gebhart/patrepeval huggingface dataset:
A 36-kilodalton Brucella abortus cell envelope protein is encoded by repeated sequences closely linked in the genomic DNA (1988)

Recombinant bacteriophage expressing Brucella abortus antigens have been isolated from a lambda gt11 expression library by using antibody raised against a sodium dodecyl sulfate-polyacrylamide gel electrophoresis-purified cell envelope protein of 36 kilodaltons. Fusion products expressed by these recombinants vary in apparent molecular mass by sodium dodecyl sulfate-polyacrylamide gel electrophoresis but only slightly exceed the size of beta-galactosidase. Western blot (immunoblot) analysis of crude lysates derived from lambda gt11 lysogens indicates that the fusion products react specifically with the original antisera used for recombinant selection and selectively bind antibody directed against the 36-kilodalton cell envelope protein. Analysis of the DNA inserts from 11 independently selected recombinants reveals similar-size EcoRI fragments which range in size from 150 to 300 base pairs (bp), all of which cross-hybridize via Southern blot analysis. Three independently selected EcoRI inserts ranging in size from 200 to 270 bp have been subcloned into M13mp18 and sequenced; all three contain a common region of about 200 bp. Southern blot analysis of B. abortus genomic DNAs digested with EcoRI, PstI, or DdeI indicates the presence of two fragments which hybridize to these DNA probes while single BamHI and HindIII fragments hybridize. The absence of these sites from the internal DNA sequence of the cloned probes suggests the presence of more than one copy of these sequences within the B. abortus genome. The same DNA probes have been used to select genomic clones of approximately 20 kbp from a lambda 2001 library. The lambda 2001 recombinants contain single BamHI fragments and two PstI fragments which hybridize to these oligonucleotide probe constructed on the basis of the amino-terminal sequence of the mature gene product hybridizes to the same BamHI and PstI fragments as the lambda gt11-derived DNA probe. Although the relative positions of the oligonucleotide sequences and the lambda gt11 insert within the genes is not known, the two sequences flank a region which corresponds to at least 40% of the size of the predicted gene. Additional experimentation must be performed to determine whether these sequences represent either two complete structural genes encoding major cell envelope proteins or repetitive sequences within a single structural gene.
Choline and Cholinergic Neurons (1983)

Mammalian neurons can synthesize choline by methylating phosphatidylethanolamine and hydrolyzing the resulting phosphatidylcholine. This process is stimulated by catecholamines. The phosphatidylethanolamine is synthesized in part from phosphatidylserine; hence the amino acids methionine (acting after conversion to S-adenosylmethionine) and serine can be the ultimate precursors of choline. Brain choline concentrations are generally higher than plasma concentrations, but depend on plasma concentrations because of the kinetic characteristics of the blood-brain-barrier transport system. When cholinergic neurons are activated, acetylcholine release can be enhanced by treatments that increase plasma choline (for example, consumption of certain foods).
Serum C-reactive Protein and Chlamydia trachomatis Antibodies in Preterm Delivery (2005)

II-2.
Noninvasive in vivo magnetic resonance imaging of injury‐induced neointima formation in the carotid artery of the apolipoprotein‐E null mouse (2000)

Mice deficient in apolipoprotein-E (apoE) experience severe hypercholesterolemia, are prone to atherosclerosis, and recently have emerged as a powerful tool in the study of plaque formation. In this study, we developed magnetic resonance (MR) imaging methods to detect the progression of atherosclerosis noninvasively in a mouse model of arterial injury. Four 14-week-old apoE-deficient mice were imaged 5 weeks after beginning an atherogenic Western diet and 4 weeks after wire denudation injury of the left common carotid artery (LCCA). Information from several images was combined into high-information content images using methods previously developed. The image resolution was 47 × 47 × 750 μm3. We acquired T1-, T2-, and proton density (PD)-weighted images (TR/TE 650/14, 2000/60, and 2000/14 msec, respectively). Each 8-bit image was placed in a separate color channel to produce a 24-bit color image (red = T1, green = PD, and blue = T2). The composite image created contrast between different tissue types that was superior to that of any single image and revealed significant luminal narrowing of the LCCA, but not the uninjured RCCA. MR images were compared with corresponding histopathology cross sections and luminal area measurements from each method correlated(r2= 0.61). Atherosclerotic luminal narrowing was successfully detected through MR imaging in a mouse model of arterial injury that is small, reproduces quickly, and lends itself to genetic analysis and manipulation. J. Magn. Reson. Imaging 2000;12:790–794. © 2000 Wiley-Liss, Inc.
Informing Eclipse API production and consumption (2007)

Application programming interfaces (APIs) inform application developers as to the functionality provided by a library and how to interact with it. APIs are a double-edged sword: if they do not permit the needed functionality to be accessed and adapted as needed, they are obstructing; if they permit all things to all people, they are complex, leading application developers to have difficulty understanding how to use them correctly. Thus, the developers of APIs have a delicate balance to strike between providing configurable functionality and simple interfaces. Inevitably, the wrong balance is sometimes chosen, as the actual usage is different from the expected usage; APIs need to evolve, or to be re-documented to account for this disparity. In this paper we propose a simple technique for quantitatively determining how existing APIs are used, and demonstrate its application to Eclipse. This technique would enable application developers to more easily understand how others have used the APIs and would allow API developers to more easily understand how their APIs are being used.
3D direct vertical interconnect microprocessors test vehicle (2003)

The current trends in high performance integrated circuits are towards faster and more powerful circuits in the giga-hertz range and even further. As the more complex Integrated Circuits (IC) such as microprocessors have been entering the giga-hertz operating frequency range, various speed related roadblocks have become increasingly difficult to overcome. The migration to smaller devices has raised serious challenges. The major impediment to fulfill Moore's Law effectively in the years to come is increasingly becoming the interconnect. ICs are using a greater fraction of their clock cycles charging interconnect wires. IC interconnect related speed degradation has stimulated much research effort in the area of low dielectric constant materials. A relatively novel approach, wafer scale 3-dimensional (3D) integration attempts to by-pass the large wire parasitics by shortening wires. This paper is going to elaborate on a 3D microprocessor test vehicle. We intend to demonstrate the speed advantages, which may be derived from 3D integration, through a combination of fabrication, testing and simulation.
AI Feynman: A physics-inspired method for symbolic regression (2020)

A core challenge for both physics and artificial intelligence (AI) is symbolic regression: finding a symbolic expression that matches data from an unknown function. Although this problem is likely to be NP-hard in principle, functions of practical interest often exhibit symmetries, separability, compositionality, and other simplifying properties. In this spirit, we develop a recursive multidimensional symbolic regression algorithm that combines neural network fitting with a suite of physics-inspired techniques. We apply it to 100 equations from the <i>Feynman Lectures on Physics</i>, and it discovers all of them, while previous publicly available software cracks only 71; for a more difficult physics-based test set, we improve the state-of-the-art success rate from 15 to 90%.
Genistein inhibits both estrogen and growth factor-stimulated proliferation of human breast cancer cells. (1996)

Genistein is a naturally occurring dietary protein tyrosine kinase (PTK) inhibitor that is hypothesized to be responsible for the lower rate of breast cancer observed in Asian women consuming soy. Although genistein is a potent in vitro PTK inhibitor, its mechanism of action in vivo is not known. In vivo, breast cancer growth is regulated by estrogens and peptide growth factors, such as epidermal growth factor (EGF), the receptor of which has intrinsic PTK activity. Therefore, genistein may block mammary epithelial cell growth by interfering with signal transduction events stimulated by estradiol or growth factors. The effect of genistein, related isoflavones, and other tyrosine kinase inhibitors on fetal bovine serum-, estradiol-, and EGF-stimulated cell growth and signal transduction pathways was examined in five human breast cancer cell lines. Genistein inhibited the growth of these cells by each of the growth stimuli with IC50 values ranging from 2.6 to over 20 micrograms/ml. Growth inhibition by genistein was cytostatic and reversible at IC50 concentrations. Related isoflavones were less potent growth inhibitors than genistein, whereas the synthetic PTK inhibitor tyrphostin A25 was an equally potent growth inhibitor. The mechanism of genistein growth inhibition in human breast cancer cells did not depend on the presence of functional estrogen receptor signaling pathways or on inhibition of EGF-receptor PTK activity. Furthermore, genistein (< or = 20 micrograms/ml) did not decrease constitutive or EGF-induced tyrosine phosphorylation as determined by Western blotting with antiphosphotyrosine antibodies. These data suggest that although genistein inhibits the growth of breast cancer cells in culture, it does so without gross inhibition of PTK activity.
Effect of Tarenflurbil on Cognitive Decline and Activities of Daily Living in Patients With Mild Alzheimer Disease<subtitle>A Randomized Controlled Trial</subtitle> (2009)

clinicaltrials.gov Identifier: NCT00105547.
High performance UV-cured optical fiber primary coating (1987)

Abstract Abstrait A new UV curable urethane acrylate (primary) coating demonstrates exceptional low temperature performance. It cures quickly and meets or surpasses other established coating requirements.
Novel use of a local drug delivery catheter for coronary perforation. (2011)

﻿Coronary perforation is a complication of percutaneous coronary intervention that may be fatal. Conventionally, a perfusion balloon catheter is used for treatment, but may not always be available. We report a case in which bleeding due to coronary perforation was successfully treated without induction of ischemia using a local drug delivery catheter as a perfusion device.
A Collaborative Extension of a Visualization System (2005)

This paper presents an extension of the single-user scientific visualization system ZoomIn to a collaborative system. We discuss the principal challenges of remote collaboration in the case of scientific visualization and present the solutions realized for ZoomIn. The main issues identified include the support of slow/fast network connections, portability, ease-of-use, privacy, configuration of the working mode and permissions. We describe why the main concepts of the original ZoomIn are well suited for a collaborative extension and how collaboration is introduced. In particular, the volume of data for scientific visualization may be very large. Therefore, the transfer of data has to be optimized. We present three different methods of data transfer for collaborative visualization and compare their efficiency with respect to particular application scenarios.
Syntactic and semantic analysis of definitions in a machine-readable dictionary (1988)

As natural language processing systems grow larger, they need larger lexicons. Furthermore, larger vocabularies require larger, more complex lexical entries to distinguish between different senses and uses. The machine-readable dictionary is a large, compact source of lexical information, but conversion of its contents to a form that a computer can use is an immense task. This thesis describes an effort to extract semantic information from Webster's Seventh New Collegiate Dictionary (W7) by a variety of methods, including parsing with Sager's Linguistic String Parser and semi-interactive text processing using UNIX utilities. It compares the effectiveness of those methods for different kinds of analysis and suggests analytical strategies exploiting the strengths of each method. Also discussed are the nature of the language of W7 and some issues in the design of a lexical database.
Recent advances in angiotensin II signaling (2002)

Angiotensin II (Ang II) is a multifunctional hormone that influences the function of cardiovascular cells through a complex series of intracellular signaling events initiated by the interaction of Ang II with AT1 and AT2 receptors. AT1 receptor activation leads to cell growth, vascular contraction, inflammatory responses and salt and water retention, whereas AT2 receptors induce apoptosis, vasodilation and natriuresis. These effects are mediated via complex, interacting signaling pathways involving stimulation of PLC and Ca2+ mobilization; activation of PLD, PLA2, PKC, MAP kinases and NAD(P)H oxidase, and stimulation of gene transcription. In addition, Ang II activates many intracellular tyrosine kinases that play a role in growth signaling and inflammation, such as Src, Pyk2, p130Cas, FAK and JAK/STAT. These events may be direct or indirect via transactivation of tyrosine kinase receptors, including PDGFR, EGFR and IGFR. Ang II induces a multitude of actions in various tissues, and the signaling events following occupancy and activation of Ang receptors are tightly controlled and extremely complex. Alterations of these highly regulated signaling pathways may be pivotal in structural and functional abnormalities that underlie pathological processes in cardiovascular diseases such as cardiac hypertrophy, hypertension and atherosclerosis.
Left Cardiac Sympathetic Denervation for Catecholaminergic Polymorphic Ventricular Tachycardia (2008)

Catecholaminergic polymorphic ventricular tachycardia is a potentially lethal disease characterized by adrenergically mediated ventricular arrhythmias manifested especially in children and teenagers. Beta-blockers are the cornerstone of therapy, but some patients do not have a complete response to this therapy and receive an implantable cardioverter-defibrillator (ICD). Given the nature of catecholaminergic polymorphic ventricular tachycardia, ICD shocks may trigger new arrhythmias, leading to the administration of multiple shocks. We describe the long-term efficacy of surgical left cardiac sympathetic denervation in three young adults with catecholaminergic polymorphic ventricular tachycardia, all of whom had symptoms before the procedure and were symptom-free afterward.
Plasma oscillations in Hall thrusters (2001)

The nature of oscillations in the 1 kHz–60 MHz frequency range that have been observed during operation of Hall thrusters is quantitatively discussed. Contours of various plasma parameters measured inside the accelerating channel of a typical Hall thruster are used to evaluate the various stability criteria and dispersion relations of oscillations that are suspected to occur. A band by band up-to-date overview of the oscillations is carried out with a description of their observed behavior and a discussion of their nature and dependencies through comparison of the calculated contours to reported observations. The discussion encompasses the excitation of low frequency azimuthal drift waves that can form a rotating spoke, axially propagating “transit-time” oscillations, azimuthal drift waves, ionization instability-type waves, and wave emission peculiar to weakly ionized inhomogeneous plasmas in crossed electric and magnetic fields.
Role of PI3K in the generation and survival of B cells (2010)

Engagement of the B-cell antigen receptor (BCR) or its precursor, the pre-BCR, induces a cascade of biochemical reactions that regulate the differentiation, selection, survival, and activation of B cells. This cascade is initiated by receptor-associated tyrosine kinases that activate multiple downstream signaling pathways. Since it is required for metabolism, cell growth, development, and survival, the activation of phosphoinositide 3-kinase (PI3K)-dependent pathways represents a crucial event of BCR/pre-BCR signaling. The phosphorylated substrates of the PI3K promote specific recruitment of selected signaling proteins to the plasma membrane, where important signaling complexes are formed to mediate the above-mentioned biological processes. Here, we review the principles of PI3K signaling and highlight the role of an important PI3K-driven module in VDJ recombination of immunoglobulin (Ig) genes during early B-cell development as compared with class switch recombination of Ig genes in mature B cells after activation by specific antigens. Furthermore, we discuss the role of PI3K in the survival of mature B cells, which is strictly dependent on BCR expression and basal BCR signaling.
Isolation and Characterization of <i>Cryptococcus neoformans</i> Spores Reveal a Critical Role for Capsule Biosynthesis Genes in Spore Biogenesis (2009)

Spores are essential particles for the survival of many organisms, both prokaryotic and eukaryotic. Among the eukaryotes, fungi have developed spores with superior resistance and dispersal properties. For the human fungal pathogens, however, relatively little is known about the role that spores play in dispersal and infection. Here we present the purification and characterization of spores from the environmental fungus Cryptococcus neoformans. For the first time, we purified spores to homogeneity and assessed their morphological, stress resistance, and surface properties. We found that spores are morphologically distinct from yeast cells and are covered with a thick spore coat. Spores are also more resistant to environmental stresses than yeast cells and display a spore-specific configuration of polysaccharides on their surfaces. Surprisingly, we found that the surface of the spore reacts with antibodies to the polysaccharide glucuronoxylomannan, the most abundant component of the polysaccharide capsule required for C. neoformans virulence. We explored the role of capsule polysaccharide in spore development by assessing spore formation in a series of acapsular strains and determined that capsule biosynthesis genes are required for proper sexual development and normal spore formation. Our findings suggest that C. neoformans spores may have an adapted cell surface that facilitates persistence in harsh environments and ultimately allows them to infect mammalian hosts.
Photonic integrated beamformers for broadband radio astronomy (2010)

For the modern radio astronomy instruments wide instantaneous bandwidth is a characteristic of great interest. This can be a difficult requirement for a phased array antenna (PAA)employing a traditional electronic beamformer: the performance of the constituting components, mainly combiners and delay elements, limits the bandwidth of the total system.
A unifying criterion for blind source separation and decorrelation: simultaneous diagonalization of correlation matrices (2002)

Blind source separation and blind output decorrelation are two well-known problems in signal processing. For instantaneous mixtures, blind source separation is equivalent to a generalized eigen-decomposition, while blind output decorrelation can be considered as an iterative method of output orthogonalization. We propose a steepest descent procedure on a new cost function based on the Frobenius norm which measures the diagonalization of correlation matrices to perform blind source separation as well as blind decorrelation. The method is applicable to both stationary and nonstationary signals and instantaneous as well as convolutive mixture models. Simulation results by Monte Carlo trials are provided to show the consistent performance of the proposed algorithm.
Bone marrow-derived lymphoid cell lines from patients with agammaglobulinemia. (1978)

In vitro infection with Epstein-Barr virus of bone marrow-derived (B) lymphocytes from blood of patients with X-linked or common varied agammaglobulinemia resulted in the establishment of long-term B-lymphoid cell lines (LCL). LCL were established only with B lymphocytes from patients whose B cells failed to respond to in vitro mitogenic stimulation. In contrast, lymphocytes from patients without small B lymphocytes or with B cells that synthesized but failed to secrete Ig failed uniformly to establish LCL. Analysis of the "nonsecretory" B lymphocytes demonstrated the presence of receptors for C3b and C3d as well as surface Ig, but absence of detectable receptors for Epstein-Barr virus. All of the six cell lines that were established formed rosettes with EAC3 but not with sheep erythrocytes. Four of the six LCL were principally surface IgD bearing and did not synthesize detectable Ig for secretion. Two of the cell lines were indistinguishable from cell lines from normal individuals: they had surface IgG, A, M, and D and synthesized and secreted Ig.
Denaturant <i>m</i> values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding (1995)

Denaturant m values, the dependence of the free energy of unfolding on denaturant concentration, have been collected for a large set of proteins. The m value correlates very strongly with the amount of protein surface exposed to solvent upon unfolding, with linear correlation coefficients of R = 0.84 for urea and R = 0.87 for guanidine hydrochloride. These correlations improve to R = 0.90 when the effect of disulfide bonds on the accessible area of the unfolded protein is included. A similar dependence on accessible surface area has been found previously for the heat capacity change (delta Cp), which is confirmed here for our set of proteins. Denaturant m values and heat capacity changes also correlate well with each other. For proteins that undergo a simple two-state unfolding mechanism, the amount of surface exposed to solvent upon unfolding is a main structural determinant for both m values and delta Cp.
New Opportunities For Diversity Twitter Journalists and Traditionally Underserved Communities (2014)

This study explores the opportunities offered by Twitter for news organizations seeking to connect with communities often underrepresented as both sources and as audiences for news. A recent study by Pew Research Center found that minority Internet users are nearly twice as likely as white Internet users to utilize Twitter, and that young Internet users are also signiicantly more likely than older Americans to adopt the social network. Through in-depth interviews, this study examines how young people and minorities are using Twitter and evaluates its potential to allow news organizations to reach and engage younger and minority audiences. For many, it is not only a site used for entertainment and connection with like-minded others, but also for keeping up with news and giving them a voice on national or local issues they did not previously perceive they possessed.