gebhart/patrepeval huggingface dataset:
Cotransplanted hepatic stellate cells enhance vascularization of islet allografts (2007)

Islet transplantation is an alternative to whole pancreas transplantation in curative therapy of diabetics. The outcome of engraftment of islet, however, remains disappointing. Rapid and adequate islet revascularization is crucial for the survival and function of transplanted islets. In this study, hepatic stellate cells (HSC) were cotransplanted with islet allografts, achieving marked prolongation of islet allografts. This was associated with enhanced revascularization within islet grafts as determined by anti-CD31 antibody staining.
Computational Advantages of Relevance Reasoning in Bayesian Belief Networks (2013)

This paper introduces a computational framework for reasoning in Bayesian belief networks that derives significant advantages from focused inference and relevance reasoning. This framework is based on d -separation and other simple and computationally efficient techniques for pruning irrelevant parts of a network. Our main contribution is a technique that we call relevance-based decomposition. Relevance-based decomposition approaches belief updating in large networks by focusing on their parts and decomposing them into partially overlapping subnetworks. This makes reasoning in some intractable networks possible and, in addition, often results in significant speedup, as the total time taken to update all subnetworks is in practice often considerably less than the time taken to update the network as a whole. We report results of empirical tests that demonstrate practical significance of our approach.
Bidirectional Image Thresholding Algorithm Using Combined Edge Detection And P-tile Algorithms (2011)

The main disadvantage of traditional global thresholding techniques is that they do not have an ability to exploit information of the characteristics of target images that they threshold. In this paper, we propose a new approach based on combination of modified p-tile and edge detection algorithms to have more accurate object segmentation. Using our proposed method, it is shown that almost all of our experiments resulted to better object segmentation than using traditional methods.
Biosynthesis of proline in <i>Pseudomonas aeruginosa</i>. Properties of ;-glutamyl phosphate reductase and 1-pyrroline-5-carboxylate reductase (1979)

gamma-Glutamyl phosphate reductase, the second enzyme of proline biosynthesis, catalyses the formation of l-glutamic acid 5-semialdehyde from gamma-glutamyl phosphate with NAD(P)H as cofactor. It was purified 150-fold from crude extracts of Pseudomonas aeruginosa PAO 1 by DEAE-cellulose chromatography and hydroxyapatite adsorption chromatography. The partially purified preparation, when assayed in the reverse of the biosynthetic direction, utilized l-1-pyrroline-5-carboxylic acid as substrate and reduced NAD(P)(+). The apparent K(m) values were: NAD(+), 0.36mm; NADP(+), 0.31mm; l-1-pyrroline-5-carboxylic acid, 4mm with NADP(+) and 8mm with NAD(+); P(i), 28mm. 3-(Phosphonoacetylamido)-l-alanine, a structural analogue of gamma-glutamyl phosphate, inhibited this enzyme competitively (K(i)=7mm). 1-Pyrroline-5-carboxylate reductase (EC 1.5.1.2), the third enzyme of proline biosynthesis, was purified 56-fold by (NH(4))(2)SO(4) fractionation, Sephadex G-150 gel filtration and DEAE-cellulose chromatography. It reduced l-1-pyrroline-5-carboxylate with NAD(P)H as a cofactor to l-proline. NADH (K(m)=0.05mm) was a better substrate than NADPH (K(m)=0.02mm). The apparent K(m) values for l-1-pyrroline-5-carboxylate were 0.12mm with NADPH and 0.09mm with NADH. The 3-acetylpyridine analogue of NAD(+) at 2mm caused 95% inhibition of the enzyme, which was also inhibited by thio-NAD(P)(+), heavy-metal ions and thiol-blocking reagents. In cells of strain PAO 1 grown on a proline-medium the activity of gamma-glutamyl kinase and gamma-glutamyl phosphate reductase was about 40% lower than in cells grown on a glutamate medium. No repressive effect of proline on 1-pyrroline-5-carboxylate reductase was observed.
Inhibition of Rabbit Brain Prolyl Endopeptidase by <i>N</i>‐Benzyloxycarbonyl‐Prolyl‐Prolinal, a Transition State Aldehyde Inhibitor (1983)

Prolyl endopeptidase cleaves peptide bonds on the carboxyl side of proline residues within a peptide chain. The enzyme readily degrades a number of neuropeptides including substance P, neurotensin, thyrotropin-releasing hormone, and luteinizing hormone-releasing hormone. The finding that the enzyme is inhibited by benzyloxycarbonyl-prolyl-proline, with a Ki of 50 microM, prompted the synthesis of benzyloxycarbonyl-prolyl-prolinal as a potential transition state analog inhibitor. Rabbit brain prolyl endopeptidase was purified to homogeneity for these studies. The aldehyde was found to be a remarkably potent inhibitor of prolyl endopeptidase with a Ki of 14 nM. This Ki is more than 3000 times lower than that of the corresponding acid or alcohol. By analogy with other transition state inhibitors, it can be assumed that binding of the prolinal residue to the S1 subsite and the formation of a hemiacetal with the active serine of the enzyme greatly contribute to the potency of inhibition. The specificity of the inhibitor is indicated by the finding that a variety of proteases were not affected at concentrations 150 times greater than the Ki for prolyl endopeptidase. The data indicate that benzyloxycarbonyl-prolyl-prolinal is a specific and potent inhibitor of prolyl endopeptidase and that consequently it should be of value in in vivo studies on the physiological role of the enzyme.
Capacitance Extraction (2005)

Abstract With the advances in integrated circuit (IC) technology, the effects of electromagnetic coupling among the metal interconnect lines have greatly influenced circuit performance in both VLSI circuits and microwave ICs. Therefore, the modeling and accurate extraction of interconnect capacitance has become a subject of advanced research in these fields. In this article, the fundamental theory, contemporary methodology, and algorithms of capacitance extraction are presented. First, the electrostatic basis of the capacitor is introduced and the capacitance for a multiconductor system is defined. Then, the practical methodologies of capacitance extraction for VLSI interconnects are presented, ranging from 1D, 2D, 2.5D to 3D methods and including the technique used for the task of current full‐chip extraction. Various numerical techniques of 3D capacitance extraction are discussed, some of which represent the frontier of this research field. For 3D capacitance extraction, the state of the art in fast boundary‐element methods and semianalytical approaches are surveyed, with a fairly complete list of references. Finally, some future tends on capacitance extraction are discussed.
Type I Adenylyl Cyclase Mutant Mice Have Impaired Mossy Fiber Long-Term Potentiation (1998)

Long-term potentiation (LTP) at the mossy fiber-->CA3 pyramidal cell synapse in the hippocampus is an NMDA-independent form of LTP that requires cAMP-dependent protein kinase (PKA) activity and can be induced by forskolin, a general activator of adenylyl cyclases. Presynaptic Ca2+ influx and elevated cAMP may be obligatory for mossy fiber LTP. Because the Ca2+-stimulated type 1 adenylyl cyclase (AC1) is expressed in the dentate gyrus and CA3 pyramidal cells, it is hypothesized that AC1 may be critical for mossy fiber LTP. To test this hypothesis, we examined several forms of hippocampal LTP in wild-type and AC1 mutant mice. Wild-type and AC1 mutant mice exhibited comparable perforant path LTP recorded in the dentate gyrus as well as decremental LTP at the Schaffer collateral-->CA1 pyramidal cell synapse. Although the mutant mice exhibited normal paired pulse facilitation, mossy fiber LTP was impaired significantly in AC1 mutants. High concentrations of forskolin induced mossy fiber LTP to comparable levels in wild-type and AC1 mutant mice, indicating that signaling components downstream from the adenylyl cyclase, including PKA, ion channels, and secretory machinery, were not affected by disruption of the AC1 gene. These data indicate that coupling of Ca2+ to activation of AC1 is crucial for mossy fiber LTP, most likely via activation of PKA and enhancement of excitatory amino acid secretion.
Etching behavior of an epoxy film in O2/CF4 plasmas (1991)

Epoxy polymers are commonly used in microelectronic packaging for printed circuit board fabrication. Exposure to plasma environments occurs during processing for purposes such as drill smear removal, surface modification, and decapsulation. In this investigation, epoxy films made from a brominated diglycidyl ether of bisphenol-A, containing aliphatic and aromatic segments, were etched in a radio-frequency plasma using a planar diode configuration. Etching rates were measured at various compositions of O2 and CF4 in the gas feed. Surface composition of etched and nonetched films were compared using x-ray photoelectron spectroscopy. Comparison of etching behavior and fluorine surface coverage is made with polymers, which are either aliphatic or aromatic. Maxima in etching rates for polyimide, epoxy, and polyethylene films occurred at 22.5%, 35%, and 37.5% CF4 in O2, respectively. Fluorine atom surface coverage was 10%, 20%, and 2%, respectively, under these conditions. It is proposed that the low affinity for fluorine atoms of the aliphatic moieties in the epoxy drives the O2/CF4 gas feed mixture, which yields maximum etching rates toward higher CF4 concentrations, similar to observations made for fully saturated polymers like polyethylene. As a consequence, the aromatic epoxy segments become more heavily fluorinated as occurs for highly aromatic polymers, like polyimide, in fluorine-rich plasmas.
A compositional approach toward dynamic phrasal thesaurus (2007)

To enhance the technology for computing semantic equivalence, we introduce the notion of phrasal thesaurus which is a natural extension of conventional word-based the saurus. Among a variety of phrases that conveys the same meaning, i.e., paraphrases, we focus on syntactic variants that are compositionally explainable using a small number of atomic knowledge, and develop a system which dynamically generates such variants. This paper describes the proposed system and three sorts of knowledge developed for dynamic phrasal thesaurus in Japanese: (i) transformation pattern, (ii) generation function, and (iii) lexical function.
Latent Herpes Simplex Virus Infection of Sensory Neurons Alters Neuronal Gene Expression (2003)

The persistence of herpes simplex virus (HSV) and the diseases that it causes in the human population can be attributed to the maintenance of a latent infection within neurons in sensory ganglia. Little is known about the effects of latent infection on the host neuron. We have addressed the question of whether latent HSV infection affects neuronal gene expression by using microarray transcript profiling of host gene expression in ganglia from latently infected versus mock-infected mouse trigeminal ganglia. (33)P-labeled cDNA probes from pooled ganglia harvested at 30 days postinfection or post-mock infection were hybridized to nylon arrays printed with 2,556 mouse genes. Signal intensities were acquired by phosphorimager. Mean intensities (n = 4 replicates in each of three independent experiments) of signals from mock-infected versus latently infected ganglia were compared by using a variant of Student's t test. We identified significant changes in the expression of mouse neuronal genes, including several with roles in gene expression, such as the Clk2 gene, and neurotransmission, such as genes encoding potassium voltage-gated channels and a muscarinic acetylcholine receptor. We confirmed the neuronal localization of some of these transcripts by using in situ hybridization. To validate the microarray results, we performed real-time reverse transcriptase PCR analyses for a selection of the genes. These studies demonstrate that latent HSV infection can alter neuronal gene expression and might provide a new mechanism for how persistent viral infection can cause chronic disease.
Pathophysiology of the Lyme Disease Spirochete, Borrelia burgdorferi, in Ixodid Ticks (1989)

The pathophysiology of Borrelia burgdorferi, the Lyme disease spirochete, is unique in tick/vector relationships, differing substantially from that of other spirochetes, e.g., Borrelia duttonii, the agent of tick-borne relapsing fever, and Borrelia recurrentis, the agent of louse-borne relapsing fever, in their respective vectors. Following ingestion by a tick, B. burgdorferi lodges in the midgut diverticula, in some instances penetrating the gut wall and invading various tissues. Certain investigators suggest that transmission of the spirochete occurs via infectious saliva, although, in light of the fact that only 5% of adult ticks are systemically infected, this mechanism is open to question. Alternatively, transmission may occur via periodic regurgitation of gut fluids during the feeding process. While ticks of the genus Ixodes were once thought to be the only vectors, it now appears that other genera, and possibly other hematophagous arthropods, may also be involved.
Intelligent Reflecting Surfaces: Physics, Propagation, and Pathloss Modeling (2019)

Intelligent reflecting surfaces can improve the communication between a source and a destination. The surface contains metamaterial that is configured to “reflect” the incident wave from the source towards the destination. Two incompatible pathloss models have been used in prior work. In this letter, we derive the far-field pathloss using physical optics techniques and explain why the surface consists of many elements that individually act as diffuse scatterers but can jointly beamform the signal in a desired direction with a certain beamwidth. We disprove one of the previously conjectured pathloss models.
A Strategy for Identifying Differences in Large Series of Metabolomic Samples Analyzed by GC/MS (2004)

In metabolomics, the purpose is to identify and quantify all the metabolites in a biological system. Combined gas chromatography and mass spectrometry (GC/MS) is one of the most commonly used techniques in metabolomics together with 1H NMR, and it has been shown that more than 300 compounds can be distinguished with GC/MS after deconvolution of overlapping peaks. To avoid having to deconvolute all analyzed samples prior to multivariate analysis of the data, we have developed a strategy for rapid comparison of nonprocessed MS data files. The method includes baseline correction, alignment, time window determinations, alternating regression, PLS-DA, and identification of retention time windows in the chromatograms that explain the differences between the samples. Use of alternating regression also gives interpretable loadings, which retain the information provided by m/z values that vary between the samples in each retention time window. The method has been applied to plant extracts derived from leaves of different developmental stages and plants subjected to small changes in day length. The data show that the new method can detect differences between the samples and that it gives results comparable to those obtained when deconvolution is applied prior to the multivariate analysis. We suggest that this method can be used for rapid comparison of large sets of GC/MS data, thereby applying time-consuming deconvolution only to parts of the chromatograms that contribute to explain the differences between the samples.
Systeme d'imagerie hybride par codage de pupille (2011)

New imaging techniques allow better and smaller systems. Among these new techniques, hybrid imaging systems with wavefront coding includes an optical system with a phase mask and a processing step. The phase function of the mask makes the system insensitive to a fault of the optical system, such as an aberration or a defocus. The price of this advantage is a deformation of the image acquired by a sensor, which is then processed. The study of the properties of these hybrid imaging systems has been completed by increasing the depth of field of an imaging system, which allows to relax some design constraints such as field curvature, thermal defocus, chromaticism… In these imaging techniques, the consideration the noise of the sensor is one the critical parameters when choosing the image processing method.The work performed during this thesis allowed to proposed an original approach for the cross-conception of the phase function of the mask and the processing step. This approach is based on a signal-to-noise criterion. Unlike known approaches, this criterion shows that a strict insensitivity of the modulation transfer function of the optics is not required. The parameters of the phase functions optimized thanks to this criterion are noticeably different from those usually proposed and lead to a significant increase of the image quality.This cross-conception approach has been validated experimentally on an uncooled thermal camera. A binary phase mask associated with a real-time processing implemented on a GPU allowed to increase the depth of field of this camera by a factor 3. Considering the important level of noise introduced by the use of a bolometric sensor, the good quality of the processed image shows the interest of the cross-conception for hybrid imaging system with wavefront coding.
4.5 GHz Lithium Niobate MEMS Filters With 10% Fractional Bandwidth for 5G Front-Ends (2019)

This paper presents a new class of micro-electro-mechanical system (MEMS) C-band filters for 5G front-ends. The filter is comprised of resonators based on the first-order asymmetric Lamb wave (A1) mode in thin-film lithium niobate. Two filters have been demonstrated at 4.5 GHz with sharp roll-off, flat in-band group delay, and spurious-free response over a wide frequency range. The first design shows a 3-dB fractional bandwidth (FBW) of 10%, an insertion loss (IL) of 1.7 dB, an out-of-band (OoB) rejection of -13 dB, and a compact footprint of 0.36 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , while the second design shows a 3-dB FBW of 8.5%, an IL of 2.7 dB, an OoB rejection of -25 dB, and a footprint of 0.9 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The demonstrations herein mark the largest FBW achieved for acoustic-only filters at 5G frequencies.
Delta variant (B.1.617.2) sublineages do not show increased neutralization resistance (2021)

Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)\n https://doi.org/10.13039/501100002347
Static verification of dynamically detected program invariants (2001)

This paper shows how to integrate two complementary techniques for manipulating program invariants: dynamic detection and static verification. Dynamic detection proposes likely invariants based on program executions, but the resulting properties are not guaranteed to be true over all possible executions. Static verification checks that properties are always true, but it can be difficult and tedious to select a goal and to annotate programs for input to a static checker. Combining these techniques overcomes the weaknesses of each: dynamically detected invariants can annotate a program or provide goals for static verification, and static verification can confirm properties proposed by a dynamic tool. We have integrated a tool for dynamically detecting likely program invariants, Daikon, with a tool for statically verifying program properties, ESC/Java. Daikon examines run-time values of program variables; it looks for patterns and relationships in those values, and it reports properties that are never falsified during test runs and that satisfy certain other conditions, such as being statistically justified. ESC/Java takes as input a Java program annotated with preconditions, postconditions, and other assertions, and it reports which annotations cannot be statically verified and also warns of potential runtime errors, such as null dereferences and out-of-bounds array indices. Our prototype system runs Daikon, inserts its output into code as ESC/Java annotations, and then runs ESC/Java, which reports unverifiable annotations. The entire process is completely automatic, though users may provide guidance in order to improve results if desired. In preliminary experiments, ESC/Java verified all or most of the invariants proposed by Daikon.
The first-order theory of subtyping constraints (2002)

We investigate the first-order of subtyping constraints. We show that the first-order theory of non-structural subtyping is undecidable, and we show that in the case where all constructors are either unary or nullary, the first-order theory is decidable for both structural and non-structural subtyping. The decidability results are shown by reduction to a decision problem on tree automata. This work is a step towards resolving long-standing open problems of the decidability of entailment for non-structural subtyping.
Towards self-healing smartphone software via automated patching (2014)

Frequent app bugs and low tolerance for loss of functionality create an impetus for self-healing smartphone software. We take a step towards this via on-the-fly error detection and automated patching. Specifically, we add failure detection and recovery to Android by detecting crashes and ``sealing off'' the crashing part of the app to avoid future crashes. In the detection stage, our system dynamically analyzes app execution to detect certain exceptional situations. In the recovery stage, we use bytecode rewriting to alter app behavior as to avoid such situations in the future. When using our implementation, apps can resume operation (albeit with limited functionality) instead of repeatedly crashing. Our approach does not require access to app source code or any system (e.g., kernel-level) modification. Experiments on several real-world, popular Android apps and bugs show that our approach manages to recover the apps from crashes effectively, timely, and without introducing overhead.
PETS2010: Dataset and Challenge (2010)

This paper describes the crowd image analysis challenge that forms part of the PETS 2010 workshop. The aim of this challenge is to use new or existing systems for i) crowd count and density estimation, ii) tracking of individual(s) within a crowd, and iii) detection of separate flows and specific crowd events, in a real-world environment. The dataset scenarios were filmed from multiple cameras and involve multiple actors.
World wide web robots: an overview (1999)

This paper traces the development of World Wide Web Robots and provides an overview of their main functions and workings. The focus is on search robots and illustrations will be drawn from two major search engines: AltaVista and Excite. In the concluding section, prblems associated with the use of Web Robots and their implications for electronic publishing will be examined.
Rectangular Symmetry Morphologies in a Topographically Templated Block Copolymer (2012)

Using an array of majority-block-functionalized posts makes it possible to locally control the self-assembly of a block copolymer and achieve several morphologies on a single substrate. A template consisting of a square symmetry array of posts produces a square-symmetry lattice of microdomains, which doubles the areal density of features.
Emotion Learning and Memory in Schizophrenia (2017)

• Prior research indicates that processing of emotional information is particularly problematic for individuals with schizophrenia. • An important component of emotional processing is the accurate encoding and recall of emotionally valenced information. • The current study addresses this matter by investigating performance on a task assessing learning, recall, and recognition in patients with schizophrenia. • In this manner, recall of emotionally valenced information may be investigated