Miracle-dz/UniFAR-FTUs huggingface dataset:
Endothelial Claudin : Claudin-5 / TMVCF Constitutes Tight Junction Strands in Endothelial Cells

Tight junctions (TJs) in endothelial cells are thought to determine vascular permeability. Recently, claudin-1 to -15 were identified as major components of TJ strands. Among these, claudin-5 (also called transmembrane protein deleted in velo-cardio-facial syndrome [TMVCF]) was expressed ubiquitously, even in organs lacking epithelial tissues, suggesting the possible involvement of this claudin species in endothelial TJs. We then obtained a claudin-6–specific polyclonal antibody and a polyclonal antibody that recognized both claudin-5/TMVCF and claudin-6. In the brain and lung, immunofluorescence microscopy with these polyclonal antibodies showed that claudin-5/TMVCF was exclusively concentrated at cell–cell borders of endothelial cells of all segments of blood vessels, but not at those of epithelial cells. Immunoreplica electron microscopy revealed that claudin-5/TMVCF was a component of TJ strands. In contrast, in the kidney, the claudin-5/TMVCF signal was restricted to endothelial cells of arteries, but was undetectable in those of veins and capillaries. In addition, in all other tissues we examined, claudin-5/TMVCF was specifically detected in endothelial cells of some segments of blood vessels, but not in epithelial cells. Furthermore, when claudin-5/TMVCF cDNA was introduced into mouse L fibroblasts, TJ strands were reconstituted that resembled those in endothelial cells in vivo, i.e., the extracellular face–associated TJs. These findings indicated that claudin-5/TMVCF is an endothelial cell–specific component of TJ strands.
SAR Calculations in Human Head Model Extracted from Thermal Infrared Images

In electromagnetic dosimetry, anatomical human models are commonly obtained by segmentation of magnetic resonance imaging (MRI) or computed tomography (CT) scans. In this paper, a human head model extracted from thermal IR images is examined in terms of its applicability to specific absorption rate (SAR) calculations. Since thermal scans are two-dimensional (2-D) representation of surface temperature, this allows researchers to overcome the extensive computational demand associated with three-dimensional (3-D) simulation. The numerical calculations are performed using the finite difference time domain (FDTD) method with mesh sizes of 2 mm at 900 MHz plane wave irradiation. The power density of the incident plane wave is assumed to be 10 W/m2. Computations were compared with a realistic anatomical head model. The results show that although there were marked differences in the local SAR distribution in the various tissues in the two models, the 1g peak SAR values are approximately similar in the two models.
Mapping chromatic pathways in the Drosophila visual system.

In Drosophila, color vision and wavelength-selective behaviors are mediated by the compound eye's narrow-spectrum photoreceptors R7 and R8 and their downstream medulla projection (Tm) neurons Tm5a, Tm5b, Tm5c, and Tm20 in the second optic neuropil or medulla. These chromatic Tm neurons project axons to a deeper optic neuropil, the lobula, which in insects has been implicated in processing and relaying color information to the central brain. The synaptic targets of the chromatic Tm neurons in the lobula are not known, however. Using a modified GFP reconstitution across synaptic partners (GRASP) method to probe connections between the chromatic Tm neurons and 28 known and novel types of lobula neurons, we identify anatomically the visual projection neurons LT11 and LC14 and the lobula intrinsic neurons Li3 and Li4 as synaptic targets of the chromatic Tm neurons. Single-cell GRASP analyses reveal that Li4 receives synaptic contacts from over 90% of all four types of chromatic Tm neurons, whereas LT11 is postsynaptic to the chromatic Tm neurons, with only modest selectivity and at a lower frequency and density. To visualize synaptic contacts at the ultrastructural level, we develop and apply a "two-tag" double-labeling method to label LT11's dendrites and the mitochondria in Tm5c's presynaptic terminals. Serial electron microscopic reconstruction confirms that LT11 receives direct contacts from Tm5c. This method would be generally applicable to map the connections of large complex neurons in Drosophila and other animals. J. Comp. Neurol. 524:213-227, 2016. © 2015 Wiley Periodicals, Inc.
hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis

Except for a small fraction of persisters, 10(-6) to 10(-5), Escherichia coli K-12 is killed by prolonged inhibition of murein synthesis. The progeny of persisters are neither more resistant to inhibition of murein synthesis nor more likely to persist than normal cells. Mutants have been isolated in which a larger fraction, 10(-2), persists. The persistent response of the mutants, Hip (high persistence), is to inhibition of murein synthesis at early or late steps by antibiotics (phosphomycin, cycloserine, and ampicillin) or by metabolic block (starvation for diaminopimelic acid). Killing of the parent strain by each of the four inhibitors has two phases: The first is rapid and lasts about 30 min; the second is slower, but still substantial, and lasts 3 to 4 h. The first phase also occurs in the Hip mutants, but then viability of the mutants remains constant after about 30 min. Neither tolerance, resistance, impaired growth, nor reversion of spheroplasts accounts for high-frequency persistence. Two of the mutations map at 33.8 min in a region containing few other recognized functions. This position and the phenotypes define hipA as a newly recognized gene. Transposons Tn5 and Tn10 have been inserted close to hipA making it possible to explore the molecular genetics of persistence, a long recognized but poorly understood phenomenon.
Partially asymmetric simple exclusion model in the presence of an impurity on a ring

We study a generalized two-species model on a ring. The original model (Mallick K 1996 J. Phys. A: Math. Gen. 29 5375) describes ordinary particles hopping exclusively in one direction in the presence of an impurity. The impurity hops with a rate different from that of ordinary particles and can be overtaken by them. Here we let the ordinary particles also hop backward with rate q . Using the matrix product ansatz we obtain the relevant quadratic algebra. A finite-dimensional representation of this algebra enables us to compute the stationary bulk density of the ordinary particles, as well as the speed of impurity on a set of special surfaces of the parameter space. We will obtain the phase structure of this model in the accessible region and show how the phase structure of the original model is modified. In the infinite-volume limit this model presents a shock in one of its phases.
Regularization of Incompletely, Irregularly and Randomly Sampled Data

In several scientific areas, data are sampled irregularly and insufficiently due to practical and economical limitations. The use of such data in applications results in some artifacts and poor spatial resolution. Therefore, before being used, the data are to be interpolated onto a regular grid. One of the methods achieving this objective is based on the Fourier reconstruction, which deals with the under-determined system of equations. The Stagewise Orthogonal Matching Pursuit (StOMP) is a recently proposed greedy algorithm. Compared to the other recent algorithms like l1- minimization techniques, StOMP admits certain promising features such as faster and simpler implementation even in large scale settings. The present work applies StOMP to the Fourier-based interpolation problem for the signals that have sparse Fourier spectra. The basic objective is to verify empirically the performance of the algorithm if, and how far, the measurement coordinates can be shifted from uniform distribution on the continuous interval. Taking kurtosis as a quantifier for the deviation of distribution from being uniform, we show numerically that the measurement coordinates can be significantly shifted from uniform distribution.
Edge-preserving disparity map estimation from stereo videos for bokeh synthesis

We present a new method of estimating disparity maps from stereo videos for bokeh effect synthesis. In this work, we develop an improved total variation regularization and the robust L1 norm in the data fidelity term (TV-L1) [4] based method to estimate edge-preserving disparity map without stereo rectification. The proposed algorithm improves the TV-L1 approach by incorporating structure edge detection, occlusion area detection, textureless region detection and applying the guided filter to alleviate the inconsistency problem between the disparity map and color image around object boundary. Furthermore, we propose a temporal filter to improve the temporal consistency of the disparity maps computed from the stereo videos. We use saliency map to focus the synthesis result on the objects which attract human attention most. Experimental comparisons on various real videos are shown to demonstrate that the proposed algorithm generates more visually pleasing bokeh video synthesis compared with those by using previous stereo matching methods.
Age‐related increase in the immunoproteasome content in rat hippocampus: molecular and functional aspects

Alterations in the proteasome activity in the CNS have been described during aging. However, a detailed study of all proteasome subunits is actually lacking. We have analyzed, in vivo, the age‐related modifications in the molecular composition of hippocampal proteasomes. We found that the immunoproteasome/proteasome ratio was increased in aged hippocampus. The processing of the low‐molecular‐mass protein (LMP)7/β5i subunit, practically absent in young hippocampus, was increased in aged animals. Among the potential factors underlying these modifications we evaluated the neuroinflammation and the transcription factor Zif268. Lipopolysaccharide (LPS)‐induced neuroinflammation in young rats, up‐regulated the expression of immunoproteasome subunits and increased the processing of the LMP7/β5i protein. Moreover, the hydrophobicity of cellular peptides, analyzed by liquid chromatography, increased in both, young LPS‐injected animals and aged rats, suggesting that immunoproteasomes including the LMP7/β5i subunit could, at least in part, account for this modification. Also, the mRNA expression of the transcription factor Zif268, which down‐regulates the immunoproteasome subunit LMP7/β5i by binding to sequences within the promoter regions, was decreased in both, aged hippocampus and young LPS‐injected animals. Finally, we found that spatial memory training in young animals, a situation in which the expression of Zif268 is increased, modified the mRNA expression of the constitutive and catalytic subunits in an opposite manner. Based on present data, we propose that the age‐related increases in the content of hippocampal immunoproteasome is mostly because of neuroinflammatory processes associated to aging.
Developing a Comprehensive Patent Related Information Retrieval Tool

In recent years, there has been a massive growth of regulatory and related information available online. This information is distributed across many different domains creating a problem for accessing and managing this data. This paper proposes a framework to access information across two such domains - patents and court cases. The framework is designed to boost the value of a set of patents based on information available in court cases by identifying and cross-referencing mutual information in the two domains. We test our framework by constructing a use case involving the hormone erythropoietin. A corpus of 1150 patents (including 135 closely related patents) and 30 court cases is gathered. Challenges associated with such integration and future plans are briefly discussed.
Mathematical Modeling for Functional Divergence after Gene Duplication

In this paper, I present a statistical framework for modeling the functional divergence after gene duplication. A rate-component model to describe the rate covariation among homologous genes of a gene family is implemented when a phylogenetic tree is known. The Markov chain model is rigorous but may require a huge amount of computational time when the number of sequences is large. On the other hand, the Poisson-based model is mathematically analytical so that computation is very fast even for a large dataset. Moreover, under the posterior framework, we have developed a site-specific profile for predicting important amino acid residues responsible for these functional differences between member genes of a gene family. Our study may have great potential for functional genomics because it is cost-effective, and these predictions can be further tested by biological experimentation.
Benchmarking Veterans Affairs Medical Centers in the Delivery of Preventive Health Services: Comparison of Methods

Objective. To identify consistent provision of clinical preventive services, we sought to benchmark all acute care Veterans Affairs Medical Centers (VAMCs) against each other nationally on the basis of multiple evidence-based, performance measures to identify facilities performing consistently higher and lower than expected. Methods. The 1998 Veterans Health Survey assessed the self-reported delivery of evidence-based clinical preventive services in a stratified national sample of 450 ambulatory care patients seen at each VAMC. Proportions appropriately receiving each service within the recommended time interval were calculated for 138 VAMCs. Percentile ranks for each outcome were assigned. Two approaches were used for benchmarking performance. First, a scaled score for each facility was calculated across the set of 12 measures. Second, facilities were ranked based on the sum of the percentile ranks over a range of specific high cutoffs (eg, 70–80%) and above a range of lower cutoffs (eg, 40–50%). Ranking was validated by comparing with deciles of ranks on chart audit (External Peer Review Program, EPRP) data using Kendall’s &tgr;-b and &khgr;2 quality-of-fit test. Differences between consistently high adherence (CHA) and low adherence (CLA) facilities were compared using the Wilcoxon rank sum test on 14 VHS and 11 EPRP outcomes. Results. Data from 39,939 patients (67% response rate) were examined. In combination, cutoffs of greater than 50th percentile and greater than 75th percentile rank yielded 12 of 14 VHS and 6 of 11 EPRP measures different between CHA and CLA facilities. The scaled-score approach resulted in 20 CHA and 14 CLA facilities. The sum of outcomes ranked above 50th percentile and over 75th percentile for CHA facilities (n = 17) was 15 or more. The sum of outcomes ranked above the same cutoffs for CLA facilities (n = 16) was 3 or less. EPRP and 1998 VHS data demonstrated that the survey measures and benchmarking approaches were both reliable and valid. Both approaches resulted in multiple differences between CHA and CLA facilities; differences were greater using the percentile rank approach. Conclusions. The VA has successfully encouraged adoption of evidence-based clinical preventive services throughout its health care system. However, facilities show wide variation in their levels of delivery and can be distinguished on the basis of their consistently high or low levels of adherence. Examining service delivery across multiple performance indicators allows identification of opportunities to improve clinical practice guideline implementation and the delivery of preventive services. This approach identifies model institutions where focused investigation of factors associated with consistent performance may be particularly fruitful.
Using a Lethality Index to Assess Susceptibility of Tribolium confusum and Oryzaephilus surinamensis to Insecticides

We evaluated knockdown caused by four insecticides: alpha-cypermethrin, chlorfenapyr, pirimiphos-methyl and fipronil against adults of Tribolium confusum Jacquelin Duval, the confused flour beetle and Oryzaephilus surinamensis (L.), the sawtoothed grain beetle. Bioassays were conducted on concrete and metal surfaces. Adults of the tested species were exposed on both surfaces treated with the above insecticides at two doses (low and high). Knockdown assessment was done after 15, 30 and 60 min of adult exposure in the treated surfaces. Also, after 1, 3, 5, 7 and 14 d of exposure, a lethality index was calculated with an equation resulting to values from 0 to 100, where 100 indicated complete mortality and 0 complete survival. We also developed a lethality index by ranking each adult on each surface from 0 to 4, 0: adults moved normally, 1: adults were knocked down, but were able to walk for short intervals, 2: adults were knocked down and unable to walk, but with visible movement of antennae etc., 3: adults were knocked down, with very minimal movement of the tarsi and the antennae and 4: adults were dead (no movement). Knockdown of adults immediately after exposure (15–60 min) was higher for pirimiphos-methyl followed by alpha-cypermethrin, for both dose rates tested and species, but only on the metal surface. The lethality index was nearly 100 for all insecticides after 5d of exposure for O. surinamensis, while for T. confusum the adult lethality index was considerably lower for alpha-cypermethrin, suggesting that that recovery from knockdown occurred. Chlorfenapyr was the only insecticide that was more effective on concrete than on metal, while the reverse was noted for the other three insecticides. These results show that knockdown has different levels, which can be used as indicators of insect mortality or recovery.
Transputers-past, present and future

The progress, products, and results of ongoing work in transputer development are discussed with particular reference to the ESPRIT Supernode project and other ESPRIT projects. The Supernode project, which lasted from Dec. 1985 to Nov. 1989, was aimed to create a low-cost, high-performance computer system from transputers and incorporated the development of the T800 floating-point transputer and the Supernode RTP (Reconfigurable Transputer Processor). The three-year GPMIMD (General-Purpose, Multiple-Instruction, MUltiple-Data) project aims to develop a standard European MIMD architecture based on H1 transputers and virtual communications. The OMI MAP (Open Microsystems Initiative Microprocessor Architecture Project) forms the core of the European-led Open Microsystems Initiative. It aims to define the architecture of a new microprocessor family designed to exploit the VLSI capabilities anticipated in the latter half of the 1990s. <<ETX>>
Association of Human Herpesvirus-6B with Mesial Temporal Lobe Epilepsy

Background Human herpesvirus-6 (HHV-6) is a β-herpesvirus with 90% seroprevalence that infects and establishes latency in the central nervous system. Two HHV-6 variants are known: HHV-6A and HHV-6B. Active infection or reactivation of HHV-6 in the brain is associated with neurological disorders, including epilepsy, encephalitis, and multiple sclerosis. In a preliminary study, we found HHV-6B DNA in resected brain tissue from patients with mesial temporal lobe epilepsy (MTLE) and have localized viral antigen to glial fibrillary acidic protein (GFAP)–positive glia in the same brain sections. We sought, first, to determine the extent of HHV-6 infection in brain material resected from MTLE and non-MTLE patients; and second, to establish in vitro primary astrocyte cultures from freshly resected brain material and determine expression of glutamate transporters. Methods and Findings HHV-6B infection in astrocytes and brain specimens was investigated in resected brain material from MTLE and non-MTLE patients using PCR and immunofluorescence. HHV-6B viral DNA was detected by TaqMan PCR in brain resections from 11 of 16 (69%) additional patients with MTLE and from zero of seven (0%) additional patients without MTLE. All brain regions that tested positive by HHV-6B variant-specific TaqMan PCR were positive for viral DNA by nested PCR. Primary astrocytes were isolated and cultured from seven epilepsy brain resections and astrocyte purity was defined by GFAP reactivity. HHV-6 gp116/54/64 antigen was detected in primary cultured GFAP-positive astrocytes from resected tissue that was HHV-6 DNA positive—the first demonstration of an ex vivo HHV-6–infected astrocyte culture isolated from HHV-6–positive brain material. Previous work has shown that MTLE is related to glutamate transporter dysfunction. We infected astrocyte cultures in vitro with HHV-6 and found a marked decrease in glutamate transporter EAAT-2 expression. Conclusions Overall, we have now detected HHV-6B in 15 of 24 patients with mesial temporal sclerosis/MTLE, in contrast to zero of 14 with other syndromes. Our results suggest a potential etiology and pathogenic mechanism for MTLE.
A New Coded Cooperation Algorithm

User cooperation provides transmit diversity even when mobile users cannot possess multiple antennas due to size constraints. Recently, a kind of user cooperation scheme called coded cooperation was proposed, in which standard channel coding methods were used to implement cooperation. This scheme achieves remarkable gains compared to non-cooperative system and other cooperation diversity scheme (such as amplify-and-forward and decoded-and-forward) while maintaining the same information rate and transmit power. In this paper, we propose a new coded cooperation algorithm. We compare the performance of our scheme with coded cooperation proposed by Hunter under a variety of conditions in slow fading, and a significant improvement is achieved.
Peak Vertical Ground Reaction Force during Two-Leg Landing: A Systematic Review and Mathematical Modeling

Objectives. (1) To systematically review peak vertical ground reaction force (PvGRF) during two-leg drop landing from specific drop height (DH), (2) to construct a mathematical model describing correlations between PvGRF and DH, and (3) to analyze the effects of some factors on the pooled PvGRF regardless of DH. Methods. A computerized bibliographical search was conducted to extract PvGRF data on a single foot when participants landed with both feet from various DHs. An innovative mathematical model was constructed to analyze effects of gender, landing type, shoes, ankle stabilizers, surface stiffness and sample frequency on PvGRF based on the pooled data. Results. Pooled PvGRF and DH data of 26 articles showed that the square root function fits their relationship well. An experimental validation was also done on the regression equation for the medicum frequency. The PvGRF was not significantly affected by surface stiffness, but was significantly higher in men than women, the platform than suspended landing, the barefoot than shod condition, and ankle stabilizer than control condition, and higher than lower frequencies. Conclusions. The PvGRF and root DH showed a linear relationship. The mathematical modeling method with systematic review is helpful to analyze the influence factors during landing movement without considering DH.
Transistor Level Test Generation for MOS Circuits

Due to inaccuracies in gate level models of VLSI digital circuits, current practice is to use transistor level simulators to analyze VLSI digital circuits. The inaccuracies of gate level models are even more severe when faults in digital circuits are considered. For this reason, recently several researchers have proposed the use of test pattern generation from digital circuits described at the transistor level. In this paper an efficient test pattern generation procedure for digital circuits described at the transistor level is given.