gebhart/patrepeval huggingface dataset:
A fast and generic hybrid simulation approach using C virtual machine (2007)

Instruction Set Simulators (ISSes) are important tools for cross-platform software development. The simulation speed is a major concern and many approaches have been proposed to improve the performance of ISSes. A prevalent technique is compiled simulation, which translates target programs into host instructions. But orders of magnitude of speed deterioration is inevitable since the difference between target and host Instruction Set Architectures (ISAs) can be large. An alternative is to emulate the program without sticking to binary compatibility. The performance problem is solved by using native execution. However, these emulators either require a special programming language, or a given Application Programming Interface (API). Last but not least, it is not trivial to integrate an emulator into a system simulator (which provides devices, external memory, etc., that the embedded programmers do care). In this paper, we propose a fast and generic hybrid simulation approach using virtualization technique to accelerate simulation and simulator-based debugging of C programs. A novel virtual coprocessor (VCP) is introduced as a processing element which executes C functions at high speed. This approach is C89 compliant and compatible with third party libraries and platform dependent code. It is also retargetable and can be integrated with existing ISSes. Two different ISAs are supported at present: MIPS and mAgic DSP. The average execution speed of the coprocessor is about 100 million simulated instructions per second.
Structures of CD200/CD200 Receptor Family and Implications for Topology, Regulation, and Evolution (2013)

CD200 is a widely distributed membrane glycoprotein that regulates myeloid cell activity through its interaction with an inhibitory receptor (CD200R). The interaction is of interest as a target for treating excessive inflammation and for treating leukemia. There are closely related proteins to CD200R that give activating signals making this a "paired receptor." We report X-ray crystallography structures for the inhibitory CD200R, the activating receptor CD200RLa, and a complex between CD200R and CD200. Both CD200 and CD200R contain two Ig-like domains and interact through their NH₂ terminal domains compatible with immunological synapse-like interactions occurring between myeloid cells and other CD200-expressing cells. The failure of the activating receptor to bind CD200 resides in subtle changes around the interface. CD200 has been acquired by herpes viruses to mimic the host interaction. CD200R has evolved rapidly presumably driven by pathogen pressure but it may also be important in homeostasis through interactions with commensal bacteria.
Neoconstitucionalismo en el Ecuador una Mirada al Jurista Ingenuo (2013)

A cinco años de la entrada en vigencia de la Constitución de Montecristi, muchas de las proclamas sobre sus bondades, han tenido una incidencia mucho menos importante en el aspecto práctico. Estamos enfrentados a la evidencia de que la sociedad no ha sufrido la trasformación radical, que se publicita sí ha tenido el ordenamiento jurídico constitucional -algo que es también discutible-. En medio de una intensa propaganda sobre la novedad del neoconstitucionalismo y la separación del pasado, aparece que la mera reforma normativa, incluso acompañada de grandilocuentes exclamaciones, no es medio suficiente para la trasformación social. En cuanto se pretende abstraer el mundo jurídico de los aspectos políticos, se está negando una realidad incontestable.
Learning to Reason: End-to-End Module Networks for Visual Question Answering (2017)

Natural language questions are inherently compositional, and many are most easily answered by reasoning about their decomposition into modular sub-problems. For example, to answer "is there an equal number of balls and boxes?" we can look for balls, look for boxes, count them, and compare the results. The recently proposed Neural Module Network (NMN) architecture implements this approach to question answering by parsing questions into linguistic substructures and assembling question-specific deep networks from smaller modules that each solve one subtask. However, existing NMN implementations rely on brittle off-the-shelf parsers, and are restricted to the module configurations proposed by these parsers rather than learning them from data. In this paper, we propose End-to-End Module Networks (N2NMNs), which learn to reason by directly predicting instance-specific network layouts without the aid of a parser. Our model learns to generate network structures (by imitating expert demonstrations) while simultaneously learning network parameters (using the downstream task loss). Experimental results on the new CLEVR dataset targeted at compositional question answering show that N2NMNs achieve an error reduction of nearly 50% relative to state-of-the-art attentional approaches, while discovering interpretable network architectures specialized for each question.
Production and Screening of Cell Hybrids Producing a Monoclonal Antibody to Human Interferon-  (1981)

Mice and rats were immunized with human lymphoblastoid interferon, a mixture of human leukocyte (interferon-alpha) and human fibroblast (interferon-beta) interferons, and their serum anti-interferon levels measured. Anti-interferon activity was detected in all animals, although the mouse sera had higher titers than the rat sera. The spleens of two mice were removed and used to prepare hybrid myelomas. Anti-interferon activity in tissue culture supernatants was measured using a direct neutralization assay and a clone (NK2) producing antibody to human interferon-alpha (leukocyte) was isolated. The anti-interferon activity of this monoclonal antibody was confirmed using a new indirect immunoprecipitation (IIP) assay, which shows some advantages over the direct neutralization assay. The antibody did not neutralize human interferon-beta (fibroblast) or mouse interferon.
Model of Sarcomeric Ca2+ Movements, Including ATP Ca2+ Binding and Diffusion, during Activation of Frog Skeletal Muscle (1998)

Cannell and Allen (1984. Biophys. J. 45:913-925) introduced the use of a multi-compartment model to estimate the time course of spread of calcium ions (Ca2+) within a half sarcomere of a frog skeletal muscle fiber activated by an action potential. Under the assumption that the sites of sarcoplasmic reticulum (SR) Ca2+ release are located radially around each myofibril at the Z line, their model calculated the spread of released Ca2+ both along and into the half sarcomere. During diffusion, Ca2+ was assumed to react with metal-binding sites on parvalbumin (a diffusible Ca2+- and Mg2+-binding protein) as well as with fixed sites on troponin. We have developed a similar model, but with several modifications that reflect current knowledge of the myoplasmic environment and SR Ca2+ release. We use a myoplasmic diffusion constant for free Ca2+ that is twofold smaller and an SR Ca2+ release function in response to an action potential that is threefold briefer than used previously. Additionally, our model includes the effects of Ca2+ and Mg2+ binding by adenosine 5'-triphosphate (ATP) and the diffusion of Ca2+-bound ATP (CaATP). Under the assumption that the total myoplasmic concentration of ATP is 8 mM and that the amplitude of SR Ca2+ release is sufficient to drive the peak change in free [Ca2+] (Delta[Ca2+]) to 18 microM (the approximate spatially averaged value that is observed experimentally), our model calculates that (a) the spatially averaged peak increase in [CaATP] is 64 microM; (b) the peak saturation of troponin with Ca2+ is high along the entire thin filament; and (c) the half-width of Delta[Ca2+] is consistent with that observed experimentally. Without ATP, the calculated half-width of spatially averaged Delta[Ca2+] is abnormally brief, and troponin saturation away from the release sites is markedly reduced. We conclude that Ca2+ binding by ATP and diffusion of CaATP make important contributions to the determination of the amplitude and the time course of Delta[Ca2+].
Self‐Organized Glycoclusters Along DNA: Effect of the Spatial Arrangement of Galactoside Residues on Cooperative Lectin Recognition (2004)

We describe herein the relationship between the spatial arrangement of self-organized galactose clusters and lectin recognition. beta-Galactose-modified deoxyuridine phosphoramidite was synthesized and applied to solid-phase synthesis to provide 18-, 20-, and 22-mers of site-specifically galactosylated oligodeoxynucleotides (Gal-ODNs). These Gal-ODNs were self-organized through hybridization with the corresponding 18-, 20-, and 22-mers of half-sliding complementary ODNs (hsc-ODNs) to give periodic galactoside clusters. The self-organization of ODNs was confirmed by size exclusion chromatography and gel electrophoresis. The binding of the Gal-clusters to the FITC-labeled RCA(120) lectin was analyzed by monitoring the change in fluorescence intensity. The assembly of 20-mer Gal-ODN with the 20-mer hsc-ODN was strongly and cooperatively recognized by the lectin. The 18-mer assembly was bound more weakly and less cooperatively, and the 22-mer assembly was minimally bound to the lectin. RCA(120) lectin recognized not only the density of galactoside residues, but also the spatial arrangement. The size of the Gal cluster was estimated from the association constant of Gal-ODN with hsc-ODN. The relationship between lectin-recognition and Gal-cluster size is also discussed.
Intramolecular Methylation of an Allyl Sulfone via Lithium Alkoxyaluminate; Application to the Enantioselective Synthesis of the CD Ring of Vitamin D<sub>3</sub> (2012)

Alcohol-directed intramolecular methylation of an enantiopure allyl sulfone using AlMe(3) provides a trans-hydrindane CD ring alcohol. The substrate cis-CD ring allyl sulfone alcohol is prepared via intramolecular allyl sulfonyl anion addition to aldehyde using Ba(OH)(2).
Concurrent Control of Mobility and Communication in Multirobot Systems (2017)

We develop a hybrid system architecture that enables a team of mobile robots to complete a task in a complex environment by self-organizing into a multihop ad hoc network and solving the concurrent communication and mobility problem. The proposed system consists of a two-layer feedback loop. An outer loop performs infrequent global coordination and a local inner loop determines motion and communication variables. This system provides the lightweight coordination and responsiveness of decentralized systems while avoiding local minima. This allows a team to complete a task in complex environments while maintaining desired end-to-end data rates. The behavior of the system is evaluated in experiments that demonstrate: 1) successful task completion in complex environments; 2) achievement of equal or greater end-to-end data rates as compared to a centralized system; and 3) robustness to unexpected events such as motion restriction.
Pathogenesis and treatment modalities of localized scleroderma (2010)

Localized scleroderma is a chronic inflammatory disease primarily of the dermis and subcutaneous fat that ultimately leads to a scar-like sclerosis of connective tissue. The disorder manifests as various plaques of different shape and size with signs of skin inflammation, sclerosis, and atrophy. This is a relatively rare inflammatory disease characterized by a chronic course, unknown etiology, and insufficiently clear pathogenesis. Many factors may influence its appearance: trauma, genetic factors, disorders of the immune system or hormone metabolism, viral infections, toxic substances or pharmaceutical agents, neurogenic factors, and Borrelia burgdorferi infection. Various therapeutic modalities are being used for the treatment of localized scleroderma. There is no precise treatment scheme for this disease. A majority of patients can be successfully treated with topical pharmaceutical agents and phototherapy, but some of them with progressive, disseminated, and causing disability localized scleroderma are in need of systemic treatment. The aim of this article is not only to dispute about the clinical and morphological characteristics of localized scleroderma, but also to present the newest generalized data about the possible origin, pathogenesis, and treatment modalities of this disease.
Combination of fluconazole and urea in a nail lacquer for treating onychomycosis (2005)

Generally, a favourable response to local treatment may be anticipated only if the distal two-thirds of the nail is affected. In view of this, and despite the fact that most of the patients were severely affected with involvement of the proximal third of the nail, the response to local therapy was appreciable.
Ultrasound-guided large-core needle biopsies of breast lesions: analysis of 962 cases to determine the number of samples for reliable tumour classification (2004)

The objective of this one-institutional study was to determine the number of large-core needle biopsies (LCNB), under three-dimensional ultrasound (3D-US) validation, that are sufficient to obtain a reliable histological diagnosis of a sonographically detectable breast lesion. Over an 28-month period, 962 sonographically guided LCNB were performed under 3D-US validation to assess 962 breast lesions. All biopsies were carried out with an automated core biopsy device fitted with 14-gauge (22 mm excursion) needles. Data of 962 biopsied breast lesions were gathered. Surgical follow-up was available for 659 lesions. Breast malignancies were diagnosed by ultrasound-guided LCNB with a sensitivity of 98.2% by performing three cores per lesion. In few cases, the open surgical specimen revealed the presence of invasive carcinomas in contrast to initial LNCB-based classification as ductal carcinomas in situ (DCIS, 11 lesions), lobular carcinoma in situ (one lesion), and atypical ductal hyperpasia (one lesion). Owing to disagreement between classification based on breast-imaging and histological findings, eight of these tumours were subsequently excised. Of the lesions that were removed at the patients' requests despite benign LCNB diagnosis, two were infiltrating carcinoma and one a DCIS. We demonstrate that three 3D-US-guided percutaneous core specimens are sufficient to achieve tissue for a reliable histological assessment of sonographically detectable breast lesions and allow the detection of malignancies with high sensitivity and low rate of false-negative diagnoses.
Force Tolerances of Hybrid Nanodevices (2002)

We have created hybrid devices consisting of nanoscale fabricated inorganic components integrated with and powered by a genetically engineered motor protein.1 We wish to increase the assembly yield and lifetime of these devices through identification, measurement, and improvement of weak internal bonds. Using dynamic force spectroscopy, we have measured the bond rupture force of (histidine)6 on a number of different surfaces as a function of loading rate. The bond sizes, lifetimes, and energy barrier heights were derived from these measurements. We compare the (His)6−nickel bonds to other bonds composing the hybrid device and describe preliminary measurements of the force tolerances of the protein itself. Pathways for improvement of device longevity and robustness are discussed.
Centaurin-α1-Ras-Elk-1 Signaling at Mitochondria Mediates β-Amyloid-Induced Synaptic Dysfunction (2013)

Alzheimer's disease is thought to be caused by β-amyloid peptide (Aβ)-dependent synaptic dysfunction. However, the signaling pathways connecting Aβ and synaptic dysfunction remain elusive. Here we report that Aβ transiently increases the expression level of centaurin-α1 (CentA1) in neurons, which induces a Ras-dependent association of Elk-1 with mitochondria, leading to mitochondrial and synaptic dysfunction in organotypic hippocampal slices of rats. Downregulation of the CentA1-Ras-Elk-1 pathway restored normal mitochondrial activity, spine structural plasticity, spine density, and the amplitude and frequency of miniature EPSCs in Aβ-treated neurons, whereas upregulation of the pathway was sufficient to decrease spine density. Elevations of CentA1 and association of Elk-1 with mitochondria were also observed in transgenic mice overexpressing a human mutant form of amyloid precursor protein. Therefore, the CentA1-Ras-Elk-1 signaling pathway acts on mitochondria to regulate dendritic spine density and synaptic plasticity in response to Aβ in hippocampal neurons, providing new pharmacological targets for Alzheimer's disease.
Color image enhancement algorithm based on logarithmic transform coefficient histogram (2011)

This paper presents a new technique for color enhancement based on manipulation of the histogram of logarithmic transform coefficients. The proposed technique is simple but more effective than some existing techniques in most case. This method is based on the properties of the histogram of DCT coefficients, also use the fact that the relationship between stimulus and perception is logarithmic and can afford a marriage between enhancement qualities and computational efficiency. A human visual system-based quantitative measurement of image contrast improvement is also used to determine the optimal parameters for the algorithm. A number of experimental results are presented to illustrate the performance of the proposed algorithm.
ABSTRACT: Large Scale Deepwater Sediment Remobilisation : examples from North Sea 3D Seismic and Outcrop (2002)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Effect of renal impairment on the pharmacokinetics of the dipeptidyl peptidase‐4 inhibitor linagliptin <sup>*</sup> (2011)

Renal impairment has only a minor effect on linagliptin pharmacokinetics. Consequently, there will be no need for adjusting the linagliptin dose in renally impaired patients with T2DM.
Nonlinear Behavior of Nickel Dissolution in Sulfuric Acid in a Cathode-Anode Cell Configuration: Effect of Cathode Area (2016)

We investigate the nonlinear behavior of anodic nickel dissolution reaction coupled to hydrogen ion reduction for different cathode sizes. In a standard three-electrode cell, transpassive nickel dissolution in sulfuric acid exhibits bistable and oscillating current states when an external resistance is added in series to the working electrode. We observed bistable and oscillating currents without any external resistance in a two-electrode (cathode-anode) cell. The oscillations are interpreted by the linear polarization resistance of the cathode reaction, hydrogen reduction on nickel surface; this resistance exhibited a maximum against cathode size. Those cathodes with resistances close to the maximum stimulated strong oscillations in the cell current. Theoretical considerations implied that such maximum differential resistance cannot be interpreted with elementary Butler-Volmer kinetics but require complex, multi-route reactions. Numerical model simulating coupled anode and cathode reactions reproduced the salient dynamical features of the cathode-anode cell configuration.
Roles of cytotoxic T lymphocytes in the pathogenesis of drug eruption (2015)

Drug eruption is a common delayed hypersensitivity reaction. Its pathogenesis can be usually explained by three theories, including haptens, pro-haptens and pharmacological interaction with immune receptors (the p-i concept). Drug-specific cytotoxic T lymphocytes (CTLs) play an important role in the pathological process of drug eruption. In classic theories, CTLs are commonly recognized as CD8 + T cells, but new evidences indicate that other immune cells with different phenotypes, such as CD4 + T cells, also have cytotoxicity. In the development of drug eruption, these immune cells are specifically activated to contact with target cells followed by the release of cytotoxins. Target cells can provide a favoring environment for the metabolism of drugs and occurrence of inflammation and apoptosis, and assist CTLs to function. In addition, the danger signal hypothesis suggests that danger signals play an important role in immune activation, which enriches our knowledge on the pathogenesis of drug eruption.


Key words: 
Drug eruptions; T-lymphocytes, cytotoxic; Risk factors; CD8-positive T-lymphocytes; CD4-positive T-lymphocytes
Powering mm-Size Wireless Implants for Brain-Machine Interfaces (2011)

Over the last couple of years, Brain-Machine Interfaces (BMI) based on microelectrode arrays have been shown to have the potential to substantially improve the quality of life for people suffering from debilitating conditions such as spinal cord injuries or limb loss. One of the most critical parts of a BMI system is the neural sensor. It is ideally implanted underneath the skull, reads out neural signals from the brain and transmits them wirelessly to a receiver outside the skull. The requirements on the electronics of such a sensor are extremely stringent, especially with respect to size and power consumption. Ideally, the overall size of the implanted sensor node is limited by the size of the sensor itself, rather than the electronics and the power source. <p>This work investigates powering options for implants of sizes ranging from 10 mm by 10 mm down to 1 mm by 1 mm. Wireless power transfer is identified as the most promising option of doing so and is investigated in detail. It is shown, that for a given implant antenna size, an optimum combination of external antenna and frequency of operation exists that minimizes the overall link loss. In combination with limitations on the maximum transmit and received power due to health concerns, the maximum power available to mm-size implants as a function of size is derived. Two different AC-to-DC conversion circuit topologies, covering the expected input power and frequency range, are analyzed in detail and design guidelines for each are given. <p>Finally, a 1 mm^3 proof-of-concept implementation of a wirelessly powered neural transponder is presented. It was tested in air and in animal and provides enough extra DC power to power a neural sensor front-end while supporting a 2 Mbps radio link. The presented tag is the smallest wireless neural tag reported to date and prooves the feasibility of remotely powered mm-size wireless neural implants.
Crystallization and preliminary X-ray diffraction analysis of diaminopimelate epimerase from<i>Escherichia coli</i> (2009)

Diaminopimelate (DAP) epimerase (EC 5.1.1.7) catalyzes the penultimate step of lysine biosynthesis in bacteria and plants, converting L,L-diaminopimelate to meso-diaminopimelate. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DAP epimerase from Escherichia coli are presented. Crystals were obtained in space group P4(1)2(1)2 and diffracted to 2.0 A resolution, with unit-cell parameters a = b = 89.4, c = 179.6 A. Molecular replacement was conducted using Bacillus anthracis DAP epimerase as a search model and showed the presence of two molecules in the asymmetric unit, with an initial R(free) of 0.456 and R(work) of 0.416.