gebhart/patrepeval huggingface dataset:
Performance of Runtime Optimization on BLAST (2005)

Optimization of a real world application BLAST is used to demonstrate the limitations of static and profile-guided optimizations and to highlight the potential of runtime optimization systems. We analyze the performance profile of this application to determine performance bottlenecks and evaluate the effect of aggressive compiler optimizations on BLAST. We find that applying common optimizations (e.g. O3) can degrade performance. Profile guided optimizations do not show much improvement across the board, as current implementations do not address critical performance bottlenecks in BLAST. In some cases, these optimizations lower performance significantly due to unexpected secondary effects of aggressive optimizations. We also apply runtime optimization to BLAST using the ADORE framework. ADORE is able to detect performance bottlenecks and deploy optimizations resulting in performance gains up to 58% on some queries using data cache prefetching.
Increased Cytosine DNA-Methyltransferase Activity During Colon Cancer Progression (1993)

Further studies are needed to determine whether this abnormal methylation capacity plays a role in establishing the abnormal DNA methylation patterns seen in human malignancies.
Evaluation of Tampon as a Suitable Self Sampling Device for Detection of HPV mRNA from Cervical Cells - A Preliminary Report (2008)

Background: In low resource settings screening by cervical cytology is often not implemented. This failure of cytological screening in the less developed world is partly due to the logistical problems inherently part of any speculum collected specimen program. It is hoped that HPV detection on self-collected specimens which does not demand the use of speculums, will become a valuable primary screening test in both developed and developing countries. Self-collection of samples for human papillomavirus (HPV) testing is also a feasible alternative method for women who decline to participate in population based cervical cancer screening programs. Objectives: This study is performed to prove the principle of tampon collection to detect high risk HPV mRNA, using the PreTect HPV-Proofer, in patients with cervical cancer.Materials and Methods: 45 patients at the Academic Hospital in Pretoria, South Africa, with newly diagnosed cervical cancer have been sampled so far. Samples have been collected with tampons inserted for one hour and with cervix brushes. After the sampling (and preparation of PAP smears) both brushes and tampons were placed in vials with PreTect TM for cell preservation and shipped to NorChip AS, Norway for analysisThe samples have been analysed with the PreTect HPV-Proofer assay detecting E6/E7 mRNA from the 5 high risk HPV types 16, 18, 31, 33 and 45.Results: Of the 45 sets of samples 43 had concordant results. In one case the internal control for sample quality was negative and also no HPV was detected in the brush sample, while the tampon was HPV positive and in one case HPV-16 was detected in the tampon sample, but not in the brush sample.Conclusions: This study demonstrates that tampon collection and mRNA based testing is feasible for women who for various reasons are not included in any conventional screening program. Molecular testing is probably superior to cytological testing of self-collected samples.
Bioretention Column Studies of Phosphorus Removal from Urban Stormwater Runoff (2007)

This study investigated the effectiveness of bioretention as a stormwater management practice using repetitive bioretention columns for phosphorus removal. Bioretention media, with a higher short-term phosphorus sorption capacity, retained more phosphorus from infiltrating runoff after 3 mg/L phosphorus loading. A surface mulch layer prevented clogging after repetitive total suspended solids input. Evidence suggests that long-term phosphorus reactions will regenerate active short-term phosphorus adsorption sites. A high hydraulic conductivity media overlaying one with low hydraulic conductivity resulted in a higher runoff infiltration rate, from 0.51 to 0.16 cm/min at a fixed 15-cm head, and was more efficient in phosphorus removal (85% mass removal) than a profile with low conductivity media over high (63% mass removal). Media extractions suggest that most of the retained phosphorus in the media layers is available for vegetative uptake and that environmental risk thresholds were not exceeded.
Compressive Sensing Hyperspectral Imager (2009)

Compressive sensing based hyperspectral imaging is investigated and compared with its raster scan counterpart. Data acquisition and compression are realized simultaneously which greatly decreases the measurement time and storage volume while increasing the signal fidelity.
Effects of postmortem positional changes on conjunctival petechiae (2018)

The present study aimed to determine whether postmortem period, physical constitution, cause of death, and cardiopulmonary resuscitation are associated with positional changes in the postmortem appearance of conjunctival petechiae. We retrospectively investigated serial forensic autopsies from 6 h to 6 days postmortem (n = 442; male, 303; female, 139; median age, 62 years; range, 0-100 years). The causes of death were sharp instrument injury, blunt force trauma, fire, intoxication, asphyxia, drowning, hypothermia, hyperthermia, acute heart failure, and natural causes. Of these, 28 (male, n = 18; female, n = 10) were aged ≤5 years. Palpebral conjunctival petechiae were initially assessed at autopsy in supine bodies, then reassessed in prone bodies after 30 min. Among 414 bodies, 291 (70.2%) and 123 (29.7%) who were aged between 6 and 100 years, and 18 (64.2%) and 10 (35.7%) aged <5 years at the time of death, were discovered in the supine and prone positions, respectively. The amounts of petechiae increased within 1.5 days postmortem, but not in those discovered in the prone position. The rates at which petechiae increased were higher in supine overweight bodies (BMI ≥ 25.0) and in those who were discovered supine and had died of asphyxia or drowning (37.5%). Cardiopulmonary resuscitation for bodies discovered in the supine and prone positions did not statistically affect the occurrence of petechiae. Several postmortem factors can cause hypostatic blood redistribution that manifests as increased amounts of petechiae in the palpebral conjunctivae.
Distributed nonnegative matrix factorization for web-scale dyadic data analysis on mapreduce (2010)

The Web abounds with dyadic data that keeps increasing by every single second. Previous work has repeatedly shown the usefulness of extracting the interaction structure inside dyadic data [21, 9, 8]. A commonly used tool in extracting the underlying structure is the matrix factorization, whose fame was further boosted in the Netflix challenge [26]. When we were trying to replicate the same success on real-world Web dyadic data, we were seriously challenged by the scalability of available tools. We therefore in this paper report our efforts on scaling up the nonnegative matrix factorization (NMF) technique. We show that by carefully partitioning the data and arranging the computations to maximize data locality and parallelism, factorizing a tens of millions by hundreds of millions matrix with billions of nonzero cells can be accomplished within tens of hours. This result effectively assures practitioners of the scalability of NMF on Web-scale dyadic data.
Correlation between Quinolone Susceptibility Patterns and Sequences in the A and B Subunits of DNA Gyrase in Mycobacteria (1998)

The in vitro activities of seven quinolones and the sequences of the quinolone resistance-determining regions (QRDR) in the A and B subunits of DNA gyrase were determined for 14 mycobacterial species. On the basis of quinolone activity, quinolones were arranged from that with the greatest to that with the least activity as follows: sparfloxacin, levofloxacin, ciprofloxacin, ofloxacin, pefloxacin, flumequine, and nalidixic acid. Based on MICs, the species could be organized into three groups: resistant (Mycobacterium avium, M. intracellulare, M. marinum, M. chelonae, M. abscessus [ofloxacin MICs, >/=8 microg/ml]), moderately susceptible (M. tuberculosis, M. bovis BCG, M. kansasii, M. leprae, M. fortuitum third biovariant, M. smegmatis [ofloxacin MICs, 0.5 to 1 microg/ml]), and susceptible (M. fortuitum, M. peregrinum, M. aurum [ofloxacin MICs, </=0.25 microg/ml]). Peptide sequences of the QRDR of GyrB were identical in all the species, including the amino acids at the three positions known to be involved in acquired resistance to quinolone, i.e., 426 (Asp), 447 (Arg), and 464 (Asn) (numbering system used for Escherichia coli). The last two residues could be involved in the overall low level of susceptibility of mycobacteria to quinolones since they differ from those found in the very susceptible E. coli (Lys-447 and Ser-464) but are identical to those found in the less susceptible Staphylococcus aureus and Streptococcus pneumoniae. Peptide sequences of the QRDR of GyrA were identical in all the species, except for the amino acid at position 83, which was an alanine in the two less susceptible groups and a serine in the most susceptible one, as in E. coli, suggesting that this amino acid is involved in the observed differences of quinolone susceptibility within the Mycobacterium genus.
Performance Evaluation of Bridgeless PFC Boost Rectifiers (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, a systematic review of bridgeless power factor correction (PFC) boost rectifiers, also called dual boost PFC rectifiers, is presented. Performance comparison between the conventional PFC boost rectifier and a representative member of the bridgeless PFC boost rectifier family is performed. Loss analysis and experimental efficiency evaluation for both CCM and DCM/CCM boundary operations are provided. </para>
Topical Cyproterone Acetate Treatment in Women With Acne (1998)

The therapeutic effect of topically applied cyproterone acetate for acne treatment was clearly demonstrated. Topically applied sexual steroids in combination with liposomes are as effective as oral antiandrogen medication in acne treatment, while reducing the risk of adverse effects and avoiding high serum cyproterone acetate concentrations.
Experiments in line quality monitoring (1976)

Data being carried by transmission links in computer networks are often subject to transmission errors resulting from various phenomena occurring on the transmission lines. This paper describes an experimental system for monitoring the quality of data transmission over common carrier leased lines and gives examples of how the information obtained from the system may be used in the daily operations of a computer center. The experiments have been carried out at several locations within IBM.
Filters, mollifiers and the computation of the Gibbs phenomenon (2007)

We are concerned here with processing discontinuous functions from their spectral information. We focus on two main aspects of processing such piecewise smooth data: detecting the edges of a piecewise smooth f , namely, the location and amplitudes of its discontinuities; and recovering with high accuracy the underlying function in between those edges. If f is a smooth function, say analytic, then classical Fourier projections recover f with exponential accuracy. However, if f contains one or more discontinuities, its global Fourier projections produce spurious Gibbs oscillations which spread throughout the smooth regions, enforcing local loss of resolution and global loss of accuracy. Our aim in the computation of the Gibbs phenomenon is to detect edges and to reconstruct piecewise smooth functions, while regaining the high accuracy encoded in the spectral data. To detect edges, we utilize a general family of edge detectors based on concentration kernels . Each kernel forms an approximate derivative of the delta function, which detects edges by separation of scales . We show how such kernels can be adapted to detect edges with one- and two-dimensional discrete data, with noisy data, and with incomplete spectral information. The main feature is concentration kernels which enable us to convert global spectral moments into local information in physical space. To reconstruct f with high accuracy we discuss novel families of mollifiers and filters . The main feature here is making these mollifiers and filters adapted to the local region of smoothness while increasing their accuracy together with the dimension of the data. These mollifiers and filters form approximate delta functions which are properly parametrized to recover f with (root-) exponential accuracy.
The Majority of Dorsal Spinal Cord Gastrin Releasing Peptide is Synthesized Locally Whereas Neuromedin B is Highly Expressed in Pain- and Itch-Sensing Somatosensory Neurons (2012)

The majority of dSC Grp is synthesized locally in dorsal spinal cord neurons. On the other hand, Nmb is highly expressed in pain- and itch-sensing DRG neurons. Our findings provide direct anatomic evidence that Grp could function locally in the dorsal spinal cord in addition to its roles in DRG neurons and that Nmb has potential roles in nociceptive and itch-sensitive neurons. These results will improve our understanding about roles of Grp and Nmb in mediating itch sensation.
Thermomechanical Reliability of Low-Temperature Sintered Silver Die Attached SiC Power Device Assembly (2006)

A thermomechanical reliability study was conducted on a low-temperature sintered silver die attached SiC power device assembly. The silver die attachment was formed by sintering nanoscale silver paste in air at 300 degC to form a strong bond between silver- or gold-coated direct-bond-copper substrates and silver-metallized SiC Schottky diodes. Using the 50% drop in the die-shear strength as the failure criterion, an accelerated thermal cycling experiment between 50 degC and 250 degC showed that the silver die attachment can survive more than 4000 cycles, indicating its high thermomechanical reliability at the interested temperature range. Established mainly by scanning electron microscopy/energy-dispersive spectroscopy, the drop of the die-shear strength during the thermal cycling was attributed to the pile-up of creeping dislocations to form microcavities at the grain boundaries of the sintered silver
Esterification of<i>Eschericia coli</i>tRNAs with<scp>D</scp>-Histidine and<scp>D</scp>-Lysine by Aminoacyl-tRNA Synthetases (2005)

It is generally believed that only L-amino acids are acceptable in protein synthesis, though some D-amino acids, including D-tyrosine, D-aspartate, and D-tryptophan are known to be bound enzymatically to tRNAs. In this report, we newly show that D-histidine and D-lysine are also able to be the substrates of respective Escherichia coli aminoacyl-tRNA synthetases.
Time‐lapse image registration using the local similarity attribute (2007)

We present a method for registration of time‐lapse time‐domain seismic images based on the local similarity attribute. Stretching and squeezing the reference image and computing its local similarity to the master image allows us to detect an optimal registration even in the presence of significant velocity changes in the overburden. The by‐product of this process is an estimate of the ratio of the interval seismic velocities in the reservoir interval. We illustrate the proposed method and demonstrate its effectiveness using both synthetic experiments and real data from the Duri experiment in Indonesia.
Orally active aldose reductase inhibitors derived from bioisosteric substitutions on tolrestat (1989)

A series of aldose reductase inhibitors was prepared in which structural modifications were made to three positions of the potent, orally active inhibitor tolrestat (1), namely, the 6-methoxy substituent, thioamide sulfur, and the N-methyl moiety. These compounds were evaluated in two in vitro systems: an isolated enzyme preparation from bovine lens to assess their intrinsic inhibitory activity and an isolated rat sciatic nerve assay to determine their ability to penetrate membranes of nerve tissue. These compounds were also evaluated in vivo as inhibitors of galactitol accumulation in the lens, sciatic nerve, and diaphragm of galactose-fed rats. Bioisosteric replacement of the 6-methoxy group of 1 with a methylthio substituent gave 5, and replacement of the thioamide substituent of 1 with a cyanoamidine gave 7. Both 5 and 7 retained high in vitro potency but were less potent in vivo than 1. Replacement of the tolrestat N-methyl group by a carbomethoxy moiety gave 10 and led to a substantial reduction in activity in each of the three assays employed. However, this same structural modification on oxo-tolrestat (2) led to 11 and resulted in an enhancement of the intrinsic activity and a comparable in vivo potency. The isolated nerve data suggest that some compounds in these series do not readily penetrate into peripheral nerves, and this presumably is a factor in their lack of oral activity.
DNA vectorgrams: Representation of cancer genes as movements on a 2D cellular lattice (1987)

A brief introduction introduction to a computer graphics characterization of cancer DNA sequences, as well as other biologically interesting sequences, is presented. The procedure described takes DNA sequences containing n bases and computes n two-dimensional real vectors. When displayed on a planar unit-cellular lattice, these characteristic patterns appear as a “DNA vectorgram,” C(n). Several demonstration plots are provided which indicate that C(n) is sensitive to certain statistical properties of the sequence of bases and allows the human observer to visually detect some important sequence structural properties and patterns not easily captured by traditional methods. The system presented has as its primary focus the fast characterization of the progression of sequence data using an interactive graphics system with several controlling parameters.
Entry of Opioid Peptides into the Central Nervous System (1980)

Cerebrovascular permeability of four modified opioid peptides--[D-Ala2]methionine enkephalin amide, beta-[D-Ala62,14C-Homoarg69]lipotropin 61 -69, alpha-[D-Ala2,14C-Homoarg9]endorphin, and beta-[D-Ala2,14C-Homoarg]endorphin--ranged from 1.4 to 3.9 X 10(-6) centimeters per second in brain regions of the conscous rat. These significant permeabilities should allow the peptides to fill the extracellular brain space with a half time of 3 to 11 minutes, as a result of a step increase in plasma concentration of unbound peptide.
Range measurement in ultrasound FMCW system (2006)

Abstract The low peak power of FMCW radar is attractive for application to various fields, such as vehicle collision warning systems and airborne radio altimeters. This paper describes a sonar system to provide ultrasound cross‐sectional images for diagnosis based on the same principle as the FMCW radar. Adoption of the sawtooth waveform is proposed for FM modulation to attain sufficient range resolution. The baseband received signal is analytically estimated to calculate the spectrum and range resolution. The calculation results suggest that the sonar system has similar range resolution to conventional pulse sonars, whose instantaneous power has a very high peak. The theoretically estimated spectrum also suggests that the FMCW sonar system operates well in the case of simultaneous acceptance of reflected signals from multiple points because its excellent range resolution enables distinguishing the contributions from different reflection points. The calculation results are verified by an experiment in which an electric delay line is used instead of human tissue to avoid ambiguity caused by unexpected reflection points in the measuring setup. © 2006 Wiley Periodicals, Inc. Electron Comm Jpn Pt 3, 90(1): 9–19, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecjc.20244
An Efficient Track Management Scheme for the Gaussian-Mixture Probability Hypothesis Density Tracker (2006)

The Gaussian mixture probability hypothesis density (GM-PHD) filter is a closed-form solution for the probability hypothesis density (PHD) filter, which was proposed for jointly estimating the time-varying number of targets and their states from a sequence of noisy measurement sets in the presence of data association uncertainty, clutter and miss-detections. Recently, a GM-PHD tracker based on the GM-PHD filter has been proposed to correctly maintain temporal association amongst target estimates by tagging individual Gaussian components, and to provide estimates of individual target trajectories and their identities. In this paper, we propose a tag and a track management scheme for the GM-PHD tracker, which is computationally efficient and provides a framework for parallel processing of data. Based on the proposed scheme, we also present a number of simpler and efficient pruning schemes for Gaussian components.
A Symbolic Functional Description Language (1984)

This paper describes a new diagrammatic hardware description language SFDL (Symbolic Functional Description Language) and a hierarchical logic design supporting system LDSS (Logic Design Supporting System). SFDL has three features that help designers design logic circuits easily and speedily; easy to describe with its simple rule, comprehensible to grasp the behavior of the circuit and suitable for computer processing. Besides, the LDSS allows designers to draw diagrams without the attention to complicated drawing rule and translate the SFDL diagrams into a text-styled hardware description language. Through experiments, the effectiveness of the SFDL for hierarchical logic design has been confirmed.
Autoantibodies to a 64-Kilodalton Islet Cell Protein Precede the Onset of Spontaneous Diabetes in the BB Rat (1984)

Spontaneous insulin-dependent diabetes mellitus (IDDM) in the BB rat is associated with the presence of antibodies to a 64-kilodalton rat islet cell protein. These protein antibodies appeared in young animals and remained for as long as 8 weeks before the clinical onset of IDDM. Antibodies to a 64-kilodalton human islet cell protein were found to be associated with human IDDM. Detection of the antibodies may therefore be used to predict an early immune reaction against pancreatic B cells.
HIVs Evasion of Hosts NK Cell Response and Novel Ways of its Countering and Boosting Anti-HIV Immunity (2003)

NK cells were characterized by their ability to spontaneously kill certain tumor and virus-infected cells. They constitute first line of defense against invading pathogens and usually become activated in viral infections particularly in early phases. Activated NK cells play a crucial role in the induction and amplification of virus-specific immunity by providing IFN-gamma and "danger signal". The functional activities of NK cells are regulated by a balance between the engagement of their inhibitory and activating receptors. In recent years, the discovery of several MHC and non-MHC binding NK receptors has provided important insights regarding NK cell biology and its role in viral infections. These receptors are increasingly being viewed as important regulators of immune response. Like many other viruses, HIV also seems to activate NK cells. However, several studies have reported compromised NK cell functions in HIV-infected individuals. The virus employs several strategies to counter the host's NK cell response, e.g., a differential downregulation of MHC class I molecules on the surface of infected cells, a dysregulated production of NK cell function-enhancing cytokines, direct inhibitory effects of certain viral proteins on NK cell functions, and changes in the expression of NK cell receptors, etc. The individuals expressing activating NK cell receptors and their cognate MHC ligands have activated NK cells. The development of AIDS is significantly delayed in these individuals after HIV infection. The discovery of NK receptors and their ligands has opened new avenues of developing AIDS vaccine and boosting innate and adaptive antiviral immunity in HIV-infected individuals.