Miracle-dz/UniFAR-FTUs huggingface dataset:
Partial Activation and Induction of Apoptosis in CD4+ and CD8+ T Lymphocytes by Conformationally Authentic Noninfectious Human Immunodeficiency Virus Type 1

ABSTRACT Increased levels of apoptosis are seen in human immunodeficiency virus (HIV) infection, and this has been proposed as an important mechanism contributing to HIV pathogenesis. However, interpretation of in vitro studies aimed at understanding HIV-related apoptosis has been complicated by the use of high concentrations of recombinant proteins or by direct cytopathic effects of replicating virus. We have developed an inactivation procedure that destroys retroviral infectivity while preserving the structural and functional integrity of the HIV surface proteins. These noninfectious virions interact authentically with target cells, providing a powerful tool to dissect mechanisms of HIV pathogenesis that do or do not require viral replication. Noninfectious CXCR4-tropic HIV-1 virions, but not microvesicles, partially activated freshly isolated CD4+ and CD8+ peripheral blood mononuclear cell T lymphocytes to express FasL and Fas, but not CD69 or CD25 (interleukin-2 receptor alpha) and eventually die via apoptosis starting 4 to 6 days postexposure. These effects required conformationally intact virions, as heat-denatured virions or equivalent amounts of recombinant gp120 did not induce apoptosis. The maximal apoptotic effect was dependent on major histocompatibility complex (MHC) class II proteins being present on the virion, but was not MHC restricted. The results suggest that the immunopathogenesis of HIV infection may not depend solely on direct cytopathic effects of HIV replication, but that effects due to noninfectious HIV-1 virions may also contribute importantly.
Exploration of Multi-thread Processing on XILKERNEL for FPGA Based Embedded Systems

The present day FPGA (Field Programmable Gate Array) technology is capable to design high performance embedded systems based on its soft core (MicroBlaze) and hard core (PowerPC) processors, embedded memories and other IP cores. Embedded system design demands use of limited hardware resources with as minimum power as possible while providing higher throughput. One way to decrease the complexity of application is to use a thread-oriented design where a process is divided into a number of manageable pieces known as threads. Each thread is responsible for some part of the application, thus providing multitasking. Further, for real-time task execution we need to have an efficient RTOS (Real Time Operating System) infrastructure on FPGA. Deciding a particular scheduling algorithm for thread execution requires the knowledge of resource utilization for the specific scheduling policy. Hence, a proper exploration of the various thread scheduling algorithms in terms of resource utilization, for a given embedded platform is of much importance. The incorporation of XILKERNEL RTOS in FPGA is a latest facility. Though there exists a few research work on analyzing the resource requirement in multitasking scenario for a given embedded RTOS environment, our work on resource estimation for the various task scheduling policies using XILKERNEL is first of its kind. Implementation of real-time scheduling algorithm like RMS on XILKERNEL has also been endeavored, using OS virtualization, since it is not directly supported by the kernel of XILKERNEL.
Silicone hydrogels grafted with natural amino acids for ophthalmological application

Abstract In this report, protein repelling silicone hydrogels with improved hydrophilicity were prepared by photo-polymerization of silicone-containing monomer and glycidyl methacrylate followed by grafting zwitterionic amino acids. The grafted silicone hydrogels possessed excellent hydrophilic surfaces due to the enrichment of amino acids, which was confirmed by attenuated total reflectance Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, contact angle, and equilibrium water content measurements. Remarkable resistance to bovine serum albumin and lysozyme fouling was observed for the silicone hydrogels immobilized with neutrally charged amino acids because of the formation of zwitterionic surfaces with pairs of protonated secondary ammonium cations and deprotonated carboxyl anions. Meanwhile, the silicone hydrogels grafted with positively or negatively charged amino acids were able to repulse same charged protein with reduced deposition and attract oppositely charged protein with increased adsorption. Preliminary cytotoxicity test indicated that the zwitterionic silicone hydrogels were non-cytotoxic. Similarly, three types of natural amino acids, including serine, aspartic acid and histidine, modified silicone hydrogel contact lenses exhibited excellent hydrophilicity and non-damage to the rabbit’s eyes, but only serine modified zwitterionic contact lens showed superior protein fouling resistance compared with the current commercial hydrogel contact lens, which may have great potential application in ophthalmology.
Examination stress and components of working memory

Previous research suggests that stress can influence a broad range of memory functions. In this study we investigated the effect of a naturalistic stressor, examination stress, on working memory in young adults. In order to accomplish this aim, participants were tested on psychological and hormonal measures of stress and on Digit Span, once during a low stress period and once during a high stress period. The high examination stress condition was associated with an increase in cortisol and subjective impressions of stress. Although Digits Forward performance did not vary with examination stress, Digits Backward performance improved. These findings suggest that mild increases in stress are associated with improvement in the manipulation component of working memory. However, no correlations were found between working memory and either cortisol or psychological stress. Thus the mechanism by which mild naturalistic stressors improve the manipulation component of working memory needs further investigation.
Selection and characterization of mutants of Phanerochaete chrysosporium exhibiting ligninolytic activity under nutrient-rich conditions

Synthesis of the ligninolytic system of the wood-degrading fungus Phanerochaete chrysosporium is induced during secondary metabolism, brought about by nitrogen, carbon, or sulfur starvation. We describe here a strategy for selection of mutants which are ligninolytic (lignin----CO2) and overproduce lignin-degrading enzymes (ligninases) under nutrient-rich conditions (during primary metabolism). The strategy is based on using an adduct of lysine and a lignin model compound. Ligninase-dependent oxidation of this adduct releases free lysine, which complements the lysine requirements of a lysine auxotroph. Accordingly, a lysine auxotroph was mutagenized by UV irradiation and survivors were plated onto medium containing the adduct and high ammonia nitrogen. Four mutants which overproduce the ligninase isozymes were isolated by this procedure. Further characterization of one of the mutants, PSBL-1, indicated that the predominant isozymes produced are H1 (pI = 4.7) and H2 (pI = 4.4). The ligninase activity of PSBL-1, measured by veratryl alcohol oxidation, peaks on day 5 at over 1,000 U.liter-1. The mutant PSBL-1 was also able to degrade [14C]lignin to 14CO2, indicating that the complete ligninolytic system is deregulated.
Intelligent Fusion and Asset Management Processor

Owing to continual advances in sensor capabilities, avionics, and inter-service C/sup 4/I, the volume of battlefield intelligence data to which the modern-day military intelligence analyst has access is increasing at an exponential rate. This has created the need for more intelligent systems capable of scanning and extracting the tactically most useful information for presentation to the human analyst. The presence of a more extensive and flexible sensor asset infrastructure also mandates more intelligent and accountable asset deployment and management. Accordingly, we describe an effort to develop for the Air Force Research Laboratory's Information Directorate an Intelligent Fusion and Asset Management Processor (IFAMP) for enhancing tactical situation awareness and for providing needs-based sensor asset planning and scheduling information to assist the C/sup 2/ staff. The IFAMP architecture incorporates three distinct modules: a fuzzy logic-based level one fusion module responsible for low-level event detection, unit/echelon type discrimination, observation-to-track gating and assignment, and track database management; a belief network-based level two situation assessment module responsible for generating probabilistic hypotheses for high-level situational state descriptors; and a fuzzy logic-based level four collection management expert system responsible for mapping informational requirements and current state information into asset resource requests.
GBP-Based Detection and Symmetric Information Rate for Granular Tiling Model in TDMR

—Two dimensional magnetic recording (TDMR) is a new paradigm in data storage which envisions densities up to 10 Tb / in 2 as a result of drastically reducing bit to grain ratio. In order to reach this goal aggressive write (shingled writing) and read process are used in TDMR. Kavcic et al. proposed a simple magnetic grain model called the granular tiling model which captures the essence of read/write process in TDMR. Capacity bounds for this model indicate that 0 . 6 user bit per grain densities are possible, however, previous attempt to reach capacities are not close to the channel capacity. In this paper, we provide a truly two-dimensional detection scheme for the granular tiling model based on generalized belief propagation (GBP). Factor graph interpretation of the detection problem is provided and formulated in this paper. Then, GBP is employed to compute marginal a posteriori probabilities for the constructed factor graph. Simulation results show huge improvements in detection. A lower bound on the symmetric information rate (SIR) is also derived for this model based on GBP detector.
Full-duplex in large-scale wireless systems

In this paper, we investigate the combination of full-duplex wireless communication with large-scale multiple-input multiple-output (MIMO) technology, which has the potential for bidirectional wireless communication at high spectral efficiency and low power consumption. In addition, we study its application to cellular (multi-user) systems that could be extended with large antenna arrays, such as 3GPP LTE. In order to solve the fundamental issue of self-interference cancellation in full-duplex cellular communication systems, we propose two schemes that exploit the excess of antennas present at the base-station (BS) of large-scale MIMO systems. We investigate the associated sum-rate and show that by carefully selecting the ratio between number of transmit and receive antennas at the BS, one is able to maximize the system capacity. We furthermore investigate the inter-user interference issue that occurs in multi-user scenarios, as well as the impact of residual transmit-side (TX) radio-frequency (RF) impairments. Our preliminary results show that large-scale MIMO is able to render full-duplex communication more resilient against inter-user interference and helps to mitigate the effects of residual TX-RF impairments.
Replication of Previous Genome-wide Association Studies of Bone Mineral Density in Premenopausal American Women

Bone mineral density (BMD) achieved during young adulthood (peak BMD) is one of the major determinants of osteoporotic fracture in later life. Genetic variants associated with BMD have been identified by three recent genome‐wide association studies. The most significant single‐nucleotide polymorphisms (SNPs) from these studies were genotyped to test whether they were associated with peak BMD in premenopausal American women. Femoral neck and lumbar spine BMD were determined by dual‐energy X‐ray absorptiometry in two groups of premenopausal women: 1524 white women and 512 black women. In premenopausal white women, two SNPs in the C6orf97/ESR1 region were significantly associated with BMD (p < 4.8 × 10−4), with suggestive evidence for CTNNBL1 and LRP5 (p < .01). Evidence of association with one of the two SNPs in the C6orf97/ESR1 region also was observed in premenopausal black women. Furthermore, SNPs in SP7 and a chromosome 4 intergenic region showed suggestive association with BMD in black women. Detailed analyses of additional SNPs in the C6orf97/ESR1 region revealed multiple genomic blocks independently associated with femoral neck and lumbar spine BMD. Findings in the three published genome‐wide association studies were replicated in independent samples of premenopausal American women, suggesting that genetic variants in these genes or regions contribute to peak BMD in healthy women in various populations. © 2010 American Society for Bone and Mineral Research
Public perception of coastal zone environmental problems in the Samsun province, Turkey

During the past few decades, the Samsun coast has been subjected to various human impacts that have led to changes in the coastal zone of this the area. This paper is an attempt to understand and define how residents and beach users perceive coastal zone problems in Samsun province based on their perceptions. For this purpose, a questionnaire survey was conducted during the months of June and July in 2005 and 2006 on 500 residents and beach users at eight beaches along the 121-kilometer Samsun shoreline on the north side of Turkey. The questionnaire data was collected through a direct interview. Analysis of interview data reveals that the respondents perceive coastal seawater pollution (89%), beach pollution, the loss of beach plain (67%), and changes in land use (91%) as the main problems of the coastal zone. The main factors blamed for coastal seawater pollution are sewage (98%), industrial waste (74%), and waste oils discharged by ships (38%). It is clear from the results of the survey that residents and beach users are not sufficiently aware of the coastal zone problems. The most important recommendation for solving these problems is increasing environmental awareness. To this end, environmental education activities are necessary for the conservation of coastal zone ecosystems.
Web Image Organization and Object Discovery by Actively Creating Visual Clusters through Crowdsourcing

In this paper, we propose to organize web images by actively creating visual clusters via crowd sourcing. We develop a two-phase framework to efficiently and effectively combine computers and a large number of human workers to build high quality visual clusters. The first phase partitions an image collection into multiple clusters, the second phase refines each generated cluster independently. In both phases, informative images are selected by computers and manually labeled by the crowds to learn improved models. Our method can be naturally extended to discover object categories in a collection of image segments. Experimental results on several data sets demonstrate the promise of our developed approach on both web image organization and object discovery tasks.
RNA-binding Motif Protein 4 Translocates to Cytoplasmic Granules and Suppresses Translation via Argonaute2 during Muscle Cell Differentiation*

The RNA-binding motif protein 4 (RBM4) plays multiple roles in mRNA metabolism, including translation control. RBM4 suppresses cap-dependent translation but activates internal ribosome entry site-mediated translation. Because of its high expression level in muscle and heart, we investigated the function of RBM4 in myoblast cells. Here, we demonstrate that RBM4 is phosphorylated and translocates to the cytoplasm in mouse C2C12 cells upon cell differentiation. Notably, RBM4 is transiently deposited into cytoplasmic granules containing microtubule assembly factors as well as poly(A)+ RNAs. Moreover, RBM4 colocalizes with the components of micro-ribonucleoproteins, including the Argonaute2 (Ago2) protein, during muscle cell differentiation. RBM4 interacts directly with Ago2 and may recruit Ago2 to suppress translation of target mRNAs. Furthermore, RBM4 selectively associates with muscle cell-specific microRNAs and potentiates their translation repression activity by promoting micro-ribonucleoprotein association with target mRNAs. Altogether, our results suggest that RBM4 translocates to the cytoplasm and participates in translation suppression during muscle cell differentiation.
A batteryless thermoelectric energy-harvesting interface circuit with 35mV startup voltage

Energy harvesting is an emerging technology with applications to handheld, portable and implantable electronics. Harvesting ambient heat energy using thermoelectric generators (TEG's) [1] is a convenient means to supply power to body-worn electronics and industrial sensors. Using TEG's for body-wearable applications limits the output voltage to 50mV for temperature differences of 1–2K usually found between the body and ambience. Several existing systems [2, 3] use a battery or an initial high voltage energy input to kick-start operation of the system from this low voltage. Further, changing external conditions cause the voltage and power generated by the TEG to vary, necessitating efficient control circuits that can adapt and extract the maximum possible power out of these systems. In this paper, a battery-less thermoelectric energy harvesting interface circuit which uses a mechanically assisted startup circuit to operate from 35mV input is presented. An efficient control circuit that performs maximal end-to-end transfer of the extracted energy to a storage capacitor and regulates the output voltage at 1.8V is demonstrated.
Methamphetamine‐induced structural plasticity in the dorsal striatum

Repeated exposure to psychostimulant drugs produces long‐lasting changes in dendritic structure, presumably reflecting a reorganization in patterns of synaptic connectivity, in brain regions that mediate the psychomotor activating and incentive motivational effects of these drugs, including the nucleus accumbens and prefrontal cortex. However, repeated exposure to psychostimulant drugs also facilitates a transition in the control of some behaviors from action–outcome associations to behavior controlled by stimulus–response (S–R) habits. This latter effect is thought to be due to increasing engagement and control over behavior by the dorsolateral (but not dorsomedial) striatum. We hypothesized therefore that repeated exposure to methamphetamine would differentially alter the density of dendritic spines on medium spiny neurons (MSNs) in the dorsolateral vs. dorsomedial striatum. Rats were treated with repeated injections of methamphetamine, and 3 months later dendrites were visualized using Sindbis virus‐mediated green fluorescent protein (GFP) expression in vivo. We report that prior exposure to methamphetamine produced a significant increase in mushroom and thin spines on MSNs in the dorsolateral striatum, but a significant decrease in mushroom spines in the dorsomedial striatum. This may be due to changes in the glutamatergic innervation of these two subregions of the dorsal striatum. Thus, we speculate that exposure to psychostimulant drugs may facilitate the development of S–R habits because this reorganizes patterns of synaptic connectivity in the dorsal striatum in a way that increases control over behavior by the dorsolateral striatum.
A new fault tolerant scheme for cascaded H-Bridge multilevel converter

Multilevel converters are mainly used in high power applications (usually more than a few hundred kW). It is therefore important that they can continue working under faulty condition. In this paper, a new method is proposed to improve performance of CHB inverter under faulty condition. The proposed method will be compared with existing methods in term of voltage availability. The converter is simulated in Simulink and the results are provided. These results confirm the effectiveness of the proposed scheme, and are in accordance with the theoretical results.
Skyline Travel Routes: Exploring Skyline for Trip Planning

In this paper, given a spatial range Q and a set of query points specified by users, the goal of this paper is to return the travel routes that fulfill two requirements: 1. ) travel routes should contain all those query points specified, and 2. ) travel routes should be within the spatial range Q. Furthermore, we claim that each query point may have its proper visiting time. As such, the travel routes should go through these query points at their corresponding proper visiting time. To avoid some redundant information in the travel routes, we utilize the skyline concept to retrieve travel routes with more diversity. Specifically, in our paper, we consider some factors, such as the visiting time information of POIs and the set of query points, in retrieving travel routes. These factors could be mapped into dimensional spaces. Then, each travel route is viewed as a data point in the dimensional space. Thus, skyline data points (referred to as skyline travel routes) are returned as the query result. Skyline travel routes could provide more diversity in the query result of trip route recommendations. To evaluate our proposed methods, we conducted extensive experiments on real datasets. The experimental results show that skyline travel routes indeed provide more diversity in the query result. In addition, we evaluate the efficiency of retrieving skyline travel routes.
BvgAS-mediated signal transduction: analysis of phase-locked regulatory mutants of Bordetella bronchiseptica in a rabbit model

Members of the Bordetella genus alternate between two distinct phenotypic phases in response to changes in their environment. This switch, termed phenotypic modulation, is mediated by the BvgAS sensory transduction system. We developed an animal model based on the interaction of Bordetella bronchiseptica with one of its natural hosts, the rabbit. To investigate the importance of BvgAS signal transduction, we constructed constitutive (RB53) and Bvg- (RB54) phase-locked derivatives of a wild-type strain, RB50. RB50 and RB53, but not RB54, established respiratory infections in B. bronchiseptica-free rabbits with an intranasal 50% infective dose of less than 200 organisms, and the course of the infection closely resembled that observed with naturally infected rabbits. Bacteria were recovered from the nasal cavity, larynx, trachea, and lungs in similar numbers from RB50- and RB53-infected rabbits, yet no pathology was detected by histological examination of lung and tracheal sections. The antibody responses in rabbits inoculated with RB50 or RB53 were quantitatively and qualitatively indistinguishable; high titers of antibodies were generated primarily against Bvg(+)-phase-specific antigens. No response against flagella, a Bvg- phase factor, was detected. Assessment of bacteria associated with alveolar macrophages indicated that only a small percentage of bacteria, if any, appear to be residing within lung macrophages. We also tested the ability of these strains to survive in a nutrient poor environment, conditions which may be encountered within certain niches in the host or in an environmental reservoir. The Bvg- phase was advantageous for growth under these conditions. Our results indicate the Bvg+ phase is sufficient for establishment of respiratory tract infection in the rabbit and the normal BvgAS-mediated response to environmental signals is not required during initial colonization. The Bvg- phase may play a role at later stages of infection, including persistence, transmission, or survival in the environment.