Miracle-dz/UniFAR-FTUs huggingface dataset:
A Patch of Positively Charged Amino Acids Surrounding the Human Immunodeficiency Virus Type 1 Vif SLVx4Yx9Y Motif Influences Its Interaction with APOBEC3G

ABSTRACT The amino-terminal region of the Vif molecule in human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus (SIV) contains a conserved SLV/Ix4Yx9Y motif that was first described in 1992, but the importance of this motif for Vif function has not yet been examined. Our characterization of the amino acids surrounding this motif in HIV-1 Vif indicated that the region is critical for APOBEC3 suppression. In particular, amino acids K22, K26, Y30, and Y40 were found to be important for the Vif-induced degradation and suppression of cellular APOBEC3G (A3G). However, mutation of these residues had little effect on the Vif-mediated suppression of A3F, A3C, or A3DE, suggesting that these four residues are not important for Vif assembly with the Cul5 E3 ubiquitin ligase or protein folding in general. The LV portion of the Vif SLV/Ix4Yx9Y motif was found to be required for optimal suppression of A3F, A3C, or A3DE. Thus, the SLV/Ix4Yx9Y motif and surrounding amino acids represent an important functional domain in the Vif-mediated defense against APOBEC3. In particular, the positively charged K26 of HIV-1 Vif is invariably conserved within the SLV/Ix4Yx9Y motif of HIV/SIV Vif molecules and was the most critical residue for A3G inactivation. A patch of positively charged and hydrophilic residues (K22x3K26x3Y30x9YRHHY44) and a cluster of hydrophobic residues (V55xIPLx4-5LxΦx2YWxL72) were both involved in A3G binding and inactivation. These structural motifs in HIV-1 Vif represent attractive targets for the development of lead inhibitors to combat HIV infection.
Robust evaluations for duals of non-negative linear programs with box-constrained uncertainties

Non-negative linear programs with box-constrained uncertainties for all input data and box-constrained variables are considered. The knowledge of upper bounds for dual variables is a useful information e.g. for presolving analysis aimed at the determination of redundant primal variables. The upper bounds of the duals are found by solving a set of special continuous knapsack problems, one for each row constraint.
Radar Polarimetry Analysis Applied to Single-Hole Fully Polarimetric Borehole Radar

A fully polarimetric borehole radar system using four combinations of dipole and slot antennas was developed to acquire fully polarimetric data sets in drilled boreholes. First, to implement radar polarimetry analysis, a processing scheme suitable for analyzing a single-hole reflection data set acquired by the system is presented. This processing consists of antenna-characteristic compensation, migration for image reconstruction, and time-frequency analysis for single-frequency data set construction. Two polarimetric target decomposition methods, namely: 1) Pauli decomposition and 2) eigenvector-based decomposition, are applied to characterize the scattering problem of the subsurface fractures. The Pauli decomposition method provided important radar polarimetry information of fractures, and the eigenvector-based decomposition method made a significant contribution to understanding the scattering mechanisms from different fractures with different properties. Furthermore, information about fracture classification can be obtained by analysis of the H-alpha distribution provided by eigenvector-based decomposition of local radar image regions. The potential of polarimetric target decomposition techniques to fracture characterization is shown, which, in turn, provides valuable information about water permeabilities of fractures in hydrogeological studies
An intelligent recommender system for stock trading

Abstract. Generating consistent profits from stock markets is considered to be a challenging task, especially due to the nonlinear nature of the stock price movements. Traders need to have a deep understanding of the market behavior patterns in order to trade successfully. In this study, a GA optimized technical indicator decision tree-SVM based intelligent recommender system is proposed, which can learn patterns from the stock price movements and then recommend appropriate one-day-ahead trading strategy. The recommender system takes the task of identifying stock price patterns on itself, allowing even a lay-user, who is not well versed in stock market behavior, to trade profitably on a consistent basis. The efficacy of the proposed system is validated on four different stocks belonging to two different stock markets (India and UK) over three different time frames for each stock. Performance of the proposed system is validated using fifteen different measures. Performance is compared with traditional technical indicator based trading and the traditional buy and hold strategy. Results indicate that the proposed system is capable of generating profits for all the stocks in both the stock markets considered.
Microbial Reduction of Fe(III) under Alkaline Conditions Relevant to Geological Disposal

ABSTRACT To determine whether biologically mediated Fe(III) reduction is possible under alkaline conditions in systems of relevance to geological disposal of radioactive wastes, a series of microcosm experiments was set up using hyperalkaline sediments (pH ∼11.8) surrounding a legacy lime working site in Buxton, United Kingdom. The microcosms were incubated for 28 days and held at pH 10. There was clear evidence for anoxic microbial activity, with consumption of lactate (added as an electron donor) concomitant with the reduction of Fe(III) as ferrihydrite (added as the electron acceptor). The products of microbial Fe(III) reduction were black and magnetic, and a range of analyses, including X-ray diffraction, transmission electron microscopy, X-ray absorption spectroscopy, and X-ray magnetic circular dichroism confirmed the extensive formation of biomagnetite in this system. The addition of soluble exogenous and endogenous electron shuttles such as the humic analogue anthraquinone-2,6-disulfonate and riboflavin increased both the initial rate and the final extent of Fe(III) reduction in comparison to the nonamended experiments. In addition, a soluble humic acid (Aldrich) also increased both the rate and the extent of Fe(III) reduction. These results show that microbial Fe(III) reduction can occur in conditions relevant to a geological disposal facility containing cement-based wasteforms that has evolved into a high pH environment over prolonged periods of time (>100,000 years). The potential impact of such processes on the biogeochemistry of a geological disposal facility is discussed, including possible coupling to the redox conditions and solubility of key radionuclides.
A Flexible Metric-Driven Framework for Software Process

In software engineering, metrics are always used for measuring the quality of software process to improve software development or maintenance. In fact, there are several metric frameworks available to make metrics work efficiently, but only for the specific industrial region. In this paper, a general metrics framework is proposed, which is following the Goal/Question/Metric paradigm of Basili and Weiss (1984), to support most of the metrics. Furthermore, a sample application based on this framework is presented to demonstrate its effect on software process. The results provide some useful insights into project management practices. Finally, some enhancements are proposed for future work.
Strong Association Rules Mining Without Using Frequent Items for Microarray Analysis

Microarray technology has created a revolution in the field of biological research. Association rules can not only group the similarly expressed genes but also discern relationships among genes. However, the efficiency of traditional method to generate association rules is not very well. We develop a novel algorithm, SAW, to generate strong association rules by combining the paired rules, which can avoid lots of unnecessary computing that traditional method often encounter. The experiments show our method is more efficiently than FARMER. KeyWords-strong association rules; forward combined; backward combined; closed rules
Telegenetics: a systematic review of telemedicine in genetics services.

PURPOSE Telemedicine is being increasingly used in many areas of health care, particularly to reduce the barriers that rural populations face in accessing health-care services. Telemedicine may also be effectively utilized in clinical genetics services—an application that has been termed “telegenetics. ” METHODS A systematic review of the literature was conducted to identify studies of genetic consultations carried out through video conferencing so as to determine whether conclusions can be drawn about the value of telegenetics. A total of 14 articles reporting data from 12 separate studies met the inclusion criteria. RESULTS In a majority of these studies, patients received their telegenetics consultation at a local clinic or outreach center, from where they communicated via a synchronous video link with a genetic spractitioner. All the studies reported high levels of patient satisfaction with telegenetics,and patients were generally more receptive to telegenetics than the genetics practitioners were. The studies had limitations of small sample sizes and lack of statistical analyses. CONCLUSIONS This review suggests that telegenetics may be a useful tool for providing routine counseling and has the potential to evaluate pediatric patients with suspected genetic conditions. Prospective,fully powered studies of telegenetics that explore the accuracy of diagnoses and patient outcomes are needed to allow informed decisions to be made about the appropriate use of telemedicine in genetics service delivery.
An experimentally validated bimorph cantilever model for piezoelectric energy harvesting from base excitations

Piezoelectric transduction has received great attention for vibration-to-electric energy conversion over the last five years. A typical piezoelectric energy harvester is a unimorph or a bimorph cantilever located on a vibrating host structure, to generate electrical energy from base excitations. Several authors have investigated modeling of cantilevered piezoelectric energy harvesters under base excitation. The existing mathematical modeling approaches range from elementary single-degree-of-freedom models to approximate distributed parameter solutions in the sense of Rayleigh–Ritz discretization as well as analytical solution attempts with certain simplifications. Recently, the authors have presented the closed-form analytical solution for a unimorph cantilever under base excitation based on the Euler–Bernoulli beam assumptions. In this paper, the analytical solution is applied to bimorph cantilever configurations with series and parallel connections of piezoceramic layers. The base excitation is assumed to be translation in the transverse direction with a superimposed small rotation. The closed-form steady state response expressions are obtained for harmonic excitations at arbitrary frequencies, which are then reduced to simple but accurate single-mode expressions for modal excitations. The electromechanical frequency response functions (FRFs) that relate the voltage output and vibration response to translational and rotational base accelerations are identified from the multi-mode and single-mode solutions. Experimental validation of the single-mode coupled voltage output and vibration response expressions is presented for a bimorph cantilever with a tip mass. It is observed that the closed-form single-mode FRFs obtained from the analytical solution can successfully predict the coupled system dynamics for a wide range of electrical load resistance. The performance of the bimorph device is analyzed extensively for the short circuit and open circuit resonance frequency excitations and the accuracy of the model is shown in all cases.
Organizing Search Results with a Reference Map

We propose a method to highlight query hits in hierarchically clustered collections of interrelated items such as digital libraries or knowledge bases. The method is based on the idea that organizing search results similarly to their arrangement on a fixed reference map facilitates orientation and assessment by preserving a user's mental map. Here, the reference map is built from an MDS layout of the items in a Voronoi treemap representing their hierarchical clustering, and we use techniques from dynamic graph layout to align query results with the map. The approach is illustrated on an archive of newspaper articles.
How to study artificial creativity

In this paper, we describe a novel approach to developing computational models of creativity that supports the multiple approaches to the study of artificial creative systems. The artificial creativity approach to the development of computational models of creative systems is described with reference to Csikszentmihalyi's systems view of creativity. Some interesting results from studies using an early implementation of an artificially creative system, The Digital Clockwork Muse, are presented. The different studies show how the artificial creativity approach supports the study of creativity from a variety of standpoints that mirror the disciplines that study human creativity. The use of artificial creativity allows these different studies to be conveniently conducted on the same computational model and integrated in to a more complete picture of the creative process.
Job communication characterization and its impact on meta-scheduling co-allocated jobs in a mini-grid

Summary form only given. We present a bandwidth-centric parallel job communication model that takes into account inter-cluster network utilization as a means by which to capture the interaction and impact of simultaneously co-allocated jobs in a mini-grid. Our model captures the time-varying utilization of shared inter-cluster network resources in the grid. We compare our dynamic model with previous research that utilizes a fixed execution time penalty for co-allocated jobs. We have found that the fixed penalty model is more generous in its prediction of job turnaround time than our dynamic communication model. Additionally, we see that the penalty co-allocated jobs may experience without causing a severe performance degradation decreases as the number of clusters increases.
A Shift from Cellular to Humoral Responses Contributes to Innate Immune Memory in the Vector Snail Biomphalaria glabrata

Discoveries made over the past ten years have provided evidence that invertebrate antiparasitic responses may be primed in a sustainable manner, leading to the failure of a secondary encounter with the same pathogen. This phenomenon called “immune priming” or "innate immune memory" was mainly phenomenological. The demonstration of this process remains to be obtained and the underlying mechanisms remain to be discovered and exhaustively tested with rigorous functional and molecular methods, to eliminate all alternative explanations. In order to achieve this ambitious aim, the present study focuses on the Lophotrochozoan snail, Biomphalaria glabrata, in which innate immune memory was recently reported. We provide herein the first evidence that a shift from a cellular immune response (encapsulation) to a humoral immune response (biomphalysin) occurs during the development of innate memory. The molecular characterisation of this process in Biomphalaria/Schistosoma system was undertaken to reconcile mechanisms with phenomena, opening the way to a better comprehension of innate immune memory in invertebrates. This prompted us to revisit the artificial dichotomy between innate and memory immunity in invertebrate systems.
Numerical simulations of electric fields in bone induced by an ultrasound wave using a piezoelectric finite-difference time-domain method

Numerical simulations of the piezoelectric effect of bone under ultrasound irradiation were attempted to perform using a three-dimensional (3D) elastic finite-difference time-domain (FDTD) method with piezoelectric constitutive equations (PE-FDTD method). The electric fields in a human femur induced by an ultrasound burst wave at 1 MHz, which was radiated perpendicular to the bone axis, were simulated by the PE-FDTD method. Two sets of the piezoelectric parameters were used to investigate the effect of the piezoelectric anisotropy. The spatial distribution of the electric field in the axial direction of the bone could strongly depend on the piezoelectric anisotropy and was not necessarily similar to the distribution of the normal stress in the same direction. Moreover, the comparison between the simulated results for the normal and fractured bone models showed that the electric field could change by the fracture.
Effects of Short- and Long-Term Hypercholesterolemia on Contrast-Induced Acute Kidney Injury

Background: Whether hypercholesterolemia is a risk factor for contrast-induced acute kidney injury (CI-AKI) remains unclear. In the present study, the effects of short- and long-term dietary hypercholesterolemia on contrast media-induced nephrotoxicity were evaluated. Methods: Rats were fed either a normal rodent diet (N) or high-cholesterol diet (H). At the end of 2 and 8 weeks, 8 rats from each diet group were given a tail vein injection of either iohexol (group NC and group HC) or vehicle (group N and group H). Blood lipids, renal function and renal hemodynamics were evaluated 1 day after contrast media administration. Renal and urinary prostaglandin E2 (PGE2) and thromboxane B2 (TXB2) were detected by radioimmunoassay. Renal nitric oxide and malondialdehyde (MDA) were measured by the Griess reaction and thiobarbituric acid method, respectively. Results: Contrast media administration increased serum creatinine levels and induced severe renal tubular necrosis in rats fed the high-cholesterol diet for 8 weeks but not in rats fed the normal diet or high-cholesterol diet for 2 weeks. The renal and urinary PGE2 and TXB2 levels increased significantly in rats in group H and group HC at the end of 8 weeks. Renal nitric oxide production decreased, and MDA levels increased markedly in group HC and group H at the end of 8 weeks. Conclusions: We conclude that long-term hypercholesterolemia appeared to be a risk factor for CI-AKI, which might be associated with disorders in intrarenal prostaglandins and abnormalities in renal nitric oxide system induced by lipid peroxidation.
Intragenic Recombination Has a Critical Role on the Evolution of Legionella pneumophila Virulence-Related Effector sidJ

SidJ is a Dot/Icm effector involved in the trafficking or retention of ER-derived vesicles to Legionella pneumophila vacuoles whose mutation causes an observable growth defect, both in macrophage and amoeba hosts. Given the crucial role of this effector in L. pneumophila virulence we investigated the mechanisms shaping its molecular evolution. The alignment of SidJ sequences revealed several alleles with amino acid variations that may influence the protein properties. The identification of HGT events and the detection of balancing selection operating on sidJ evolution emerge as a clear result. Evidence suggests that intragenic recombination is an important strategy in the evolutionary adaptive process playing an active role on sidJ genetic plasticity. This pattern of evolution is in accordance with the life style of L. pneumophila as a broad host-range pathogen by preventing host-specialization and contributing to the resilience of the species.
Analog Placement Based on Novel Symmetry-Island Formulation

In this paper, we present the first amortized linear-time packing algorithm for the placement with symmetry constraints. We first introduce the concept of a symmetry island which is formed by modules of the same symmetry group in a single connected placement. Based on this concept and the B*-tree representation, we propose automatically symmetric-feasible B*-trees (ASF-B*-trees) to directly model the placement of a symmetry island. Unlike the previous works that can handle only ID symmetry constraints, our ASF-B*-tree is the first in the literature to additionally consider 2D symmetry. We then present hierarchical B*-trees (HB*-trees) which can simultaneously optimize the placement with both symmetry islands and non-symmetry modules. Unlike the previous works, our approach can guarantee the close proximity of symmetry modules and significantly reduce the search space based on the symmetry-island formulation. In particular, the packing time for an ASF-B*- tree or an HB*-tree is the same as that for a plain B*-tree (only amortized linear) and much faster than previous works which need at least loglinear time. Experimental results show that our approach achieves the best published quality and runtime efficiency for analog placement.
Mica: A Wireless Platform for Deeply Embedded Networks

Low-power integration of sensing, communication, and computation requires a new approach to wireless design. Flexible interfaces and primitive accelerators enable aggressive system-level optimizations. Mica's flexible design serves as a building block for creating efficient application-specific protocols. Instead of defining narrow, standardized application interfaces, Mica provides a set of richly interconnected primitives (such as data serializers and timing extractors) to facilitate cross-layer optimizations. To explore novel systems approaches, researchers can develop customized protocols tailored to their application; Mica does not require use of predefined protocols.
P‐selectin glycoprotein‐ligand‐1 regulates pulmonary recruitment of neutrophils in a platelet‐independent manner in abdominal sepsis

Background and purpose: Neutrophil‐mediated lung injury is an insidious feature in sepsis although the mechanisms regulating pulmonary recruitment of neutrophils remain elusive. Here, we investigated the role of P‐selectin glycoprotein‐ligand‐1 (PSGL‐1) in sepsis‐induced neutrophil recruitment and tissue injury in the lung.
Broadcasting in massive MIMO using OSTBC with reduced dimension

An analysis of broadcasting in massive MIMO (multiple-input and multiple-output) systems with a limited coherence interval is presented. When broadcasting common information, such as control signals, the base station does not have channel state information to the terminals. We propose that the base station broadcasts this common information using a low dimensional orthogonal space-time block code (OSTBC). This code is mapped onto the large antenna array with the use of a dimension reducing matrix, effectively “shrinking” the channel. The terminal can estimate the effective channel and decode the information, even when the coherence interval is short compared to the number of base station antennas. Different OSTBCs are compared in terms of outage capacity in practical scenarios using estimated CSI. In particular, the trade-off between diversity and rate, when little or no time/frequency diversity is available, is investigated.