gebhart/patrepeval huggingface dataset:
Cyclophosphamide-Potentiated West Nile Viral Encephalitis: Relative Influence of Cellular and Humoral Factors (1974)

Intraperitoneal inoculation of 106 LD50 of West Nile virus produces an inapparent infection in the central nervous system of the mouse; the infection is converted into lethal encephalitis by a single dose of cyclophosphamide (150 mg/kg) given 24 hr after infection. Cyclophosphamide-potentiated infection is characterized by suppressed response of neutralizing antibody, prolonged viremia, enhanced titers of virus in the brain, and concomitant histologic encephalitis; death occurs eight to 16 days after infection. A single intraperitoneal injection of immune serum given as late as six days after infection reduces mortality to 15%. A comparable reduction in mortality follows the transfer of 108 syngeneic splenocytes from mice immune to West Nile virus. However, these cells are effective only when given within two days after infection. In this model neutralizing antibody appears to play a critical role in recovery from potentially fatal encephalitis, and immune lymphoid cells may act primarily through production of antibody.
4‐[18F]fluorophenyl ureas via carbamate‐4‐nitrophenyl esters and 4‐[18F]fluoroaniline (2006)

Abstract Four different no carrier added (n.c.a.) 4‐[ 18 F]fluorophenylurea derivatives are synthesized as model compounds via two alternative routes. In both cases carbamate‐4‐nitrophenylesters are used as intermediates. Either n.c.a. 4‐[ 18 F]fluoroaniline reacts with carbamates of several amines, or the carbamate of n.c.a. 4‐[ 18 F]fluoroaniline is formed at first and an amine is added subsequently to yield the urea derivative. The choice of the appropriate way of reaction depends on the possibilities of precursor synthesis. The radiochemical yields reach up to 80% after 50 min of synthesis time while no radiochemical by‐products can be determined. These high yields were possible due to an optimized preparation of n.c.a. 4‐[ 18 F]fluoroaniline with a radiochemical yield of up to 90%. From the various ways of its radiosynthesis, the substitution with n.c.a. [ 18 F]fluoride on dinitrobenzene is chosen, using phosphorous acid and palladium black for reduction of the second nitro group. Copyright © 2006 John Wiley &amp; Sons, Ltd.
Automatically Tuning Background Subtraction Parameters using Particle Swarm Optimization (2007)

A common trait of background subtraction algorithms is that they have learning rates, thresholds, and initial values that are hand-tuned for a scenario in order to produce the desired subtraction result; however, the need to tune these parameters makes it difficult to use state-of-the-art methods, fuse multiple methods, and choose an algorithm based on the current application as it requires the end-user to become proficient in tuning a new parameter set. The proposed solution is to automate this task by using a Particle Swarm Optimization (PSO) algorithm to maximize a fitness function compared to provided ground-truth images. The fitness function used is the F-measure, which is the harmonic mean of recall and precision. This method reduces the total pixel error of the Mixture of Gaussians background subtraction algorithm by more than 50% on the diverse Wallflower data-set.
A New Class of Small Molecule Inhibitor of BMP Signaling (2013)

Growth factor signaling pathways are tightly regulated by phosphorylation and include many important kinase targets of interest for drug discovery. Small molecule inhibitors of the bone morphogenetic protein (BMP) receptor kinase ALK2 (ACVR1) are needed urgently to treat the progressively debilitating musculoskeletal disease fibrodysplasia ossificans progressiva (FOP). Dorsomorphin analogues, first identified in zebrafish, remain the only BMP inhibitor chemotype reported to date. By screening an assay panel of 250 recombinant human kinases we identified a highly selective 2-aminopyridine-based inhibitor K02288 with in vitro activity against ALK2 at low nanomolar concentrations similar to the current lead compound LDN-193189. K02288 specifically inhibited the BMP-induced Smad pathway without affecting TGF-β signaling and induced dorsalization of zebrafish embryos. Comparison of the crystal structures of ALK2 with K02288 and LDN-193189 revealed additional contacts in the K02288 complex affording improved shape complementarity and identified the exposed phenol group for further optimization of pharmacokinetics. The discovery of a new chemical series provides an independent pharmacological tool to investigate BMP signaling and offers multiple opportunities for pre-clinical development.
Nonlinear estimation of PSK-modulated carrier phase with application to burst digital transmission (1983)

Burst transmission of digital data and voice has become commonplace, particularly in satellite communication systems employing time-division multiple-access (TI)MA) and packet demand-assignment multiple-access (DAMA) techniques. In TDMA systems particularly, phase estimation on each successive burst is a requirement, while bit timing and carrier frequency can be accurately tracked between bursts. A class of nonlinear estimation algorithms is described to estimate the unknown phase of a carrier which is fully modulated by <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</tex> -ary PSK modulation. Performance of the method is determined in closed form and compared to the Cramér-Rao lower bound for the variance of the estimation error in the phase of an unmodulated carrier. Results are also obtained when the carrier frequency is imprecisely known. Finally, the effect of quantization and finite read-only-memory (ROM) implementation of the nonlinearity are determined by computer simulation.
Expression of a Drosophila heat shock protein in mammalian cells: transient association with nucleoli after heat shock (1984)

We transformed mouse L cells with a cloned Drosophila hsp70 gene and obtained cells with either heat-inducible or constitutively expressed copies of the gene. The distribution of hsp70 in these cells was examined by indirect immunofluorescence with monoclonal antibodies specific to the Drosophila protein. In constitutive cells, hsp70 was present in both cytoplasm and nucleus. After heat shock, the nuclear hsp70 was transiently concentrated in nucleoli, from which it had previously been excluded; the cytoplasmic hsp70 moved to a perinuclear location, a result consistent with it being associated with intermediate filaments of the cytoskeleton. The nucleolar migration took several hours and was partly inhibited by actinomycin D, but was independent of protein synthesis; it may reflect binding to newly-synthesized rRNA. Drosophila hsp70 was also expressed from replicating plasmids in monkey COS cells, and was found to be concentrated in nuclei even at low temperature. Migration to nucleoli occurred after heat shock. These results indicate that a single protein can have multiple interactions with cellular components, and form the basis for future studies of these interactions by in vitro mutagenesis and expression of the hsp70 gene.
Invasion of Human Mucosal Epithelial Cells byNeisseria gonorrhoeaeUpregulates Expression of Intercellular Adhesion Molecule 1 (ICAM-1) (1999)

Infection of the mucosa by Neisseria gonorrhoeae involves adherence to and invasion of epithelial cells. Little is known, however, about the expression by mucosal epithelial cells of molecules that mediate cellular interactions between epithelial cells and neutrophils at the site of gonococcal infection. The aim of this study was to determine the expression of intercellular adhesion molecule 1 (ICAM-1) by epithelial cells during the process of gonococcal invasion. The highly invasive strain FA1090 and the poorly invasive strain MS11 were incubated with human endometrial adenocarcinoma (HEC-1-B) or human cervical carcinoma (ME-180) epithelial cells, after which ICAM-1 expression was measured by flow cytometry. After 15 h of infection with FA1090, expression of ICAM-1 increased 4.7- and 2.1-fold for HEC-1-B and ME-180 cells, respectively, whereas 15 h of infection of HEC-1-B cells with MS11 increased ICAM-1 expression only 1.6-fold. ICAM-1 expression was restricted to the cell surface, since no soluble ICAM-1 was detected. The distribution of staining was heterogeneous and mimicked that seen after treatment of HEC-1-B cells with the ICAM-1 agonist tumor necrosis factor alpha (TNF-alpha) in the absence of bacteria. PCR and dot blot analyses of ICAM-1 mRNA showed no change in levels over time in response to infection. Although TNF-alpha was produced by HEC-1-B cells after infection, the extent of ICAM-1 upregulation was not affected by neutralizing anti-TNF-alpha antiserum. Dual-fluorescence flow cytometry showed that the cells with the highest levels of ICAM-1 expression were cells with associated gonococci. We conclude that epithelial cells upregulate the expression of ICAM-1 in response to infection with invasive gonococci. On the mucosa, upregulation of ICAM-1 by infected epithelial cells may function to maintain neutrophils at the site of infection, thereby reducing further invasion of the mucosa by gonococci.
Depression and Anxiety as Predictors of 2-Year Cardiac Events in Patients With Stable Coronary Artery Disease (2008)

Anxiety and depression predict greater MACE risk in patients with stable CAD, supporting future research into common genetic, environmental, and pathophysiologic pathways and treatments.
Cementing High-Angle Wells Using Cement-Expanded Formation Packers and/or Casing Rotation (1987)

ABSTRACT This paper describes an ongoing program to improve primary cementing results for casing in high angle or deviated wells. Thums Long Beach Company, acting as Contractor for the City of Long Beach, Operator of the Long Beach Unit, has drilled and completed over 1100 wells from four man-made islands and four land filled pier locations. The average well exceeds 55° hole angle with some wells exceeding 80° from vertical. Two techniques have been recently utilized to provide a competent shut-off between the completion interval and the surface. The first technique employs the installation of a twenty foot (20′) Cement Expanded Formation Packer usually set in a competent shale immediately above the completion interval. The CEFP is expanded with cement at the completion of the primary cement job. This method employing specifically approved equipment has proven so successful that the State of California will accept a successful installation as a substitute for the normally required water shut-off test. The second technique involves the rotation of a selected length of casing at the bottom of the casing string. A specially designed casing swivel is integral to the casing string and is rotated by a spline drive installed on drill pipe. The casing segment is rotated during a conditioning period and while the cement is being placed. Up to 600′ of centralized casing has been rotated with excellent results in high angle wells.
Information about movement direction obtained from synchronous activity of motor cortical neurons (1998)

Although neuronal synchronization has been shown to exist in primary motor cortex (MI), very little is known about its possible contribution to coding of movement. By using cross-correlation techniques from multi-neuron recordings in MI, we observed that activity of neurons commonly synchronized around the time of movement initiation. For some cell pairs, synchrony varied with direction in a manner not readily predicted by the firing of either neuron. Information theoretic analysis demonstrated quantitatively that synchrony provides information about movement direction beyond that expected by simple rate changes. Thus, MI neurons are not simply independent encoders of movement parameters but rather engage in mutual interactions that could potentially provide an additional coding dimension in cortex.
Macrophage and smooth muscle cell proliferation in atherosclerotic lesions of WHHL and comparably hypercholesterolemic fat-fed rabbits. (1990)

Lesions of atherosclerosis were analyzed at varying stages of development in Watanabe heritable hyperlipidemic (WHHL) and comparably hypercholesterolemic fat-fed (FF) rabbits for the capacity to incorporate thymidine into proliferating cells within both the intima and the underlying media. An identical inverse relationship between the intimal/medial ratio (which reflects both lesion size and severity) and the labeling index was observed for both the WHHL and FF rabbits. Analysis of the spatial distribution of the labeled cells within each lesion revealed the highest rates of thymidine incorporation in cells situated within the superficial areas and lateral margins of the lesions. Up to 12% of the labeled cells were foam cells, which were predominantly located immediately beneath the endothelium and within the lateral margins. Some labeled macrophages were also observed within the necrotic core of advanced lesions. There were no differences in the labeling indexes at differing sites in the aorta, providing lesions of comparable size were compared. Simultaneous thymidine autoradiography and immunostaining with cell type-specific monoclonal antibodies revealed that approximately 30% of the labeled cells were macrophages and 45% were smooth muscle cells in advanced lesions from both WHHL and FF rabbits.
MEK Kinase 3 Directly Activates MKK6 and MKK7, Specific Activators of the p38 and c-Jun NH2-terminal Kinases (1999)

Mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase kinase kinase 3 (MEKK3) activates the c-Jun NH2-terminal kinase (JNK) pathway, although no substrates for MEKK3 have been identified. We have examined the regulation by MEKK3 of MAPK kinase 7 (MKK7) and MKK6, two novel MAPK kinases specific for JNK and p38, respectively. Coexpression of MKK7 with MEKK3 in COS-7 cells enhanced MKK7 autophosphorylation and its ability to activate recombinant JNK1 in vitro. MKK6 autophosphorylation and in vitro activation of p38alpha were also observed following coexpression of MKK6 with MEKK3. MEKK2, a closely related homologue of MEKK3, also activated MKK7 and MKK6 in COS-7 cells. Importantly, immunoprecipitates of either MEKK3 or MEKK2 directly activated recombinant MKK7 and MKK6 in vitro. These data identify MEKK3 as a MAPK kinase kinase specific for MKK7 and MKK6 in the JNK and p38 pathways. We have also examined whether MEKK3 or MEKK2 activates p38 in intact cells using MAPK-activated protein kinase-2 (MAPKAPK2) as an affinity ligand and substrate. Anisomycin, sorbitol, or the expression of MEKK3 in HEK293 cells enhanced MAPKAPK2 phosphorylation, whereas MEKK2 was less effective. Furthermore, MAPKAPK2 phosphorylation induced by MEKK3 or cellular stress was abolished by the p38 inhibitor SB-203580, suggesting that MEKK3 is coupled to p38 activation in intact cells.
OS3: Photoemission from gold thin films for application in multiphotocathode arrays for electron beam lithography (1998)

Photoemission is a promising approach to electron sources for electron beam lithography because of the ease with which various shapes or arrays of independently modulated sources can be fabricated. However, most high-quantum-efficiency photoemitters are extremely sensitive to even partial monolayers of contamination, and therefore require some combination of differential pumping systems and photoemitter surface protection after activation. Here we propose to use a high-power 257 nm laser in combination with the relatively high work function and low quantum efficiency of gold films to produce practical multicathode electron sources for electron beam lithography. Gold films have the offsetting advantages that their photoemission characteristics are relatively reproducible and stable even in contaminating environments. It is possible, therefore, to prepare and handle them in air as well as operate them in less demanding vacuum environments. It is shown that a back-illuminated 15 nm gold film on a quartz or sapphire substrate exhibits a quantum efficiency of approximately 10−4 at 257 nm, producing photocurrents greater than 1 μA at a laser power of under 200 mW. The quantum efficiency is very reproducible and relatively stable under a variety of environmental and operational conditions. Slow changes, by as much as a factor of 3, over time periods of several weeks following sample preparation have been observed, consistent with variations of the gold work function of approximately 0.2 eV. The results are in good agreement with a straightforward extension of existing photoemission models for bulk material.
Transition Metal Catalyzed Asymmetric Oxidation of Sulfides (2008)

In the past two decades, chiral sulfoxides have been finding increasing use, reflecting growing interest both in convenient auxiliaries in asymmetric synthesis and products with biological properties containing a chiral sulfinyl group. In 1984, groups of Kagan and Modena discovered that titanium(IV) isopropoxide - diethyltartrate based systems (also known as “modified Katsuki-Sharpless reagents”) are capable of asymmetric oxidizing of prochiral sulfides by alkylhydroperoxides. Later, catalytic versions of the titanium tartrate systems were developed (with up to 90 % yield and 90 % ee for certain sulfides) that remain the most applied systems for asymmetric sulfoxidations. However, the low turnover numbers (5-20), complexity and expensiveness of such systems stimulated the search for other transition metal based catalytic systems. This review will cover the progress in transition metal catalyzed asymmetric sulfides oxidations achieved since the discoveries of early 1980s to the present days.
Multielectrode analysis of coordinated, multisite, rhythmic bursting in cultured CNS monolayer networks (1986)

Laser-deinsulated, printed-circuit electrodes integrated into the floor of culture chambers have been used to monitor the spontaneous activity of mouse spinal monolayer cell cultures. This technique has allowed a multisite analysis of activity over long periods of time in closed chambers. In 63 cultures investigated 3-5 weeks after seeding, 89% included single- or multiunit bursting. Based on a subset of 40 cultures in which all electrodes were sequentially scanned, bursting was found on 41% of the active electrodes (approximately 38% of all units monitored). A total of 35% of the electrodes monitoring spontaneous bursting activity revealed rhythmic sequences that were usually coupled among multiple electrodes. Although most of this coupling was in-phase, three out of 40 cultures exhibited antiphasic bursting. In all cases where coupling was observed, each electrode monitored different burst compositions, demonstrating that the activity was generated by different units. Some rhythmic patterns persisted for over 12 hr and were observed in 400 mm2 monolayer cultures, as well as in much smaller 3 mm2 adhesion islands. The addition of 10 mM MgCl2 consistently blocked both random and patterned (i.e., bursting) spontaneous activity at all recording sites. Strychnine (10(-6) M) typically increased firing frequencies and either disrupted pretest bursting or generated rhythmic activity from random phasic patterns. In certain cases, strychnine also blocked activity on specific electrodes, indicating that glycine is not the only inhibitory transmitter involved. The spontaneous appearance of rhythmic activity in low-density, monolayer cell cultures established from dissociated and randomly seeded spinal tissue can be explained by one or a combination of two hypotheses: an inherent specificity of some interconnections in developing mammalian cultures and the generation of organized activity by random circuits at certain stages of complexity.
Epidemiology of sports-related concussion in seven US high school and collegiate sports (2015)

Sports-related concussions present with a diverse range of symptoms and are associated with previous concussion history.
Interactive wrapper generation with minimal user effort (2006)

While much of the data on the web is unstructured in nature, there is also a significant amount of embedded structured data, such as product information on e-commerce sites or stock data on financial sites. A large amount of research has focused on the problem of generating wrappers, i.e., software tools that allow easy and robust extraction of structured data from text and HTML sources. In many applications, such as comparison shopping, data has to be extracted from many different sources, making manual coding of a wrapper for each source impractical. On the other hand, fully automatic approaches are often not reliable enough, resulting in low quality of the extracted data.We describe a complete system for semi-automatic wrapper generation that can be trained on different data sources in a simple interactive manner. Our goal is to minimize the amount of user effort for training reliable wrappers through design of a suitable training interface that is implemented based on a powerful underlying extraction language and a set of training and ranking algorithms. Our experiments show that our system achieves reliable extraction with a very small amount of user effort.
A Hybrid CFHR3-1 Gene Causes Familial C3 Glomerulopathy (2012)

Controlled activation of the complement system, a key component of innate immunity, enables destruction of pathogens with minimal damage to host tissue. Complement factor H (CFH), which inhibits complement activation, and five CFH-related proteins (CFHR1-5) compose a family of structurally related molecules. Combined deletion of CFHR3 and CFHR1 is common and confers a protective effect in IgA nephropathy. Here, we report an autosomal dominant complement-mediated GN associated with abnormal increases in copy number across the CFHR3 and CFHR1 loci. In addition to normal copies of these genes, affected individuals carry a unique hybrid CFHR3-1 gene. In addition to identifying an association between these genetic observations and complement-mediated kidney disease, these results provide insight into the protective role of the combined deletion of CFHR3 and CFHR1 in IgA nephropathy.
Silicon Odometer: An On-Chip Reliability Monitor for Measuring Frequency Degradation of Digital Circuits (2007)

A fully-digital reliability monitor is presented for high resolution frequency degradation measurements of digital circuits. The proposed scheme measures the beat frequency of two ring oscillators, one which is stressed and the other which is unstressed, to achieve 50X higher delay sensing resolution compared to prior techniques. A reliability monitor test chip has been fabricated in a 1.2 V, 130 nm CMOS technology.
Using H.264 coded block patterns for fast inter-mode selection (2008)

The support of variable block-sizes, though significantly improves the compression efficiency, imposes a big computational challenge on an H.264 encoder. In this paper, we present a new fast inter-mode decision algorithm based on the coded block pattern (CBP). Specifying which blocks within a macroblock are uncoded, CBP is a good indicator of block-matching accuracy and can be used to reduce the rate-distortion calculation required for mode selection. Experimental results show that the proposed method achieves more than 50% reduction in computation time relative to the exhaustive mode search with negligible degradation in visual quality. Other merits of the proposed method include (1) no extra computation is needed for obtaining CBP; (2) no ad-hoc threshold is involved in the algorithm; (3) in contrast to the previous early-skip algorithm that yields very limited improvement for high-activity videos, the proposed method is highly reliable for various video characteristics.