gebhart/patrepeval huggingface dataset:
Engineering the Protein Folding Landscape in Gram-Negative Bacteria (2008)

Gram-negative bacteria, especially Escherichia coli, are often the preferred hosts for recombinant protein production because of their fast doubling times, ability to grow to high cell density, propensity for high recombinant protein titers and straightforward protein purification techniques. The utility of simple bacteria in such studies continues to improve as a result of an ever-increasing body of knowledge regarding their native protein biogenesis machinery. From translation on the ribosome to interaction with cytosolic accessory factors to transport across the inner membrane into the periplasmic space, cellular proteins interact with many different types of cellular machinery and each interaction can have a profound effect on the protein folding process. This review addresses key aspects of cellular protein folding, solubility and expression in E. coli with particular focus on the elegant biological machinery that orchestrates the transition from nascent polypeptide to folded, functional protein. Specifically highlighted are a variety of different techniques to intentionally alter the folding environment of the cell as a means to understand and engineer intracellular protein folding and stability.
Effect of Sulfur on Grain Growth in UO <sub>2</sub> Pellets (1984)

The influence of sulfur content in the range of 20 to 200 μg/g on grain growth in sintered pellets of ceramic uranium dioxide(UO 2 ) fuel originating from the ammonium uranate (AU) process was investigated. Results indicate a strong dependence of discontinuous grain growth on sulfur content and on sintering rates. The data show that, in the absence of sulfur, normal microstructures are obtained by sintering, whereas the presence of sulfur can cause coring. A possible mechanism is proposed based on the effect of the sintering atmosphere, hydrogen.
A new paradigm for parallel optical interconnects (2003)

A highly redundant, self-routing architecture is described utilizing parallel optical interconnects. The fundamental hardware component is a monolithically integrated module consisting of an array of VCSELs, resonant detectors, and waveguide couplers. Different types of interconnect specific architectures, including a reconfigurable, non-blocking crossbar will be presented.
Orthorhombic model for geomechanical applications in unconventional shale reservoirs (2015)

Summary Geomechanics of orthorhombic media (a relatively appropriate model for fractured shales), with the assumption of linear elasticity, was investigated using theoretical data. This paper presents the equations for computing anisotropic mechanical properties of orthorhombic media (Poisson's ratios “vij”, Young's moduli “Ei”, and minimum/maximum horizontal stresses “σh and σH”). Although nine independent parameters (nine stiffness matrix, Cij, components) are used to define the elastic properties of orthorhombic media, only six Cij components are used to define the above mechanical properties. Simplified equations for computing anisotropic stresses in orthorhombic media (simplified orthorhombic model) are also presented; these equations yield accurate estimates of the anisotropic stresses in heavily fractured media (shear wave splitting or SWS > 10%). Although the simplified equations for the anisotropic stresses are defined using six Cij components, σij or σij can be defined using only three mechanical properties (e.g., two Poisson's ratio values and one Young's modulus value). To investigate the mechanical behavior of an orthorhombic medium, a theoretical model was used to create data for fractured shales with two sets of vertical fractures (VTI background + two sets of rectangular, vertical fractures), with variable fracture density (which results in variable SWS values). Based on the modeling results, the values of Poisson's ratios and Young's moduli decrease with increasing fracture density (although a few moduli will remain almost unchanged). For all fracture densities, the magnitude of stress anisotropy (σH − σh) can be accurately computed using the simplified orthorhombic model and, for higher fracture densities, the simplified model converge to the exact values. σh can be accurately computed using a simpler VTI model, whereas the σH calculation using VTI or isotropic models will result in significant errors.
The Effects of Diaspirin Cross-Linked Hemoglobin on Hemodynamics, Metabolic Acidosis, and Survival in Burned Rats (1999)

Early resuscitation with DCLHb is superior to non-oxygen-carrying resuscitative fluids in improving hemodynamics and survival in this model of burn shock. DCLHb might improve general tissue perfusion in the acute postburn period, and it could be useful in the early management of patients with severe burns.
Gamma-ray compton imaging of multitracer in bio-samples by strip germanium telescope (2005)

The feasibility of a Compton camera for /spl gamma/-ray emission imaging of radioactive multi-nuclide tracer (multitracer) has been proved by the results of some bio-sample imaging experiments. The distribution of the multitracer administered to a soybean sample and a tumor-bearing mouse has been visualized for each nuclide simultaneously. Some three-dimensional images of the multitracer have been obtained though the samples were measured from a fixed direction.
Localization of handheld devices inside vehicles using audio masking (2013)

This paper addresses the problem of locating a handheld device (a smartphone or a tablet) inside a car. Based on the location of the device in the car, one can determine whether the device is being used by a driver or not so that a software can enable or disable certain features and functions of the device to reduce the distraction to the driver. We provide several predesigned audio signals to play from the car audio system that can be received by a handheld device inside the car. Using some prior knowledge of the predesigned audio signal, the handheld device can post-process the received signal in order to locate its position. Another key element in this paper is the technique to make the audio signal inaudible from users. Two audio hiding methods are proposed that are based on audio masking and playing in the out-of-hearing band.
Production of L-tryptophan by azaserine-resistant mutants of Brevibacterium flavum. (1982)

Azaserine-resistant mutants derived from a 5-fluorotryptophan-resistant, L-tryptophan-producing mutant of Brevibacterium flavum, accumulated 10.3 g/liter of L-tryptophan at maximum. The production increased to 11.4 g/liter when L-serine was added. In the mutant, only anthranilate synthase among enzymes of the tryptophan-specific biosynthetic pathway increased in activity to a 2-fold higher level than that in the parent strain, No. 187. Sensitivity of anthranilate synthase to the feedback inhibition was not altered by the mutation. Activity of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, the first common enzyme for aromatic amino acid biosynthesis, also increased 2.7-fold and was less sensitive to the feedback inhibition by phenylalanine and tyrosine. Tryptophan transport activity in strain A-100 was similar as that in the parent. Azaserine inhibited anthranilate synthase activity by 50% at 0.075 mM. The inhibition was of a mixed type with respect to both the two substrates. Anthranilate synthase of strain A-100 was inhibited in a similar manner to that of the parent.
The Electro optic Characteristics of Multi-Cell Gap Fringe-Field Switching Mode (2005)

The electro optic characteristics of the fringe-field switching (FFS) mode can be investigated by a combination of in-plane switching (IPS) at electrode center and low-twist TN (= electrode edge). In other words, the smaller optimal optical retardation and higher operating voltage of the IPS mode compared with the low-twist TN mode mean that the retardation and operating voltage (= V op ) of the FFS mode can not be optimized for maximum transmittance at both the center and the edge of the electrode. In the multi-cell gap (= MCG)-FFS mode, the operating voltage at the edge is increased by heightening the cell gap at the edge and is shifted near V op at the center. One notable result is that the transmittance at the center with increased value D (= the cell gap at the near edge) becomes higher owing to the increased twist angle. In conclusion, the novel FFS mode has a higher transmittance than the conventional FFS mode.
Leveraging Randomized Compiling for the QITE Algorithm (2021)

The success of the current generation of Noisy Intermediate-Scale Quantum (NISQ) hardware shows that quantum hardware may be able to tackle complex problems even without error correction. One outstanding issue is that of coherent errors arising from the increased complexity of these devices. These errors can accumulate through a circuit, making their impact on algorithms hard to predict and mitigate. Iterative algorithms like Quantum Imaginary Time Evolution are susceptible to these errors. This article presents the combination of both noise tailoring using Randomized Compiling and error mitigation with a purification. We also show that Cycle Benchmarking gives an estimate of the reliability of the purification. We apply this method to the Quantum Imaginary Time Evolution of a Transverse Field Ising Model and report an energy estimation and a ground state infidelity both below 1\%. Our methodology is general and can be used for other algorithms and platforms. We show how combining noise tailoring and error mitigation will push forward the performance of NISQ devices.
High Temperature Strain Gage Apparent Strain Compensation (1992)

Once an installed strain gage is connected to a strain indicating device and the instrument is balanced, a subsequent change in temperature of the gage installation will generally produce a resistance change in the gage. This purely temperature-induced resistance will be registered by the indicating device as a strain and is referred to as 'apparent strain' to distinguish it from strain due to applied stress. One desirable technique for apparent strain compensation is to employ two identical gages with identical mounting procedures which are connected with a 'half bridge' configuration where gages see the same thermal environment but only one experiences a mechanical strain input. Their connection in adjacent arms of the bridge will then balance the thermally induced apparent strains and, in principle, only the mechanical strain remains. Two approaches that implement this technique are discussed.
A Pipeline for Computer Aided Polyp Detection (2006)

We present a novel pipeline for computer-aided detection (CAD) of colonic polyps by integrating texture and shape analysis with volume rendering and conformal colon flattening. Using our automatic method, the 3D polyp detection problem is converted into a 2D pattern recognition problem. The colon surface is first segmented and extracted from the CT data set of the patient's abdomen, which is then mapped to a 2D rectangle using conformal mapping. This flattened image is rendered using a direct volume rendering technique with a translucent electronic biopsy transfer function. The polyps are detected by a 2D clustering method on the flattened image. The false positives are further reduced by analyzing the volumetric shape and texture features. Compared with shape based methods, our method is much more efficient without the need of computing curvature and other shape parameters for the whole colon surface. The final detection results are stored in the 2D image, which can be easily incorporated into a virtual colonoscopy (VC) system to highlight the polyp locations. The extracted colon surface mesh can be used to accelerate the volumetric ray casting algorithm used to generate the VC endoscopic view. The proposed automatic CAD pipeline is incorporated into an interactive VC system, with a goal of helping radiologists detect polyps faster and with higher accuracy.
Development of energy-efficient algorithms for wireless sensor networks (2012)

Wireless sensor networks (WSNs) require very efficient algorithms for data processing, compression and routing due to the limited resources of sensor nodes. As WSNs are commonly deployed for monitoring the remote and hazardous environments, it is not feasible to recharge or replace the battery of sensor nodes. Therefore, sensor nodes should use their energy very efficiently even when a power harvesting technique is used with the battery of limited capacity. Moreover, most of the sensors' energy is consumed by data transmission and idle listening. Therefore, the lifetime of WSNs can be significantly prolonged by using energy-efficient protocols for topology control, duty-cycling, routing, and data aggregation and compression. Aiming at developing energy efficient algorithms for WSNs, this dissertation proposes several algorithms for clock synchronization, coverage, connectivity, communication and dust storm detection. First, a recursive time synchronization protocol (RTSP) for global clock synchronization in WSNs is proposed, which provides an average accuracy of 0.23µs per hop in a large multi-hop clustered network using 7-times lesser energy than that of state-of-the-art FTSP algorithm in the long run. Second, an integrated protocol for coverage, connectivity and communication (C3) is proposed, which ensures partial coverage of more than 90% of the total deployment area, guarantees at least 1-connected network, and enables energy-efficient communication in WSNs. Finally, a sand and dust storm detection system (SDSDS) is developed, which incorporates the proposed algorithms in order to achieve high level of accuracy, reliability and energy-efficiency.
Automatic uncertainty calculation for smart measurement systems (2002)

The design of software for automatic calculation of uncertainty is described. Using a mathematical model of a measurement, expressions for uncertainty can be derived, establishing the sensitivity of a result to any variation in the uncertain input terms. We show how software suitable for measurement systems can be designed to automate the evaluation of uncertainty.
Inhibitors of sterol synthesis. Metabolism of 5 alpha-cholest-8(14)-en-3 beta-ol-15-one after intravenous administration to bile duct-cannulated rats. (1988)

The metabolism of 5 alpha-cholest-8(14)-en-3 beta-ol-15-one has been studied after intravenous administration to bile duct-cannulated rats. Very rapid and substantial conversion of the 15-ketosterol to polar biliary metabolites was observed in both male and female rats. For example, upon intravenous injection of [4-14C]5 alpha-cholest-8(14)-en-3 beta-ol-15-one to male bile duct-cannulated rats, approximately 86% of the administered 14C was recovered in bile in the first 38 h. Of the total amount of 14C recovered in bile in 38 h, approximately 50% was excreted in bile in the first 70 min and approximately 90% was excreted within 8 h after the injection of the 15-ketosterol. A substantial fraction of the polar biliary metabolites was shown to undergo enterohepatic circulation. Of the radioactivity derived from the labeled 15-ketosterol which was not recovered in bile or other excreta at 48 h after the intravenous administration of the 15-ketosterol, most (approximately 79%) was recovered in the form of cholesterol and cholesteryl esters of blood and the various tissues. The very substantial and rapid biliary excretion of polar metabolites of the 15-ketosterol (or of cholesterol derived from the 15-ketosterol), coupled with inhibition of the intestinal absorption of cholesterol by the 15-ketosterol, may contribute to the overall hypocholesterolemic action of the 15-ketosterol which has been observed in rodents and in nonhuman primates by providing a metabolic pathway(s) wherein a substantial fraction of the absorbed 15-ketosterol is rapidly removed from the body by biliary excretion in the form of polar metabolites.
Self-mode-locking in quantum cascade lasers (2000)

We report on the first observation of mode-locking of quantum cascade lasers (QCLs). Both self-mode locking (SML) and active mode-locking have been achieved, although this talk will primarily focus on SML.
A Cell Culture-Adapted Vaccine Virus against the Current African Swine Fever Virus Pandemic Strain (2021)

African swine fever virus (ASFV) causes a virulent, deadly infection in wild and domestic swine and is currently causing a pandemic covering a contiguous geographical area from Central and Eastern Europe to Asia. No commercial vaccines are available to prevent African swine fever (ASF), resulting in devastating economic losses to the swine industry. The most advanced vaccine candidates are live attenuated strains developed using a genetically modified virulent parental virus. Recently, we developed a vaccine candidate, ASFV-G-ΔI177L, by deleting the I177L gene from the genome of the highly virulent ASFV pandemic strain Georgia (ASFV-G). ASFV-G-ΔI177L is safe and highly efficacious in challenge studies using parental ASFV-G. Large-scale production of ASFV-G-ΔI177L has been limited because it can replicate efficiently only in primary swine macrophages. Here, we present the development of an ASFV-G-ΔI177L derivative strain, ASFV-G-ΔI177L/ΔLVR, that replicates efficiently in a stable porcine cell line. In challenge studies, ASFV-G-ΔI177L/ΔLVR maintained the same level of attenuation, immunogenic characteristics, and protective efficacy as ASFV-G-ΔI177L. ASFV-G-ΔI177L/ΔLVR is the first rationally designed ASF vaccine candidate that can be used for large-scale commercial vaccine manufacture. <b>IMPORTANCE</b> African swine fever is currently causing a pandemic resulting in devastating losses to the swine industry. Experimental ASF vaccines rely on the production of vaccine in primary swine macrophages, which are difficult to use for the production of a vaccine on a commercial level. Here, we report a vaccine for ASFV with a deletion in the left variable region (LVR). This deletion allows for growth in stable cell cultures while maintaining the potency and efficacy of the parental vaccine strain. This discovery will allow for the production of an ASF vaccine on a commercial scale.
Inactivating mutations targeting the chfr mitotic checkpoint gene in human lung cancer. (2003)

A hallmark of cancer is inactivation of cell cycle checkpoints. However, very few mutations targeting mitotic checkpoint genes have been described, and in those instances, a wild-type copy of the gene was retained. chfr is a mitotic checkpoint gene that functions in early prophase delaying chromosome condensation in response to microtubule poisons. In a panel of 53 lung carcinomas for which matched normal tissue was available, we identified three missense mutations in the chfr gene, at least one of which was associated with loss of heterozygosity. In tissue culture checkpoint assays, the tumor-associated missense mutants had reduced activity or were inactive. Together with recent data suggesting that the chfr gene is frequently silenced in various tumors because of methylation of its promoter, these findings suggest that chfr is inactivated by multiple mechanisms in human cancer.
Persistent high density spectral holeburning in CaS:Eu and CaS:Eu,Sm phosphors (1998)

Persistent spectral hole-burning has been reported for singly, Eu-doped, and doubly, Eu- and Sm-doped, CaS phosphors. Efficient photon gated holeburning in the 4f7 (8S7/2)−4f65d1 transition of Eu2+ is a result of photoionization of Eu2+ to Eu3+. These holes have a width of &lt;5 GHz (2 K), survive thermal cycling of the phosphor up to the room temperature, 300 K, and have no detectable deterioration over more than a day of storage time at low temperature (2 K). Although self-gated holeburning is observed with the reading laser at higher powers, the photon budget for reading these holes is so small that in excess of 1000 reading cycles can be performed without destroying the optical signal. The nature of holes burned by photon-gating is found to be very different from the self-gated holes. The characteristics for the holeburning are the same in singly and doubly doped phosphors, suggesting that under the conditions of our experiments, Sm traps do not play any significant role in spectral holeburning. Possibilities of high density optical memory storage using photon-gated holeburning in this THz broad transition are discussed.
Design and Synthesis of Bicyclic Pyrimidinones as Potent and Orally Bioavailable HIV-1 Integrase Inhibitors (2008)

HIV integrase is one of the three enzymes encoded by HIV genome and is essential for viral replication, but integrase inhibitors as marketed drugs have just very recently started to emerge. In this study, we show the evolution from the N-methylpyrimidinone structure to bicyclic pyrimidinones. Introduction of a suitably substituted amino moiety modulated the physical-chemical properties of the molecules and conferred nanomolar activity in the inhibition of spread of HIV-1 infection in cell culture. An extensive SAR study led to sulfamide (R)- 22b, which inhibited the strand transfer with an IC50 of 7 nM and HIV infection in MT4 cells with a CIC95 of 44 nM, and ketoamide (S)- 28c that inhibited strand transfer with an IC50 of 12 nM and the HIV infection in MT4 cells with a CIC95 of 13 nM and exhibited a good pharmacokinetic profile when dosed orally to preclinical species.
Ultra High Flux 2-D CdZnTe Monolithic Detector Arrays for X-Ray Imaging Applications (2007)

The performance of 2-D CdZnTe monolithic detector arrays designed for high flux X-ray imaging applications was studied. For the first time we have obtained 5 times 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> counts/s/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> count-rate for a CdZnTe pixelated detector array. This count-rate is more than twice the highest count-rate ever achieved using a CdZnTe detector array. Such excellent performance was demonstrated for more than 600 individual CdZnTe detector arrays. The 2-D CdZnTe monolithic arrays were 16 x 16 pixel devices with 0.4 mm times 0.4 mm area pixels on a 0.5 mm pitch and were fabricated using 8.7 mm times 8.7 mm times 3.0 mm CdZnTe single crystals grown by the high-pressure, electro-dynamic gradient freeze technique. The CdZnTe detector arrays were bonded to a ceramic substrate with the Z-bondtrade technique. This enabled performance testing of the individual detector arrays before bonding to the read-out ASIC chip. The detector arrays were characterized in a custom designed test system. The measurement and data acquisition system consisted of a 16 times 16 pin probe head and 256-channel read-out electronics controlled by a host PC. We utilized our 8-channel fast bipolar ASIC chip and computer controlled 120 kVp X-ray source. In order to measure the true throughput of the CdZnTe devices a counts correction method was developed and implemented that compensates for the counting system non-linearity caused by pile-up and amplifier shaping time effects. Survey of detector array performance as a function of CdZnTe charge transport properties showed that the maximum achievable count-rate of these detectors strongly depends on the hole charge transport properties of the crystals.
Optical gain control of a GaAs MMIC distributed amplifier (1988)

Abstract This paper reports on experimental results of an optical gain control of a GaAs microwave monolithic integrated circuit (MMIC) distributed amplifier. The amplifier gain was varied by 15 dB and was controlled by a LED (250 μW) over the frequency range of 5‐8 GHz. The key to this investigation is the development of a simple inexpensive optical control mechanism that is compatible with MMIC fabrication methods.