Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of an ATP-binding Cassette Transporter for Export of the O-antigen across the Inner Membrane inRhizobium etli Based on the Genetic, Functional, and Structural Analysis of an lps Mutant Deficient in O-antigen*

For O-antigen lipopolysaccharide (LPS) synthesis in bacteria, transmembrane migration of undecaprenyl pyrophosphate-bound O-antigen oligosaccharide subunits or polysaccharide occurs before ligation to the core region of the LPS molecule. In this study, we identified by mutagenesis an ATP-binding cassette transporter in Rhizobium etli CE3 that is likely responsible for the translocation of the O-antigen across the inner plasma membrane. Mutant FAJ1200 LPS lacks largely the O-antigen, as shown by SDS-polyacrylamide gel electrophoresis and confirmed by immunoblot analysis. Furthermore, LPS isolated from FAJ1200 is totally devoid of any O-chain glycosyl residues and contains only those glycosyl residues that can be expected for the inner core region. The membrane component and the cytoplasmic ATP-binding component of the ATP-binding cassette transporter are encoded by wzm andwzt, respectively. The Tn5 transposon in mutant FAJ1200 is inserted in the wzm gene. This mutation resulted in an Inf− phenotype in bean plants.
Mathematical and Computer Modelling of Dynamical Systems Methods , Tools and Applications in Engineering and Related Sciences

Neuronal models based on the Hodgkin–Huxley equation form a fundamental framework in the field of computational neuroscience. While the neuronal state is often modelled deterministically, experimental recordings show stochastic fluctuations, presumably driven by molecular noise from the underlying microphysical conditions. In turn, the firing of individual neurons gives rise to an electric field in extracellular space, also thought to affect the firing pattern of nearby neurons. We develop a multiscale model which combines a stochastic ion channel gating process taking place on the neuronal membrane, together with the propagation of an action potential along the neuronal structure. We also devise a numerical method relying on a split-step strategy which effectively couples these two processes and we experimentally test the feasibility of this approach. We finally also explain how the approach can be extended with Maxwell’s equations to allow the potential to be propagated in extracellular space. ARTICLE HISTORY Received 28 October 2016 Accepted 12 June 2018
Detectability of Absorption and Reduced Scattering Coefficients in Frequency-Domain Measurements Using a Realistic Head Phantom

Detection limits of the changes in absorption and reduced scattering coefficients were investigated using a frequency-domain near-infrared system in a realistic head phantom. The results were quantified in terms of the maximum detectable depth for different activation volumes in the range of 0.8–20 microliters. The non-linear relation between the maximum detectable depth and the magnitude of changes in the absorption coefficient conform well with the Born approximation to the diffusion equation. The minimal detectable changes in the reduced scattering coefficient measured in terms of the phase signal were found to be approximately twice as large as that of the absorption coefficient using the AC signal for the same volume and at the same depth. The phase delay, which can be used to quantify the fast neuronal optical response in the human brain, showed a linear dependence on the reciprocal of the reduced scattering coefficient, as predicted by the Rytov approximation.
An efficient real-time routing with presence of concave voids in wireless sensor networks

To bypass voids in sensor networks, most existing geographic routing protocols tend to route packets along the boundary nodes. Generally, a packet will be either forwarded along a void boundary by the right-hand rule or pushed back to find another route when it encounters the void. The two techniques consume more energy of boundary nodes, drop many packets and may incur data collisions if multiple communication sessions share the same boundary nodes. We propose in this paper an alternative and efficient void avoidance scheme. The proposed on-demand scheme consists of void discovery, void announce and packet rerouting steps. After discovering a void, a sender node inside the void's announce-area reroutes all data packets to get around the void in advance by selecting one appropriate forwarding side. The double objective of our scheme is to prevent data packets from traveling along the boundaries of voids and to avoid them the concave zones of voids. By achieving this objective we can reduce the energy consumption of boundary nodes and data collisions in these nodes. We can also reduce the packets rerouting overhead and the number of packets dropped by nodes on the boundaries of voids. Simulation showed the efficiency of our scheme.
Agent-based tactics for goal-oriented requirements elaboration

Goal orientation is an increasingly recognized paradigm for eliciting, structuring, analyzing and documenting system requirements. Goals are statements of intent ranging from high-level, strategic concerns to low-level, technical requirements on the software-to-be and assumptions on its environment. Achieving goals require the cooperation of agents such as software components, input/output devices and human agents. The assignment of responsibilities for goals to agents is a critical decision in the requirements engineering process as alternative agent assignments define alternative system proposals. The paper describes a systematic technique to support the process of refining goals, identifying agents, and exploring alternative responsibility assignments. The underlying principles are to refine goals until they are assignable to single agents, and to assign a goal to an agent only if the agent can realize the goal. There are various reasons why a goal may not be realizable by an agent, e.g., the goal may refer to variables that are not monitorable or controllable by the agent. The notion of goal realizability is first defined on formal grounds; it provides a basis for identifying a complete taxonomy of realizability problems. From this taxonomy we systematically derive a catalog of tactics for refining goals and identifying agents so as to resolve realizability problems. Each tactics corresponds to the application of a formal refinement pattern that relieves the specifier from verifying the correctness of refinements in temporal logic. Our techniques have been used in two case studies of significant size; excerpts are shown to illustrate the main ideas.
Autonomous evolution of gaits with the Sony Quadruped Robot

A trend in robotics is towards legged robots. One of the issues with legged robots is the development of gaits. Typically gaits arc developed manually. In this paper we report our results of autonomous evolution of dynamic gaits for the Sony Quadruped Robot. Fitness is determined using the robot's digital camera and infrared sensors. Using this system we evolve faster dynamic gaits than previously manually developed.
Universal estimation of directed information via sequential probability assignments

We propose four approaches to estimating the directed information rate between a pair of jointly stationary ergodic processes with the help of universal probability assignments. The four approaches yield estimators with different merits such as nonnegativity and boundedness. We establish consistency of these estimators in various senses and derive near-optimal rates of convergence in the minimax sense under mild conditions. The estimators carry over directly to estimating other information measures of stationary ergodic processes, such as entropy rate and mutual information rate, and provide alternatives to classical approaches in the existing literature. Guided by the theoretical results, we use context tree weighting as the vehicle for the implementations of the proposed estimators. Experiments on synthetic and real data are presented, demonstrating the potential of the proposed schemes in practice and the efficacy of directed information estimation as a tool for detecting and measuring causality and delay.
Hubble Space Telescope Imaging in the Chandra Deep Field South : III . Quantitative Morphology of the 1 Million Second Chandra Counterparts and Comparison with the Field Population 1

We present quantitative morphological analyses of 37 HST/WFPC2 counterparts of X-ray sources in the 1 Ms Chandra Deep Field–South (CDFS). We investigate: 1) one-dimensional surface brightness profiles via isophotal ellipse fitting; 2) two-dimensional, PSF-convolved, bulge+disk+nucleus profile-fitting; 3) asymmetry and concentration indices compared with all ∼ 3000 sources in our three WFPC2 fields; and 4) near-neighbor analyses comparing local environments of X-ray sources versus the field control sample. Significant nuclear pointsource optical components appear in roughly half of the resolved HST/WFPC2 counterparts, showing a narrow range of FX/Fopt,nuc consistent with the several HST-unresolved X-ray sources (putative type 1 active galactic nuclei [AGNs]) in our fields. We infer roughly half of the HST/WFPC2 counterparts host unobscured AGN, comparable to analogous low-redshift AGN samples and suggesting no steep decline in the type 1/type 2 ratio out to the redshifts z ∼ 0.5−1 typical of our sources. The concentration indices of the CDFS counterparts are clearly larger on average than those of the field distribution, at 5-sigma, suggesting that Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218, USA Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218, USA Associated Universities, Inc., 1400 16th Street NW, Washington, DC 20036, USA European Southern Observatory, Karl-Schwarzschild-Strasse 2, Garching, D-85748, Germany Max-Planck-Institut Für extraterrestrische Physik, Giessenbachstrasse PF 1312, Garching D-85748, Germany Harvard-Smithsonian Center for Astrophysics, 60 Garden St., Cambridge, MA 02138,USA Osservatorio Astronomico di Trieste, Via G. B. Tiepolo 11, 34131 Trieste, Italy
Factors predictive of urinary retention after a tension-free vaginal tape procedure for female stress urinary incontinence.

PURPOSE We performed this study to evaluate factors related to urinary retention after a tension-free vaginal tape (TVT) procedure for female stress urinary incontinence. MATERIALS AND METHODS We retrospectively analyzed the records of 375 women with a followup of at least 6 months from among patients who underwent the TVT procedure between March 1999 and May 2002 at our institution. We analyzed multiple parameters, including patient characteristics, symptoms and urodynamic studies, using univariate and multivariate regression analyses with respect to postoperative urinary retention, as defined by the need for intermittent catheterization for at least 3 days after the procedure. All patients in the nonretention (343) and retention (32) groups answered a global satisfaction question. RESULTS In answer to a global satisfaction question 338 of the 375 patients (90.1%) favored the procedure. Univariate analysis demonstrated that patient mean age, parity, peak urinary flow and a history of hysterectomy predicted urinary retention. However, on multivariate analyses the peak urinary flow rate was the only significant independent predictive factor (p = 0.007). While 28 patients (87.5%) in the retention group regained normal voiding without a specific procedure, 4 required tape release or cutting within 3 month of surgery. The global satisfaction question showed a significant difference between the nonretention and retention groups (91.5% vs 75% satisfaction, p = 0.03). CONCLUSIONS An accurate measurement of the peak urinary flow rate could predict women at risk for postoperative urinary retention that compromises global satisfaction after the highly curative TVT procedure.
Comparative study regarding friction coefficient for three epoxy resins

Three commercial epoxy diglycidylether of bisphenol-A (DGEBA) were used in this study namely Epiphen RE4020-DE 4020 (Bostik), Epoxy Resin C (R&G Gmbh Waldenbuch), and Epoxy Resin HT-2 (R&G Gmbh Waldenbuch). Epoxy resins are often used for the friction purpose but their friction resistance is quite low and it is thus necessary to enhance their friction resistance. In this paper it is shown how load, sliding velocity, and distance affect friction coefficient of epoxy resins.
Why systolic architectures?

f High-performance, special-purpose computer systems are typically used to meet specific application requirements or to off-load computations that are especially taxing to general-purpose computers. As hardware cost and size continue to drop and processing requirements become well-understood in areas such as signal and image processing, more special-purpose systems are being constructed. However, since most of these systems are built on an ad hoc basis for specific tasks, methodological work in this area is rare. Because the knowledge gaited from individual experiences is neither accumulated nor properly organized, the same errors are repeated. I/O and computation imbalance is a notable example-often, the fact that I/O interfaces cannot keep up with device speed is discovered only after constructing a high-speed, special-purpose device. We intend to help correct this ad hoc approach by providing a general guideline-specifically, the concept of systolic architecture, a general methodology for mapping high-level computations into hardware structures. In a systolic system, data flows from the computer memcory in a rhythmic fashion, passing through many processing elements before it returns to memory, much as blood circulates to and from the heart. The system works like an autombbile assembly line where different people work on the same car at different times and many cars are assembled simultaneously. An assembly line is always linear, however, and systolic systems are sometimes two-dimensional. They can be rectangular, triangular, or hexagonal to make use of higher degrees of parallelism. Moreover, to implement a variety of computations, data flow in a systolic system may be at multiple speeds in multiple directions-both inputs and (partial) results flow, whereas only results flow in classical pipelined systems. Generally speaking, a systolic system is easy to implement because of its regularity and easy to reconfigure (to meet various outside constraints) because of its modularity. The systolic architectural concept was developed at Carnegie-Mellon University,'17 and versions of systolic processors are being designed and built by several industrial and governmental organizations.840 This article reviews the basic principle of systolic architectures and explains why they should result in cost-effective, highperformance special-purpose systems for a wide range of problems.
The coactivator host cell factor-1 mediates Set1 and MLL1 H3K4 trimethylation at herpesvirus immediate early promoters for initiation of infection

Originally identified as an essential component of the herpes simplex virus immediate early (IE) gene enhancer complex, the transcriptional coactivator host cell factor-1 (HCF-1) has been implicated in a broad range of cellular regulatory circuits. The protein mediates activation through multiple interactions with transcriptional activators, coactivators, and chromatin remodeling complexes. However, the mechanisms involved in HCF-1-dependent transcriptional stimulation were undefined. By using a minimal HCF-1-dependent promoter and a model activator, the varicella zoster IE62 protein, it was determined that HCF-1 was not required for the assembly of the RNAPII basal complex, which depended solely on IE62 in conjunction with the cellular factor Sp1. In contrast, HCF-1 was required for recruitment of the histone methyltransferases Set1 and MLL1 (mixed-lineage leukemia 1), leading to histone H3K4 trimethylation and transcriptional activation. Similarly, in a varicella zoster virus lytic infection, HCF-1, Set1, and MLL1 were recruited to the viral genomic IE promoter, suggesting an essential role for HCF-1 in chromatin modification and remodeling during initiation of lytic infection. The results indicate that one biological rationale for the incorporation of the viral IE activators in the viral particle is to recruit HCF-1/histone methyltransferase complexes and promote assembly of the viral IE gene promoters into transcriptionally active chromatin. These studies also contribute to the model whereby the induced nuclear transport of HCF-1 in sensory neurons may be critical to the reactivation of latent herpesviruses by promoting the activation of chromatin modifications.
Discrete laplace operators: no free lunch

Discrete Laplace operators are ubiquitous in applications spanning geometric modeling to simulation. For robustness and efficiency, many applications require discrete operators that retain key structural properties inherent to the continuous setting. Building on the smooth setting, we present a set of natural properties for discrete Laplace operators for triangular surface meshes. We prove an important theoretical limitation: discrete Laplacians cannot satisfy all natural properties; retroactively, this explains the diversity of existing discrete Laplace operators. Finally, we present a family of operators that includes and extends well-known and widely-used operators.
Variable millimetre radiation from the colliding-wind binary Cygnus OB2 #8A

CONTEXT: Massive binaries have stellar winds that collide. In the colliding-wind region, various physically interesting processes occur, leading to enhanced X-ray emission, non-thermal radio emission, as well as non-thermal X-rays and gamma-rays. Non-thermal radio emission (due to synchrotron radiation) has so far been observed at centimetre wavelengths. At millimetre wavelengths, the stellar winds and the colliding-wind region emit more thermal free-free radiation, and it is expected that any non-thermal contribution will be difficult or impossible to detect. AIMS: We aim to determine if the material in the colliding-wind region contributes substantially to the observed millimetre fluxes of a colliding-wind binary. We also try to distinguish the synchrotron emission from the free-free emission. METHODS: We monitored the massive binary Cyg OB2 #8A at 3 mm with the NOrthern Extended Millimeter Array (NOEMA) interferometer of the Institut de Radioastronomie Millimetrique (IRAM). The data were collected in 14 separate observing runs (in 2014 and 2016), and provide good coverage of the orbital period. RESULTS: The observed millimetre fluxes range between 1.1 and 2.3 mJy, and show phase-locked variability, clearly indicating that a large part of the emission is due to the colliding-wind region. A simple synchrotron model gives fluxes with the correct order of magnitude, but with a maximum that is phase-shifted with respect to the observations. Qualitatively this phase shift can be explained by our neglect of orbital motion on the shape of the colliding-wind region. A model using only free-free emission results in only a slightly worse explanation of the observations. Additionally, on the map of our observations we also detect the O6.5 III star Cyg OB2 #8B, for which we determine a 3 mm flux of 0.21 ± 0.033 mJy. CONCLUSIONS: The question of whether synchrotron radiation or free-free emission dominates the millimetre fluxes of Cyg OB2 #8A remains open. More detailed modelling of this system, based on solving the hydrodynamical equations, is required to give a definite answer.
The Acinetobacter baumannii Omp33-36 Porin Is a Virulence Factor That Induces Apoptosis and Modulates Autophagy in Human Cells

ABSTRACT Acinetobacter baumannii is an extracellular opportunistic human pathogen that is becoming increasingly problematic in hospitals. In the present study, we demonstrate that the A. baumannii Omp 33- to 36-kDa protein (Omp33-36) is a porin that acts as a channel for the passage of water. The protein is found on the cell surface and is released along with other porins in the outer membrane vesicles (OMVs). In immune and connective cell tissue, this protein induced apoptosis by activation of caspases and modulation of autophagy, with the consequent accumulation of p62/SQSTM1 (sequestosome 1) and LC3B-II (confirmed by use of autophagy inhibitors). Blockage of autophagy enables the bacterium to persist intracellularly (inside autophagosomes), with the subsequent development of cytotoxicity. Finally, we used macrophages and a mouse model of systemic infection to confirm that Omp33-36 is a virulence factor in A. baumannii. Overall, the study findings show that Omp33-36 plays an important role in the pathogenesis of A. baumannii infections.
Towards Maintainable Architecture for Process Control Applications

Development of software systems utilizes only 20%-40% of the overall project cost; the rest is consumed by maintenance. Systems with poor maintainability are difficult to modify and to extend. Maintainability based risk is defined as a product of two factors: the probability of carrying out maintenance tasks and the impact of these tasks. The decision of adopting a single architecture over others should be verified through some pre-implementation analysis. This paper assesses different architectures for process control applications using a maintainability risk analysis. The paper illustrates the methodology using a simple example of a Gas Burner process control system.
Collaboration activity function: an interaction analysis tool for supported collaborative learning activities

During the last years, an increased interest has been observed on tools analyzing collaborative interactions that could be useful for researchers, teachers, or even students. The paper presents such a tool, based on the formally defined collaborative activity function (CAF). The empirical evaluation of CAF is also presented. The evaluation is focused on teachers using CAF during and after sessions of synchronous collaborative problem solving among students.
Skip RNN: Learning to Skip State Updates in Recurrent Neural Networks

Recurrent Neural Networks (RNNs) continue to show outstanding performance in sequence modeling tasks. However, training RNNs on long sequences often face challenges like slow inference, vanishing gradients and difficulty in capturing long term dependencies. In backpropagation through time settings, these issues are tightly coupled with the large, sequential computational graph resulting from unfolding the RNN in time. We introduce the Skip RNN model which extends existing RNN models by learning to skip state updates and shortens the effective size of the computational graph. This model can also be encouraged to perform fewer state updates through a budget constraint. We evaluate the proposed model on various tasks and show how it can reduce the number of required RNN updates while preserving, and sometimes even improving, the performance of the baseline RNN models. Source code is publicly available at this https URL .
Convergence and rate of convergence of a foraging ant model

We present an ant model that solves a discrete foraging problem. We describe simulations and provide a complete convergence analysis: we show that the ant population computes the solution of some optimal control problem and converges in some well defined sense. We discuss the rate of convergence with respect to the number of ants: we give experimental and theoretical arguments that suggest that this convergence rate can be superlinear with respect to the number of agents. Furthermore, we explain how this model can be extended in order to solve optimal control problems in general and argue that such an approach can be applied to any problem that involves the computation of the fixed point of a contraction mapping. This allows to design a large class of formally well understood ant like algorithms for problem solving.