Miracle-dz/UniFAR-FTUs huggingface dataset:
Thioredoxin Promotes ASK1 Ubiquitination and Degradation to Inhibit ASK1-Mediated Apoptosis in a Redox Activity-Independent Manner

It has been shown that thioredoxin (Trx) in a reduced form binds to and inhibits apoptosis signal-regulating kinase 1 (ASK1). Apoptotic stimuli such as tumor necrosis factor (TNF) and reactive oxygen species (ROS) activate ASK1 in part by oxidizing Trx (forming intramolecular disulfide between C32 and C35) to release Trx from ASK1. In the present study, we examined if Trx affects ASK1 protein stability and whether the redox activity of Trx is critical in regulating ASK1 activity. First, we showed that overexpression of the wild-type Trx (Trx-WT) in endothelial cells induced ASK1 ubiquitination and degradation. Trx-induced ASK1 ubiquitination/degradation could be blocked by ASK1 activators TNF and TRAF2. We then tested the single-mutation of Trx at the catalytic site C32 or C35 (Trx-C32S or Trx-C35S) and the double-mutation (Trx-CS). The results showed that the single mutants (but not Trx-CS) retained the binding activity for ASK1 and the ability to induce ASK1 ubiquitination/degradation. Unlike Trx-WT, Trx-C32S and Trx-C35S mutants constitutively bind to ASK1 even in the presence of hydrogen peroxide in vitro and TNF in vivo. Finally, we showed that the single mutants (not Trx-WT) significantly (n=4 and P <0.05) inhibited ASK1-induced JNK activation, caspase 3 activity, and apoptosis in TNF/ROS-resistant manner. Our data suggest that association of Trx with ASK1 through a single Cysteine (C32 or C35) is necessary and sufficient for Trx activity in inducing ASK1 ubiquitination/degradation leading to inhibition of ASK1-induced apoptosis.
Beamspace channel estimation for 3D lens-based millimeter-wave massive MIMO systems

Lens-based mmWave massive MIMO can significantly reduce the number of required RF chains without obvious performance loss, where the accurate information of beamspace channel is required. However, existing beamspace channel estimation schemes are based on the 2D beamspace channel model. In this paper, we consider the more general 3D beamspace channel model, and propose an adaptive support detection (ASD)-based channel estimation scheme. The basic idea is to decompose the 3D beamspace channel estimation problem into several sub-problems, and each one only deals with a sparse channel component. For each channel component, we first adaptively detect its support with high accuracy by exploiting the horizontal and vertical sparsity of 3D beamspace channel. Then, we remove the influence of this channel component to detect the support of the next channel component. After the support detections of all channel components, we can estimate the nonzero elements of the beamspace channel with low pilot overhead. Simulation results verify that the proposed scheme enjoys satisfying accuracy, even with low SNR.
Gadget: A Tool for Extracting the Dynamic Structure of Java Programs

Source code analysis and inspection does not provide enough information to describe the structure of an objectoriented program completely because there are components and relations that only exist during its runtime. This paper presents a tool, called Gadget, that helps software engineers extract the dynamic structure of objectoriented programs written in the Java programming language. The tool uses program profiling, filtering, and graph clustering techniques. In this work we show how Gadget is used to analyze a standard graphical user interface library for Java, called Swing. This library has a complex structure, part of which we expose using data gathered by Gadget during the execution of a simple Java program that uses Swing.
Efficacy of Type 2 porcine reproductive and respiratory syndrome virus (PRRSV) vaccine against the 2010 isolate of Vietnamese highly pathogenic PRRSV challenge in pigs

The efficacy of a commercial attenuated live type 2 porcine reproductive and respiratory syndrome (PRRS) vaccine was tested under experimental infection with a highly virulent Vietnamese virus isolated from a diseased pig affected with highly pathogenic PRRS (HP-PRRS) using specific pathogen-free (SPF) pigs. Twenty-five 4-week-old SPF pigs were divided into three groups as follows: pigs vaccinated with a single dose of the vaccine (Group 1, n=10), unvaccinated pigs (Group 2, n=10) and unvaccinated and non-infectious control pigs (Group 3, n=5). Four weeks later, Groups 1 and 2 were challenged with a 1 ml inoculum containing 1 × 105.5 50% tissue culture infectious dose (TCID50)/ml of a Vietnamese HP-PRRS virus isolated in 2010 via the intranasal route. Animals were monitored during the subsequent two-week period post-challenge and necropsied for virological and pathological assays. Results showed a significant reduction in viral replication and shedding in vaccinated pigs compared to unvaccinated pigs. The non-vaccinated pigs showed severe pyrogenic and respiratory illness with marked systematic lesions including interstitial pneumonia and thymic atrophy. In contrast, vaccinated pigs recovered quickly from fever with only mild pathological manifestations. Therefore, although viral shedding was still noted, immunization with the live PRRS vaccine did indeed reduce viral replication and disease severity, suggesting its utility in minimizing outbreaks of HP-PRRS.
Utilizing Various Natural Language Processing Techniques for Biomedical Interaction Extraction

The vast number of biomedical literature is an important source of biomedical interaction information discovery. However, it is complicated to obtain interaction information from them because most of them are not easily readable by machine. In this paper, we present a method for extracting biomedical interaction information assuming that the biomedical Named Entities (NEs) are already identified. The proposed method labels all possible pairs of given biomedical NEs as INTERACTION or NO- INTERACTION by using a Maximum Entropy (ME) classifier. The features used for the classifier are obtained by applying various NLP techniques such as POS tagging, base phrase recognition, parsing and predicate-argument recognition. Especially, specific verb predicates (activate, inhibit, diminish and etc.) and their biomedical NE arguments are very useful features for identifying interactive NE pairs. Based on this, we devised a two- step method: 1) an interaction verb extraction step to find biomedically salient verbs, and 2) an argument relation identification step to generate partial predicate-argument structures between extracted interaction verbs and their NE arguments. In the experiments, we analyzed how much each applied NLP technique improves the performance. The proposed method can be completely improved by more than 2% compared to the baseline method. The use of external contextual features, which are obtained from outside of NEs, is crucial for the performance improvement. We also compare the performance of the proposed method against the co-occurrence-based and the rule-based methods. The result demonstrates that the proposed method considerably improves the performance.
Comparison of the validity of Hill and Huxley muscle–tendon complex models using experimental data obtained from rat m. soleus in situ

ABSTRACT The relationship between mechanical and metabolic behaviour in the widely used Hill muscle–tendon complex (MTC) model is not straightforward, whereas this is an integral part of the Huxley model. In this study, we assessed to what extent Huxley- and Hill-type MTC models yield adequate predictions of mechanical muscle behaviour during stretch–shortening cycles (SSCs). In fully anaesthetized male Wistar rats (N=3), m. soleus was dissected completely free, except for the insertion. Cuff electrodes were placed over the n. ischiadicus. The distal end of the tendon was connected to a servo motor, via a force transducer. The setup allowed for full control over muscle stimulation and length, while force was measured. Quick-release and isovelocity contractions (part 1), and SSCs (part 2) were imposed. Simulations of part 2 were made with both a Hill and a Huxley MTC model, using parameter values determined from part 1. Modifications to the classic two-state Huxley model were made to incorporate series elasticity, activation dynamics, and active and passive force–length relationships. Results were similar for all rats. Fitting of the free parameters to the data of part 1 was near perfect (R2>0.97). During SSCs, predicted peak force and force during relaxation deviated from the experimental data for both models. Overall, both models yielded similarly adequate predictions of the experimental data. We conclude that Huxley and Hill MTC models are equally valid with respect to mechanical behaviour. Summary: Huxley and Hill muscle–tendon-complex models yield similar predictions of rat soleus muscle force, under physiological contraction conditions.
Nutritional Status and Other Baseline Predictors of Mortality among HIV-Infected Children Initiating Antiretroviral Therapy in Tanzania

Background: We assembled a prospective cohort of 3144 children less than 15 years of age initiating antiretroviral therapy (ART) in Dar es Salaam, Tanzania. Methods: The relationships of nutritional status and other baseline characteristics in relation to mortality were examined using Cox proportional hazards model. Results: Compared with children with weight for age (WAZ) > -1, those with WAZ ≤ -2 to < -3 had a nearly double risk of death (relative risk [RR], 1.85; 95% confidence interval [CI], 1.10-3.11), and among those with WAZ ≤ -3, the risk more than tripled (RR, 3.36; 95% CI, 2.12-5.32). Other baseline risk factors for overall mortality included severe anemia (P < .001), severe immune suppression (P = .02), history of tuberculosis (P = .01), opportunistic infections (P < .001), living in the poorest district (P < .001), and advanced World Health Organization stage (P = .003). Conclusions: To sustain the obtained benefit of ART in this setting, interventions to improve nutritional status may be used as an adjunct to ART.
1 2 3 D S 1 2 3 D S 1 2 3 D 4 4 4

In adhoc networks connection failure between source and destination often occurs, due to mobility of nodes. After every failure the connection between source and destination gets disconnected.The problem is while sending data packets from source to destination, there is a possibility of occurring congestion at any node incurring high packet loss and long delay, which cause the performance degradation of a network. This paper presents predictive congestion control routing protocol for wireless Ad-hoc networks called as PCCAODV. Unlike traditional AODV, predictive congestion index of a node as the ratio of current queue occupancy over total queue size at node level. Based on a congestion index, PCCAODV utilizes the upstream nodes and down stream nodes of a congested node and initiates route finding process Bi-directionally to find alternate non congested path between them for transmitting data. Suppose that the process find more non congested multipaths and decides a finest single path for transmitting data. The protocol is implemented and simulated using Ns-2 simulator. Performance comparisons of the proposed PCCAODV protocol against AODV is presented and shown that the proposed algorithm performs well.
Actin filament destruction by osmium tetroxide

We have studied the destruction of purified muscle actin filaments by osmium tetroxide (OsO4) to develop methods to preserve actin filaments during preparation for electron microscopy. Actin filaments are fragmented during exposure to OsO4. This causes the viscosity of solutions of actin filaments to decrease, ultimately to zero, and provides a convenient quantitative assay to analyze the reaction. The rate of filament destruction is determined by the OsO4 concentration, temperature, buffer type and concentration, and pH. Filament destruction is minimized by treatment with a low concentration of OsO4 in sodium phosphate buffer, pH 6.0, at 0 degrees C. Under these conditions, the viscosity of actin filament solutions is stable and actin filaments retain their straight, unbranched structure, even after dehydration and embedding. Under more severe conditions, the straight actin filaments are converted into what look like the microfilament networks commonly observed in cells fixed with OsO4. Destruction of actin filaments can be inhibited by binding tropomyosin to the actin. Cross-linking the actin molecules within a filament with glutaraldehyde does not prevent their destruction by OsO4. The viscosity decrease requires the continued presence of free OsO4. During the time of the viscosity change, OsO4 is reduced and the sulfur-containing amino acids of actin are oxidized, but little of the osmium is bound to the actin. Over a much longer time span, the actin molecules are split into discrete peptides.
Stochastic modelling of muscle recruitment during activity

Muscle forces can be selected from a space of muscle recruitment strategies that produce stable motion and variable muscle and joint forces. However, current optimization methods provide only a single muscle recruitment strategy. We modelled the spectrum of muscle recruitment strategies while walking. The equilibrium equations at the joints, muscle constraints, static optimization solutions and 15-channel electromyography (EMG) recordings for seven walking cycles were taken from earlier studies. The spectrum of muscle forces was calculated using Bayesian statistics and Markov chain Monte Carlo (MCMC) methods, whereas EMG-driven muscle forces were calculated using EMG-driven modelling. We calculated the differences between the spectrum and EMG-driven muscle force for 1–15 input EMGs, and we identified the muscle strategy that best matched the recorded EMG pattern. The best-fit strategy, static optimization solution and EMG-driven force data were compared using correlation analysis. Possible and plausible muscle forces were defined as within physiological boundaries and within EMG boundaries. Possible muscle and joint forces were calculated by constraining the muscle forces between zero and the peak muscle force. Plausible muscle forces were constrained within six selected EMG boundaries. The spectrum to EMG-driven force difference increased from 40 to 108 N for 1–15 EMG inputs. The best-fit muscle strategy better described the EMG-driven pattern (R2 = 0.94; RMSE = 19 N) than the static optimization solution (R2 = 0.38; RMSE = 61 N). Possible forces for 27 of 34 muscles varied between zero and the peak muscle force, inducing a peak hip force of 11.3 body-weights. Plausible muscle forces closely matched the selected EMG patterns; no effect of the EMG constraint was observed on the remaining muscle force ranges. The model can be used to study alternative muscle recruitment strategies in both physiological and pathophysiological neuromotor conditions.
Interactive-rate motion planning for concentric tube robots

Concentric tube robots may enable new, safer minimally invasive surgical procedures by moving along curved paths to reach difficult-to-reach sites in a patient's anatomy. Operating these devices is challenging due to their complex, unintuitive kinematics and the need to avoid sensitive structures in the anatomy. In this paper, we present a motion planning method that computes collision-free motion plans for concentric tube robots at interactive rates. Our method's high speed enables a user to continuously and freely move the robot's tip while the motion planner ensures that the robot's shaft does not collide with any anatomical obstacles. Our approach uses a highly accurate mechanical model of tube interactions, which is important since small movements of the tip position may require large changes in the shape of the device's shaft. Our motion planner achieves its high speed and accuracy by combining offline precomputation of a collision-free roadmap with online position control. We demonstrate our interactive planner in a simulated neurosurgical scenario where a user guides the robot's tip through the environment while the robot automatically avoids collisions with the anatomical obstacles.
Image Recoloring Induced by Palette Color Associations

In this paper we present a non-interactive method for recoloring a destination image according to the color scheme found in a source image. The approach is motivated by trying to invert the working process employed in oil painting, and results are demonstrated by application to several well-known oil paintings. The algorithm uses several color models, but leans most heavily on the Lαβ color space. We first color segment each image bottomup by iteratively merging groups of pixels into connected regions of similar color. During color segmentation, a color “texture” tree is generated and associated to each region. Next, we construct classes of regions by compensating for color duplication and color similarity within the set of averaged color values obtained from regions. We extract a color palette for each image by choosing the colors of canonical region representatives from these classes. Once this palette is constructed for each image, any inverse map from the set of destination palette colors to the set of source palette colors induces a forward map from the classes of regions in the source image to sets of classes of regions in the destination image. For each source class in the range of the inverse map we transfer color from its canonical region representative to each of the associated destination regions. Color transfer occurs at the level of pixels, and uses the color texture trees associated to the regions. Our recoloring method attempts to maintain the destination image’s original value structure. This is accomplished by transferring only the α and β channels from the source. To make our method computationally tractable, we work within an image pyramid, transferring color layer by layer.
A combined backstepping and wavelet neural network control approach for mechanical system

A combined backstepping and wavelet neural network control approach for mechanical system is proposed in this paper. The proposed control approach comprises a neural controller and a robust compensator. The neural controller using a wavelet neural network (WNN) is the main controller based on backstepping method; and the parameters of WNN are on-line tune by adaptation laws from the Lyapunov stability theorem. The robust compensator is designed to dispel the approximation error, so the asymptotic stability of the system can be guaranteed. Finally, a mass-spring-damper system is performed to verify the effectiveness of the proposed control scheme.
Trends in the Epidemiological Aspects and Mortality of Alcoholic Liver Disease in Korea in the Decade Between 2000 and 2009

Background Alcohol consumption and related alcohol liver disease (ALD) have substantially increased in Korea during the last decade. The objective of this study was to evaluate the trends in the epidemiological aspects and mortality rate (MR) of Korea in the decade between 2000 and 2009. Methods The raw data analyzed in this study were obtained from the website of “the ALD” managed by Korea Center for Disease Control and Prevention (KCDC), Korea Public Health Association (KPHA), and statistics website of Statistics Korea. The data analyses were performed using Excel 2007 statistical software (Microsoft Corp., USA). Results The amount of alcohol-consumption-per-capita-per-year (ACCY) in Korea was 8.38 L in 2000 and 8.54 L in 2009. The most taken alcoholic beverage was soju, followed by beer. There were a total of 1,403 case-fatalities (CF) with an MR of 2.98 per 100,000 populations of ALD in 2000, while a total of 3,588 CF with an MR of 7.21 in 2009 (P < 0.01). The CF and MR of ALD in males were significantly higher than those in females (P < 0.01). In over 40-year-old age groups, the CF and MR were significantly increased (P < 0.01). Moreover, occupational classification revealed that the mistress/students/jobless (MSJ) were the most risky group. The comparison of overall CF and MR of ALD by six key classifications (International Classification of Diseases (ICD)) showed that alcoholic cirrhosis (229 CF and 16.3%) in 2000 tended to be increased in 2009 (2,803 CF and 78.1%), while alcoholic fibrosis and sclerosis (607 CF and 43.3%) in 2000 significantly decreased in 2009 (120 CF and 3.3%), respectively. Conclusion ALD is one of the most severe diseases in Korea, as indicated by its high CF and MR in this study. As over-consumption of alcoholic beverages is relatively common in Korea, more efforts should be made toward prevention of ALD by raising awareness of the risk factors of ALD by public health education.
Compiler support for selective page migration in NUMA architectures

Current high-performance multicore processors provide users with a non-uniform memory access model (NUMA). These systems perform better when threads access data on memory banks next to the core where they run. However, ensuring data locality is difficult. In this paper, we propose compiler analyses and code generation methods to support a lightweight runtime system that dynamically migrates memory pages to improve data locality. Our technique combines static and dynamic analyses and is capable of identifying the most promising pages to migrate. Statically, we infer the size of arrays, plus the amount of reuse of each memory access instruction in a program. These estimates rely on a simple, yet accurate, trip count predictor of our own design. This knowledge let's us build templates of dynamic checks, to be filled with values known only at runtime. These checks determine when it is profitable to migrate data closer to the processors where this data is used. Our static analyses are quadratic on the number of variables in a program, and the dynamic checks are O(1) in practice. Our technique does not require any form of user intervention, neither the support of a third-party middleware, nor modifications in the operating system's kernel. We have applied our technique on several parallel algorithms, which are completely oblivious to the asymmetric memory topology, and have observed speedups of up to 4×, compared to static heuristics. We compare our approach against Minas, a middleware that supports NUMA-aware data allocation, and show that we can outperform it by up to 50% in some cases.