Miracle-dz/UniFAR-FTUs huggingface dataset:
TargetATPsite : A

The front cover illustrates the parallel molecular docking of large databases on the Sequoia, a petascale IBM Blue Gene/Q supercomputer at Lawrence Livermore National Laboratory. A mixed parallel scheme that combines MPI and multithreading is implemented by on page 915 in the Vina molecular docking program named VinaLC, where LC stands for Livermore Computing. Parallel performance analysis shows the code scales up to more than 15K CPUs with a very low overhead cost of 3.94%. One million flexible compound docking calculations take only 1.4 hours on about 15K CPUs. The picture shows ligands that have been docked into various receptors to form ligand–receptor complexes via calculations on the Sequoia. TargetATPsite, a new method based on residue evolution image sparse representation and classifier ensemble, is developed for predicting ATP-binding sites from primary sequences, as presented by on page 974. The high performance of TargetATPsite originates from the good discriminative capability of the new image sparse representation feature and the power of the modified AdaBoost classifier ensemble. TargetATPsite also features the capability of further identifying the binding pockets from the predicted binding residues through a spatial clustering algorithm. Look for these important papers in upcoming issues PHI: A powerful new program for the analysis of anisotropic monomeric and exchange-coupled polynuclear d-and f-block complexes Keith S. Murray et al. A new and extensively parallelized code for the calculation of the magnetic properties of large spin systems or complex orbitally degenerate compounds is presented. The program can simulate theoretical systems or fit experimental data with a specific Hamiltonian. Parameterization of a reactive force field (ReaxFF) is performed using a robust Metropolis Monte Carlo algorithm for a system of magnesium sulfate hydrates. This new method for optimizing the force field is efficient especially without good initial conditions. The stochastic nature enables one to arrive at the global minimum in the parameter space and thereby the best obtainable force field. [a] Understanding the interactions between proteins and ligands is critical for protein function annotations and drug discovery. We report a new sequence-based template-free predictor (TargetATPsite) to identify the Adenosine-5 0-triphosphate (ATP) binding sites with machine-learning approaches. Two steps are implemented in TargetATPsite: binding residues and pockets predictions, respectively. To predict the binding residues, a novel image sparse representation technique is proposed to encode residue evolution information treated as the input features. An ensemble classifier constructed based on support vector machines (SVM) from multiple random under-samplings is …
A game theory approach to the Iranian forest industry raw material market

Dynamic game theory is applied to analyze the timber market in northern Iran as a duopsony. The Nash equilibrium and the dynamic properties of the system based on marginal adjustments are determined. When timber is sold, the different mills use mixed stra tegies to give sealed bids. It is found that the decision probability combination of the different mills follow a special form of attractor and that centers should be expected to appear in unconstrained games. Since the probabilities of different strategies are always found in the interval [0,1], the boundaries of the feasible set are sometimes binding constraints. Then, the attractor becomes a constrained probability orbit. In the studied game, the probability that the Nash equilibrium will be reached is almost zero. The dynamic properties of timber prices derived via the duopsony game model are also found in the real empirical price series from the north of Iran.
Piezoelectric wind power harnessing – an overview

As fossil energy resources deplete, wind energy gains ever more importance. Recently, piezoelectric energy harvesting methods are emerging with the advancements in piezoelectric materials and its storage elements. Piezoelectric materials can be utilized to convert kinetic energy to electrical energy. Utilization of piezoelectric wind harvesting is a rather new means to convert renewable wind energy to electricity. Piezoelectric generators are typically low cost and easy to maintain. This work illustrates an overview of piezoelectric wind harvesting technology. In wind harvesting, piezoelectric material choice is of the first order of importance. Due to their strain rate, robustness is a concern. For optimum energy harvesting efficiency resonant frequency of the selected materials and overall system configuration plays important role. In this work, existing piezoelectric wind generators are grouped and presented in following categories: leaf type, rotary type, rotary to linear type and beam type wind generators.
On the degrees of freedom of three-user MIMO broadcast channel with delayed CSIT

We investigate the three-user MIMO Gaussian broadcast channel with i.i. d. fading and the same number of antennas at each receiver, and with the delayed channel state information at the transmitter (CSIT). We obtain achievability results on the degrees of freedom (DoF) of this channel and also show that our achievable DoF is tight for some ranges of transmit-receive antenna ratio. It is observed that when the number of antennas at the transmitter is strictly greater than that at each receiver, the DoF with delayed CSIT lies strictly between the DoF with perfect CSIT and DoF with no CSIT.
Predicting species distributions for conservation decisions

Species distribution models (SDMs) are increasingly proposed to support conservation decision making. However, evidence of SDMs supporting solutions for on-ground conservation problems is still scarce in the scientific literature. Here, we show that successful examples exist but are still largely hidden in the grey literature, and thus less accessible for analysis and learning. Furthermore, the decision framework within which SDMs are used is rarely made explicit. Using case studies from biological invasions, identification of critical habitats, reserve selection and translocation of endangered species, we propose that SDMs may be tailored to suit a range of decision-making contexts when used within a structured and transparent decision-making process. To construct appropriate SDMs to more effectively guide conservation actions, modellers need to better understand the decision process, and decision makers need to provide feedback to modellers regarding the actual use of SDMs to support conservation decisions. This could be facilitated by individuals or institutions playing the role of ‘translators’ between modellers and decision makers. We encourage species distribution modellers to get involved in real decision-making processes that will benefit from their technical input; this strategy has the potential to better bridge theory and practice, and contribute to improve both scientific knowledge and conservation outcomes.
Prolactin Prevents Chronic Stress-Induced Decrease of Adult Hippocampal Neurogenesis and Promotes Neuronal Fate

Chronic exposure to stress results in a reduction of hippocampal neurogenesis and of hippocampal volume. We examined whether prolactin (PRL), a regulator of the stress response and stimulator of neurogenesis in the subventricular zone, influences neurogenesis in the hippocampal dentate gyrus (DG) of chronically stressed adult C57BL/6 male mice. Chronically stressed (4 h daily immobilization for 21 d) or nonstressed mice were treated with either ovine PRL or vehicle between days 1–14. BrdU was injected daily between days 1–7 to evaluate cell survival and fate, or twice on day 21 to evaluate cell proliferation. Hippocampal cell proliferation was unchanged by either stress exposure or PRL at the end of the treatments. In contrast, the number of cells in the DG that incorporated BrdU during the first phase of the experiment and survived to the end of the experiment was decreased in vehicle-treated stressed mice compared with PRL- or vehicle-treated nonstressed control mice. Stressed animals receiving PRL had significantly more BrdU-labeled cells than vehicle-treated stressed mice at this time point. Cell fate analysis revealed a higher percentage of neurons in PRL- compared with vehicle-treated stressed mice. The results demonstrate that PRL protects neurogenesis in the DG of chronically stressed mice and promotes neuronal fate.
Inhibits Induction of Apoptosis in Mammalian Cells Its Transactivation Function and DNA-binding Activity but Enhances Both α Deletion of the COOH-Terminal Region of p 73 Updated Version

The candidate tumor suppressor p73 has a high sequence homology with p53 within the NH 2-terminal transactivation domain, the sequencespecific DNA-binding region, and the oligomerization domain. However, p73a, which is most abundantly expressed in many tissues and cells among the alternatively spliced forms of p73, has an additional long COOH-terminal tail that might distinguish the function of p53 and p73a or other p73 splicing variants. To examine the functional role of the p73a COOH-terminal region, we generated a series of p73 a truncation mutants including p73a(1–247) (retaining only a transactivation domain), p73a(1– 427) (lacking the most COOH-terminal region including a SAM domain), and p73a(1–548) (deleting an extreme COOH-terminal region except a SAM domain). When transfected into COS cells, all of p73 a, p73a(1–548), and p73a(1–427) localized in the cellular nucleus, whereas p73 a(1–247) localized in both nucleus and cytoplasm. Intriguingly, when compared with p73a, both p73a(1–427) and p73a(1–548) showed a significant stimulation of the transcription of luciferase reporters harboring three p53responsive promoters ( p21, Mdm2, andBax) in p53-deficient SAOS-2 cells. Gel retardation assays showed that DNA-binding activity of p73 a(1– 427) and p73a(1–548) was increased as compared with that of the fulllength p73a. However, the colony formation assays using SAOS-2 cells demonstrated that, contrary to p73a, transfection of p73a(1–427) or p73a(1–548) resulted in no significant reduction of the number of colonies. These suggest that the distal COOH-terminal region of p73 a is a cisor trans-acting regulatory domain and regulates its functions diversely.
Permanence for a predator-prey model with Schenk functional response

This paper deals with a diffusive predator-prey model with a functional response presented by Schenk based on the experiment tests. Based on an auxiliary lemma and by comparison principles, the ultimate boundedness, extinction of prey and permanence of system are investigated. The presented results are all applicable to such realistic cases as Hassell-Varley constant σ = 1,1/2 and 1/3.
Consensus Problem of Multi-agent Systems with Sensing Constraint on Range

Consensus problem of multi-agent systems with sensing constraint on range is studied in this paper. It is known that sensors have limited sensing capabilities although they are very important components and play a vital role in networked control systems. This paper discusses the consensus problem of the multi-agent systems in which some agents are outside the sensing ranges of their neighbors. We introduce an initial-state-dependent switching parameter into the consensus protocol, and show that the consensus can be obtained as long as some conditions are satisfied. an example is proposed to illustrate the effectiveness of the method.
A New Zearalenone Biodegradation Strategy Using Non-Pathogenic Rhodococcus pyridinivorans K408 Strain

Zearalenone (hereafter referred to as ZEA) is a nonsteroidal estrogenic mycotoxin produced by several Fusarium spp. on cereal grains. ZEA is one of the most hazardous natural endocrine disrupting chemicals (EDC) which induces hyper estrogenic responses in mammals. This can result in reproductive disorders in farm animals as well as in humans. Consequently, detoxification strategies for contaminated crops are crucial for food safety. In this study we have developed a bacterial based detoxification system using a non-pathogen Rhodococcus pyridinivorans K408 strain. Following 5 days treatment of ZEA with R. pyridinivorans K408 strain HPLC analyses showed an 87.21% ZEA-degradation efficiency of the bacterial enzyme systems. In another approach, the strain biotransformation ability has also been confirmed by a bioluminescent version of the yeast estrogen screening system (BLYES), which detected an 81.75% of biodegradability of ZEA, in a good agreement with the chemical analyses. Furthermore, the capacity of R. pyridinivorans to eliminate the estrogenic effects of ZEA was tested by using an immature uterotrophic assay. Prepubertal female rats were treated with vehicle (olive oil), 17β-estradiol, ZEA (0.1-1-5-10 mg/kg body weight) and LB broth containing 500 mg/l ZEA that has already been incubated with or without Rhodococcus pyridinivorans K408 strain. Uterine weights were measured and the mRNA level changes relating to apelin, aquaporin 5, complement component 2, and calbindin-3 genes were measured by qRT-PCR. These genes represent the major pathways that are affected by estromimetic compounds. Zearalenone feeding significantly increased the uterus weight in a dose dependent manner and at the same time upregulated complement component 2 and calbindin-3 expression as well as decreased apelin and aquaporin 5 mRNA levels comparable to that seen in 17β-estradiol exposed rats. In contrast, LB broth in which ZEA was incubated with Rhodococcus pyridinivorans K408 prior to the feeding did not display any estrogenic effect neither on uterine weight nor on the expression of estrogen-regulated genes. Consequently, the identification of Rhodococcus pyridinivorans K408 strain in ZEA biodegradation proved to be a very efficient biological tool that is able to eliminate the complete estrogenic effects of ZEA. It is also remarkable that this biotransformation pathway of ZEA did not result in any residual estrogenic effects.
Integrating Cross-Language Hierarchies and Its Application to Retrieving Relevant Documents

Internet directories such as Yahoo! are an approach to improvethe efficacy and efficiency of Information Retrieval (IR) on theWeb, as pages (documents) are organized into hierarchicalcategories, and similar pages are grouped together. Most of thesearch engines on the Web service find documents that are assignedto a single classification hierarchy. Categories in the hierarchyare carefully defined by human experts and documents are wellorganized. However, a single hierarchy in one language is ofteninsufficient to find all relevant material, as each hierarchy tendsto have some bias in both defining hierarchical structure andclassifying documents. Moreover, documents written in a languageother than the users native language often include large amounts ofinformation related to the users request. In this article, wepropose a method of integrating cross-language (CL) categoryhierarchies, that is, Reuters 96 hierarchy and UDC code hierarchyof Japanese by estimating category similarities. The method doesnot simply merge two different hierarchies into one large hierarchybut instead extracts sets of similar categories, where each elementof the sets is relevant with each other. It consists of threesteps. First, we classify documents from one hierarchy intocategories with another hierarchy using a cross-language textclassification (CLTC) technique, and extract category pairs of twohierarchies. Next, we apply Ç2 statisticsto these pairs to obtain similar category pairs, and finally weapply the generating function of the Apriori algorithm(Apriori-Gen) to the category pairs, and find sets of similarcategories. Moreover, we examined whether integrating hierarchieshelps to support retrieval of documents with similar contents. Theretrieval results showed a 42.7% improvement over the baselinenonhierarchy model, and a 21.6% improvement over a singlehierarchy.
A robust hardwired interwoven fault-masking technique

The process technology scales below 100 nanometers at present. Such miniaturizations of components has created reliability-threats to the designers, specially in the case of critical or semi-critical systems, whose failures can bring catastrophes in terms of human or great financial losses. Reliable working of such be ensured. In this paper, first the causes of such reliability-threats have been discussed and then a robust fault-masking technique has been presented to improve the reliability of a system. The technique presented restricts a system, even to generate momentary errors.
Analysis of tidal data via the blockwise bootstrap

We analyze tidal data from Port Mansfield, TX, using Kunsch's blockwise bootstrap in the regression setting. In particular, we estimate the variability of parameter estimates in a harmonic analysis via block subsampling of residuals from a least-squares fit. We see that naive least-squares variance estimates can be either too large or too small, depending on the strength of correlation and the design matrix. We argue that the block bootstrap is a simple, omnibus method of accounting for correlation in a regression model with correlated errors.
Dexmedetomidine versus Remifentanil for Sedation during Awake Fiberoptic Intubation

This study compared remifentanil and dexmedetomidine as awake fiberoptic intubation (AFOI) anesthetics. Thirty-four adult ASA I-III patients were enrolled in a double-blinded randomized pilot study to receive remifentanil (REM) or dexmedetomidine (DEX) for sedation during AFOI (nasal and oral). Thirty patients completed the study and received 2 mg midazolam IV and topical anesthesia. The REM group received a loading dose of 0.75 mcg/kg followed by an infusion of 0.075 mcg/kg/min. The DEX group received a loading dose of 0.4 mcg/kg followed by an infusion of 0.7 mcg/kg/hr. Time to sedation, number of intubation attempts, Ramsay sedation scale (RSS) score, bispectral index (BIS), and memory recall were recorded. All thirty patients were successfully intubated by AFOI (22 oral intubations/8 nasal). First attempt success rate with AFOI was higher in the REM group than the DEX group, 72% and 38% (P = 0.02), respectively. The DEX group took longer to attain RSS of ≥3 and to achieve BIS <80, as compared to the REM group. Postloading dose verbal recall was poorer in the DEX group. Dexmedetomidine seems a useful adjunct for patients undergoing AFOI but is dependent on dosage and time. Further studies in the use of dexmedetomidine for AFOI are warranted.
The Meaning and Concept of Financial Education in the Society of Economic Changes

The changes of economic, demographic, technologic and other conditions in Europe and the world leads to a delegation of responsibility in the field of financial activities and the security of individuals as consumers (also the young) from the country and institutions to individuals. Above all they also modify the habits, requirements, expectations and behaviour of individuals and the forms of risk they are exposed to. The appropriate system of financial education stimulates different factors of an active citizenship like socially responsible behaviour and decision, cooperation, better mobility and the rise of ethics and morals. So the level of risk lowers significantly in the field of the financial activity of individuals. Individuals improve with the appropriate level of financial literacy their understanding of financial products and concepts. The financial literacy is worldwide acknowledged as an important element of the economic and financial stability and development. Early enough the individuals who are able to financial literacy contribute positively also to an effective function of the financial system, economy and the society generally. Financial education represents a lifelong process. The article presents the meaning of financial education in the modern society of economic changes. The advantages of financial education for individuals, economy and society are presented. In the article a suggestion of the concept of financial education and the position of financial education within public policy on national level is presented.
Design of Access Algorithm for VANET MAC Layer Based on Multi-serviced P-persistent Model

A Real-time Listening Based Self-adaptive Algorithm has been proposed in this paper. This algorithm is based on multi-serviced p-persistent model, it computes the collision/idle ratio according to four priorities of VANET to adjust the transmission probability with a self-adaptive strategy to enhance the channel efficiency. The algorithm improves system through reduces collision probability among nodes by real-time interception of channels state, calculation of collision to free ratio and sending probability. Therefore it can guarantee the equality of services with different priorities.
Regulated Expression of ADAMTS-12 in Human Trophoblastic Cells: A Role for ADAMTS-12 in Epithelial Cell Invasion?

Metastatic carcinoma cells exploit the same molecular machinery that allows human placental cytotrophoblasts to develop an invasive phenotype. As altered expression levels of ADAMTS (A Disintegrin And Metalloproteinase with ThromboSpondin repeats) subtypes have been associated with cancer progression, we have examined the function and regulation of members of this gene family in epithelial cell invasion using cultures of highly invasive extravillous cytotrophoblasts and the poorly invasive JEG-3 cytotrophoblast cell line as model systems. Of the multiple ADAMTS subtypes identified in first trimester human placenta and these two trophoblastic cell types, only ADAMTS-12 was preferentially expressed by extravillous cytotrophoblasts. Transforming growth factor-β1 and interleukin-1β, two cytokines that promote and restrain cytotrophoblast invasion in vitro, were also found to differentially regulate trophoblastic ADAMTS-12 mRNA levels. Loss- or gain-of-function studies confirmed that ADAMTS-12, independent of its proteolytic activity, plays a specific, non-redundant role in trophoblast invasion. Furthermore, we demonstrated that ADAMTS-12 regulated cell-extracellular matrix adhesion and invasion through a mechanism involving the αvβ3 integrin heterodimer. This study identifies a novel biological role for ADAMTS-12, and highlights the importance and complexity of its non-proteolytic domain(s) pertaining to its function.
Short leukocyte telomere length predicts incidence and progression of carotid atherosclerosis in American Indians: The Strong Heart Family Study

Short leukocyte telomere length (LTL) has been associated with atherosclerosis in cross-sectional studies, but the prospective relationship between telomere shortening and risk of developing carotid atherosclerosis has not been well-established. This study examines whether LTL at baseline predicts incidence and progression of carotid atherosclerosis in American Indians in the Strong Heart Study. The analysis included 2,819 participants who were free of overt cardiovascular disease at baseline (2001-2003) and were followed through the end of 2006-2009 (average 5.5-yr follow-up). Discrete atherosclerotic plaque was defined as focal protrusion with an arterial wall thickness ≥50% the surrounding wall. Carotid progression was defined as having a higher plaque score at the end of study follow-up compared to baseline. Associations of LTL with incidence and progression of carotid plaque were examined using Cox proportional hazard regression, adjusting for standard coronary risk factors. Compared to participants in the highest LTL tertile, those in the lowest tertile had significantly elevated risk for both incident plaque (HR, 1.49; 95% CI, 1.09–2.03) and plaque progression (HR, 1.61; 95% CI, 1.26–2.07). Our results provide initial evidence for a potential prognostic utility of LTL in risk prediction for atherosclerosis.