Miracle-dz/UniFAR-FTUs huggingface dataset:
Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose

Plant cell-wall polysaccharides represent a vast source of food in nature. To depolymerize polysaccharides to soluble sugars, many organisms use multifunctional enzyme mixtures consisting of glycoside hydrolases, lytic polysaccharide mono-oxygenases, polysaccharide lyases, and carbohydrate esterases, as well as accessory, redox-active enzymes for lignin depolymerization. Many of these enzymes that degrade lignocellulose are multimodular with carbohydrate-binding modules (CBMs) and catalytic domains connected by flexible, glycosylated linkers. These linkers have long been thought to simply serve as a tether between structured domains or to act in an inchworm-like fashion during catalytic action. To examine linker function, we performed molecular dynamics (MD) simulations of the Trichoderma reesei Family 6 and Family 7 cellobiohydrolases (TrCel6A and TrCel7A, respectively) bound to cellulose. During these simulations, the glycosylated linkers bind directly to cellulose, suggesting a previously unknown role in enzyme action. The prediction from the MD simulations was examined experimentally by measuring the binding affinity of the Cel7A CBM and the natively glycosylated Cel7A CBM-linker. On crystalline cellulose, the glycosylated linker enhances the binding affinity over the CBM alone by an order of magnitude. The MD simulations before and after binding of the linker also suggest that the bound linker may affect enzyme action due to significant damping in the enzyme fluctuations. Together, these results suggest that glycosylated linkers in carbohydrate-active enzymes, which are intrinsically disordered proteins in solution, aid in dynamic binding during the enzymatic deconstruction of plant cell walls.
Mining network traffic for application category recognition on Android platform

Signature-based static mobile malware detection is fragile when facing code obfuscation and transformation attacks. Behavior based malware detection mechanisms have been widely studied and experimented. So far only the application's running behaviors, such as API calls and resource consumption are used, which can also be easily concealed and obfuscated with various coding tricks. Most mobile malware need either cellular or network connection to conduct their malicious activities. We propose to monitor an application's network behavior and interaction to characterize application behaviors. An integrated testbed system has been designed and prototyped for such network behavior collection. Statistical features are derived from application network traffic, which are further fed to a machine-learning based classifier to build one general model for each typical category of mobile applications. Experiments show that applications in each category with identical functionality exhibit similar network behaviors, which makes it possible to use the derived category model of network behaviors to evaluate future unknown application for its trustworthiness.
Molecular mechanisms of invadopodium formation

Invadopodia are actin-rich membrane protrusions with a matrix degradation activity formed by invasive cancer cells. We have studied the molecular mechanisms of invadopodium formation in metastatic carcinoma cells. Epidermal growth factor (EGF) receptor kinase inhibitors blocked invadopodium formation in the presence of serum, and EGF stimulation of serum-starved cells induced invadopodium formation. RNA interference and dominant-negative mutant expression analyses revealed that neural WASP (N-WASP), Arp2/3 complex, and their upstream regulators, Nck1, Cdc42, and WIP, are necessary for invadopodium formation. Time-lapse analysis revealed that invadopodia are formed de novo at the cell periphery and their lifetime varies from minutes to several hours. Invadopodia with short lifetimes are motile, whereas long-lived invadopodia tend to be stationary. Interestingly, suppression of cofilin expression by RNA interference inhibited the formation of long-lived invadopodia, resulting in formation of only short-lived invadopodia with less matrix degradation activity. These results indicate that EGF receptor signaling regulates invadopodium formation through the N-WASP–Arp2/3 pathway and cofilin is necessary for the stabilization and maturation of invadopodia.
Fibrogenesis in Kidney Transplantation: Potential Targets for Prevention and Therapy

Kidney allograft fibrosis results from a reactive process mediated by humoral and cellular events and the activation of transforming growth factor &bgr;1. It is a process that involves both parenchymal and graft infiltrating cells and can lead to organ failure if injury persists or if the response to injury is excessive. In this review, we will address the role of preventive and therapeutic strategies that target kidney allograft fibrogenesis. We conclude that in addition to preventive strategies, therapies based on bone morphogenetic protein 7, hepatocyte growth factor, connective tissue growth factor, and pirfenidone have shown promising results in preclinical studies. Clinical trials are needed to examine the effect of these therapies on long-term outcomes.
QM/MM Molecular Dynamics Studies of Metal Binding Proteins

Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.
Equi-Reward Utility Maximizing Design in Stochastic Environments

We present the Equi-Reward Utility Maximizing Design (ER-UMD) problem for redesigning stochastic environments to maximize agent performance. ER-UMD ﬁts well contemporary applications that require ofﬂine design of environments where robots and humans act and cooperate. To ﬁnd an optimal modiﬁcation sequence we present two novel solution techniques: a compilation that embeds design into a planning problem, allowing use of off-the-shelf solvers to ﬁnd a so-lution, and a heuristic search in the modiﬁcations space, for which we present an admissible heuristic. Evaluation shows the feasibility of the approach using standard benchmarks from the probabilistic planning competition and a benchmark we created for a vacuum cleaning robot setting.
AERODYNAMIC AND AEROACOUSTIC OPTIMIZATION OF AIRFOI LS VIA A PARALLEL GENETIC ALGORITHM

A parallel genetic algorithm (GA) was used to generate, in a single run, a family of aerodynamically efficient, low-noise rotor blade designs representing th e Pareto optimal set. The n-branch tournament, uniform crossover genetic algorithm operates on twenty design variables, which constitute the control points for a spline representing the airfoil surface. The GA takes advantage of available computer resources by operating in either serial mode or “manager/worker” parallel mode. The multiple objectives of this work were to maximize lift-to-drag of a rotor airfoil shape and to minimize an overall noise measure including effects of loading and thickness noise of the airfoil. Constraint s are placed on minimum lift coefficient, pitching moment and boundary layer convergence. The program XFOIL provides the aerodynamic analysis, and the code WOPWOP provides the aeroacoustic analysis. The Pareto-optimal airfoil set has been generated and is compared to the performance of a typical rotorcraft airfoil under identical flight conditions.
Cheetah: Fast Graph Kernel Tracking on Dynamic Graphs

Graph kernels provide an expressive approach to measuring the similarity of two graphs, and are key building blocks behind many real-world applications, such as bioinformatics, brain science and social networks . However, current methods for computing graph kernels assume the input graphs are static, which is often not the case in reality. It is highly desirable to track the graph kernels on dynamic graphs evolving over time in a timely manner. In this paper, we propose a family of Cheetah algorithms to deal with the challenge. Cheetah leverages the low rank structure of graph updates and incrementally updates the eigen-decomposition or SVD of the adjacency matrices of graphs. Experimental evaluations on real world graphs validate our algorithms (1) are significantly faster than alternatives with high accuracy and (b) scale sub-linearly.
MAP kinases MPK9 and MPK12 are preferentially expressed in guard cells and positively regulate ROS-mediated ABA signaling

Reactive oxygen species (ROS) mediate abscisic acid (ABA) signaling in guard cells. To dissect guard cell ABA-ROS signaling genetically, a cell type-specific functional genomics approach was used to identify 2 MAPK genes, MPK9 and MPK12, which are preferentially and highly expressed in guard cells. To provide genetic evidence for their function, Arabidopsis single and double TILLING mutants that carry deleterious point mutations in these genes were isolated. RNAi-based gene-silencing plant lines, in which both genes are silenced simultaneously, were generated also. Mutants carrying a mutation in only 1 of these genes did not show any altered phenotype, indicating functional redundancy in these genes. ABA-induced stomatal closure was strongly impaired in 2 independent RNAi lines in which both MPK9 and MPK12 transcripts were significantly silenced. Consistent with this result, mpk9-1/12-1 double mutants showed an enhanced transpirational water loss and ABA- and H2O2-insensitive stomatal response. Furthermore, ABA and calcium failed to activate anion channels in guard cells of mpk9-1/12-1, indicating that these 2 MPKs act upstream of anion channels in guard cell ABA signaling. An MPK12-YFP fusion construct rescued the ABA-insensitive stomatal response phenotype of mpk9-1/12-1, demonstrating that the phenotype was caused by the mutations. The MPK12 protein is localized in the cytosol and the nucleus, and ABA and H2O2 treatments enhance the protein kinase activity of MPK12. Together, these results provide genetic evidence that MPK9 and MPK12 function downstream of ROS to regulate guard cell ABA signaling positively.
Interpreting Neural Response Variability as Monte Carlo Sampling of the Posterior

The responses of cortical sensory neurons are notoriously variable, with the number of spikes evoked by identical stimuli varying significantly from trial to trial. This variability is most often interpreted as 'noise', purely detrimental to the sensory system. In this paper, we propose an alternative view in which the variability is related to the uncertainty, about world parameters, which is inherent in the sensory stimulus. Specifically, the responses of a population of neurons are interpreted as stochastic samples from the posterior distribution in a latent variable model. In addition to giving theoretical arguments supporting such a representational scheme, we provide simulations suggesting how some aspects of response variability might be understood in this framework.
Real - time Embedded Software Systems - An Introduction

A digital facsimile system suitable for the facsimile transmission of newspaper pages having screened picture portions and printed character portions is disclosed. The transmitter receives a digitized facsimile signal which is a train of pel codes formed by scanning a picture to be transmitted. In response to the digitized facsimile signal, a first reference generator produces first pel codes neighboring the present pel code, a second pel code spaced by the pitch of the screened picture from the present pel code, and third pel codes neighboring the second pel code. A ROM is addressed by the first, second and third pel codes to produce a first prediction code for the present pel code. The output of the ROM and the digitized facsimile signal are supplied to an Exclusive OR which provides a prediction error code according to the difference between the first prediction code and the present pel code. A train of prediction errors codes constitutes a prediction error signal which is encoded and transmitted. The receiver receives the encoded prediction error signal and decodes it to reproduce the prediction error signal. Another Exclusive OR produces the present pel code from each error code of the prediction error signal. A second reference code generator produces a second reference code corresponding to the first reference code on the basis of the output of the second Exclusive OR. A second ROM produces a second prediction code corresponding to the first prediction code on the basis of the second reference code and applies the second prediction code to the second Exclusive OR.
Design and implementation of SET-CMOS hybrid half subtractor

A hybrid SET-CMOS based half subtractor is presented in this paper. Combination of CMOS and SET technology facilitates new advantageous functionalities. The proposed hybrid SET-CMOS based half subtractor is implemented and simulated using T-SPICE. The simulation results are successfully verified with the truth table for the half subtractor. Two different approaches of SET-CMOS hybrid design is explained in this paper. Two main parts of the circuit is formed with the Single electron transistor based network and MOS transistor based network. The circuit of the half subtractor designed using both the approaches is presented in this paper. The stability analysis of the designed circuit is also explained in this paper with the stability plot. Also a performance comparison is given to justify the proposed work.
Yersinia pestis: mechanisms of entry into and resistance to the host cell

During infection, Yersinia, a facultative intracellular bacterial species, exhibits the ability to first invade host cells and then counteract phagocytosis by the host cells. During these two distinct stages, invasion or antiphagocytic factors assist bacteria in manipulating host cells to accomplish each of these functions; however, the mechanism through which Yersinia regulates these functions during each step remains unclear. Here, we discuss those factors that seem to function reversely and give some hypothesis about how bacteria switch between the two distinct status.
Fast Desynchronization for Decentralized Multichannel Medium Access Control

Distributed desynchronization algorithms are key to wireless sensor networks as they allow for medium access control in a decentralized manner. In this paper, we view desynchronization primitives as iterative methods that solve optimization problems. In particular, by formalizing a well established desynchronization algorithm as a gradient descent method, we establish novel upper bounds on the number of iterations required to reach convergence. Moreover, by using Nesterov's accelerated gradient method, we propose a novel desynchronization primitive that provides for faster convergence to the steady state. Importantly, we propose a novel algorithm that leads to decentralized time-synchronous multichannel TDMA coordination by formulating this task as an optimization problem. Our simulations and experiments on a densely-connected IEEE 802.15. 4-based wireless sensor network demonstrate that our scheme provides for faster convergence to the steady state, robustness to hidden nodes, higher network throughput and comparable power dissipation with respect to the recently standardized IEEE 802.15. 4e-2012 time-synchronized channel hopping (TSCH) scheme.
2‐Methylhopanoids are maximally produced in akinetes of Nostoc punctiforme: geobiological implications

2‐Methylhopanes, molecular fossils of 2‐methylbacteriohopanepolyol (2‐MeBHP) lipids, have been proposed as biomarkers for cyanobacteria, and by extension, oxygenic photosynthesis. However, the robustness of this interpretation is unclear, as 2‐methylhopanoids occur in organisms besides cyanobacteria and their physiological functions are unknown. As a first step toward understanding the role of 2‐MeBHP in cyanobacteria, we examined the expression and intercellular localization of hopanoids in the three cell types of Nostoc punctiforme: vegetative cells, akinetes, and heterocysts. Cultures in which N. punctiforme had differentiated into akinetes contained approximately 10‐fold higher concentrations of 2‐methylhopanoids than did cultures that contained only vegetative cells. In contrast, 2‐methylhopanoids were only present at very low concentrations in heterocysts. Hopanoid production initially increased threefold in cells starved of nitrogen but returned to levels consistent with vegetative cells within 2 weeks. Vegetative and akinete cell types were separated into cytoplasmic, thylakoid, and outer membrane fractions; the increase in hopanoid expression observed in akinetes was due to a 34‐fold enrichment of hopanoid content in their outer membrane relative to vegetative cells. Akinetes formed in response either to low light or phosphorus limitation, exhibited the same 2‐methylhopanoid localization and concentration, demonstrating that 2‐methylhopanoids are associated with the akinete cell type per se. Because akinetes are resting cells that are not photosynthetically active, 2‐methylhopanoids cannot be functionally linked to oxygenic photosynthesis in N. punctiforme.
The role of thyroid hormone in blood pressure homeostasis: evidence from short-term hypothyroidism in humans.

Arterial hypertension is known to be frequently associated with thyroid dysfunction, with a particularly high prevalence in chronic hypothyroidism. However, to our knowledge no comprehensive study addressed causal mechanisms possibly involved in this association. We here report the physiological relationships between blood pressure and neuro-humoral modifications induced by acute hypothyroidism in normotensive subjects. Twelve normotensive patients with previous total thyroidectomy were studied. Ambulatory 24-h blood pressure monitoring was performed, and free T(3), free T(4), TSH, PRA, aldosterone, cortisol, adrenaline, and noradrenaline were assayed 6 wk after oral L-T(4) withdrawal (phase 1) and 2 months after resumption of treatment (phase 2). During the hypothyroid state (TSH, 68.1 +/- 27.7 microIU/ml; mean +/- SD), daytime arterial systolic levels slightly, but significantly, increased (125.5 +/- 9.7 vs. 120.4 +/- 10.8 mm Hg; P < 0.05), and daytime diastolic levels (84.6 +/- 7.9 vs. 76.4 +/- 6.8 mm Hg; P < 0.001), noradrenaline (2954 +/- 1578 vs. 1574 +/- 962 pmol/liter; P < 0.001), and adrenaline (228.4 +/- 160 vs. 111.3 +/- 46.1 pmol/liter; P < 0.05) also increased. PRA remained unchanged (0.49 +/- 0.37 vs. 0.35 +/- 0.21 ng/ml.h; P = NS), whereas both aldosterone (310.3 +/- 151 vs. 156.9 +/- 67.5 pmol/liter; P < 0.005) and cortisol (409.2 +/- 239 vs. 250.9 +/- 113 pmol/liter; P < 0.02) significantly increased. By using univariate logistic regression daytime arterial diastolic values, noradrenaline and aldosterone were found to be significantly related to the hypothyroid state (P < 0.02, P < 0.036, and P < 0.024, respectively). In conclusion, our data show that thyroid hormones participate in the control of systemic arterial blood pressure homeostasis in normotensive subjects. The observed sympathetic and adrenal activation in hypothyroidism, which is reversible with thyroid hormone treatment, may also contribute to the development of arterial hypertension in human hypothyroidism.
Dynamic Traveling Repairperson Problem for dynamic systems

In this paper, we study the dynamic traveling repairman problem (DTRP) for dynamic systems. In the DTRP, customers are arising dynamically and randomly in a bounded region R, and when customers arrive, they wait for the repairperson to visit their location and offer a ¿service¿-that will take a certain random amount of time s-. In our study, the repairperson is modeled as a dynamic system whose output space contains R and our objective is the average time a customer has to wait to be serviced. We present schemes (for low and high traffic intensities) that guarantee that the expected waiting time for a customer scales within a constant factor of the optimum in terms of traffic intensity.
CPU, SMP and GPU implementations of Nohalo level 1, a fast co-convex antialiasing image resampler

This article introduces Nohalo level 1 ("Nohalo"), the simplest member of a family of image resamplers which straighten diagonal interfaces without adding noticeable nonlinear artifacts. Nohalo is interpolatory, co-monotone, co-convex, antialiasing, local average preserving, continuous, and exact on linears. Like many edge-enhancing methods, Nohalo has two main stages: first, nonlinear interpolation is used to create a double-density version of the original image; this double-density image is then resampled with bilinear interpolation. Nohalo is especially suited for GPU computing because the nonlinear slopes can be computed once and stored in a low bit-depth texture without rounding error, because the final bilinear stage can be performed in hardware, and because monotonicity allows full use of the texture's dynamic range. Demand-driven implementations for CPU's and SMPs are more complex, and require extra work to fix bottlenecks. Efficient implementations of the minmod function are key to performance. Three implementations of Nohalo are presented and bench-marked: a CPU version in C for the graphics library GEGL, an SMP version in C++ for the graphics library VIPS and a GPU version in HLSL for DirectX. The GPU implementation is branch-free thanks to the discovery of a simple formula for the pixel values of the double density image. Branches are eliminated in the demand-driven C/C++ implementations by reflecting, if needed, Nohalo's 12-point stencil with pointer shifts. Overall, Nohalo is not much slower than standard bicubic resamplers. Compared to twenty-three alternatives in tests involving the re-enlargement of images downsampled with nearest neighbour, Nohalo gets the best PSNRs.
New converter for switched reluctance motor drive with wide speed range operation

This paper offers a new converter for switched reluctance motor (SRM) drive which uses one switch in each phase. One switch for each phase is the least number of switches among the converters used in the switch reluctance motor drive. Also, the proposed converter enjoy from an important characteristic which makes it suitable for high speed drive applications. This is due to the fast phase current commutation capability of this converter. Therefore, the generation of negative torque and consequently, large generated torque ripples in SRM drive are resolved. SRM drive simulation using the proposed converter is presented and the results are compared with the asymmetric converter which is usually used in SRM drives.