gebhart/patrepeval huggingface dataset:
Sentiment Mining and Indexing in Opinmind (2007)

This paper presents a production system that efficiently mines social networking sites for sentiments and indexes the expressions for fast retrieval via a web search interface. Sentiment mining is a computational approach used to identify expressions made about topics within a span of text. Social networks represent a particularly rich corpus for mining sentiments because writers express sentiments about a wide variety of topics in their online journals. We introduce a streamlined approach to extract sentiment expressions and target subjects from unstructured and grammatically imperfect text. In addition, we discuss our approach to index sentiment expressions. 1.
Genetic and antigenic characterization of sigma C protein from avian reovirus (2010)

Avian reovirus (ARV) causes viral arthritis, tenosynovitis, liver infection and immunosuppression in birds. Live-attenuated and inactivated vaccines for ARV are available, but do not efficiently protect against recent variants. Sigma C, which mediates virus attachment to target cells, is the most variable protein in ARV. Antibodies to this protein neutralize viral infection. The purpose of the present study was to characterize sigma C in isolates of ARV from infected birds, as compared with the vaccine strain. Amino acids 27 to 293 of sigma C from 28 Israeli isolates were compared, classified and analysed using bioinformatics tools. Large variations were found among the isolates, and the vaccine strain was shown to differ from most of the studied strains, which could explain the failure of commonly used vaccinations in protecting birds against ARV infection. Based on sigma C protein sequences from all over the world, ARV can be divided into four groups. Isolates from all groups were found in the field simultaneously, possibly explaining the insufficient protection achieved by the vaccine strain, which is represented in one of the groups. The results point out the need and the difficulty in producing a wide-ranging vaccine. Several conserved regions among all reported ARV sigma C proteins were identified. These peptides were further studied for structural and functional properties, and for antigenic characterization. The results of this study shed light on peptide selection for a broad and efficient vaccine.
Experimental Allergic Encephalomyelitis: Synthesis of Disease-Inducing Site of the Basic Protein (1970)

A highly encephalitogenic peptide whose structure resembles the sequence of amino acids surrounding the single tryptophan residue in the encephalitogenic A1 protein from bovine myelin was synthesized. This peptide is similar in the sequence to peptic peptide E and tryptic T27, derived directly from the A1 protein, and is as active on a molar basis as the A1 protein. The major disease-inducing site of the A1 protein resides in a linear sequence of nine amino acids: H-Phe-Ser-Trp-Gly-Ala-Glu-Gly-Gln-Lys-OH. This region of the A1 protein is apparently the major encephalitogenic determinant since specific modification of the tryptophan residue in the A1 protein with 2-hydroxy-5-nitrobenzyl bromide destroyed its encephalitogenic activity.
Activation of the T-Cell Oncogene<i>LMO2</i>after Gene Therapy for X-Linked Severe Combined Immunodeficiency (2004)

Gene therapy, in which a retrovirus was used to carry the relevant gene (IL2Rγc) into a patient's hematopoietic stem cells, was used to treat 10 boys with X-linked severe combined immunodeficiency (SCID). A syndrome resembling T-cell leukemia developed in two of the boys. In both boys — and a third in whom leukemia has not developed — the retrovirus integrated into the same genomic site, the locus of LMO2, which is involved in childhood lymphocytic leukemia. This article reviews the molecular biology of these events and discusses their implications for the future of gene therapy.
Cytochrome P450 2C19 Polymorphism is Associated with Reduced Clopidogrel Response in Cerebrovascular Disease (2011)

Intermediate and poor metabolizing CYP2C19 polymorphism is associated with reduced clopidogrel antiplatelet activity in patients with cerebrovascular disease. The clinical implications of this finding require further investigation.
An empirical investigation into learning bug-fixing patches in the wild via neural machine translation (2018)

Millions of open-source projects with numerous bug fixes are available in code repositories. This proliferation of software development histories can be leveraged to learn how to fix common programming bugs. To explore such a potential, we perform an empirical study to assess the feasibility of using Neural Machine Translation techniques for learning bug-fixing patches for real defects. We mine millions of bug-fixes from the change histories of GitHub repositories to extract meaningful examples of such bug-fixes. Then, we abstract the buggy and corresponding fixed code, and use them to train an Encoder-Decoder model able to translate buggy code into its fixed version. Our model is able to fix hundreds of unique buggy methods in the wild. Overall, this model is capable of predicting fixed patches generated by developers in 9% of the cases.
GaAs traveling-wave electrooptic waveguide modulator with bandwidth >20 GHz at 1.3 μm (1987)

A GaAs traveling-wave electrooptic waveguide polarization modulator In the coplanar strip configuration has been fabricated and characterized at an optical wavelength of 1.3 μm. The –3-dB optical bandwidth is measured to be >20 GHz. The device consists of an optical waveguide with a double-heterojunction structure of Al0.032Ga0.968As/GaAs/Al0.032Ga0.968As with dimensions of 2, 1.6, and 5 μm, respectively, for vertical confinement and a chemically etched ridge for lateral confinement. The ridge width Is 4.5 pm etched to a depth of 1.2 μm for dielectric loading. The optical waveguide is single mode. The structure is grown by organometallic vapor phase epitaxy at low pressure in a horizontal reactor. All epitaxial layers have doping n < 3 × 1014 cm−3 and are grown on a (001) semi-insulating GaAs substrate.1
Clinicopathological correlation—a case of complex congenitally corrected transposition (1994)

Summary A 29-year-old man, with a diagnosis of congenitally corrected transposition (discordant atrioventricular and ventriculoarterial connections) with associated multiple ventricular septal defects, mild pulmonary valvar stenosis and Ebstein's malformation of a stenotic left-sided morphologically tricuspid valve, died after closure of the ventricular septal defect and insertion of a valved homograft conduit between the morphologically left ventricle and the pulmonary trunk. Death occurred because of failure to appreciate the bizarre and rather stenotic anomaly of the morphologically tricuspid valve, in which the anterosuperior leaflet divided the morphologically right ventricle into an inlet portion and a smaller outlet portion. After closure of the ventricular septal defects, this ventricle could no longer support the systemic circulation. We discuss the natural history and the reasons for the erroneous interpretation of the echocardiographic images of the left-sided tricuspid valve.
The performance of independent checkpointing in distributed systems (2002)

The paper describes performance measurements of an implementation of independent checkpointing in a network of workstations. Independent checkpointing is a simple technique for providing fault tolerance in distributed systems. Because processes do not coordinate during checkpointing, this technique has a low run-time overhead. To avoid the classical domino effect, our implementation relies on a message logging mechanism. We have measured fault management overhead for different kinds of parallel applications. The costs of checkpointing are very low. However, message logging introduces a sizeable overhead. We compare these results to other works implementing different checkpointing policies, and we show that independent checkpointing is an efficient way to provide fault tolerance for long-running distributed applications composed of processes exchanging small streams of data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Uric Acid and Coronary Heart Disease Risk: Evidence for a Role of Uric Acid in the Obesity-Insulin Resistance Syndrome (1995)

Various epidemiologic studies have linked an increase in serum uric acid level to an increased risk of coronary heart disease. The reasons for this finding are unclear. The authors examined the influence of a number of cardiovascular disease risk factors on serum uric acid level in 886 middle-aged and older men participating in the Normative Aging Study. The men were examined between 1987 and 1991. In a multivariate regression model predicting serum uric acid level, uric acid was positively associated with body mass index (weight (kg)/height (m)2 beta = 0.041 mg/dl per kg/m2, p = 0.003), abdomen: hip circumference ratio (beta = 1.88 mg/dl per cm/cm, p = 0.048), log alcohol intake (beta = 0.150 mg/dl per g/week, p = 0.0001), and log postcarbohydrate insulin level (beta = 0.157 mg/dl per log(microIU/ml), p = 0.005). Serum uric acid level was negatively associated with age (beta = -0.012 mg/dl per year of age, p = 0.017) and log physical activity (beta = -0.152 mg/dl per kcal/week, p = 0.0001). The data suggest that serum uric acid may be involved in the obesity-insulin resistance syndrome, which in turn may explain the relation of serum uric acid to coronary atherosclerosis.
Fiber optic current sensor calibration (2002)

Fiber optic current sensors have been touted for their potential ability to measure currents with accuracy better than 0.1% over a dynamic range extending from literally milliamps to hundreds of kiloamps. Such claims have a good theoretical basis but it is quite difficult to verify such claims, especially at the two extremes of this range. At the lower end of the current range, white noise in the output compares to, or exceeds the signal level and thus interferes with the measurement process. At the upper end of the range, equipment limitations come into play. In our laboratory we have undertaken a careful study of calibration techniques appropriate to manufacture fiber optic current sensors in the range from 1 to 3600 amps. The main results of our study are reported in this paper. Voltage techniques applied yielded errors of about 0.015% in the range from 1 to 100 amps, and 0.054% in the range from 100 to 3600 amps. The current techniques applied can yield 0.001% errors in the range from 1 to 100 amps (though practically, this would be degraded to save time) and 0.054% in the range from 100 to 3600 amps.
A constant-temperature gas flowmeter with a silicon micromachined package (2003)

A micromachined flowmeter based on convective heat transfer from hot, heavily doped polycrystalline silicon bridges was designed, fabricated, packaged, and tested. The flowmeter consists of two basic sensing units: one is exposed to the flow while the other acts as a reference. A silicon cap with a micromachined laminar-flow channel is placed on top of the sensor chip to confine the flow. The polysilicon bridge resistors operate at a constant temperature under the control of external circuits. An output signal voltage of 35 mV is obtained for air flow in the range of 0-100 SCCM at an average device temperature of 250 degrees C. The applied heating power is 8 mW.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Aerodynamic performance of 1.38-pressure-ratio, variable-pitch fan stage (1979)

The performance of a variable pitch fan stage tested over a range of blade setting angles, speeds, and flows is presented. The fan was designed for a tip speed of 289.6 m/sec and a flow of 29.6 kg/sec. The measured performance agreed reasonably well with the design point. The stall margin was only 5 percent. Static thrust values along an operating line ranged from less than 15 to over 115 percent of that at design angle as the blade setting angle was varied from 25 degrees (closed) to -8 degrees (opened). The use of casing treatment increased the stall margin to 20.6 percent but decreased efficiency by 4 percentage points.
In<i>x</i>Ga(1−<i>x</i>)N/In<i>y</i>Ga(1−<i>y</i>)N superlattices grown on GaN films (1993)

High-quality In0.22Ga0.78N/In0.06Ga0.94N superlattices were grown on GaN films with periods of 60 and 200 Å by the two-flow metalorganic chemical-vapor deposition method. The double-crystal x-ray rocking curve measurements showed satellite peaks which indicated the existence of the In0.22Ga0.78N/In0.06Ga0.94N superlattices. The quantum effects were observed through room-temperature photoluminescence (PL) measurements. These PL spectra were compared to theoretical solutions for the In0.22Ga0.78N/In0.06Ga0.94N superlattices.
Trace-Driven Memory Access Pattern Recognition in Computational Kernels (2014)

Classifying memory access patterns is paramount to the selection of the right set of optimizations and determination of the parallelization strategy. Static analyses suffer from ambiguities present in source code, which modern compilation techniques, such as profile-guided optimization, alleviate by observing runtime behavior and feeding back into the compilation flow. This paper discusses a dynamic analysis technique for recognizing memory access patterns, with application to the stencils domain, and presents our design and C++ implementation using the memory-tracing tool Gleipnir. Finally, we evaluate and discuss the performance and matching capability of our classifiers in the context of the Polybench scientific benchmark suite, which includes both stencil and matrix computations.
A soluble form of the F3 neuronal cell adhesion molecule promotes neurite outgrowth (1992)

The F3 molecule is a member of the immunoglobulin superfamily anchored to membranes by a glycane-phosphatidylinositol, and is predominantly expressed on subsets of axons of the central and peripheral nervous system. In a previous paper (Gennarini, G., P. Durbec, A. Boned, G. Rougon, and C. Goridis. 1991. Neuron. 6:595-606), we have established that F3 fulfills the operational definition of a cell adhesion molecule and that it stimulates neurite outgrowth when presented to sensory neurons as a surface component of transfected CHO cells. In the present study the question as to whether soluble forms of F3 would be functionally active was addressed in vitro on cultures of mouse dorsal root ganglion neurons. We observed that preparations enriched in soluble F3 had no effect on neuron attachment but enhanced neurite initiation and neurite outgrowth in a dose-dependent manner. By contrast, soluble NCAM-120 does not have any measurable effect on these phenomena. Addition of anti-F3 monovalent antibodies reduced the number of process-bearing neurons and the neuritic output per neuron to control values. Addition of cerebrospinal fluid, a natural source of soluble F3, also stimulated neurite extension, and this effect was partially blocked by anti-F3 antibodies. Our results suggest that the soluble forms of adhesive proteins with neurite outgrowth-promoting properties could act at a distance from their site of release in a way reminiscent of growth and trophic factors.
Coexisting stable conformations of gaseous protein ions. (1993)

For further insight into the role of solvent in protein conformer stabilization, the structural and dynamic properties of protein ions in vacuo have been probed by hydrogen-deuterium exchange in a Fourier-transform mass spectrometer. Multiply charged ions generated by electrospray ionization of five proteins show exchange reactions with 2H2O at 10(-7) torr (1 torr = 133.3 Pa) exhibiting pseudo-first-order kinetics. Gas-phase compactness of the S-S cross-linked RNase A relative to denatured S-derivatized RNase A is indicated by exchange of 35 and 135 hydrogen atoms, respectively. For pure cytochrome c ions, the existence of at least three distinct gaseous conformers is indicated by the substantially different values--52, 113, and 74--of reactive H atoms; the observation of these same values for ions of a number--2, 7, and 5, respectively--of different charge states indicates conformational insensitivity to coulombic forces. For each of these conformers, the compactness in vacuo indicated by these values corresponds directly to that of a known conformer structure in the solution from which the conformer ions are produced by electrospray. S-derivatized RNase A ions also exist as at least two gaseous conformers exchanging 50-140 H atoms. Gaseous conformer ions are isometrically stable for hours; removal of solvent greatly increases conformational rigidity. More specific ion-molecule reactions could provide further details of conformer structures.
Timing of defoliation and its effect on bud development, starch reserves, and sap sugar concentration in sugar maple (1986)

Sapling sugar maple (Acersaccharum Marsh.) trees were defoliated artificially at 10-day intervals beginning May 27 and ending August 5, 1981. Refoliation, terminal bud and shoot development, and xylem starch and sap sugar concentration were observed in defoliated and control trees. All defoliated trees refoliated, but decreasingly with later defoliation. Defoliation caused an acceleration in the rate of primordia initiation in terminal shoot apices. After early season defoliations, the developing buds in the axils of the removed leaves abscissed, but axillary and terminal buds on the refoliated terminal shoots survived through winter. In late season defoliation, most buds of refoliated shoots did not survive and the next year's growth depended on axillary buds formed prior to defoliation. Thus, when progressing from early to late defoliations, the next year's shoot growth depended decreasingly on the last-formed and increasingly on the first-formed portions of the previous year's shoot. Early October starch concentration in xylem decreased with later defoliation and was nearly absent in shoots and roots of trees defoliated in late July. There was not, however, a corresponding decrease in sap sugar concentration. Mortality occurred only in late defoliated trees and was associated with starch depletion.
Understanding and Managing Methotrexate Nephrotoxicity (2006)

Methotrexate (MTX) is one of the most widely used anti-cancer agents, and administration of high-dose methotrexate (HDMTX) followed by leucovorin (LV) rescue is an important component in the treatment of a variety of childhood and adult cancers. HDMTX can be safely administered to patients with normal renal function by the use of alkalinization, hydration, and pharmacokinetically guided LV rescue. Despite these measures, HDMTX-induced renal dysfunction continues to occur in approximately 1.8% of patients with osteosarcoma treated on clinical trials. Prompt recognition and treatment of MTX-induced renal dysfunction are essential to prevent potentially life-threatening MTX-associated toxicities, especially myelosuppression, mucositis, and dermatitis. In addition to conventional treatment approaches, dialysis-based methods have been used to remove MTX with limited effectiveness. More recently carboxypeptidase-G(2) (CPDG(2)), a recombinant bacterial enzyme that rapidly hydrolyzes MTX to inactive metabolites, has become available for the treatment of HDMTX-induced renal dysfunction. CPDG(2) administration has been well tolerated and resulted in consistent and rapid reductions in plasma MTX concentrations by a median of 98.7% (range, 84%-99.5%). The early administration of CPDG(2) in addition to LV may be beneficial for patients with MTX-induced renal dysfunction and significantly elevated plasma MTX concentrations.
Choline supplementation mitigates trace, but not delay, eyeblink conditioning deficits in rats exposed to alcohol during development (2011)

Children exposed to alcohol prenatally suffer from a range of physical, neuropathological, and behavioral alterations, referred to as fetal alcohol spectrum disorders (FASD). Both the cerebellum and hippocampus are affected by alcohol exposure during development, which may contribute to behavioral and cognitive deficits observed in children with FASD. Despite the known neuropathology associated with prenatal alcohol exposure, many pregnant women continue to drink (heavy drinkers, in particular), creating a need to identify effective treatments for their children who are adversely affected by alcohol. We previously reported that choline supplementation can mitigate alcohol's effects on cognitive development, specifically on tasks which depend on the functional integrity of the hippocampus. The present study examined whether choline supplementation could differentially mitigate alcohol's effects on trace eyeblink classical conditioning (ECC, a hippocampal-dependent task) and delay ECC (a cerebellar-dependent task). Long-Evans rats were exposed to 5.25 g/kg/day alcohol via gastric intubation from postnatal days (PD) 4-9, a period of brain development equivalent to late gestation in humans. A sham-intubated control group was included. From PD 10-30, subjects received subcutaneous injections of 100 mg/kg choline chloride or vehicle. Beginning on PD 32-34, subjects were trained on either delay or trace eyeblink conditioning. Performance of subjects exposed to alcohol was significantly impaired on both tasks, as indicated by significant reductions in percentage and amplitude of conditioned eyeblink responses, an effect that was attenuated by choline supplementation on the trace, but not delay conditioning task. Indeed, alcohol-exposed subjects treated with choline performed at control levels on the trace eyeblink conditioning task. There were no significant main or interactive effects of sex. These data indicate that choline supplementation can significantly reduce the severity of trace eyeblink conditioning deficits associated with early alcohol exposure, even when administered after the alcohol insult is complete. These findings have important implications for the treatment of fetal alcohol spectrum disorders.
Investigating sepsis with biomarkers (2015)

#### The bottom line A 65 year old man presents with lethargy, fever, and rigors. On examination his arterial blood pressure is 120/50 mm Hg, he has a mild tachycardia (105 beats/min), and he is febrile (38.7°C), with no other abnormalities. His urine is cloudy and urinary dipstick test shows the presence of leucocytes and nitrate. There is no history of recent travel, urinary symptoms, or drug allergy (including antibiotic sensitivity) and no relevant findings on systems review (such as liver or kidney disease). You promptly establish intravenous access, draw blood for laboratory tests (including blood culture), send a urine sample for microbiology, and administer the first dose of an empirical broad spectrum antibiotic. These clinical signs and symptoms strongly suggest sepsis. However, in a third of patients with sepsis, the causative pathogen cannot be identified.1 The lack of confirmatory evidence of infection often makes the diagnosis of sepsis a challenge. This difficulty is reflected by the inclusion of the words “probable infection” in defining sepsis in the Surviving Sepsis Campaign guidelines (box 1).2 #### Box 1: Definitions and classification of sepsis syndrome2 ##### Systemic inflammatory response syndrome An abnormal increase in two or more of the following parameters: