gebhart/patrepeval huggingface dataset:
Web ontology segmentation (2006)

Ontologies are at the heart of the semantic web. They define the concepts and relationships that make global interoperability possible. However, as these ontologies grow in size they become more and more difficult to create, use, understand, maintain, transform and classify. We present and evaluate several algorithms for extracting relevant segments out of large description logic ontologies for the purposes of increasing tractability for both humans and computers. The segments are not mere fragments, but stand alone as ontologies in their own right. This technique takes advantage of the detailed semantics captured within an OWL ontology to produce highly relevant segments. The research was evaluated using the GALEN ontology of medical terms and procedures.
Motion-compensated temporal filtering for denoising in video encoder (2004)

A DCT-domain temporal filtering in a video encoder is presented. It is proven that the multiplication of every DCT coefficient in an inter block with a proper weight is equivalent to motion-compensated temporal filtering in the spatial domain for the inter block. Thus, a temporal filtering in the DCT-domain is proposed, which determines properly the weight by using an effective noise estimation scheme.
Genistein elicits pleiotropic molecular effects on head and neck cancer cells. (2001)

Genistein (4,5,7-trihydroxyisoflavone) has been reported to induce cell cycle arrest and apoptosis in different cancer cell lines in vitro and to show antitumor activity against a variety of tumors in animal models. We have previously reported (S. A. Alhasan et al., Nutr. Cancer, 34:12-19, 1999; S. A. Alhasan et al., Int. J. Oncol., 16: 333-338, 2000) that genistein induces cell cycle arrest and apoptosis by up-regulating p21(WAF1) and Bax, and down-regulating cyclin B1 and Bcl-2 in a head and neck cancer cell line. However, the precise molecular mechanism(s) by which genistein elicits its effects on head and neck cancer cells still remains to be elucidated. In the present study, we report that genistein induces several specific molecular changes in head and neck cancer cells, such as down-regulation of c-erbB-2 expression, down-regulation of MMP-2 and MMP-9 secretion, inhibition of tumor cell invasion and down-regulation of nuclear factor-kappaB DNA binding activity. In addition, genistein inhibited the levels of phosphorylated Akt and the expression of 14-3-3 protein. Moreover, genistein induces telomere shortening in treated cells without affecting telomerase activity in vitro. We also observed that genistein inhibits the translocation of telomerase catalytic subunit [human telomerase reverse transcriptase (hTERT)] to the nucleus, which may result in telomere shortening, although the activity of telomerase is unaffected, along with the inhibition of metaphase spread of chromosomes. From these results, together with our previously published reports, (S. A. Alhasan et al., Nutr. Cancer, 34: 12-19, 1999; S. A. Alhasan et al., Int. J. Oncol., 16: 333-338, 2000) we conclude that genistein elicits pleiotropic molecular changes that resulting in the inhibition of cell growth and the induction of apoptotic cell death of head and neck cancer cells, which suggests that genistein may be useful as a chemotherapeutic and/or chemopreventive agent for head and neck cancer.
Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line. (1992)

Methylation patterns of specific genes have been studied by polymerase chain reaction and found to undergo dynamic changes in the germ line and early embryo. Some CpG sites are methylated in sperm DNA and unmodified in mature oocytes, indicating that the parental genomes have differential methylation profiles. These differences, however, are erased by a series of early embryonic demethylation and postblastula remodification events, which serve to reestablish the basic adult methylation pattern prior to organogenesis. During gametogenesis, all of these sites are unmethylated in primordial germ cells but eventually become remodified by 18.5 days postcoitum in both males and females. The final methylation profile of the mature germ cells is then formed by a multistep process of site-specific demethylation events. These results form a basis for the understanding of the biochemical mechanisms and role of DNA methylation in embryonic development.
Biophysical aspects of epithelial adhesion to stroma. (1978)

The affinity of various corneal boundary surfaces, such as mucus-coated epithelium, demucinized epithelium, denuded basement membrane, and keratectomized cornea, to water and hydrophobic liquids was determined by contact angle goniometry on enucleated rabbit eyes. The mucus-coated surface and the bare stromal surface without the basement membrane were found to be more hydrophilic than the surfaces of the epithelium and the basement membrane. If at least one of the surfaces forming a joint boundary is hydrophilic, then conditions become favorable for the accumulation of water at the interface, forming a weak boundary layer that is detrimental to adhesion, due to its low shear resistance. Thus, even in a normal eye, mucus does not adhere strongly to the epithelium; when the basement membrane is damaged or absent, the epithelium does not adhere well to the stroma. External dehydrating factors such as hyperosmotic conditions favor adhesion, whereas edematic conditions have an adhesive (adhesion-decreasing) effect. Experimental ophthalmic solutions containing macromolecules at hyperosmotic concentrations may demonstrate a therapeutic effect when applied to eyes with recurrent epithelial erosion or other epithelial trauma.
Local immunity in ulcerative colitis: evidence for defective secretory IgA production. (1988)

To investigate local humoral immunity in ulcerative colitis (UC), immunoglobulin (Ig) contents and net Ig production in vitro was assessed using organ cultures of colonic biopsies from 21 patients with quiescent disease and 11 controls. Ig was estimated by enzyme linked immunoassay (ELISA) for IgA, secretory IgA (sIgA), IgM, and IgG. In parallel, numbers of IgA plasma cells were estimated by indirect immunoperoxidase staining of tissue sections for IgA. IgA was the dominant Ig isotype found pre-existing in colonic mucosae, and secreted in vitro. In UC patients, preformed tissue IgA and IgA produced in vitro were significantly increased compared with controls. There was no concomitant increase in amounts of sIgA synthesised in culture, however, although numbers of IgA plasma cells were increased in UC patients by an amount comparable with the increased in vitro IgA production. These results directly show a dysfunction of transepithelial IgA secretion in quiescent ulcerative colitis. Despite a significantly raised concentration of tissue IgG in UC patients, little was produced in vitro in patient and control groups alike, suggesting that mucosal IgG was serum derived, and not linked to local IgA production.
Albumin Storage Proteins in the Protein Bodies of Castor Bean (1978)

Of the total protein in the protein bodies of castor bean (Ricinus communis L.), approximately 40% is represented by a group of closely related albumins localized in the matrix of the organelle. This group of albumins has a sedimentation value of 2S and is resolved into several proteins of molecular weight around 12,000 daltons by sodium dodecyl sulfate-acrylamide gel electrophoresis. It has a high content of glutamate/glutamine and undergoes rapid degradation during the early stage of germination. In view of the abundance and ubiquitous occurrence of albumins in various seeds, we suggest that albumins, in addition to globulins, glutelins, and prolamines, are important storage proteins in seeds.
CMOS VLSI Potentiostat for Portable Environmental Sensing Applications (2010)

This paper reports an integrated CMOS potentiostat for detection of heavy metal ions in water and other solvents based on electrochemical sensing. The proposed potentiostat features a low-input impedance, high sensitivity, high gain and low power transimpedance amplifier front end, with programmable control of electrode potential, thus facilitating continuous bidirectional measurement of reduction-oxidation (redox) current in a potentiostat for cyclic voltammetry (CV) experiment. For proof of concept, we use the proposed integrated potentiostat to perform CV on a reference ferricyanide (K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> Fe(CN) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> ) using external microelectrodes. Results compared with standard benchtop potentiostat confirm microelectrode behavior with accurate estimate of redox potential with varying redox currents proportional to the ferricyanide concentration.
Non‐producer human cells induced by murine sarcoma virus (1975)

Non-produces (NP) human cells were isolated from transformed foci induced by the Kirsten mouse sarcoma virus. These morphologically altered NP cells produced neither infectious virus nor complement-fixing antigens of the murine sarcoma-leukemia virus complex. However, the sarcoma virus genome could be rescued from these NF cells by co-cultivation with cells carrying "helper" Kirsten mouse leukemia virus or Woolly Monkey leukemia virus. The possible usefulness of these cells in efforts designed to detect covert or repressed RNA tumor viruses in various animal and human tissues is discussed.
Scale Driven Convolutional Neural Network Model for People Counting and Localization in Crowd Scenes (2019)

Counting and localization of people in videos consisting of low density to high density crowds encounter many key challenges including complex backgrounds, scale variations, nonuniform distributions, and occlusions. For this purpose, we propose a scale driven convolutional neural network (SD-CNN) model, which is based on the assumption that heads are the dominant and visible features regardless of the density of crowds. To deal with the problem of different scales of heads in different regions of the videos, we annotate a set of heads in random locations of the videos to develop a scale map representing the mapping of head sizes. We then extract scale aware proposals based on the scale map which are fed to the SD-CNN model acting as a head detector. Our model provides a response matrix rendering accurate head positions via nonmaximal suppression. For experimental evaluations, we consider three standard datasets presenting low density to high density crowd scenes. Our proposed SD-CNN model outperforms the state-of-the-art methods in terms of both frame-level and pixel-level analyses.
Baculovirus gene ME53, which contains a putative zinc finger motif, is one of the major early-transcribed genes (1993)

We have been investigating the first viral genes to be transcribed in Spodoptera frugiperda cells after the infection with Autographa california nuclear polyhedrosis virus in order to identify regulatory proteins required for the activation of early and/or late gene transcription. By screening a cDNA library from polyadenylated RNA transcribed at 1 h postinfection, we identified a gene which is designated ME53. This newly identified gene is located upstream of the late p74 gene and forms a divergent promoter unit with the immediate-early gene IE0. The determination of the nucleotide sequence of ME53 has revealed an open reading frame encoding a gene product of 53 kDa. Furthermore, the sequence data suggest a putative DNA binding motif, a zinc finger, whose functional significance has yet to be shown. Transcription of ME53 does not require previous viral protein synthesis, and during infection, the level of promoter activity seems to be independent of trans-acting viral factors, as suggested by transient expression studies.
Involvement of IFN-<i>gamma</i> in <i>Bacillus Calmette-Guérin</i>-induced but not in tumor-induced sensitization to TNF-induced lethality. (1995)

In healthy mice, murine (m) TNF is fairly lethal, whereas human (h) TNF (a selective murine TNF-R55 agonist) is rather harmless. However, we and others observed that mice suffering from a bacterial infection, such as Bacillus Calmette-Guérin (BCG), or bearing i.m. some types of tumor, develop a hypersensitivity to the IL-6-inducing and lethal properties of hTNF. This is a cardinal problem as it severely limits the potential use of hTNF-R55-specific agonists for systemic treatment of human cancer. Using mice carrying a targeted disruption in the gene encoding the IFN-gamma receptor (IFN-gamma Ro/o), we here report that endogenous IFN-gamma plays a crucial role in the development of TNF hypersensitivity during BCG infection. Indeed, both the lethality and the IL-6 induced by hTNF were drastically reduced in IFN-gamma Ro/o mice as compared with control mice. These results demonstrate that the enhancement of TNF effects is at least an equally important mechanism by which IFN-gamma contributes to BCG-induced hypersensitivity as the previously described augmentation of TNF production. Experiments in athymic nude mice, either depleted of NK cells or not, revealed that the latter cell population is an important source of the sensitizing IFN-gamma during BCG infection. In contrast, IFN-gamma Ro/o mice were as susceptible as control mice to the sensitizing effects of tumors. mTNF, which interacts with both mTNF-R55 and mTNF-R75 and causes lethality on its own, is as toxic in IFN-gamma Ro/o mice as in wt control mice; this means that TNF-induced IFN-gamma does not play a role in mTNF-induced lethality.
A low power digital beamformer for handheld ultrasound systems (2001)

The digital part of a low power single chip digital beamformer for use in low-cost handheld ultrasound imaging systems is presented. To ensure lowest power dissipation for battery operated systems, a quantitative optimization strategy from system down to physical layout level was employed. A cascadable test chip comprising a single processing channel was realized in a 0.5 µm CMOS technology. Operating at 40 MHz the digital part dissipates 25mW from a dual 1.8 V/3.3 V power supply.
Probabilistic, modular and scalable inference of typestate specifications (2011)

Static analysis tools aim to find bugs in software that correspond to violations of specifications. Unfortunately, for large and complex software, these specifications are usually either unavailable or sophisticated, and hard to write. This paper presents ANEK, a tool and accompanying methodology for inferring specifications useful for modular typestate checking of programs. In particular, these specifications consist of pre and postconditions along with aliasing annotations known as access permissions. A novel feature of ANEK is that it can generate program specifications even when the code under analysis gives rise to conflicting constraints, a situation that typically occurs when there are bugs. The design of ANEK also makes it easy to add heuristic constraints that encode intuitions gleaned from several years of experience writing such specifications, and this allows it to infer specifications that are better in a subjective sense. The ANEK algorithm is based on a modular analysis that makes it fast and scalable, while producing reliable specifications. All of these features are enabled by its underlying probabilistic analysis that produces specifications that are very likely . Our implementation of ANEK infers access permissions specifications used by the PLURAL [5] modular typestate checker for Java programs. We have run ANEK on a number of Java benchmark programs, including one large open-source program(approximately 38K lines of code), to infer specifications that were then checked using PLURAL. The results for the large benchmark show that ANEK can quickly infer specifications that are both accurate and qualitatively similar to those written by hand, and at 5% of the time taken to manually discover and hand-code the specifications.
Multimode Strong Coupling in Superconducting Cavity Piezoelectromechanics (2016)

High-frequency mechanical resonators subjected to low thermal phonon occupancy are easier to be prepared to the ground state by direct cryogenic cooling. Their extreme stiffness, however, poses a significant challenge for external interrogations. Here we demonstrate a superconducting cavity piezoelectromechanical system in which multiple modes of a bulk acoustic resonator oscillating at 10 GHz are coupled to a planar microwave superconducting resonator with a cooperativity exceeding 2×10^{3}, deep in the strong coupling regime. By implementation of the noncontact coupling scheme to reduce mechanical dissipation, the system exhibits excellent coherence characterized by a frequency-quality-factor product of 7.5×10^{15} Hz. Interesting dynamics of classical temporal oscillations of the microwave energy is observed, implying the coherent conversion between phonons and photons. The demonstrated high-frequency cavity piezoelectromechanics is compatible with superconducting qubits, representing an important step towards hybrid quantum systems.
Simulation of light scattering from Brownian particles (2015)

This project is a computational exploration of the light scattering from Brownian particles. We simulate laser light scattering to produce fluctuating light intensity at a detector located in the far-field. By analyzing the statistical properties of this intensity fluctuation, and knowing physical parameters of the system, we can deduce the size of the scattering particles. The computer simulation is in excellent agreement with theory.
Effect of spironolactone on endothelial dysfunction in rheumatoid arthritis (2008)

The study suggests that, in RA, endothelial dysfunction is part of the disease process and treatment with spironolactone improves both endothelial dysfunction and inflammatory disease activity in RA.
Predicated software pipelining technique for loops with conditions (2002)

An effort to formalize the process of software pipelining loops with conditions is presented. A formal framework for scheduling such loops, based on representing sets of paths by matrices of predicates, has been proposed. Usual set operations and relationships may then be applied to such matrices. Operations of a loop body are placed into a single schedule with the flow of control implicitly encoded in predicate matrices. An algorithm that generates loop code from such an encoded schedule has been described. The framework is supported by a concrete proposed technique that iteratively parallelize loops, as well as with heuristics driven by data dependencies to efficiently shorten loop execution. Preliminary experimental results of our prototype implementation prove that the proposed framework, technique, and heuristics produce efficient code at acceptable cost.
Transmission at different scales (2015)

Abstract The term ‘transmission’ defines infectious disease. Respiratory viruses such as influenza are airborne; diseases such as HIV and hepatitis are transmitted through direct, usually sexual, exchange of bodily fluids; water-borne diseases such as cholera can survive in the environment; and vector-borne pathogens have evolved to use other organisms, especially blood-sucking insects and mites, to travel from one host to another. ‘Transmission at different scales’ considers the filters for encounter and compatibility, mathematical modelling of epidemic dynamics, and the key factors of virulence, resistance, and tolerance.
The Influence of Potassium Ion on the Electrodeposition and Electrochemistry of Electrolytic Manganese Dioxide (1992)

Electrolytic manganese dioxide (EMD) has been prepared with varying levels of incorporated K+, in the range 54 to 5150 ppm K, by varying the amount of K+ in the electrolyte. Higher acid concentrations or higher current densities decrease the amount of incorporated K+. X‐ray diffraction patterns reveal the presence of an phase (containing potassium) as a minor component along with the usual . Cyclic voltammograms in 9.0 mol dm−3 show that the Mn(IV) reduction peaks shift to more negative potentials while the peak currents decrease with increasing K+, reflecting the increased levels of in the EMD. Chronopotentiometry reveals that voltages (corrected for iR loss) measured during reduction at 0.02 A g−1 are lower for EMDs containing > 590 ppm K, consistent with the presence of in the EMDs. Potassium levels ≤ 590 ppm K do not prima facie effect the electrochemical behavior of EMD under the conditions of this study.
Two-Dimensional Numerical Optimization of MIS Solar Cell on n-Type Silicon (2008)

The studies on metal oxides and mixed system have shown, that some of them form a negative fixed charge at the interface when deposited on silicon substrate. After deposition of dielectric layers with negative fixed charge on p-type silicon substrate an inversion layer is formed, leading to a back surface field for the minority carriers and thereby reducing the surface recombination velocity. The experiments with metal-insulator-semiconductor solar cells on n-type silicon, using (Al2O3)x(TiO2)1-x as a dielectric with a negative fixed charge are under way. In this paper, our two-dimensional device simulator MINIMOS-NT is applied for the optimization of these novel devices. The impact of various cell parameters, such as the spacing between the contact metal fingers, the substrate resistivity, and the negative fixed charge density) on the cell’s current-voltage (I-V) characteristics is investigated.
Molecular Imaging of Cancer with Radiolabeled Peptides and PET (2012)

Radiolabeled peptides hold promise for diagnosis and therapy of cancer as well as for early monitoring of therapy outcomes, patient stratification, etc. This manuscript focuses on the development of peptides labeled with 18F, 64Cu, 68Ga and other positron-emitting radionuclides for PET imaging. The major techniques for radionuclide incorporation are briefly discussed. Then, examples of positron-emitting peptides targeting somatostatin receptors, integrins, gastrin-releasing peptide receptors, vasointestinal peptide receptors, melanocortin 1 receptors and others are reviewed.
Selective Acetylation of Berbin-8-one. Synthesis of 2-Methoxyberbine (1993)

In the presence of excess aluminum chloride, berbin-8-one (1) could be selectively acetylated at the C-2 position to give 2-acetylberbin-8-one (2) in good yield. In fact this exclusive orientation was due to a complex between the amide carbonyl and the Lewis acid which deactivated the aromatic ring D for electrophilic substitution. Further chemical degradation of the acetyl group afforded the corresponding phenol derivative (3) which was converted to 2-methoxyberbin-8-one (4). Reduction of this latter gave finally 2-methoxyberbine (5). Spectral data comparison of compound (4) and 3-methoxyberbin-8-one permitted us to conclude unambiguously in favour of the C-2 orientation of the acetylation
Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation (2012)

Genome diversity in L. casei has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a L. casei supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like L. casei.
<i>SYNGAP1</i> encephalopathy (2018)

<i>SYNGAP1</i> mutations cause a generalized DEE with a distinctive syndrome combining epilepsy with eyelid myoclonia with absences and myoclonic-atonic seizures, as well as a predilection to seizures triggered by eating.