gebhart/patrepeval huggingface dataset:
The Kinase Homology Domain of Retinal Guanylyl Cyclases 1 and 2 Specifies the Affinity and Cooperativity of Interaction with Guanylyl Cyclase Activating Protein-2 (1998)

RetGC-1 and RetGC-2 are photoreceptor membrane guanylyl cyclases that are regulated by the Ca2+-binding protein, GCAP-2. We used a protease protection assay to localize regions of the intracellular domains of RetGCs important for the interaction with GCAP-2 and found that GCAP-2 reduces the access of trypsin to a site in the kinase homology domain (KHD) of RetGC-1. The protective effect of GCAP-2 is independent of Ca2+. We also found that RetGC-2 and GCAP-2 interact cooperatively with high affinity, but RetGC-1 and GCAP-2 interact noncooperatively with low affinity. By analyzing RetGC-1/RetGC-2 chimeras we demonstrated that the affinity and cooperativity of the interaction with GCAP-2 is dictated by the structure of the KHD. These findings suggest that GCAP-2 interacts constituitively with the KHDs of RetGC-1 and RetGC-2 and that cGMP synthesis is controlled by Ca2+-dependent conformational changes in the RetGC/GCAP complex.
Complete Genome of Pseudomonas mendocina NK-01, Which Synthesizes Medium-Chain-Length Polyhydroxyalkanoates and Alginate Oligosaccharides (2011)

Pseudomonas mendocina NK-01 can synthesize medium-chain-length polyhydroxyalkanoate (PHA(MCL)) and alginate oligosaccharides (AO) simultaneously from glucose under conditions of limited nitrogen. Here, we report the complete sequence of the 5.4-Mbp genome of Pseudomonas mendocina NK-01, which was isolated from farmland soil in Tianjin, China.
Neutron Diffraction Study of the Structure of Cubic CsPbBr<sub>3</sub> (1979)

The Debye-Waller factor of cubic CsPbBr 3 was investigated by neutron diffraction technique at 152°C. The perovskite structure model with anisotropic thermal vibrations can explain the characteristics of the thermal behavior of this substance, which turned out to be essentially the same as that of CsPbCl 3 ; that is, anomalously large thermal parameters for the cesium and halogen atoms are obtained.
Carbon Exchange in Hot Alkaline Degradation of Glucose (2002)

The decomposition of 1-13C-D-glucose, 6-13C-D-glucose, and 1-13C-sodium lactate has been studied in hot (145 +/- 3 degrees C) alkaline (3.5 M) sodium hydroxide solution in order to understand the mechanisms of carbon exchange in the alkaline degradation of glucose. The results show that in the formation of lactate from glucose the carboxylate (COO-) carbon is formed preferentially from C1 carbons but methyl (CH3) carbon is formed preferentially from C6 carbons. However, on further decomposition of lactate to ethanol and carbonate, 13C-labeled carboxylate (COO-) is scrambled equally among carbonate and both carbons in product ethanol molecules. In the production of glycolate, the labeled C1 carbon mainly ends up as carboxylate (COO-) carbon, while for C6-labeled glucose the labeled carbon mainly ends up as alcoholic (CH2OH) carbon. In the production of acetate and formate there is also discrimination between C1 and C6 label.
TwinAx Differential Cable Helical Shield Wrap Modeling (2007)

This paper presents a Full-Wave FEM simulation technique for the shield wrap discontinuities that result in a 'suckout' effect in TwinAx differential cables.
Spontaneous Parametric Down-Conversion and Quantum Entanglement (2014)

Quantum entanglement has been a topic of much research in modern physics, and an application in quantum computing is envisioned. This thesis address the use of polarization entangled photon pairs produced by spontaneous parametric down-conversion (SPDC) in entanglement transfer process and quantum computing. The simplicity of SPDC entanglement relative to other quantum phenomena is first emphasized by developing a complete classical theory of the photon-crystal interactions characteristic of SPDC. The methods of achieving polarization superposition via the Type-I and Type-II SPDC are described. A combination of superposition and polarization correlation between down-converted photons is shown to violate Bell’s inequality, thus revealing the entangled nature of the photon pairs. Finally, the possibility of controlling entangled photons through the manipulation of surface plasmons is highlighted as a way to transfer entanglement from photons to material particles.
Proteomic Profiling of Cereal Aphid Saliva Reveals Both Ubiquitous and Adaptive Secreted Proteins (2013)

The secreted salivary proteins from two cereal aphid species, Sitobion avenae and Metopolophium dirhodum, were collected from artificial diets and analysed by tandem mass spectrometry. Protein identification was performed by searching MS data against the official protein set from the current pea aphid (Acyrthosiphon pisum) genome assembly and revealed 12 and 7 proteins in the saliva of S. avenae and M. dirhodum, respectively. When combined with a comparable dataset from A. pisum, only three individual proteins were common to all the aphid species; two paralogues of the GMC oxidoreductase family (glucose dehydrogenase; GLD) and ACYPI009881, an aphid specific protein previously identified as a putative component of the salivary sheath. Antibodies were designed from translated protein sequences obtained from partial cDNA sequences for ACYPI009881 and both saliva associated GLDs. The antibodies detected all parent proteins in secreted saliva from the three aphid species, but could only detect ACYPI009881, and not saliva associated GLDs, in protein extractions from the salivary glands. This result was confirmed by immunohistochemistry using whole and sectioned salivary glands, and in addition, localised ACYPI009881 to specific cell types within the principal salivary gland. The implications of these findings for the origin of salivary components and the putative role of the proteins identified are discussed in the context of our limited understanding of the functional relationship between aphid saliva and the plants they feed on. The mass spectrometry data have been deposited to the ProteomeXchange and can be accessed under the identifier PXD000113.
A broader view on jamming: from spring networks to circle packings (2019)

Jamming occurs when objects like grains are packed tightly together (e.g. grain silos). It is highly cooperative and can lead to phenomena like earthquakes, traffic jams, etc. In this paper we point out the paramount importance of the underlying contact network for jammed systems; the network must have one contact in excess of isostaticity and a finite bulk modulus. Isostatic means that the number of degrees of freedom is exactly balanced by the number of constraints. This defines a large class of networks that can be constructed without the necessity of packing particles together compressively (either in the lab or computationally). One such construction, which we explore here, involves setting up the Delaunay triangulation of a Poisson disk sampling and then removing edges to maximize the bulk modulus until the isostatic plus one edge is reached. This construction works in any dimensions and here we give results in 2D where we also show how such networks can be transformed into disk packs.
Input/Output (1981)

Input/output I/O ports are the only method by which the CPU can communicate with devices in the ‘real’ world. They provide the means not only by which the user can input data to the CPU, but also the means by which the CPU outputs information to peripheral devices. Simplified I/O ports were introduced earlier in the book (see sections 1.5, 3.17 and 4.3); in this chapter we take a more detailed look at their operation together with methods of chip selection.
How the Quantum no-Communication Theorem Misuses the Formalism and Loses Phase Information (2015)

This paper follows on from the author’s previous thoughts on the subject of the “No-communication Theorem” and Ghirardi’s critique of a communication scheme by the author and then his response to this. It is an addendum to lay bare the inadequate use of the formalism by Ghirardi, Hall et-al. To make our argument convincing, we find it necessary to explicitly lay out the machinery of the density matrix formulated argument, so that it can be seen by the incredulous, the gapping hole in the Ghirardi-Hall belief. We shall see that phase information, crucial to the interferometer setup in previous papers, is lost when: the joint evolution of the system is not considered, superposition is not explicitly brought in as an operation itself and finally, when the act of taking the reduced trace is taken too early (the act of exclusion of one system). This has lead to the limiting belief that components of entangled systems considered in isolation, are only ever in a mixed state. We shall see that when the reduced trace is taken at the right point in the analysis, phase information pertaining to the remote system is still present and this concurs with the state vector approach used to analyse the same problem.
A Novel Low-Temperature Cu-Cu Direct Bonding with Cr Wetting Layer and Au Passivation Layer (2020)

In this study, Cu-Cu direct bonding at the ultra-low bonding temperature has been successfully demonstrated by using the Cr/Au layer, which can protect Cu from oxidation before the thermocompression bonding (TCB) process and greatly improve the diffusion of Cu atoms into the surface during the thermal process. The bonding quality has been carefully investigated by analyzing Auger depth, observing the SAT, AFM, SEM images, and measuring electrical performance of the samples. In addition, the mechanical test and reliability test have been performed to verify the reliability of the novel structure with the Cr/Au layer in this study.
Elevated Plasma Factor VIII and D-Dimer Levels as Predictors of Poor Outcomes of Thrombosis in Children (2004)

Elevated levels of plasma factor VIII, D-dimer, or both at diagnosis and a persistent elevation of at least one of these factors after standard-duration anticoagulant therapy predict a poor outcome in children with thrombosis.
Differential flotation centrifugation study of hepatitis C virus and response to interferon therapy (1997)

Hepatitis C virus (HCV) appears to circulate in various forms such as native virion, immune complexes, and nucleocapsids during chronic infections. To determine the association of the physicochemical properties of HCV and its response to interferon therapy in patients with chronic hepatitis C, we examined pretreatment serum samples from 43 patients with HCV RNA who had received interferon therapy, using differential flotation centrifugation in a NaCl solution with a density of 1.063 g/ml. After centrifugation, the ratio of HCV RNA in the top and bottom fractions was determined by the polymerase chain reaction and expressed as T/B. Patients with a sustained response to IFN therapy were found to have higher T/B ratios than transient responders who relapsed after treatment (P < 0.01) and nonresponders (P < 0.01). With regards to HCV genotypes, patients with genotype 1b had higher T/B ratios in the sustained response group than in the nonsustained response group (P = 0.001), but patients with genotype 2 had a similar distribution of T/B among the 3 response groups (not significant). These findings indicate that the physicochemical properties of HCV affect the effectiveness of interferon therapy, particularly in patients with genotype 1b. J. Med. Virol. 52:190–194, 1997. © 1997 Wiley-Liss, Inc.
Recent progress in P-glycoprotein research. (1999)

P-glycoprotein can extrude a variety of structurally diverse, toxic xenobiotic compounds from cells. It is believed to be one of key molecules which can cause multidrug resistance in cancer. This paper deals with recent progress in P-glycoprotein research, especially in its structure, mechanisms for substrate recognition and transport. The review also discusses specific modulators of multidrug resistance in cancer and gene therapy using the MDR1 gene.
Benefits of the virtualization technologies with intrusion detection and prevention systems (2013)

In recent years, virtualization technologies were settled faster than anyone imagined and got placed big areas in our lives. Virtualization is a technology that eliminates the “uniqueness” dependency by creating an abstraction layer between the hardware and the software that runs on it. The aim of virtualization is to centralize the information system for facilitating administrative task while improving scalability. Virtualization technology which allows more efficient use of existing physical hardware, as well as some advantages including cost reduction, labor loss and performance improvement, contains several innovations in security, especially in system security. Software applications such as antivirus, firewall, end point security installed on the servers to ensure system security causes performance loss on the network and servers. Hence, security applications must be implemented on virtualization layer (hypervisor, Virtual Machine Monitor) to cover all the virtual system. In this paper, we aim to explain usage of Intrusion Detection Systems and Intrusion Prevention Systems in virtualization technologies and prologue possible security threats in virtual area.
A Method for Measuring Foot Pressures Using a High Resolution, Computerized Insole Sensor: The Effect of Heel Wedges on Plantar Pressure Distribution and Center of Force (1992)

A new, high resolution, pressure-sensitive insole was tested and found to provide reproducible measurements of static and dynamic plantar pressures inside the shoe of normal test subjects under certain conditions. However, calibration between separate sensors was poor and the sensor pads showed significant wear with use. This system was also used to investigate the effect of heel wedges on plantar foot pressure to determine whether this system was sensitive enough to detect the effect of a gross shoe modification on plantar foot pressure. Medial heel wedges decreased plantar pressures under the first and second metatarsals as well as under the first toe, and shifted the center of force laterally in all portions of the foot. Lateral heel wedges decreased pressures under the third, fourth, and fifth metatarsals, increased pressures under the first and second metatarsals, and shifted the center of force medially in all portions of the foot. Our evaluations indicate that it is possible to measure static and dynamic plantar foot pressures within shoes and to study the possible effect of shoe modifications on plantar pressures in controlled gait trials.
HARTS: a distributed real-time architecture (1991)

The design, implementation, and evaluation of a distributed real-time architecture called HARTS (hexagonal architecture for real-time systems) are discussed, emphasizing its support of time-constrained, fault-tolerant communications and I/O (input/output) requirements. HARTS consists of shared-memory multiprocessor nodes, interconnected by a wrapped hexagonal mesh. This architecture is intended to meet three main requirements of real-time computing: high performance, high reliability, and extensive I/O. The high-level and low-level architecture is described. The evaluation of HARTS, using modeling and simulation with actual parameters derived from its implementation, is reported. Fault-tolerant routing, clock synchronization and the I/O architecture are examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Front-end design issues in soft-x-ray projection lithography (1993)

We present a protocol for the design of an illumination system (front end) for a soft-x-ray projection lithography tool. The protocol is illustrated by specific front-end designs. The most complete design analysis is for a laser-driven system. Other drivers; undulator, synchrotron orbital radiation, and plasma discharge, are also discussed.
Bovine Viral Diarrhea (1987)

Bovine viral diarrhea virus is the most important viral pathogen of the bovine fetus. After birth it is responsible for two clinically dissimilar conditions: BVD and mucosal disease. It also causes significant losses as a result of its interaction with other pathogens, enhancing their morbidity in dual infections. Currently available prophylactic vaccines may be inadequate because they are not totally safe or afford incomplete protection; Our understanding of the pathogenesis of BVD virus infections in cattle is in a very dynamic state at the present time, as a result of work carried out by several groups (1-5). In contrast, progress in areas such as the molecular events of virus replication, the antigenic structure of the virus and the specificity of the immune response of the host has been slower.
Omni-directional face detection based on real adaboost (2005)

We propose an omni-directional face detection method based on the confidence-rated AdaBoost algorithm, called real AdaBoost, proposed by R.E. Schapire and Y. Singer (see Machine Learning, vol.37, p.297-336, 1999). To use real AdaBoost, we configure the confidence-rated look-up-table (LUT) weak classifiers based on Haar-type features. A nesting-structured framework is developed to combine a series of boosted classifiers into an efficient object detector. For omni-directional face detection, our method has achieved a rather high performance and the processing speed can reach 217 ms per 320/spl times/240 image. Experiment results on the CMU+MIT frontal and the CMU profile face test sets are reported to show its effectiveness.
Real-time traffic measurements on MAGNET II (1990)

Real-time traffic measurements on MAGNET II, an integrated network testbed based on asynchronous time sharing (ATS), are reported. The quality of service is evaluated by monitoring the buffer occupancy distribution, the packet time delay distribution, the packet loss, and the gap distribution of the consecutively lost packets. Experiments show that both time delay and buffer occupancy distributions of multiplexed video sources display a marked bimodal behavior, which does not seem to depend on the buffer size. The reliance of the network designer on traffic sources that do not exhibit substantial correlations can lead to implementations with serious congestion problems. For ATS-based networks with different traffic classes, the impact of a traffic class on the performance of the other classes tends to be diminished when compared with single-class-based ATM (asynchronous transfer mode) networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Effect of polymorphism in the human glutathione S-transferase A1 promoter on hepatic GSTA1 and GSTA2 expression (2001)

The patterns of expression of glutathione S-transferases A1 and A2 in human liver (hGSTA1 and hGSTA2, respectively) are highly variable, notably in the ratio of hGSTA1/hGSTA2. We investigated if this variation had a genetic basis by sequencing the proximal promoters (-721 to -1 nucleotides) of hGSTA1 and hGSTA2, using 55 samples of human liver that exemplified the variability of hGSTA1 and hGSTA2 expression. Variants were found in the hGSTA1 gene: -631T or G, -567T, -69C, -52G, designated as hGSTA1*A; and -631G, -567G, -69T, -52A, designated as hGSTA1*B. Genotyping for the substitution -69C > T by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP), showed that the polymorphism was widespread in Caucasians, African-Americans and Hispanics, and that it appeared to conform to allelic variation. Constructs consisting of the proximal promoters of hGSTA1*A, hGSTA1*B or hGSTA2, with luciferase as a reporter gene, showed differential expression when transfected into HepG2 cells: hGSTA1*A approximately hGSTA2 > hGSTA1*B. Similarly, mean levels of hGSTA1 protein expression in liver cytosols decreased significantly according to genotype: hGSTA1*A > hGSTA1-heterozygous > hGSTA1*B. Conversely, mean hGSTA2 expression increased according to the same order of hGSTA1 genotype. Consequently, the ratio of GSTA1/GSTA2 was highly hGSTA1 allele-specific. Because the polymorphism in hGSTA1 correlates with hGSTA1 and hGSTA2 expression in liver, and hGSTA1-1 and hGSTA2-2 exhibit differential catalysis of the detoxification of carcinogen metabolites and chemotherapeutics, the polymorphism is expected to be of significance for individual risk of cancer or individual response to chemotherapeutic agents.
Characteristics of human prostasomes isolated from three different sources (2003)

Since the three prostasome types were isolated from different environments, our data support the view that the common characteristics were prostasome-genuine.
High-throughput templated multisegment synthesis of gold nanowires and nanorods (2009)

A cost-effective, high-throughput method for generating gold nanowires and/or nanorods based on a multisegment template electrodeposition approach is described. Using this method, multiple nanowires/nanorods can be generated from a single pore of alumina template membranes by alternately depositing segments of desirable (e.g., gold) and non-desirable metals (e.g., silver), followed by dissolution of the template and the non-desirable metal. Critical cost analysis indicates substantial savings in material requirements, processing times, and processing costs compared to the commonly used single-segment method. In addition to solid gold nanowires/nanorods, high yields of porous gold nanowires/nanorods are obtained by depositing alternate segments of gold-silver alloy and silver from the same gold-silver plating solution followed by selective dissolution of the silver from both segments. It is anticipated that this high-throughput method for synthesizing solid and porous gold nanowires and nanorods will accelerate their use in sensing, electronic, and biomedical applications.
Optically addressable molecular spins for quantum information processing (2020)

Spin-bearing molecules are promising building blocks for quantum technologies as they can be chemically tuned, assembled into scalable arrays, and readily incorporated into diverse device architectures. In molecular systems, optically addressing ground-state spins would enable a wide range of applications in quantum information science, as has been demonstrated for solid-state defects. However, this important functionality has remained elusive for molecules. Here, we demonstrate such optical addressability in a series of synthesized organometallic, chromium(IV) molecules. These compounds display a ground-state spin that can be initialized and read out using light and coherently manipulated with microwaves. In addition, through atomistic modification of the molecular structure, we vary the spin and optical properties of these compounds, indicating promise for designer quantum systems synthesized from the bottom-up.
High‐temperature adsorption of alkali vapors on solid sorbents (1989)

Abstract Vapors of alkali metal compounds can be removed from coal combustion and gasification flue gases using high‐temperature aluminosilicate sorbents. The fundamentals of alkali adsorption on kaolinite, bauxite, and emathlite are compared and analyzed both experimentally and through theoretical modeling. The results show that the process is not a simple physical condensation, but a complex combination of diffusion and reaction. The kinetics of adsorption on these sorbents have similarities: the process is diffusion‐influenced, the rate decreases with time, and there is a final saturation limit. There are, however, differences in reaction mechanisms leading to potentially different applications for each sorbent. In adsorbing alkali chloride vapors, kaolinite and emathlite release all the chlorine back to the gas phase while bauxite retains some of the chlorine. Moreover, the products of reaction with emathlite have a melting point significantly lower than those for kaolinite and bauxite. Therefore, emathlite is more suitable for lower‐temperature sorption systems downstream of the combustors/gasifiers, while kaolinite and bauxite are suitable as in ‐ situ additives.