gebhart/patrepeval huggingface dataset:
Automatically learning semantic features for defect prediction (2016)

Software defect prediction, which predicts defective code regions, can help developers find bugs and prioritize their testing efforts. To build accurate prediction models, previous studies focus on manually designing features that encode the characteristics of programs and exploring different machine learning algorithms. Existing traditional features often fail to capture the semantic differences of programs, and such a capability is needed for building accurate prediction models.
Inhibitory Potential of Herbal Medicines on Human Cytochrome P450-Mediated Oxidation: Properties of Umbelliferous or Citrus Crude Drugs and Their Relative Prescriptions (2001)

To investigate the possible drug interaction with herbal medicine, hot water decoctions or 40% ethanol infusions of several Umbelliferous or Citrus crude drugs and their prescriptions were examined in vitro for their abilities to inhibit human cytochrome P450 3A (CYP3A). Addition of each decoction or infusion from Baizhi (Angelica dahurica and varieties), Qianghuo (Notopterygium incisum or N. forbesii), Duhuo (Angelica biserrata), Fangfeng (Saposhnikovia divaricata), Danggui (Angelicasinensis), Zhishi or Zhiqiao (Citrus aurantium) resulted in various degrees of human CYP3A inhibition as determined by microsomal testosterone 6beta-hydroxylation. The inhibitory potency was consistent with the abundance of the hydrophobic components for each sample. Experiments on the infusion of a Japanese Baizhi (BZ1) showed the major role of furanocoumarins on human CYP3A inhibition. Some of the crude drugs and a related prescription showed increased inhibition after the preincubation, suggesting the involvement of a mechanism-based inhibition. Some formulated prescriptions, however, showed intense inhibition with their hydrophobic fractions rather than with their hydrophobic fractions, suggesting that components other than furanocoumarins in herbal prescriptions may also cause CYP3A inhibition. These results indicate the necessity of intensive investigations on the possible drug interaction with traditional medicines.
Epstein-Barr Virus BGLF4 Kinase Suppresses the Interferon Regulatory Factor 3 Signaling Pathway (2008)

The BGLF4 protein kinase of Epstein-Barr virus (EBV) is a member of the conserved family of herpesvirus protein kinases which, to some extent, have a function similar to that of the cellular cyclin-dependent kinase in regulating multiple cellular and viral substrates. In a yeast two-hybrid screening assay, a splicing variant of interferon (IFN) regulatory factor 3 (IRF3) was found to interact with the BGLF4 protein. This interaction was defined further by coimmunoprecipitation in transfected cells and glutathione S-transferase (GST) pull-down in vitro. Using reporter assays, we show that BGLF4 effectively suppresses the activities of the poly(I:C)-stimulated IFN-beta promoter and IRF3-responsive element. Moreover, BGLF4 represses the poly(I:C)-stimulated expression of endogenous IFN-beta mRNA and the phosphorylation of STAT1 at Tyr701. In searching for a possible mechanism, BGLF4 was shown not to affect the dimerization, nuclear translocation, or CBP recruitment of IRF3 upon poly(I:C) treatment. Notably, BGLF4 reduces the amount of active IRF3 recruited to the IRF3-responsive element containing the IFN-beta promoter region in a chromatin immunoprecipitation assay. BGLF4 phosphorylates GST-IRF3 in vitro, but Ser339-Pro340 phosphorylation-dependent, Pin1-mediated downregulation is not responsible for the repression. Most importantly, we found that three proline-dependent phosphorylation sites at Ser123, Ser173, and Thr180, which cluster in a region between the DNA binding and IRF association domains of IRF3, contribute additively to the BGLF4-mediated repression of IRF3(5D) transactivation activity. IRF3 signaling is activated in reactivated EBV-positive NA cells, and the knockdown of BGLF4 further stimulates IRF3-responsive reporter activity. The data presented here thus suggest a novel mechanism by which herpesviral protein kinases suppress host innate immune responses and facilitate virus replication.
Data mining for identification and prediction of safety and reliability characteristics of complex industrial systems and processes (2009)

The model of the operation process of the complex technical system with the distinguished their operation states is proposed in (Kolowrocki & Soszynska, 2008). The semi-markov process is used to construct a general probabilistic model of the considered complex industrial system operation process. To construct this model there were defined the vector of the probabilities of the system initial operation states, the matrix of the probabilities of transitions between the operation states, the matrix of the distribution functions and the matrix of the density functions of the conditional sojourn times in the particular operation states. To describe the system operation process conditional sojourn times in the particular operation states the uniform distribution, the triangular distribution, the double trapezium distribution, the quasi-trapezium distribution, the exponential distribution, the Weibull’sand the chimney in (Kolowrocki & Soszynska, 2008). In this paper, the formulae estimating unknown parameters of these distributions are presented and the chi-square test (Rice, 2007, Stapleton, 2009) is applied to verifying the hypotheses about these distributions validity.
Electromagnetically-induced transparency and squeezed light (2009)

We report theoretical and experimental studies of the transmission and storage of squeezed vacuum under the conditions of electromagnetically induced transparency in rubidium vapor. A model based on a three‐level atom allows us to evaluate the linear losses and extra noise that degrade nonclassical properties of the squeezed vacuum during the atomic interaction and eventually predict the quantum states of the transmitted light with a high precision. Experimentally, we show that squeezing is preserved after storage in rubidium vapor for 1 μs.
Interactions of Rabconnectin-3 with Cav2 calcium channels (2019)

This study describes the interaction between Cav2 calcium channels and Rabconnectin-3, a di-subunit protein that is associated with synaptic vesicles. Immunostaining reveals that both Rabconnectin-3α (RB-3α) and Rabconnectin-3β (RB-3β) are colocalized in mouse hippocampal neurons. Co-immunoprecipitations from brain tissue is consistent with the formation of a protein complex between RB-3α and RB-3β and both Cav2.2 and the related Cav2.1 calcium channel. The coexpression of either RB-3α or RB-3β with Cav2.2 calcium channels in tsA-201 cells led to a reduction in Cav2.2 current density without any effects on the voltage-dependence of activation or inactivation. Coexpression of both Rabconnectin-3 subunits did not cause an additive effect on current densities. Finally, the presence of Rabconnectin-3 did not interfere with μ-opioid receptor mediated Gβγ modulation of Cav2.2 channels. Altogether, our findings show that Rabconnectin-3 has the propensity to regulate calcium entry mediated by Cav2.2 channels.
Analytic expressions for emission in sharp field emitter diodes (1995)

We present a complete analytical treatment of elliptical field emitting structures in a diode geometry which correctly includes image charge effects off axis and the variation of field along the tip. The methodology may be extended to other geometries. The angular distribution of electron emission along the tip, the total emitted current, and the area factor may all be calculated as a function of emitter to anode distance, tip radius, tip height, and the anode-tip voltage difference. We show not only where errors arise if the planar Fowler–Nordheim (FN) equation is used to govern electron emission, but also how the FN equation may be modified to correctly address the complications due to atomically sharp tips. Finally, we present an analytic form of the area factor and compare it to the exact calculation and the various approximations.
Multiplex ligation‐dependent probe amplification (MLPA) and prenatal diagnosis (2012)

Multiplex ligation-dependent probe amplification (MLPA) is a recent technique for the relative quantitation of up to 40 to 45 nucleic acid targets. Due to its relative simplicity, low cost, and availability of laboratory-developed and more than 300 commercially-developed assays, MLPA has become more widely used for both research and diagnostic applications. The MLPA platform is now extensively applied for postnatal diagnosis of genetic disorders and has recently been used for prenatal diagnosis. The published uses of MLPA for prenatal diagnosis include detection of aneuploidies, common microdeletion syndromes and subtelomeric copy-number changes, identification of marker chromosomes, and detection of familial copy-number changes in single genes. This review describes the technique of MLPA in detail and offers considerations for the interpretation of results in the clinical diagnostic setting. © 2012 John Wiley & Sons, Ltd.
Migraine headache and its association with emesis and gastric motility: A brief review (2004)

66 CLINICAL MANIFESTATIONS AND EPIDEMIOLOGY Migraine headache is a chronic, debilitating disorder characterized by severe head pain that is usually unilateral and throbbing in nature (1). If left untreated, a can persist for up to 72 hours (2). It is frequently associated with nausea (87%) and/or vomiting (56%), and other symptoms such as photophobia and phonophobia are also quite common (3). As reported in a review in The New England Jour nal of Medicine on the pathophysiology and treatment of headaches (4), fifteen percent of sufferers will experience transient focal neurological symptoms that typically precede their headaches. This phenomenon is known as migraine with aura, and the neurological symptoms are usually manifested as visual disturbances. However, some studies show that up to 31% of patients report the presence of aura with their migraines at one time or an another (5). It is the Migraine Headache and Its Association with Emesis and Gastric Motility: A Brief Review A SPECIAL ARTICLE
“Candidatus Brocadiales” ord. nov (2015)

Abstract Bro.ca.di.a'les. N.L. fem. n. “ Candidatus Brocadia” type genus of the order; ‐ ales ending to denote an order; N.L. fem. pl. n. Brocadiales the order of “ Candidatus Brocadia”. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Candidatus Brocadiales is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Planctomycetota / Candidatus Brocadiia / Candidatus Brocadiales The order Candidatus Brocadiales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Brocadiales (version v220) ** . GTDB classification: d__Bacteria / p__Planctomycetota / c__Brocadiia / o__Brocadiales * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776
Automatic Cloud Classification (1986)

In this paper, design and implementation of an automatic cloud classifier is discussed. It is assumed that the pattern classes obey the multivariate normal distribution. Maximum Likelihood with threshold and penalised Declassification algorithms have been implemented both on host computer VAX-11/750 and Array Processor FPS-100. This technique classifies not only different cloud types but land, sea and snow as well. The result of classification and the time required on host as well as on array processor for various complexities is presented. NOAA satellite pictures have been used for testing.
Accurate Determination of Interstrand Distances and Alignment in Amyloid Fibrils by Magic Angle Spinning NMR (2016)

Amyloid fibrils are structurally ordered aggregates of proteins whose formation is associated with many neurodegenerative and other diseases. For that reason, their high-resolution structures are of considerable interest and have been studied using a wide range of techniques, notably electron microscopy, X-ray diffraction, and magic angle spinning (MAS) NMR. Because of the excellent resolution in the spectra, MAS NMR is uniquely capable of delivering site-specific, atomic resolution information about all levels of amyloid structure: (1) the monomer, which packs into several (2) protofilaments that in turn associate to form a (3) fibril. Building upon our high-resolution structure of the monomer of an amyloid-forming peptide from transthyretin (TTR&lt;sub&gt;105−115&lt;/sub&gt;), we introduce single 1-&lt;sup&gt;13&lt;/sup&gt;C labeled amino acids at seven different sites in the peptide and measure intermolecular carbonyl−carbonyl distances with an accuracy of ∼0.11 A. Our results conclusively establish a parallel, in register, topology for the packing of this peptide into a β-sheet and provide constraints essential for the determination of an atomic resolution structure of the fibril. Furthermore, the approach we employ, based on a combination of a double-quantum filtered variant of the DRAWS recoupling sequence and multispin numerical simulations in SPINEVOLUTION, is general and should be applicable to a wide range of systems.
Measurement System of Bubbly Flow Using Ultrasonic Velocity Profile Monitor and Video Data Processing Unit, (II) (1997)

The authors have developed a measurement system which is composed of an ultrasonic velocity profile monitor and a video data processing unit in order to clarify its multi-dimensional flow characteristics in bubbly flows and to offer a data base to validate numerical codes for multi-dimensional two-phase flow. In this paper, the measurement system was applied for bubbly countercurrent flows in a vertical rectangular channel. At first, both bubble and water velocity profiles and void fraction profiles in the channel were investigated statistically. Next, turbulence intensity in a continuous liquid phase was defined as a standard deviation of velocity fluctuation, and the two-phase multiplier profile of turbulence intensity in the channel was clarified as a ratio of the standard deviation of flow fluctuation in a bubbly countercurrent flow to that in a water single phase flow. Finally, the distribution parameter and drift velocity used in the drift flux model for bubbly countercurrent flows were calculated from the obtained velocity profiles of both phases and void fraction profile, and were compared with the correlation proposed for bubbly countercurrent flows.
Association of progression‐free survival, overall survival, and patient‐reported outcomes by skin toxicity and KRAS status in patients receiving panitumumab monotherapy (2009)

More severe ST, by both clinical grading and PRO, is associated with better CRC symptoms and HRQOL and with longer OS and PFS among panitumumab-treated patients. The associations for PFS were more pronounced in patients with WT KRAS tumors.
A-Site Ordered Double Perovskite CaMnTi2O6 as a Multifunctional Piezoelectric and Ferroelectric–Photovoltaic Material (2017)

The double perovskite CaMnTi<sub>2</sub>O<sub>6</sub>, is a rare A-site ordered perovskite oxide that exhibits a sizable ferroelectric polarization and relatively high Curie temperature. Using first-principles calculations combined with detailed symmetry analyses, we identify the origin of the ferroelectricity in CaMnTi<sub>2</sub>O<sub>6</sub>. We further explore the material properties of CaMnTi<sub>2</sub>O<sub>6</sub>, including its ferroelectric polarization, dielectric and piezoelectric responses, magnetic order, electronic structure, and optical absorption coefficient. It is found that CaMnTi<sub>2</sub>O<sub>6</sub> exhibits room-temperature-stable ferroelectricity and moderate piezoelectric responses. Moreover, CaMnTi<sub>2</sub>O<sub>6</sub> is predicted to have a semiconducting energy band gap similar to that of BiFeO<sub>3</sub>, and its band gap can further be tuned via distortions of the planar Mn-O bond lengths. CaMnTi<sub>2</sub>O<sub>6</sub> exemplifies a new class of single-phase semiconducting ferroelectric perovskites for potential applications in ferroelectric photovoltaic solar cells.
Highly sensitive silicon photomultipliers for ATP bioluminescence detection on 3D printe lab-on-a-chip (2018)

Adenosine triphosphate (ATP) bioluminescence has been widely used for biosensing applications. Commercially available platforms to perform biological testing are expensive, bulky, and require subst ...
Merit Aid and Inequality: Evidence from Baccalaureate & Beyond (2001)

This study examines the distribution of merit-based and need-based financial aid packages among a nationally representative sample of baccalaureate degree recipients. The results show that students from underrepresented race and class backgrounds are less likely to receive merit aid and that students with minimal financial need are more likely to receive merit aid. Because the majority of financial aid flows through student loan programs, shifting financial aid resources toward merit-based scholarships may increase the costs of higher education for students with high financial need. Thus, awarding financial aid regardless of student need is counterproductive to the goal of equal opportunity in postsecondary education.
Metallo-organic compounds containing metal–nitrogen bonds. Part VI. Infrared and nuclear magnetic resonance of dialkylamidoderivatives of titanium, vanadium, zirconium, niobium, hafnium, tantalum, and thorium (1969)

I.r. and n.m.r. spectra have been measured on solutions of a number of dialkylamido-compounds M(NR2)x of titanium, vanadium, zirconium, niobium, hafnium, tantalum, and thorium and on the alkylimido-trisdialkylamidotantalums RNTa(NR2)3. Assignments of characteristic bands are made and the metal–nitrogen stretching frequencies are discussed in terms of a significant contribution of nitrogen → metal pπ–dπ bonding. The variable temperature n.m.r. studies on Zr(NMe2)4 confirmed the presence of polymeric species in solution.
Mutation of conserved aspartates affect maturation of presenilin 1 and presenilin 2 complexes (2000)

Presenilin (PS1 and PS2) holoproteins are transiently incorporated into low molecular weight (MW) complexes. During subsequent incorporation into a higher MW complex, they undergo endoproteolysis to generate stable N- and C-terminal fragments (NTF/CTF). Mutation of either of two conserved aspartate residues in transmembrane domains inhibits both presenilin-endoproteolysis and the proteolytic processing of APP and Notch. We show that aspartate-mutant holoprotein presenilins are not incorporated into the high molecular weight, NTF/CTF-containing complexes. Aspartate-mutant presenilin holoproteins also preclude entry of endogenous wild-type PS1/PS2 into the high molecular weight complexes, but do not affect the incorporation of wild-type holoproteins into lower molecular weight holoprotein complexes. These data suggest that the loss-of-function aspartate-mutants cause altered PS complex maturation, and argue that the functional presenilin moieties are contained in the high molecular weight presenilin NTF/CTF-containing complexes.
Pneumocystis jirovecii pneumonia Suspected Due to Low-Dosage Prednisolone Treatment for Acute Autoimmune Hepatitis: Case Report and Literature Review (2017)

(1) Background: Preventative treatment for Pneumocystis jirovecii pneumonia (PCP) has been recommended for patients receiving ≥20 mg/day prednisolone. We describe a patient who developed PCP while receiving a dose of 15 mg/day prednisolone, and consider criteria for the initiation of preventative therapy for PCP in patients with autoimmune hepatitis (AIH) treated with prednisolone. (2) Case Report: A 71-year-old woman initially possessed dark-colored urine, white stool, and decreased appetite, which indicated hepatic dysfunction. Further comprehensive investigation suggested a diagnosis of acute hepatitis with probable autoimmune etiology. Treatment was initiated at 60 mg/day prednisolone. Following a positive response by the patient, the dose was gradually reduced to 15 mg/day. Seventy days after the start of prednisolone treatment, respiratory symptoms appeared, and PCP was diagnosed following examination of bronchoalveolar lavage samples. The patient responded positively to treatment with sulfamethoxazole/trimethoprim combination therapy. (3) Conclusions: Preventative therapy for PCP may be indicated for AIH patients treated with steroids with (1) a dose of prednisolone of 12–15 mg/day or more, (2) a CD4+ lymphocyte count of 200–250/mm3 or less, or (3) a total lymphocyte count of 600/mm3 or less.
Decoherence in ion traps due to laser intensity and phase fluctuations (1998)

We consider one source of decoherence for a single trapped ion due to intensity and phase fluctuations in the exciting laser pulses. For simplicity we assume that the stochastic processes involved are white noise processes, which enables us to give a simple master equation description of this source of decoherence. This master equation is averaged over the noise, and is sufficient to describe the results of experiments that probe the oscillations in the electronic populations as energy is exchanged between the internal and electronic motion. Our results are in good qualitative agreement with recent experiments and predict that the decoherence rate will depend on vibrational quantum number in different ways depending on which vibrational excitation sideband is used.
Rhodium-catalyzed Sommelet–Hauser type rearrangement of α-diazoimines: synthesis of functionalized enamides (2020)

An efficient rhodium catalyzed Sommelet-Hauser type rearrangement of sulfur ylides derived from α-thioesters and N-sulfonyl-1,2,3-triazoles has been successfully accomplished for the synthesis of various functionalized enamides. The developed reaction involves the unprecedented [2,3]-sigmatropic rearrangement of sulfur ylides with the imine motif. Importantly, the method works well with various substituted α-thioesters/-amides/-ketones and substituted N-sulfonyl-1,2,3-triazoles and allows the synthesis of diverse enamide derivatives in good to excellent yields. The reaction was also successfully extended to the one-pot synthesis of enamides from terminal alkynes.
Reduction of variance in statistical estimates of spectra for use in correction of ultrasonic aberration (2004)

Parameters of ultrasonic aberration can be obtained from power spectra of scattering when individual scattering measurements from which the spectra are estimated have a common aberration and the same nominal geometry. However, the scattering volumes are then confined to a small spatial region and use of finitely many overlapping volumes that result in a nonzero variance is necessary for the measurements. Assuming the scattering is from a spatially uncorrelated medium, the variance of the spectral estimates is expressed as the product of the variance for a single measurement and a reduction factor that depends on the amount of overlap between each volume pair. This factor describes the rate of convergence and the accuracy of the estimates as a function of the number and the overlap of the scattering volumes. Assuming further that the individual volumes are localized by a Gaussian window and that the centers of the volumes are located on orbits of an icosahedral rotation group, the variance is minimized by adjusting the weight and radius of each orbit. Numerical evaluations using orbits formed by icosahedral vertices, face centers, and edge midpoints show that a significant reduction of variance can be achieved from volumes in a confined region.