Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporo-Spatial Model Construction Using the MML and Software Framework

Development of complex temporo-spatial biological computational models can be a time consuming and arduous task. These models may contain hundreds of differential equations as well as realistic geometries that may require considerable investment in time to ensure that all model components are correctly implemented and error free. To tackle this problem, the Modeling Markup Languages (MML) and software framework is a modular XML/HDF5-based specification and toolkits that aims to simplify this process. The main goal of this framework is to encourage reusability, sharing and storage. To achieve this, the MML framework utilizes the CellML specification and repository, which comprises an extensive range of curated models available for use. The MML framework is an open-source project available at http://mml.gsbme. unsw.edu. au.
Rethinking roles, relationships and voices in studies of undergraduate student writers

Undergraduate students have a complex and often problematic history of representation in research on writing pedagogy. They have been described as novices and outsiders, while having minimal input into how they are studied and represented. In this piece, I share my efforts to rethink the roles and relationships among researchers and student participants, and particularly to rethink how students contribute to pedagogical research. In my recent experience working with six, undergraduate, student co-researchers, I found myself complicating not only the roles of students as research participants but also my own role as researcher, a role that became increasingly hard to extricate from those of teacher, colleague, advocate and friend. Such complications, I argue, are actually strengths and sources of especially rich data, for strong interpersonal connections lead to increased trust and engagement. Trusting, engaged students contribute information and examples that a researcher may not think to ask for. By blurring researcher and participant roles and foregrounding student voices, then, we can deepen the connections and conclusions made in pedagogical research, and students can be not just participants in our research but skilled researchers in their own lives.
Improving Information Extraction Using Knowledge Model

This paper describes the work on automated Information Extraction that accepts arbitrary text and extracts information from the text. A new approach to implement Information Extraction system is proposed in this paper. Firstly, the article will be decomposed according to paragraph, sentence and phrase. Every sentence will be compared with the knowledge node, and then append the information extracted to the knowledge model. Finally, the answers are generated to the questions about the input text. With the experimental corpus the accuracy rate of knowledge matching is 63.5%, and accuracy rate of question answering is 65.0% with the system knowledge model.
Valproate in combat-related posttraumatic stress disorder.

BACKGROUND The symptoms of posttraumatic stress disorder (PTSD) suggest sympathetic nervous system hyperarousal and hyperreactivity. Pathophysiology of this condition may include stress-activated limbic kindling. Antikindling agents lithium and carbamazepine have been found effective for PTSD symptoms of intrusive reexperiencing and increased arousal. These facts suggest that valproate, another drug shown to interfere with limbic kindling, could also be effective for treatment of PTSD. METHOD An open clinical trial of valproate was conducted in 16 Vietnam veterans diagnosed with DSM-III-R combat-related PTSD. RESULTS Ten of 16 patients showed significant improvement, especially in hyperarousal/hyperreactivity symptoms. CONCLUSIONS The efficacy of valproate in the treatment of PTSD should be rigorously studied.
High Quality Graph-Based Similarity Search

SimRank is an influential link-based similarity measure that has been used in many fields of Web search and sociometry. The best-of-breed method by Kusumoto et. al., however, does not always deliver high-quality results, since it fails to accurately obtain its diagonal correction matrix D. Besides, SimRank is also limited by an unwanted "connectivity trait": increasing the number of paths between nodes a and b often incurs a decrease in score s(a,b). The best-known solution, SimRank++, cannot resolve this problem, since a revised score will be zero if a and b have no common in-neighbors. In this paper, we consider high-quality similarity search. Our scheme, SR#, is efficient and semantically meaningful: (1) We first formulate the exact D, and devise a "varied-D" method to accurately compute SimRank in linear memory. Moreover, by grouping computation, we also reduce the time of from quadratic to linear in the number of iterations. (2) We design a "kernel-based" model to improve the quality of SimRank, and circumvent the "connectivity trait" issue. (3) We give mathematical insights to the semantic difference between SimRank and its variant, and correct an argument: "if D is replaced by a scaled identity matrix, top-K rankings will not be affected much". The experiments confirm that SR# can accurately extract high-quality scores, and is much faster than the state-of-the-art competitors.
A Systematic Review of Bayesian Articles in Psychology: The Last 25 Years

Although the statistical tools most often used by researchers in the field of psychology over the last 25 years are based on frequentist statistics, it is often claimed that the alternative Bayesian approach to statistics is gaining in popularity. In the current article, we investigated this claim by performing the very first systematic review of Bayesian psychological articles published between 1990 and 2015 (n = 1,579). We aim to provide a thorough presentation of the role Bayesian statistics plays in psychology. This historical assessment allows us to identify trends and see how Bayesian methods have been integrated into psychological research in the context of different statistical frameworks (e.g., hypothesis testing, cognitive models, IRT, SEM, etc.). We also describe take-home messages and provide “big-picture” recommendations to the field as Bayesian statistics becomes more popular. Our review indicated that Bayesian statistics is used in a variety of contexts across subfields of psychology and related disciplines. There are many different reasons why one might choose to use Bayes (e.g., the use of priors, estimating otherwise intractable models, modeling uncertainty, etc.). We found in this review that the use of Bayes has increased and broadened in the sense that this methodology can be used in a flexible manner to tackle many different forms of questions. We hope this presentation opens the door for a larger discussion regarding the current state of Bayesian statistics, as well as future trends.
The state after statism : new state activities in the age of liberalization

List of Tables and Figures Preface Introduction: The State also Rises: The Roots of Contemporary State Activism Jonah Levy I. VARIETIES OF STATISM 1. The Transformation of the British State: From Club Government to State-Administered High Modernism Michael Moran 2. The Forgotten Center: State Activism and Corporatist Adjustment in Holland and Germany Anton Hemerijck and Mark Vail 3. Exiting Etatisme? New Directions in State Policy in France and Japan Jonah Levy, Mari Miura, and Gene Park II. THE STATE AND SOCIAL GROUPS 4. The State and the Reconstruction of Industrial Relations Institutions after Fordism: Britain and France Compared Chris Howell 5. Building Finance Capitalism: The Regulatory Politics of Corporate Governance Reform in the United States and Germany John Cioffi 6. From Maternalism to "Employment for All": State Policies to Promote Women's Employment across the Affluent Democracies Ann Shola Orloff III. THE MARKET-MAKING STATE 7. The State in the Digital Economy John Zysman and Abraham Newman 8. Building Global Service Markets: Economic Structure and State Capacity Peter Cowhey and John Richards 9. The Transformation of European Trading States Richard Steinberg Conclusion: The State after Statism: From Market Direction to Market Support Jonah Levy Notes References Contributors Index
A new wavelet thresholding approach for SAS images denoising

SAS (Synthetic Aperture Sonar) is actively used in sea bed imagery. Indeed high resolution images provided by SAS are of great interest, especially for the detection, localization and eventually classification of objects lying on sea bed. Unfortunately, SAS images are highly corrupted by a granular multiplicative noise, called speckle noise, which reduces spatial and radiometric resolutions. The purpose of this article is to present a new wavelet thresholding approach, which ensures both a strong denoising and a spatial resolution preservation. Results obtained on real SAS data are presented and compared with those obtained using classing wavelet-based denoising approaches
Query transformation method by delaunay triangulation for multi-source distributed spatial database systems

One of the difficulties in building a distributed GIS comes from the heterogeneity of spatial databases. In particular, positional mismatches between spatial databases arise due to several reasons, such as different scales, or different ground control points. They result in unreliable outputs of query processing. One simple solution is to correct positional data in spatial databases at each site, according to the most accurate one. This solution is however not practical in most of the cases where the autonomy of each database should be respected. In this paper, we propose a spatial query processing method without correcting positional data in each spatial database. Instead of correcting positional data, we dynamically transform a given query region or position onto each space where spatial objects of each site are located. Our method is based on an elastic transformation method by delaunay triangulation.
Multi-State Quantum Dissipative Dynamics in Sub-Ohmic Environment: The Strong Coupling Regime

We study the dissipative quantum dynamics and the asymptotic behavior of a particle in a bistable potential interacting with a sub-Ohmic broadband environment. The reduced dynamics, in the intermediate to strong dissipation regime, is obtained beyond the two-level system approximation by using a real-time path integral approach. We find a crossover dynamic regime with damped intra-well oscillations and incoherent tunneling and a completely incoherent regime at strong damping. Moreover, a nonmonotonic behavior of the left/right well population difference is found as a function of the damping strength.
Adenovirus E1B 55-Kilodalton Oncoprotein Binds to Daxxand Eliminates Enhancement of p53-Dependent Transcription byDaxx

ABSTRACT The adenovirus E1B 55-kDa protein impairs the p53 pathway and enhances transformation, although the underlying mechanisms remain to be defined. We found that Daxx binds to the E1B 55-kDa protein in a yeast two-hybrid screen. The two proteins interact through their C termini. Mutation of three potential phosphorylation sites (S489/490 and T494 to alanine) within the E1B 55-kDa protein did not affect its interaction with Daxx, although such mutations were previously shown to inhibit E1B's ability to repress p53-dependent transcription and to enhance transformation. In addition to their coimmunoprecipitation in 293 extracts, purified Daxx interacted with the E1B 55-kDa protein in vitro, indicating their direct interaction. In 293 cells, Daxx colocalized with the E1B 55-kDa protein within discrete nuclear dots, where p53 was also found. Such structures were distinct from PML (promyelocytic leukemia protein) bodies, and it appeared that Daxx was displaced from PML bodies. Thus, the Daxx concentration was diminished in dots with a prominent presence of PML and vice versa. Indeed, PML overexpression led to dramatic redistribution of Daxx from p53-E1B 55-kDa protein complexes to PML bodies. Additionally, expression of the E1B 55-kDa protein in Saos2 osteosarcoma cells reduced the number of PML bodies. Our data suggest that E1B and PML compete for available Daxx in the cell. Surprisingly, Daxx significantly augmented p53-mediated transcription and the E1B 55-kDa protein eliminated this effect. Thus, it is likely that the E1B 55-kDa protein sequesters Daxx and p53 in specific nuclear locations, where p53 cannot activate transcription. One consequence of the Daxx-E1B interaction might be an alteration of normal interactions of Daxx, PML, and p53, which may contribute to cell transformation.
First-principles calculations of large-scale semiconductor systems on the earth simulator

First-principles simulations of large-scale semiconductor systems using the PHASE code on the Earth Simulator (ES) demonstrate high performance with respect to the theoretical peak performance. PHASE, designed for vector-parallel systems like the ES, demonstrates excellent parallel efficiency. We simulated an arsenic donor in silicon using up to 8,000 atom unit cell. A sustained peak performance of 14.6 TFlop/s was measured on 3,072 processing elements, which corresponds to 59% of the theoretical peak performance. Preliminary results using 10,648 atom unit cell are also presented.
Empirical Measurements of Disk Failure Rates and Error Rates

The SATA advertised bit error rate of one error in 10 terabytes is frightening. We moved 2 PB through low-cost hardware and saw five disk read error events, several controller failures, and many system reboots caused by security patches. We conclude that SATA uncorrectable read errors are not yet a dominant system-fault source - they happen, but are rare compared to other problems. We also conclude that UER (uncorrectable error rate) is not the relevant metric for our needs. When an uncorrectable read error happens, there are typically several damaged storage blocks (and many uncorrectable read errors.) Also, some uncorrectable read errors may be masked by the operating system. The more meaningful metric for data architects is Mean Time To Data Loss (MTTDL.)
Characterization of the SpaCBA Pilus Fibers in the Probiotic Lactobacillus rhamnosus GG

ABSTRACT Lactobacillus rhamnosus GG is a human intestinal isolate that has been studied intensively because of its probiotic properties. We have previously shown that L. rhamnosus GG produces proteinaceous pili that earlier had been observed only in Gram-positive pathogens (M. Kankainen et al., Proc. Natl. Acad. Sci. U. S. A. 106:17193–17198, 2009). These pili were found to be encoded by the spaCBA gene cluster, and the pilus-associated SpaC pilin was shown to confer on the cells a mucus-binding ability. In addition to the spaCBA cluster, another putative pilus cluster, spaFED, was predicted from the L. rhamnosus GG genome sequence. Herein, we show that only SpaCBA pili are produced by L. rhamnosus, and we describe a detailed analysis of cell wall-associated and affinity-purified SpaCBA pili by Western blotting and immunogold electron microscopy. Our results indicate that SpaCBA pili are heterotrimeric protrusions with a SpaA subunit as the shaft-forming major pilin. Only a few SpaB subunits could be observed in pilus fibers. Instead, SpaB pilins were found at pilus bases, as assessed by immunogold double labeling of thin sections of cells, suggesting that SpaB is involved in the termination of pilus assembly. The SpaC adhesin was present along the whole pilus length at numbers nearly equaling those of SpaA. The relative amount and uniform distribution of SpaC within pili not only makes it possible to exert both long-distance and intimate contact with host tissue but also provides mucus-binding strength, which explains the prolonged intestinal residency times observed for L. rhamnosus GG compared to that of nonpiliated lactobacilli.
Activation of NF‐κB protects hippocampal neurons against oxidative stress‐induced apoptosis: Evidence for induction of manganese superoxide dismutase and suppression of peroxynitrite production and protein tyrosine nitration

The transcription factor NF‐κB is expressed in neurons wherein it is activated in response to a variety of stress‐ and injury‐related stimuli including exposure to cytokines such as tumor necrosis factor‐α (TNFα), and excitotoxic and oxidative insults. NF‐κB may play a role in the anti‐death actions of TNFα in cultured hippocampal neurons exposed to metabolic and oxidative insults. We now report that pretreatment of hippocampal cell cultures with agents that activate NF‐κB (TNFα and C2‐ceramide) confers resistance of neurons to apoptosis induced by the oxidative insults FeSO4 and amyloid β‐peptide (Aβ25–35). The neuroprotective actions of TNFα and ceramide were abolished in cultures cotreated with κB decoy DNA demonstrating a requirement for NF‐κB activation for prevention of cell death. Levels of manganese superoxide dismutase (Mn‐SOD) in neurons were increased following exposure of cultures to TNFα and ceramide in control cultures, but not in cultures cotreated with κB decoy DNA. FeSO4and Aβ25–35 induced accumulation of mitochondrial peroxynitrite, and membrane lipid peroxidation, in neurons. Peroxynitrite accumulation and lipid peroxidation were largely prevented in neurons pretreated with TNFα and ceramide prior to exposure to FeSO4 and Aβ25–35, an effect blocked by κB decoy DNA. Immunoreactivity of neurons with an anti‐nitrotyrosine antibody was increased following exposure to FeSO4 and Aβ25–35; TNFα and C2‐ceramide suppressed protein tyrosine nitration, and κB decoy DNA blocked the effects of TNFα and C2‐ceramide. Finally, the peroxynitrite scavenger uric acid protected neurons against apoptosis induced by FeSO4 and Aβ, and suppressed peroxynitrite accumulation. We conclude that, by inducing production of Mn‐SOD and suppressing peroxynitrite formation and membrane lipid peroxidation, NF‐κB plays an anti‐apoptotic role in neurodegenerative conditions that involve oxidative stress. The data further suggest important roles for peroxynitrite and NF‐κB in the pathogenesis of neuronal degeneration in Alzheimer's disease. J. Neurosci. Res. 49:681–697, 1997. © 1997 Wiley‐Liss, Inc.
Improve Search by Optimization or Personalization, A Case Study in Sogou Log

With the development of information technology, especially when the Web is developing and widespread, the information resource grows explosively. The information retrieval(IR) system becomes more and more important as an indispensable way of accessing the information. Generally speaking the search engine returns results for user community rather than each person so there is also considerable room for improvement. But, the user of search engine cares about the personal results for him. And many personalization strategies have been investigated. We present a large-scale research of Sogou Logs and do the following work. 1) Analyze the performance of the search engine, 2) According to current information on the user logs, calculate the optimal performance of the search engine without personalization. 3) Process the current user logs and calculate the optimal performance of the search engine with personalization. 4) Adopt two possible personalized approaches and calculate their performance respectively. 5) Reveal the relationship between the performance of personalization and the results returned by the search engine. All of our experiments are carried out on Sogou Logs.
Robust multihypothesis discrimination of controlled i.i.d. processes

This paper describes a general framework for the robust discrimination of objects represented as a family of i.i. d. random distributions. Testing is based on accumulating evidences on the discrimination between all-pairs of hypotheses by sampling the family of distributions according to an optimal control law. The optimality criterion is built on constraint satisfaction issues. An application on 2D rotation invariant shape recognition with noisy contours illustrates the approach.
Learning to Be a Teacher of the Gifted: The Importance of Examining Opinions and Challenging Misconceptions

Abstract In Australia, most teachers enter the profession without having completed any dedicated studies pertaining to gifted education, yet many go on to teach gifted students. There is a substantive body of research supporting the value of professional learning in enhancing attitudes and practices that are conducive to appropriate provisioning for gifted students. In 2008, Monash University began offering a new elective in gifted education which by the end of 2010 had been completed by almost 500 pre-service teachers. This article reports on research conducted with 332 of those participants, using Gagné and Nadeau’s (1985) Opinionnaire and a reflective journal. Findings illustrate a strong positive growth in opinions relating to gifted education, particularly in regard to social justice. Respondents’ reflections suggest that access to research and literature on giftedness had been instrumental in assisting pre-service teachers to challenge their previous opinions, many of which they now regarded as uninformed misconceptions.
On Self-Adaptive Mutation Restarts for Evolutionary Robotics with Real Rotorcraft

Self-adaptive parameters are increasingly used in the field of Evolutionary Robotics, as they allow key evolutionary rates to vary autonomously in a context-sensitive manner throughout the optimisation process. A significant limitation to self-adaptive mutation is that rates can be set unfavourably, which hinders convergence. Rate restarts are typically employed to remedy this, but thus far have only been applied in Evolutionary Robotics for mutation-only algorithms. This paper focuses on the level at which evolutionary rate restarts are applied in population-based algorithms with more than 1 evolutionary operator. After testing on a real hexacopter hovering task, we conclude that individual-level restarting results in higher fitness solutions without fitness stagnation, and population restarts provide a more stable rate evolution. Without restarts, experiments can become stuck in suboptimal controller/rate combinations which can be difficult to escape from.
Effects of combinations of curcumin, linalool, rutin, safranal, and thymoquinone on glucose/serum deprivation-induced cell death

Objective: Several phytochemical agents have been known to exhibit a neuroprotective effect. Among them, curcumin, linalool, rutin, safranal, and thymoquinone were widely investigated and neuroprotective activity of each of them was shown by several studies. This work was planned to investigate whether different combinations of them could induce better neuroprotective effect against glucose/serum deprivation (GSD)-induced cytotoxicity. Materials and Methods: PC12 cells were cultivated for 8 h in GSD condition in both the absence and presence of curcumin, linalool, rutin, safranal, thymoquinone, or combinations of them. At the end of the experiment, the cell viability was determined using MTT assay. Results: The cells cultured in GSD condition showed a significant decrease in viability (28±1%) as compared with those cultured in standard condition (100±2%). In the presence of curcumin (10 µg/ml), linalool (16 µg/ml), rutin (200 µg/ml), safranal (50 µg/ml), and thymoquinone (1 µg/ml), the cell viability increased to 69±3.4% (p<0.001), 44±1.4% (p<0.01), 64±0.5% (p<0.001), 49±2% (p<0.001), and 70±3.2% (p<0.001), respectively. When different combinations of the agents were tested, the best cytoprotective activity was obtained from safranal + curcumin + thymoquinone (97±5%, p<0.01 vs. untreated cells). Conclusions: The present study demonstrated that a combination of safranal + curcumin + thymoquinone can block GSD-induced cell death and has the potential to be considered for management of cerebral ischemia and neurodegenerative diseases.