gebhart/patrepeval huggingface dataset:
Lysine 68 acetylation directs MnSOD as a tetrameric detoxification complex versus a monomeric tumor promoter (2019)

Manganese superoxide dismutase (MnSOD) functions as a tumor suppressor; however, once tumorigenesis occurs, clinical data suggest MnSOD levels correlate with more aggressive human tumors, implying a potential dual function of MnSOD in the regulation of metabolism. Here we show, using in vitro transformation and xenograft growth assays that the MnSOD-K68 acetylation (Ac) mimic mutant (MnSOD<sup>K68Q</sup>) functions as a tumor promoter. Interestingly, in various breast cancer and primary cell types the expression of MnSOD<sup>K68Q</sup> is accompanied with a change of MnSOD's stoichiometry from a known homotetramer complex to a monomeric form. Biochemical experiments using the MnSOD-K68Q Ac-mimic, or physically K68-Ac (MnSOD-K68-Ac), suggest that these monomers function as a peroxidase, distinct from the established MnSOD superoxide dismutase activity. MnSOD<sup>K68Q</sup> expressing cells exhibit resistance to tamoxifen (Tam) and cells selected for Tam resistance exhibited increased K68-Ac and monomeric MnSOD. These results suggest a MnSOD-K68-Ac metabolic pathway for Tam resistance, carcinogenesis and tumor progression.
Improvements in Network Parameter Error Identification via Synchronized Phasors (2009)

This paper is concerned about the identification of network parameter errors, which are known to bias the state estimation solution. Previously proposed parameter error identification techniques implicitly assume the availability of a set of conventional measurements. In this paper, it is first shown that identification of certain parameter errors based on such conventional measurements, no matter how redundant they are, may not always be possible. The paper then describes the need for phasor measurements to overcome this limitation and presents an identification method that requires the use of such measurements. Examples are also included to describe the application of the proposed method to a number of typical topologies and measurement configurations.
A novel negative expansion substrate material for athermalizing fiber Bragg gratings (1996)

/spl beta/-eucryptite solid solution glass-ceramic substrates have a negative thermal expansion ideally suited for athermalizing fiber Bragg gratings. Gratings with thermal variations of 0.0022 nm//spl deg/C from -40 to +85/spl deg/C are reported.
A New Approach to AIDS Research and Prevention: The Use of Gene‐Mutated HIV‐1/SIV Chimeric Viruses for Anti‐HIV‐1 Live‐Attenuated Vaccines (1998)

The lack of a suitable animal model is a major obstacle to developing anti-HIV-1 vaccines. We successfully generated an SIVmac/HIV-1 chimeric virus (SHIV) (designated as NM-3rN) that contains the HIV-1 env gene and is infectious to macaque monkeys. Challenging the vaccinated macaque monkeys with NM-3rN, we developed an evaluation system for anti-HIV-1 Env-targeted vaccines. For the purpose of making the vaccine, a series of gene-mutated SHIVs were constructed. The monkeys vaccinated with these SHIVs had long-term anti-virus immunities without manifesting the disease, and became resistant to a challenge inoculation with NM-3rN. The sera from a monkey showed that, after the vaccination, the neutralizing antibodies not only against the parental HIV-1 but also against an antigenically different HIV-1 were raised. In vivo experiments confirmed that the vaccinated monkeys were protected from the challenge inoculum of an antigenically different SHIV-MN. Vaccination of monkeys with the attenuated SHIVs showed that further gene-deletion of the SHIV resulted in less immunogenicity. Nevertheless, the attenuated SHIVs had a vaccine effect against the challenge inoculation. In addition to specific immunities including neutralizing antibodies and cytotoxic T cells, a more complicated immune mechanism induced by live vaccine appears to play a role in this protection. Our data suggest that the live vaccine can induce strong and wide-range immunity against HIV-1. These SHIVs should contribute to understanding the pathogenicity of AIDS and to the development of future anti-HIV-1 live vaccines for humans.
ACE -- An Anomaly Contribution Explainer for Cyber-Security Applications (2019)

In this paper, we introduce Anomaly Contribution Explainer or ACE, a tool to explain security anomaly detection models in terms of the model features through a regression framework, and its variant, ACE-KL, which highlights the important anomaly contributors. ACE and ACE-KL provide insights in diagnosing which attributes significantly contribute to an anomaly by building a specialized linear model to locally approximate the anomaly score that a black-box model generates. We conducted experiments with these anomaly detection models to detect security anomalies on both synthetic data and real data. In particular, we evaluate performance on three public data sets: CERT insider threat, netflow logs, and Android malware. The experimental results are encouraging: our methods consistently identify the correct contributing feature in the synthetic data where ground truth is available; similarly, for real data sets, our methods point a security analyst in the direction of the underlying causes of an anomaly, including in one case leading to the discovery of previously overlooked network scanning activity. We have made our source code publicly available.
Natural Philosophy and Thermodynamics: William Thomson and ‘The Dynamical Theory of Heat’ (1976)

William Thomson's image as a professional mathematical physicist who adheres, particularly in his work in classical thermodynamics, to a strict experimental basis for his science, avoids speculative hypotheses, and becomes renowned for his omission of philosophical declarations has been reinforced in varying degrees by those historians who have attempted, as either admirers or critics of Thomson, to describe and assess his life. J. G. Crowther, for example, sees him as a thinker of great intellectual strength, but deficient in intellectual taste; a scientist aware only of his immediate work and without depth of vision. Not well read in the literature of the subjects of his research, Thomson is seen, moreover, as one whose achievements owe little to the work of others, and whose great personality ‘is an expression in the realm of ideas of the power and blindness of capitalism’, especially through ‘his view of the world in terms of engineering conceptions’. On the other hand, even Sir Joseph Larmor, for whom Thomson was nothing less than a hero, is to be found ascribing to him the epithet of pragmatist.
Functional studies on the influenza A virus M2 protein (1996)

The M2 protein of influenza A viruses is a homotetramer composed of four 97 amino acid subunits which form an ion permeable channel. It plays an important role both in the process of virus uncoating and in modulating the pH of the transport pathway which is necessary for haemagglutinin (HA) maturation. \nM2 was stably expressed in mouse erythroleukaemia (MEL) cells under the control of the inducible β-globin locus control region (LCR). The production of M2 peaked at 4-6 days post induction and was at a level comparable to that in virus-infected MDCK cells. The expressed M2 was structurally similar to that produced in virus-infected MDCK cells, in particular with regard to the formation and stability of the tetramer and was also phosphorylated and palmitoylated. \nThe function of the M2 protein expressed in MEL cells was studied using three assays, 1) co-expression of HA and M2, 2) determination of intracellular pH and 3) measurements of ion conductance. Analysis of MEL cells showed that they provided a suitable environment for the co-expression of M2 and HA. Expression of M2 resulted in a decrease in intracellular pH, indicating that the M2 protein is responsible for the decrease in cytoplasmic pH during virus infection. Voltage clamp measurements showed that the expressed M2 formed a proton-selective channel which was specifically inhibited by rimantadine. Two features of the results indicated that the current was due to a proton conductance. At zero membrane potential, both the direction and magnitude of the current were dependent on the proton gradient and secondly the reversal potential was equal to the proton equilibrium potential. Neither the reversal potential nor the amplitude of the current were influenced by the presence of other small ions, including Na+, or K+ or CI-. These results are consistent with the biochemical role that M2 is perceived to play during virus infection. Structure/activity studies were also undertaken to identify residues in the transmembrane domain of the M2 protein which affected both the activation and thermal stability of the tetramer. In particular amino acid differences between the Weybridge and Rostock M2 proteins were studied.
Epidemiological Association of Airway Inflammation with Asthma Symptoms and Airway Hyperresponsiveness in Childhood (1998)

The role of airway inflammation in childhood asthma is not well defined, despite modern treatment approaches recommending potent anti-inflammatory therapy for an increasing number of children. In this study, induced sputum analysis was used to investigate the relationships among sputum inflammatory cells (eosinophils and mast cells), asthma symptoms, and airway hyperresponsiveness to hypertonic saline in a cohort of 170 children aged 8-14 years. Children who reported asthma symptoms in the past 2 wk had a 2. 25-fold (95% to CI, 1.20-4.24) increased odds of having significant sputum eosinophilia. Hyperresponsiveness to hypertonic saline was strongly associated with higher levels of sputum eosinophils ([OR] 4. 36, 1.70-11.20), sputum mast cells (OR 7.46, 2.48-22.75), and nasal eosinophils (OR 4.73, 1.89-11.86). Interestingly, boys were more likely than girls to have features of airway inflammation (sputum mast cells, OR 3.33, 1.15-9.65; nasal eosinophils, OR 3.25, 1.72-5. 97), which is consistent with the known increase in asthma prevalence in boys in this age group. Airway inflammation with eosinophils and mast cells is likely to be important in the pathogenesis of asthma in childhood. Induced sputum analysis can be used to evaluate this problem and has the potential to be a useful tool for monitoring therapy.
Novel substrates for improved cooling of power electronics (2017)

The thermal management of power electronics is critical to the long term reliability of these devices. In this work, three concepts which allow the placement of advanced cooling solutions close to power electronic die are investigated through the creation of advanced substrate technologies. First, two phase cooling was integrated with direct bonded copper power substrates by sintering copper particles directly onto the back side to allow for evaporative two phase cooling. The work experimentally investigated the impact of the thickness of the copper microporous layer as well as its size relative to the thermal test die on the heat transfer performance. The second methodology developed a novel substrate that replaces the DBC by having a cold plate with integrated AlN dielectric and circuit layer. A low-cost bonding method which created a low thermal resistance composite bonding layer was developed and demonstrated which allows low thermal resistance between the die and the cooling fluid. Finally, a third technique which uses a glass interposer with copper vias to bond the power die was investigated as a third packaging methodology. This strategy was explored through finite element analysis. Overall, this thesis presents several new pathways to improving the thermal management of wide bandgap power electronic and RF devices.
Genotyping of forensic short tandem repeat (STR) systems based on sizing precision in a capillary electrophoresis instrument (1998)

Automated fluorescence analysis of polymerase chain reaction (PCR)-amplified short tandem repeat (STR) systems by capillary electrophoresis (CE) is becoming an established tool both in forensic casework and in the implementation of both state and national convicted offender DNA databases. A new capillary electrophoresis instrument, the ABI Prism 310 Genetic Analyzer, along with the Performance Optimized Polymer 4 (POP-4) provides an automated and precise method for simultaneously analyzing ten fluorescently labeled STR loci from a single PCR amplification kit, which provides a power of discrimination of approximately one in five billion from a single PCR amplification. Data are presented on sizing precision, sizing accuracy, and resolution for the STR loci in the AmpFlSTR Profiler kit. Sizing accuracy is highly dependent on the electrophoresis system, and therefore the reporting of alleles based on the nucleotide size obtained from an electrophoresis system is not recommended for forensic work. The precision of the 310 capillary electrophoresis system, coupled with software developed for automated genotyping of alleles based on the use of an allelic ladder, allows for accurate genotyping of STR loci. Sizing precision of < or = 0.16 nucleotide standard deviation was obtained with this system, thus allowing for accurate genotyping of length variants that differ in length by a single nucleotide.
Enhancing the Structural Performance of Additively Manufactured Objects (2018)

The ability to accurately quantify the performance an additively manufactured (AM) product is important for a widespread industry adoption of AM as the design is required to: (1) satisfy geometrical constraints, (2) satisfy structural constraints dictated by its intended function, and (3) be cost effective compared to traditional manufacturing methods. Optimization techniques offer design aids in creating cost-effective structures that meet the prescribed structural objectives. The fundamental problem in existing approaches lies in the difficulty to quantify the structural performance as each unique design leads to a new set of analyses to determine the structural robustness and such analyses can be very costly due to the complexity of in-use forces experienced by the structure. This work develops computationally tractable methods tailored to maximize the structural performance of AM products. A geometry preserving build orientation optimization method as well as data-driven shape optimization approaches to structural design are presented. Proposed methods greatly enhance the value of AM technology by taking advantage of the design space enabled by it for a broad class of problems involving complex in-use loads.
The Involvement of Arg265 of Mouse Ribonucleotide Reductase R2 Protein in Proton Transfer and Catalysis (2006)

Ribonucleotide reductase class I enzymes consist of two non-identical subunits, R1 and R2, the latter containing a diiron carboxylate center and a stable tyrosyl radical (Tyr*), both essential for catalysis. Catalysis is known to involve highly conserved amino acid residues covering a range of approximately 35 A and a concerted mechanism involving long range electron transfer, probably coupled to proton transfer. A number of residues involved in electron transfer in both the R1 and R2 proteins have been identified, but no direct model has been presented regarding the proton transfer side of the process. Arg265 is conserved in all known sequences of class Ia R2. In this study we have used site-directed mutagenesis to gain insight into the role of this residue, which lies close to the catalytically essential Asp266 and Trp103. Mutants to Arg265 included replacement by Ala, Glu, Gln, and Tyr. All mutants of Arg265 were found to have no or low catalytic activity with the exception of Arg265 to Glu, which shows approximately 40% of the activity of native R2. We also found that the Arg mutants were capable of stable tyrosyl radical generation, with similar kinetics of radical formation and R1 binding as native R2. Our results, supported by molecular modeling, strongly suggest that Arg265 is involved in the proton-coupled electron transfer pathway and may act as a proton mediator during catalysis.
Rhinovirus Outbreak in a Long Term Care Facility for Elderly Persons Associated with Unusually High Mortality (2005)

During a 6-week period in 2003, 56 residents and 26 staff developed respiratory illness in a long-term facility; 12 residents died. Seven of 13 respiratory specimens were culture-positive for rhinovirus; 6 of the isolates were serotype 82. In elderly populations, severe illness may be associated with organisms typically considered to be "benign," such as rhinovirus.
Role of Planar Laser-Induced Fluorescence in Combustion Research (2009)

Laser diagnostics are now considered an indispensable tool in fluid dynamics research. Such measurements provide a deeper understanding of the inner physical and chemical processes, which is required to validate and improve computer-based simulations and to assist applied research in practical combustors. This paper presents an overview of the potential of planar laser-induced fluorescence (PLIF), which currently allows for the imaging of scalar properties such as species concentration, temperature, velocity, pressure and density over wide pressure and temperature ranges with high temporal and spatial resolution. Although a complete picture of the present research and PLIF applications to fluid mechanics is beyond the scope of this article, this overview focuses rather on the basic concepts underlying the technique and its application to various flowfields at Onera. These examples cover applications to primarily gas flows like mixing experiments under isothermal and isobaric conditions, fuel/air mixing and temperature measurements in heated jet flows, subsonic and supersonic flame structures and improvement of combustion processes using nanosecond pulsed discharges. Several examples of measurements of fuel concentration in multiphase flows, flame structure around isolated droplets and fuel/air mixing processes in kerosene/air combustion at high pressure are presented. The paper concludes with a section that addresses key issues that remain as challenges for continued research towards the improvement of quantitative PLIF measurements.
Time Synchronization Attack in Smart Grid: Impact and Analysis (2013)

Many operations in power grids, such as fault detection and event location estimation, depend on precise timing information. In this paper, a novel Time Synchronization Attack (TSA) is proposed to attack the timing information in smart grid. Since many applications in smart grid utilize synchronous measurements and most of the measurement devices are equipped with global positioning system (GPS) for precise timing, it is highly probable to attack the measurement system by spoofing the GPS. The effectiveness of TSA is demonstrated for three applications of phasor measurement unit (PMU) in smart grid, namely transmission line fault detection, voltage stability monitoring and event locationing. The validity of TSA is demonstrated by numerical simulations.
Proteomic mapping of p53 immunogenicity in pancreatic, ovarian, and breast cancers (2016)

In this comprehensive analysis, mutations in tumor p53 induce strong, polyclonal autoantibodies with broadly reactive epitope specificity.
Neurophysiology of Skin Thermal Sensations (2016)

ABSTRACT Undoubtedly, adjusting our thermoregulatory behavior represents the most effective mechanism to maintain thermal homeostasis and ensure survival in the diverse thermal environments that we face on this planet. Remarkably, our thermal behavior is entirely dependent on the ability to detect variations in our internal (i.e., body) and external environment, via sensing changes in skin temperature and wetness. In the past 30 years, we have seen a significant expansion of our understanding of the molecular, neuroanatomical, and neurophysiological mechanisms that allow humans to sense temperature and humidity. The discovery of temperature‐activated ion channels which gate the generation of action potentials in thermosensitive neurons, along with the characterization of the spino‐thalamo‐cortical thermosensory pathway, and the development of neural models for the perception of skin wetness, are only some of the recent advances which have provided incredible insights on how biophysical changes in skin temperature and wetness are transduced into those neural signals which constitute the physiological substrate of skin thermal and wetness sensations. Understanding how afferent thermal inputs are integrated and how these contribute to behavioral and autonomic thermoregulatory responses under normal brain function is critical to determine how these mechanisms are disrupted in those neurological conditions, which see the concurrent presence of afferent thermosensory abnormalities and efferent thermoregulatory dysfunctions. Furthermore, advancing the knowledge on skin thermal and wetness sensations is crucial to support the development of neuroprosthetics. In light of the aforementioned text, this review will focus on the peripheral and central neurophysiological mechanisms underpinning skin thermal and wetness sensations in humans. © 2016 American Physiological Society. Compr Physiol 6:1279‐1294, 2016.
Pulse compression ultrasound for minimization of transmitted peak power (2002)

Spread spectrum pulse compression can be used as a method for reducing peak power so that it is within the bounds of safety guidelines set by the American Institute of Ultrasonic Measurements (AIUM). Pulse compression accomplishes this by implementing a longer length transmitted pulse of lower amplitude while maintaining the same signal gain, resolution, and signal-to-noise ratios. Here, correlation algorithms for implementing such a subsystem are described, as well as computer simulation results for methods that reduce correlation sidelobe levels resulting from that process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Organic Molecules Entrapped In A Silica Host For Use As Biosensor Probe Materials (1988)

Optically active organic molecules have been entrapped in a porous silica gel host for use as an opto-chemical transducer. Organic dye molecules were incorporated into the inorganic glassy matrix via the so called "sol-gel" technique. Sol-gel derived glasses are typically synthesized at room temperature and result in the formation of a relatively low density network structure, capable of supporting the rapid transport of atoms and small molecules. This "cage-like" network, however, serves to entrap larger molecules, such as organic dyes. The guest probe molecules do not migrate through the silica host. Fluorescence characteristics of optically active dye species, in many cases, are known to change in solution with respect to the activity of factors such as oxygen and pH. We have fabricated silica gel films containing organic probes, and measured changes in emission spectra of entrapped pyranine dye due to variations in the pH of ambient aqueous solution.
The ninth component of human complement: purification and physicochemical characterization. (1980)

A procedure for the isolation of the human complement (C) protein C9 is described. The procedure allowin. The purified protein has the electrophoretic mobility of an alpha-globulin, and is a single polypeptide chain with a m.w. of 71,000. No impurities were detected either on gel electrophoretic or immunochemical examination. C9 is a glycoprotein containing 7.8% carbohydrate, and in terms of residues per mole, 3.0 glucosamine, 17.6 neutral hexose, and 7.4 sialic acid. Its amino acid composition is typical of a globular serum protein. Upon automated Edman degradation of reduced and alkylated C9, no amino acid residues were released, suggesting a blocked N-terminus. The concentration of C9 in normal human serum is 58 +/- 8 microgram/ml. A high titer rabbit antiserum was produced and employed to immunochemically deplete serum of C9. The CH50 of the C9-depleted serum was identical to that of whole human serum; however, membrane fragments of erythrocytes lysed by C9-depleted serum lacked the typical ultrastructural C lesions, which constitute the dimeric membrane attack complex.