Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Interaction Between the ESCRT‐I Component TSG101 and the HSV‐1 Tegument Ubiquitin Specific Protease

Similar to phosphorylation, transient conjugation of ubiquitin to target proteins (ubiquitination) mediated by the concerted action of ubiquitin ligases and de‐ubiquitinating enzymes (DUBs) can affect substrate function. As obligate intracellular parasites, viruses rely on different cellular pathways for their own replication and the well conserved ubiquitin conjugating/de‐conjugating system is not an exception. Viruses not only usurp the host proteins involved in the ubiquitination/de‐ubiquitination process, but they also encode their own ubiquitin ligases and DUBs. Here we report that an N‐terminal variant of the herpes simplex virus (HSV) type‐1 large tegument protein VP1/2 (VP1/21–767), encompassing an active DUB domain (herpesvirus tegument ubiquitin specific protease, htUSP), and TSG101, a component of the endosomal sorting complex required for transport (ESCRT)‐I, functionally interact. In particular, VP1/21–767 modulates TSG101 ubiquitination and influences its intracellular distribution. Given the role played by the ESCRT machinery in crucial steps of both cellular pathways and viral life cycle, the identification of TSG101 as a cellular target for the HSV‐1 specific de‐ubiquitinating enzyme contributes to the clarification of the still under debate function of viral encoded DUBs highly conserved throughout the Herpesviridae family. J. Cell. Physiol. 230: 1794–1806, 2015. © 2014 Wiley Periodicals, Inc.
Exploiting known latitudinal variations for improved limited-angle tomographic reconstruction of the plasmasphere

A new technique that exploits physical constraints for improved accuracy in volume reconstruction of the terrestrial plasmasphere's plasma density is presented. The goal of the work is to support volume reconstruction given a small number of 2D external views from locally close viewing positions. The technique is aimed at allowing exploitation of time-series 2D image data from the EUV sensor on NASA's IMAGE satellite. Reconstruction quality benchmarking results on synthetic data are also presented.
Blaming Halo: The Effects of Violent Video Games and What Should Be Done about Them

In the wake of such incidents as the Newtown, Connecticut; and Aurora, Colorado, shootings, much scrutiny has been applied to the topic of violent video games, because there appears to be a link between school shooters and video games that contain gratuitous violence. This paper examines the alleged link between video game violence and real-world violence. Copious amounts of research have been dedicated to this topic. Although many researchers conclude that violent video games lead to increases in aggression, a causal link between violent video games and real-life acts of violence remains unseen. This paper explores the origins of this controversy, and then seeks to find a solution to the problem of children playing video games that they should not. Additionally, this paper strives to dispel certain erroneous beliefs that many people have about violent video games. VIOLENT VIDEO GAMES 4 Blaming Halo The Effects of Violent Video Games and What Should Be Done About Them
Single Parameter Model for Free Recall And the Nature of Partially Filled Working Memory

I present a single parameter model of free recall and fit the one parameter, the probability per time unit of an item in working memory entering the next memory store (similar to Atkinson and Shiffrin, 1968), to the original Murdock (1962) data. Working memory is modeled as having space for a maximum of 4 items (Cowan, 2001). The first four probability values convey precise information about how items in the partially filled working memory enter the next memory store. In particular, one can distinguish between four separate “sub-stores” and a single store model. Two alternatives follow for the probability of an item in the initially partially filled working memory store to enter the next memory store: the same probability as a single item in the filled working memory or a probability proportional to the total space that exists in working memory. I find that the latter alternative is a better fit (though not a perfect fit), suggesting that working memory is not divided into four separate sub-stores. It is suggested that new high statistics (low noise) experiments on short lists will either settle the issue or prove theory incorrect.
Leveraging employee creativity through high performance work systems : a multilevel perspective

Research has looked at single rather than a configuration of human resource management (HRM) practices to influence creativity so it is not yet clear how these practices synergistically facilitate creativity and organisational performance. I address this significant but unanswered question in a three-part study. In Study 1, I develop a high performance work system (HPWS) for creativity scale. I use Study 2 sample to test the validity of the new scale. In Study 3, I test a multilevel model of the intervening processes through which branch HPWS for creativity influences creativity and branch performance. Specifically, at the branch level, I draw on social context theory and hypothesise that branch HPWS for creativity relates to climate for creativity which, in turn, leads to creativity, and ultimately, to profit. Furthermore, I hypothesise environmental dynamism as a boundary condition of the creativity-profit relationship. At the individual level, I hypothesise a cross-level effect of branch HPWS for creativity on employee-perceived HPWS. I draw on self-determination theory and argue that perceived HPWS for creativity relate to need satisfaction and the psychological pathways of intrinsic motivation and creative process engagement to predict creativity. I also hypothesise climate for creativity as a cross-level moderator of the intrinsic motivation-creativity and creative process engagement-creativity relationships. Results of hierarchical linear modeling (HLM) indicate that ten out of the fifteen hypotheses were supported. The findings of this study respond to calls for HPWS to be designed around a strategic focus by developing and providing initial validity evidence of an HPWS for creativity scale. The results reveal the underlying mechanisms through which HPWS for creativity simultaneously influences individual and branch creativity leading to profit. Lastly, results indicate environmental dynamism to be an important boundary condition of the creativity-profit relationship and climate for creativity as a cross-level moderator of the creative process engagement-creativity.
Two-Level Microprocessor-Accelerator Partitioning

The integration of microprocessors and field-programmable gate array (FPGA) fabric on a single chip increases both the utility and necessity of tools that automatically move software functions from the microprocessor to accelerators on the FPGA to improve performance or energy. Such hardware/software partitioning for modern FPGAs involves the problem of partitioning functions among two levels of accelerator groups - tightly-coupled accelerators that have fast single-clock-cycle memory access to the microprocessor's memory, and loosely-coupled accelerators that access memory through a bridge to avoid slowing the main clock period with their longer critical paths. This new two-level accelerator-partitioning problem was introduced, and a novel optimal dynamic programming algorithm was described to solve the problem. By making use of the size constraint imposed by FPGAs, the algorithm has what is effectively quadratic runtime complexity, running in just a few seconds for examples with up to 25 accelerators, obtaining an average performance improvement of 35% compared to a traditional single-level bus architecture
Two Sodium/Calcium Exchanger Gene Products, NCX1 and NCX3, Play a Major Role in the Development of Permanent Focal Cerebral Ischemia

Background and Purpose— The Na+/Ca2+ exchanger, by mediating Ca2+ and Na+ fluxes in a bidirectional way across the synaptic plasma membrane, may play a pivotal role in the events leading to anoxic damage. In the brain, there are 3 different genes coding for 3 different proteins: NCX1, NCX2, and NCX3. The aim of this study was to determine whether NCX1, NCX2, and NCX3 might play a differential role in the development of cerebral injury induced by permanent middle cerebral artery occlusion (pMCAO). Methods— By means of Western blotting, NCX1, NCX2, and NCX3 protein expression was evaluated in the ischemic core and in the remaining nonischemic area of the slice at different time intervals starting from ischemia induction. The role of each isoform was also assessed with antisense oligodeoxynucleotides (ODNs) targeted for each isoform. These ODNs were continuously intracerebroventricularly infused with an osmotic minipump (1 &mgr;L/h) for 48 hours, 24 hours before pMCAO. Results— The results showed that after pMCAO all 3 NCX proteins were downregulated in ischemic core; NCX3 decreased in periinfarctual area whereas NCX1 and NCX2 were unchanged. The ODNs for NCX1 and NCX3 gene products were capable of inducing an increase in the ischemic lesion and to worsen neurological scores. Conclusions— The results of this study suggest that in the neuroprotective effect exerted by NCX during ischemic injury, the major role is prevalently exerted by NCX1 and NCX3 gene products.
Variations in the abundances of potassium and thorium on the surface of Mercury: Results from the MESSENGER Gamma‐Ray Spectrometer

[1] A technique for converting gamma-ray count rates measured by the Gamma-Ray Spectrometer on the MESSENGER spacecraft to spatially resolved maps of the gamma-ray emission from the surface of Mercury is utilized to map the surface distributions of the elements Si, O, and K over the planet's northern hemisphere. Conversion of the K gamma-ray count rates to elemental abundances on the surface reveals variations from 300 to 2400 ppm. A comparison of these abundances with models for the maximum surface temperature suggests the possibility that a temperature-related process is controlling the K abundances on the surface as well as providing K to the exosphere. The abundances of K and Th have been determined for several geologically distinct regions, including Mercury's northern smooth plains and the plains interior to the Caloris basin. The lack of a significant variation in the measured Th abundances suggests that there may be considerable variability in the K/Th abundance ratio over the mapped regions.
Leveraging Social Connections to Improve Peer Assessment in MOOCs

With the advent of Massive Open Online Courses (MOOCs), students from all over the world can access to quality courses via a web browser. Due to their great convenience, a popular MOOC can easily attract tens of thousands of students to enroll. Hence, a challenging problem in MOOCs is to find an efficient way to grade a large scale of assignments. To address this problem, peer assessment was proposed to grade the assignments in a scalable way. In peer assessment, each student is asked to access a subset of his/her peers' assignments via a web interface, then all these peer grades are aggregated to predict a final grade for each submitted assignment. These peer grades are very noisy due to the fact that different students have different bias and reliability. Several probabilistic models were proposed to improve the accuracy of the predicted grades by explicitly modeling the bias and reliability of each student. However, existing methods assumed that all students are independent of each other while ignoring the social interactions among the students. In real life, students' grading bias are easily affected by their friends. For example, a student tends to have a tough grading standard if his/her friends are harsh graders. Following this intuition, we propose three probabilistic models for peer assessment by incorporating social connections to model the dependencies of bias among the students. Moreover, we evaluate our models in a new peer grading dataset, which is enhanced with the social information of users in the discussion forums of the MOOC platform. Experimental results show that our models improve the accuracy of the predicted grades by leveraging social connections of students.
Towards a Unified Behavioral Model for Component-Based and Service-Oriented Systems

There is no clear distinction between service-oriented systems (SOS) and component-based systems (CBS). However, there are several characteristics that could let one consider SOS as a step further from CBS. In this paper, we discuss the general features of CBS and SOS, while accounting for behavioral modeling in the language called REMES. First, we present REMES in the context of CBS modeling, and then we show how it can become suitable for SOS. We also discuss the relation between our model and the current state of the art.
Intrusion Response System in AODV for MANET

The mobile adhoc network (MANET) requires effective intrusion response system. In this paper, we present an intrusion response system that supports the infrastructureless nature of MANETs. We propose a NHELLO and Link Layer based solution towards excluding malicious node which is robust against address spoofing from the attacker. In particular, we investigate how power adaption can be used to keep a malicious node away from normal node’s transmission range. Important issue in this strategy is to select optimal transmission power so that malicious node goes out of operating zone of network, as well as node adapting power itself remains in the operating zone. We also provide a detailed performance evaluation based on various network parameters i.e. a series of simulation studies. Our results show that the proposed concept significantly improves the overall security of mobile ad hoc network without having geographical information of nodes.
Stabilization methods of bubble type for the Q1/Q1-element applied to the incompressible Navier-Stokes equations

In this paper, a general technique is developed to enlarge the velocity space of the unstable -element by adding spaces such that for the extended pair the Babuska-Brezzi condition is satisfied. Examples of stable elements which can be derived in such a way imply the stability of the well-known Q2 /Q1 -element and the 4Q1 /Q1 -element. However, our new elements are much more cheaper. In particular, we shall see that more than half of the additional degrees of freedom when switching from the Q 1 to the Q 2 and 4Q1 , respectively, element are not necessary to stabilize the Q1 /Q1 -element. Moreover, by using the technique of reduced discretizations and eliminating the additional degrees of freedom we show the relationship between enlarging the velocity space and stabilized methods. This relationship has been established for triangular elements but was not known for quadrilateral elements. As a result we derive new stabilized methods for the Stokes and Navier-Stokes equations. Finally, we show how the Brezzi-Pitkaranta stabilization and the SUPG method for the incompressible Navier-Stokes equations can be recovered as special cases of the general approach. In contrast to earlier papers we do not restrict ourselves to linearized versions of the Navier-Stokes equations but deal with the full nonlinear case.
Cooperative Strategies and Fairness-Aware Resource Allocation in Selection-Based OFDM Networks

This paper considers a multi-source orthogonal frequency division multiplexing (OFDM)-based network of access points wherein dedicated relays use the decode-and-forward relaying. We investigate the joint problem of transmission strategy selection (relaying v/s direct), relay assignment, and power allocation to maximize the minimum rate across sources in two different cooperative scenarios: subcarrier-based and block-based relaying. In the subcarrier-based scheme, each subcarrier is treated as an independent transmission; however, in addition to the synchronization problems caused, it is likely impractical for a relay to decode a subset of subcarriers. Thus, we study relay selection for the entire OFDM block. The key difference from previous work is that we consider resource allocation across source-relay, relay-destination, and source-destination channels. Second, a simple, distributed, block-based scheme is proposed. Simulation results using the COST-231 channel model reveals that the performance of this heuristic scheme tracks that of the optimum block-based scheme while it significantly decreases the required computational complexity.
Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank

We have developed GeneBase, a full parser of the National Center for Biotechnology Information (NCBI) Gene database, which generates a fully structured local database with an intuitive user-friendly graphic interface for personal computers. Features of all the annotated eukaryotic genes are accessible through three main software tables, including for each entry details such as the gene summary, the gene exon/intron structure and the specific Gene Ontology attributions. The structuring of the data, the creation of additional calculation fields and the integration with nucleotide sequences allow users to make many types of comparisons and calculations that are useful for data retrieval and analysis. We provide an original example analysis of the existing introns across all the available species, through which the classic biological problem of the ‘minimal intron’ may find a solution using available data. Based on all currently available data, we can define the shortest known eukaryotic GT-AG intron length, setting the physical limit at the 30 base pair intron belonging to the human MST1L gene. This ‘model intron’ will shed light on the minimal requirement elements of recognition used for conventional splicing functioning. Remarkably, this size is indeed consistent with the sum of the splicing consensus sequence lengths.
Regulation of Glucagon Secretion in Normal and Diabetic Human Islets by γ-Hydroxybutyrate and Glycine*

Background: β-Cells regulate α-cells via paracrine mechanisms. Results: A GABA shunt defect impairs glucose suppression of glucagon secretion in diabetic human islets. Glucagon secretion is inhibited by γ-hydroxybutyrate produced by β-cells but is stimulated by glycine via plasma membrane receptors. Conclusion: γ-Hydroxybutyrate and glycine serve as counterbalancing receptor-based regulators of glucagon secretion. Significance: Amino acids and their metabolites are central regulators of α-cell function. Paracrine signaling between pancreatic islet β-cells and α-cells has been proposed to play a role in regulating glucagon responses to elevated glucose and hypoglycemia. To examine this possibility in human islets, we used a metabolomic approach to trace the responses of amino acids and other potential neurotransmitters to stimulation with [U-13C]glucose in both normal individuals and type 2 diabetics. Islets from type 2 diabetics uniformly showed decreased glucose stimulation of insulin secretion and respiratory rate but demonstrated two different patterns of glucagon responses to glucose: one group responded normally to suppression of glucagon by glucose, but the second group was non-responsive. The non-responsive group showed evidence of suppressed islet GABA levels and of GABA shunt activity. In further studies with normal human islets, we found that γ-hydroxybutyrate (GHB), a potent inhibitory neurotransmitter, is generated in β-cells by an extension of the GABA shunt during glucose stimulation and interacts with α-cell GHB receptors, thus mediating the suppressive effect of glucose on glucagon release. We also identified glycine, acting via α-cell glycine receptors, as the predominant amino acid stimulator of glucagon release. The results suggest that glycine and GHB provide a counterbalancing receptor-based mechanism for controlling α-cell secretory responses to metabolic fuels.
Exact solutions of the isoholonomic problem and the optimal control problem in holonomic quantum computation

The isoholonomic problem in a homogeneous bundle is formulated and solved exactly. The problem takes a form of a boundary value problem of a variational equation. The solution is applied to the optimal control problem in holonomic quantum computer. We provide a prescription to construct an optimal controller for an arbitrary unitary gate and apply it to a k-dimensional unitary gate which operates on an N-dimensional Hilbert space with N⩾2k. Our construction is applied to several important unitary gates such as the Hadamard gate, the CNOT gate, and the two-qubit discrete Fourier transformation gate. Controllers for these gates are explicitly constructed.
Manipulability optimization for trajectory generation

In this paper, we present an algorithm for manipulability based trajectory generation for any serial manipulator that has an inverse kinematic model that can obtain all solutions. Our strategy is a search based approach that analyzes candidate configurations at discrete points along the work-space trajectory. Given such a model we prove the configuration-space trajectories generated are optimal within the limit of the discretization of the work-space trajectory
Gaussian Process Volatility Model

The prediction of time-changing variances is an important task in the modeling of financial data. Standard econometric models are often limited as they assume rigid functional relationships for the evolution of the variance. Moreover, functional parameters are usually learned by maximum likelihood, which can lead to over-fitting. To address these problems we introduce GP-Vol, a novel non-parametric model for time-changing variances based on Gaussian Processes. This new model can capture highly flexible functional relationships for the variances. Furthermore, we introduce a new online algorithm for fast inference in GP-Vol. This method is much faster than current offline inference procedures and it avoids overriding problems by following a fully Bayesian approach. Experiments with financial data show that GP-Vol performs significantly better than current standard alternatives.
Observational tests of open strings in braneworld scenarios

We consider some consequences of describing the gauge and matter degrees of freedom in our universe by open strings, as suggested by the braneworld scenario. We focus on changes in causal structure described by the open string metric and investigate their observational implications. The causal structure is described not by the usual metric g"", but instead by the open string metric, that incorporates the electromagnetic background and the NS-NS two-form, G"" = g"" i (2…fi 0 ) 2 (F 2 )"". The speed of light on the brane is now slower when propagating along directions transverse to electromagnetic flelds or NS- NS two-forms, so that Lorentz invariance is explicitly broken. We describe experiments designed to detect the predicted variations in the open string causal structure on the brane: interferometric laboratory based experiments, experiments exploiting astrophysical electro- magnetic flelds, and experiments that rely on modiflcation to special relativity. We show that current technology cannot probe beyond open string lengths of 10 i13 cm, correspond- ing to MeV string scales. We also point out that in a braneworld scenario, constraints on large scale electromagnetic flelds together with a modest phenomenological bound on the NS-NS two-form naturally lead to a bound on the scale of canonical noncommutativity that is two orders of magnitude below the string length. We show that theoretical constraints on the NS-NS two-form bound the scale of noncommutativity to be well below the Planck length, p jµjmax < 10 i35 cm£ ( TeV string scale ) 2 .