Miracle-dz/UniFAR-FTUs huggingface dataset:
A Gaussia Luciferase Cell-Based System to Assess the Infection of Cell Culture- and Serum-Derived Hepatitis C Virus

Robust replication of hepatitis C virus (HCV) in cell culture occurs only with the JFH-1 (genotype 2a) recombinant genome. The aim of this study was to develop a system for HCV infection quantification analysis and apply it for the selection of patient sera that may contain cell culture infectious viruses, particularly of the most clinically important genotype 1. Initially, a hepatoma cell line (designated Huh-7.5/EG(4A/4B)GLuc) was generated that stably expressed the enhanced green fluorescent protein (EGFP) fused in-frame to the secreted Gaussia luciferase via a recognition sequence of the viral NS3/4A protease. Upon HCV infection, NS3/4A cleaved at its signal and the Gaussia was secreted to the culture medium, thus facilitating the infection quantification. The Huh-7.5/EG(4A/4B)GLuc cell line provided a rapid and highly sensitive quantification of HCV infection in cell culture using JFH-1-derived viruses. Furthermore, the Huh-7.5/EG(4A/4B)GLuc cells were also shown to be a suitable host for the discovery of anti-HCV inhibitors by using known compounds that target distinct stages of the HCV life cycle; the Ź-factor of this assay ranged from 0.72 to 0.75. Additionally, eighty-six sera derived from HCV genotype 1b infected liver transplant recipients were screened for their in vitro infection and replication potential. Approximately 12% of the sera contained in vitro replication-competent viruses, as deduced by the Gaussia signal, real time quantitative PCR, immunofluorescence and capsid protein secretion. We conclude that the Huh-7.5/EG(4A/4B)GLuc cell line is an excellent system not only for the screening of in vitro replication-competent serum-derived viruses, but also for the subsequent cloning of recombinant isolates. Additionally, it can be utilized for high-throughput screening of antiviral compounds.
Economic forecasts with Bayesian autoregressive distributed lag model: choosing optimal prior in economic downturn

Bayesian inference requires an analyst to set priors. Setting the right prior is crucial for precise forecasts. This paper analyzes how optimal Litterman prior changes when an economy is hit by a recession. For this task, an autoregressive distributed lag model is chosen. The results show that a sharp economic slowdown changes the optimal prior in two directions. First, it changes the structure of the optimal weight prior by setting smaller weight on the lagged dependent variable compared to variables containing more recent information. Second, greater uncertainty brought by a rapid economic downturn requires more space for coefficient variation which is set by the overall tightness parameter. It is shown that the optimal overall tightness parameter may increase to such an extent that Bayesian ADL becomes equivalent to frequentist ADL.
The Using Artificial Neural Network to Estimate of Chemical Oxygen Demand

Nowadays, the increase of human population every year results in increasing of water usage and demand. Saen Saep canal is important canal in Bangkok. The main objective of this study is using Artificial Neural Network (ANN) model to estimate the Chemical Oxygen Demand (COD) on data from 11 sampling sites. The data is obtained from the Department of Drainage and Sewerage, Bangkok Metropolitan Administration, during 2007-2011. The twelve parameters of water quality are used as the input of the models. These water quality indices affect the COD. The experimental results indicate that the ANN model provides a high correlation coefficient (R=0.89). Keywords—Artificial neural network, chemical oxygen demand, estimate, surface water.
Periostin Responds to Mechanical Stress and Tension by Activating the MTOR Signaling Pathway

Current knowledge about Periostin biology has expanded from its recognized functions in embryogenesis and bone metabolism to its roles in tissue repair and remodeling and its clinical implications in cancer. Emerging evidence suggests that Periostin plays a critical role in the mechanism of wound healing; however, the paracrine effect of Periostin in epithelial cell biology is still poorly understood. We found that epithelial cells are capable of producing endogenous Periostin that, unlike mesenchymal cell, cannot be secreted. Epithelial cells responded to Periostin paracrine stimuli by enhancing cellular migration and proliferation and by activating the mTOR signaling pathway. Interestingly, biomechanical stimulation of epithelial cells, which simulates tension forces that occur during initial steps of tissue healing, induced Periostin production and mTOR activation. The molecular association of Periostin and mTOR signaling was further dissected by administering rapamycin, a selective pharmacological inhibitor of mTOR, and by disruption of Raptor and Rictor scaffold proteins implicated in the regulation of mTORC1 and mTORC2 complex assembly. Both strategies resulted in ablation of Periostin-induced mitogenic and migratory activity. These results indicate that Periostin-induced epithelial migration and proliferation requires mTOR signaling. Collectively, our findings identify Periostin as a mechanical stress responsive molecule that is primarily secreted by fibroblasts during wound healing and expressed endogenously in epithelial cells resulting in the control of cellular physiology through a mechanism mediated by the mTOR signaling cascade.
Resolving It, This, and That in Unrestricted Multi-Party Dialog

We present an implemented system for the resolution of it, this, and that in transcribed multi-party dialog. The system handles NP-anaphoric as well as discoursedeictic anaphors, i.e. pronouns with VP antecedents. Selectional preferences for NP or VP antecedents are determined on the basis of corpus counts. Our results show that the system performs significantly better than a recency-based baseline.
Autonomous Agents as Competent Assistants : Better Interpretation of Pen Gestures

Interaction between users and synthetic hardware systems have provided opportunities to utilise an important sensing modality through the use of a digital pen (stylus). Ambient learning environments insist on recognising and reacting to users’ input sketches and gestures for expediting the responses needed to improve user-interface (UI) supports for more natural communications. This paper focuses on the techniques and methodologies used in ciphering information obtained from digital ink compositions that gave way to the conceptions of elaborate and intelligent programs. We present our classification of sketch-objects for identification purposes while maintaining their native attributes, and discuss our approaches for interpreting them as valid intended gestures through autonomous agents.
Group Therapy: Essential Component for Success with Sexually Acting Out Problems among Men

Sexual acting out behavior has become a major issue in the United States, with more mental health care professionals seeking assistance in providing effective treatment for this complex and interesting population. Reviews of the literature support the fact that specialized treatments often can be effective (Schwartz, 1995); however, without targeted interventions, recidivistic behaviors can be very high. Innovative approaches are all too uncommon. Many suggest group therapy is an essential, as well as cost-effective, component of a comprehensive treatment program (Schwartz, 1995; Freeman-Longo & Blanchard, 1998). In this article, a model for group therapy for men with a range of sexually acting out problems is presented. This semi-structured group therapy model combines psychodynamic cognitive-behavioral theoretical perspectives in a 16-week module in which structured exercises and group process-oriented interventions are employed. In this article we discuss group format, content, and process in an effort to elucidate the specific challenges and common issues of this population.
The sound-object: A hypothesis about prenatal auditory experience and memory

Abstract The exploration of the area of possible prenatal experience suggests that the sound of the mother's voice, alternating with silence, may give the child a proto-experience of both presence and absence. This experience may, on the one hand, give rise to primitive defensive reactions and, on the other, become the basis for the constitution of a prenatal proto-object with sound qualities called tentatively ‘sound-object’. The hypothesis is made that this object could be connected with the preconception of the breast, and could also be considered as a precursor of the postnatal maternal inner object. Two dreams of adults and clinical material of a child patient are examined with special attention to sound aspects and their possible connection with prenatal experiences. The importance of integrating sound aspects, especially in analytic work with borderline and psychotic patients, is discussed.
Are Two Report Cards Better than One? The Case of CABG Surgery and Patient Sorting

Public reporting of information regarding quality may encourage sellers to improve product quality. In this paper, I study how quality disclosure affect health care providers’ behavior. In particular, I examine the impact of mortality report cards on the degree of within-hospital sorting using hospital discharge data on coronary artery bypass graft (CABG) surgery in New York State from 1986 to 1993. Hospital report cards may encourage surgeons to allocate patients in more efficient ways to boost hospital scores. However, surgeon report cards may provide incentives for surgeons to avoid risky patients. I find that the level of within-hospital sorting increased immediately following the publication of hospital report cards but fell after the publication of surgeon report cards for hospitals in Manhattan, but not hospitals elsewhere. This phenomenon may have been driven by the intense competition faced by hospitals and surgeons in Manhattan. ∗Paul Merage School of Business, University of California, Irvine. yang.zhang@uci.edu. I am indebted to David Dranove for his continuous guidance and support. I am also grateful to Bernard Black, Leemore Dafny, and Craig Garthwaite for their advice. I would like to thank Jennifer Brown, Cory Capps, Kitt Carpenter, Steven Farmer, Jie Gong, Mark Satterthwaite, Todd Sarver, Tuan-Hwee Sng, and Bruce Spencer for valuable discussions. Conversations with Robert Bonow, Angelo Costas, and Steven Farmer vastly improved my understanding of medical and institutional background information. Chieko Maene provided generous GIS support. This work has also benefited from the comments of seminar participants at Kellogg School of Management, Institute for Policy Research at Northwestern University, Department of Economics at National University of Singapore, Bates White, Paul Merage School of Business at University of California, Irvine, Acumen LLC. , and Cornerstone Research. All errors are mine.
Eigenvalue correction results in face recognition

Eigenvalues of sample covariance matrices are often used in biometrics. It has been known for several decades that even though the sample covariance matrix is an unbiased estimate of the real covariance matrix [Fukunaga,1990], the eigenvalues of the sample covariance matrix are biased estimates of the real eigenvalues [Silverstein,1986]. This bias is particularly dominant when the number of samples used for estimation is in the same order as the number of dimensions, as is often the case in biometrics. We investigate the effects of this bias on error rates in verification experiments and show that eigenvalue correction can improve recognition performance.
A game theoretic scheme for relay service in heterogeneous content centric networks

To cope with the rapidly expanding network scale and population, the heterogeneous content centric networks (HCCNs) have emerged, where the naming content can be shared among different sub-networks by using interest packets. However, In the HCCNs, as these sub-networks are managed by different operators and some sub-network may exhibit selfish behaviors due to the limited resource, how to design a cooperative scheme for relay service to deliver naming content becomes a new challenge. Therefore, this paper proposes a bargaining game based cooperative scheme for relay service in HCCNs. Specifically, at first we present an incentive framework that each sub-network can obtain currency by providing other subnetworks with relay service. Then, by using a cooperative node as an agent, a sub-network can select an optimal adjacent subnetwork to obtain content. Next, a bargaining game is introduced to model the interaction between two sub-networks, which leads to a Subgame perfect Nash equilibrium as the agreement of two players to maximize their benefits. Finally, simulation experiments prove that the proposed scheme can outperform other conventional methods to reduce the delay and overhead.
Fracture risk in patients with monoclonal gammopathy of undetermined significance

Little information is available on the risk of fractures in patients with monoclonal gammopathy of undetermined significance (MGUS). We identified 1535 patients with MGUS between 1978 and 2003 in North Jutland County, Denmark. The population control group consisted of 15 350 persons selected from the Danish Central Population Registry, matched by age and sex. Data on fractures in the two groups were obtained from the regional Hospital Discharge Registry. In the MGUS cohort, 187 first‐time fractures were identified during 9754 person‐years of follow‐up, corresponding to an incidence rate of 19/1000 person‐years. The adjusted relative risk for fractures among MGUS patients compared with population controls was 1·4 [95% confidence interval (CI), 1·2–1·6]. After 5 years of follow‐up, the risk difference was 1·8% (95% CI, 0·5–3·0). Six of the 187 MGUS patients with fractures were later diagnosed with malignant transformation. Relative risks for fractures were increased in IgG‐type MGUS [1·3 (95% CI,1·1–1·6)], IgM‐type MGUS [1·6 (95% CI, 1·1–2·2)] and MGUS with kappa light chain [1·4 (95% CI, 1·1–1·7)]. MGUS patients had an increased risk of fractures, which could not be explained by comorbidity, advanced age, gender or malignant transformation.
The Chemoprevention of Chronic Degenerative Disease Through Dietary Antioxidants: Progress, Promise and Evidences

In countries such as Australia, Austria, Belgium, Canada, Denmark, Finland, France, Ger‐ many, Greece, Ireland, Italy, Japan, Luxembourg, Netherlands, New Zealand, Norway, Portugal, Spain, Sweden, Switzerland, the United Kingdom, and the United States, incor‐ porated to the OECD (Organization for Economic Cooperation and Development), mortal‐ ity due to those diseases has diminished up to 38% in people between 35 and 69 years old. Likewise, the risk of mortality before age 70 has diminished up to the 23%. Those re‐ ductions have been the result of social changes and of the improvement of preventive methods of infectious diseases. However, in recent years the prevalence of chronic degen‐ erative diseases has increased [1].
Biotechnologically Relevant Enzymes and Proteins

Biochemical and functional characterizations of tyrosine phosphatases from pathogenic and nonpathogenic mycobacteria: as tyrosine phosphatase inhibitors Abstract Tyrosine phosphorylation is one of the most common means of posttranslational modifications which can generate novel recognition motifs for protein interactions and thereafter affecting cellular localization, protein stability, and enzyme activity. Mycobacterium tuberculosis (Mtb) possesses a wide range of signal transduction systems, including two protein tyrosine phosphatases (PtpA and PtpB). Since functional diversities between protein tyrosine phosphatases (PTPases) are illustrated by regulatory domains and subunits, we have characterized the nature of tyrosine phosphatases from slow-grower pathogenic species Mtb and from fast-grower nonpathogenic species Mycobacterium smegmatis (MS). The findings delineate that the enzymes present in MS have significantly lesser phosphatase activity than PTPases of Mtb as evidenced by low K cat /K m of recombinantly expressed proteins. The K cat /K m for Mtb PtpA was 500–1000-fold higher than MS PTPases. We have designed and synthesized phenyl cyclopropyl methyl-/phenyl butenyl azoles which inhibit growth of mycobacteria, in culture and in macrophages. The mechanism of efficacy of these compounds against mycobacteria was identified and suggested that the inhibition may possibly be mediated via the targeting of Mtb tyrosine phosphatase. The results further added that these compounds exclusively inhibit PtpA of Mtb.
Lynx1 Limits Dendritic Spine Turnover in the Adult Visual Cortex

Dendritic spine turnover becomes limited in the adult cerebral cortex. Identification of specific aspects of spine dynamics that can be unmasked in adulthood and its regulatory molecular mechanisms could provide novel therapeutic targets for inducing plasticity at both the functional and structural levels for robust recovery from brain disorders and injuries in adults. Lynx1, an endogenous inhibitor of nicotinic acetylcholine receptors, was previously shown to increase its expression in adulthood and thus to limit functional ocular dominance plasticity in adult primary visual cortex (V1). However, the role of this “brake” on spine dynamics is not known. We examined the contribution of Lynx1 on dendritic spine turnover before and after monocular deprivation (MD) in adult V1 with chronic in vivo imaging using two-photon microscopy and determined the spine turnover rate of apical dendrites of layer 5 (L5) and L2/3 pyramidal neurons in adult V1 of Lynx1 knock-out (KO) mice. We found that the deletion of Lynx1 doubled the baseline spine turnover rate, suggesting that the spine dynamics in the adult cortex is actively limited by the presence of Lynx1. After MD, adult Lynx1-KO mice selectively exhibit higher rate of spine loss with no difference in gain rate in L5 neurons compared with control wild-type counterparts, revealing a key signature of spine dynamics associated with robust functional plasticity in adult V1. Overall, Lynx1 could be a promising therapeutic target to induce not only functional, but also structural plasticity at the level of spine dynamics in the adult brain. SIGNIFICANCE STATEMENT Dendritic spine turnover becomes limited in the adult cortex. In mouse visual cortex, a premier model of experience-dependent plasticity, we found that the deletion of Lynx1, a nicotinic “brake” for functional plasticity, doubled the baseline spine turnover in adulthood, suggesting that the spine dynamics in the adult cortex is actively limited by Lynx1. After visual deprivation, spine loss, but not gain rate, remains higher in adult Lynx1 knock-out mice than in control wild-type mice, revealing a key signature of spine dynamics associated with robust functional plasticity. Lynx1 would be a promising target to induce not only functional, but also structural plasticity at the level of spine dynamics in adulthood.
A simple, doubly robust, efficient estimator for survival functions using pseudo observations

Survival functions are often estimated by nonparametric estimators such as the Kaplan‐Meier estimator. For valid estimation, proper adjustment for confounding factors is needed when treatment assignment may depend on confounding factors. Inverse probability weighting is a commonly used approach, especially when there is a large number of potential confounders to adjust for. Direct adjustment may also be used if the relationship between the time‐to‐event and all confounders can be modeled. However, either approach requires a correctly specified model for the relationship between confounders and treatment allocation or between confounders and the time‐to‐event. We propose a pseudo‐observation–based doubly robust estimator, which is valid when either the treatment allocation model or the time‐to‐event model is correctly specified and is generally more efficient than the inverse probability weighting approach. The approach can be easily implemented using standard software. A simulation study was conducted to evaluate this approach under a number of scenarios, and the results are presented and discussed. The results confirm robustness and efficiency of the proposed approach. A real data example is also provided for illustration.
CMAC: An Energy Efficient MAC Layer Protocol Using Convergent Packet Forwarding for Wireless Sensor Networks

Low duty cycle operation is critical to conserve energy in wireless sensor networks. Traditional wake-up scheduling approaches either require periodic synchronization messages or incur high packet delivery latency due to the lack of any synchronization. In this paper, we present the design of a new low duty-cycle MAC layer protocol called Convergent MAC (CMAC). CMAC avoids synchronization overhead while supporting low latency. By using zero communication when there is no traffic, CMAC allows operation at very low duty cycles. When carrying traffic, CMAC first uses any cast to wake up forwarding nodes, and then converges from route-suboptimal any cast with unsynchronized duty cycling to route-optimal unicast with synchronized scheduling. To validate our design and provide a usable module for the community, we implement CMAC in TinyOS and evaluate it on the Kansei testbed consisting of 105 XSM nodes. The results show that CMAC at 1% duty cycle significantly outperforms BMAC at 1% in terms of latency, throughput and energy efficiency. We also compare CMAC with other protocols using simulations. The results show for 1% duty cycle, CMAC exhibits similar throughput and latency as CSMA/CA using much less energy, and outperforms SMAC and GeRaF in all aspects.
The School Short-Form Coopersmith Self-Esteem Inventory: Revised and Improved

The school short form of the Coopersmith Self-Esteem Inv entory is a widely used measure of children’s global self-esteem. Unlike the full-length scale, howev er, it has been generally understood that the short form does not allow differentiation between the major indiv idual sources of self-esteem. The present study has examined the internal structure of the school short form by exploratory and confirmatory analysis on data prov ided by 3,056 adolescents between the ages of 13 and 15 years and has demonstrated that after the remov al of 6 redundant items, the newly rev ised scale not only possesses improv ed psychometric properties but also contains three clear factors that correspond to personal self-esteem and self-esteem deriv ed from parents and peers, respectiv ely. The presentation of a rev ised v ersion of the school short form of the Coopersmith Self-Esteem Inv entory that is psychometrically robust and demonstrates three clear subscales will allow clearer distinctions to be made among the sources of children’s self-esteem in future studies. La v ersion abrégée, pour le milieu scolaire, de l’Inv entaire d’estime de soi de Coopersmith est grandement utilisée pour mesurer l’estime de soi globale chez les jeunes. On croit généralement que cette v ersion ne permet pas de différencier entre les principales sources d’estime de soi, contrairement à ce qu’on obtient de la v ersion complète. La présente étude porte sur l’examen de la structure de la v ersion abrégée, au moyen d’analyses exploratoires et confirmatoires sur des données prov enant de 3 056 adolescents, âgés de 13 à 15 ans. Or, il appert que la nouv elle échelle rév isée, si on enlèv e six questions redondantes, possède non seulement de meilleures propriétés psychométriques, mais comporte trois facteurs distincts qui correspondent à l’estime de soi dériv ée du soi, des parents et des pairs, dans l’ordre. C’est donc dire qu’une v ersion rév isée de l’Inv entaire d’estime de soi de Coopersmith pour le milieu scolaire, qui comprend des propriétés psychométriques robustes et dégage aussi trois souséchelles claires, permettra de distinguer, à l’av enir, les sources d’estime de soi chez les jeunes.