gebhart/patrepeval huggingface dataset:
Visualizing program memory behavior using memory reference traces (2012)

Computer programs have complex interactions with their underlying hardware, exhibiting complex behaviors as a result. It is critical to understand these programs, as they serve an important role: researchers use them to express new ideas in computer science, while many others derive production value from them. In both cases, program understanding leads to mastery over these functions, adding value to human endeavors. Memory behavior is one of the hallmarks of general program behavior: it represents the critical function of retrieving data for the program to work on; it often reflects the overall actions taken by the program, providing a signature of program behavior; and it is often an important performance bottleneck, as the the memory subsystem is typically much slower than the processor. These reasons justify an investigation into the memory behavior of programs. 
A memory reference trace is a list of memory transactions performed by a program at runtime, a rich data source capturing the whole of a program's interaction with the memory subsystem, and a clear starting point for investigating program memory behavior. However, such a trace is extremely difficult to interpret by mere inspection, as it consists solely of many, many addresses and operation codes, without any more structure or context. This dissertation proposes to use visualization to construct images and animations of the data within a reference trace, thereby visually transmitting structures and events as encoded in the trace. These visualization approaches are designed with different focuses, meant to expose various aspects of the trace. For instance, the time dimension of the reference traces can be handled either with animation, showing events as they occur, or by laying time out in a spatial dimension, giving a view of the entire history of the trace at once. The approaches also vary in their level of abstraction from the hardware: some are concretely connected to representations of the memory itself, while others are more free-form, using more abstract metaphors to highlight general behaviors and patterns, which in turn characterize the program behavior. Each approach delivers its own set of insights, as demonstrated in this dissertation.
Non-Intrusive Sensor for In Situ Measurement of Recession Rate of Heat Shield Ablatives (2010)

The development of a new sensor for in-situ non-intrusive measurements of recession rate of heat shield ablative materials is described. The sensor utilizes a focused ultrasound approach to non-intrusively detect the ablative material's surface loss while simultaneously correcting for acoustic velocity dependencies on temperature. The latter correction is done via a closed loop feedback approach that yields the average acoustic velocity through the ablative material. The multi-source focusing approach is atypical of current ultrasound based sensors used for ablation recession rate measurement, which require a-priori knowledge of temperature distribution within the ablative to yield accurate data on recession rate. The paper describes the early development of the sensor system resulting in a proof-of-concept breadboard system that demonstrates its unique operational aspects and possibilities as a heat shield health monitoring system for future spacecraft.
<i>Staphylococcus aureus</i> Fibronectin-Binding Protein Serves as a Substrate for Coagulation Factor XIIIa:  Evidence for Factor XIIIa-Catalyzed Covalent Cross-Linking to Fibronectin and Fibrin (2003)

In this study, we have investigated the interactions of a Staphylococcal recombinant fibronectin-binding protein A (rFnbA) with fibronectin, fibrinogen, and fibrin. Using analytical size-exclusion chromatography, we evaluated the stoichiometry of reversible binding of FnbA to fibronectin and demonstrated that, in solution, it can accommodate at least two molecules of fibronectin. Results of ELISA experiments demonstrated that rFnbA binds with equally high affinity to both immobilized fibrinogen and fibrin. When included into a thrombin-induced fibrin polymerization reaction, rFnbA strongly inhibited fibrin assembly in a dose-dependent manner. In this study, we have shown that rFnbA can act as a substrate for coagulation factor XIIIa. Factor XIIIa catalyzes the incorporation of amine donor (dansylacadaverine) and amine acceptor (peptide patterned on the N-terminal sequence of fibronectin) synthetic probes into rFnbA, suggesting that it serves as a bifunctional substrate containing reactive glutamine and lysine residues. We have demonstrated that the reversible complex formed by rFnbA and fibronectin or rFnbA and fibrin is covalently stabilized by the transglutaminase action of factor XIIIa. Incubation of rFnbA in the presence of either of its ligands and factor XIIIa results in the introduction of intermolecular epsilon-(gamma-glutamyl)lysine isopeptide bond(s) and the formation of high molecular mass heteropolymers. These findings suggest a novel mechanism by which pathogenic Staphylococcus aureus may utilize the transglutaminase activity of factor XIIIa for attachment to soluble proteins, cell surfaces, and matrixes.
Novel Optical Fiber Cable with Small Cable Diameter Employing Rollable 20-Fiber Ribbons (2010)

This letter proposes novel optical fiber cables with extremely small cable diameter that employs rollable 20-fiber ribbons, which will improve fiber ribbon and cable productivity compared with optical fiber cable employing rollable 4-fiber ribbons. We fabricated the cables and investigated its feasibility in terms of high-count compactness, cable productivity, fiber strain induced by cable bending, optical loss characteristics and capacity for mass splicing. As a result, we confirmed the excellence of these cables and their fiber splicing workability.
Bu-2470, a new peptide antibiotic complex. I. Production, isolation and properties of Bu-2470 A, B1 and B2. (1983)

A strain of Bacillus circulans produced a complex of basic peptide antibiotics designated Bu-2470, which was found to contain four active components, A, B1, B2a and B2b. Bu-2470 A specifically inhibited various Pseudomonas species including P. aeruginosa, P. maltophilia and P. putida, but otherwise its antibacterial spectrum was limited to certain Gram-negative organisms. Bu-2470 B1 and B2 (B2a + B2b) showed broad antibiotic activity against Gram-positive and Gram-negative bacteria including Pseudomonas species. The physicochemical and biological properties of Bu-2470 B1 and B2 are very similar to those of the octapeptin group of antibiotics.
Imide/arylene ether block copolymers (1991)

Two series of imide/arylene either block copolymers were prepared using an arylene ether block and either an amorphous or semi-crystalline imide block. The resulting copolymers were characterized and selected physical and mechanical properties were determined. These results, as well as comparisons to the homopolymer properties, are discussed.
Traveltime Inversion of Walkaway VSP Data for a Model with Dipping TI Layers (2015)

Walkaway vertical seismic profiling (VSP) data potentially provides the most reliable anisotropy estimates. In many cases, a 1D model is not quite adequate for real data. If walkaway first break function is not symmetrical with respect to the well, then we need a velocity model with dipping/curvilinear boundaries. In this paper, I present a traveltime inversion approach for transverse isotropy (TI) parameter estimation that takes into account lateral velocity changes in the overburden. I describe these changes with dipping boundaries above the shallowest receiver. Dipping boundaries, interval velocities and anisotropic TI parameters in the overburden are included, together with simultaneous estimations of anisotropic parameters within the receiver array depth interval. Tests on model data show reliable anisotropy estimates. This approach was applied to multi-azimuthal walkaway data.
Plasma Renin Activity by LC-MS/MS: Development of a Prototypical Clinical Assay Reveals a Subpopulation of Human Plasma Samples with Substantial Peptidase Activity (2010)

Our method requires reduced sample handling when compared with an RIA and eliminates the need for extended generation times for samples with low renin activity. Degradation of Ang I during generation appears to be a confounding variable in the interpretation of results from some clinical samples. Samples with profound degradation activity can be identified using a degradation standard that is added at the start of generation.
Effect of Combination Therapy with Lactoferrin and Antibiotics against Staphylococcal Mastitis on Drying Cows (2006)

We examined combination therapy with both lactoferrin (Lf) and antibiotics on clinical mastitis due to Staphylococcus aureus (S.aureus) on drying cows. The clinical symptoms of mastitic quarters were cured 81% of combination therapeutic quarters at 7 days post injection (dpi). Moreover, most of mammary gland secretions (MGSs) in combination therapeutic quarters were normal at 7 days after parturition. In the quarters with combination therapy, S.aureus counts, Lf concentrations and content rate of concanavalin A (Con A) low-affinity Lf decreased and were lower than in the quarters treated with Lf or antibiotics alone. The mRNA expression of tumor necrosis factor alpha (TNFalpha) of the quarters with combination therapy also decreased and was lower than that of the Lf or antibiotics treated. The mRNA expression of pro-inflammatory cytokines and chemokines in bovine mammary gland epithelial lined cells (BMEC) stimulated with Lf were lower than those of Con A low-affinity Lf stimulated BMEC. Moreover, Lf showed an inhibitory effect to the induction of pro-inflammatory cytokine mRNA expression when co-stimulated with Lf and Con A low-affinity Lf. Nuclear factor kappa B (NFkappaB) activation was also induced with Con A low-affinity Lf, and the inhibitory effects of Lf were also confirmed on BMEC co-stimulated with Lf and Con A low-affinity Lf. These results indicated that the efficacy of combination therapy with antibiotics and Lf caused antibacterial effect of antibiotics and inhibition of pro-inflammatory cytokine and chemokine production with Lf via the inhibition of NFkappaB activation.
Formal Cross-Coupling of Diaryl Ethers with Ammonia by Dual C(Ar)–O Bond Cleavages (2018)

The conversion of renewable resources and inexpensive inorganic chemicals directly into higher value-added organic chemicals is becoming more and more important for our society’s future sustainable development. Lignin, being the second most abundant organic carbon renewable resource on Earth, has been treated as waste in the pulp and paper industry. The 4-O-5 linkage diaryl ether bond is the strongest among the three types of ether linkages in lignins. Selective cleavage of this linkage can potentially generate smaller processable bio-based aromatic polymeric materials and compounds. Furthermore, there has been a long synthetic interest in coupling reactions with aryl ethers via C(Ar)–O bond cleavage, for example, for polyphenylene oxide (PPO) waste recycling. On the other hand, ammonia is a very inexpensive industrial inorganic chemical. Herein, we report a direct conversion of diaryl ethers and ammonia into aniline derivatives and arenes, providing a model for selective lignin 4-O-5 linkage modification and PPO recycling with inexpensive ammonia. Both symmetrical and unsymmetrical diaryl ethers were successfully cross-coupled with ammonia via dual C(Ar)–O bond cleavages, generating the corresponding cyclohexylanilines and arenes.
Resorcinol-Based Grp94-Selective Inhibitors (2017)

Glucose regulated protein 94 (Grp94) is the endoplasmic reticulum resident of the 90 kDa heat shock protein (Hsp90) family and represents a promising therapeutic target for the treatment of several diseases. Grp94 is the most unique member of the 90 kDa heat shock protein family due to a five amino acid insertion into its primary sequence, which creates hydrophobic subpockets exclusive to Grp94 that can be utilized for selective inhibition. The first resorcinol-based Grp94-selective inhibitor to take advantage of the hydrophobic S2 subpocket has been developed and shown to manifest low nanomolar affinity and ∼10-fold selectivity for Grp94. Furthermore, these Grp94-selective inhibitors manifest low micromolar GI<sub>50</sub> values against multiple myeloma cells, supporting Grp94 as an emerging target for the treatment of this disease.
Spin switches for compact implementation of neuron and synapse (2014)

Nanomagnets driven by spin currents provide a natural implementation for a neuron and a synapse: currents allow convenient summation of multiple inputs, while the magnet provides the threshold function. The objective of this paper is to explore the possibility of a hardware neural network implementation using a spin switch (SS) as its basic building block. SS is a recently proposed device based on established technology with a transistor-like gain and input-output isolation. This allows neural networks to be constructed with purely passive interconnections without intervening clocks or amplifiers. The weights for the neural network are conveniently adjusted through analog voltages that can be stored in a non-volatile manner in an underlying CMOS layer using a floating gate low dropout voltage regulator. The operation of a multi-layer SS neural network designed for character recognition is demonstrated using a standard simulation model based on coupled Landau-Lifshitz-Gilbert equations, one for each magnet in the network.
Ebp1, an ErbB‐3 binding protein, interacts with Rb and affects Rb transcriptional regulation (2001)

Ebp1, an ErbB-3 binding protein, inhibits the proliferation and induces the differentiation of human breast cancer cells. The mechanisms of these effects are unknown. Rb, the product of the retinoblastoma gene, is an important modulator of cell cycle progression and cellular differentiation. We report that Rb is a binding target for Ebp1. Ebp1 was localized to both the nucleus and the cytoplasm of logarithmically growing AU565 breast cancer cells and HeLa cells as determined by confocal immunofluorescent microscopy. Ebp1 was present in Rb immunoprecipitates derived from AU565 breast cancer cells. GST-Rb also bound endogenous Ebp1. Using GST-Ebp1 constructs, we determined that the 72 C-terminal amino acids of Ebp1 were sufficient to bind Rb. Dephosphorylation of Ebp1 enhanced the interaction of Ebp1 with Rb. The overexpression of Ebp1 in MCF-7 and AU565 (Rb(+)) cells inhibited the activity of the E2F1 regulated cyclin-E promoter. Ebp1 bound E2F1 indirectly via Rb in lysates of MCF-7 cells. The interaction of Ebp1 with Rb may prove to be an important mechanism of Ebp1 induced changes in cell proliferation and differentiation.
Quantum Dot Photonic Integrated Circuits on Silicon (2018)

Quantum dot lasers, amplifiers, modulators and photodetectors epitaxially grown on Si are promising for photonic integrated circuits. Laser performance is improving rapidly with continuous-wave threshold currents below 1 mA, injection efficiency of 87% and output power of 185 mW at 20 °C. Reliability tests show an extrapolated mean-time-to-failure of more than a million hours. This represents a significant stride toward efficient, scalable, and reliable III-V lasers on Si substrates for photonic integrated circuits that are compatible with CMOS foundries.
Probability interval partitioning entropy coding using systematic variable-to-variable length codes (2011)

The recently emerging probability interval partitioning entropy (PIPE) coding scheme offers high coding efficiency at a comparably low complexity level. In this paper, a new set of systematic variable-to-variable length (v2v) codes is proposed for use within the PIPE coding concept that allows the complexity requirements to be reduced even further. The proposed systematic v2v codes can be efficiently implemented by using simple counters instead of memory consuming tables. At the same time, the average number of operations per decoded binary symbol can be reduced by more than a factor of 2 relative to a fast multiplication-free binary arithmetic decoder. In terms of coding efficiency, experimental results show that in a typical video coding environment the average Bjontegaard delta (BD) rate increase is typically less than 0.5% when compared to the use of nearly optimal binary arithmetic codes.
Preliminary Observations About Providing Problem Resolution Advisories to Air Traffic Controllers (2000)

This paper reports on research being conducted by The MITRE Corporation’s Center for Advanced Aviation System Development (CAASD) into providing a set of problem resolution advisories to air traffic controllers. The goal of this research is to assist the controller in the generation of strategic resolution maneuvers in complex, heavy traffic situations, and consequently facilitate an efficient, strategic mode of Air Traffic Control (ATC) in these situations. These capabilities are currently being developed as an extension to the User Request Evaluation Tool (URET) prototype, and build on the URET capabilities to support a strategic mode of ATC operation. The primary focus of this research is termed Problem Analysis, Resolution and Ranking (PARR), which provides a ranked set of resolution maneuvers for aircraft-to-aircraft, aircraft-toairspace, and metering problems. Resolutions are generated in a range of dimensions and directions, and support is provided for the rapid evaluation and implementation of the results. Additional efforts involve the generation of automatically probed sets of *Daniel Kirk joined the MITRE Corporation in 1988. His work at MITRE has included the development of problem resolution algorithms and requirements for the Automated En Route ATC (AERA) 2 project, and various aspects of the User Request Evaluation Tool (URET) project. He is currently the Task Lead for the problem resolution enhancements to URET described in this report. altitude, direct-to-downstream fix, and speed maneuvers to enhance the existing URET menu displays. A graphical display is also being developed to assist the controller in the evaluation of the altitude probe results. This paper describes these resolution capabilities, presents data from real world scenarios, and discusses the results of initial laboratory analyses.
MULTI-TRANSGENIC PIGS FOR XENOTRANSPLANTATION (2012)

Successful development of somatic cell nuclear transfer (cloning) technology in pigs has allowed for precise genetic manipulation of the pig genome. For xenotransplantation applications, pigs have been produced in which both copies of the a1,3-galactosyl transferase (GT) gene were inactivated (GTKO pigs). Analysis of tissues from GTKO pigs demonstrated a complete lack of immunogenic Gala1,3Gal (Gal) sugars, while in vivo pre-clinical studies in nonhuman primates, using cells (i.e. pancreatic islets) or whole organs (heart, kidney, liver, lung), demonstrated the elimination of hyperacute rejection, and prolonged survival compared to wild-type controls. While survival of GTKO xenografts was extended, challenges including induced antibody responses to non-gal antigens, thrombosis, inflammation, and cell-mediated rejection remained, pointing to the need for further genetic modification of the source pig. Towards this goal, through a combination of cloning and breeding, in combination with GTKO, we have produced multi-transgenic pigs (some with 5 different transgenes) with controlled expression of genes for (1) complement regulation to address the humoral response to anti-non-gal targets (DAF, CD46); (2) inhibition of inflammation and thrombosis (TFPI, CD39, thrombomodulin, EPCR); and (3) local protection against the human cellular response (CTLA4Ig, CIITA-DN). For some transgenes a constitutive promoter system can be used for expression in all tissues, such that one animal can be used for multiple transplant applications, however, our results have shown that for certain transgenes, tissue-specific gene expression is preferred. Since inhibition of thrombosis, complement modulation, and suppression of T-cell responses are important to delayed xenograft rejection of both whole organs and islet cell xenografts, pigs have been produced with tissue-specific transgene expression in either the vascular endothelium or endocrine pancreas compartments, or constitutively in all tissues. In vivo results in nonhuman primates have demonstrated complete normalization of blood glucose for up to 1 year in diabetic monkeys, and 8-month survival of multigenic pig hearts in baboons, evidence for the promise of this technology for human clinical applications.
Combinatorial development of novel polymers resistant to bacterial attachment (2012)

Bacterial attachment and subsequent biofilm formation are key challenges to the long term performance of many medical devices. Here, a high throughput approach coupled with the analysis of surface structure-property relationships using a chemometics approach has been developed to simultaneously investigate the interaction of bacteria with hundreds of polymeric materials on a microarray format. Using this system, a new group of materials comprising ester and hydrophobic moieties are identified that dramatically reduce the attachment of clinically relevant, pathogenic bacteria (Pseudomonas aeruginosa, Staphylococcus aureus and uropathogenic Escherichia coli). Hit materials coated on silicone catheters resulted in up to a 30 fold reduction in coverage compared to a commercial silver embedded catheter, which has been proven to half the incidence of clinically acquired infection. These polymers represent a new class of materials resistant to bacterial attachment that could not have been predicted from the current understanding of bacteria-surface interactions.
Tissue Engineering: Composite Three‐Dimensional Woven Scaffolds with Interpenetrating Network Hydrogels to Create Functional Synthetic Articular Cartilage (Adv. Funct. Mater. 47/2013) (2013)

A 3D woven fiber scaffold infiltrated with an interpenetrating network hydrogel mimics the load-bearing and tribological properties of native cartilage. The woven fiber scaffold, created by X. Zhao, F. Guilak, and co-workers on page 5833, provides controlled tensile and compressive mechanical properties in three dimensions, while the infused hydrogel, consisting of an interpenetrating network of alginate and polyacrylamide, provides high toughness and a low coeffecient of friction. This biomimetic, fiber-reinforced composite structure has potential as an acellular or cell-based replacement for cartilage.
Adenosine and Its Receptors During Inflammation (1999)

The number of endogenous mediators of inflammation is large and growing, but the list of endogenous inhibitors of inflammation has remained relatively small. Most investigators are familiar with glucocorticoids, and there is an increasing appreciation of lipid mediators, select cytokines, and endogenous cytokine inhibitors as anti-inflammatory mediators. Adenosine, a purine nucleoside, is another agent that has received increasing interest as an endogenous anti-inflammatory agent. In this chapter the author will discuss the generation of adenosine at inflamed sites, the cell surface receptors for adenosine, which, when occupied, affect inflammatory cell function and the functional effects of adenosine on the various inflammatory cells and the inflammatory process. Finally, the author will discuss the potential pharmacologic uses of adenosine as an anti-inflammatory agent.