (sp39), the accuracy of a fourfold cross-validation is 61% for disulfide connectivity pattern prediction when the bonding state of cysteines is not known in advance. With the prior knowledge of bonding state, the accuracy increases to 71%.
Neutral Biogeography and the Evolution of Climatic Niches

Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than from adaptive scenarios. We developed a model inspired by neutral biodiversity theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sampled the climatic niches of species according to their geographic position and showed that even when species evolve independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time.
Flexibly Cooperative Spectrum Sensing and Allocation in cognitive radio networks: An auction-based framework

Cognitive radio networks have made a dramatic shift towards variously cooperative paradigm to achieve fast, reliable spectrum sensing and effective spectrum usage in recent past. In this paper, we develop a Flexibly Cooperative Spectrum Sensing and Allocation (FCSSA) framework in cognitive radio networks. The proposed FCSSA framework captures the essential interactive function between cooperative spectrum sensing and allocation, which allows licensed channel and secondary users bargaining on their decisions, such as the enforceable requirements of spectrum sensing time, energy detection threshold and secondary users' payment for spectrum access, to maximize their utilities respectively. Moreover, we apply Stackelberg game to formulate the joint cooperative spectrum sensing and allocation design. The leader (authorized agent of licensed channel) decides spectrum sensing time and energy detection threshold according to the predictable behavior of secondary users. The followers (secondary users) make their payment decision underlying a non-cooperative game according to the limited information from licensed channel. Numeric simulations verify that our proposed jointly design framework in cooperative spectrum sensing and allocation can increase the agility and effectiveness of dynamic spectrum usage.
Direct Manipulation: A Step Beyond Programming Languages

These feelings are not, of course, universal, but the amalgam does convey an image of the truly pleased user. As I talked with these enthusiasts and examined the systems they used, I began to develop a model of the features that produced such delight. The central ideas seemed to be visibility of the object of interest; rapid, reversible, incremental actions; and replacement of complex command language syntax by direct manipulation of the object of interest-hence the term "direct manipulation. " Examples of direct manipulation systems
Complete blockage of the mevalonate pathway results in male gametophyte lethality

Plants have two isoprenoid biosynthetic pathways: the cytosolic mevalonate (MVA) pathway and the plastidic 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Since the discovery of the MEP pathway, possible metabolic cross-talk between these pathways has prompted intense research. Although many studies have shown the existence of such cross-talk using feeding experiments, it remains to be determined if native cross-talk, rather than exogenously applied metabolites, can compensate for complete blockage of the MVA pathway. Previously, Arabidopsis mutants for HMG1 and HMG2 encoding HMG-CoA reductase (HMGR) were isolated. Although it was shown that HMGR1 is a functional HMGR, the enzyme activity of HMGR2 has not been confirmed. It is demonstrated here that HMG2 encodes a functional reductase with similar activity to HMGR1, using enzyme assays and complementation experiments. To estimate the contribution of native cross-talk, an attempt was made to block the MVA pathway by making double mutants lacking both HMG1 and HMG2, but no double homozygotes were detected in the progeny of self-pollinated HMG1/hmg1 hmg2/hmg2 plants. hmg1 hmg2 male gametophytes appeared to be lethal based on crossing experiments, and microscopy indicated that ∼50% of the microspores from the HMG1/hmg1 hmg2/hmg2 plant appeared shrunken and exhibited poorly defined endoplasmic reticulum membranes. In situ hybridization showed that HMG1 transcripts were expressed in both the tapetum and microspores, while HMG2 mRNA appeared only in microspores. It is concluded that native cross-talk from the plastid cannot compensate for complete blockage of the MVA pathway, at least during male gametophyte development, because either HMG1 or HMG2 is required for male gametophyte development.
A Malware Analysis Platform Based on Taint Analysis

Nowadays, malware has become one of the most serious threats to information security, which causes incalculable economic losses. In this paper, we introduce a malware analysis platform based on taint analysis. Our platform focuses on the overflow attack (Of all attacks, more than 60% is the overflow attack) and the condition-related malware protection technology (which is one of the most popular malware protection technologies). Experiments show that our platform is efficient for malware detection and analysis.