gebhart/patrepeval huggingface dataset:
Mechanisms of Plaque Formation and Rupture (2014)

Atherosclerosis causes clinical disease through luminal narrowing or by precipitating thrombi that obstruct blood flow to the heart (coronary heart disease), brain (ischemic stroke), or lower extremities (peripheral vascular disease). The most common of these manifestations is coronary heart disease, including stable angina pectoris and the acute coronary syndromes. Atherosclerosis is a lipoprotein-driven disease that leads to plaque formation at specific sites of the arterial tree through intimal inflammation, necrosis, fibrosis, and calcification. After decades of indolent progression, such plaques may suddenly cause life-threatening coronary thrombosis presenting as an acute coronary syndrome. Most often, the culprit morphology is plaque rupture with exposure of highly thrombogenic, red cell-rich necrotic core material. The permissive structural requirement for this to occur is an extremely thin fibrous cap, and thus, ruptures occur mainly among lesions defined as thin-cap fibroatheromas. Also common are thrombi forming on lesions without rupture (plaque erosion), most often on pathological intimal thickening or fibroatheromas. However, the mechanisms involved in plaque erosion remain largely unknown, although coronary spasm is suspected. The calcified nodule has been suggested as a rare cause of coronary thrombosis in highly calcified and tortious arteries in older individuals. To characterize the severity and prognosis of plaques, several terms are used. Plaque burden denotes the extent of disease, whereas plaque activity is an ambiguous term, which may refer to one of several processes that characterize progression. Plaque vulnerability describes the short-term risk of precipitating symptomatic thrombosis. In this review, we discuss mechanisms of atherosclerotic plaque initiation and progression; how plaques suddenly precipitate life-threatening thrombi; and the concepts of plaque burden, activity, and vulnerability.
Formation of micro lens by laser polymerization (2012)

Abstract Recently, micro lenses have been in demand for uniting laser devices and optical fibers. We have fabricated a new type of plastic micro lens by laser polymerization. The amount of resin polymerized by exposure to laser light (light curing) depends on the laser power and the exposure time. The shape of the lens can be controlled by changing the conditions of laser irradiation. In this paper, the characteristics of the lens formed by this method are examined. The relation between the lens shape and the conditions of laser irradiation are investigated, and the conditions for reducing transverse spherical aberration are examined. A lens 390 μm in diameter was formed. The area that can be used for light coupling from a laser diode to a multimode fiber will be 81% of the total lens area. © 2012 Wiley Periodicals, Inc. Electron Comm Jpn, 95(2): 59–67, 2012; Published online in Wiley Online Library ( wileyonlinelibrary.com ). DOI 10.1002/ecj.10339
X Rays Induce Interallelic Homologous Recombination at the Human Thymidine Kinase Gene (1992)

We have developed a human lymphoblast cell line for the study of interchromosomal homologous recombination at the endogenous thymidine kinase (tk) gene on chromosome 17 (M. B. Benjamin, H. Potter, D. W. Yandell, and J. B. Little, Proc. Natl. Acad. Sci. USA 88:6652-6656, 1991). This cell line (designated 6:86) carries unique heterozygous frameshift mutations in exons 4 and 7 of its endogenous tk alleles and can revert to TK+ by frame-restoring mutations, gene conversion, or reciprocal recombination. Line 6:86 reverts spontaneously to TK+ at a frequency of 10(-7) to 10(-8), and exposures to X-irradiation or the frameshift mutagen ICR-191 induce increased reversion frequencies in a dose-dependent manner. Another cell line (designated 4:2) carries a homozygous exon 7 frameshift and is not expected to revert through mechanisms other than frame-restoring mutation. Line 4:2 reverts to TK+ at a lower spontaneous frequency than does 6:86 but can be induced with similar kinetics by ICR-191. In contrast to line 6:86, however, X rays did not induce detectable reversion of line 4:2. We have characterized a number of 6:86-derived revertants by means of restriction fragment length polymorphism analysis at tk and linked loci, single-strand conformation polymorphisms, and direct transcript sequencing. For X rays, most revertants retain both original mutations in the genomic DNA, and a subset of these frameshift-retaining revertants produce frameshift-free message, indicating that reversion is the result of reciprocal recombination within the tk gene. Frame-restoring point mutations, restoration of original sequences, and phenocopy reversion by acquisition of aminopterin resistance were also found among X-ray-induced revertants, whereas the ICR-191-induced revertants examined show only loss of the exon 7 frameshift.
Partial self-ordering observed in silicon nanoclusters deposited on silicon oxide substrates by chemical vapor deposition (2005)

The formation of Si dots by chemical vapor deposition is studied from the very early stages of the dot formation up to about 25% of substrate coverage. Structural characterization is mainly performed by means of energy filtered transmission electron microscopy, which couples chemical information to very high spatial resolution. The dots are shown to be surrounded by Si-free regions and this is attributed to the Si adatom capture mechanism from each nucleus. The data are discussed in the framework of a self-similar model, which takes into account the dot local environment, the adatom diffusion and the continuous nucleation of new islands. From the fit to the data the correlation between the dot size and the capture area is obtained and the number of deactivated nucleation sites is quantified.
Influence of the Evaporation Rate on the Packing Order of Polydisperse Latex Monofilms (1997)

A new strategy to create well-ordered latex particle monofilms from polydisperse latex solutions was developed. Due to size-dependent segregation, the spherical particles assemble in grains with a uniform sphere size within each grain. The size-dependent segregation process can be deduced from the action of a single force, the lateral capillary force. A strong temperature dependence can be observed, and the process becomes evident when the substrate is cooled. The samples are characterized by scanning force microscopy. Finally, to prove the theoretical model, a computer simulation is performed, supporting the experimental results.
SNF2β-BRG1 is Essential for the Viability of F9 Murine Embryonal Carcinoma Cells (1997)

The yeast and animal SNF-SWI and related multiprotein complexes are thought to play an important role in processes, such as transcription factor binding to regulatory elements, which require nucleosome remodeling in order to relieve the repressing effect of packaging DNA in chromatin. There are two mammalian homologs of the yeast SNF2-SWI2 subunit protein, SNF2alpha-brm and SNF2beta-BRG1, and overexpression of either one of them has been shown to enhance transcriptional activation by glucocorticoid, estrogen, and retinoic acid (RA) receptors in transiently transfected cells. We have investigated here the function of SNF2beta-BRG1 in the RA receptor-retinoid X receptor-mediated transduction of the retinoid signal in F9 embryonal carcinoma (EC) cells which differentiate into endodermal-like cells upon RA treatment. The two SNF2beta-BRG1 alleles have been targeted by homologous recombination and subsequently disrupted by using a conditional Cre recombinase. We show that F9 EC cells inactivated on both SNF2beta alleles are not viable and that heterozygous mutant cells are affected in proliferation but not in RA-induced differentiation. Thus, in F9 EC cells, SNF2beta-BRG1 appears to play an essential role in basal processes involved in cell proliferation, in addition to its putative role in the activation of transcription mediated by nuclear receptors.
Inhibition of initiation of bacteriophage T4 DNA replication by perturbation of Escherichia coli host membrane composition (1979)

3-Decynoyl-N-acetylcysteamine (3-decynoyl-NAC) is an analog which specifically causes the immediate cessation of the biosynthesis of unsaturated fatty acids in Escherichia coli, whereas the synthesis of saturated fatty acids is actually stimulated. As a result, the cell membrane accumulates saturated fatty acids in its phospholipid. Addition of the inhibitor at the time of infection of E. coli by T4 phage had no effect on normal phage replication and development, implying that the synthesis of unsaturated fatty acids per se has little effect on T4 DNA replication. However, if the integrity and composition of the bacterial membrane was grossly perturbed by first treating the cells with the inhibitor for 60 min before infection, the proper initiation and the attainment of a rapid rate of T4 DNA synthesis were not observed. Under these conditions, a full complement of T4 early proteins was synthesized. The membrane associability of the known DNA delay proteins induced by wild-type T4 phage in the treated cells resembled that expected of a culture of untreated cells infected with a DNA delay mutant. When any one of three DNA delay mutants was used to infect 3-decynoyl-NAC-treated cells, T4 DNA replication was aborted. These findings suggest that some kind of specific interactions among the initiation proteins defined by the DNA delay mutants and the bacterial membrane may be necessary to facilitate the normal initiation and rapid rate of T4 DNA replication. A model for the involvement of the three different initiation proteins and the subsequent attainment of rapid DNA synthesis is discussed.
Cyclin-Binding Motifs Are Essential for the Function of p21<i><sup>CIP1</sup></i> (1996)

The cyclin-dependent kinase (Cdk) inhibitor p21 is induced by the tumor suppressor p53 and is required for the G1-S block in cells with DNA damage. We report that there are two copies of a cyclin-binding motif in p21, Cy1 and Cy2, which interact with the cyclins independently of Cdk2. The cyclin-binding motifs of p21 are required for optimum inhibition of cyclin-Cdk kinases in vitro and for growth suppression in vivo. Peptides containing only the Cy1 or Cy2 motif partially inhibit cyclin-Cdk kinase activity in vitro and DNA replication in Xenopus egg extracts. A monoclonal antibody which recognizes the Cy1 site of p21 specifically disrupts the association of p21 with cyclin E-Cdk2 and with cyclin D1-Cdk4 in cell extracts. Taken together, these observations suggest that the cyclin-binding motif of p21 is important for kinase inhibition and for formation of p21-cyclin-Cdk complexes in the cell. Finally, we show that the cyclin-Cdk complex is partially active if associated with only the cyclin-binding motif of p21, providing an explanation for how p21 is found associated with active cyclin-Cdk complexes in vivo. The Cy sequences may be general motifs used by Cdk inhibitors or substrates to interact with the cyclin in a cyclin-Cdk complex.
<title>Dual frequency piezoelectric transducer for medical applications</title> (1992)

Recent advances in the field of medical ultrasound requires a dual frequency transducer capable of operation at two frequencies. This is usually achieved by having a broadband transducer which can be excited at two different frequencies. Such frequency characteristics will allow echo-amplitude imaging at the higher frequency where a high resolution is required and color flow imaging (CFI) at the lower frequency for improved sensitivity. In this paper a novel dual frequency transducer design, demonstrating two distinct resonance, is presented. This is achieved by varying the geometry of the piezoelectric ceramic in a manner which results in two distinct thickness mode resonance. The results showing the temporal characteristics of such transducer are presented. The parameters influencing the temporal response of this transducer are discussed. It is also shown that the two resonance frequencies are independent. Finally, the advantages of this new design over the conventional techniques are discussed.
A new W3C markup standard for text-to-speech synthesis (2002)

A new set of XML-based markup standards developed for the purpose of enabling voice browsing of the Internet are emerging from the Voice Browser working group, organized under the auspices of the W3C. Among the first in this series of specifications is the speech synthesis text markup standard. The Speech Synthesis Markup Language (SSML) specification is largely based on Java Speech Markup Language (JSML), but also incorporates elements and concepts from SABLE, previously published text markup standards, and from Voice eXtensible Markup Language (VoiceXML), which is itself based on JSML and SABLE. SSML also includes new elements designed to optimize the capabilities of contemporary speech synthesis engines in the task of converting text into speech. This paper summarizes the markup element design philosophy and includes descriptions of each of the speech synthesis markup elements.
The DLV system for knowledge representation and reasoning (2006)

Disjunctive Logic Programming (DLP) is an advanced formalism for knowledge representation and reasoning, which is very expressive in a precise mathematical sense: it allows one to express every property of finite structures that is decidable in the complexity class Σ P 2 (NP NP ). Thus, under widely believed assumptions, DLP is strictly more expressive than normal ( disjunction-free ) logic programming, whose expressiveness is limited to properties decidable in NP. Importantly, apart from enlarging the class of applications which can be encoded in the language, disjunction often allows for representing problems of lower complexity in a simpler and more natural fashion.This article presents the DLV system, which is widely considered the state-of-the-art implementation of disjunctive logic programming, and addresses several aspects. As for problem solving, we provide a formal definition of its kernel language, function-free disjunctive logic programs (also known as disjunctive datalog ), extended by weak constraints, which are a powerful tool to express optimization problems. We then illustrate the usage of DLV as a tool for knowledge representation and reasoning, describing a new declarative programming methodology which allows one to encode complex problems (up to Δ P 3 -complete problems) in a declarative fashion. On the foundational side, we provide a detailed analysis of the computational complexity of the language of DLV, and by deriving new complexity results we chart a complete picture of the complexity of this language and important fragments thereof.Furthermore, we illustrate the general architecture of the DLV system, which has been influenced by these results. As for applications, we overview application front-ends which have been developed on top of DLV to solve specific knowledge representation tasks, and we briefly describe the main international projects investigating the potential of the system for industrial exploitation. Finally, we report about thorough experimentation and benchmarking, which has been carried out to assess the efficiency of the system. The experimental results confirm the solidity of DLV and highlight its potential for emerging application areas like knowledge management and information integration.
Persistent Diarrhea and Fecal Shedding of Retroviral Nucleic Acids in Children Infected with Human Immunodeficiency Virus (1991)

Gastrointestinal dysfunction is a serious problem in many children infected with human immunodeficiency virus (HIV), the etiology of which has not been clearly defined. Quantitative nucleic acid amplification was used to study the correlation between shedding of HIV nucleic acids and gastrointestinal symptoms in HIV-infected infants and children. Many with HIV infection and persistent diarrheal disease shed HIV nucleic acids in their feces, as did an HIV-infected patient without apparent diarrheal disease. HIV nucleic acids were not found in feces of non-HIV-infected individuals. Intestinal infection with HIV appears to be important in the pathophysiology of gastrointestinal dysfunction in infants and children with HIV infection. Furthermore, the fecal shedding of HIV may play a role in HIV transmission in environments prone to high levels of fecal-oral contamination.
Carrier concentration and surface electron accumulation in indium nitride layers grown by high pressure chemical vapor deposition (2007)

Electronic and structural properties of InN layer grown by high pressure chemical vapor deposition have been studied by high-resolution electron energy loss spectroscopy (HREELS) and room temperature infrared reflection measurements. HREEL spectra after atomic hydrogen cleaning exhibit N–H bending and stretching vibrations with no indications of an indium overlayer or droplet formation. Broad conduction band plasmon excitations are observed centered at 3100–4200cm−1 at various locations across the surface in HREEL spectra acquired with 25eV incident electron energy. The plasmon excitations are shifted about 300cm−1 higher in spectra acquired using 7eV electrons due to higher plasma frequency and carrier concentration at the surface than in the bulk which indicates surface electron accumulation. Infrared reflectance data acquired at various spots across the surface showed a similar variation in bulk plasma frequency. A three phase thin film reflection model fitted to the infrared data yielded carrier concentrations from 8.2×1019to1.5×1020cm−3 and carrier mobilities from 105 to 210cm2∕Vs.
The Farnesoid X Receptor Modulates Adiposity and Peripheral Insulin Sensitivity in Mice (2006)

The farnesoid X receptor (FXR) is a bile acid (BA)-activated nuclear receptor that plays a major role in the regulation of BA and lipid metabolism. Recently, several studies have suggested a potential role of FXR in the control of hepatic carbohydrate metabolism, but its contribution to the maintenance of peripheral glucose homeostasis remains to be established. FXR-deficient mice display decreased adipose tissue mass, lower serum leptin concentrations, and elevated plasma free fatty acid levels. Glucose and insulin tolerance tests revealed that FXR deficiency is associated with impaired glucose tolerance and insulin resistance. Moreover, whole-body glucose disposal during a hyperinsulinemic euglycemic clamp is decreased in FXR-deficient mice. In parallel, FXR deficiency alters distal insulin signaling, as reflected by decreased insulin-dependent Akt phosphorylation in both white adipose tissue and skeletal muscle. Whereas FXR is not expressed in skeletal muscle, it was detected at a low level in white adipose tissue in vivo and induced during adipocyte differentiation in vitro. Moreover, mouse embryonic fibroblasts derived from FXR-deficient mice displayed impaired adipocyte differentiation, identifying a direct role for FXR in adipocyte function. Treatment of differentiated 3T3-L1 adipocytes with the FXR-specific synthetic agonist GW4064 enhanced insulin signaling and insulin-stimulated glucose uptake. Finally, treatment with GW4064 improved insulin resistance in genetically obese ob/ob mice in vivo. Although the underlying molecular mechanisms remain to be unraveled, these results clearly identify a novel role of FXR in the regulation of peripheral insulin sensitivity and adipocyte function. This unexpected function of FXR opens new perspectives for the treatment of type 2 diabetes.
Transport Layer Security (TLS) Next Protocol Extension (2011)

This document describes a Transport Layer Security (TLS) extension for
application layer protocol probing and announcement. This allows the
application client to specify which protocol will be performed over
the secure connection.
DAC nonlinearity and residue gain error correction in a pipelined ADC using a split-ADC architecture (2006)

A split-ADC architecture is used to calibrate both the non-linearity errors introduced by capacitor mismatches in the DAC, and gain errors in the residue amplifier of the first stage in a pipelined ADC. The background scheme only requires 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> clock cycles to perform the calibration to more than 12b accuracy. Simulated in Simulink and Spice, the digital calibration scheme improves the ADC's SNDR/SFDR from 54dB/58dB before calibration to 78dB/85dB after calibration
Polymorph Selection with Morphology Control Using Solvents (2007)

Sulfathiazole is a highly polymorphic model system exhibiting at least five polymorphic forms: I, II, III, IV, and V. Polymorph stability is known to be susceptible to solvent environment, and it is established that 1-propanol stabilizes the most metastable form I. This study examines the effect of a range of alcohols on polymorph selection and attempts to elucidate the mechanism. The role of the alcohol functional group in the polymorph selection process is thus investigated and evaluated. Crystals were characterized using optical microscopy, SEM, PXRD, DSC, IR, and single-crystal X-ray diffraction for their polymorphic identity. The role of solvent in the stabilization of polymorphs was investigated by visualizing and calculating energy requirements for the interaction of each solvent molecule with α- and β-dimers of sulfathiazole, using Cerius2 modeling software. This study showed that solvent had a significant impact on polymorph selection. In common with 1-propanol, 1-butanol was found to stabilize form I by inhibiting the formation of the β-dimer, which is necessary for nucleation of and transformation to forms II−IV. Shorter chain alcohols and branched chain alcohols such as methanol, 2-propanol, and ethanol did not stabilize form I but stabilized forms II, III, and IV, respectively, showing that it is not only the alcohol functionality but also the steric effects of the alkyl chain that contributed to the effect. Sulfathiazole form I normally has a needlelike morphology. Form I with a modified rodlike morphology was produced by crystallization from 1-propanol with the addition of methanol in low concentration, showing that it is possible to control the morphology and selectively isolate polymorphs.
Synthesis of two substance P analogs, [8-tyr] and [5-asn] substance P. (1978)

In a conventional manner, two substance P analogs, [8-Tyr] and [5-Asn]-substance P, were synthesized. When contractility on isolated guinea-pig ileum was examined, [8-Tyr] and [5-Asn]-analogs exhibited the activities of 1.73 and 2.08 times higher than that of synthetic substance P respectively.
Back surface reflectors for solar cells (1980)

Sample solar cells were fabricated to study the effects of various back surface reflectors on the device performance. They are typical 50 micrometers thick, space quality, silicon solar cells except for variations of the back contact configuration. The back surfaces of the sample cells are polished to a mirror like finish, and have either conventional full contacts or grid finger contacts. Measurements and evaluation of various metallic back surface reflectors, as well as cells with total internal reflection, are presented. Results indicate that back surface reflectors formed using a grid finger back contact are more effective reflectors than cells with full back metallization and that Au, Ag, or Cu are better back surface reflector metals than Al.