gebhart/patrepeval huggingface dataset:
Influence of Outer-Shell Metal Ligands on the Structural and Electronic Properties of Horse Liver Alcohol Dehydrogenase Zinc Active Site (2003)

An analysis of the high resolution 3D structures of zinc enzymes shows that the Zn−His−carboxyl(ate)−HX (X = OH or NH) H-bond motif is common. We investigate here the influence of this motif in the active site of horse liver alcohol dehydrogenase, which features the Zn−His−Asp−H2O motif. Density functional theory calculations are carried out on models of the active site complexed with the NAD+ cofactor, in which the metal ion binds either the alcohol substrate [Bahnson et al. Proc. Natl. Acad. Sci. U. S.A 1997, 94, 12797−12802]1 or a water molecule [Meijers et al. J. Biol. Chem. 2001, 276, 9316−9321].2 Our calculations suggest that in both complexes the presence of Asp49 significantly affects the structural and electronic properties of the metal site. Furthermore, they show that inclusion of the Asp bound water molecule is required to describe the energetics correctly. Finally, they suggest that the Asp49/water pattern could play a role in the enzymatic reaction.
Activin receptor‐like kinase5 inhibition suppresses mouse melanoma by ubiquitin degradation of Smad4, thereby derepressing eomesodermin in cytotoxic T lymphocytes (2014)

Varieties of transforming growth factor-β (TGF-β) antagonists have been developed to intervene with excessive TGF-β signalling activity in cancer. Activin receptor-like kinase5 (ALK5) inhibitors antagonize TGF-β signalling by blocking TGF-β receptor-activated Smad (R-Smad) phosphorylation. Here we report the novel mechanisms how ALK5 inhibitors exert a therapeutic effect on a mouse B16 melanoma model. Oral treatment with a novel ALK5 inhibitor, EW-7197 (2.5 mg/kg daily) or a representative ALK5 inhibitor, LY-2157299 (75 mg/kg bid) suppressed the progression of melanoma with enhanced cytotoxic T-lymphocyte (CTL) responses. Notably, ALK5 inhibitors not only blocked R-Smad phosphorylation, but also induced ubiquitin-mediated degradation of the common Smad, Smad4 mainly in CD8(+) T cells in melanoma-bearing mice. Accordingly, T-cell-specific deletion of Smad4 was sufficient to suppress the progression of melanoma. We further identified eomesodermin (Eomes), the T-box transcription factor regulating CTL functions, as a specific target repressed by TGF-β via Smad4 and Smad3 in CD8(+) T cells. Thus, ALK5 inhibition enhances anti-melanoma CTL responses through ubiquitin-mediated degradation of Smad4 in addition to the direct inhibitory effect on R-Smad phosphorylation.
Estradiol administration controls eosinophilia through estrogen receptor-α activation during acute peritoneal inflammation (2011)

Estrogens influence the incidence and the course of numerous immune or inflammatory diseases in humans and in experimental models. For instance, estrogens prevent the accumulation of granulocytes in acute inflammatory murine models, but the respective actions on neutrophil and eosinophil trafficking remain to be clarified. We demonstrate here that in a model of TGC-induced sterile peritonitis in ovx mice, chronic E2 administration electively and strongly inhibited peritoneal eosinophil accumulation. E2 decreased BM eosinophil number, contributing to a marked prevention of the TGC-induced eosinophil blood mobilization. These effects on eosinophil mobilization and peritoneal accumulation were abolished in ER-α(-/-) mice, demonstrating the crucial role of this nuclear receptor. Grafting ER-α(-/-) mice with ER-α(+/+) BM cells restored the suppressive effect of E2 on peritoneal eosinophilia, although the action on eosinophil blood mobilization was still abrogated. We therefore explored additional mechanisms and found that E2 reduced the peritoneal concentrations of key eosinophil prosurvival factors (IL-5, IL-9, and IL-25) and enhanced eosinophil apoptosis during the inflammatory process. Furthermore, this proapoptotic effect of E2 was abrogated in IL-5-overexpressing Tg mice. To conclude, we demonstrate for the first time that ER-α activation by exogenous E2 administration strongly inhibits eosinophil accumulation during acute inflammation in a nonreproductive target site for estrogen through combined actions on eosinophil mobilization and apoptosis. This specific, suppressive effect of chronic E2 replacement therapy on eosinophils has to be integrated to further understand the evolution of eosinophil-associated diseases in menopausal women.
Interpreter prototypes from formal language definitions (1993)

Denotational semantics is now used widely for the formal definition of programming languages but there is a lack of appropriate tools to support language development. General purpose language implementation systems are oriented to syntax with poor support for semantics. Specialised denotational semantics based systems correspond closely to the formalism but are rendered inflexible for language experimentation by their monolithic multiple stages Exploratory language development with formal definitions is better served by a unitary notation, encompassing syntax and semantics, which is close to but simpler than denotational semantics. Interactive implementation of the notation then facilitates language investigation through the direct execution of a formal definition as an interpreter for the defined language. This thesis presents Navel, a run-time typed, applicative order, pure functional programming language with integrated context free grammar rules. Navel has been used to develop prot...
Oligomeric-Induced Activity by Thienyl Pyrimidine Compounds Traps Prion Infectivity (2011)

Accumulation of PrP(Sc), an abnormal form of cellular prion protein (PrP), in the brain of animals and humans leads to fatal neurodegenerative disorders known as prion diseases. Limited protease digestion of PrP(Sc) produces a truncated form called PrP(27-30) that retains prion infectivity and is the main marker of disease targeted in most diagnostic tests. In the search for new anti-prion molecules, drug-screening assays on prion-infected murine cells have been oriented toward decreasing levels of PrP(27-30). In contrast, we screened for drugs promoting multimers of PrP(27-30), illustrating a possible stabilization of mouse PrP(Sc) species, because recent studies aiming to characterize the conformational stability of various prion strains showed that stable recombinant amyloids produced more stable prion strain, leading to longest incubation time. We identified a family of thienyl pyrimidine derivatives that induce SDS-resistant dimers and trimers of PrP(27-30). Bioassays performed on mice brain homogenates treated with these compounds showed that these thienyl pyrimidine derivatives diminished prion infectivity in vivo. Oligomeric-induced activity by thienyl pyrimidine compounds is a promising approach not only to understanding the pathogenesis of prions but also for prion diagnostics. This approach could be extended to other neurodegenerative "prionopathies," such as Alzheimer's, Huntington, or Parkinson's diseases.
External Cavity Laser with Alignment Tolerant III-V Gain Chip to PIC Edge Coupler in Silicon Nitride (2021)

We present an external cavity laser formed by coupling a III-V gain chip to a silicon nitride chip using an alignment tolerant multimode edge coupler, resulting in a misalignment tolerance of 12 &#x03BC;m. The ECL has a 42 kHz linewidth and 83 nm tuning range.
Excitation Control to Improve Powerline Stability (1968)

The influence of generator voltage regulators upon powerline stability is closely scrutinized by analog techniques. Contrary to common concepts, it is shown that high-speed control of excitation to maintain constant terminal voltage actually hampers rather than aids damping and powerline stability. It is further shown that damping and stability are greatly improved by supplementing excitation control with a specially derived function of frequency deviation. Results of the studies are verified in actual performance obtained in field tests.
MONITORING BY FIBER OPTICAL SENSORS OF RELIABILITY OF OPERATION OF BUILDING STRUCTURES WITH EXTERNAL COMPOSITE REINFORCEMENT (2020)

This article describes of the actual state of building structures by the example of structures of reinforced concrete and metal bridges. It is shown that a high degree of wear of artificial structures leads to the need for a reliable assessment of their actual condition using modern methods and means of non-destructive testing and diagnostics, as well as strengthening exploited structures with polymer composite materials. The results of researches on fiber-optic monitoring and strengthening of bridge spans with composite materials based on domestic and foreign carbon reinforcing fillers and epoxy polymer matrices are presented. It has been experimentally shown that for reinforced concrete structures it is advisable to use composite strengthening systems using external reinforcement installed directly on the damaged object by contact molding. For metal structures, this approach is not applicable due to a significant difference in the coefficients of linear thermal expansion of composites and metals. In this case, an amplification system based on prefabricated composite truss systems made by autoclave and unautoclave molding can be applied. The obtained research results also indicate the advisability of joint use of monitoring systems and strengthening of damaged bridge structures by composites.
TRE signal processing by positive photon discrimination (2004)

IC debug is facilitated with time resolved photon emission. Latest technologies are now working at ultra low power supply voltages, <1 V. At such voltages, background noise begins to mask commutation peaks, thus biasing the analysis. With the positive photon discrimination approach, signal is extracted even below the noise level.
n Vivo Evaluation of a Gastroretentive Drug Delivery System Based on Enteric-Coated Floating Tablets (2015)

Floating dosage forms are supposed to exhibit an enhanced gastric residence time. Their development is challenging as the prediction of the retention potential in humans based on in vitro studies and animal models is difficult.
Non-invasive time-resolved measurements of anomalous collision frequency in a Hall thruster (2019)

The time-resolved cross-field electron anomalous collision frequency in a Hall thruster is inferred from minimally invasive laser-based measurements. This diagnostic is employed to characterize the relationship between the dominant low-frequency “breathing” oscillations and anomalous electron transport mechanisms. The ion Boltzmann equation combined with a generalized Ohm's law is used to infer key quantities including the ionization rate and axial electric field strength which are necessary in computing the total electron cross-field collision frequency. This is accomplished by numerically integrating functions of velocity moments of the ion velocity distribution function measured with laser-induced fluorescence, in conjunction with current density measurements at a spatial boundary. Estimates of neutral density are used to compute the classical collision frequency profile and the difference in the total collision frequency, and this quantity describes the anomalous collision frequency. This technique reveals the anticipated trends in electron transport: few collisions in the acceleration region but a collision frequency approaching the cyclotron frequency farther downstream. The time-resolved transport profiles indicate that the anomalous collision frequency fluctuates by several orders of magnitude during a breathing cycle. At troughs in the discharge current, classical collisions may dominate; at peaks in the discharge current, anomalous collisions dominate. These results show that the breathing mode and electron transport are directly correlated. This finding is discussed with regard to existing numerical models for the breathing mode and interpretations of anomalous electron transport.
Broadband wavefront control in a pupil mapping coronagraph (2007)

Pupil mapping (a.k.a. Phase-Induced Amplitude Apodization, or PIAA) is a promising technique in high-dynamic range stellar coronagraphy that obtains higher throughput and better inner working angle than any other known approach. As with any coronagraph, the optical surface requirements and the diameter of the controllable region in the image plane are tied to the wavefront control system and optical bandpass. For example, in a monochromatic bandpass, a single ideal deformable mirror (DM) can create a dark hole with a diameter limited by its Nyquist frequency, even for highly aberrated optics. In broadband light, the depth of the dark hole is linked to the wavelength dependence of aberrations, their spatial frequency content, and their propagation through the system. We derive requirements on the surface height and reflectivity power spectral densities for optics in the PIAA system and describe a sequential-DM architecture that will achieve high-contrast over a large optical bandwidth.
Effect of W-Mo balance on properties of high alloy PM high speed tool steel. (1989)

The effect of W-Mo balance on the characteristics of high speed tool steels containing 1.8-1.9%C, 4%Cr, 5%V, 10%Co and 2Mo+W=23% made by powder metallurgical process was studied. Increasing W content brought higher tempering hardness and toughness to the steels. The 23%W steel with no Mo content had best wear resistance and tool life of milling cutter.These characteristic improvements were due to greater solid-solution strengthening by W than Mo.
A cooperative GPU-based Parallel Multistart Simulated Annealing algorithm for Quadratic Assignment Problem (2018)

GPU hardware and CUDA architecture provide a powerful platform to develop parallel algorithms. Implementation of heuristic and metaheuristic algorithms on GPUs are limited in literature. Nowadays developing parallel algorithms on GPU becomes very important. In this paper, NP-Hard Quadratic Assignment Problem (QAP) that is one of the combinatorial optimization problems is discussed. Parallel Multistart Simulated Annealing (PMSA) method is developed with CUDA architecture to solve QAP. An efficient method is developed by providing multistart technique and cooperation between threads. The cooperation is occurred with threads in both the same and different blocks. This paper focuses on both acceleration and quality of solutions. Computational experiments conducted on many Quadratic Assignment Problem Library (QAPLIB) instances. The experimental results show that PMSA runs up to 29x faster than a single-core CPU and acquires best known solution in a short time in many benchmark datasets.
Development and Migration of Pre-Plasma Cells in the Mouse Lymph Node (44.5) (2010)

Abstract Plasma cells (PCs) play important roles in the acute response to infection and the long-term protection of the host by acting as antibody factories. In this study, we imaged the differentiation and migratory behavior of nascent plasma cells (PC) in lymph nodes of mice by intravital two-photon microscopy using a Blimp-1-YFP transgene. Pre-PCs differentiate in the germinal center and migrate to the medullary cords where they become sessile plasma cells. Their migration has been shown to be chemokine-dependent based on in vitro chemotaxis assays and histological sections using chemokine receptor-deficient cells. Here we identify a novel migration pattern for pre-PCs, which is unique among previously-described lymphocytes and uses an alternative pathway for motility.
Precoding and postcoding schemes for wireless video transmission in overloaded MIMO systems (2017)

Image and video transmission is highly expected to proliferate with the wide spread of Wi-Fi devices and the introduction of multiple-input multiple-output (MIMO) systems. This paper proposes a novel precoder for video transmission in overloaded MIMO systems, which is based on an eigenbeam space division multiplexing (E-SDM) technique. This paper also proposes a low complexity postcoder, which detects some of data symbols by a linear approach and the others by a prevoting vector cancellation (PVC) approach. It is shown from simulation results that the proposed precoder and postcoder achieve 40 dB in peak signal-to-noise ratio while reducing the computational complexity by over 61 compared to the conventional PVC-based detection when received signal-to-noise ratio is higher than 10 dB.
Pathogenesis of Myeloproliferative Neoplasms: Role and Mechanisms of Chronic Inflammation (2015)

Myeloproliferative neoplasms (MPNs) are a heterogeneous group of clonal diseases characterized by the excessive and chronic production of mature cells from one or several of the myeloid lineages. Recent advances in the biology of MPNs have greatly facilitated their molecular diagnosis since most patients present with mutation(s) in the JAK2, MPL, or CALR genes. Yet the roles played by these mutations in the pathogenesis and main complications of the different subtypes of MPNs are not fully elucidated. Importantly, chronic inflammation has long been associated with MPN disease and some of the symptoms and complications can be linked to inflammation. Moreover, the JAK inhibitor clinical trials showed that the reduction of symptoms linked to inflammation was beneficial to patients even in the absence of significant decrease in the JAK2-V617F mutant load. These observations suggested that part of the inflammation observed in patients with JAK2-mutated MPNs may not be the consequence of JAK2 mutation. The aim of this paper is to review the different aspects of inflammation in MPNs, the molecular mechanisms involved, the role of specific genetic defects, and the evidence that increased production of certain cytokines depends or not on MPN-associated mutations, and to discuss possible nongenetic causes of inflammation.
An SRAM Design in 65nm and 45nm Technology Nodes Featuring Read and Write-Assist Circuits to Expand Operating Voltage (2006)

This paper describes a 32Mb SRAM that has been designed and fabricated in a 65nm low-power CMOS technology. The design has also been migrated to 45nm bulk and SOI technologies. The 68mm die features read and write-assist circuit techniques that expand the operating voltage range and improve manufacturability across technology platforms
Challenges in tactical support functions for fighter aircraft (2009)

Fighter pilots operate in environments where an erroneous decision may have fatal consequences. A tactical decision support system (TDSS) could aid the pilots to analyze the situation and make correct decisions. The TDSS can, for instance, highlight important information and suggest suitable actions. The aim of this thesis is to provide a situation analysis model of combat survival that can be utilized in a TDSS. The first part of this thesis describes an analysis of what the model needs to describe and how it can be used. It is concluded that the model should evaluate the outcome of different actions with respect to combat survival. This evaluation can guide the pilot’s decision making, so that actions leading to dangerous situations are avoided. The analysis also highlights the need of handling uncertainties, both measurement precision uncertainty regarding the locations and capabilities of the threats (enemies) and inference uncertainties regarding the prediction of how the threats will act. Finally, arguments for focusing the rest of the work on a single fighter aircraft and threats located on the ground are presented. The second part of the thesis suggests a model, which describes the survivability, i.e., the probability that the aircraft can fly a route without being hit by fire from ground-based threats. Thus, the model represents the inference uncertainty, since it describes the probability of survival. The model’s characteristics are discussed, e.g., that the model is implementable and can be adapted to describe different kinds of ground-based threats. Uncertainty in terms of measurement precision influences the estimate of the survivability. Two different ways of representing this is discussed: calculating the worst case scenario or describing the input as random variables and the resulting survivability as a random variable with a probability distribution. Monte Carlo simulations are used for estimating the distribution for survivability in a few illustrative scenarios, where the input is represented as random variables. The simulations show that when the uncertainty in input is large, the survivability distribution may be both multimodal and mixed. Two uncertainty measures are investigated that condense the information in the distributions into a single value: standard deviation and entropy. The simulations show that both of these measures reflect the uncertainty. Furthermore, the simulations indicate that the uncertainty measures can be used for sensor management, since they point out which information that is the most valuable to gather in order to decrease the uncertainty in the survivability. Finally, directions for future work are suggested. A number of TDSS functions that can be developed based on the model are discussed e.g., warnings, countermeasure management, route-planning and sensor management. The design of these functions could require extending the threat model to incorporate airborne threats and the effects of countermeasures. Further investigations regarding the uncertainty in the model are also suggested.
Visible light activated coumarin photocages: an interplay between radical and organobase generation to govern thiol–ene polymerizations (2023)

Novel coumarinylmethyl photobase generators (PBGs) that induce polymerization upon exposure to visible light are described. PBG composition governs anionic vs. radical mechanisms, which will lead to disparate polymer topologies and properties.
Propagation Diagnostics Measurements. Microwave Diagnostics of the ATA Electron Beam Propagating in Air (1988)

Abstract : Experiments on conductivity profiling around a propagating electron beam were successfully performed during the Spring 1987 series of open-air propagation experiments on ATA at LLNL. Our measurements of both 10- and 35-GHz microwave interferometer measurements of real imaginary conductivity histories along chords at various y-offsets from the beam centerline and at two different locations along the propagating beam line. Keywords: Electron beams, Conductivity, Afterglows, Microwave diagnostics, Plasmas.
Organo-Mineral Composite Materials Based on Sodium Liquid Glass, Tolylene-2,4-diisocyanate, Epoxy Oligomer, and Polyisocyanate (2018)

Organo-mineral composite materials based on sodium liquid glass combined with tolylene-2,4-diisocyanate (TDI), polyisocyanate, and epoxy oligomer have been synthesized. When heated, the organic components of the composites form a polymer network through the trimerization reaction and TDI curing of the epoxy oligomer. The composite materials after heating to 130°C have a uniform structure. The resulting hybrid composite materials are not brittle and exhibit enhanced heat resistance as compared to common polyisocyanurate compositions. Hybrid composites can find wide application in various fields of engineering.
Effect of corn endosperm hardness on different stages of dry grind corn process (2004)

Ethanol yields from six yellow dent corn hybrids of different endosperm hardness were studied. Corn samples were milled, liquefied, saccharified and fermented.Endosperm hardness of hybrids was classified according to their true density. Ethanol and sugar levels in the mash were monitored using an HPLC method. Solids in the thin stillage and wet distillers grains were measured using a standard oven method. It was observed that ethanol yields increased with true density of corn hybrids. Thin stillage and wet distillers grain did not show any significant correlation (R2 <0.45) with bulk density.