Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic Analysis of Pathogenic and Attenuated Alcelaphine Herpesvirus 1

ABSTRACT The gammaherpesvirus alcelaphine herpesvirus 1 (AlHV-1) causes malignant catarrhal fever in susceptible ungulates but infects its natural host, wildebeest, without obvious clinical signs. In tissue culture, AlHV-1 is initially predominantly cell associated and virulent but on extended culture becomes cell-free and attenuated. We wanted to determine what changes in protein composition had taken place during the transition from virulent to attenuated virus in culture. Purified virus preparations were fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and proteins were analyzed by liquid chromatography-electrospray ionization-tandem mass spectrometry. Peptides were identified in serial gel slices by using MASCOT software to interrogate virus-specific and nonredundant sequence databases. Twenty-three AlHV-1-encoded proteins and six cellular proteins were identified in the attenuated and virulent viruses. Two polypeptides were detected in only the virulent virus preparations, while one other protein was found in only the attenuated virus. Two of these virus-specific proteins were identified by a single peptide, suggesting that these may be low-abundance virion proteins rather than markers of attenuation or pathogenesis. The results suggest that attenuation of AlHV-1 is not the result of gross changes in the composition of the virus particle but probably due to altered viral gene expression in the infected cell.
Distraction during learning with hypermedia: difficult tasks help to keep task goals on track

In educational hypermedia environments, students are often confronted with potential sources of distraction arising from additional information that, albeit interesting, is unrelated to their current task goal. The paper investigates the conditions under which distraction occurs and hampers performance. Based on theories of volitional action control it was hypothesized that interesting information, especially if related to a pending goal, would interfere with task performance only when working on easy, but not on difficult tasks. In Experiment 1, 66 students learned about probability theory using worked examples and solved corresponding test problems, whose task difficulty was manipulated. As a second factor, the presence of interesting information unrelated to the primary task was varied. Results showed that students solved more easy than difficult probability problems correctly. However, the presence of interesting, but task-irrelevant information did not interfere with performance. In Experiment 2, 68 students again engaged in example-based learning and problem solving in the presence of task-irrelevant information. Problem-solving difficulty was varied as a first factor. Additionally, the presence of a pending goal related to the task-irrelevant information was manipulated. As expected, problem-solving performance declined when a pending goal was present during working on easy problems, whereas no interference was observed for difficult problems. Moreover, the presence of a pending goal reduced the time on task-relevant information and increased the time on task-irrelevant information while working on easy tasks. However, as revealed by mediation analyses these changes in overt information processing behavior did not explain the decline in problem-solving performance. As an alternative explanation it is suggested that goal conflicts resulting from pending goals claim cognitive resources, which are then no longer available for learning and problem solving.
Numerical analysis of the axially loaded concrete filled steel tube columns with debonding separation at the steel-concrete interface

The interaction between steel tube and concrete core is the key design considerations for concrete-filled steel tube columns. In a concrete-filled steel tube (CFST) column, the steel tube provides confinement to the concrete core which permits the composite action among the steel tube and the concrete. Due to construction faults and plastic shrinkage of concrete, the debonding separation at the steel-concrete interface weakens the confinement effect, and hence affects the behaviour and bearing capacity of the composite member. This study investigates the axial loading behavior of the concrete filled circular steel tube columns with debonding separation. A three-dimensional nonlinear finite element model of CFST composite columns with introduced debonding gap was developed. The results from the finite element analysis captured successfully the experimental behaviours. The calibrated finite element models were then utilized to assess the influence of concrete strength, steel yield stress and the steel-concrete ratio on the debonding behaviour. The findings indicate a likely significant drop in the load carrying capacity with the increase of the size of the debonding gap. A design formula is proposed to reduce the load carrying capacity with the presence of debonding separation.
On Efficient Retiming of Fixed-Point Circuits

Retiming of digital circuits is conventionally based on the estimates of propagation delays across different paths in the data-flow graphs (DFGs) obtained by discrete component timing model, which implicitly assumes that operation of a node can begin only after the completion of the operation(s) of its preceding node(s) to obey the data dependence requirement. Such a discrete component timing model very often gives much higher estimates of the propagation delays than the actuals particularly when the computations in the DFG nodes correspond to fixed-point arithmetic operations like additions and multiplications. On the other hand, very often it is imperative to deal with the DFGs of such higher granularity at the architecture-level abstraction of digital system design for mapping an algorithm to the desired architecture, where the overestimation of propagation delay leads to unwanted pipelining and undesirable increase in pipeline overheads. In this paper, we propose the connected component timing model to obtain adequately precise estimates of propagation delays across different combinational paths in a DFG easily, for efficient cutset-retiming in order to reduce the critical path substantially without significant increase in register-complexity and latency. Apart from that, we propose novel node-splitting and node-merging techniques that can be used in combination with the existing retiming methods to achieve reduction of critical path to a fraction that of the original DFG with a small increase in overall register complexity.
Residue 41 of the Eurasian Avian-Like Swine Influenza A Virus Matrix Protein Modulates Virion Filament Length and Efficiency of Contact Transmission

ABSTRACT Position 41 of the influenza A virus matrix protein encodes a highly conserved alanine in human and avian lineages. Nonetheless, strains of the Eurasian avian-like swine (Easw) lineage contain a change at this position: position 41 of A/swine/Spain/53207/04 (H1N1) (SPN04) encodes a proline. To assess the impact of this naturally occurring polymorphism on viral fitness, we utilized reverse genetics to produce recombinant viruses encoding wild-type M1 41P (rSPN04-P) and consensus 41A (rSPN04-A) residues. Relative to rSPN04-A, rSPN04-P virus displayed reduced growth in vitro. In the guinea pig model, rSPN04-P was transmitted to fewer contact animals than rSPN04-A and failed to infect guinea pigs that received a low-dose inoculum. Moreover, the P41A change altered virion morphology, reducing the number and length of filamentous virions, as well as reducing the neuraminidase activity of virions. The lab-adapted human isolate, A/PR/8/34 (H1N1) (PR8), is nontransmissible in the guinea pig model, making it a useful background in which to identify certain viral factors that enhance transmissibility. We assessed transmission in the context of single-, double-, and triple-reassortant viruses between PR8 and SPN04; PR8/SPN04 M, PR8/SPN04 M+NA, and PR8/SPN04 M+NA+HA, encoding either matrix 41 A or P, were generated. In each case, the virus possessing 41P transmitted less well than the corresponding 41A-encoding virus. In summary, we have identified a naturally occurring mutation in the influenza A virus matrix protein that impacts transmission efficiency and can alter virion morphology and neuraminidase activity. IMPORTANCE We have developed a practical model for examining the genetics underlying transmissibility of the Eurasian avian-like swine lineage viruses, which contributed M and NA segments to the 2009 pandemic strain. Here, we use our system to investigate the impact on viral fitness of a naturally occurring polymorphism at matrix (M1) position 41 in an Easw isolate. Position 41 has been implicated previously in adaptation to laboratory substrates and to mice. Here we show that the polymorphism at M1 41 has a limited effect on growth in vitro but changes the morphology of the virus and impacts growth and transmission in the guinea pig model.
Mechanism of recruitment of DnaB helicase to the replication origin of the plasmid pSC101.

Although many bacterial chromosomes require only one replication initiator protein, e.g., DnaA, most plasmid replicons depend on dual initiators: host-encoded DnaA and plasmid-encoded Rep initiator protein for replication initiation. Using the plasmid pSC101 as a model system, this work investigates the biological rationale for the requirement for dual initiators and shows that the plasmid-encoded RepA specifically interacts with the replicative helicase DnaB. Mutations in DnaB or RepA that disrupt RepA-DnaB interaction cause failure to load DnaB to the plasmid ori in vitro and to replicate the plasmid in vivo. Although, interaction of DnaA with DnaB could not substitute for RepA-DnaB interaction for helicase loading, DnaA along with integration host factor, DnaC, and RepA was essential for helicase loading. Therefore, DnaA is indirectly needed for helicase loading. Instead of a common surface of interaction with initiator proteins, interestingly, DnaB helicase appears to have at least a limited number of nonoverlapping surfaces, each of which interacts specifically with a different initiator protein.
Design recommendations to support automated explanation and tutoring

The after-action review is an essential component of military training exercises. The use of constructive simulations for training poses a challenge when conducting such reviews, because behavior models are typically designed to simulate satisfactorially, without explicit concern for the interrogation of synthetic entities afterward. Ideally, users could obtain knowledge about not only the choices made by a simulator’s behavior models, but also the rationale for those choices. This requires a rich representation of behavioral knowledge within the software system. We have integrated our explainable AI system with behavior models and log information from two simulation systems. Selecting examples from these simulators, we identify areas for improvement to facilitate the automation of explanation and tutoring.
Pubertal Development, Emotion Regulatory Styles, and the Emergence of Sex Differences in Internalizing Disorders and Symptoms in Adolescence

Adolescence marks the emergence of sex differences in internalizing symptoms and disorders, with girls at increased risk for depression and anxiety during the pubertal transition. However, the mechanisms through which puberty confers risk for internalizing psychopathology for girls, but not boys, remain unclear. We examined two pubertal indicators (pubertal status and timing) as predictors of the development of emotion regulation styles (rumination and emotional clarity) and depressive and anxiety symptoms and disorders in a three-wave study of 314 adolescents. Path analyses indicated that early pubertal timing, but not pubertal status, predicted increased rumination, but not decreased emotional clarity, in adolescent girls, but not boys. Additionally, rumination mediated the association between early pubertal timing and increased depressive, but not anxiety, symptoms and disorder onset among adolescent girls. These findings suggest that the sex difference in depression may result partly from early maturing girls’ greater tendency to develop ruminative styles than boys.
DDOS Attack Detection Based on an Ensemble of Neural Classifier

This Paper Reviews the Detection of DDoS Attck.This DDoS attacks could be detected using the existing machine learning techniques such as neural classifiers. These classifiers lack generalization capabilities which result in less performance leading to high false positives. This paper evaluates the performance of a comprehensive set of machine learning algorithms for selecting the base classifier using the publicly available KDD Cup dataset. Based on the outcome of the experiments, Resilient Back Propagation (RBP) was chosen as base classifier for our research. The improvement in performance of the RBP classifier is the focus of this paper. Our proposed classification algorithm, RBPBoost, is achieved by combining ensemble of classifier outputs and Neyman Pearson cost minimization strategy, for final classification decision. Publicly available datasets such as KDD Cup, DARPA 1999, DARPA 2000, and CONFICKER were used for the simulation experiments. RBPBoost was trained and tested with DARPA, CONFICKER, and our own lab datasets. Detection accuracy and Cost per sample were the two metrics evaluated to analyze the performance of the RBPBoost classification algorithm. From the simulation results, it is evident that RBPBoost algorithm achieves high detection accuracy (99.4%) with fewer false alarms and outperforms the existing ensemble algorithms. RBPBoost algorithm outperforms the existing algorithms with maximum gain of 6.6% and minimum gain of 0.8%
Study on the Performance of the “Pendulor” Wave Energy Converter in an Array Configuration

For over three decades the “Pendulor” wave energy device has had a significant influence in this field, triggering several research endeavours. It includes a top-hinged flap propelled by the standing waves produced in a caisson with a back wall on the leeward side. However, one of the main disadvantages which impedes its progress is the enormous expense involved in the construction of the custom made typical caisson structure, about a little more than one-quarter of the wave length. In this study, the influence of such design parameters on the performance of the device is investigated, via numerical modelling for a device arranged in an array configuration, for irregular waves. The potential wave theory is applied to derive the frequency-dependent hydrodynamic parameters by making a distinction in the fluid domain into a separate sea side and lee side. The Cummins equation was utilised for the development of the time domain equation of motion while the transfer function estimation methods were used to solve the convolution integrals. Finally, the device was tested numerically for irregular wave conditions for a 50 kW class unit. It was observed that in irregular wave operating conditions, the caisson chamber length could be reduced by 40% of the value estimated for the regular waves. Besides, the device demonstrated around 80% capture efficiency for irregular waves thus allowing provision for avoiding the employment of any active control.
Approximate Policy Iteration Schemes: A Comparison

We consider the infinite-horizon discounted optimal control problem formalized by Markov Decision Processes. We focus on several approximate variations of the Policy Iteration algorithm: Approximate Policy Iteration (API) (Bertsekas & Tsitsiklis, 1996), Conservative Policy Iteration (CPI) (Kakade & Langford, 2002), a natural adaptation of the Policy Search by Dynamic Programming algorithm (Bagnell et al., 2003) to the infinite-horizon case (PSDP∞), and the recently proposed Non-Stationary Policy Iteration (NSPI(m)) (Scherrer & Lesner, 2012). For all algorithms, we describe performance bounds with respect the per-iteration error e, and make a comparison by paying a particular attention to the concentrability constants involved, the number of iterations and the memory required. Our analysis highlights the following points: 1) The performance guarantee of CPI can be arbitrarily better than that of API, but this comes at the cost of a relative--exponential in 1/e increase of the number of iterations. 2) PSDP1 enjoys the best of both worlds: its performance guarantee is similar to that of CPI, but within a number of iterations similar to that of API. 3) Contrary to API that requires a constant memory, the memory needed by CPI and PSDP∞ is proportional to their number of iterations, which may be problematic when the discount factor γ is close to 1 or the approximation error e is close to 0; we show that the NSPI(m) algorithm allows to make an overall trade-off between memory and performance. Simulations with these schemes confirm our analysis.
ImgWordle: image and text visualization for events in microblogging services

With the wide usage of microblogging services, microposts grow at high rate and provide a rich source of information related to important social events and trends. However, analyzing microposts is challenging due to its high complexity and large volume. In this paper, we present ImgWordle, an interactive visualization prototype to help people perceive and analyze the image and text information in microblogging services. The prototype extends tag cloud by involving images as well as words, and provides multiple coordinated views for a given event, including keywords of various topics, representative images, geographic sentiments and amounts of microposts, and popular microposts over time. We implement ImgWordle on Sina Weibo, the most popular microblogging service in China, and illustrate the usefulness of this visual interface.
Analysis of Interactive Intonation in Unaccompanied SATB Ensembles

Unaccompanied ensemble singing is common in many musical cultures, yet it requires great skill for singers to listen to each other and adjust their pitch to stay in tune. The aim of this research is to investigate interaction in four-part (SATB) singing from the point of view of pitch accuracy (intonation). In particular we compare intonation accuracy of individual singers and collaborative ensembles. 20 participants (five groups of four) sang two pieces of music in three different listening conditions: solo, with one vocal part missing and with all vocal parts. After semi-automatic pitch extraction and manual correction, we annotated the recordings and calculated the pitch error, melodic interval error, harmonic interval error and note stability. We observed significant differences between individual and interactional intonation, more specifically: 1) Singing without the bass part has less mean absolute pitch error than singing with all vocal parts; 2) Mean absolute melodic interval error increases when participants can hear the other parts; 3) Mean absolute harmonic interval error is higher in the one-way interaction condition than the two-way interaction condition; and 4) Singers produce more stable notes when singing solo than with their partners.
The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes

Recent genome-wide association studies (GWAS) have identified a number of novel genetic associations with complex human diseases. In spite of these successes, results from GWAS generally explain only a small proportion of disease heritability, an observation termed the ‘missing heritability problem’. Several sources for the missing heritability have been proposed, including the contribution of many common variants with small individual effect sizes, which cannot be reliably found using the standard GWAS approach. The goal of our study was to explore a complimentary approach, which combines GWAS results with functional data in order to identify novel genetic associations with small effect sizes. To do so, we conducted a GWAS for lymphocyte count, a physiologic quantitative trait associated with asthma, in 462 Hutterites. In parallel, we performed a genome-wide gene expression study in lymphoblastoid cell lines from 96 Hutterites. We found significant support for genetic associations using the GWAS data when we considered variants near the 193 genes whose expression levels across individuals were most correlated with lymphocyte counts. Interestingly, these variants are also enriched with signatures of an association with asthma susceptibility, an observation we were able to replicate. The associated loci include genes previously implicated in asthma susceptibility as well as novel candidate genes enriched for functions related to T cell receptor signaling and adenosine triphosphate synthesis. Our results, therefore, establish a new set of asthma susceptibility candidate genes. More generally, our observations support the notion that many loci of small effects influence variation in lymphocyte count and asthma susceptibility.
Cooling-Sensitive TRPM8 Is Thermostat of Skin Temperature against Cooling

We have shown that cutaneous cooling-sensitive receptors can work as thermostats of skin temperature against cooling. However, molecule of the thermostat is not known. Here, we studied whether cooling-sensitive TRPM8 channels act as thermostats. TRPM8 in HEK293 cells generated output (y) when temperature (T) was below threshold of 28.4°C. Output (y) is given by two equations: At T >28.4°C, y = 0; At T <28.4°C, y = -k(T – 28.4°C). These equations show that TRPM8 is directional comparator to elicits output (y) depending on negative value of thermal difference (ΔT = T – 28.4°C). If negative ΔT-dependent output of TRPM8 in the skin induces responses to warm the skin for minimizing ΔT recursively, TRPM8 acts as thermostats against cooling. With TRPM8-deficient mice, we explored whether TRPM8 induces responses to warm the skin against cooling. In behavioral regulation, when room temperature was 10°C, TRPM8 induced behavior to move to heated floor (35°C) for warming the sole skin. In autonomic regulation, TRPM8 induced activities of thermogenic brown adipose tissue (BAT) against cooling. When menthol was applied to the whole trunk skin at neutral room temperature (27°C), TRPM8 induced a rise in core temperature, which warmed the trunk skin slightly. In contrast, when room was cooled from 27 to 10°C, TRPM8 induced a small rise in core temperature, but skin temperature was severely reduced in both TRPM8-deficient and wild-type mice by a large heat leak to the surroundings. This shows that TRPM8-driven endothermic system is less effective for maintenance of skin temperature against cooling. In conclusion, we found that TRPM8 is molecule of thermostat of skin temperature against cooling.
Jointed Pricing Decision of Brick-and-Click Retailers under Uncertain Demand

This paper studies on jointed pricing decision of Brick-and-Click Retailers under uncertain demand, based on the two-item newsvendor model. Firstly, the two-item newsvendor model is built based on profit maximization. Then, the concavity of objective function is proved and the solving method is given. Moreover, the solutions of the model and the influence of demand transfer coefficient to pricing, productivity and profit are analyzed numerically. The results show that the traditional retail channels pricing and productivity will decrease while e-commerce channels pricing and productivity and retailer profits will grow with the increase of demand transfer coefficient.