Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural determinants of growth factor binding and specificity by VEGF receptor 2

Vascular endothelial growth factors (VEGFs) regulate blood and lymph vessel formation through activation of three receptor tyrosine kinases, VEGFR-1, -2, and -3. The extracellular domain of VEGF receptors consists of seven immunoglobulin homology domains, which, upon ligand binding, promote receptor dimerization. Dimerization initiates transmembrane signaling, which activates the intracellular tyrosine kinase domain of the receptor. VEGF-C stimulates lymphangiogenesis and contributes to pathological angiogenesis via VEGFR-3. However, proteolytically processed VEGF-C also stimulates VEGFR-2, the predominant transducer of signals required for physiological and pathological angiogenesis. Here we present the crystal structure of VEGF-C bound to the VEGFR-2 high-affinity-binding site, which consists of immunoglobulin homology domains D2 and D3. This structure reveals a symmetrical 2∶2 complex, in which left-handed twisted receptor domains wrap around the 2-fold axis of VEGF-C. In the VEGFs, receptor specificity is determined by an N-terminal alpha helix and three peptide loops. Our structure shows that two of these loops in VEGF-C bind to VEGFR-2 subdomains D2 and D3, while one interacts primarily with D3. Additionally, the N-terminal helix of VEGF-C interacts with D2, and the groove separating the two VEGF-C monomers binds to the D2/D3 linker. VEGF-C, unlike VEGF-A, does not bind VEGFR-1. We therefore created VEGFR-1/VEGFR-2 chimeric proteins to further study receptor specificity. This biochemical analysis, together with our structural data, defined VEGFR-2 residues critical for the binding of VEGF-A and VEGF-C. Our results provide significant insights into the structural features that determine the high affinity and specificity of VEGF/VEGFR interactions.
Comparison of efficient small antennas for wireless microsensors through simulation and experiment

This work presents the results of a study on a set of small antennas for wireless microsensor devices. We consider antennas that are small compared to the wavelength, and can be fitted on a small PCB. The key point regarding small antennas is that their performance is heavily dependent on their electrical size. The product of the bandwidth and the gain is a function of the size of the antenna, so that the gain can only be increased at the expense of bandwidth, and vice versa. Our goal was not only to miniaturize the elements, but to maintain acceptable radiation characteristics as well. A reasonable figure of merit is suggested, in an attempt to gather all fundamental antenna parameters in a single quantity. The behavior of the examined schemes was characterized through simulation and experimental validation.
Technical Introduction: A primer on probabilistic inference

Research in computer science, engineering, mathematics, and statistics has produced a variety of tools that are useful in developing probabilistic models of human cognition. We provide an introduction to the principles of probabilistic inference that are used in the papers appearing in this special issue. We lay out the basic principles that underlie probabilistic models in detail, and then briefly survey some of the tools that can be used in applying these models to human cognition.
Progress: an approach for defining and monitoring non deterministic design-to-time methods

Guaranteed response time is one of the most important issues encountered in designing real time systems. The AI community has developed various approaches to solve this problem, e.g. anytime algorithms, approximate processing, design to time scheduling and progressive reasoning. All these approaches rely on a trade-off between run time and quality of results. In the framework of the ESPRIT projects Nos. 5145 and 7805 REAKT (Real time Knowledge Tool), we have developed a similar approach called PROGRESS (PROGressive REasoning System). PROGRESS manages AI tasks with hard and soft deadlines, provided that competing methods are available for the tasks to be solved. A comparison was made between our model and a conventional algorithm (Earliest Deadline Algorithm) and showed the higher robustness and efficiency of PROGRESS.
Complex frequency shifted (CFS) PML for the WLP-FDTD method

This paper proposes a complex frequency shifted PML absorbing boundary condition for the unconditionally stable finite difference time-domain method based on weighted Laguerre polynomials (WLPs). The method offers a number of advantages over the traditional implementations of the PML in the WLP-FDTD method. Numerical results show the CFS PML is effective.
Biomechanical Factors in Planning of Periacetabular Osteotomy

Objective: This study addresses the effects of cartilage thickness distribution and compressive properties in the context of optimal alignment planning for periacetabular osteotomy (PAO). Background: The Biomechanical Guidance System (BGS) is a computer-assisted surgical suite assisting surgeon’s in determining the most beneficial new alignment of a patient’s acetabulum. The BGS uses biomechanical analysis of the hip to find this optimal alignment. Articular cartilage is an essential component of this analysis and its physical properties can affect contact pressure outcomes. Methods: Patient-specific hip joint models created from CT scans of a cohort of 29 dysplastic subjects were tested with four different cartilage thickness profiles (one uniform and three non-uniform) and two sets of compressive characteristics. For each combination of thickness distribution and compressive properties, the optimal alignment of the acetabulum was found; the resultant geometric and biomechanical characterization of the hip were compared among the optimal alignments. Results: There was an average decrease of 49.2 ± 22.27% in peak contact pressure from the preoperative to the optimal alignment over all patients. We observed an average increase of 19 ± 7.7° in center-edge angle and an average decrease of 19.5 ± 8.4° in acetabular index angle from the preoperative case to the optimized plan. The optimal alignment increased the lateral coverage of the femoral head and decreased the obliqueness of the acetabular roof in all patients. These anatomical observations were independent of the choice for either cartilage thickness profile, or compressive properties. Conclusion: While patient-specific acetabular morphology is essential for surgeons in planning PAO, the predicted optimal alignment of the acetabulum was not significantly sensitive to the choice of cartilage thickness distribution over the acetabulum. However, in all groups the biomechanically predicted optimal alignment resulted in decreased joint contact pressure and improved acetabular coverage.
Groupware implementation: reinvention in the sociotechnical frame

ciotechnical systems theory suggests several themes about implementation, including continuous mutual adaptation of tool and context, task emphasis, the priority of process, and changes in evaluative criteria over time. The effectiveness of these ideas is illustrated in the experience of the World Bank in its implementation of a group decision support system, GroupSystems.
Chandra High Resolution Camera Imaging of GRS 1758–258

We observed the "microquasar" GRS 1758-258 four times with Chandra. Two observations with the imaging detector of the High Resolution Camera (HRC-I) were made in 2000 September-October spanning an intermediate-to-hard spectral transition (identified with the Rossi X-Ray Timing Explorer). Another HRC-I observation and an Advanced CCD Imaging Spectrometer/High Energy Transmission Grating (HETG) observation were made in 2001 March following a hard-to-soft transition to a very low flux state. Based on the three HRC images and the HETG zero-order image, the accurate position (J2000) of the X-ray source is R.A. = 18h01m12. ˢ39, decl. = -25°44'36. ″1 (90% confidence radius = 0.″45), consistent with the purported variable radio counterpart. All three HRC images are consistent with GRS 1758-258 being a point source, indicating that any bright jet is less than ~1 lt-month in projected length, assuming a distance of 8.5 kpc.
Markov Perfect Equilibrium: I. Observable Actions

Abstract We define Markov strategy and Markov perfect equilibrium (MPE) for games with observable actions. Informally, a Markov strategy depends only on payoff-relevant past events. More precisely, it is measurable with respect to the coarsest partition of histories for which, if all other players use measurable strategies, each player's decision-problem is also measurable. For many games, this definition is equivalent to a simple affine invariance condition. We also show that an MPE is generically robust: if payoffs of a generic game are perturbed, there exists an almost Markovian equilibrium in the perturbed game near the initial MPE. Journal of Economic Literature Classification Numbers: C72, C73.
The TRAC mission manager autonomous control executive

Present autonomy technologies do not compensate for a vehicle's structural, perceptual and control limitations through reflexive responses and rapid adaptation as a pilot typically does. For Uninhabited Air Vehicles (UAVs) to have more general application the mishap rates must be much reduced. Therefore the vehicle control systems must be capable of rigorously analyzing and predicting in real-time, component failures and other disturbance effects to determine the appropriate response much as a pilot does. The purpose of the Reliable Autonomous Control Technology (REACT) program, a jointly-developed mission management architecture by Lockheed Martin Aeronautics, General Electric, NASA Dryden, and Jet Propulsion Lab. , is to autonomously accomplish this complex mission and subsystem management task. Based on prior analysis of recent UAV data, the Autonomous Control Executive (ACE) could play a role in preventing up to about 36% of these mishaps. We describe the ACE that would be part the Mission Management architecture and some initial results from rapid prototype of the architecture implemented using a PC based simulator.
Meshless Local Petrov-Galerkin (MLPG) Mixed Finite Difference Method for Solid Mechanics

The Finite Difference Method (FDM), within the framework of the Meshless Local PetrovGalerkin (MLPG) approach, is proposed in this paper for solving solid mechanics problems. A “mixed” interpolation scheme is adopted in the present implementation: the displacements, displacement gradients, and stresses are interpolated independently using identical MLS shape functions. The system of algebraic equations for the problem is obtained by enforcing the momentum balance laws at the nodal points. The divergence of the stress tensor is established through the generalized finite difference method, using the scattered nodal values and a truncated Taylor expansion. The traction boundary conditions are imposed in the stress equations directly, using a local coordinate system. Numerical examples show that the proposed MLPG mixed finite difference method is both accurate and efficient, and stable. keyword: Meshless method, Finite difference method, MLPG
Defending the Sybil attack in P2P networks: taxonomy, challenges, and a proposal for self-registration

The robustness of peer-to-peer (P2P) networks, in particular of DHT-based overlay networks, suffers significantly when a Sybil attack is performed. We tackle the issue of Sybil attacks from two sides. First, we clarify, analyze, and classify the P2P identifier assignment process. By clearly separating network participants from network nodes, two challenges of P2P networks under a Sybil attack become obvious: i) stability over time, and ii) identity differentiation. Second, as a starting point for a quantitative analysis of time-stability of P2P networks under Sybil attacks and under some assumptions with respect to identity differentiation, we propose an identity registration procedure called self-registration that makes use of the inherent distribution mechanisms of a P2P network.
HCMV Infection of Human Trophoblast Progenitor Cells of the Placenta Is Neutralized by a Human Monoclonal Antibody to Glycoprotein B and Not by Antibodies to the Pentamer Complex

Human cytomegalovirus (HCMV) is the major viral cause of congenital infection and birth defects. Primary maternal infection often results in virus transmission, and symptomatic babies can have permanent neurological deficiencies and deafness. Congenital infection can also lead to intrauterine growth restriction, a defect in placental transport. HCMV replicates in primary cytotrophoblasts (CTBs), the specialized cells of the placenta, and inhibits differentiation/invasion. Human trophoblast progenitor cells (TBPCs) give rise to the mature cell types of the chorionic villi, CTBs and multi-nucleated syncytiotrophoblasts (STBs). Here we report that TBPCs are fully permissive for pathogenic and attenuated HCMV strains. Studies with a mutant virus lacking a functional pentamer complex (gH/gL/pUL128-131A) showed that virion entry into TBPCs is independent of the pentamer. In addition, infection is blocked by a potent human neutralizing monoclonal antibody (mAb), TRL345, reactive with glycoprotein B (gB), but not mAbs to the pentamer proteins pUL130/pUL131A. Functional studies revealed that neutralization of infection preserved the capacity of TBPCs to differentiate and assemble into trophospheres composed of CTBs and STBs in vitro. Our results indicate that mAbs to gB protect trophoblast progenitors of the placenta and could be included in antibody treatments developed to suppress congenital infection and prevent disease.
Oscillatory interaction between amygdala and hippocampus coordinates behavioral modulation based on reward expectation

The aim of this study is to examine how the amygdala and hippocampus interact for behavioral performance modulated by different Reward-expectations (REs). We simultaneously recorded neuronal spikes and local field potential from the basolateral amygdala and hippocampal CA1 while rats were performing a light-side discrimination task with different expectations of a high or low probability of reward delivery. Here, we report the following results. First, the rats actually modulated their behavioral performance on their expectations of a high or low probability of reward. Second, we found more neurons related to RE in the amygdala and more neurons related to task performance in the hippocampus. Third, a prominent increase in the coherence of high-frequency oscillations (HFOs) (90–150 Hz) between the amygdala and the hippocampus was present during high RE. Fourth, coherent HFOs during inter-trial intervals and theta coherence during trials had significant correlations with the behavioral goal-selection time. Finally, cross-frequency couplings of LFPs within and across the amygdala and hippocampus occurred during ITI. These results suggest that the amygdala and hippocampus have different functional roles in the present task with different REs, and the distinctive band of coherence between the amygdala and the hippocampus contributes to behavioral modulation on the basis of REs. We propose that the amygdala influences firing rates and the strength of synchronization of hippocampal neurons through coherent oscillation, which is a part of the mechanism of how reward expectations modulate goal-directed behavior.
A FML-based hybrid reasoner combining fuzzy ontology and Mamdani inference

Fuzzy ontologies have been employed to represent and reason over fuzzy information, which often occurs in real-world applications. Fuzzy inference systems (FIS) are well-known computational intelligence systems whose inferences can also be exploited in fuzzy ontology-based applications. Specifically, the combination of fuzzy ontologies and Mamdani-type FIS can provide inferences involving fuzzy rules and numerical property values, which can be considered in other fuzzy ontology reasoning tasks. In this sense, this paper proposes a hybrid reasoner combining fuzzy ontology and Mamdani inference to provide meaningful inferences that are not available to fuzzy ontology-based applications in an integrated way. Fuzzy rules are represented with Fuzzy Markup Language, providing an abstraction level with regard to the underlying FIS implementation. Some experiments are presented regarding a recommender system context, including a comparison with a fuzzy description logic reasoner in terms of fuzzy rule reasoning semantics and integration issues.
Performance analysis of network-level QoS with encoding configurations for unicast video streaming over IEEE 802.11 WLAN networks

Video streaming has a large impact on the resource requirements of the WLAN. However, there are many variables involved in video streaming, such as the video content being streamed, how the video is encoded and how it is sent. This makes the role of radio resource management extremely difficult. In this paper we investigate the effect that video encoding configurations has on the network resource requirements for unicast video streaming in a WLAN environment. We compare the network resource requirements of several content types encoded at various encoding configurations with varying I-frame frequencies, target encoding bit rates and hint track settings. We present two key findings. We show that by halving the hint track MTU values, the access requirements of the WLAN are increased by 20%. Furthermore, we show how the I-frame frequency of the encoded file relates to the resource requirements of the WLAN.
Modeling and Performance Analysis of Scalable Web Servers Deployed on the Cloud

Over the last few years, cloud computing has become quite popular. It offers Web-based companies the advantage of scalability. However, this scalability adds complexity which makes analysis and predictable performance difficult. There is a growing body of research on load balancing in cloud data centres which studies the problem from the perspective of the cloud provider. Nevertheless, the load balancing of scalable web servers deployed on the cloud has been subjected to less research. This paper introduces a simple queueing model to analyse the performance metrics of web server under varying traffic loads. This assists web server managers to manage their clusters and understand the trade-off between QoS and cost. In this proposed model two thresholds are used to control the scaling process. A discrete-event simulation (DES) is presented and validated via an analytical solution.
Bi‐stable block by 4‐aminopyridine of a transient K+ channel (Kv1.4) cloned from ferret ventricle and expressed in Xenopus oocytes.

1. Using the two‐microelectrode, ‘cut open’ oocyte, and ‘torn off’ macropatch voltage clamp techniques, we studied the blocking effects of 4‐aminopyridine (4‐AP) on two cloned K+ channels expressed in Xenopus oocytes, an inactivating K+ channel isolated from ferret ventricle (FK1), and its NH2‐terminal deletion mutant (delta NCO) which lacks fast N‐type inactivation. 2. Experiments with a permanently charged, impermeant 4‐AP derivative, 4‐aminopyridine‐methyliodide, indicated that the cationic form of 4‐AP blocks at an intracellular site. 3. Block accumulated from pulse to pulse and was sensitive to the applied potential during hyperpolarizing deactivating pulses, indicating trapping of 4‐AP in deactivated channels. For long trains of depolarizing pulses (‐90 to +50 mV, 0.1 Hz), 4‐AP block increased with decreasing pulse duration. Block of FK1 was much more sensitive to pulse duration than was block of delta NCO, consistent with competition between N‐type inactivation and 4‐AP binding. 4. To elucidate these mechanisms further, in the absence of fast N‐type inactivation the following results were obtained on delta NCO channels: (1) application of 4‐AP caused the appearance of apparent inactivation; (2) 4‐AP, however, did not cause cross‐over of deactivating tail currents; (3) 4‐AP block developed with time for potentials positive to ‐40 mV; and (4) trapping of 4‐AP by delta NCO was insensitive to the degree of C‐type inactivation. 5. We conclude that the kinetics of 4‐AP block of FK1 and delta NCO channels cannot be accounted for by either a pure open channel or closed channel blocking scheme.
On the nature of superoutbursts in dwarf novae

We present the first detailed hydrodynamic simulation of a superoutburst to incorpo- rate the full tidal potential of a binary system. A two-dimensional smoothed particle hydrodynamics code is used to simulate a superoutburst in a binary with the param- eters of the SU UMa system Z Chamaeleontis. The simulated light curves shows all the features observed in such systems. Analysis of the mass flux through the disc and the growth rate of the superhumps and disc eccentricity show that the superoutburst- superhump phenomenon is a direct result of tidal instability. No enhanced mass trans- fer from the secondary is required to initiate or sustain these phenomena. Comparisons of superoutbursts with normal outbursts are made and we show that the model can be reconciled with the behavior of U Geminorum type dwarf novae, which show no superoutbursts.
A REAL-TIME POLYPHONIC MUSIC TRANSCRIPTION SYSTEM

In this paper, we describe a real-time polyphonic transcription system submitted to the multiple F0 n ote tracking task of 2008 Music Retrieval Evaluation eXchange (MIREX). The Resonator Time-Frequency Image (RTFI) is used as the basic time-frequency analysis tool. The evaluation of this system unde r the MIREX task is also discussed.
A Unified Monitoring Framework for Distributed Environment

Distributed computing is a field of computer science that studies distributed systems. With the increasing computing capacity of computers it is widely used to solve large problems. Monitoring system is one of the key components in distributed computing. Although there have been varieties of monitoring systems developed by different organizations, it is still a great challenge to monitor a heterogeneous distributed environment in a unified and transparent way. In this paper, we present a unified monitoring framework for distributed environment (UMFDE) with heterogeneous monitoring systems, and then propose a comprehensive method based on the Enterprise Service Bus (ESB) to integrate the monitoring systems in the environment as a unified monitoring system. A representative case study is given to show the feasibility of this framework.
Exploration and Exploitation of Action Selection in the Motor Cortex and Basal Ganglia.

The basal ganglia (BG) have been proposed as a possible neural substrate for action selection in the vertebrate brain. This hypothesis has been developed primarily through pathological observations. Human neurological disorders of the basal ganglia can result in movements that are slowed or eliminated (bradykinesia/akinesia in Parkinson’s Disease) or conversely, uncontrolled or unwanted (e.g. in Huntington’s Disease and Tourette Syndrome). However, the precise mechanisms by which BG circuits influence behavior remain to be understood. In this thesis, I have focused on determining the role of BG circuits in selection of well-trained actions, and how these findings can be applied for use in neuroprosthetic devices. In the first study, I investigated one proposed mechanism to help resolve competition between actions in the BG: feedforward inhibition of striatal medium spiny cells (MSNs) by fast-spiking interneurons (FSIs). I recorded single unit activity from presumed MSNs and FSIs together with motor cortex and globus pallidus (GP), in rats performing a simple choice task. My findings support the idea that FSIs contribute to action selection processes within striatal microcircuits, but suggest that the feedback pathway from GP to FSIs may be particularly important for the suppression of highly trained yet unwanted actions. In my second study, I examined the role of large neuronal ensembles of the BG and motor cortex during two variations on a simple action selection task. Analysis of local field potential (LFP) oscillations revealed that ∼20Hz rhythms (β20) were prominent during the hold period, but only if subjects were instructed on which direction to move during the hold period. This finding is consistent with the hypothesis that β20