Miracle-dz/UniFAR-FTUs huggingface dataset:
CG2AA: backmapping protein coarse-grained structures

UNLABELLED Coarse grain (CG) models allow long-scale simulations with a much lower computational cost than that of all-atom simulations. However, the absence of atomistic detail impedes the analysis of specific atomic interactions that are determinant in most interesting biomolecular processes. In order to study these phenomena, it is necessary to reconstruct the atomistic structure from the CG representation. This structure can be analyzed by itself or be used as an onset for atomistic molecular dynamics simulations. In this work, we present a computer program that accurately reconstructs the atomistic structure from a CG model for proteins, using a simple geometrical algorithm. AVAILABILITY AND IMPLEMENTATION The software is free and available online at http://www.ic. fcen.uba.ar/cg2aa/cg2aa.py SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT lula@qi.fcen.uba.ar.
Purchasing pirated software: an initial examination of Chinese consumers

Purpose – To analyze Chinese consumers in purchasing pirated software; to establish and empirically validate a model for analyzing consumers in software piracy; and to help software companies understand the software piracy issue in China and design anti‐piracy strategies.Design/methodology/approach – A research model was established by extending a model used by Ang et al. in studying Singaporeans' purchasing pirated CD. A survey was conducted. Hypotheses were tested through stepwise regressions. An exploratory factor analysis was carried out to analyze Chinese consumers' attitude toward software piracy.Findings – Four personal and social factors were found important in influencing Chinese consumers' attitude toward software piracy, including value consciousness, normality susceptibility, novelty seeking, and collectivism. Five attitude measures, which were important in influencing consumer purchase intention, were identified as reliability of pirated software, recognized social benefits of piracy, functio.
PREVENTION, THE APPROPRIATE TARGET OF INFANT PSYCHOTHERAPY

The aim of this paper is to evaluate the case for preventive interventions in infancy aimed at the reduction of childhood psychopathology. The paper considers the terminology of prevention and the case for prevention in infancy. It is argued that increased knowledge concerning the developmental pathways involved in many psychological disorders opens the door to prevention initiatives. An overview of recent prevention trials is provided and the implications from treatment evaluation studies are explored. The case for prevention of conduct disorders is taken as an illustration of the potential for interventions in infancy. A developmental model of conduct disorder implicates a vicious cycle of parent- child inter- actions, a process that may arguably be preempted by early intervention. Three modalities are considered in detail: parent training; enhancement of attachment security; and (c) the facilitation of (a) early (b) the the development of reflective function. Studies in each of these areas are reviewed. The paper concludes that increased emphasis on the prevention aspect of infant mental health interventions is justified and desirable.
Knowledge on cassava disease management: The case of cassava brown streak disease awareness in Northern Uganda

The cassava brown streak disease (CBSD) has spread rapidly in Northern Uganda since its emergence in Uganda in 2005. Field surveys conducted in 2010 and 2011 by Ngetta Zonal Agricultural Research and Development Institute (Ngetta ZARDI) revealed high CBSD prevalence in the zone. CBSD epidemic has severely affected livelihood of smallholder farmers in the region. Lack of knowledge on disease recognition and management contributed significantly to rapid spread of CBSD in the zone. Addressing this aspect to increase and improve the knowledge base of cassava farmers was an important component in integrated disease management. Ngetta ZARDI through the Agricultural Technology Agribusiness and Advisory Services (ATAAS) project developed a multi-displinary effort to reduce the spread and impact of CBSD, partly through promotion of adoption of tolerant cassava varieties, and educating and training of smallholder farmers and other stakeholders. Participants were carefully selected from farmer groups, extension and political leadership. Training involved lectures and field visits for practical demonstration of CBSD symptoms. The training increased the number of people with knowledge on CBSD management up to farmer level. Overall, the training program significantly strengthened the human resource base employed against CBSD in the zone. Key words: Cassava brown streak disease, Northern Uganda.
Pricing of Eco-Labels for Salmon in UK Supermarkets

Eco-labels are important features of many natural resource and food markets. They certify that a product has a desirable intrinsic quality, typically related to a public good such as being sustainably produced. In an increasing number of markets, consumers can choose between different labels that certify different attributes. Two issues that have received limited attention are whether pricing varies across different eco-labels and to what extent different retailers have adopted different pricing strategies for eco-labels. This paper investigates these issues by estimating a hedonic price model for salmon sold in Glasgow, U.K. for eight different retail chains, two eco-labels, and one label of origin. The results show substantial variation in the prices of the different eco-labels and that eco-label premiums vary across retail chains.
Irritable bowel syndrome: an update on therapeutic modalities

Irritable bowel syndrome (IBS) is the most common condition that a physician faces in the GI clinic. Of the general population, 10 - 25% suffer from symptoms judged to be IBS. The negative impact of this disease includes not only pain, suffering and direct medical expenses but also significant social and job-related consequences. IBS can be the result of dysfunction in any part of the brain-gut axis: alterations in the CNS caused by psychological or other factors, abnormal gastrointestinal motility, or heightened visceral sensations. Diagnosis is based on either the Manning or Rome-II criteria. Education, reassurance and emotional support are the cornerstones of successful treatment. The mainstays of the current therapeutic approach continue to be: stress management strategies, dietary modification entailing addition of dietary fibre and pharmacotherapy. Pharmacotherapy is still limited to treating symptoms. Newer drugs that modulate motility or drugs that modulate visceral sensation may be useful in selected cases. Psychopharmacological agents are useful in the treatment of IBS, especially in those with psychological co-morbidity. Alternative therapies such as homeopathy, acupuncture, special diets, herbal medication and several forms of psychological treatments and hypnotherapy are sought by many patients and are now being offered by physicians as treatment options, either alone or in conjunction with conventional forms of therapy in patients with refractory symptoms.
Bounds on the Error Probability of Block Codes over the q-Ary Erasure Channel

In this paper, tight bounds on the block error probability of linear block codes over order-q finite fields for the q-ary erasure channel, under maximum-likelihood (ML) decoding, are developed. Upper bounds are obtained for uniform parity-check ensembles, sparse parity-check ensembles, general parity-check ensembles (e.g., Gallager regular nonbinary low-density parity-check ensembles), and for any given linear code with known distance spectrum. The tightness of the upper bounds is confirmed both by the comparison with simple lower bounds and, for Gallager low-density parity-check ensembles, by extensive Monte Carlo simulations. Exploiting the derived bounds, it is shown how already for short blocks and small q>2 sparse ensembles attain block error probabilities close to those of idealized maximum distance separable (MDS) codes, down to low error probabilities, whereas in the same regime binary codes show visible losses with respect to the Singleton bound. Thanks to the accurate performance estimates, the developed bounds can support the design of near-optimum erasure correcting codes with short and moderate lengths.
Variation in phenology of hibernation and reproduction in the endangered New Mexico meadow jumping mouse (Zapus hudsonius luteus)

Hibernation is a key life history feature that can impact many other crucial aspects of a species’ biology, such as its survival and reproduction. I examined the timing of hibernation and reproduction in the federally endangered New Mexico meadow jumping mouse (Zapus hudsonius luteus), which occurs across a broad range of latitudes and elevations in the American Southwest. Data from museum specimens and field studies supported predictions for later emergence and shorter active intervals in montane populations relative to lower elevation valley populations. A low-elevation population located at Bosque del Apache National Wildlife Refuge (BANWR) in the Rio Grande valley was most similar to other subspecies of Z. hudsonius: the first emergence date was in mid-May and there was an active interval of 162 days. In montane populations of Z. h. luteus, the date of first emergence was delayed until mid-June and the active interval was reduced to ca 124–135 days, similar to some populations of the western jumping mouse (Z. princeps). Last date of immergence into hibernation occurred at about the same time in all populations (mid to late October). In montane populations pregnant females are known from July to late August and evidence suggests that they have a single litter per year. At BANWR two peaks in reproduction were expected based on similarity of active season to Z. h. preblei. However, only one peak was clearly evident, possibly due to later first reproduction and possible torpor during late summer. At BANWR pregnant females are known from June and July. Due to the short activity season and geographic variation in phenology of key life history events of Z. h. luteus, recommendations are made for the appropriate timing for surveys for this endangered species.
Experimental study of a microstrip-probe feed for U-slot patch array antennas

We propose a new type of feeding method for the two-element array of U-slot rectangular patches. We combine the microstrip line and the probe to form a microstrip-probe feed. As confirmed by our experimental measurements, by placing the feeder between the patch and the ground plane, we improved the matching and the front to back ratio (F/B) characteristic over a wide bandwidth, compared to the conventional coaxial-probe feeding method used by Lee (Electron. Lett., vol.31, no.5, p.819-420, 1996).
Sustainable Computing: Informatics and Systems Hero: a Smart-phone Application for Location Based Emissions Estimates

Keywords: Electricity Emissions Locational marginal price Smart-phone Household energy a b s t r a c t A smartphone application has been created that provides consumers with real-time information about local air emissions resulting from their energy consumption. The purpose of the application is to provide information to enable consumers to consider emissions as they schedule their energy use. This tool provides one mechanism for demand-side optimization through optimal timing of energy use for environmental benefit. The application relies on a model that estimates air emission rates of user-selected pollutants based on real-time spatially accurate information on the electric grid. The development of this smartphone application, its potential use, and opportunities for future improvement are presented.
License plate image patch filtering using HOG descriptor and bio-inspired optimization

Automatic license plate detection (ALPD) is one of the widespread research topics in the area of intelligent transportation systems. A challenging issue that affects ALPD performance is the complex image background, where possibility of misclassification of non-license plate (non-LP) objects as a license plate (LP) object is high. One of the ways to resolve the issue is to use an efficient filter to correctly classify the license plate and non-license plate objects. In this paper, we propose an efficient general technique for the classification of LP and non-LP images based on Histogram Oriented Gradient (HOG) features, and mixture of experts model (binary classifiers). To maximize the classification performance, Genetic Algorithm (GA) is applied to find the best feature subset and adjust the weights of the mixture model. Performance of the proposed method is evaluated on a new database of 2360 LP and non-LP images created by us. Experimental results achieve image classification with a high accuracy of 85.16%. The filter is also tested by plugging it into a recent ALPD system which improves the detection performance by 6.7%.
3D simulation of tennis game using learning algorithms by application of virtual reality

replicating a human-like behavior for a Non-player character (NPC) was always a challenge in sports simulations. Having a non-repetitive and intelligent behavior can dramatically increase the entertainment value of the game. To achieve this, many developers used some rule based or expert system methods which result in a controlled NPC behavior, but recently some machine learning methods are deployed in various types of games. In this paper we propose a method for an NPC to learn main skills in the tennis game. The method is based on the multi layered perceptron (MLP) network. We created a virtual 3D environment of the tennis game which can be interacted with via virtual reality devices. Then, after collecting required data from this environment, implemented a virtual opponent that learns the fundamental skills required to play a tennis game. Finally we compared results of different learning methods.
Nucleotide sequence of the Escherichia coli micA gene required for A/G-specific mismatch repair: identity of micA and mutY

The Escherichia coli methylation-independent repair pathway specific for A/G mismatches has been shown to require the gene product of micA. Extracts prepared from micA mutants do not form an A/G mismatch-specific DNA-protein complex and do not contain an A/G mismatch-specific nicking activity. Moreover, a partially purified protein fraction containing both A/G mismatch-specific nicking and binding activities restores repair activity in micA mutant extracts. The DNA sequence of a 2.3-kb fragment containing the micA gene has been determined. There are two open reading frames (ORF) in this DNA fragment: one ORF encodes a 25.7-kDa protein whose function is still unknown, the other ORF codes for a protein with an Mr of 39,147, but this ORF can be transcribed and the mRNA can be translated to yield a protein with an apparent Mr of 36 kDa on a sodium dodecyl sulfate-polyacrylamide gel. Deletion analysis showed that this 39.1-kDa ORF is the micA gene as judged by the capacity of the encoded protein to restore the A/G mismatch-specific nicking activity of micA mutant extracts. Furthermore, our results suggest that micA is the same gene as the closely mapped mutY, which encodes the A/G mismatch-specific glycosylase.
A Test Data Generation Method for C/C++ Projects

This research proposes an automated test data generation method for C/C++ projects to generate the lower number of test data while gaining higher code coverage in comparison with KLEE, CAUT, PathCrawler, and CREST. In order to do that, the proposed method contributes an algorithm named loop depth first search by combining both static testing and concolic testing together. Besides, the paper also provides an improvement symbolic execution for avoiding the initial test data problem in the concolic testing. Currently, a tool supporting the proposed method has been developed and applied to test on different C/C++ projects in several software companies. The experimental results show the higher coverage with the lower number of test data compared with the existing methods. The experimental results display the effectiveness and practical usefulness of the proposed method for automated test data generation in practice.
Production of Hepatitis C Virus Lacking the Envelope-Encoding Genes for Single-Cycle Infection by Providing Homologous Envelope Proteins or Vesicular Stomatitis Virus Glycoproteins in trans

ABSTRACT Hepatitis C virus (HCV) infection is a major worldwide health problem. The envelope glycoproteins are the major components of viral particles. Here we developed a trans-complementation system that allows the production of infectious HCV particles in whose genome the regions encoding envelope proteins are deleted (HCVΔE). The lack of envelope proteins could be efficiently complemented by the expression of homologous envelope proteins in trans. HCVΔE production could be enhanced significantly by previously described adaptive mutations in NS3 and NS5A. Moreover, HCVΔE could be propagated and passaged in packaging cells stably expressing HCV envelope proteins, resulting in only single-round infection in wild-type cells. Interestingly, we found that vesicular stomatitis virus (VSV) glycoproteins could efficiently rescue the production of HCV lacking endogenous envelope proteins, which no longer required apolipoprotein E for virus production. VSV glycoprotein-mediated viral entry could allow for the bypass of the natural HCV entry process and the delivery of HCV replicon RNA into HCV receptor-deficient cells. Our development provides a new tool for the production of single-cycle infectious HCV particles, which should be useful for studying individual steps of the HCV life cycle and may also provide a new strategy for HCV vaccine development.
Adoption of technology-based services: the role of customers’ willingness to co-create

Purpose – The purpose of this paper is to develop and empirically evaluate an adoption model for technology-based services (TBS) that integrates a customer’s willingness to co-create (WCC) as mediator complementing the well-known individual differences and innovation characteristics in predicting customer adoption of TBS. Design/methodology/approach – The manuscript uses structural equation modeling to analyze survey data from two empirical studies (n=781 and n=181). Findings – The empirical results show that WCC represents a key mediator between established antecedent predictors (innovation characteristics and individual differences) and the likelihood of TBS adoption. Additionally, the analysis reveals that WCC can even better explain and predict adoption intention of TBS than the commonly used individual differences and innovation characteristics. Finally, the results also suggest that a lack of customers’ WCC may help to explain persuasion-decision discrepancies within TBS adoption. Research limitatio.
Biodistribution and Retention Time of Retrovirally Labeled T Lymphocytes in Mice is Strongly Influenced by the Culture Period Before Infusion

T lymphocytes used for adoptive immunotherapy are often cultured before transfer to generate sufficient amounts of effector cells with desired specificity. Modification of lymphocytes induced by in vitro activation and expansion may influence their potential effector capacity by altering the survival and trafficking patterns after transfer. In this report, the authors show that the culture period of T cells after ConA/IL-2 stimulation strongly influences the retention and tissue distribution of these cells after infusion into syngeneic C57BL/6 mice. Infused labeled cells that have been cultured for 3 days remained in the peripheral blood and organs in at least a ten-fold higher number than cells cultured for 8 days. In addition, cells cultured for 3 days preferentially migrate to lungs and liver shortly after infusion and subsequently to lymph nodes and spleen. Cells cultured for 8 days preferentially migrate to liver and can be hardly detected in lymph nodes. In contrast, labeled cells cultured for 3 days are predominantly present in lymph nodes starting from day 8 until day 28. We showed that accurate monitoring of transferred cells is feasible, which may contribute to understanding response to adoptive immunotherapy.
The Relationship Between Corporate Governance And Financial Reporting Timeliness For Companies Listed On Egyptian Stock Exchange “An Empirical Study”

This study empirically investigates the relationship between the timeliness of corporate financial reporting and Corporate Governance for companies listed on Egyptian stock exchange during the period from 1998 to 2007. It investigates the role of corporate governance level on the timeliness of corporate financial reporting; it also investigates the relationship between industry type, company size, gearing, leverage, earnings quality, earnings management, electronic disclosure, audit opinion and the timeliness of corporate financial reporting. The results show that Egyptian publicly listed firms have taken less timeliness to publish their annual financial reporting since application corporate governance principals, the average of days lag between the end of the financial year and the publication of annual reporting has decreased from 134 days in 1998 to 72 days in 2007.
Anthropogenic and climate-change impacts on salt marshes of Jamaica Bay, New York City

Field studies and aerial photograph interpretation suggest that large sections of Jamaica Bay salt marshes in New York City near John F. Kennedy International Airport are deteriorating rapidly. The relatively recent salt marsh losses may be caused by a variety of factors, potentially interacting synergistically. Possible factors include reduced sediment input, dredging for navigation channels, boat traffic, and regional sea-level rise. Field work included aboveground biomass measurements of Spartina alterniflora, mapping plant community distribution, and documenting biogeomorphological indicators of marsh loss. Current productivity (standing crop biomass), which ranged from approximately 700 to 1500 g m−2, was typical of healthy marshes in this region, in spite of other indicators of marsh degradation. Historical aerial photographs of several islands showed that sampled marshes have diminished in size by ≈12% since 1959. Overall island low marsh vegetation losses since 1974 averaged 38%, with smaller islands losing up to 78% of their vegetation cover. Ground observations indicate that major mechanisms of marsh loss include increased ponding within marsh interiors, slumping along marsh edges, and widening of tidal inlets. Projections of future sea-level rise, using outputs from several global climate models and data from local tide gauges, in conjunction with a range of plausible accretion rates, suggest that under current stresses, Jamaica Bay salt marshes are unlikely to keep pace with accelerated rates of sea-level rise in the future.