Miracle-dz/UniFAR-FTUs huggingface dataset:
A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding

High-resolution structures reveal that yeast ribosomal protein L11 and its bacterial/archael homologs called L5 contain a highly conserved, basically charged internal loop that interacts with the peptidyl-transfer RNA (tRNA) T-loop. We call this the L11 ‘P-site loop’. Chemical protection of wild-type ribosome shows that that the P-site loop is inherently flexible, i.e. it is extended into the ribosomal P-site when this is unoccupied by tRNA, while it is retracted into the terminal loop of 25S rRNA Helix 84 when the P-site is occupied. To further analyze the function of this structure, a series of mutants within the P-site loop were created and analyzed. A mutant that favors interaction of the P-site loop with the terminal loop of Helix 84 promoted increased affinity for peptidyl-tRNA, while another that favors its extension into the ribosomal P-site had the opposite effect. The two mutants also had opposing effects on binding of aa-tRNA to the ribosomal A-site, and downstream functional effects were observed on translational fidelity, drug resistance/hypersensitivity, virus maintenance and overall cell growth. These analyses suggest that the L11 P-site loop normally helps to optimize ribosome function by monitoring the occupancy status of the ribosomal P-site.
Denotational semantics for a program logic of objects

The object-calculus is an imperative and object-based programming language in which every object comes equipped with its own method suite. Consequently, methods need to reside in the store (‘higher-order store’), which complicates the semantics. Abadi and Leino defined a program logic for this language enriching object types by method specifications. We present a new soundness proof for their logic using denotational semantics. It turns out that denotations of store specifications are predicates defined by mixed-variant recursion. A benefit of our approach is that derivability and validity can be kept distinct. Moreover, it reveals which of the limitations of Abadi and Leino's logic are incidental design decisions and which follow inherently from the use of a higher-order store. We discuss the implications for the development of other, more expressive, program logics.
Noise reduction and estimation in multiple micro-electro-mechanical inertial systems

This research studies the reduction and the estimation of the noise level within a redundant configuration of low-cost (MEMS-type) inertial measurement units (IMUs). Firstly, independent observations between units and sensors are assumed and the theoretical decrease in the system noise level is analyzed in an experiment with four MEMS-IMU triads. Then, more complex scenarios are presented in which the noise level can vary in time and for each sensor. A statistical method employed for studying the volatility of financial markets (GARCH) is adapted and tested for the usage with inertial data. This paper demonstrates experimentally and through simulations the benefit of direct noise estimation in redundant IMU setups.
Prevalence of SXT/R391-like integrative and conjugative elements carrying blaCMY-2 in Proteus mirabilis.

OBJECTIVES To characterize the vectors involved in the dissemination of bla(CMY-2) genes in clinical isolates of Proteus mirabilis collected between 1999 and 2007. METHODS Plasmid analysis of 19 P. mirabilis carrying ampC genes was performed by PCR-based replicon typing, S1-PFGE and Southern hybridization with ampC and replicon probes. Isolates that could not be characterized were examined for the presence of SXT/R391-like elements. To demonstrate the involvement of these elements in the dissemination of bla(CMY-2), we performed a PCR amplification of the integrase (int) and toxin/antitoxin (TA) genes from SXT/R391-like integrative conjugative elements (ICEs). Later on, I-Ceu-I PFGE gels and hybridization with bla(CMY-2), int and prfC probes were performed. The genetic organization of bla(CMY-2) was also studied. RESULTS ampC genes were located on large conjugative plasmids in 11 of the 19 (58%) P. mirabilis studied. However, in eight of these isolates a plasmid was not involved in the mobilization of ampC genes. I-Ceu-I PFGE and hybridization analyses revealed that bla(CMY-2) were chromosomally located in these eight P. mirabilis isolates. The genetic organization of bla(CMY-2) and hybridization analyses revealed that bla(CMY-2) was carried by an ICE almost identical to ICEPmiJpan1 in seven out of these eight isolates. CONCLUSIONS The prevalence of ICEs carrying bla(CMY-2) was surprisingly high [37% (7 out of 19)]. This is the first study giving prevalence data on ICEs carrying bla(CMY-2) genes. These results suggest the need to study these mobile genetic elements in the context of dissemination of acquired AmpC β-lactamases and also of other β-lactamases, such as extended-spectrum β-lactamases and carbapenemases.
Mapping Interdisciplinary Fields: Efficiencies, Gaps and Redundancies in HIV/AIDS Research

While interdisciplinarity continues to increase in popularity among funders and other scientific organizations, its potential to promote scientific advances remains under-examined. For HIV/AIDS research, we examine the dynamics of disciplinary integration (or lack thereof) providing insight into a field's knowledge base and those questions that remain unresolved. Drawing on the complete histories of two interdisciplinary journals, we construct bibliographic coupling networks based on overlapping citations to identify segregation into research clusters and estimate topic models of research content. We then compare how readily those bibliographic coupling clusters account for the structuring of topics covered within the field as it evolves over two decades. These comparisons challenge one-dimensional and/or cross-sectional approaches to interdisciplinarity. Some topics are increasingly coordinated across disciplinary boundaries (e.g., vaccine development); others remain relatively segmented into disconnected disciplinary domains for the full period (e.g., drug resistance). This divergence indicates heterogeneity in interdisciplinarity and emphasizes the need for critical approaches to studying the organization of science.
Increased mortality among HIV-positive men on antiretroviral therapy: survival differences between sexes explained by late initiation in Uganda

Background We aimed to assess the relationship between gender and survival among adult patients newly enrolled on antiretroviral therapy (ART) in Uganda. We also specifically examined the role of antenatal services in favoring women’s access to HIV care. Methods From an observational cohort study, we assessed survival and used logistic regression and differences in means to compare men and women who did not access care through antenatal services. Differences were assessed on measures of disease progression (WHO stage and CD4 count) and demographic (age, marital status, and education), behavioral (sexual activity, disclosure to partner, and testing), and clinical variables (hepatitis B and C, syphilis, malaria, and anemia). A mediational analysis that considered gender as the initial variable, time to death as the outcome, initial CD4 count as the mediator, and age as a covariate was performed using an accelerated failure time model with a Weibull distribution. Results Between 2004 and 2011, a total of 4775 patients initiated ART, and after exclusions 4537 (93.2%) were included in analysis. Men initiating ART were more likely to have a WHO disease stage III or IV (odds ratio: 1.46, 95% confidence interval [CI]: 1.29–1.66), and lower CD4 cell counts compared to women (median baseline CD4 124 cells/mm3, interquartile range [IQR]: 43–205 versus 147 cells/mm3, IQR: 68–212, P-value < 0.0001). Men were at an increased risk of death compared to women (hazard ratio: 1.38, 95% CI: 1.03–1.83). Baseline CD4 cell counts accounted for 43% of the increased risk of death in men (95% CI: 22%–113%). Access to care via antenatal services did not explain differences in outcomes. Conclusion In this cohort there is a marked increase in risk of mortality for men and approximately half of it can be attributed to their later engagement in care. More effort is required to engage men in care in a timely manner.
Temperature-aware register reallocation for register file power-density minimization

Increased chip temperature has been known to cause severe reliability problems and to significantly increase leakage power. The register file has been previously shown to exhibit the highest temperature compared to all other hardware components in a modern high-end embedded processor, which makes it particularly susceptible to faults and elevated leakage power. We show that this is mostly due to the highly clustered register file accesses where a set of few registers physically placed close to each other are accessed with very high frequency. We propose compile-time temperature-aware register reallocation methodologies for breaking such groups of registers and to uniformly distribute the accesses to the register file. This is achieved with no performance and no hardware overheads. We show that the underlying problem is NP-hard, and subsequently introduce and evaluate two efficient algorithmic heuristics. Our extensive experimental study demonstrates the efficiency of the proposed methodology.
Selecting the best system in steady-state simulations using batch means

Suppose that we want to compare k different systems, where /spl mu//sub i/ denotes the steady state mean performance of system i. Our goal is to use simulation to pick the "best" system (i.e., the one with the largest or smallest steady state mean). To do this, we present some two stage procedures based on the method of batch means. Our procedures also construct multiple comparisons with the best (MCB) confidence intervals for /spl mu//sub i/-max/sub j/spl ne/i//spl mu//sub j/, i=1,. ,k. Under the assumption of an indifference zone of (absolute or relative) width /spl delta/, we can show that asymptotically (as /spl delta//spl rarr/0 with the size of the batches proportional to 1//spl delta//sup 2/), the joint probability of correctly selecting the best system and of the MCB confidence intervals simultaneously containing /spl mu//sub i/-max/sub j/spl ne/i//spl mu//sub j/, i=1,. ,k, is at least 1-/spl alpha/, where /spl alpha/ is prespecified by the user.
Stability Analysis for High-Order Dynamic Neural Networks with Time Delays

This paper studies the problem of asymptotic stability for a class of high-order dynamic neural networks with time delays. Several useful lemmas are proved in this paper first. After that, the sufficient conditions for the asymptotic stability of the system with constant time delays are introduced, and also this asymptotic stability problem for the system with time-varying delays is put forward. In order to obtain above results, the Lyapunov-Krasovskii stability theory for functional differential equations and the linear matrix inequality (LMI) approach are employed to investigate this kind of problems. Finally, some numerical examples are given to illustrate the advantages of our approach
Knowledge and Attitude of Hungarian Athletes towards Long-term Sports Injuries

Abstract The purpose of this study was to investigate long-term sports injuries, their prevalence, general identification of and consultation about injuries, and the knowledge among Hungarian athletes related to injury prevention. A questionnaire was designed to survey athletes regarding these topics. Olympic medal winners, nationally selected athletes, and amateur athletes were surveyed, and altogether 502 completed questionnaires were obtained. The data was analyzed with the Chi-square test for dichotomous variables and the Kruskal-Wallis H-test for questions with the Likert scale to try the statistical power of the hypotheses. The results of our analysis show that athletes suffer injuries regardless of their level of play, and that athletes regard their sports to be moderately dangerous. Most athletes would compete despite the risk of permanent injury; they compete with injuries mostly of their own volition; and they will risk potential injuries or long-term health damage to gain exceptional outcomes. Success is the first and foremost desire of athletes, and the risk of injuries or even long-term health damage does not play an important role in the value system of Hungarian athletes. Sport managers and officers of sport federations must be made aware that the first line of prevention of sport injuries is comprehensive medical consultation with proper medical coverage.
Dynamic Noise Adaptation

We consider the problem of robust speech recognition in the car environment. We present a new dynamic noise adaptation algorithm, called DNA, for the robust front-end compensation of evolving semi-stationary noise as typically encountered in the car setting. A large dataset of in-car noise was collected for the evaluation of the new algorithm. This dataset was combined with the Aurora II framework to produce a new, publicly available framework, called DNA + AURORA II, for the evaluation of adaptive noise compensation algorithms. We show that DNA consistently outperforms several existing, related state-of-the-art front-end denoising techniques
Toward a political economy of complex interdependence

How should we theorize about international political economy in an era of complex interdependence? The global economy is much more interdependent today than it was 40 years ago. As a result, there is a widening appreciation that we need new theoretical tools to understand how complex interdependence arose, how it operates, and where it might be headed. I argue that to develop such tools, we must embrace new theoretical logics that more readily accommodate and explain change. I develop this point by drawing on complexity theories, ecology, and information theory. I first develop the core elements of a complexity-based approach and contrast it to the central assumptions of the Open Economy Politics approach. I then illustrate this complexity-oriented approach by using the logic of coevolution and the information–entropy cycle to explain key elements in the development of the 2008 global financial crisis.
PECAM-1 is required for transendothelial migration of leukocytes

Platelet/endothelial cell adhesion molecule 1 (PECAM-1; CD31) is crucial to the process of leukocyte transmigration through intercellular junctions of vascular endothelial cells. A monoclonal antibody to PECAM, or recombinant soluble PECAM, blocks transendothelial migration of monocytes by 70-90%. Pretreating either the monocytes or the endothelial junctions with antibody blocks transmigration. If the endothelium is first activated by cytokines, anti-PECAM antibody or soluble recombinant PECAM again block transmigration of both monocytes and neutrophils. Anti-PECAM does not block chemotaxis of either cell type. Light and electron microscopy reveal that leukocytes blocked in transmigration remain tightly bound to the apical surface of the endothelial cell, precisely over the intercellular junction. Thus, the process of leukocyte emigration can be dissected into three successive stages: rolling, mediated by the selectin class of adhesion molecules; tight adhesion, mediated by the leukocyte integrins and their endothelial cell counter-receptors; and now transmigration, which, based on these studies, requires PECAM-1.
Bisphosphonates in bone cement inhibit PMMA particle induced bone resorption

OBJECTIVE Wear particle induced bone resorption is thought to be one of the mechanisms that contribute to implant loosening. It has previously been shown that macrophages, in response to polymethylmethacrylate (PMMA) particles, differentiate into bone resorbing osteoclasts, and that this process is inhibited by a bisphosphonate, etidronate (EHDP). The aim of this study was to determine whether incorporating EHDP in bone cement could reduce PMMA associated bone resorption. METHODS Two concentrations of EHDP were mixed with PMMA monomer before polymerisation. Particles of PMMA (1–10 μm) were generated then added to mouse monocytes cocultured with UMR106 rat osteoblast-like cells and the extent of osteoclast differentiation was determined by assessing the extent of tartrate resistant acid phosphatase (TRAP) staining and measuring the amount of lacunar bone resorption. RESULTS The addition of PMMA to monocyte-UMR106 cocultures resulted in a marked increase in the number of TRAP positive osteoclast-like cells and a significant increase in the number of lacunar resorption pits compared with control cultures to which no particles had been added. After the addition of particles of PMMA + 20 mg EHDP, significantly fewer lacunar pits (p=0.00006) and fewer TRAP positive cells were noted compared with cocultures containing PMMA particles alone. CONCLUSIONS These results indicate that by mixing a bisphosphonate with bone cement, it is possible to inhibit PMMA particle induced bone resorption. This bisphosphonate inhibition of PMMA biomaterial wear particle containing macrophage-osteoclast differentiation and bone resorption may provide a possible therapeutic strategy to prevent or to control the osteolysis of aseptic loosening.
Fe b 20 07 Galaxy Clusters Associated with Short GRBs . II . Predictions for the Rate of Short GRBs in Field and Cluster Early-Type Galaxies

We determine the relative rates of short GRBs in cluster and field early-type galaxies as a function of the age probability distribution of their progenitors, P (τ) ∝ τ n. This analysis takes advantage of the difference in the growth of stellar mass in clusters and in the field, which arises from the combined effects of the galaxy stellar mass function, the early-type fraction, and the dependence of star formation history on mass and environment. This approach complements the use of the early-to late-type host galaxy ratio, with the added benefit that the star formation histories of early-type galaxies are simpler than those of late-type galaxies, and any systematic differences between progenitors in early-and late-type galaxies are removed. We find that the ratio varies from R cluster /R field ∼ 0.5 for n = −2 to ∼ 3 for n = 2. Current observations indicate a ratio of about 2, corresponding to n ∼ 0 − 1. This is similar to the value inferred from the ratio of short GRBs in early-and late-type hosts, but it differs from the value of n ≈ −1 for NS binaries in the Milky Way. We stress that this general approach can be easily modified with improved knowledge of the effects of environment and mass on the build-up of stellar mass, as well as the effect of globular clusters on the short GRB rate. It can also be used to assess the age distribution of Type Ia supernova progenitors.
Controllability of the 1D Schrodinger equation by the flatness approach

We derive in a straightforward way the exact controllability of the 1-D Schrodinger equation with a Dirichlet boundary control. We use the so-called flatness approach, which consists in parameterizing the solution and the control by the derivatives of a "flat output". This provides an explicit control input achieving the exact controllability in the energy space. As an application, we derive an explicit pair of control inputs achieving the exact steering to zero for a simply-supported beam.
PRAS40 and PRR5-Like Protein Are New mTOR Interactors that Regulate Apoptosis

TOR (Target of Rapamycin) is a highly conserved protein kinase and a central controller of cell growth. TOR is found in two functionally and structurally distinct multiprotein complexes termed TOR complex 1 (TORC1) and TOR complex 2 (TORC2). In the present study, we developed a two-dimensional liquid chromatography tandem mass spectrometry (2D LC-MS/MS) based proteomic strategy to identify new mammalian TOR (mTOR) binding proteins. We report the identification of Proline-rich Akt substrate (PRAS40) and the hypothetical protein Q6MZQ0/FLJ14213/CAE45978 as new mTOR binding proteins. PRAS40 binds mTORC1 via Raptor, and is an mTOR phosphorylation substrate. PRAS40 inhibits mTORC1 autophosphorylation and mTORC1 kinase activity toward eIF-4E binding protein (4E-BP) and PRAS40 itself. HeLa cells in which PRAS40 was knocked down were protected against induction of apoptosis by TNFα and cycloheximide. Rapamycin failed to mimic the pro-apoptotic effect of PRAS40, suggesting that PRAS40 mediates apoptosis independently of its inhibitory effect on mTORC1. Q6MZQ0 is structurally similar to proline rich protein 5 (PRR5) and was therefore named PRR5-Like (PRR5L). PRR5L binds specifically to mTORC2, via Rictor and/or SIN1. Unlike other mTORC2 members, PRR5L is not required for mTORC2 integrity or kinase activity, but dissociates from mTORC2 upon knock down of tuberous sclerosis complex 1 (TSC1) and TSC2. Hyperactivation of mTOR by TSC1/2 knock down enhanced apoptosis whereas PRR5L knock down reduced apoptosis. PRR5L knock down reduced apoptosis also in mTORC2 deficient cells. The above suggests that mTORC2-dissociated PRR5L may promote apoptosis when mTOR is hyperactive. Thus, PRAS40 and PRR5L are novel mTOR-associated proteins that control the balance between cell growth and cell death.
An adaptive BCI system for virtual navigation

A brain computer interface (BCI) builds an additional pathway between the brain and external devices. This paper introduces a BCI system combined with virtual reality (VR) technology that allows users to navigate in the virtual apartment by motor imagery. Since performance in online sessions is sometimes found to decrease due to non-stationarity of electroencephalogram (EEG) signals, we proposed a method based on adaptive probabilistic neural network (APNN) to overcome this phenomenon. Online experiments were carried out using the BCI system and offline analysis was conducted to make a comparison among different methods. Online results demonstrated that most subjects were able to perform well on the system, and offline analysis showed that the APNN was comparatively predominant.
OPTIMAL WITHDRAWALS IN COASTAL AQUIFERS UNDER SALINE INTRUSIONS 1

Saltwater intrusion in coastal aquifers is nowadays one of the main causes of groundwater quality degradation. These intrusions are often due to excessive withdrawals in sensible parts of coastal aquifers. Because seawater is denser than freshwater, it invades aquifers hydraulically connected with the sea where hydrostatic equilibrium has been disturbed by important water abstraction levels. The scope of this paper is to identify specific problems set by optimal management of coastal aquifers under saline intrusion conditions. To this end, we use a simplified model describing a coastal aquifer. We focuse our attention on hydraulic interface moves resulting from freshwater withdrawals level changes. Water abstaction shifts landward the last feasible withdrawals point. This relation between water abstraction and pumping point position creates a specific externality that has to be taken into account in order to determine optimal use of resource.
A password-based authenticator: P-Auth

At present most of the existing authenticators require the input of high entropy keys. However, these keys are hard to remember and a great deal of the existing authentication protocols are based on passwords, the low entropy ones, which are given by users in practice. In this paper, we propose a password-based authenticator P-Auth. P-Auth uses ldquoreputationrdquo to generate high entropy unite secrets that are build on password and session key. It also employs threshold scheme to resist offline dictionary attack and provide forward security.