gebhart/patrepeval huggingface dataset:
Hypermethylation of the caveolin‐1 gene promoter in prostate cancer (2001)

CpG sites at the 5' promoter of Cav-1 are more methylated in tumor than in adjacent normal prostate cells. Hypermethylation of the Cav-1 promoter supports the notion that Cav-1 may function as a tumor suppressor gene in prostate cancer and evidence is presented suggesting that methylation status of this gene is not only a marker for cancer but also may be predictive of outcome.
Longevit of British breeds of dog and its relationships with‐sex, size, cardiovascular variables and disease (1999)

The results of a questionnaire provided data about owners' perceptions of the cause of death of over 3000 British dogs. The mean age at death (all breeds, all causes) was 11 years one month, but in dogs dying of natural causes it was 12 years eight months. Only 8 per cent of dogs lived beyond 15, and 64 per cent of dogs died of disease or were euthanased as a result of disease. Nearly 16 per cent of deaths were attributed to cancer, twice as many as to heart disease. Neutered females lived longer than males or intact females, but among dogs dying of natural causes entire females lived slightly longer. In neutered males the importance of cancer as a cause of death was similar to heart disease. Mongrels lived longer than average but several breeds lived longer than mongrels, for example, Jack Russells, miniature poodles and whippets. There was no correlation between longevity and cardiovascular parameters (heart rate, systolic, diastolic, pulse and mean arterial pressure, or the combination of heart rate and pulse pressure) but smaller dogs had longer lifespans. The results also include breed differences in lifespan, susceptibility to cancer, road accidents and behavioural problems as a cause of euthanasia.
Exact analysis of the cache behavior of nested loops (2001)

We develop from first principles an exact model of the behavior of loop nests executing in a memory hicrarchy, by using a nontraditional classification of misses that has the key property of composability. We use Presburger formulas to express various kinds of misses as well as the state of the cache at the end of the loop nest. We use existing tools to simplify these formulas and to count cache misses. The model is powerful enough to handle imperfect loop nests and various flavors of non-linear array layouts based on bit interleaving of array indices. We also indicate how to handle modest levels of associativity, and how to perform limited symbolic analysis of cache behavior. The complexity of the formulas relates to the static structure of the loop nest rather than to its dynamic trip count, allowing our model to gain efficiency in counting cache misses by exploiting repetitive patterns of cache behavior. Validation against cache simulation confirms the exactness of our formulation. Our method can serve as the basis for a static performance predictor to guide program and data transformations to improve performance.
LiteMat: A scalable, cost-efficient inference encoding scheme for large RDF graphs (2015)

The number of linked data sources and the size of the linked open data graph keep growing every day. As a consequence, semantic RDF services are more and more confronted with various "big data" problems. Query processing in the presence of inferences is one them. For instance, to complete the answer set of SPARQL queries, RDF database systems evaluate semantic RDFS relationships (subPropertyOf, subClassOf) through time-consuming query rewriting algorithms or space-consuming data materialization solutions. To reduce the memory footprint and ease the exchange of large datasets, these systems generally apply a dictionary approach for compressing triple data sizes by replacing resource identifiers (IRIs), blank nodes and literals with integer values. In this article, we present a structured resource identification scheme using a clever encoding of concepts and property hierarchies for efficiently evaluating the main common RDFS entailment rules while minimizing triple materialization and query rewriting. We will show how this encoding can be computed by a scalable parallel algorithm and directly be implemented over the Apache Spark framework. The efficiency of our encoding scheme is emphasized by an evaluation conducted over both synthetic and real world datasets.
Glutamate Receptor Anchoring Proteins and the Molecular Organization of Excitatory Synapses (1999)

Ionotropic glutamate receptors are concentrated at postsynaptic sites in excitatory synapses. The cytoplasmic C-terminal tail of certain glutamate receptor subunits interact with specific PDZ domain-containing proteins. NMDA receptor NR2 subunits bind to the PSD-95 family of proteins, whereas AMPA receptor subunits GluR2/3 bind to GRIP. These interactions may underlie the clustering, targeting, and immobilization of the glutamate receptors at postsynaptic sites. By virtue of their multiple protein-binding domains (e.g., three PDZs in PSD-95 and seven PDZs in GRIP), PSD-95 and GRIP can function as multivalent proteins that organize a specific cytoskeletal and signaling complex associated with each class of glutamate receptor. The network of protein-protein interactions mediated by these abundant PDZ proteins is likely to contribute significantly to the molecular scaffold of the postsynaptic density.
Smallest k point enclosing rectangle of arbitrary orientation. (2004)

Given a set of points in 2D, the problem of identi- fying the smallest rectangle of arbitrary orientation, and contain- ing exactly points is studied in this paper. The worst case time and space complexities of the proposed algorithm are and respectively. The algorithm is then used to identify the smallest square of arbitrary orientation containing points in time.
Bandwidth controllable filter using the chirped fiber Bragg gratings (2003)

We demonstrated a novel bandpass filter of which bandwidth can be controlled from 0.1 nm to 2.89 nm using a pair of chirped fiber Bragg gratings and a fiber stretcher based on piezoelectric transducer.
File updating revisited (1986)

Abstract Expositions of sequential master file updating are usually concerned only with insertions of new records, alterations or deletions of existing records and with the joint processing of these transactions. In actual practice other types of file transactions may also be needed, such as printing of (parts of) records, preventing possible alterations of certain records, etc. A general framework for dealing as well with such transactions in one processing run is presented. Simplifications of this framework are possible for random‐access files.
Study of high explosives by optical thermal analysis (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudy of high explosives by optical thermal analysisBilly D. FaubionCite this: Anal. Chem. 1971, 43, 2, 241–247Publication Date (Print):February 1, 1971Publication History Published online1 May 2002Published inissue 1 February 1971https://pubs.acs.org/doi/10.1021/ac60297a003https://doi.org/10.1021/ac60297a003research-articleACS PublicationsRequest reuse permissionsArticle Views91Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Use of the Fused NS4A Peptide−NS3 Protease Domain To Study the Importance of the Helicase Domain for Protease Inhibitor Binding to Hepatitis C Virus NS3-NS4A (2009)

The NS3 protein of hepatitis C virus is unusual because it encodes two unrelated enzymatic activities in linked protease and helicase domains. It has also been intensively studied because inhibitors targeting its protease domain have potential to significantly improve treatment options for those infected with this virus. Many enzymological studies and inhibitor discovery programs have been carried out using the isolated protease domain in complex with a peptide derived from NS4A which stimulates activity. However, some recent publications have suggested that the NS3 helicase domain may influence inhibitor binding and thus suggest work should focus on the full-length NS3-NS4A protein. Here we present the characterization of a single-chain protease in which the NS4A peptide activator is linked to the N-terminus of the NS3 protease domain. This protein behaves well in solution, and its protease activity is very similar to that of full-length NS3-NS4A. We find that this fusion protein, as well as the noncovalent complex of the NS4A peptide with NS3, gives similar Ki values, spanning 3 orders of magnitude, for a set of 25 structurally diverse inhibitors. We also show that simultaneous mutation of three residues on the surface of the helicase domain which has been hypothesized to interact with the protease does not significantly affect enzymatic activity or inhibitor binding. Thus, the protease domain with the NS4A peptide, in a covalent or noncovalent complex, is a good model for the protease activity of native NS3-NS4A.
Sequence CLEAN: a modified deconvolution technique for microwave images of contiguous targets (2002)

High resolution range profiles usually suffer from range sidelobe artifacts which cause reduction in the dynamic range. The sidelobes can be greatly reduced by a deconvolution technique called Coherent CLEAN. The Coherent CLEAN algorithm is based on the assumption that the scene consists of isolated and independent targets. However, many real-life targets are contiguous. Even if we approximate the contiguous targets by very closely spaced point sources, they can hardly be assumed to radiate independently. The sidelobes and the mainlobes of these closely spaced point sources can interact constructively and destructively causing spurious peaks and peak mislocations. These problems are studied and a variation in the existing Coherent CLEAN algorithm, called Sequence CLEAN, is proposed. Sequence CLEAN is found to work well with actual targets.
Blood Viscosity of Psychotics and Nonpsychotics under Stress (1954)

Summary An ultrasonic instrument was used to measure continuously the changes in blood viscosity of 3 groups of experimental subjects. Group 1, 4 neurotic patients showing no overt anxiety, and Group 2, neurotic subjects showing overt anxiety, were subjected to a mild stress. No behavioral or physiological changes were noted in the first group. Behavioral evidence of increased anxiety was associated with the rise in blood viscosity in Group 2. Group 3, 6 psychotic subjects, were tested just prior to the administration of electroshock therapy; these subjects all showed intense anxiety. Significant blood viscosity increases were noted in this group. These findings were found to be consistent with previous studies of changes in blood coagulation in emotional stress. Pertinence of the results to further study of blood viscosity changes under emotional stress, especially in thromboembolic diseases, was suggested.
Interaction of Retinal Pigmented Epithelial Cells and CD4 T Cells Leads to T-Cell Anergy (2007)

RPE cells directly presented extracellular peptides through MHC class II to naive CD4 T cells, leading to an anergic state in the T cells. The anergic T cells survived, but were not immunoregulatory. The ability to modulate T-cell responsiveness in this manner may underlie the contribution of the RPE to immune privilege.
Choose your own viewpoint: A high-quality/low-complexity free-viewpoint 3D visual system (2012)

Choosing one's own viewpoint when watching a video program has long been a desire for viewers. To achieve this goal, view synthesis and depth map generation are two fundamental techniques. View synthesis is a signal processing procedure which creates dense virtual views based on sparse real views. Each object inside a frame is warped to a proper position according to its depth information to form the viewpoint changing perception for viewers. Hence, the correctness of depth map influences the view synthesis quality. To increase the accuracy of depth map, this paper proposes an edge-adaptive block matching scheme cooperated with an unreliable region repairing approach. The former avoid finding local minimum in stereo matching, and the latter repairs the errors caused by occlusion regions. As for view synthesis, this paper proposes a special warping method that can detect errors caused by boundary mismatches of objects between corresponding depth and color images to improve quality of the synthesized view. Besides, we also propose a compensative-filling method that can fix tiny cracks due to round-off errors. Because of these two features, the proposed view synthesis becomes more robust to tolerate errors inside depth maps when compared with previous schemes. Both the depth generation and view synthesis are extremely complex computations. Therefore, this paper also proposes a low-complexity computing technology based on group-of-pixels which increases 30 times of performance for depth map generation, and reduces 60% computation time of view synthesis.
Object oriented programming (OOP) and its relevance to designing intelligent software systems (2003)

The development of large software packages requires not only modularity but also the capability to experiment and change. Such a capability is akin to self-organization characteristics of adaptive systems. It is suggested that computer-aided software engineering (CASE) can benefit from the development retrainable software modules, where both the data structures and the algorithms performing on them are subject to evolutionary change. Such an approach is modeled after the AI (artificial-intelligence) methodology of reasoning by analogy, and it can be naturally implemented through the paradigm of object-oriented programming languages, which provide an exploratory software environment in which changes resulting from feedback to the system are easy to track and implement. The benefits of OOP to major software development areas involved with resource allocation, computer vision, and the service industry are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Seamless multi-reticle photonics (2021)

While Moore's law predicted shrinking transistors would enable exponential scaling of electronic circuits, the footprint of photonic components is limited by the wavelength of light. Thus, future high-complexity photonic integrated circuits (PICs) such as petabit-per-second transceivers, thousand-channel switches, and photonic quantum computers will require more area than a single reticle provides. In our novel approach, we overlay and widen waveguides in adjacent reticles to stitch a smooth transition between misaligned exposures. In SiN waveguides, we measure ultralow loss of 0.0004 dB per stitch, and produce a stitched delay line 23 m in length. We extend the design to silicon channel waveguides, and predict 50-fold lower loss or 50-fold smaller footprint versus a multimode-waveguide-based method. Our approach enables large-scale PICs to scale seamlessly beyond the single-reticle limit.
Processor-efficient parallel solution of linear systems. II. The positive characteristic and singular cases (1992)

For pt.I see Proc. 3rd Ann. ACM Symp. Parallel Algms. Architecture, p. 180-91 (1991). The authors show that over any field, the solution set to a system of n linear equations in n unknowns can be computed in parallel with randomization simultaneously in poly-logarithmic time in n and with only as many processors as are utilized to multiply two n * n matrices. A time unit represents an arithmetic operation in the field. For singular systems the parallel timings are asymptotically as fast as those for non-singular systems, due to the avoidance of binary search in the matrix rank problem, except when the field has small positive characteristic; in that case, binary search is avoided at a somewhat higher processor count measure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Elevated free nitrotyrosine levels, but not protein-bound nitrotyrosine or hydroxyl radicals, throughout amyotrophic lateral sclerosis (ALS)-like disease implicate tyrosine nitration as an aberrant <i>in vivo</i> property of one familial ALS-linked superoxide dismutase 1 mutant (1997)

Mutations in superoxide dismutase 1 (SOD1; EC 1.15.1.1) are responsible for a proportion of familial amyotrophic lateral sclerosis (ALS) through acquisition of an as-yet-unidentified toxic property or properties. Two proposed possibilities are that toxicity may arise from imperfectly folded mutant SOD1 catalyzing the nitration of tyrosines [Beckman, J. S., Carson, M., Smith, C. D. & Koppenol, W. H. (1993) Nature (London) 364, 584] through use of peroxynitrite or from peroxidation arising from elevated production of hydroxyl radicals through use of hydrogen peroxide as a substrate [Wiedau-Pazos, M., Goto, J. J., Rabizadeh, S., Gralla, E. D., Roe, J. A., Valentine, J. S. & Bredesen, D. E. (1996) Science 271, 515-518]. To test these possibilities, levels of nitrotyrosine and markers for hydroxyl radical formation were measured in two lines of transgenic mice that develop progressive motor neuron disease from expressing human familial ALS-linked SOD1 mutation G37R. Relative to normal mice or mice expressing high levels of wild-type human SOD1, 3-nitrotyrosine levels were elevated by 2- to 3-fold in spinal cords coincident with the earliest pathological abnormalities and remained elevated in spinal cord throughout progression of disease. However, no increases in protein-bound nitrotyrosine were found during any stage of SOD1-mutant-mediated disease in mice or at end stage of sporadic or SOD1-mediated familial human ALS. When salicylate trapping of hydroxyl radicals and measurement of levels of malondialdehyde were used, there was no evidence throughout disease progression in mice for enhanced production of hydroxyl radicals or lipid peroxidation, respectively. The presence of elevated nitrotyrosine levels beginning at the earliest stages of cellular pathology and continuing throughout progression of disease demonstrates that tyrosine nitration is one in vivo aberrant property of this ALS-linked SOD1 mutant.
Large scale content distribution protocols (2005)

This paper introduces large scale content distribution protocols, which are capable of scaling to massive numbers of users and providing low delay end-to-end delivery. Delivery of files and static objects is described, with real-time content streaming being outside the scope of this paper. The focus is on solutions provided by the IETF Reliable Multicast Transport Working Group. More precisely, the paper explains FLUTE, ALC and the associated building blocks. Then it discusses how these components are used in the Multimedia Broadcast Multicast Service (MBMS) for 3G systems and in the IP Datacast (IPDC) service for Digital Video Broadcast for Handheld devices (DVB-H).
Curcumin activates the aryl hydrocarbon receptor yet significantly inhibits (-)-benzo(a)pyrene-7R-trans-7,8-dihydrodiol bioactivation in oral squamous cell carcinoma cells and oral mucosa. (2002)

The development of oral squamous cell carcinoma (SCC) shows a positive correlation with the carcinogen exposure that occurs during tobacco and alcohol use. The purpose of this study was to investigate whether the naturally occurring chemopreventive agent, curcumin, modulates expression and function of carcinogen- metabolizing enzymes in human keratinocytes isolated from oral SCC tumors. Dose-response studies demonstrated that curcumin concentrations of >or=25 micro M were cytotoxic for oral SCC cells. Curcumin increased both expression (reverse transcription-PCR analyses) and function (high-performance liquid chromatography determination of ethoxyresorufin metabolism) of cytochrome P-450 (CYP) 1A1 and/or CYP1B1. The aryl hydrocarbon receptor (AhR), which up-regulates a battery of genes associated with carcinogen metabolism, is activated by polycyclic aromatic hydrocarbons such as the tobacco-associated carcinogen benzo(a)pyrene. Electromobility shift assays demonstrated that similar to the established AhR ligand 2,3,7,8,-tetrachlorodibenzo-p-dioxin, curcumin inclusion resulted in AhR nuclear translocation and formation of the transcriptionally active AhR-aryl hydrocarbon receptor nuclear translocator complex. Cellular capacity to bioactivate the tobacco-associated carcinogen (-)-benzo(a)pyrene-7R-trans-7,8-dihydrodiodiol was determined by evaluating conversion of the carcinogenic metabolite diol epoxide to stable tetrols via high-performance liquid chromatography. Results of our metabolism studies showed that curcumin significantly inhibited CYP1A1-mediated benzo(a)pyrene diol bioactivation in both oral SCC cells and intact oral mucosa. Because CYP1A1 is one of the primary carcinogen-activating enzymes in oral mucosa, the use of curcumin as an oral cavity chemopreventive agent could have significant clinical impact via its ability to inhibit carcinogen bioactivation.
Laboratory evaluation of two passive alcohol sensors. (1992)

Passive alcohol sensors are screening devices designed to sample nonintrusively the exhaled breath of a person to determine whether or not it contains alcohol and if so approximately how much. Two production passive alcohol sensors (NPAS passive alcohol sensor and the Life-Loc PBA 2000) were evaluated in a laboratory environment to establish appropriate threshold measurements that indicate probable alcohol impairment. The laboratory evaluation was conducted using both instrument types with 12 drinking subjects. Both sensors were able to identify alcohol in exhaled breath with sufficient accuracy to identify persons with high blood alcohol concentrations (BACs). The accuracy of both sensors was related to the distance from the subject's mouth: the further away they were from a subject's mouth the greater the chance that high BACs would not be detected. Under ideal conditions, it was estimated that the Life-Loc sensor could be expected to correctly detect 80% of drivers at 0.10% BAC (99% at 0.15% BAC) as being impaired while incorrectly identifying only about one in eight drivers with BACs of 0.02% (false positives). In comparison, the NPAS sensor could be expected to correctly detect about 75% of drivers at 0.10% BAC (97% at 0.15% BAC) while incorrectly identifying one in five drivers at 0.02% BAC.