Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural and Biochemical Basis for Ubiquitin Ligase Recruitment by Arrestin-related Domain-containing Protein-3 (ARRDC3)*

Background: ARRDC proteins bind ubiquitin ligases and are involved in receptor down-regulation. Results: ARRDC3 recruitment of Nedd4 is explained. Conclusion: The first PPXY motif of ARRDC3 binds to the third WW domain of Nedd4 with high affinity, whereas other domains also contribute. Significance: The structure explains aspects of high affinity recognition. After protracted stimulation, the β2-adrenergic receptor and many other G-protein-coupled receptors are ubiquitinated and down-regulated. Arrestin-related domain-containing protein-3 (ARRDC3) has been proposed to recruit the ubiquitin ligase Nedd4 to the β2-adrenergic receptor. ARRDC3 contains two PPXY motifs that could potentially interact with any of the four WW domains of Nedd4. Here we dissect the interaction determinants. ARRDC3 PPXY-Nedd4 WW dissociation constants vary from unmeasurable to Kd = 3 μm for the third WW domain of Nedd4 binding to the first PPXY motif of ARRDC3. Structures of the uncomplexed and PPXY1-bound WW3 domain were determined at 1.1 and 1.7 Å resolution. The structures revealed conformational changes upon binding and the hydrogen bonding network in exquisite detail. Tight packing of ARRDC3 Val-352′, part of a 310 helix at the C terminus of PPXY1, is important for high affinity binding to WW3. Although no single WW domain is strictly essential for the binding of Nedd4 and ARRDC3 expressed in HEK293 cells, high affinity binding of full-length ARRDC3 and Nedd4 is driven by the avid interaction of both PPXY motifs with either the WW2-WW3 or WW3-WW4 combinations, with Kd values as low as 300 nm.
A Multi-resolution Approach for Combining Visual Information using Nuclei Segmentation and Classification in Histopathological Images

This paper describes a multi-resolution technique to combine diagnostically important visual information at different magnifications in H&E whole slide images (WSI) of gastric cancer. The primary goal is to improve the results of nuclei segmentation method for heterogeneous histopathological datasets with variations in stain intensity and malignancy levels. A minimum-model nuclei segmentation method is first applied to tissue images at multiple resolutions, and a comparative evaluation is performed. A comprehensive set of 31 nuclei features based on color, texture and morphology are derived from the nuclei segments. AdaBoost classification method is used to classify these segments into a set of pre-defined classes. Two classification approaches are evaluated for this purpose. A relevance score is assigned to each class and a combined segmentation result is obtained consisting of objects with higher visual significance from individual magnifications, thereby preserving both coarse and fine details in the image. Quantitative and visual assessment of combination results shows that they contain comprehensive and diagnostically more relevant information than in constituent
Misspecification versus bubbles in hyperinflation data: Monte Carlo and interwar European evidence

This paper analyzes tests of the Cagan hyperinflation-money demand model that have several advantages relative to those in the literature. They do not confound specification error with rational bubbles, are implementable with a linear procedure, and are frequently able to detect periodically collapsing bubbles that have challenged existing tests. After a Monte Carlo analysis, the tests are applied to data from hyperinflations in Austria, Germany, Hungary, and Poland. Strong evidence of model misspecification is found for Austria, while the model with a rational, explosive component well characterizes the Polish data. Inferences for Germany and Hungary are mixed.
Flame Retardant Emissions from Spray Polyurethane Foam Insulation

The desire to build more energy efficient homes in the United States has led to the expansion of the residential spray polyurethane foam (SPF) insulation industry. Upon application of SPF, reacting chemicals form expanding polyurethane foam that fills cracks and gaps, reducing infiltration and thermal conductivity of the building envelope. However, more information is being sought on chemical emissions from SPF to better understand occupant exposures and any potential impacts on health. The objective of this investigation was to investigate the emission of flame retardant tris (1-chloro-2-propyl) phosphate (TCPP) from SPF using both micro-chambers and a full scale residential test facility. Two high pressure, open cell foams and one high pressure, closed cell foam were tested using micro-chambers. After 100 hours, TCPP concentrations from the open cell samples were 100 times higher than TCPP concentrations from the closed cell SPF. TCPP emissions from open cell foam were found to correlate exponentially with temperature and vary with flow rate, indicating emission factors from SPF micro-chamber experiments may not directly predict TCPP concentrations in buildings without consideration of material mass transfer properties. Due to the use of TCPP in furniture, SPF has not previously been positively identified as a primary source of indoor TCPP concentrations in actual buildings. This research measured airborne TCPP concentrations in the furniture-free National Institute of Standards and Technology (NIST) Net Zero Energy Residential Test Facility (NZERTF) that contained 15 m of exposed, two-year-old, open cell SPF. The measured NZERTF TCPP emission rates were not directly predicted by emission factors from the micro-chamber measurements, which suggests a mass transfer-based modelling approach is needed for predicting TCPP concentrations from open cell SPF. More research is needed to determine how data from micro-chamber studies can be used to predict exposures of residential occupants to emissions from SPF foam.
Using Kinect to Capture Human Motion for Mechanism Synthesis, Motion Generation and Visualization

In this paper, we are presenting a framework for capturing human motions using Microsoft Kinect sensor for the purpose of 1) generating task positions for mechanism and robot synthesis, and 2) generation and visualization of B-spline interpolated and approximated motion from the captured task positions. The theoretical foundation of this work lies in Kinematic Mapping, Dual and Bi-quaternions, and NURBS (Non-Uniform Rational B-spline) geometry. Lately, Kinect has opened doors for creation of natural and intuitive human-machine interactive (HMI) systems in medicine, robotic manipulation, CAD, and many other fields, where visual-sensing and -capture is a central theme. Kinect has made a huge impact in physical therapy area, achieving new benchmarks in tele-rehabilitation by improving physical exercise assessment, monitoring and supervision using the skeletal data. Moreover, Kinect’s depth sensing capability has helped in retrieving depth information required for robotic vision in grasping, object recognition which was previously done using computationally demanding computer vision algorithms. Kinect’s point cloud data with interactive gestures has proven to be useful in various CAD software for conceptual design of shapes. Mechanism synthesis is one of the areas in Kinematics, where Kinect-provided skeletal data can be leveraged to design and develop highly customized end-user collaborated mechanism solutions. We demonstrate that using Kinect, OpenGL, and Openframeworks, we can capture discrete (or, key) rigid body displacements, continuous motions, and generate and visualize rational B-spline motions from captured key positions. Capturing only a few key positions results in significant data savings and also provides a natural way to create tasks for mechanism synthesis problems. The output is a set of dual quaternions and 4× 4 homogeneous transforms representing a task motion, which can be used as an input for mechanism synthesis applications. The tool produced also allows users to generate trajectories of various points on a moving rigid body interactively. A Kinectbased capture of such motions can help create highly-customized assistive devices for people who suffer from a range of motionrelated difficulties due to old age or disabilities.
Uncovering New Pathogen–Host Protein–Protein Interactions by Pairwise Structure Similarity

Pathogens usually evade and manipulate host-immune pathways through pathogen–host protein–protein interactions (PPIs) to avoid being killed by the host immune system. Therefore, uncovering pathogen–host PPIs is critical for determining the mechanisms underlying pathogen infection and survival. In this study, we developed a computational method, which we named pairwise structure similarity (PSS)-PPI, to predict pathogen–host PPIs. First, a high-quality and non-redundant structure–structure interaction (SSI) template library was constructed by exhaustively exploring heteromeric protein complex structures in the PDB database. New interactions were then predicted by searching for PSS with complex structures in the SSI template library. A quantitative score named the PSS score, which integrated structure similarity and residue–residue contact-coverage information, was used to describe the overall similarity of each predicted interaction with the corresponding SSI template. Notably, PSS-PPI yielded experimentally confirmed pathogen–host PPIs of human immunodeficiency virus type 1 (HIV-1) with performance close to that of in vitro high-throughput screening approaches. Finally, a pathogen–host PPI network of human pathogen Mycobacterium tuberculosis, the causative agent of tuberculosis, was constructed using PSS-PPI and refined using filtration steps based on cellular localization information. Analysis of the resulting network indicated that secreted proteins of the STPK, ESX-1, and PE/PPE family in M. tuberculosis targeted human proteins involved in immune response and phagocytosis. M. tuberculosis also targeted host factors known to regulate HIV replication. Taken together, our findings provide insights into the survival mechanisms of M. tuberculosis in human hosts, as well as co-infection of tuberculosis and HIV. With the rapid pace of three-dimensional protein structure discovery, the SSI template library we constructed and the PSS-PPI method we devised can be used to uncover new pathogen–host PPIs in the future.
A spiking-timing-based model for classification

With a similar capability of processing spikes as biological neural systems, networks of spiking neurons are expected to achieve a performance similar to that of living brains. In recent days, many great achievements have been made in spiking neuron models and its learning algorithm. We build an integrated model using spiking neural networks (SNNs), which performs phase encoding method and delay learning-based ReSuMe (DL-ReSuMe) supervised learning algorithm to solve optical character recognition (OCR) task. In this way, the superiority of spiking-timing-based model will be displayed.
SOA and the Enterprise -- Lessons from the City

Enterprise wide rather than departmental focus differentiates SOA from the earlier legacy technologies like client server and object oriented programming. This enterprise focus not only includes the IT personnel, but also the business personnel into the broader SOA ecosystem. This paper presents lessons learnt from three years of SOA implementation at a large city government in the US from an enterprise wide application perspective
Prediction by partial approximate matching for lossless image compression

Summary form only given. In this paper, motivated by the characteristics of natural images, we introduce PPAM - prediction by partial approximate matching, a modification of the context model used by the prediction by partial matching (PPM) family of text compression algorithms, for images. Unless there is a strong edge boundary, natural images usually contain locally homogeneous areas. However, the correlation within these local neighborhoods is usually not exact. Repeating contexts often occur in an approximate (rather than exact) form. In PPAM, we exploit these inexact contexts using methods from text pattern matching with errors. In PPM, context searching starts by looking for the maximum-order context and then escapes to shorter contexts until a match is found. PPAM uses a simple context quantization scheme to avoid potentially huge time and space requirements. We group the contexts based on the square of their Euclidean distances (SED) from a reference context. We tested the performance of the proposed PPAM on standard test images and good results were obtained.
Universität Augsburg Monocular 3d Human Pose Estimation by Classification Institut F ¨ Ur Informatik D-86135 Augsburg Monocular 3d Human Pose Estimation by Classification

We present a novel approach to 2D and 3D human pose estimation in monocular images by building on and improving recent advances in this field. We take the full body pose as a combination of a 3D pose and a viewpoint and in this way define classes that are then learned by a classifier. Compared to part based approaches, our approach does not suffer from self–occluded body parts since such occlusions are characteristic for certain classes and thus are captured during class definition. Moreover, we significantly relax the requirements posed on training data by the fact that we do neither require labeled viewpoints nor background subtracted images, and the carried out action does not need to be cyclic. By combining an efficient classifier with efficient image features, we present a generic and fast way to estimate human poses in images and achieve comparable results to state–of–the art approaches which we demonstrate on a public benchmark.
Design of Piecewise Linear LQ Control by Multivariable Circle Criterion for Dynamic Positioning System

A model of servomechanism used for high-powered actuators in mechanical systems consists of a position feedback loop around the cascade connection of a saturation function with an integrator. The saturation function constrains the position change rate and so for a position demand rate faster than the maximum rate of the actuator servosystem, the time lag of the actuator response behind the demand results in the actual plant input different from the controller output and may exhibit undesirable behavior such as excessive overshoot and further the control system may become unstable. This paper clarifies a design of piecewise linear LQ control (PLC) whose control gain switching variable is an input of the saturation function in the actuator servomechanism and which makes the controlled system stable even under drastic disturbances. In design procedures the permissible maximum absolute value of the input to the saturation function as a reciprocal number of the permissible minimum sector bound is decided by the multivariable circle criterion enabling to ensure the local absolute stability of the total system according to each level of LQ controller gain groups determined beforehand. In control procedures the gain switching function selects a control gain group by monitoring the inputs of the saturation functions, for example the gain switching function selects the smaller gain group when the input absolute value to the saturation function exceeds the permissible maximum absolute value decided for the used control gain group. Evaluation of the design method is made by computer simulation for dynamic positioning (DP) system by PLC using the controller gain switching function, which holds the position and heading of a ship under wind disturbances by controlled thrusters and the results as expected are obtained
Compact Resolved Ejecta in the Nearest Tidal Disruption Event

Tidal disruption events (TDEs) occur when a star or substellar object passes close enough to a galaxy’s supermassive black hole to be disrupted by tidal forces. NGC 4845 (d = 17 Mpc) was host to a TDE, IGR J12580+0134, detected in 2010 November. Its proximity offers us a unique close-up of the TDE and its aftermath. We discuss new Very Long Baseline Array (VLBA) and Karl G. Jansky Very Large Array observations, which show that the radio flux from the active nucleus created by the TDE has decayed in a manner consistent with predictions from a jet-circumnuclear medium interaction model. This model explains the source’s broadband spectral evolution, which shows a spectral peak that has moved from the submillimeter (at the end of 2010) to GHz radio frequencies (in 2011–2013) to in 2015. The milliarcsecond-scale core is circularly polarized at 1.5 GHz but not at 5 GHz, consistent with the model. The VLBA images show a complex structure at 1.5 GHz that includes an east–west extension that is ∼40 mas (3 pc) long, as well as a resolved component that is 52 mas (4.1 pc) northwest of the flat-spectrum core, which is all that can be seen at 5 GHz. If ejected in 2010, the northwest component must have had over five years. However, this is unlikely, as our model suggests strong deceleration to speeds within months and a much smaller, sub-parsec size. In this interpretation, the northwest component could have either a non-nuclear origin or be from an earlier event.
Improving the performance of intrusion detection using Dialog-based Payload Aggregation

We propose Dialog-based Payload Aggregation (DPA) that extracts relevant payload data from TCP/IP packet streams based on sequence numbers in the TCP header for improved intrusion detection performance. Typical network-based Intrusion Detection Systems (IDSs) like Snort, which use rules for matching payload data, show severe performance problems in high-speed networks. Our detailed analysis based on live network traffic reveals that most of the signature matches either occur at the beginning of TCP connections or directly after direction changes in the data streams. Our DPA approach exploits protocol semantics intrinsic to bidirectional communication, i.e., most application layer protocols rely on requests and associated responses with a direction change in the data stream in between. DPA forwards the next N bytes of payload whenever a connection starts, or when the direction of the data transmission changes. All data transferred after this window is discarded. According to experimental results, our method reduces the amount of data to be analyzed at the IDS to around 3:7% for typical network traffic. At the same time, more than 89% of all potential events can be detected. Assuming a linear relationship between data rate and processing time of an IDS, this results in a speedup of more than one order of magnitude in the best case. Our performance analysis that combines DPA with Snort shows a 400% increase in packet processing throughput on commodity hardware.
The Macrophage Scavenger Receptor A Is Host-Protective in Experimental Meningococcal Septicaemia

Macrophage Scavenger Receptor A (SR-A) is a major non-opsonic receptor for Neisseria meningitidis on mononuclear phagocytes in vitro, and the surface proteins NMB0278, NMB0667, and NMB1220 have been identified as ligands for SR-A. In this study we ascertain the in vivo role of SR-A in the recognition of N. meningitidis MC58 (serogroup B) in a murine model of meningococcal septicaemia. We infected wild-type and SR-A−/− animals intraperitoneally with N. meningitidis MC58 and monitored their health over a period of 50 hours. We also determined the levels of bacteraemia in the blood and spleen, and measured levels of the pro-inflammatory cytokine interleukin-6 (IL-6). The health of SR-A−/− animals deteriorated more rapidly, and they showed a 33% reduction in survival compared to wild-type animals. SR-A−/− animals consistently exhibited higher levels of bacteraemia and increased levels of IL-6, compared to wild-type animals. Subsequently, we constructed a bacterial mutant (MC58-278-1220) lacking two of the SR-A ligands, NMB0278 and NMB1220. Mutation of NMB0667 proved to be lethal. When mice were infected with the mutant bacteria MC58-278-1220, no significant differences could be observed in the health, survival, bacteraemia, and cytokine production between wild-type and SR-A−/− animals. Overall, mutant bacteria appeared to cause less severe symptoms of septicaemia, and a competitive index assay showed that higher levels of wild-type bacteria were recovered when animals were infected with a 1∶1 ratio of wild-type MC58 and mutant MC58-278-1220 bacteria. These data represent the first report of the protective role of SR-A, a macrophage-restricted, non-opsonic receptor, in meningococcal septicaemia in vivo, and the importance of the recognition of bacterial protein ligands, rather than lipopolysaccharide.
Full-duplex communication in cooperative cognitive radio networks: Preliminary results

We address the design of cooperative cognitive radio networks (CCRN) adopting a full-duplex (FD) technique. In order to enable FD communication in the CCRN, simultaneous transmitting and receiving antennas are employed for the secondary users. Some preliminary results from numerical evaluation indicate that the proposed FD multiple-input-multiple-output CCRN framework can provide a considerable performance gain over the conventional CCRN frameworks.
Hyponatraemia in patients with crush syndrome during the Wenchuan earthquake

Background Although sodium disturbances are common in hospitalised patients, no study has specifically investigated the epidemiology of hyponatraemia in patients with crush syndrome. Objectives To describe the incidence of hyponatraemia and assess its effect on outcome in patients with crush syndrome during the Wenchuan earthquake. Methods A retrospective study was conducted in 17 reference hospitals during the Wenchuan earthquake. We excluded patients younger than 15 years and those with missing sodium values within 3 days after being rescued from the ruins. Results Hyponatraemia (serum sodium concentration <135 mmol/l) was seen in 91/180 (50.6%) patients on admission. Compared with patients with normonatraemia, those with hyponatraemia were younger, had more severe traumatic injury and renal failure, underwent more fasciotomies, received more blood transfusion and renal replacement therapy. In the multivariable-adjusted model, the number of extremity injuries (OR=1.59, 95% CI 1.08 to 2.33) and serum creatinine (OR=1.30, 95% CI 1.07 to 1.59) were independently associated with the occurrence of hyponatraemia. Covariate adjusted multiple logistic regression analysis showed an independent mortality risk rising with hyponatraemia (OR=5.74, 95% CI 1.18 to 28.00). Conclusions Hyponatraemia was common in the patients with crush syndrome during the Wenchuan earthquake and associated with poor prognosis. Water, commercial drinks and hypotonic intravenous fluids should be supplied carefully to patients with crush syndrome.
Simulation of human locomotion using a musculoskeletal model

Human gaits in a sagittal plane are simulated throughout a musculoskeletal model with a simple feedback postural controller. Hill-type muscletendon models generate joint motions over each leg. Typical human gait data about joint torques and angles is used to estimate muscular activation signal profiles by a simple optimization technique. A simple feedback controller updates the activation profiles to achieve stable dynamical walking simulation through optimization with a genetic algorithm. Simulation study demonstrates the proposed approach achieves realistic human walking behavior with neurophysiologically plausible muscular activations.