gebhart/patrepeval huggingface dataset:
Extracellular Superoxide Dismutase Protects Against Matrix Degradation of Heparan Sulfate in the Lung (2007)

Asbestosis is a form of interstitial lung disease caused by the inhalation of asbestos fibers, leading to inflammation and pulmonary fibrosis. Inflammation and oxidant/antioxidant imbalances are known to contribute to the disease pathogenesis. Extracellular superoxide dismutase (EC-SOD) is an antioxidant enzyme that has been shown to protect the lung from oxidant-mediated damage, inflammation, and interstitial fibrosis. Extracellular matrix (ECM) components, such as collagen and glycosaminoglycans, are known to be sensitive to oxidative fragmentation. Heparan sulfate, a glycosaminoglycan, is highly abundant in the ECM and tightly binds EC-SOD. We investigated the protective role of EC-SOD by evaluating the interaction of EC-SOD with heparan sulfate in the presence of reactive oxygen species (ROS). We found that ROS-induced heparin and heparan sulfate fragments induced neutrophil chemotaxis across a modified Boyden chamber, which was inhibited by the presence of EC-SOD by scavenging oxygen radicals. Chemotaxis in response to oxidatively fragmented heparin was mediated by Toll-like receptor-4. In vivo, bronchoalveolar lavage fluid from EC-SOD knockout mice at 1, 14, and 28 days after asbestos exposure showed increased heparan sulfate shedding from the lung parenchyma. We demonstrate that one mechanism through which EC-SOD inhibits lung inflammation and fibrosis in asbestosis is by protecting heparin/heparan sulfate from oxidative fragmentation.
Boundary conditions for open quantum systems driven far from equilibrium (1990)

This is a study of simple kinetic models of open systems, in the sense of systems that can exchange conserved particles with their environment. The system is assumed to be one dimensional and situated between two particle reservoirs. Such a system is readily driven far from equilibrium if the chemical potentials of the reservoirs differ appreciably. The openness of the system modifies the spatial boundary conditions on the single-particle Liouville---von Neumann equation, leading to a non-Hermitian Liouville operator. If the open-system boundary conditions are time reversible, exponentially growing (unphysical) solutions are introduced into the time dependence of the density matrix. This problem is avoided by applying time-irreversible boundary conditions to the Wigner distribution function. These boundary conditions model the external environment as ideal particle reservoirs with properties analogous to those of a blackbody. This time-irreversible model may be numerically evaluated in a discrete approximation and has been applied to the study of a resonant-tunneling semiconductor diode. The physical and mathematical properties of the irreversible kinetic model, in both its discrete and its continuum formulations, are examined in detail. The model demonstrates the distinction in kinetic theory between commutator superoperators, which may become non-Hermitian to describe irreversible behavior, and anticommutator superoperators, which remain Hermitian and are used to evaluate physical observables.
Observations of Water Line Emission Near Three Compact Infrared Sources (1975)

Observations of the water line emission from regions near three compact infrared sources are reported. A new water vapour source has been dicovered in S140. New components have been observed in NGC 1333, one of which decreased in intensity by a factor of 2.5 over three days. The position of the W51(N) water source differs by 9<sup>ø</sup>±10<sup>ø</sup> from that of the compact HII/infrared source IRS-2 in W51.
Molecular and systemic mechanisms of general anaesthesia: the ‘multi-site and multiple mechanisms’ concept (2005)

Clinical anaesthesia is based on drug actions at multiple anatomical sites in the brain. The finding that amnesia, hypnosis and immobility involve distinct molecular targets opens new avenues for developing improved therapeutic strategies in anaesthesia.
Monocyte activation markers during cardiopulmonary bypass (2003)

Extracorporeal support during cardiac surgery initiates an inflammatory response, causing damage to cardiac, pulmonary and renal tissue [Post Pump Syndrome (PPS)]. This is accompanied by a neutrophil leucocytosis and lymphopenia, but less is known about the role of monocytes and markers of monocyte activity. We studied 19 patients undergoing cardiac surgery, obtaining blood samples from the aortic root (AR) and from the coronary sinus ( < s) before the cardiopulmonary bypass (CPB), 1 min after release of the aortic crossclamp and 10 min after weaning from CPB (periods 1, 2 and 3). Leucocyte count, monocyte count and HLA-DR, CD15, CD11b and CD62L activation markers were measured. In samples obtained from the coronary sinus (CS), HLA-DR, expressed as a percentage of the monocyte count, decreased between periods 1, 2 and 3 by 78%, 66% and 43%, respectively. A similar change was observed in samples from the AR. Conversely, CD62L increased in the CS samples (55%, 68% and 73%), but revealed a lesser increase in the AR samples (51%, 68% and 63%). The other markers showed little change throughout the procedure. Reduced immunological competence could result from the decrease in HLA-DR counts. Increases in CD62L sensitizes monocytes to the tethering effects of endothelial integrins and might contribute to the atherosclerotic process.
Representing Java classes in a typed intermediate language (1999)

We propose a conservative extension of the polymorphic lambda calculus (Fω) as an intermediate language for compiling languages with name-based class and interface hierarchies. Our extension enriches standard Fω with recursive types, existential types, and row polymorphism, but only ordered records with no subtyping. Basing our language on Fω makes it also a suitable target for translation from other higher-order languages; this enables the safe interoperation between class-based and higher-order languages and the reuse of common type-directed optimization techniques, compiler back ends, and runtime support.We present the formal semantics of our intermediate language and illustrate its features by providing a formal translation from a subset of Java, including classes, interfaces, and private instance variables. The translation preserves the name-based hierarchical relation between Java classes and interfaces, and allows access to private instance variables of parameters of the same class as the one defining the method. It also exposes the details of method invocation and instance variable access and allows many standard optimizations to be performed on the object-oriented code.
NVCR: A Transparent Checkpoint-Restart Library for NVIDIA CUDA (2011)

Today, CUDA is the de facto standard programming framework to exploit the computational power of graphics processing units (GPUs) to accelerate various kinds of applications. For efficient use of a large GPU-accelerated system, one important mechanism is checkpoint-restart that can be used not only to improve fault tolerance but also to optimize node/slot allocation by suspending a job on one node and migrating the job to another node. Although several checkpoint-restart implementations have been developed so far, they do not support CUDA applications or have some severe limitations for CUDA support. Hence, we present a checkpoint-restart library for CUDA that first deletes all CUDA resources before check pointing and then restores them right after check pointing. It is necessary to restore each memory chunk at the same memory address. To this end, we propose a novel technique that replays memory related API calls. The library supports both CUDA runtime API and CUDA driver API. Moreover, the library is transparent to applications, it is not necessary to recompile the applications for check pointing. This paper demonstrates that the proposed library can achieve checkpoint-restart of various applications at acceptable overheads, and the library also works for MPI applications such as HPL.
The IP-meter, design concept and example implementation of an Internet enabled power line quality meter (2002)

An Internet Protocol enabled meter, IP-meter, has been designed. As an example of the IP-meter a power line quality meter fully accessible over the Internet has been implemented. The meter is capable of measuring line frequency harmonics with spectral information, transients, line voltage RMS with sags and swells analysis. The Internet access for this application is made over a thin Ethernet medium. The Internet connection is made with a three part design concept: sensor part, microprocessor part and communication part. Served by the built in Webserver the meter is fully accessible via a standard internet browser. Meter setup, data display etc. are made using html pages and Java applets.
Reducing Resource Redundancy for Concurrent Error Detection Techniques in High Performance Microprocessors (2006)

With reducing feature size, increasing chip capacity, and increasing clock speed, microprocessors are becoming increasingly susceptible to transient (soft) errors. Redundant multi-threading (RMT) is an attractive approach for concurrent error detection and recovery. However, redundant threads significantly increase the pressure on the processor resources, resulting in dramatic performance impact. In this paper, we propose reducing resource redundancy as a means to mitigate the performance impact of redundancy. In this approach, all the instructions are redundantly executed, however, the redundant instructions do not use many of the resources used by an instruction. The approach taken to reduce resource redundancy is to exploit the runtime profile of the leading thread to optimally allocate resources to the trailing thread in a staggered RMT architecture. The key observation used in this approach is that, even with a small slack between the two threads, many instructions in the leading thread have already produced their results before their trailing counterparts are renamed. We investigate two techniques in this approach (i) register bits reuse technique that attempts to use the same register (but different bits) for both the copies of the same instruction, if the result produced by the instruction is of small size, and (ii) register value reuse technique that attempts to use the same register for a main instruction and a distinct redundant instruction, if both the instructions produce the same result. These techniques, along with some others, are used to reduce redundancy in register file, reorder buffer, and load/store buffer. The techniques are evaluated in terms of their performance, power, and vulnerability impact on an RMT processor. Our experiments show that the techniques achieve about 95% performance improvement and about 17% energy reduction. The vulnerability of the RMT remains the same with the techniques.
Using measured characteristics of surface mount components in time-domain simulation of high speed analog circuit (2004)

Although surface mount components are widely used in high frequency circuit design, the distortion of the characteristics of these devices at high frequencies should be considered during analog circuit design. The work reported in this paper employs a novel combination of measurement results and fast computational tools to provide the circuit response in both time and frequency domains. In particular, this method allows very fast computation of the circuit response (in the time or frequency domain) for systems composed of a variety of elements - including those for which the equivalent circuit is not known. This technique allows the designer to carefully (and quickly) investigate the contribution of individual components to the overall response. In this paper a brief overview is provided of the methods employed.
Band-gap renormalization in semiconductors with multiple inequivalent valleys (1992)

The narrowing of direct and indirect band gaps is investigated in highly excited semiconductor materials with multiple inequivalent valleys in the conduction band. The model substance chosen is ${\mathrm{Al}}_{\mathit{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$As close to the crossover from a direct-band-gap to an indirect-band-gap semiconductor. A theoretical model is presented, which is an extension of the universal formula for band-gap renormalization (BGR) to a multivalley scenario. This model accounts explicitly for the electron-exchange contribution to BGR in each conduction-band minimum. Its applicability to the case of high carrier densities is demonstrated by comparison to band-gap energies experimentally determined from time-resolved luminescence spectra. In a scenario of essentially unoccupied higher-energy conduction-band minima, one finds a renormalization of the fundamental gap by full correlation and exchange effects. The higher-energy gaps, on the other hand, narrow mainly due to the interactions between the holes in the valence band, while the electron-exchange effect in the empty valleys is negligible. The case of the electrons being distributed among several minima, such as in direct band-gap ${\mathrm{Al}}_{\mathit{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$As just below the crossover point, is treated with a self-consistent routine for the population and renormalization of each valley. The agreement with experimental data is excellent and the alleged enhancement of the BGR in this scenario is quantitatively explained. The differential renormalization of minima with different populations is utilized to achieve a laser-induced transition from a direct-band-gap to an indirect-band-gap semiconductor in ${\mathrm{Al}}_{0.42}$${\mathrm{Ga}}_{0.58}$As. Crossings of various conduction-band minima due to BGR is predicted from the self-consistent multivalley model and demonstrated by the properties of indirect stimulated emission.
Rule-based Approach in Arabic Natural Language Processing (2010)

The rule-based approach has successfully been used in developing many natural language processing systems. Systems that use rule-based transformations are based on a core of solid linguistic knowledge. The linguistic knowledge acquired for one natural language processing system may be reused to build knowledge required for a similar task in another system. The advantage of the rule-based approach over the corpus-based approach is clear for: 1) less-resourced languages, for which large corpora, possibly parallel or bilingual, with representative structures and entities are neither available nor easily affordable, and 2) for morphologically rich languages, which even with the availability of corpora suffer from data sparseness. These have motivated many researchers to fully or partially follow the rule- based approach in developing their Arabic natural processing tools and systems. In this paper we address our successful efforts that involved rule-based approach for different Arabic natural language processing tasks.
Engineering in genomics-automating the Genome Center (1994)

Engineering enters genomics principally through the development of hardware and software tools or processes (operations research) to aid the biologist/geneticist to take different, more, or higher quality data. The Human Genome Project, in order to meet its goals for mapping and sequencing, is pushing to advance the state of the art in instrumentation, automation and computational biology. The focus of the project was to develop the necessary strategies, hardware, and software to complete the identification of all the genes, and obtain the sequence for the entire genome for humans and a select set of relevant organisms (mouse, fruit fly, yeast, E.coli, etc.) by the year 2006. The project has already produced a significant amount of data, is contributing to medicine and is ahead of schedule. But to keep on track, laboratories conducting research in genomics must move into a period where production data gathering is performed in a factory-like setting. The author focuses on some of the research activities of his group, which is developing automation and informatics systems for the Human Genome Project, specifically human genome centers where the production mapping and sequencing will be done. A multidisciplinary group has been assembled from personnel from the Salk Institute (a biological research organization) and General Atomics (an energy and basic sciences research company). The center is conducting research to map and sequence chromosome 11 and Giardia, for starters, and becoming more highly automated daily.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A study on the capacitance–voltage characteristics of metal-Ta2O5-silicon capacitors for very large scale integration metal-oxide-semiconductor gate oxide applications (1999)

In this work, the capacitance–voltage characteristics of Au/Ta2O5/Si capacitors are studied. The Ta2O5 films are deposited by plasma-enhanced chemical vapor deposition system. Constant voltage stress is applied to the Ta2O5 capacitors. The flatband voltage VFB is measured before and after the constant voltage stress. The flatband voltage shift due to the stress is explained by the trapping of electrons and holes. An interface trapped charge density (Dit) about 2×1011 eV−1 cm−2 in the midgap of silicon is extracted by using the conductance method. The discharging transient current after a constant voltage stress is measured and correlated with the electron and hole trapping. The trapped electron and hole densities in Ta2O5 are calculated by using the tunneling front model. The VFB shift and the discharging transient currents are explained based on the energy band diagram of the metal/Ta2O5/silicon system.
Leg-length discrepancy measured by ultrasonography (1991)

Leg-length discrepancy was determined by real-time ultrasonography (ultrasound) in 45 patients, and the measurements were compared with those of erect-posture radiography. A special device for holding and moving the ultrasound transducer was constructed, and the leg length was measured as the highest level of the femoral head in the standing position. The correlation coefficient r between ultrasound and radiography was 0.94, the mean difference was -1.9 mm, and the limits of agreement (mean +/- 2 SD) were -9.1 to 5.3 mm. The mean difference between examiners 1 and 2 was 1.7 mm, and the 95 percent confidence interval was +/- 7 mm. We conclude that leg-length discrepancy can be reliably determined by ultrasound, although the accuracy is less than that obtained by radiographic methods. Because ultrasound is not limited by radiation hazards, our technique can be used for clinical screening.
Boundary Representation-Based Feature Recognition (1997)

This paper introduces an ongoing research which is aimed at the development of an intelligent form feature extraction system from Computer Aided Design (CAD) database, a high level data structure form useful for Computer Aided Manufacturing (CAM) such as Automated Process Planning System (APPS). Part description in CAD models is the form of basic geometry and topology that is unsuitable for direct application in APPS. Furthermore, CAD software does not incorporate sufficient manufacturing specific data to be used in APPS. Therefore, feature recognition systems will provide the capabilities for bridging the gap between the CAD database and the CAM database. A solid boundary representation (B-rep) model of the part is used to describe the part. This paper concentrates on the recognition of machinable features of either depression or protrusion types to be used in Automated Process Planning System. Logical procedures were developed to recognise these features which consists of both simple and intersecting features.
A comprehensive functional analysis of tissue specificity of human gene expression (2008)

A comprehensive functional analysis of housekeeping and tissue-specific genes showed that the biological function of housekeeping and tissue-specific genes was consistent with tissue origin. Network analysis revealed that tissue-specific networks have distinct network properties related to each tissue's function. Tissue 'signature networks' promise to be a rich source of targets and biomarkers for disease treatment and diagnosis.
Regulation by glucagon (cAMP) and insulin of the promoter of the human phosphoenolpyruvate carboxykinase gene (cytosolic) in cultured rat hepatocytes and in human hepatoblastoma cells (2000)

A promoter fragment (-457 to +65) of the human cytosolic phosphoenolpyruvate carboxykinase gene, which by analogy to the rat promoter contains regulatory regions conferring glucagon (cAMP) and insulin responsiveness to the phosphoenolpyruvate carboxykinase gene, was cloned into a luciferase expression vector and transfected into cultured rat hepatocytes and human hepatoblastoma cells (HepG2) to study the regulation of the transgene by glucagon (cAMP) and insulin. A reporter gene that contained the rat promoter sequence from -493 to +33 was used for comparison. In cultured rat hepatocytes glucagon and its second messenger cAMP increased luciferase expression 4-6-fold over basal levels. Insulin reduced this effect by 40-70%. Luciferase expression was also stimulated by the combination of dexamethasone and cAMP in HepG2 cells and this effect was inhibited by insulin. The phosphoinositide 3-kinase (PI 3-kinase) inhibitor, wortmannin, abolished this action of insulin in cultured rat hepatocytes. The results show that the promoter of the human phosphoenolpyruvate carboxykinase gene mediates the stimulatory action of glucagon and its second messenger cAMP. The inhibitory action of insulin was exerted through the PI 3-kinase pathway in cultured rat hepatocytes.
Viral Gastroenteritis (1981)

ACUTE infectious diarrheal illness is the leading cause of disease and death in many areas of the world. Indeed, by one estimate there were 3 to 5 billion cases of diarrhea accounting for 5 to 10 million deaths in Asia, Africa, and Latin America during the year 1977 to 1978.1 Although the cause of a large proportion of this infectious gastroenteritis remains unknown, recently discovered viral agents have joined certain bacteria and parasites on the list of pathogens involved in serious diarrheal disease worldwide.Acute viral gastroenteritis is an extremely common illness that affects all age groups and occurs in . . .
Airborne Cell Analysis (2000)

A miniaturized analysis system for the study of living cells and biochemical reactions in microdroplets was developed. The technique utilizes an in-house-developed piezoelectric flow-through droplet dispenser for precise reagent supply and an ultrasonic levitator for contactless sample handling. A few-cell study was performed with living primary adipocytes. Droplets (500 nL) containing 3-15 individual cells were acoustically levitated. The addition of beta-adrenergic agonists into the levitated droplet using the droplet dispenser stimulated adipocyte lipolysis, leading to free fatty acid release and a consequent pH decrease of the surrounding buffer. The addition of insulin antagonized lipolysis and hence also the decrease in pH. The changes in pH, i.e., the cell response in the droplet, were followed using a pH-dependent fluorophore continuously monitored by fluorescence imaging detection. An image analysis computer program was employed to calculate the droplet intensities. To counteract droplet evaporation, found to affect the fluorescence intensities, a separate dispenser was used to continually add water, thus keeping the droplet volume constant.