Miracle-dz/UniFAR-FTUs huggingface dataset:
Techniques to cope with missing data in host–pathogen protein interaction prediction

Motivation: Approaches that use supervised machine learning techniques for protein–protein interaction (PPI) prediction typically use features obtained by integrating several sources of data. Often certain attributes of the data are not available, resulting in missing values. In particular, our host–pathogen PPI datasets have a large fraction, in the range of 58–85% of missing values, which makes it challenging to apply machine learning algorithms. Results: We show that specialized techniques for missing value imputation can improve the performance of the models significantly. We use cross species information in combination with machine learning techniques like Group lasso with ℓ1/ℓ2 regularization. We demonstrate the benefits of our approach on two PPI prediction problems. In our first example of Salmonella–human PPI prediction, we are able to obtain high prediction accuracies with 77.6% precision and 84% recall. Comparison with various other techniques shows an improvement of 9 in F1 score over the next best technique. We also apply our method to Yersinia–human PPI prediction successfully, demonstrating the generality of our approach. Availability: Predicted interactions, datasets, features are available at: http://www.cs.cmu.edu/~mkshirsa/eccb2012_paper46. html. Contact: judithks@cs.cmu.edu Supplementary Information: Supplementary data are available at Bioinformatics online.
LET-767 Is Required for the Production of Branched Chain and Long Chain Fatty Acids in Caenorhabditis elegans*

LET-767 from Caenorhabditis elegans belongs to a family of short chain dehydrogenases/reductases and is homologous to 17β-hydroxysterol dehydrogenases of type 3 and 3-ketoacyl-CoA reductases. Worms subjected to RNA interference (RNAi) of let-767 displayed multiple growth and developmental defects in the first generation and arrested in the second generation as L1 larvae. To determine the function of LET-767 in vivo, we exploited a biochemical complementation approach, in which let-767 (RNAi)-arrested larvae were rescued by feeding with compounds isolated from wild type worms. The arrest was only rescued by the addition of triacylglycerides extracted from worms but not from various natural sources, such as animal fats and plant oils. The mass spectrometric analyses showed alterations in the fatty acid content of triacylglycerides. Essential for the rescue were odd-numbered fatty acids with monomethyl branched chains. The rescue was improved when worms were additionally supplemented with long chain even-numbered fatty acids. Remarkably, let-767 completely rescued the yeast 3-ketoacyl-CoA reductase mutant (ybr159Δ). Because worm ceramides exclusively contain a monomethyl branched chain sphingoid base, we also investigated ceramides in let-767 (RNAi). Indeed, the amount of ceramides was greatly reduced, and unusual sphingoid bases were observed. Taken together, we conclude that LET-767 is a major 3-ketoacyl-CoA reductase in C. elegans required for the bulk production of monomethyl branched and long chain fatty acids, and the developmental arrest in let-767 (RNAi) worms is caused by the deficiency of the former.
Phase separation and structure formation in gadolinium based liquid and glassy metallic alloys

In this PhD research the liquid-liquid phase separation phenomena in Gd-based alloys was investigated in terms of phase equilibria, microstructure formation upon quenching the melt and corresponding magnetic properties of phase-separated metallic glasses. The phase diagrams of the binary subsystems Gd-Zr and Gd-Ti were experimentally reassessed. Especially the phase equilibria with the liquid phase could be determined directly by combining in situ high energy synchrotron X-ray diffraction with electrostatic levitation of the melt. The Gd-Zr system is of eutectic type with a metastable miscibility gap. The eutectic composition at 18 ± 2 at. % Zr, the liquidus line and the coexistence of bcc-Zr and bcc-Gd at elevated temperature could be determined. The Gd-Ti system is a monotectic system. The experimental observations in this work led to improved new Gd-Zr and Gd-Ti phase diagrams. The phase equilibria of the ternary Gd-Ti-Co system were analyzed for two alloy compositions. The XRD patterns for molten Gd35Ti35Co30 gave direct evidence for the coexistence of two liquid phases formed by liquid-liquid phase separation. The first experimental and thermodynamic assessment of the ternary Gd–Ti–Co system revealed that the stable miscibility gap of binary Gd–Ti extends into the ternary Gd–Ti–Co system (up to about 30 at.% Co). New phase-separated metallic glasses were synthesized in Gd-TM-Co-Al (TM = Hf, Ti or Zr) alloys. The microstructure was characterized in terms of composition and cooling rate dependence of phase separation. Due to large positive enthalpy of mixing between Gd on the one side and Hf, Ti or Zr on the other side, the alloys undergo liquid-liquid phase separation during rapid quenching the melt. The parameters determining the microstructure development during phase separation are the thermodynamic properties of the liquid phase, kinetic parameters and quenching conditions. By controlling these parameters and conditions the microstructure can be tailored both at microscopic and macroscopic length scales. This includes either droplet-like or interconnected microstructures at the microscopic level and glass-glass or glass-crystalline composites at the macroscopic level. Essential parameter for the quenched in microstructure is the temperature dependence of liquid-liquid phase separation, which is determined by the chemical
Boundary Lubrication Studies on Undulated Titanium Surfaces

It is customary in tribological research, and especially in practice, to employ smooth surfaces, for it is generally believed that smooth surfaces should have low sliding friction. However the wear particles produced during sliding get trapped at the interfaces, and plowing by the wear particles becomes the principal mechanism of friction. Through experimental and theoretical investigations, it is shown that the plowing friction component can be substantially reduced by means of surface undulations. Steel-titanium and titanium-titanium pairs were tested to investigate the role of surface undulations in boundary lubricated sliding. Compared with the experimental results of flat titanium surfaces, friction coefficient and wear rate were considerably reduced with the undulated titanium surfaces, especially when lubricants considered ineffective for titanium were used. In addition, the effects of pad width and cavity volume fraction of the undulated surface were also investigated. A plowing model proposed for.
Estimating Relatedness in the Presence of Null Alleles

Studies of genetics and ecology often require estimates of relatedness coefficients based on genetic marker data. However, with the presence of null alleles, an observed genotype can represent one of several possible true genotypes. This results in biased estimates of relatedness. As the numbers of marker loci are often limited, loci with null alleles cannot be abandoned without substantial loss of statistical power. Here, we show how loci with null alleles can be incorporated into six estimators of relatedness (two novel). We evaluate the performance of various estimators before and after correction for null alleles. If the frequency of a null allele is <0.1, some estimators can be used directly without adjustment; if it is >0.5, the potency of estimation is too low and such a locus should be excluded. We make available a software package entitled PolyRelatedness v1.6, which enables researchers to optimize these estimators to best fit a particular data set.
Metal Chalcogenides: A Rich Source of Nonlinear Optical Materials

Materials chemistry and the pursuit of new compounds through exploratory synthesis are having a strong impact in many technological fields. The field of nonlinear optics is directly impacted by the availability of enabling materials with high performance. Nonlinear optical (NLO) phenomena such as second harmonic and difference frequency generation (SHG and DFG, respectively) are effective at producing a coherent laser beam in difficult to reach frequency regions of the electromagnetic spectrum. Such regions include the infrared (IR), far-infrared, and terahertz frequencies. High performance NLO crystals are critical for applications utilizing these coherent light sources, and new materials are continuously sought for better conversion efficiency and performance. The class of metal chalcogenides is the most promising source of potential NLO materials with desirable properties particularly in the IR region where most classes of materials face various fundamental challenges. We review the recent developments.
Driving vision systems by communication

Proposes a new multi-agent system architecture which is dedicated to building distributed computer vision systems. This architecture incorporates a communication language which provides a great degree of flexibility: firstly, the language permits the construction of flexible and self-organizing vision systems; secondly, it is capable of expressing complex facts and tasks; thirdly, it is simple, i.e. human-readable and writable; and lastly, the messages provided by the communication language can be interpreted efficiently. We describe in detail the basic concepts of the multi-agent system architecture, including the communication language as well as the agent architecture and the interaction strategy. As a testbed for the proposed architecture, we have modelled an object recognition system as a society of autonomous agents which organize themselves according to a given recognition task by employing communication.
Evaluation of Initial Active Phase Laminitis in Equine Hoofs using MRI

Introduction Laminitis is an expensive and emotionally draining disease for the equine industry, whose pathophysiology remains unclear. The disease carries a higher morbidity and mortality rate compared to other causes of equine lameness. The appearance of chronic laminitis with magnetic resonance imaging (MRI) in cadavers has been described, but the usefulness of MRI in evaluating laminitis in the acute patient remains open. Clinical assessment and radiographs are the current standard for assessment of laminitis despite the inability to directly evaluate the soft tissues that are affected. This cadaver study evaluates the use of MRI during the initial active phase of laminitis as a means to increase the understanding of the disease and also serves as a justification for the development of an experiment involving live horses. Methods Seven feet from horses in the initial active stage of laminitis at the time of euthanasia and thirteen feet from horses without laminitis were imaged on a 4.7T/40cm magnet controlled by a Bruker Avance Console (Ettlingen, Germany). After a localizer spin echo sequence, T2* weighted images were acquired using 3D gradient echo (GRE) sequences with FOV = 12x12x8 cm, matrix = 384x384x40, TR/TE = 16.5/3.7 ms and 2 NEX. Furthermore proton density weighted images (20 slices, thickness 2.5 mm) were created using a 2D gradient echo sequence with TR/TE = 700/4.3 ms, 256x256 matrix and 12x12 cm FOV. Representative T2* 3D GRE images from the proximal, middle and distal thirds of each foot were evaluated by two boarded veterinary radiologists and a boarded equine surgeon. All reviewers were blinded to the animals clinical status and histological findings. All histological samples were evaluated by a boarded veterinary pathologist. Each MR image was examined for alteration of the following: corium architecture, corium signal intensity, laminar architecture, laminar signal intensity and laminar separation. Each change was graded normal, mild, moderate or severe (1-4). Specific quantitative measurements of the MR images included: width of the corium, width of the lamina, width of the dermal tissue (lamina plus corium), ratio of lamina to total dermal tissue (lamina:dermis). Measurements and rankings for each of the MR images (proximal, middle and distal) were evaluated for their ability to accurately predict the histological diagnosis for each foot using data plots and logistic regression. Digital radiographs and MR images of the limbs were evaluated separately for evidence of laminitis and the resulting diagnoses were compared to the histological diagnosis for correlation.
A FAST AND SIMPLE METHOD OF BUILDING DETECTION FROM LIDAR DATA BASED ON SCAN LINE ANALYSIS

One of the major problems in processing LiDAR (Light Detection And Ranging) data is its huge data volume which causes very high computational load when dealing with large areas with high point density. A fast and simple algorithm based on scan line analysis is proposed for automatic detection of building points from LiDAR data. At first, ground/non-ground classification is performed to filter out the ground points. Douglas–Peucker algorithm is then used to segment the scan line into segment objects based on height variation. These objects are preliminarily classified into buildings and vegetation based on local analysis using simple rules. At last, the region growing method is used to improve the quality of the extraction. The test data provided by the ISPRS test project on urban object extraction, containing a lot of buildings with complex roof structures, various sizes, and different heights, is used to test the algorithm. The experimental results show that the proposed algorithm can extract building regions effectively.
Progressive Renal Disease: Fibroblasts, Extracellular Matrix, and Integrins

Progressive renal disease is characterized by expansion of the tubulo-interstitium and accumulation of extracellular matrix within this tissue compartment. Interstitial fibroblasts are the primary producers of the interstitial matrix, and in the evolution of tubulo-interstitial fibrosis these cells undergo changes, namely increased proliferation, differentiation to myofibroblasts, and altered extracellular matrix metabolism, all of which, in other cell types, have been shown to be regulated by the major family of extracellular matrix receptors, the integrins. In the normal kidney, interstitial fibroblasts express α1, α4, α5, and β1 integrins, and fibrosis is associated with increased expression of α1, α2, α5, αv, and β1 integrins. In particular, α5, β1, and αv are suggested to be linked with the fibrotic process. In vitro, renal fibroblasts express a similar range of integrins, and ligation of selected receptors is associated with specific functions. Ligation of α6 stimulates proliferation, while α5 promotes expression of myofibroblastic phenotype, and β1 integrin has been implicated in cell contraction. Recent studies suggest that renal fibroblasts also express the non-integrin matrix receptors, discoidin domain receptors, and that changes in activation of these receptors may be associated with fibrogenic events. Thus the current, albeit limited, data suggest an important role for receptors for extracellular matrix molecules in the pathogenesis of progressive renal fibrosis.
Field programmable gate array-based acceleration of shortest-path computation

There exist several practical applications that require high-speed shortest-path computations. In many situations, especially in embedded applications, an field programmable gate array (FPGA)-based accelerator for computing the shortest paths can help to achieve high performance at low cost. This study presents an FPGA-based distributed architecture for solving the single-source shortest-path problem in a fast and efficient manner. The proposed architecture is based on the Bellman-Ford algorithm adapted to facilitate early termination of computation. One of the novelties of the architecture is that it does not involve any centralised control and the processing elements (PEs), which are identical in construction, operate in perfect synchronisation with each other. The functional correctness of the design has been verified through simulations and also in actual hardware. It has been shown that the implementation on a Xilinx Virtex-5 FPGA is more than twice as fast as a software implementation of the algorithm on a high-end general-purpose processor that runs at an order-of-magnitude faster clock. The speed-up offered by the design can be further improved by adopting an interconnection topology that maximises the data transfer rate among the PEs.
Design and development of an 11kV H-bridge multilevel STATCOM

This tutorial paper outlines the design and development of a "state-of-the-art" 11 kV direct connection multilevel static compensator (STATCOM) based on cascaded H-bridges. This STATCOM is currently being developed at the University of Newcastle under a linkage project with industrial partner, ResTech Pty Ltd, which is a company jointly owned by Ampcontrol Pty Ltd and the University of Newcastle. This is a large scale project involving a high degree of innovation - there are currently no commercially available direct connect STATCOMs using this topology. The paper will concentrate on the hardware and software design issues.
Reification: Reflection without metaphysics

We consider how the data structures of an interpreter may be made available to the program it is running, and how the program may alter its interpreter's structures. We refer to these processes as reification and reflection. We show how these processes may be considered as an extension of the fexpr concept in which not only the form and the environment, but also the continuation, are made available to the body of the procedure. We show how such a construct can be used to effectively add an unlimited variety of “special forms” to a very small base language. We consider some trade-offs in how interpreter objects are reified. Our version of this construct is similar to one in 3-Lisp [Smith 82, 84], but is independent of the rest of 3-Lisp. In particular, it does not rely on the notion of a tower of interpreters.
A novel aging sensor with programmable resolution

From year to year there are lot of new requirements regarding to the lifetime and reliability of integrated circuits (IC) especially in automotive applications. In align with technology scaling the amount of device's reliability issues are increasing but the quality requirements becoming stronger. Now the aging phenomena becomes one of the critical issues in applications with longer life time. Hence the aging sensors becoming one of the key part of today's ICs. In this paper a new aging sensor will be presented. This new sensor can predict various failures in ICs by showing low level of sensitivity to process, power and temperature variations. Sensor circuit was realized by 32 nm technology node and proved results usefulness by simulations presented in the paper.
Yet Another Proof of the Strong Equivalence Between Propositional Theories and Logic Programs

Recently, the stable model semantics was extended to the syntax of arbitrary propositional formulas, which are beyond the traditional rule form. Cabalar and Ferraris, as well as Cabalar, Pearce, and Valverde, showed that any propositional theory under the stable model semantics can be turned into a logic program. In this note, we present yet another proof of this result. Unlike the other approaches that are based on the logic of here-and-there, our proof uses familiar properties of classical logic. Based on this idea, we present a prototype implementation for computing stable models of propositional theories using the answer set solver DLV. We also note that every first-order formula under the stable model semantics is strongly equivalent to a prenex normal form whose matrix has the form of a logic program.
On the performance of non-coherent transmission schemes with equal-gain combining in generalized Κ-fading

The generalized κ-fading model, characterized by two parameters, κ and m, is a very versatile model and was recently shown to accurately capture the effects of composite shadowing and multipath fading in wireless communication systems. Furthermore, it can be used to model cascade multipath fading, which is relevant in, e.g., mobile-to-mobile communication scenarios. In this paper, we derive closed-form expressions for the bit error probability of two non-coherent transmission schemes over L diversity branches being subject to generalized κ-fading. Specifically, focus is on binary differential phase-shift keying (DPSK) and binary non-coherent frequency-shift keying (FSK) modulation with (post-detection) equal-gain combining at the receiver. We also discuss the extension of our results to M-ary modulation schemes. Considering both independent and correlated fading across the L branches, we derive expressions for the asymptotic diversity order, which reveal an interesting interplay between the two fading parameters κ and m. Moreover, we show that the diversity order of the considered non-coherent transmission schemes is the same as in the case of a coherent transmission scheme. Finally, numerical performance results are presented, and our analytical results are corroborated by means of Monte-Carlo simulations.
Arm-Reaching Tasks Kinematics and Kinetics During Isometric-Force and Motor Cortex Neural Correlates of Output

[PDF] [Full Text] [Abstract] , November 17, 2009; 106 (46): 19563-19568. PNAS and Emilio Bizzi Vincent C. K. Cheung, Lamberto Piron, Michela Agostini, Stefano Silvoni, Andrea Turolla Stability of muscle synergies for voluntary actions after cortical stroke in humans [PDF] [Full Text] [Abstract] , February , 2010; 103 (2): 986-1006. J Neurophysiol Jacques-Étienne Andujar, Kim Lajoie and Trevor Drew Guided Locomotion: Limb-Specific and Limb-Independent Effects A Contribution of Area 5 of the Posterior Parietal Cortex to the Planning of Visually [PDF] [Full Text] [Abstract] , August , 2010; 104 (2): 1090-1102. J Neurophysiol Emmanuel Guigon Active Control of Bias for the Control of Posture and Movement [PDF] [Full Text] [Abstract] , February 23, 2011; 31 (8): 3110-3128. J. Neurosci. Weiguo Song and Simon F. Giszter Locomotion in Rats Adaptation to a Cortex-Controlled Robot Attached at the Pelvis and Engaged during [PDF] [Full Text] [Abstract] , June , 2011; 25 (5): 398-411. Neurorehabil Neural Repair Michelle L. Harris-Love, Susanne M. Morton, Monica A. Perez and Leonardo G. Cohen Hemiparetic Stroke Patients : A TMS Study Mechanisms of Short-Term Training-Induced Reaching Improvement in Severely