gebhart/patrepeval huggingface dataset:
Synthesis and Preliminary Biological Evaluations of Ionic and Nonionic Amphiphilic α-Phenyl-<i>N</i>-<i>tert</i>-butylnitrone Derivatives (2003)

In this study we report the synthesis of a series of new amphiphilic compounds derived from alpha-phenyl-N-tert-butylnitrone (PBN). The nitrone function was fitted into the core of the molecule between its polar and apolar groups. The polar head consisted of a lactobionamide, an ammonium, or a carboxylate group. The hydrophobic part consisted of a hydro- or a perfluorocarbon chain. The hydrophobic chain was linked to the tert-butyl group of the PBN derivatives using an urethane, a thioether, or an amide bond. The impact of these different parameters on the hydrophilic lipophilic balance of these compounds and their spin trap activity were studied. The various ESR measurements indicated that the aromatic and tert-butyl functional groups of PBN did not affect its spin trap properties. Moreover, these compounds were found to increase the viability of cultured human skin fibroblasts harboring the neurogenic ataxia retinitis pigmentosa mutation and presenting a severe ATPase deficiency.
PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production (2019)

Lignocellulosic biomass offers a sustainable source for biofuel production that does not compete with food-based cropping systems. Importantly, two critical bottlenecks prevent economic adoption: many industrially relevant microorganisms cannot ferment pentose sugars prevalent in lignocellulosic medium, leaving a significant amount of carbon unutilized. Furthermore, chemical biomass pretreatment required to release fermentable sugars generates a variety of toxins, which inhibit microbial growth and metabolism, specifically limiting pentose utilization in engineered strains. Here we dissected genetic determinants of anaerobic xylose fermentation and stress tolerance in chemically pretreated corn stover biomass, called hydrolysate. We previously revealed that loss-of-function mutations in the stress-responsive MAP kinase HOG1 and negative regulator of the RAS/Protein Kinase A (PKA) pathway, IRA2, enhances anaerobic xylose fermentation. However, these mutations likely reduce cells' ability to tolerate the toxins present in lignocellulosic hydrolysate, making the strain especially vulnerable to it. We tested the contributions of Hog1 and PKA signaling via IRA2 or PKA negative regulatory subunit BCY1 to metabolism, growth, and stress tolerance in corn stover hydrolysate and laboratory medium with mixed sugars. We found mutations causing upregulated PKA activity increase growth rate and glucose consumption in various media but do not have a specific impact on xylose fermentation. In contrast, mutation of HOG1 specifically increased xylose usage. We hypothesized improving stress tolerance would enhance the rate of xylose consumption in hydrolysate. Surprisingly, increasing stress tolerance did not augment xylose fermentation in lignocellulosic medium in this strain background, suggesting other mechanisms besides cellular stress limit this strain's ability for anaerobic xylose fermentation in hydrolysate.
Low friction in mixed-mu superconducting bearings (1995)

Individual magnetic steel rotors were levitated by combining the attractive force between permanent magnets and the steel with the repulsive force between high-temperature superconductors and the steel. The free spindown of several rotors was observed, and the effective coefficient of friction for the bearing was calculated as a function of geometry. Low-speed coefficients of &lt;10−8 were observed, and the velocity dependence of MnZn ferrite rotors suggest that coefficients of &lt;10−6 are attainable at bearing rim velocities of 100 m/s.
Molecular Encapsulation beyond the Aperture Size Limit through Dissociative Linker Exchange in Metal–Organic Framework Crystals (2014)

Under linker exchange conditions, large guests with molecular diameters 3-4 times the framework aperture size have been encapsulated into preformed nanocrystals of the metal-organic framework ZIF-8. Guest encapsulation is facilitated by the formation of short-lived "open" states of the pores upon linker dissociation. Kinetic studies suggested that linker exchange reactions in ZIF-8 proceed via a competition between dissociative and associative exchange mechanisms, and guest encapsulation was enhanced under conditions where the dissociative pathway predominates.
De-jittering in the transport of MPEG-4 and MPEG-2 video over ATM (2003)

In this paper a de-jittering scheme which can be used in the transport of MPEG-4 and MPEG-2 video to absorb any introduced network jitter is proposed. The essence of the de-jittering scheme is based on the statistical approximation of delay variation in the arrival times of video packets carrying encoded clock reference values and a filtering and re-stamping mechanism. In addition, a brief overview of the MPEG-4 system is presented.
Nonallosteric Sirtuin Enzyme Activation: Characterization of Hit Compounds (2020)

ABSTRACT Mammalian sirtuins (SIRT1-SIRT7) are a family of nicotinamide adenine dinucleotide (NAD + )-dependent protein deacylases that play critical roles in lifespan and age-related diseases. The physiological importance of sirtuins has stimulated intense interest in designing sirtuin-activating compounds. However, except for allosteric activators of SIRT1-catalyzed reactions that are limited to particular substrates, a general framework for the design of sirtuin-activating compounds has been lacking. Recently, we introduced a general mode of sirtuin activation that is distinct from the known modes of enzyme activation, establishing biophysical properties of small molecule modulators that can, in principle, result in enzyme activation for various sirtuins and substrates. Here, we characterize small molecules reported in the literature to activate the SIRT3 enzyme using a variety of computational, biochemical and biophysical techniques including protein-ligand docking, molecular dynamics simulation, nonlinear reaction dynamics simulation, kinetic assays and thermodynamic assays with multiple substrates and protocols. In particular, we identify the mechanism of action of the compound honokiol on the human SIRT3 enzyme, modeling its effect on active site conformational degrees of freedom and demonstrating how it nonallosterically activates the human SIRT3 enzyme under physiologically relevant conditions. We show that honokiol constitutes a hit compound for the design of a new generation of nonallosteric activators that can activate SIRT3 through the proposed mechanism-based mode of activation.
Facilitation of endoglin-targeting cancer therapy by development/utilization of a novel genetically engineered mouse model expressing humanized endoglin (CD105) (2014)

Endoglin (ENG) is a TGF-β coreceptor and essential for vascular development and angiogenesis. A chimeric antihuman ENG (hENG) monoclonal antibody (mAb) c-SN6j (also known as TRC105) shows promising safety and clinical efficacy features in multiple clinical trials of patients with various advanced solid tumors. Here we developed a novel genetically engineered mouse model to optimize the ENG-targeting clinical trials. We designed a new targeting vector that contains exons 4-8 of hENG gene to generate novel genetically engineered mice (GEMs) expressing functional human/mouse chimeric (humanized) ENG with desired epitopes. Genotyping of the generated mice confirmed that we generated the desired GEMs. Immunohistochemical analysis demonstrated that humanized ENG protein of the GEMs expresses epitopes defined by 7 of our 8 anti-hENG mAbs tested. Surprisingly the homozygous GEMs develop normally and are healthy. Established breast and colon tumors as well as metastasis and tumor microvessels in the GEMs were effectively suppressed by systemic administration of anti-hENG mAbs. Additionally, test result indicates that synergistic potentiation of antitumor efficacy can be induced by simultaneous targeting of two distinct epitopes by anti-hENG mAbs. Sorafenib and capecitabine also showed antitumor efficacy in the GEMs. The presented novel GEMs are the first GEMs that express the targetable humanized ENG. Test results indicate utility of the GEMs for the clinically relevant studies. Additionally, we generated GEMs expressing a different humanized ENG containing exons 5-6 of hENG gene, and the homozygous GEMs develop normally and are healthy.
The Evolution and Design of Flat-Panel Loudspeakers for Audio Reproduction (2021)

The underlying physics and the design of loudspeakers that radiate sound through the bending vibrations of elastic panels, here referred to generically as flat-panel loudspeakers, are reviewed in this paper. The form factor, reduced weight, and aesthetic appeal of flat-panel speakers have made them a topic of interest for more than 90 years, but these advantages have been overshadowed by acoustical shortcomings, specifically the uneven frequency response and directivity in comparison to conventional cone-radiator loudspeakers. Fundamentally, the design challenges of flat-panel speakers arise from the intrinsically large number of mechanical degrees of freedom of a panel radiator. A number of methods have been explored to compensate for the acoustical shortcomings of flat-panel speakers, such as employing inverse filters, equalization, canceling mechanical resonances with actuator arrays, and modifying the panel material, shape, structure, and boundary conditions. Such methods have been used in various combinations to achieve significant audio performance improvements, and carefully designed flat-panel loudspeakers have been rated in blind listening tests as competitive with some prosumer-grade conventional loudspeakers. This review presents a brief historical account of the evolution of flat-panel loudspeakers and summarizes the essential physics and design methodologies that have been developed to optimize their fidelity and directional response.
Contribution of novel choline‐binding proteins to adherence, colonization and immunogenicity of <i>Streptococcus pneumoniae</i> (1997)

The surface of Streptococcus pneumoniae is decorated with a family of choline-binding proteins (CBPs) that are non-covalently bound to the phosphorylcholine of the teichoic acid. Two examples (PspA, a protective antigen, and LytA, the major autolysin) have been well characterized. We identified additional CPBs and characterized a new CBP, CbpA, as an adhesin and a determinant of virulence. Using choline immobilized on a solid matrix, a mixture of proteins from a pspA-deficient strain of pneumococcus was eluted in a choline-dependent fashion. Antisera to these proteins passively protected mice challenged in the peritoneum with a lethal dose of pneumococci. The predominant component of this mixture, CbpA, is a 75-kDa surface-exposed protein that reacts with human convalescent antisera. The deduced sequence from the corresponding gene showed a chimeric architecture with a unique N-terminal region and a C-terminal domain consisting of 10 repeated choline-binding domains nearly identical to PspA. A cbpA-deficient mutant showed a >50% reduction in adherence to cytokine-activated human cells and failed to bind to immobilized sialic acid or lacto-N-neotetraose, known pneumococcal ligands on eukaryotic cells. Carriage of this mutant in an animal model of nasopharyngeal colonization was reduced 100-fold. There was no difference between the parent strain and this mutant in an intraperitoneal model of sepsis. These data for CbpA extend the important functions of the CBP family to bacterial adherence and identify a pneumococcal vaccine candidate.
Segmentation architecture of multi-axis SMA array actuators inspired by biological muscles (2005)

A new approach to artificial muscle actuators assimilating the morphological and kinesiological structure of biological muscles is presented and is implemented using shape memory alloys. Like a biological muscle consisting of short muscle fibers arranged in an overlapping series, an array of SMA actuators are segmented into many independently controlled, spatially discrete volumes, each contributing a small displacement to create a large motion. Furthermore, the segmented architecture of SMA wires is extended to a multi-axis actuator array by arranging them in a two-dimensional array. The multi-axis control is streamlined and coordinated using a two-dimensional segmentation method in order to activate multiple bones (links) of a skeletal robot structure in a coordinated manner. Moreover, the 2-D segmentation is so designed that coordinated gross motion as well as independent fine movements may be generated with minimum complexity and minimum control loops.
An internal Mg–Li alloy composite process for the fabrication of MgB<sub>2</sub>wire (2007)

This paper proposes a composite process for the fabrication of MgB2 wire utilizing the excellent room temperature workability of Mg–Li alloy (LA141) as one of the promising processes for scale-up production. The starting composite is a Fe sheath tube with a coaxial internal Mg–Li alloy rod and powder mixture of B and nano-SiC filling the space between the inner wall of the Fe tube and the Mg–Li alloy rod. The composite can be deformed uniformly into the final wire with large cross-sectional area reduction and no intermediate annealing. During the subsequent heat treatment, Mg and Li in the liquid state infiltrate into the B layer and react with B forming a reacted layer along the inner wall of the Fe tube and a hole at the centre. The reacted layer is composed of a MgB2 matrix composed of equi-axed grains with sub-micron size. Li is little incorporated into the MgB2 phase and does not degrade the superconducting properties. The superconducting transition temperature Tc is 38 K and the transport critical current density Jc(core) for the core is 3 × 104 A cm−2 at 4.2 K and 4 T.
Range and Doppler information from fourth-order spectra (1991)

In an active sonar system setting, a novel method is evaluated that extracts range and Doppler information from a Doppler-spread active sonar echo. The Doppler spreading is based on H. Van Trees' (1971) Gaussian amplitude modulating model, and the new method is based on the Fourier transform of a special case of the fourth-order cumulant. Specifically, from the envelope of the Gaussian amplitude modulated echo of a transmitted coded pulse train, the second-order spectrum and the Fourier transform of a special case of the fourth-order cumulant are derived and analyzed for this ability to extract range and Doppler information. It is shown that the method can theoretically extract range and Doppler information without degradation. The reason for this result is that a special case of the fourth-order cumulant is independent of the covariance of the Gaussian amplitude modulating function. These methods are also simulated and compared with the simulated results of the range-Doppler ambiguity function. This shows that the ambiguity function and the second-order spectrum are degraded due to the Gaussian amplitude modulation. The results are further demonstrated by simulating the three range-Doppler extraction methods for the received echo in noise.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Thin film interaction between titanium and polycrystalline silicon (1980)

The low resistivity of the titanium disilicide makes this material attractive for gate and interconnect metallizations. TiSi2 has been formed by reacting Ti films with polycrystalline and monocrystalline silicon in the temperature range 400–1100 °C. The interaction is investigated by use of sheet resistance, x-ray diffraction, and stress measurements. It has been found that Ti and Si react very rapidly to form both TiSi and TiSi2 at temperatures ? 700 °C and only TiSi2 at temperatures ≳ 700 °C. The TiSi2 films are associated with a very low resistivity (∼15 μΩ cm), high tensile stress [∼ (1–2) ×1010 dyn/cm2)], and a rough surface. Silicided structures are mechanically stable. It is proposed that the silicon, as the predominant diffusing species, first diffuses into titanium to completely convert titanium into TiSi and then into TiSi to form TiSi2.
Discovery of MK-7145, an Oral Small Molecule ROMK Inhibitor for the Treatment of Hypertension and Heart Failure (2016)

ROMK, the renal outer medullary potassium channel, is involved in potassium recycling at the thick ascending loop of Henle and potassium secretion at the cortical collecting duct in the kidney nephron. Because of this dual site of action, selective inhibitors of ROMK are expected to represent a new class of diuretics/natriuretics with superior efficacy and reduced urinary loss of potassium compared to standard-of-care loop and thiazide diuretics. Following our earlier work, this communication will detail subsequent medicinal chemistry endeavors to further improve lead selectivity against the hERG channel and preclinical pharmacokinetic properties. Pharmacological assessment of highlighted inhibitors will be described, including pharmacodynamic studies in both an acute rat diuresis/natriuresis model and a subchronic blood pressure model in spontaneous hypertensive rats. These proof-of-biology studies established for the first time that the human and rodent genetics accurately predict the in vivo pharmacology of ROMK inhibitors and supported identification of the first small molecule ROMK inhibitor clinical candidate, MK-7145.
Predicting and optimizing the territory of blood–brain barrier opening by superselective intra-arterial cerebral infusion under dynamic susceptibility contrast MRI guidance (2015)

Interventional neuroradiology techniques are minimally invasive and allow for superselective drug delivery to specific brain regions. The passage of most agents, however, is impaired by the blood-brain barrier (BBB). Despite its discovery over 40 years ago, hyperosmotic BBB opening (BBBO) remains highly variable, preventing its widespread implementation. Here, we report on a technique that enables the prediction and optimization of the BBBO territory. We found that the microcatheter tip position and the speed of hyperosmolar mannitol injection, both major determinants of the targeted territory, can be modulated in real-time as guided by trans-catheter perfusion MRI.
22.4 A reconfigurable bidirectional wireless power transceiver with maximum-current charging mode and 58.6% battery-to-battery efficiency (2017)

Wireless power transfer (WPT) is currently on the critical point of an explosive growth. Here, as projected in Fig. 22.4.1, we propose a future WPT eco-system of consumer electronics, which includes three layers: 1) wireless charging pads being the fundamental energy plants that can charge a wireless power bank and mobile devices; 2) wireless power banks that get energy from plants and feed mobile devices; and 3) power hungry mobile devices that get energy from all the other sources. To enable the mobile devices charging others without additional hardware, we propose a reconfigurable bidirectional 6.78MHz WPT transceiver (TRX) that reuses the LC resonant tank and 4 area-consuming power transistors for the differential Class-D power amplifier (PA) and the full-wave rectifier. With such WPT TRX embedded, one can provide a first-aid to his/her smart watch or friend's device of which the battery is dying.
Highly Stretchable, Weavable, and Washable Piezoresistive Microfiber Sensors (2018)

A key challenge in electronic textiles is to develop an intrinsically conductive thread of sufficient robustness and sensitivity. Here, we demonstrate an elastomeric functionalized microfiber sensor suitable for smart textile and wearable electronics. Unlike conventional conductive threads, our microfiber is highly flexible and stretchable up to 120% strain and possesses excellent piezoresistive characteristics. The microfiber is functionalized by enclosing a conductive liquid metallic alloy within the elastomeric microtube. This embodiment allows shape reconfigurability and robustness, while maintaining an excellent electrical conductivity of 3.27 ± 0.08 MS/m. By producing microfibers the size of cotton threads (160 μm in diameter), a plurality of stretchable tubular elastic piezoresistive microfibers may be woven seamlessly into a fabric to determine the force location and directionality. As a proof of concept, the conductive microfibers woven into a fabric glove were used to obtain physiological measurements from the wrist, elbow pit, and less accessible body parts, such as the neck and foot instep. Importantly, the elastomeric layer protects the sensing element from degradation. Experiments showed that our microfibers suffered minimal electrical drift even after repeated stretching and machine washing. These advantages highlight the unique propositions of our wearable electronics for flexible display, electronic textile, soft robotics, and consumer healthcare applications.
Redundancy removal and test generation for circuits with non-Boolean primitives (1997)

Production VLSI circuits typically consist of primitives like tristate buffers, bidirectional buffers, and bus configurations that assume non-Boolean values like the high-impedance state. We describe a systematic methodology for extending test generation algorithms that work on combinational circuits with only Boolean primitives to full-scan production circuits. Key features of the methodology are illustrated using the energy minimization based test generation algorithm for combinational circuits. The main features of our methodology that make the test generation algorithm practical for large production circuits are: (1) only one Boolean variable is used to represent the value on a signal and all signals assume only Boolean values during the test generation procedure; (2) the function of non-Boolean primitives is separated into Boolean and non-Boolean components with energy functions required only for the Boolean component; and (3) non-Boolean components are implicitly considered in the energy minimization procedure. In this process, no new energy functions other than the normal Boolean gate energy functions are needed. We give a method for identifying and removing redundancies in production circuits using energy minimization. The formulation is also applicable to Boolean satisfactorily and BDD methods. We first use the test generation algorithm for identifying undetectable faults and then relax specific constraints in the original test generation problem by ignoring the non-Boolean components. We show that undetectability in the relaxed formulation implies redundancy. We report redundancy removal results for production VLSI circuits, ISCAS 85, and full-scan versions of the ISCAS 89 benchmark circuits.
Two‐Phase Catalysis: A Strategy for Avoiding Consecutive Reactions as Exemplified in the Telomerization of Butadiene and Ammonia (1996)

The industrially interesting primary octadienylamines 1 and 2 can be synthesized selectively for the first time from 1,3-butadiene and ammonia. The use of an aqueous catalyst phase together with an organic solvent as a second phase are the key to the success of this process. Consecutive reactions of the primary amines 1 and 2, which are more nucleophilic than ammonia, can thus be avoided.