Miracle-dz/UniFAR-FTUs huggingface dataset:
Hybrid Cluster Proteins and Flavodiiron Proteins Afford Protection to Desulfovibrio vulgaris upon Macrophage Infection

ABSTRACT Desulfovibrio species are Gram-negative anaerobic sulfate-reducing bacteria that colonize the human gut. Recently, Desulfovibrio spp. have been implicated in gastrointestinal diseases and shown to stimulate the epithelial immune response, leading to increased production of inflammatory cytokines by macrophages. Activated macrophages are key cells of the immune system that impose nitrosative stress during phagocytosis. Hence, we have analyzed the in vitro and in vivo responses of Desulfovibrio vulgaris Hildenborough to nitric oxide (NO) and the role of the hybrid cluster proteins (HCP1 and HCP2) and rubredoxin oxygen oxidoreductases (ROO1 and ROO2) in NO protection. Among the four genes, hcp2 was the gene most highly induced by NO, and the hcp2 transposon mutant exhibited the lowest viability under conditions of NO stress. Studies in murine macrophages revealed that D. vulgaris survives incubation with these phagocytes and triggers NO production at levels similar to those stimulated by the cytokine gamma interferon (IFN-γ). Furthermore, D. vulgaris hcp and roo mutants exhibited reduced viability when incubated with macrophages, revealing that these gene products contribute to the survival of D. vulgaris during macrophage infection.
Survey on applications of biased-random key genetic algorithms for solving optimization problems

This paper presents a survey on studies devising biased-random key genetic algorithms (BRKGAs), a novel variant of the ordinary genetic algorithms (GAs) introduced in 2000s, for solving numerous optimization problems up to 2015. The aim is to provide a comprehensive picture of the development of the algorithms and the areas of implementation in literature yet. From the survey, a number of findings include: (1) number of studies tends to increase over the last five years dealing with various combinatorial optimization problems, however limited research deals with continuous variables, (2) local search procedure is the typical hybridization method used to enhance the performance of the algorithms, hence others improvement methods are still potential avenues for future research.
A constant conversion factor for retrieval of PWV from GPS signals in tropical region

In this paper, a constant conversion factor PI is proposed for retrieval of Precipitable Water Vapor (PWV) from Global Positioning System (GPS) signal delay in Tropical region. The factor PI is calculated using water-vapor weighted mean temperature (Tm). For Tropical region, Tm doesn't vary much and thus range of PI values is also small. Therefore, using the data obtained from 5 different sites of Tropical region, a constant PI value of 0.163 is proposed for calculation of PWV from GPS signals in Tropical region. The proposed conversion factor allows for the ease of PWV retrieval, which is useful in meteorological studies and also applicable in satellite communications.
Singular perturbation of smoothly evolving Hele-Shaw solutions.

We present analytical scaling results, confirmed by accurate numerics, to show that there exists a class of smoothly evolving zero surface tension solutions to the Hele-Shaw problem that are significantly perturbed by an arbitrarily small amount of surface tension in order one time. {copyright} {ital 1996 The American Physical Society. }
Lack of any Association between the Hogg1 Ser326Cys Polymorphism and Breast Cancer Risk: a Systematic Review And Meta-Analysis Of 18 Studies

Background: The human 8-oxoguanine DNA glycosylase (hOGG1) gene may be linked with cancer susceptibility. The aim of this study was to quantitatively summarize any association between the hOGG1 Ser326Cys polymorphism and breast cancer (BC) risk. Materials and Methods: A comprehensive search of the PubMed, Embase, and ISI web of knowledge databases for papers published before 1 October 2016 was conducted. Summary odds ratios (ORs) with corresponding 95 % confidence intervals (95 %CIs) were estimated, with fixed-effects or random-effects models when appropriate, to assess any association. Results: A total of 9,434 cases and 10,497 controls from 18 studies were included in this meta-analysis. When the eligible studies were pooled, there was no evidence found for a significant association between the hOGG1 Ser326Cys polymorphism and BC in in all genetic contrast models G vs. C (OR=1.19, 95% CI 0.92– 1.53), CG vs. CC (OR = 0.97, 95% CI 0.91-1.04, p = 0.46), GG vs. CC (OR = 1.11, 95% CI 0.91-1.35, p = 0.30), GG + CG vs. CC (OR = 0.98, 95% CI 0.92-1.05, p = 0.67), and GG vs. CG + CC (OR = 1.22, 95% CI 0.98-1.52, p = 0.07). According to subgroup analysis, we also did not find a significant association between the hOGG1 Ser326Cys polymorphism and BC risk in Asians and Caucasians considered separately. Conclusions: The current meta-analysis suggests that the hOGG1 Ser326Cys polymorphism is not significantly associated with BC risk.
Measurement of Free Ca in Sarcoplasmic Reticulum in Perfused Rabbit Heart Loaded with 1,2-Bis(2-amino-5,6-difluorophenoxy)ethane-N,N,N′,N′-tetraacetic Acid by F NMR (*)

Measurements of free calcium ion concentration in the sarcoplasmic reticulum ([Ca]) and an evaluation of its relationship to changes in cytosolic free calcium and energy state of the cell, as well as heterogeneity of the SR calcium pool, were performed using F NMR in Langendorff perfused rabbit hearts loaded with acetoxymethyl ester of 1,2-bis(2-amino-5,6-difluorophenoxy)ethane-N,N,N′,N′-tetraacetic acid. We report a base-line time-average [Ca] value of 1.5 mM (n = 13) in the beating heart, similar to the value measured at diastole. We further report that [Ca] decreases by 30% at the start of systole and that there is no evidence of spacial heterogeneity in [Ca] during the contraction cycle. However, there appears to be a heterogeneous response to SR calcium channel release activator (caffeine) and SR calcium-ATPase inhibitor (cyclopiazonic acid), consistent with studies suggesting that there are subpopulations of SR. Raising cytosolic free calcium by depolarizing the cell with 30 mM extracellular KCl, resulted in an increase in [Ca]; however, the calcium gradient was unchanged. Lowering cell phosphorylation potential, which would reduce the free energy available for the SR Ca-ATPase, leads to a decrease in the calcium gradient across the SR, but this reduced gradient was primarily due to an increase in cytosolic free calcium and not a net release of SR calcium.
Cellular Force Microscopy for in Vivo Measurements of Plant Tissue Mechanics1[W][OA]

Although growth and morphogenesis are controlled by genetics, physical shape change in plant tissue results from a balance between cell wall loosening and intracellular pressure. Despite recent work demonstrating a role for mechanical signals in morphogenesis, precise measurement of mechanical properties at the individual cell level remains a technical challenge. To address this challenge, we have developed cellular force microscopy (CFM), which combines the versatility of classical microindentation techniques with the high automation and resolution approaching that of atomic force microscopy. CFM’s large range of forces provides the possibility to map the apparent stiffness of both plasmolyzed and turgid tissue as well as to perform micropuncture of cells using very high stresses. CFM experiments reveal that, within a tissue, local stiffness measurements can vary with the level of turgor pressure in an unexpected way. Altogether, our results highlight the importance of detailed physically based simulations for the interpretation of microindentation results. CFM’s ability to be used both to assess and manipulate tissue mechanics makes it a method of choice to unravel the feedbacks between mechanics, genetics, and morphogenesis.
Burst kinetics of single calcium‐activated potassium channels in cultured rat muscle.

Burst kinetics of single Ca‐activated K channels in excised patches of surface membrane from cultured rat muscle were studied using the patch‐clamp technique. Channel activity was separated into bursts using a calculated gap derived from the distribution of shut intervals. Shut intervals greater than the calculated gap were taken as gaps between bursts. The distribution of burst duration was described as the sum of two exponentials with mean durations of about 0.8 and 24 msec (1 microM‐Cai, + 20 mV), suggesting two classes of bursts (short and long). The composition of short and long bursts was determined from comparisons of the distributions of open intervals, unit bursts (bursts of single openings), and openings/burst. Short bursts consisted mainly of single openings to the open channel state of short mean lifetime. Long bursts consisted of one or more openings to the (compound) open‐channel state of long mean lifetime, plus, in fewer than 70% of the long bursts, one or more openings to the short open‐channel state. The frequency of occurrence of bursts from each class first increased and then decreased with increasing [Ca]i, with the number of long bursts increasing at a greater rate than the number of short bursts. The number of openings/short burst was relatively independent of [Ca]i, while the number of openings/long burst increased, often more than linearly, with increasing [Ca]i. This increase arose almost entirely from an increase in openings to the long open state. These results suggest that openings to the long open state typically require the binding of three or more Ca ions, and openings to the short open state typically require the binding of at least one Ca ion. This is the case whether the openings occur in isolation as bursts of single openings or in bursts composed of both types of openings. An obvious burst of channel activity would occur when the channel opens and closes several times without losing all its bound Ca. The power relationship between [Ca]i and the percentage of time spent in the open state is accounted for in terms of the effects of [Ca]i upon mean channel open time, openings/burst, and burst rate. A model is presented that describes quantitatively many features of the burst kinetics of the Ca‐activated K channel for constant [Ca]i.
Comparison of the Effects of Central and Peripheral Dopamine Receptor Activation on Evoked Firing in the Trigeminocervical Complex

Dopaminergic mechanisms have been suggested to play a role in migraine. Here, electrophysiological techniques were used to study the effects of intravenously administered centrally or peripherally active dopamine receptor agonists and antagonists on evoked firing in the trigeminocervical complex (TCC). After establishing baseline firing evoked by electrical stimulation of the dural middle meningeal artery (MMA) and mechanical noxious and innocuous stimulation of the ophthalmic dermatome, D1- or D2-like receptor agonists or antagonists were administered intravenously and the effect on firing was determined. In addition, with use of intravital microscopy, we monitored changes in dural vessel diameter in response to varying doses of D1- or D2-like receptor agonists to determine whether their effects were related to blood vessel caliber. The central D2-like receptor agonist quinpirole hydrochloride inhibited firing in the TCC evoked by stimulation of the MMA. Conversely, the central D2-like receptor antagonists, eticlopride hydrochloride and remoxipride hydrochloride, facilitated MMA-evoked firing and also firing evoked by noxious and innocuous stimulation of the ophthalmic dermatome. Both the peripheral D1-like receptor agonist fenoldopam and the central D1-like receptor agonists cis-(±)-1-(aminomethyl)-3,4-dihydro-3-phenyl-1H-2-benzopyran-5,6-diol hydrochloride (A68930 hydrochloride) and dihydrexidine facilitated innocuous brush-evoked firing, with A68930 hydrochloride having the greatest effect. The data suggest that dopamine binding to peripheral D1-like receptors may play a role in peripheral sensitization, and that the inhibitory or excitatory effects seen with administration of dopamine receptor agonists are independent of blood vessel changes. In addition, these studies maintain that central D2-like receptors inhibit trigeminocervical neurons, and may provide insight into the conflicting literature on the role of dopamine and its receptors in migraine.
Stability Analysis and Control of Discrete Type-1 and Type-2 TSK Fuzzy Systems: Part II. Control Design

This paper proposes a new control system design methodology for type-1 and type-2 Takagi-Sugeno-Kang (TSK) fuzzy systems that are based on new stability conditions. The stability conditions are discussed in a companion paper (Part I) and are used in the proofs of our main results. A major advantage of the new methodology is that it does not require a common Lyapunov function and is therefore applicable to systems with nonstabilizable consequents. Our controllers include fuzzy type-1 proportional and proportional-integral (PI) controllers, as well as constant state feedback for the same systems. The controller results in an exponentially stable system, and the designer can specify the rate of exponential convergence. The controller designs can be tested by the usage of linear matrix inequalities (LMIs). The design methodology is demonstrated by the usage of simple examples where methods that are based on a common Lyapunov function fail and physical systems where the new methodology provides better performance.
Assistance to maintenance in industrial process using an augmented reality system

Augmented reality (AR) application is an excellent domain for maintenance task in industrial environment. It allows the user to see computer generated virtual objects superimposed upon the real world through the see-through head mounted display. Technician of maintenance when using this system can interact with the virtual world and have additional information, such as instruction for performing maintenance tasks inform of text messages, images, 3-D models of pieces or audio such as speech instruction. In this paper, we describe a prototype of a maintenance system based on distributed augmented reality in industrial context. For the good results of the virtual overlays, aspect of the usage of optical tracking system and the calibration procedures based on computer vision techniques are discussed.
A New Supervised Learning Algorithm for Spiking Neurons

The purpose of supervised learning with temporal encoding for spiking neurons is to make the neurons emit a specific spike train encoded by the precise firing times of spikes. If only running time is considered, the supervised learning for a spiking neuron is equivalent to distinguishing the times of desired output spikes and the other time during the running process of the neuron through adjusting synaptic weights, which can be regarded as a classification problem. Based on this idea, this letter proposes a new supervised learning method for spiking neurons with temporal encoding; it first transforms the supervised learning into a classification problem and then solves the problem by using the perceptron learning rule. The experiment results show that the proposed method has higher learning accuracy and efficiency over the existing learning methods, so it is more powerful for solving complex and real-time problems.
Flavobacterium hibisci sp. nov., isolated from the rhizosphere of Hibiscus syriacus L.

A Gram-stain-negative, smooth, bright-yellow-pigmented, rod-shaped bacterial strain, slightly motile by gliding, catalase- and oxidase-positive and aerobic, but growing weakly under anaerobic conditions, was isolated from the rhizosphere of the flower mugunghwa (Hibiscus syriacus L.) located in Kyung Hee University, Yongin, Gyeonggi, South Korea. The strain named THG-HG1.4T grew at 15-35 °C, pH 6.5-9.0 and in the presence of 0-2.5 % (w/v) NaCl. The phylogenetic analysis based on 16S rRNA gene sequence showed that strain THG-HG1.4T was most closely related to Flavobacterium gyeonganense HME7524T (98.83 %) and Flavobacterium arsenitoxidans S2-3HT (97.28 %). The DNA G+C content of strain THG-HG1.4T was 41.2 mol%. In DNA-DNA hybridization, the DNA-DNA relatedness between strain THG-HG1.4T and its closest phylogenetic neighbour was below 64.1 %. The predominant isoprenoid quinone detected in strain THG-HG1.4T was menaquinone-6 (MK-6). The major polar lipids were found to be phosphatidylethanolamine, three unidentified lipids, two unidentified glycolipids and an unidentified aminolipid. The major fatty acids were identified as iso-C15 : 0, iso-C15 : 0 3-OH, C16 : 0, iso-C17 : 0 3-OH and summed feature 3. Thus, based on the report of the phenotypic, genotypic and phylogenetic characterization of strain THG-HG1.4T, it has been concluded that the novel isolate represents a novel species of the genus Flavobacterium.Flavobacterium hibisci sp. nov. is proposed, with THG-HG1.4T (=KACC 18852T=CCTCC AB 2016178T) as the type strain.
Towards Multi-tenant GPGPU : Event-driven Programming Model for System-wide Scheduling on Shared GPUs

Graphics processing units (GPUs) are attractive to the generalpurpose computing (GPGPU) beyond the graphics purpose. Sharing GPUs among such GPGPU applications is a key requirement especially for cloud platforms whose resources are utilized by various cloud users. However, consolidating recent GPU applications, referred to as GPU eaters, on a GPU poses a new challenge. Such advanced applications are designed based on the assumption that only one GPU application runs on a GPU at a time. In this paper, we present GLoop, a GPGPU framework that allows multiple GPU eaters to share a GPU. GLoop offers an event-driven programming model that generates scheduling points in GPU kernels. It achieves resource isolation among GPU applications and schedules applications by suspending/resuming GPU kernels only if necessary to reduce the number of kernel launches. The preliminary experiments demonstrate that GLoop model is applicable to a GPU eater. The results also show that GLoop enables two GPGPU applications to run concurrently on a shared GPU by interleaving GPU kernel execution.
A Modified Asymptotical Regularization of Nonlinear Ill-Posed Problems

In this paper, we investigate the continuous version of modified iterative Runge–Kutta-type methods for nonlinear inverse ill-posed problems proposed in a previous work. The convergence analysis is proved under the tangential cone condition, a modified discrepancy principle, i.e., the stopping time T is a solution of ∥ F ( x δ ( T ) ) − y δ ∥ = τ δ + for some δ + > δ , and an appropriate source condition. We yield the optimal rate of convergence.
The mouse grid-shock analgesia test: pharmacological characterization of latency to vocalization threshold as an index of antinociception.

Latency to vocalization and jump/flinch behaviors were scored as the nociceptive endpoints in mice in a grid-shock apparatus that delivered increasing shock levels through a grid floor. Morphine produced a dose-dependent increase in latency to vocalization and was equieffective at a 70- or 80-dB vocalization level. The jump/flinch behavior was not dose dependently modified by morphine. The mouse grid-shock procedure was pharmacologically characterized by using the 70-dB level endpoint. The antinociceptive potencies of the mu opioid receptor agonist analgesics, morphine, methadone, fentanyl, oxycodone, meperidine, etorphine and codeine, correlated well (R = .989) with their clinical doses. The mixed opioid agonist-antagonist, pentazocine, and the partial mu receptor opioid agonist, buprenorphine, were partially effective. The alpha-2 adrenergic agonists clonidine and flupirtine and the serotonergic 5-HT1B agonists 1-(m-trifluoromethyl)piperazine and anpirtoline, were all effective antinociceptives with potencies 20 times less to one-half that of morphine. The gamma-aminobutyric acid agonist 4,5,6,7-tetrahydroisoxazolo[5,4- c]pyridin-3(2H)-one was partially effective, whereas the gamma-aminobutyric acid uptake inhibitors SKF 100300A [N-(4,4-diphenyl-3-butenyl)-guvacine] and tiagabine were highly effective and 6 and 2 times less potent than morphine, respectively. The muscarinic agonists, oxotremorine and arecoline, and the cholinesterase inhibitor, physostigmine, were also antinociceptive, ranging from 7 times less to 100 times more potent than morphine. The nonsteroidal anti-inflammatory analgesic, aspirin, was inactive. The present studies show that the latency to a defined level of vocalization as the nociceptive endpoint provides a reliable, highly reproducible and high through-put test for antinociception in nonrestrained mice.
Approximate Analysis of Fork/Join Synchronization in Parallel Queues

An approximation technique, called scaling approximation, is introduced and applied to the analysis of homogeneous fork/join queuing systems consisting of K>or=2 servers. The development of the scaling approximation technique is guided by both experimental and theoretical considerations. The approximation is based on the observation that there exist upper and lower bounds on the mean response time that grow at the same rate as a function of K. Simple, closed-form approximate expressions for the mean response time are derived and compared to simulation results. The relative error in the approximation is less than 5% for K >
Preliminary study on proportional and simultaneous estimation of hand posture using surface EMG based on synergy concept

Most of current myoelectric prostheses are using sequential and on-off control strategy within pattern classification framework, which is of robustness. But it is not a natural neuromuscular control scheme. On the other hand, there are two difficulties to control the prosthesis proportionally and simultaneously. First, human hand is high dimensional with more than 20 degrees-of-freedom (DOFs); Second, extracting such control information from EMG is hard due to signal crosstalk and noises. This paper is aimed at proposing a new method for proportional and simultaneous myoelectric control, taking advantage of synergy concept. The hand motion and corresponding forearm EMG signals were collected simultaneously. Principal component analysis (PCA) is used to reduce hand motion dimension. And support vector regression (SVR) is adopted to build the connection between hand posture and EMG. Offline analysis validated the effectiveness of this method, and preliminary and positive results have been obtained.
Regression-based trust model for mobile ad hoc networks

The focus of this study is to propose a generalised trust-model over routing protocols in mobile ad hoc networks (MANETs). It is observed that the presence of malicious nodes is a critical factor affecting the network performance in an ad hoc network. The novelty in the approach is that the notion of trust can be easily incorporated into any routing protocol in MANETs. The vector auto regression based trust model is introduced to identify malicious nodes that launch multiple attacks in the network. The proposed trust model is incorporated over ad hoc on-demand distance vector (AODV) routing protocol and optimised link state routing (OLSR) protocol in MANETs. The performance evaluations show that by carefully setting the trust parameters, substantial benefit in terms of throughput can be obtained with minimal overheads. The computed trust and confidence values are introduced into the path computation process of the ad hoc routing protocols. It was observed that the nodes in the network were able to learn the malicious activities of their neighbours and hence, alternate trustworthy paths are taken to avoid data loss in the network, with trade-offs in end-to-end packet delay and routing traffic.