gebhart/patrepeval huggingface dataset:
Definition of the Interferon-α Receptor-binding Domain on the TYK2 Kinase (1998)

Interferons and cytokines modulate gene expression via a simple, direct signaling pathway containing receptors, JAK tyrosine kinases, and STAT transcription factors. The interferon-alpha pathway is a model for these cascades. Two receptors, IFNaR1 and IFNaR2, associate exclusively in a constitutive manner with two JAK proteins, TYK2 and JAK1, respectively. Defining the molecular interface between JAK proteins and their receptors is critical to understanding the signaling pathway and may contribute to the development of novel therapeutics. This report defines the IFNaR1 interaction domain on TYK2. In vitro binding studies demonstrate that the amino-terminal half of TYK2, which is approximately 600 amino acids long and contains JAK homology (JH) domains 3-7, comprises the maximal binding domain for IFNaR1. A fragment containing amino acids 171-601 (JH3-6) also binds IFNaR1, but with reduced affinity. Glutathione S-transferase-TYK2 fusion proteins approximating either the JH6 or JH3 domain affinity-precipitate IFNaR1, suggesting that these are major sites of interaction within the larger binding domain. TYK2 amino acids 1-601 act in a dominant manner to inhibit the transcription of an interferon-alpha-dependent reporter gene, presumably by displacing endogenous TYK2 from the receptor. This same fragment inhibits interferon-alpha-dependent tyrosine phosphorylation of TYK2, STAT1, and STAT2.
Optimization of Chloronitrobenzamides (CNBs) as Therapeutic Leads for Human African Trypanosomiasis (HAT) (2013)

We previously reported the discovery of the activity of chloronitrobenzamides (CNBs) against bloodstream forms of Trypanosoma brucei . Herein we disclose extensive structure-activity relationship and structure-property relationship studies aimed at identification of tractable early leads for clinical development. These studies revealed a promising lead compound, 17b, that exhibited nanomolar potency against T. brucei (EC50 = 27 nM for T. b. brucei, 7 nM for T. b. rhodesiense, and 2 nM for T. b. gambiense ) with excellent selectivity for parasite cells relative to mammalian cell lines (EC50 > 25 μM). In addition compound 17b displayed suitable physiochemical characteristics and microsomal stability (t1/2 > 4 h for human and mouse) to justify pursuing in vivo studies.
Interferon-induced transmembrane protein-3 genetic variant rs12252-C is associated with severe influenza in Chinese individuals (2013)

The SNP rs12252-C allele alters the function of interferon-induced transmembrane protein-3 increasing the disease severity of influenza virus infection in Caucasians, but the allele is rare. However, rs12252-C is much more common in Han Chinese. Here we report that the CC genotype is found in 69% of Chinese patients with severe pandemic influenza A H1N1/09 virus infection compared with 25% in those with mild infection. Specifically, the CC genotype was estimated to confer a sixfold greater risk for severe infection than the CT and TT genotypes. More importantly, because the risk genotype occurs with such a high frequency, its effect translates to a large population-attributable risk of 54.3% for severe infection in the Chinese population studied compared with 5.4% in Northern Europeans. Interferon-induced transmembrane protein-3 genetic variants could, therefore, have a strong effect of the epidemiology of influenza in China and in people of Chinese descent.
Glycoform and Net Charge Heterogeneity in gp120 Immunogens Used in HIV Vaccine Trials (2012)

MN- and A244-rgp120 used in the RV144 trial exhibited extensive heterogeneity in net charge due to variation in sialic acid-containing glycoforms. These differences were cell line-dependent, affected the antigenicity of recombinant envelope proteins, and may affect assays used to measure neutralization. These studies, together with recent reports documenting broadly neutralizing antibodies directed against carbohydrate epitopes of gp120, suggest that glycoform variation is a key variable to be considered in the production and evaluation of subunit vaccines designed to prevent HIV infection.
A new self-aligned well-isolation technique for CMOS devices (1986)

This paper presents the development of a new well-isolation technique for advanced CMOS LSI's. The technique comprises narrow deep trench fabrication utilizing undercut, in addition to silicon-oxide cap formation, which leaves a cavity. The predominant feature of this technique is that well isolation self-aligned to the well region is realized utilizing the trench fabrication technique. Additionally, no crystal defects are observed around the well isolation even after 1000°C annealing following silicon-oxide cap formation. Since the well isolation produced also prevents the latchup phenomenon from occurring due to its depth, this technique enables the CMOS device dimensions to be considerably reduced.
Cobalt‐mediated catalytic chain‐transfer polymerization (CCTP) in water and water/alcohol solution (2001)

Abstract This article describes the use of cobalt‐mediated catalytic chain transfer in aqueous solution under fed conditions for the preparation of macromonomers of acidic, hydroxy, and zwitterionic functional monomers. Use of a batch reaction leads to hydrolysis of catalyst, a mixture of mechanisms and poor control of the reaction. A feed process is described that adds catalyst as a solution in monomer over the course of the reaction. The feed process is applied to a range of monomers of methacrylic acid ( 2 ), 2‐aminoethyl methacrylate hydrochloride ( 3 ), 2‐hydroxyethyl methacrylate ( 4 ), 2‐methacryloxyethyl phosphoryl choline ( 5 ), glycerol monomethyl methacrylate ( 6 ), and 3‐ O ‐methacryloyl‐1,2:5,6‐di‐ O ‐isopropylidene‐ D ‐glucofuranose ( 7 ). Use of the feed process for water‐soluble monomers in conjunction with 1 as a catalytic chain‐transfer agent gives high‐conversion, > 90%, water‐soluble macromonomers. The number‐average molecular mass ( M n was determined by integration of the 1 H NMR spectrum comparing the vinylic end group with the remainder of the backbone. Pseudo‐Mayo plots were constructed by measuring the M n at high conversion as a function of [monomer]/[catalyst] to give observed chain‐transfer constants of 1120, 958, and 1058 for 4, 6, and 2, respectively. All products were obtained as relatively high‐solid, homogeneous, low‐viscosity aqueous solutions. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 2378–2384, 2001
Fully integrated CMOS data and clock recovery for wireless biomedical implants (2011)

In order to minimize the size and improve the efficiency of power consumption, most of wireless implantable Microsystems use Amplitude Shift Keying (ASK) modulator to transmit, through a RF link, data and energy to the internal implants. In this paper, we propose a new structure of wireless data and clock recovery dedicated for biomedical implants. It consists in a fully integrated ASK demodulator unit and a digital Manchester decoder. The demodulator is based on active components instead of the passive elements, as resistance or capacitance, to extract a robust data with a low modulation index. The whole digital Manchester decoder intends to recover data and clock from the demodulated signal. The following design has been validated by CADENCE environment using Specter simulation in a standard AMS 0.35μm CMOS process. The data rate is simulated by 1Mbps speed for 10MHz carrier frequency and 20% modulation index.
Near-field optics simulation of a solid immersion lens combining with a conical probe and a highly efficient solid immersion lens-probe system (2004)

A solid immersion lens (SIL) combined with near-field probes which are the conic dielectric probe and the local metallic coating on the SIL probe is designed for optical recording by means of a three-dimensional rather than two-dimensional finite difference time domain method to gain more insight in the near-field distribution. Our computation model is realistic to match the real SIL-probe system. The optical properties of near-field distributions between the SIL probe and recording layers are investigated. A promising idea for fabricating a type of the SIL-probe system is proposed. Results of our designation of an optimal SIL-probe system can achieve higher performance (in terms of high throughput and low reflection of the light beam) for optical data storage and microscopy than the conventional metal NSOM probe or SIL used alone.
BioVision: A Biomimetics Platform for Intrinsically Motivated Visual Saliency Learning (2018)

We present BioVision, a bio-mimetics platform based on the human visual system. BioVision relies on the foveal vision principle based on a set of cameras with wide and narrow fields of view. We present in this platform a mechanism for learning visual saliency in an intrinsically motivated fashion. This model of saliency, learned and improved on-the-fly during the robot's exploration provides an efficient tool for localizing relevant objects within their environment. The proposed approach includes two intertwined components. On the one hand, a method for learning and incrementally updating a model of visual saliency from foveal observations. On the other hand, we investigate an autonomous exploration technique to efficiently learn such a saliency model. The proposed exploration, based on the intelligent adaptive curiosity (IAC) algorithm is able to drive the robot's exploration so that samples selected by the robot are likely to improve the current model of saliency. We then demonstrate that such a saliency model learned directly on a robot outperforms several state-of-the-art saliency techniques, and that IAC can drastically decrease the required time for learning a reliable saliency model. We also investigate the behavior of IAC in a non static environment, and how well this algorithm can adapt to changes.
The Chemical Composition and Biological Properties of Coconut (Cocos nucifera L.) Water (2009)

Coconut water (coconut liquid endosperm), with its many applications, is one of the world's most versatile natural product. This refreshing beverage is consumed worldwide as it is nutritious and beneficial for health. There is increasing scientific evidence that supports the role of coconut water in health and medicinal applications. Coconut water is traditionally used as a growth supplement in plant tissue culture/micropropagation. The wide applications of coconut water can be justified by its unique chemical composition of sugars, vitamins, minerals, amino acids and phytohormones. This review attempts to summarise and evaluate the chemical composition and biological properties of coconut water.
Application of the Solid Dispersion Method to the Controlled Release of Medicine. VI. Release Mechanism of a Slightly Water Soluble Medicine and Interaction between Flurbiprofen and Hydroxypropyl Cellulose in Solid Dispersion. (1994)

Solid dispersion (SD) was prepared with a slightly water soluble medicine (flurbiprofen (FP)) and a water soluble polymer (hydroxypropyl cellulose (HPC)) having five grades of different molecular weights. The release mechanism of FP from the SD granules and the interaction between FP and HPC in the SD were studied.The release rate of FP from the SD granules increased with decreasing HPC molecular weight or increase in the composition ratio of HPC. The powder X-ray diffraction patterns and DSC curves suggest that FP exists in an amorphous state in the SD. The IR spectra show an interaction of hydrogen bonding between FP and HPC. The percent of FP forming a hydrogen bond with HPC in the SD increased with decreasing HPC molecular weight or increase in the composition ratio of HPC. A linear relationship was found between the release rate of FP and the percent of the hydrogen bonded FP in the SD. An increase in the dispersibility of FP and the degree of mixing of FP and HPC will cause an increase in the effective surface area of FP and HPC for dissolution, thus increasing the release of FP and the percent of hydrogen bonded FP.
The Role of Contract Law in Developing the Chinese Legal Culture (1987)

The economic reforms initiated during the past decade in China have created an additional need for legal reforms. One reform which greatly affects commercial transactions between Chinese and foreign entities is the establishment of a legal framework for analyzing contractual relationships. This Article outlines some of the provisions of the Economic Contract Law, which governs contracts between Chinese entities, and the Foreign Economic Contract Law, which governs contracts used in foreign trade. After noting the interdependence of these laws, the author examines the treatment of several issues which are of great concern to foreign businesses, including choice of law, contract formation, performance and breach of contractual obligations, and dispute resolution. The author strongly recommends that contracts with Chinese parties follow the language of the Chinese contract laws, in order to assure enforceability.
Spätkomplikationen nach Silikonölinjektion. Langzeitbeobachtungen an 100 Fällen* (1986)

The authors report on late complications in 100 eyes in which silicone oil injection had been used to treat complicated retinal detachment; the follow-up-period was two years. Redetachment developed in 28 of 100 eyes (30%) during the first year, cataract in 43 of 54 phakic eyes, and glaucoma in 22 of 100 eyes (= 22%). Keratopathy developed in 29 of 46 aphakic eyes up to the 18th postoperative month. After treatment of these complications a visual acuity of 1/50 to 0.4 was observed in 50 percent of the eyes two years after the operation.
Fabrication and Analysis of Josephson and Weak-Link Junctions and Arrays. (1992)

Abstract : The work took two main avenues in order to prepare the ground for the main goal of the program: planar junctions made with the use of scanning tunneling microscope and atomic force microscopes in conjunction with some novel ideas of etching and metal deposition. The first avenue was the fabrication of ultra small bridges on which junctions will be written. The second avenue was a theoretical analysis of a single junction as well as arrays of many sections of that type.
Effects of atabrine and of certain related substances on the development of liver tumors due to azo dyes. (1952)

1. Atabrine, auramine, and quinine were without consistent effect on tumor incidence when the alkaloids were fed to rats with 4-dimethylaminoazobenzene (DAB).

2. Atabrine increased the incidence of liver tumors when fed between two doses of 3′-methyl-4-dimethylaminoazobenzene (3′-Me-DAB). The increase was approximately equal to that observed when carcinogens such as DAB, 2-acetylaminofluorene, or urethan were fed between the two doses of 3′-Me-DAB. Quinine, auramine, or methylcholanthrene did not increase the incidence of liver tumors under these conditions.

3. The concentration of riboflavin was diminished in the livers of rats fed atabrine. The observed increase in tumors, however, appeared to be associated with some other (unknown) effect of atabrine upon the liver.
Selection of fuzzy control rules using automatic tuning of membership functions (2002)

Tuning of membership functions using learning procedure in a neuro-like approach has been developed to select fuzzy control rules. The tuning method is applied to simulation of driving control of a model car to run on a straight road. Simulation results bring out similar optimal trajectories of the car in both cases of 3/spl times/3 (=9 rules) and 7/spl times/7 (=49 rules) control rule types after tuning. Estimation function of errors used in the tuning of 3/spl times/3 rule type rapidly decreases to the convergent value of that used in 7/spl times/7 with increasing learning iteration.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
In vitro susceptibilities of aerobic and facultatively anaerobic Gram-negative bacilli isolated from patients with intra-abdominal infections worldwide: 2004 results from SMART (Study for Monitoring Antimicrobial Resistance Trends) (2006)

Antimicrobial resistance among GNB isolated from intra-abdominal infections continued to be a problem worldwide in 2004, with the highest rates of resistance overall in the Asia/Pacific region. The carbapenems and amikacin were the most consistently active agents in vitro against Enterobacteriaceae isolated from intra-abdominal infections worldwide.
Charge-coupled device imaging system for precision beam steering in laser communications (1995)

A CCD imaging system has been developed for precision laser beam pointing. The system contains a high frame rate CCD camera operated in windowing mode under command of an embedded processor. A laser pointing and tracking update rate of 2 kHz has been achieved.
On parameter optimization approach to optimal control problems (2002)

A user-friendly window-driven interactive environment called Op/sup ti/A for the effective solution of mathematical programming problems is described. It enables solution of various frequently encountered classes of parameter optimization problems including nonsmooth, minimax and multicriterial. Reciting the fact that most of the optimal control problems, either continuous-time or discrete-time, can be alternatively expressed in a mathematical programming framework, one can use the current system for their solution, at least for some classes of problems. Especially for continuous-time optimal control problems the appropriate parametrization results in reasonably manageable nonlinear mathematical programming problems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis (2016)

Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial infections. Conjugative pheromone-responsive plasmids are narrow-host-range mobile genetic elements (MGEs) that are rapid disseminators of antibiotic resistance in the faecalis species. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification confer acquired and innate immunity, respectively, against MGE acquisition in bacteria. Most multidrug-resistant E. faecalis isolates lack CRISPR-Cas and possess an orphan locus lacking cas genes, CRISPR2, that is of unknown function. Little is known about restriction-modification defense in E. faecalis. Here, we explore the hypothesis that multidrug-resistant E. faecalis strains are immunocompromised. We assessed MGE acquisition by E. faecalis T11, a strain closely related to the multidrug-resistant hospital isolate V583 but which lacks the ~620 kb of horizontally acquired genome content that characterizes V583. T11 possesses the E. faecalis CRISPR3-cas locus and a predicted restriction-modification system, neither of which occurs in V583. We demonstrate that CRISPR-Cas and restriction-modification together confer a 4-log reduction in acquisition of the pheromone-responsive plasmid pAM714 in biofilm matings. Additionally, we show that the orphan CRISPR2 locus is functional for genome defense against another pheromone-responsive plasmid, pCF10, only in the presence of cas9 derived from the E. faecalis CRISPR1-cas locus, which most multidrug-resistant E. faecalis isolates lack. Overall, our work demonstrated that the loss of only two loci led to a dramatic reduction in genome defense against a clinically relevant MGE, highlighting the critical importance of the E. faecalis accessory genome in modulating horizontal gene transfer. Our results rationalize the development of antimicrobial strategies that capitalize upon the immunocompromised status of multidrug-resistant E. faecalis. IMPORTANCE Enterococcus faecalis is a bacterium that normally inhabits the gastrointestinal tracts of humans and other animals. Although these bacteria are members of our native gut flora, they can cause life-threatening infections in hospitalized patients. Antibiotic resistance genes appear to be readily shared among high-risk E. faecalis strains, and multidrug resistance in these bacteria limits treatment options for infections. Here, we find that CRISPR-Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, significantly impact the spread of antibiotic resistance genes in E. faecalis populations. The loss of these systems in high-risk E. faecalis suggests that they are immunocompromised, a tradeoff that allows them to readily acquire new genes and adapt to new antibiotics.
Electron transfer in ruthenium-modified proteins (1992)

The electron-transfer (ET) reactions of metalloproteins\nare potentially far more complex than those of small molecules. The structural intricacies of proteins are largely responsible for the added complexity. Reactive centers are surrounded by polypeptide matrices that shield these sites from solvent and separate them from their redox partners. The nonuniform charge distributions on the protein surfaces create anisotropic interactions between redox partners, confounding the interpretation of bimolecular reactions. Covalent or electrostatic coupling of redox partners can be exploited to simplify the problem but does not eliminate all of the complicating factors in metalloprotein ET reactions. The energetics and dynamics\nof nuclear reorientations accompanying protein ET reactions continue to be a source of inquiry. Multiple conformational states in the polymer surrounding the redox sites create the potential for "gating" and directional electron transfer. The peptide matrix also separates the redox sites, leading to questions of how protein ET can be efficient over such long (> 10 Å) distances. One line of research aimed at addressing many of the fundamental issues in protein ET involves the use of proteins modified by the coordination of Ru complexes to surface amino acid residues.
Reversible data hiding with histogram-based difference expansion for QR code applications (2011)

In this paper, we propose a new algorithm in reversible data hiding, with the application associated with the quick response (QR) codes. QR codes are random patterns, which can be commonly observed on the corner of posters or webpages. The goal of QR codes aims at convenienceoriented applications for mobile phone users. People can use the mobile phone cameras to capture QR code at the corner of web page, and then the hyperlink corresponding to the QR code can be accessed instantly. Since QR code looks like random noise and it occupies a corner of the original image, its existence can greatly reduce the value of the original content. Thus, how to retain the value of original image, while keeping the capability for the instant access for webpages, would be the major concern of this paper. With the aid of our reversible data hiding technique, the QR codes can be hidden into the original image, and considerable increase in embedding capacity can be expected. Next, we propose a scheme such that when the image containing the QR code is browsed, the hyperlink corresponding to the QR code is accessed first. Then, the QR code could get vanished and the original image would be recovered to retain the information conveyed therein. Simulation results demonstrate the applicability of the proposed algorithm.
Build up and decay of mode instability in a high power fiber amplifier (2012)

State-of-the-art high power Yb-doped large mode area fibers have been developed to a performance level able to reach the so-called mode instability threshold. In this contribution we will discuss the experimental results regarding the temporal evolution (build up and decay) of this effect to come closer to a comprehensive understanding of its driving mechanisms. Our investigations prove that the relevant time scale for build up and decay of mode instability is in the millisecond range and thus deliver experimental evidence of underlying thermal effects. To the best of our knowledge these are the first systematic, time resolved investigations on that topic.