gebhart/patrepeval huggingface dataset:
Fay (2012)

Fay is a flexible platform for the efficient collection, processing, and analysis of software execution traces. Fay provides dynamic tracing through use of runtime instrumentation and distributed aggregation within machines and across clusters. At the lowest level, Fay can be safely extended with new tracing primitives, including even untrusted, fully optimized machine code, and Fay can be applied to running user-mode or kernel-mode software without compromising system stability. At the highest level, Fay provides a unified, declarative means of specifying what events to trace, as well as the aggregation, processing, and analysis of those events. We have implemented the Fay tracing platform for Windows and integrated it with two powerful, expressive systems for distributed programming. Our implementation is easy to use, can be applied to unmodified production systems, and provides primitives that allow the overhead of tracing to be greatly reduced, compared to previous dynamic tracing platforms. To show the generality of Fay tracing, we reimplement, in experiments, a range of tracing strategies and several custom mechanisms from existing tracing frameworks. Fay shows that modern techniques for high-level querying and data-parallel processing of disagreggated data streams are well suited to comprehensive monitoring of software execution in distributed systems. Revisiting a lesson from the late 1960s [Deutsch and Grant 1971], Fay also demonstrates the efficiency and extensibility benefits of using safe, statically verified machine code as the basis for low-level execution tracing. Finally, Fay establishes that, by automatically deriving optimized query plans and code for safe extensions, the expressiveness and performance of high-level tracing queries can equal or even surpass that of specialized monitoring tools.
Defining the Putative Inhibitory Site for a Selective Negative Allosteric Modulator of Human α4β2 Neuronal Nicotinic Receptors (2012)

Neuronal nicotinic receptors (nAChRs) have been implicated in several diseases and disorders such as autism spectrum disorders, Alzheimer's disease, Parkinson's disease, epilepsy, and nicotine addiction. To understand the role of nAChRs in these conditions, it would be beneficial to have selective molecules that target specific nAChRs in vitro and in vivo. Our laboratory has previously identified a novel allosteric site on human α4β2 nAChRs using a series of computational and in vitro approaches. At this site, we have identified negative allosteric modulators that selectively inhibit human α4β2 nAChRs, a subtype implicated in nicotine addiction. This study characterizes the allosteric site via site-directed mutagenesis. Three amino acids (Phe118, Glu60, and Thr58) on the β2 subunit were shown to participate in the inhibitory properties of the selective antagonist KAB-18 and provided insights into its antagonism of human α4β2 nAChRs. SAR studies with KAB-18 analogues and various mutant α4β2 nAChRs also provided information concerning how different physiochemical features influence the inhibition of nAChRs through this allosteric site. Together, these studies identify the amino acids that contribute to the selective antagonism of human α4β2 nAChRs at this allosteric site. Finally, these studies define the physiochemical features of ligands that influence interaction with specific amino acids in this allosteric site.
Multi-functional integrated photonics in the mid-infrared with suspended\n AlGaAs on silicon (2019)

The microscale integration of mid- and longwave-infrared photonics could\nenable the development of fieldable, robust chemical sensors, as well as highly\nefficient infrared frequency converters. However, such technology would be\ndefined by the choice of material platform, which immediately determines the\nstrength and types of optical nonlinearities available, the optical\ntransparency window, modal confinement, and physical robustness. In this work,\nwe demonstrate a new platform, suspended AlGaAs waveguides integrated on\nsilicon, providing excellent performance in all of these metrics. We\ndemonstrate low propagation losses within a span of nearly two octaves (1.26 to\n4.6 $\\mu$m) with exemplary performance of 0.45 dB/cm at $\\lambda = 2.4$ $\\mu$m.\nWe exploit the high nonlinearity of this platform to demonstrate 1560 nm-pumped\nsecond-harmonic generation and octave-spanning supercontinuum reaching out to\n2.3 $\\mu$m with 3.4 pJ pump pulse energy. With mid-IR pumping, we generate\nsupercontinuum spanning from 2.3 to 6.5 $\\mu$m. Finally, we demonstrate the\nversatility of the platform with mid-infrared passive devices such as low-loss\n10 $\\mu$m-radius bends, compact power splitters with 96 $\\pm$ 1% efficiency and\nedge couplers with 3.0 $\\pm$ 0.1 dB loss. This platform has strong potential\nfor multi-functional integrated photonic systems in the mid-IR.\n
Production and characterization of human induced pluripotent stem cells (iPSC) CSSi007-A (4383) from Joubert Syndrome (2019)

Joubert syndrome (JS) is an autosomal recessive neurodevelopmental disorder, characterized by congenital cerebellar and brainstem defects, belonging to the group of disorders known as ciliopathies, which are caused by mutations in genes encoding proteins of the primary cilium and basal body. Human induced pluripotent stem cells (hiPSCs) from a patient carrying a homozygous missense mutation (c.2168G > A) in AHI1, the first gene to be associated with JS, were produced using a virus-free protocol.
Cryogenic and High Temperature Performance of 4H-SiC Vertical Junction Field Effect Transistors (VJFETs) for Space Applications (2005)

In this paper, we present an investigation on the different aspects of the performance of a 600V, 3A 4H-SiC vertical-trench junction field effect transistor (VJFET) at cryogenic and high temperatures. Some critical device physics related factors that affect the DC characteristics and switching performance of the device are explored. In particular, the experimental low-temperature performance of 4H-SiC VJFETs (down to 30K or -243/spl deg/C) is presented for the first time to our knowledge.
Efficient plasmid mobilization by pIP501 in Lactococcus lactis subsp. lactis (1993)

pIP501 is a streptococcal conjugative plasmid which can be transmitted among numerous gram-positive strains. To identify a minimal mobilization (mob) locus of pIP501, DNA fragments of pIP501 were cloned into nonconjugative target plasmids and tested for mobilization by pIP501. We show that nonmobilizable plasmids containing a specific fragment of pIP501 are transmitted at high frequencies between Lactococcus lactis subsp. lactis strains if transfer (tra) functions are provided in trans by a pIP501 derivative. Independent transfer of the mobilized plasmid was observed in up to 44% of transconjugants. A 2.2-kb segment containing mob was sequenced. This DNA segment is characterized by three palindromes (palI, palII, and palIII) and a 202-amino-acid open reading frame (ORFX) of unknown function. The smallest DNA fragment conferring high frequency mobilization was localized to a 1.0-kb region (extending from pIP501 coordinates 3.60 to 4.60 on the 30.2-kb map) which contains palI (delta G = -27 kcal/mol [ca. -110,000 J/mol]). A 26-bp sequence identical to palI is present on pIP501, upstream of the plasmid copy control region. Further homologies with the palI sequence are also found with the related Enterococcus faecalis conjugative plasmid pAM beta 1. The region containing mob maps outside the previously described segment mediating pIP501 conjugation. Our results with recA strains indicate that the mob site is a hot spot for cointegrate formation.
Simulations of realistic multifunctional nanoantenna enabled detectors (2017)

The goal of this paper is to investigate full-wave simulations of realistic implementations of multifunctional nanoantenna enabled detectors (NEDs). We realize a 2×2 pixelated array structure that supports two wavelengths of operation. After designing each resonating structure independently using full-wave simulations with periodic boundary conditions mimicking the whole infinite array, we construct a supercell made of a 2×2 pixelated array with periodic boundary conditions mimicking the full NED. In the NED, each pixel comprises 10-20 nanoantennas. Our simulations account for the cross-talk between contiguous pixels. We observe that, even though there are finite extent effects, the pixels work as designed, each responding at the respective wavelength of operation. We want to stress that realistic simulations of multifunctional NEDs need to be performed to verify the design functionality by taking into account finite extent and cross-talk effects.
Understanding the Effect of Confinement on the Liquid−Gas Transition: A Study of Adsorption Isotherms in a Family of Metal−Organic Frameworks (2010)

We present here a molecular simulation study of the adsorption of CO2 in three IRMOFs, a family of metal−organic frameworks with varying pore size and chemical nature, as controlled by the linker length and the strength of the MOF−CO2 interactions. This extension of previous theoretical and experimental characterizations (Walton, K. S.; Millward, A. R.; Dubbeldam, D.; Frost, H.; Low, J. J.; Yaghi, O. M.; Snurr, R. Q. J. Am. Chem. Soc. 2008, 130, 406−407) provides a coherent explanation and a generic framework in which to understand the presence or absence of step in the sorption isotherms in terms of the effect of confinement on the liquid−gas transition in the phase diagram of the adsorbate. This branch of the phase diagram is calculated explicitly for CO2@IRMOFs and is compared to previous work on families of zeolites and other metal−organic frameworks.
Sequence analysis of bovine lens aldose reductase. (1990)

The covalent structure of bovine lens aldose reductase (alditol-NADP+ oxidoreductase, EC 1.1.1.21) was determined by sequence analysis of peptides generated by specific and chemical cleavage of the homogeneous apoenzyme. Peptides, purified by reverse-phase high performance liquid chromatography were subjected to compositional analysis and sequencing by gas-phase automated Edman degradation. Aldose reductase was found to contain 315 amino acid residues. The enzyme is blocked at the amino terminus, and mass spectrometry was employed to identify the blocking acetyl group and to sequence the amino-terminal tryptic peptide. The aldose reductase was shown to contain no carbohydrate despite the fact that the enzyme contains the consensus sequence -Asn-Lys-Thr- for N-linked glycosylation. Comparative sequence analysis and application of algorithms for prediction of secondary structure and nucleotide binding domains are consistent with the view that aldose reductase is a double-domain protein with a beta-alpha-beta secondary structural organization. The NADPH binding site appears to be associated with the amino-terminal half of the enzyme. Modeling studies based on the tertiary structures of dihydrofolate and glutathione reductases indicate that the NADPH binding site begins at Lys-11 and continues with a beta-alpha-beta fold characteristic of nucleotide binding proteins.
Pericardial patch anterior leaflet extension in rheumatic mitral insufficiency (2010)

This report describes a technique for anterior leaflet extension using an autologous pericardial patch in patients suffering from rheumatic mitral regurgitation. The technique has recently evolved and now enables us to correct both vertical and transversal fibrotic leaflet retraction.
A New Approach for Treatment of Hypertension: Modifying D1 Dopamine Receptor Function (2006)

Essential hypertension is a major factor for myocardial infarction, heart failure and kidney failure. Dopamine plays an important role in the pathogenesis of hypertension by regulating epithelial sodium transport and vasodilatation directly or indirectly with other hormones and humoral factors, such as reactive oxygen species and the renin-angiotensin system. Dopamine receptors are classified into five subtypes based on their structure and pharmacology. Among those dopamine receptor subtypes, D(1) receptor is the most important one, during conditions of moderate sodium intake, more than 50% of renal sodium excretion is regulated by D(1)-like receptors. Decreased renal dopamine production and/or impaired D(1) receptor function have been reported in hypertension. Disruption of D(1) receptor results in hypertension. In this paper, we review the mechanisms by which hypertension develops when D(1) receptor function is perturbed. We also discuss possible new approaches developing anti-hypertensive medicine by increasing renal dopamine production, enhancing D(1) receptor function, or modifying its interactions with other blood pressure-regulating systems.
Current knowledge of primary prostatic extra-gastrointestinal stromal tumor: a case report and review of the literature (2021)

The patient was a 62-year-old man diagnosed as having prostatic extra-gastrointestinal stromal tumor (EGIST) who was treated with imatinib. No recurrence or metastasis was found after a 6-month follow-up. We identified 14 cases of prostatic primary EGIST in PubMed and summarized these cases with our case. The patients' ages ranged from 31 to 78 years (average: 53.6 years), and most patients' prostate-specific antigen (PSA) concentrations were within normal limits (92.9%, 13/14). All patients underwent imaging examinations; prostatic masses measured 6 to 14.2 cm (mean: 9.43 cm), and imaging excluded secondary prostatic masses from the intestinal tract. By immunohistochemical staining, the tumors were positive for cluster of differentiation (CD)117 (71.4%, 10/14), DOG1 (100%, 7/7), and CD34 (100%, 14/14), and negative for smooth muscle actin (SMA) (71.4%, 10/14), desmin (100%, 11/11), and S100 (100%, 12/12). Treatment depended on the results of the gene mutation detection as well as the risk estimation according to tumor size and microscopic mitotic rates (>5 per 50 high-power fields: 60%, 6/10). Among the 12 patients with reported outcomes, nine achieved good results (no recurrence or metastasis), one achieved reduced mass volume, one experienced recurrence, and one died.
Topologically controlled multiskyrmions in photonic gradient-index lenses (2023)

Skyrmions are topologically protected quasiparticles, originally studied in condensed-matter systems and recently in photonics, with great potential in ultra-high-capacity information storage. Despite the recent attention, most optical solutions require complex and expensive systems yet produce limited topologies. Here we demonstrate an extended family of quasiparticles beyond normal skyrmions, which are controlled in confined photonic gradient-index media, extending to higher-order members such as multiskyrmions and multimerons, with increasingly complex topologies. We introduce new topological numbers to describe these complex photonic quasiparticles and propose how this new zoology of particles could be used in future high-capacity information transfer. Our compact creation system lends integrated and programmable solutions of complex particle textures, with potential impacts on both photonic and condensed-matter systems for revolutionizing topological informatics and logic devices.
Chamber maintenance and fault detection technique for a gate etch process via self-excited electron resonance spectroscopy (2005)

With the introduction of 300mm wafer and sub-100nm technology processes, semiconductor manufacturers are gradually paying attention to efficient methods for process and equipment control, which is conventionally called advanced process control (APC) and advanced equipment control (AEC). As a potential strategy, an APC∕AEC technique by self-excited electron resonance spectroscopy (SEERS) was evaluated in a dynamic random access memory gate etch process, in terms of chamber maintenance and process control. Small changes in the chamber conditions after wet cleaning, which could not be detected under conventional monitoring methods, were identified by analyzing the electron collision rate of plasma. This event justifies that plasma monitoring is inevitable in chamber maintenance, especially considering that process results gradually tend to be affected by even small chamber changes in sub-100nm technology process era. Also, the first wafer effect, one of the most serious process drifts in an etch process, could be clearly detected by comparing average electron collision rates of plasma during each wafer process. In addition, a strong correlation between average electron collision rate and remaining oxide thickness enables us to control the gate etch process more tightly. Consequently, the APC∕AEC technique by SEERS is expected to be a potent strategy for plasma etch processes in semiconductor manufacturing.
Nipple aspirate fluid and its use for the early detection of breast cancer (2022)

Nipple aspirate fluid is the physiological biofluid lining ductal epithelial cells. Historically, cytology of nipple fluid has been the gold standard diagnostic method for assessment of ductal fluid in patients with symptomatic nipple discharge. The role of biomarker discovery in nipple aspirate fluid for assessment of asymptomatic and high-risk patients is highly attractive but evaluation to date is limited by poor diagnostic accuracy. However, the emergence of new technologies capable of identifying metabolites that have been previously thought unidentifiable within such small volumes of fluid, has enabled testing of nipple biofluid to be re-examined. This review evaluates the use of new technologies to evaluate the components of nipple fluid and their potential to serve as biomarkers in screening.
Infection of mature dendritic cells with herpes simplex virus type 1 dramatically reduces lymphoid chemokine-mediated migration (2005)

Herpes simplex virus type 1 (HSV-1) is able to establish latency in infected individuals. In order to characterize potential new immune-escape mechanisms, mature dendritic cells (DCs) were infected with HSV-1 and total cellular RNA was isolated from infected and mock-infected populations at different time points. RNA profiling on Affymetrix Human Genome U133A arrays demonstrated a dramatic downregulation of the migration-mediating surface molecules CCR7 and CXCR4, an observation that was further confirmed by RT-PCR and fluorescence-activated cell sorting analyses. Furthermore, migration assays revealed that, upon infection of mature DCs, CCR7- and CXCR4-mediated migration towards the corresponding CCL19 and CXCL12 chemokine gradients was strongly reduced. It is noteworthy that the infection of immature DCs with HSV-1 prior to maturation led to a failure of CCR7 and CXCR4 upregulation during DC maturation and, as a consequence, also induced a block in their migratory capacity. Additional migration assays with a Deltavhs mutant virus lacking the virion host shutoff (vhs) gene, which is known to degrade cellular mRNAs, suggested a vhs-independent mechanism. These results indicate that HSV-1-infected mature DCs are limited in their capacity to migrate to secondary lymphoid organs, the areas of antigen presentation and T-cell stimulation, thus inhibiting an antiviral immune response. This represents a novel, previously unrecognized mechanism for HSV-1 to escape the human immune system.
A variable field strength system for hyperpolarized noble gas MR imaging of rodent lungs (2008)

Abstract Hyperpolarized Noble Gas (HNG), 3 He (helium) or 129 Xe (xenon), MR imaging has become a promising approach for visualizing lung anatomy and function. It has been theoretically predicted that low field strengths (0.05–0.2 T) may provide optimal signal‐to‐noise ratio (SNR) and spatial resolution for clinical HNG MR imaging. These optimum field strengths correspond to frequencies between 1.62–6.5 MHz and 0.59–2.35 MHz for 3 He and 129 Xe respectively. The optimum field strength depends on the size and geometry of the sample and radiofrequency (RF) coil as well as the field dependence of the HNG MR properties in the lung (e.g., relaxation times, susceptibility effects). In particular, little is known about the field dependence of the apparent transverse relaxation time, T , which is expected to strongly influence HNG signal. In this paper, a broadband (0.1–100 MHz) variable field strength MR imaging system for rodents is described. A custom‐built resistive magnet was constructed and shimmed to provide the necessary homogeneity for imaging. RF coils and transmit/receive switches for different frequencies were also developed. Preliminary proton ( 1 H) and hyperpolarized 129 Xe images of test objects are presented, including a desiccated lung phantom. In vivo 129 Xe signals from rat lungs were acquired at 73.5 mT and T was estimated to be approximately 80 ± 8 ms, in good agreement with previously reported values. The MR system developed should be useful for imaging rodent lungs at different field strengths to verify the expected SNR and spatial resolution possible using HNG imaging and to investigate long range diffusion and oxygen‐induced transverse relaxation. © 2008 Wiley Periodicals, Inc. Concepts Magn Reson Part B (Magn Reson Engineering) 33B: 124–137, 2008
Sidewall Covalent Functionalization of Single Wall Carbon Nanotubes through C-N Bond Forming Reactions of Fluoronanotubes with Urea, Guanidine and Thiourea (Preprint) (2007)

Sidewall covalent functionalization of carbon nanotubes is necessary to achieve smaller bundles, link to other functional moieties, and to aid in better dispersion in composites. In the present study, we present a one-step functionalization method which uses fluorinated single wall carbon nanotubes (F-SWNTs) as starting materials in the reactions with either urea, thiourea, or guanidine. Through these reactions, the derivatives with terminal amide and heteroamide groups on the nanotube sidewalls have been prepared. The products still contain some residual fluorine creating bifunctional nanotubes. These derivatives were characterized by Raman spectroscopy, Fourier transform infrared (FTIR), thermo gravimetric analysis (TGA), scanning electron microscopy (SEM), x-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) and atomic force microscopy (AFM). Compared to fluorinated tubes, the urea-F-SWNTs, among the three derivatives, have shown the highest stability in water and aqueous urea solutions, thereby creating new opportunities for biomedical applications with nanotubes. These bifunctional derivatives will aid in creating an interface between the SWNTs and polymers, which will result in much stronger composites. The three derivatives are easily and rapidly synthesized, and the method can be easily scaled up for applications such as creating an integrated polymer network for stronger composites, coatings, for use in biomedical applications and nanoelectronic devices.