Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of Reovirus σ1 in Complex with Its Receptor Junctional Adhesion Molecule-A

Viral attachment to specific host receptors is the first step in viral infection and serves an essential function in the selection of target cells. Mammalian reoviruses are highly useful experimental models for studies of viral pathogenesis and show promise as vectors for oncolytics and vaccines. Reoviruses engage cells by binding to carbohydrates and the immunoglobulin superfamily member, junctional adhesion molecule-A (JAM-A). JAM-A exists at the cell surface as a homodimer formed by extensive contacts between its N-terminal immunoglobulin-like domains. We report the crystal structure of reovirus attachment protein σ1 in complex with a soluble form of JAM-A. The σ1 protein disrupts the JAM-A dimer, engaging a single JAM-A molecule via virtually the same interface that is used for JAM-A homodimerization. Thus, reovirus takes advantage of the adhesive nature of an immunoglobulin-superfamily receptor by usurping the ligand-binding site of this molecule to attach to the cell surface. The dissociation constant (KD) of the interaction between σ1 and JAM-A is 1,000-fold lower than that of the homophilic interaction between JAM-A molecules, indicating that JAM-A strongly prefers σ1 as a ligand. Analysis of reovirus mutants engineered by plasmid-based reverse genetics revealed residues in σ1 required for binding to JAM-A and infectivity of cultured cells. These studies define biophysical mechanisms of reovirus cell attachment and provide a platform for manipulating reovirus tropism to enhance vector targeting.
Frequency-Hopped Quadrature Frequency Synthesizer in 0.13-$\mu$m Technology

This paper presents a Wireless-USB/WiMedia-compliant fast-hopping frequency synthesizer architecture with quadrature outputs based on sub-harmonic injection-locking. The synthesizer features a cross-coupled quadrature digitally-controlled oscillator, that is injection-locked to a sub-harmonic frequency. An intuitive closed-form expression for the dynamics of the quadrature injection-locked oscillator and a technique to achieve fast frequency-hopping, are presented. The overall architecture, based on this technique, is a CMOS-only implementation and has been fabricated in a 0.13-μm SiGe BiCMOS process. On-chip mixers have been implemented to measure the quadrature accuracy of the outputs. Measurement results indicate lock-times of less than 2.5 ns, a locked phase noise of -114 dBc/Hz at 1 MHz offset and a quadrature accuracy of better than 0.5°. The frequency synthesizer (excluding output buffers) occupies an area of 0.27 mm2 and consumes 14.5 mW of power. The best and worst case spur suppression achieved are 47 and 31 dB, respectively. This is the lowest power fast-hopping quadrature frequency synthesizer that has been reported to date.
Edge-Directed Interpolation in a Bayesian Framework

In this paper we present a novel framework for Edge-Directed Interpolation (EDI) of still images. The problem is treated as finding maximum a posteriori estimates of each interpolated pixel type and intensity value. The pixel type may be one of the pre-defined edge directions or "non-edge". Instead of the separate steps of edge orientation detection and intensity interpolation, maximizing the joint probability density function of type and intensity provides a better fit to the local image structure. Such a technique allows an effective discrimination between edges and non-edges (uniform areas and texture), thus leading to the suppression of artifacts which are common to existing EDI methods. Objective and subjective comparisons with conventional EDI methods corroborate the advantages of the proposed one. Moreover, the locality and the low computational complexity of the method make it suitable for a hardware implementation.
High-Performance Parallel Implementations of the NAS Kernel Benchmarks on the IBM SP2

Recently, researchers at NASA Ames have defined a set of computational benchmarks designed to measure the performance of parallel supercomputers. In this paper, we describe the parallel implementation of the five kernel benchmarks from this suite on the IBM SP2™, a scalable, distributed memory parallel computer. High-performance implementations of these kernels have been obtained by mapping the computation of these kernels to the underlying architecture of the SP2 machine. Performance results for the SP2 are compared with publicly available results for other high-performance computers.
Complete Genome Sequence of a Street Rabies Virus Isolated from a Dog in Nigeria

ABSTRACT A canine rabies virus (RABV) was isolated from a trade dog in Nigeria. Its entire genome was sequenced and found to be closely related to canine RABVs circulating in Africa. Sequence comparison indicates that the virus is closely related to the Africa 2 RABV lineage. The virus is now termed DRV-NG11.
IBM IPAM RIPS 2010 Program Topic Detection and Causal Influence in Microblogs

The emergence of the web2.0 phenomenon has set in place a planetary-scale infrastructure for rapid proliferation of information and ideas. Social media platforms such as blogs, twitter accounts and online discussion sites are large-scale forums where every individual can voice a potentially influential public opinion. According to recent surveys, a massive number of internet users are turning to such forums to collect recommendations and reviews for products and services – shaping their choices and stances by the commentary of the online community as a whole.
Delay-driven layer assignment for advanced technology nodes

This paper addresses a delay-driven layer assignment problem with consideration of via delay and coupling effect in the global routing stage. A negotiation-based framework is proposed to balance delay, congestion, and via count. Coupling capacitance is considered using a probabilistic look-up table. Finally, the proposed algorithm uses both parallel wires and wide wires to reduce wire delay. The effectiveness of our layer assignment algorithm is supported by extensive experimental results.
Constraint-enhanced role engineering via answer set programming

Role engineering (RE) aims to develop and maintain appropriate role-based access control (RBAC) configurations. However, RE with constraints in place is not well-studied. Constraints usually describe organizations' security and business requirements. An inconsistency between configurations and constraints compromises security and availability, as it may authorize otherwise forbidden access and deprive users of due privileges. In this paper, we apply answer set programming (ASP) to discover RBAC configurations that comply with constraints and meet various optimization objectives. We first formulate the need of supporting constraints as a problem independent of and complementary to existing RE problems. We then present a flexible framework for translating the proposed problem to ASP programs. In this way, the problem can be addressed via ASP solvers. Finally, we demonstrate the effectiveness and efficiency of our approach through experimental results.
A fully automated system for retinal vessel tortuosity diagnosis using scale dependent vessel tracing and grading

A fully automated system for retinal vessel tortuosity system diagnosis is proposed in this paper. Our diagnosis system includes: (1) automated retinal vessel segmentation and tracing; (2) computerized tortuosity grading. In recent years, many works have been done on computerized diagnosis of retinal vessel tortuosity. But there are few researchers working on a fully automated system. The major difficulties in producing a fully automated system includes: (1) automated tracing of vessels to identify each individual branch; (2) global tortuosity grading of a retinal vessel image. In this paper, we propose a scheme to trace and grade retinal vessels using scale (variant widths and lengths of vessel segments) dependent techniques. The experimental results show that our system is useful in clinical applications.
Localization of cell surface sites involved in fibronectin fibrillogenesis

Fibronectin binding sites on cultured human fibroblasts were localized by high voltage electron microscopy using either 5- or 18-nm colloidal gold beads (Au5 or Au18) bound to intact fibronectin, the 70-kD amino- terminal fragment of fibronectin that blocks incorporation of exogenous fibronectin into extracellular matrix, or 160-180-kD fragments of fibronectin with cell adhesion and heparin-binding activities. Binding sites for Au18-fibronectin on the cell surface were localized to specific regions along the edge of the fibroblast and on retraction fibers. Au18-fibronectin complexes at these sites were initially localized in clusters that co-aligned with intracellular microfilament bundles. With longer incubations, Au18-fibronectin complexes were arranged into long fibrillar networks on the cell surface and in the extracellular space. The appearance of Au18-fibronectin in these fibrillar networks and disappearance of clusters of Au18-fibronectin suggest that Au18-fibronectin complexes are arranged into matrix at specific regions of the cell surface. Au18-70-kD fragment complexes initially had a similar distribution to Au18-fibronectin complexes. With longer incubations, Au18-70-kD fragment complexes were found in long linear arrangements on the cell surface. Double labeling experiments using Au18-70-kD fragment and Au5-160-180-kD fragments showed that the 70-kD fragment and the 160-180-kD fragments bind to different regions of the cell.
High-Speed Per-Flow Traffic Measurement with Probabilistic Multiplicity Counting

On today's high-speed backbone network links, measuring per-&#64258;ow traf&#64257;c information has become very challenging. Maintaining exact per-&#64258;ow packet counters on OC-192 or OC-768 links is not practically feasible due to computational and cost constrains. Packet sampling as implemented in today's routers results in large approximation errors. Here, we present Probabilistic Multiplicity Counting (PMC), a novel data structure that is capable of accounting traf&#64257;c per &#64258;ow probabilistically. The PMC algorithm is very simple and highly parallelizable, and therefore allows for ef&#64257;cient implementations in software and hardware. At the same time, it provides very accurate traf&#64257;c statistics. We evaluate PMC with both arti&#64257;cial and real-world traf&#64257;c data, demonstrating that it outperforms other approaches.
Tumor necrosis factor is dispensable for the success of immunogenic anticancer chemotherapy

The antineoplastic effects of anthracyclines have been shown to rely, at least in part, on a local immune response that involves dendritic cells (DCs) and several distinct subsets of T lymphocytes. Here, we show that the administration of anthracyclines to mice bearing established neoplasms stimulates the intratumoral secretion of tumor necrosis factor α (TNFα). However, blocking the TNFα/TNF receptor (TNFR) system by three different strategies—namely, (1) neutralizing antibodies, (2) etanercept, a recombinant protein in which TNFR is fused to the constant domain of an IgG1 molecule, and (3) gene knockout—failed to negatively affect the therapeutic efficacy of anthracyclines in three distinct tumor models. In particular, TNFα-blocking strategies did not influence the antineoplastic effects of doxorubicin (a prototypic anthracycline) against MCA205 fibrosarcomas growing in C57BL/6 mice, F244 sarcomas developing in 129/Sv hosts and H2N100 mammary carcinomas arising in BALB/c mice. These findings imply that, in contrast to other cytokines (such as interleukin-1β, interleukin-17 and interferon γ), TNFα is not required for anthracyclines to elicit therapeutic anticancer immune responses.
Postinduction Requirement of NMDA Receptor Activation for Late-Phase Long-Term Potentiation of Developing Retinotectal Synapses In Vivo

Spaced patterns of repetitive synaptic activation often result in a long-lasting, protein synthesis-dependent potentiation of synaptic transmission, known as late-phase long-term potentiation (L-LTP) that may serve as a substrate for long-term memory. Behavioral studies showed that posttraining blockade of NMDA subtype of the glutamate receptor (NMDAR) impaired long-term memory, although NMDAR activation is generally known to be required during LTP induction. In this study, we found that the establishment of L-LTP in vivo requires NMDAR activation within a critical time window after LTP induction. In the developing visual system of Xenopus laevis tadpole, L-LTP of retinotectal synapses could be induced by three episodes of theta burst stimulation (TBS) of the optic nerve with 5 min spacing (“spaced TBS”), but not by three TBS episodes applied en masse or spaced with intervals ≥10 min. Within a time window of ∼30 min after the spaced TBS, local perfusion of the tectum with NMDAR antagonist d-AP5 or Ca2+-chelator EGTA-AM impaired the establishment of L-LTP, indicating the requirement of postinduction activation of NMDAR/Ca2+ signaling. Moreover, inhibiting spontaneous spiking activity in the tectum by local application of tetrodotoxin (TTX) prevented L-LTP when TTX was applied for 15 min immediately after the spaced TBS but not 1 h later, whereas the same postinduction TTX application in the retina had no effect. These findings offer new insights into the synaptic basis for the requirement of postlearning activation of NMDARs and point to the importance of postlearning spontaneous circuit activity in memory formation.
On Discovering Community Trends in Social Networks

Real-world social networks (e.g., blogosphere) often evolve over time and thus poses challenges on conventional social network analysis techniques which model the underlying networks as static graphs. In this paper, we are interested in detecting dynamic communities and their trend of evolution in a social network by examining the structural and dynamic patterns of interactions. In doing so, we propose an iterative mining algorithm for computing the intensities and bursts of some hidden communities over time. Our method is probabilistic in nature and can be applied to both undirected graphs and directed graphs. Quantitative and qualitative performance comparisons between the proposed method and some representative methods for social network analysis are provided. Evaluation results based on three benchmark datasets, including Reuters terror news network, political blogosphere, and Enron emails, show that the proposed method is both effective and efficient.
Collaborative voice activity detection for hearing aids

Most binaural hearing aid systems have separate processing for each ear. Collaborative processing allows the left and right hearing aids to share information and resources. In this paper, collaborative processing is used to take advantage of head shadow effects to improve Voice Activity Detection (VAD). We emphasize here that while a variety of improvements in VAD and speech enhancement are possible, contributions have meaning only if the advances fit into the framework of the limited computing resources available in current hearing aid devices. The proposed approach leads to an absolute speech hit rate improvement of up to 25% at low SNR in the ear closest to noise source. The cost is a lower noise hit rate in the other ear. It is however sufficient to ensure proper noise spectrum magnitude estimation.
The science of deriving dense linear algebra algorithms

In this article we present a systematic approach to the derivation of families of high-performance algorithms for a large set of frequently encountered dense linear algebra operations. As part of the derivation a constructive proof of the correctness of the algorithm is generated. The article is structured so that it can be used as a tutorial for novices. However, the method has been shown to yield new high-performance algorithms for well-studied linear algebra operations and should also be of interest to those who wish to produce best-in-class high-performance codes.
Gel versus aerogel to collect high velocity ejectas from laser shock-loaded metallic targets for postrecovery analyses

Soft recovery of fast objects is an issue of considerable interest for many applications involving shock wave loading, such as ballistics, armor design, or more recently laser-driven inertial confinement fusion, where the characterization of the debris ejected from metallic shells subjected to intense laser irradiation conditions the design of the experiments. In this work, we compare the high velocity ejecta recovery efficiency of two materials: silica aerogel (density 0.03 g/cm3), which has been used as fragment collector for many years, and “varagel” (density 0.9 g/cm3), which we have tested recently in laser shock experiments. Ejected fragments have been recovered in both types of collectors. Then, samples have been analyzed by X-ray tomography at the European Synchrotron Radiation Facility (ESRF). Three-dimensional reconstructions of the fragments populations have been achieved, and quantitative comparisons between both collecting materials, used in the same conditions, have been performed.
Deterministic Reductions in an Asynchronous Parallel Language

Reduction operations are a common and important feature in many parallel programming models. In this paper, we present a new reduction construct for Concurrent Collections (CnC). CnC is a deterministic, asynchronous parallel programming model in which data production and reduction can overlap. While reductions are most frequently incorporated in synchronous contexts where all data is available before parallel reduction begins, our solution works for the asynchronous CnC model. We retain the determinism of the CnC parallel programming model while providing an efficient high-level construct for specifying reductions. Keywords-reductions; declarative languages; singleassignment languages; determinism; parallelism.
Cytosolic inositol 1,4,5-trisphosphate dynamics during intracellular calcium oscillations in living cells

We developed genetically encoded fluorescent inositol 1,4,5-trisphosphate (IP3) sensors that do not severely interfere with intracellular Ca2+ dynamics and used them to monitor the spatiotemporal dynamics of both cytosolic IP3 and Ca2+ in single HeLa cells after stimulation of exogenously expressed metabotropic glutamate receptor 5a or endogenous histamine receptors. IP3 started to increase at a relatively constant rate before the pacemaker Ca2+ rise, and the subsequent abrupt Ca2+ rise was not accompanied by any acceleration in the rate of increase in IP3. Cytosolic [IP3] did not return to its basal level during the intervals between Ca2+ spikes, and IP3 gradually accumulated in the cytosol with a little or no fluctuations during cytosolic Ca2+ oscillations. These results indicate that the Ca2+-induced regenerative IP3 production is not a driving force of the upstroke of Ca2+ spikes and that the apparent IP3 sensitivity for Ca2+ spike generation progressively decreases during Ca2+ oscillations.
The FD-TD analysis of aperture antennas using a triplate transmission line structure

An aperture antenna (APA) is a flat element that radiates a linearly polarized wave. This antenna has been fabricated using a triplate transmission line (TTL). The measured data has shown that the TTL structure with a cavity improves the radiation characteristics. The purpose of this paper is to obtain a theoretical reason why the APA with the cavity improves the radiation characteristics. For this, two APAs are analyzed and compared: one has a flat conducting bottom without a cavity, and the other has a cavity in the bottom plate. Special attention is paid to a comparison of Poynting vectors in the two APAs. The radiation pattern and input impedance are also evaluated and discussed.
Untreated Human Infections by Trypanosoma brucei gambiense Are Not 100% Fatal

The final outcome of infection by Trypanosoma brucei gambiense, the main agent of sleeping sickness, has always been considered as invariably fatal. While scarce and old reports have mentioned cases of self-cure in untreated patients, these studies suffered from the lack of accurate diagnostic tools available at that time. Here, using the most specific and sensitive tools available to date, we report on a long-term follow-up (15 years) of a cohort of 50 human African trypanosomiasis (HAT) patients from the Ivory Coast among whom 11 refused treatment after their initial diagnosis. In 10 out of 11 subjects who continued to refuse treatment despite repeated visits, parasite clearance was observed using both microscopy and polymerase chain reaction (PCR). Most of these subjects (7/10) also displayed decreasing serological responses, becoming progressively negative to trypanosome variable antigens (LiTat 1.3, 1.5 and 1.6). Hence, in addition to the “classic” lethal outcome of HAT, we show that alternative natural progressions of HAT may occur: progression to an apparently aparasitaemic and asymptomatic infection associated with strong long-lasting serological responses and progression to an apparently spontaneous resolution of infection (with negative results in parasitological tests and PCR) associated with a progressive drop in antibody titres as observed in treated cases. While this study does not precisely estimate the frequency of the alternative courses for this infection, it is noteworthy that in the field national control programs encounter a significant proportion of subjects displaying positive serologic test results but negative results in parasitological testing. These findings demonstrate that a number of these subjects display such infection courses. From our point of view, recognising that trypanotolerance exists in humans, as is now widely accepted for animals, is a major step forward for future research in the field of HAT.
Relationship between atherosclerosis and late-life depression: the Rotterdam Study.

CONTEXT Depression in late life has been associated with vascular abnormalities. Several studies have demonstrated that persons with brain infarcts are more likely to have depressive disorders. Furthermore, depression is related to the subsequent development of ischemic heart disease. OBJECTIVE To investigate the relationship between atherosclerosis at different locations and depression in the general population. DESIGN Cross-sectional population-based study. SETTING The Rotterdam Study, a population-based cohort study. PARTICIPANTS In 4019 men and women 60 years and older, we assessed atherosclerosis at different locations, including common carotid intima-media thickness, plaques in the carotid arteries, the ankle-brachial blood pressure index, and aortic atherosclerosis. An overall measure of extracoronary atherosclerosis was obtained in 3747 persons by computing the principal component of these extracoronary atherosclerosis measures. In a subgroup of 1986 persons, we additionally measured coronary calcifications. MAIN OUTCOME MEASURE All subjects were screened for depressive symptoms. Screen-positive subjects had a psychiatric interview to diagnose depressive disorder. RESULTS More severe extracoronary atherosclerosis was associated with a higher prevalence of depressive disorders. For every 1-standard deviation increase, the prevalence increased by 30%. Furthermore, we found a strong relationship of severe coronary and aortic calcifications with depressive disorders (odds ratio, 3.89; 95% confidence interval, 1.55-9.77; and odds ratio, 2.00; 95% confidence interval, 1.02-3.96, respectively). CONCLUSIONS Atherosclerosis and depression are associated in the elderly. This finding is compatible with the vascular depression hypothesis. However, the cross-sectional nature of the study does not allow causal inferences. In particular, earlier depressive episodes may have contributed to the development of atherosclerosis.