gebhart/patrepeval huggingface dataset:
Structure of the HIV-1 Nucleocapsid Protein Bound to the SL3 Ψ-RNA Recognition Element (1998)

The three-dimensional structure of the human immunodeficiency virus-type 1 (HIV-1) nucleocapsid protein (NC) bound to the SL3 stem-loop recognition element of the genomic Psi RNA packaging signal has been determined by heteronuclear magnetic resonance spectroscopy. Tight binding (dissociation constant, approximately 100 nM) is mediated by specific interactions between the amino- and carboxyl-terminal CCHC-type zinc knuckles of the NC protein and the G7 and G9 nucleotide bases, respectively, of the G6-G7-A8-G9 RNA tetraloop. A8 packs against the amino-terminal knuckle and forms a hydrogen bond with conserved Arg32, and residues Lys3 to Arg10 of NC form a 310 helix that binds to the major groove of the RNA stem and also packs against the amino-terminal zinc knuckle. The structure provides insights into the mechanism of viral genome recognition, explains extensive amino acid conservation within NC, and serves as a basis for the development of inhibitors designed to interfere with genome encapsidation.
tRNA<sup>His</sup> guanylyltransferase adds G<sub>−1</sub> to the 5′ end of tRNA<sup>His</sup> by recognition of the anticodon, one of several features unexpectedly shared with tRNA synthetases (2006)

All eukaryotic tRNA(His) molecules are unique among tRNA species because they require addition of a guanine nucleotide at the -1 position by tRNA(His) guanylyltransferase, encoded in yeast by THG1. This G(-1) residue is both necessary and sufficient for aminoacylation of tRNA by histidyl-tRNA synthetase in vitro and is required for aminoacylation in vivo. Although Thg1 is presumed to be highly specific for tRNA(His) to prevent misacylation of tRNAs, the source of this specificity is unknown. We show here that Thg1 is >10,000-fold more selective for its cognate substrate tRNA(His) than for the noncognate substrate tRNA(Phe). We also demonstrate that the GUG anticodon of tRNA(His) is a crucial Thg1 identity element, since alteration of this anticodon in tRNA(His) completely abrogates Thg1 activity, and the simple introduction of this GUG anticodon to any of three noncognate tRNAs results in significant Thg1 activity. For tRNA(Phe), k(cat)/K(M) is improved by at least 200-fold. Thg1 is the only protein other than aminoacyl-tRNA synthetases that is known to use the anticodon as an identity element to discriminate among tRNA species while acting at a remote site on the tRNA, an unexpected link given the lack of any identifiable sequence similarity between these two families of proteins. Moreover, Thg1 and tRNA synthetases share two other features: They act in close proximity to one another at the top of the tRNA aminoacyl-acceptor stem, and the chemistry of their respective reactions is strikingly similar.
3.6 A 45Gb/s PAM-4 transmitter delivering 1.3Vppd output swing with 1V supply in 28nm CMOS FDSOI (2016)

The development of next-generation electrical link technology to support 400Gb/s standards is underway [1-5]. Physical constraints paired to the small area available to dissipate heat, impose limits to the maximum number of serial interfaces and therefore their minimum speed. As such, aggregation of currently available 25Gb/s systems is not an option, and the migration path requires serial interfaces to operate at increased rates. According to CEI-56G and IEEE P802.3bs emerging standards, PAM-4 signaling paired to forward error correction (FEC) schemes is enabling several interconnect applications and low-loss profiles [1]. Since the amplitude of each eye is reduced by a factor of 3, while noise power is only halved, a high transmitter (TX) output amplitude is key to preserve high SNR. However, compared to NRZ, the design of a PAM-4 TX is challenged by tight linearity constraints, required to minimize the amplitude distortion among the 4 levels [1]. In principle, current-mode (CM) drivers can deliver a differential peak-to-peak swing up to 4/3(VDD-VOV), but they struggle to generate high-swing PAM-4 levels with the required linearity. This is confirmed by recently published CM PAM-4 drivers, showing limited output swings even with VDD raised to 1.5V [2-4]. Source-series terminated (SST) drivers naturally feature better linearity and represent a valid alternative, but the maximum differential peak-to-peak swing is bounded to VDD only. In [5], a dual-mode SST driver supporting NRZ/PAM-4 was presented, but without FFE for PAM-4 mode. In this paper, we present a PAM-4 transmitter leveraging a hybrid combination of SST and CM driver. The CM part enhances the output swing by 30% beyond the theoretical limit of a conventional SST implementation, while being calibrated to maintain the desired linearity level. A 5b 4-tap FIR filter, where equalization tuning can be controlled independently from output matching, is also embedded. The transmitter, implemented in 28nm CMOS FDSOI, incorporates a half-rate serializer, duty-cycle correction (DCC), ≫2kV HBM ESD diodes, and delivers a full swing of 1.3V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ppd</sub> at 45Gb/s while drawing 120mA from a 1V supply. The power efficiency is ~2 times better than those compared in this paper.
Compact and reliable protection of single-fiber and ribbon-fiber fusion splices (1993)

Arc fusion splicing is the result of fiber preparation, bare fiber welding, and protection application. Fiber preparation is performed through a sequence of operations like coating stripping (chemical, mechanical, thermal), cleaning and cleaving of stripped fibers. Welding process involves placing the fibers in the splicing machine, alignment and fusion. The length of bare fiber in the splice falls in the range 8 divided by 30 mm depending on splicer type. At the end a protection is applied to seal the bare splice from the environment and to increase its strength. In this paper the influence of the different steps of splicing process on the reliability of the splices is analyzed. All tests have been performed on single-mode reduced-core fibers made by OVD technology and coated by means of a double layer acrylate material or ribboned together by means of an additional common extruded coating.
Role for Emulsan in Growth of <i>Acinetobacter calcoaceticus</i> RAG-1 on Crude Oil (1986)

When Acinetobacter calcoaceticus RAG-1 was grown together with an emulsan-deficient mutant on crude oil, only the emulsan-producing RAG-1 was found to grow, regardless of whether the medium was supplemented with emulsan. The results suggested that the cell-associated form of the bioemulsifier is the biologically active species required for growth on crude oil. A revertant of an emulsan-deficient strain was isolated which simultaneously regained the ability to produce both cell-associated and cell-free emulsan as well as the ability to grow on crude oil.
Local nitroglycerin for treatment of anal fissures (1997)

Topical application of nitroglycerine represents a new, easily handled, and effective alternative in the treatment of anal fissures. All of our patients reported a dramatic reduction in acute anal pain. However, it should be noted that a lack of sphincter tone reduction is a likely reason for the great tendency of chronic anal fissures to recur.
Electrical properties of mim and mis structures with Langmuir-Blodgett poly diacetylene films (2005)

Electrical properties are investigated for metal-insulator-metal (MIM) and metal-insulator-semiconductor (MIS) structures with Langmuir-Blodgett poly diacetylene (LB PDA) insulators. Capacitance-voltage (C-V) characteristics are measured for the Al / LB PDA / p-Si (MIS) devices. The C-V curves show hysteresis, and flat-band voltage shifts are observed under the application of bias voltages. These results show charge injection from Si into the MIS devices. Thermally stimulated currents (TSCs) are measured for Al / LB PDA / Al (MIM) structures. TSC peaks caused by dipole polarization and charge injection are observed in the low and in the high temperature regions, re spectively.Furthermore, remarkable change of TSC curves is observed for this structures between before and after annealing.
Autonomous grid scheduling using probabilistic job runtime forecasting. (2008)

Computational Grids are evolving into a global, service-oriented architecture a universal platform for delivering future computational services to a range of applications of varying complexity and resource requirements. The thesis focuses on developing a new scheduling model for general-purpose, utility clusters based on the concept of user requested job completion deadlines. In such a system, a user would be able to request each job to finish by a certain deadline. and possibly to a certain monetary cost. Implementing deadline scheduling is dependent on the ability to predict the execution time of each queued job. and on an adaptive scheduling algorithm able to use those predictions to maximise deadline adherence. The thesis proposes novel solutions to these two problems and documents their implementation in a largely autonomous and self-managing way. The starting point of the work is an extensive analysis of a representative Grid workload revealing consistent workflow patterns, usage cycles and correlations between the execution times of jobs and its properties commonly collected by the Grid middleware for accounting purposes. An automated approach is proposed to identify these dependencies and use them to partition the highly variable workload into subsets of more consistent and predictable behaviour. A range of time-series forecasting models, applied in this context for the first time, were used to model the job execution times as a function of their historical behaviour and associated properties. Based on the resulting predictions of job runtimes a novel scheduling algorithm is able to estimate the latest job start time necessary to meet the requested deadline and sort the queue accordingly to minimise the amount of deadline overrun. The testing of the proposed approach was done using the actual job trace collected from a production Grid facility. The best performing execution time predictor (the auto-regressive moving average method) coupled to workload partitioning based on three simultaneous job properties returned the median absolute percentage error eentroid of only 4.75CX. This level of prediction accuracy enabled the proposed deadline scheduling method to reduce the average deadline overrun time ten-fold compared to the benchmark batch scheduler. Overall, the thesis demonstrates that deadline scheduling of computational jobs on the Grid is achievable using statistical forecasting of job execution times based on historical information. The proposed approach is easily implementable, substantially self-managing and better matched to the human workflow making it well suited for implementation in the utility Grids of the future.
Receiver Orientation versus Transmitter Orientation in Linear MIMO Transmission Systems (2004)

In conventional transmission schemes, the transmitter algorithms are a priori given, whereas the algorithms to be used by the receivers have to be a posteriori adapted. Such schemes can be termed transmitter (Tx) oriented and have the potential of simple transmitter implementations. The opposite to Tx orientation would be receiver (Rx) orientation in which the receiver algorithms are a priori given, and the transmitter algorithms have to be a posteriori adapted. An advantage of the rationale Rx orientation is the possibility to arrive at simple receiver structures. In this paper, linear versions of the rationales Tx orientation and Rx orientation are applied to radio transmission systems with multiantennas both at the transmitter and receiver. After the introduction of adequate models for such multiple-input multiple-output (MIMO) systems, different system designs are evaluated by simulations, and recommendations for proper system solutions are given.
New metallochromic indicator for barium: Determination of sulfate in water and soil extracts (2006)

A new metallochromic indicator for barium, Orthanilic NM, is synthesized and proposed. The color reaction of Orthanilic NM with barium ions is compared with the reactions of carboxyarsenazo and other orthanilic group reagents, such as Orthanilic K, nitchromazo, etc. The quantitative characteristics of the reactions are determined. It is shown that Orthanilic NM can be used for the titrimetric (down to 20 mg/L) and photometric (down to 0.2 mg/L) determinations of sulfate. Substantial amounts of conventional anions, alkali, alkaline-earth, and nonferrous metals do not interfere with the titrimetric determination (at pH 2.5). For the photometric determination, a 1:1 Ba2+-Orthanilic NM complex is used at pH 2. In these conditions, sulfite and phosphate do not interfere with the determination either. Procedures are developed for the determination of sulfate in various types of water and soil extracts. Examples of their practical application are given.
Self‐Assembly of Imidazolium‐Based Rodlike Ionic Liquid Crystals: Transition from Lamellar to Micellar Organization (2010)

By using aryl-amination chemistry, a series of rodlike 1-phenyl-1H-imidazole-based liquid crystals (LCs) and related imidazolium-based ionic liquid crystals (ILCs) has been prepared. The number and length of the C-terminal chains (at the noncharged end of the rodlike core) and the length of the N-terminal chain (on the imidazolium unit in the ILCs) were modified and the influence of these structural parameters on the mode of self-assembly in LC phases was investigated by polarizing microscopy, differential scanning calorimetry, and X-ray diffraction. For the single-chain imidazole derivatives nematic phases (N) and bilayer SmA2 phases were found, but upon increasing the number of alkyl chains the LC phases were lost. For the related imidazolium salts LC phases were preserved upon increasing the number and length of the C-terminal chains and in this series it leads to the phase sequence SmA-columnar (Col)-micellar cubic (CubI /Pm3n). Elongation of the N-terminal chain gives the reversed sequence. Short N-terminal chains prefer an end-to-end packing of the mesogens in which these chains are separated from the C-terminal chains. Elongation of the N-terminal chain leads to a mixing of N- and C-terminal chains, which is accompanied by complete intercalation of the aromatic cores. In the smectic phases this gives rise to a transition from bilayer (SmA2) to monolayer smectic (SmA) phases. For the columnar and cubic phases the segregated end-to-end packing leads to core-shell aggregates. In this case, elongation of the N-terminal chains distorts core-shell formation and removes CubI and Col phases in favor of single-layer SmA phases. Hence, by tailoring the length of the N-terminal chain, a crossover from taper-shaped to polycatenar LC tectons was achieved, which provides a powerful tool for control of self-assembly in ILCs.
Crystal Structure of the Entire Ectodomain of gp130 (2010)

gp130 is the shared signal-transducing receptor subunit for the large and important family of interleukin 6-like cytokines. Previous x-ray structures of ligand-receptor complexes of this family lack the three membrane-proximal domains that are essential for signal transduction. Here we report the crystal structure of the entire extracellular portion of human gp130 (domains 1-6, D1-D6) at 3.6 A resolution, in an unliganded form, as well as a higher resolution structure of the membrane-proximal fibronectin type III domains (D4-D6) at 1.9 A. This represents the first atomic resolution structure of the complete ectodomain of any "tall" cytokine receptor. These structures show that other than a reorientation of the D1 domain, there is little structural change in gp130 upon ligand binding. They also reveal that the interface between the D4 and D5 domains forms an acute bend in the gp130 structure. Key residues at this interface are highly conserved across the entire tall receptor family, suggesting that this acute bend may be a common feature of these receptors. Importantly, this geometry positions the C termini of the membrane-proximal fibronectin type III domains of the tall cytokine receptors in close proximity within the transmembrane complex, favorable for receptor-associated Janus kinases to trans-phosphorylate and activate each other.
Novelty and Inductive Generalization in Human Reinforcement Learning (2015)

In reinforcement learning (RL), a decision maker searching for the most rewarding option is often faced with the question: What is the value of an option that has never been tried before? One way to frame this question is as an inductive problem: How can I generalize my previous experience with one set of options to a novel option? We show how hierarchical Bayesian inference can be used to solve this problem, and we describe an equivalence between the Bayesian model and temporal difference learning algorithms that have been proposed as models of RL in humans and animals. According to our view, the search for the best option is guided by abstract knowledge about the relationships between different options in an environment, resulting in greater search efficiency compared to traditional RL algorithms previously applied to human cognition. In two behavioral experiments, we test several predictions of our model, providing evidence that humans learn and exploit structured inductive knowledge to make predictions about novel options. In light of this model, we suggest a new interpretation of dopaminergic responses to novelty.
A competitive quantitative polymerase chain reaction method for characterizing the population dynamics during kimchi fermentation (2014)

The aim of this study was to develop a competitive quantitative-PCR (CQ-PCR) method for rapid analysis of the population dynamics of lactic acid bacteria (LAB) in kimchi. For this, whole chromosome sequences of Leuconostoc mesenteroides, Lactobacillus plantarum, and Lb. brevis were compared and species-specific PCR primers targeting dextransucrase, 16S rRNA, and surface layer protein D (SlpD) genes, respectively, were constructed. The tested strains were quantified both in medium and kimchi by CQ-PCR and the results were compared with the data obtained using a conventional plate-counting method. As a result, the three species were successfully detected and quantified by the indicated primer sets. Our results show that the CQ-PCR method targeting species-specific genes is suitable for rapid estimation of LAB population to be used in the food fermentation industry.
An improved diversity-guided particle swarm optimisation for numerical optimisation (2014)

Particle swarm optimisation (PSO) is a global optimisation technique, which has shown a good performance on many problems. However, PSO easily falls into local minima because of quick losing of diversity. Some diversity-guided PSO algorithms have been proposed to maintain diversity, but they often slow down the convergence rate. In this paper, we propose an improved diversity-guided PSO algorithm, namely IDPSO, which employs a local search to enhance the exploitation. In addition, a concept of generalised opposition-based learning (GOBL) is utilised for population initialisation and generation jumping to find high quality of candidate solutions. Experiments are conducted on a set of benchmark functions. Results show that our approach obtains a promising performance when compared with other PSO variants.
The Preparation of <i>N</i>-Protected Amino Alcohols and <i>N</i>-Protected Peptide Alcohol by Reduction of the Corresponding Esters with Sodium Borohydride. An Improved Procedure Involving a Slow Addition of a Small Amount of Methanol (1984)

Abstract Esters of N-protected amino acids and an N-protected peptide were reduced selectively to the corresponding alcohols in high yields using lesser amounts of sodium borohydride than does the conventional method by the slow addition of methanol to the mixture of ester and NaBH4 in t-butyl alcohol or tetrahydrofuran at 50°C.
Sound velocity of a sandstone saturated with oil and brine at different concentrations (1986)

We have measured the velocity of sound in a sandstone saturated with oil and brine at different concentrations. The velocity variations with the concentration depend drastically on the way of entering the fluids in the sample : injection of non‐wetting fluid in a sandstone fully saturated with a totally wetting fluid (drainage) or vice versa (imbibition). We interpret our measurements with an extension of the Biot‐Gassmann theory to a wetted frame of the sandstone saturated with an effective oil‐brine fluid.
Characterization of transducin from bovine retinal rod outer segments. Use of monoclonal antibodies to probe the structure and function of the subunit. (1988)

A panel of monoclonal antibodies has been developed against the T alpha, T beta and T gamma subunits of bovine transducin. Two anti-T alpha antibodies from this panel (TF15 and TF16) and a third one (4A) against frog T alpha (Witt, P. L., Hamm, H. E., and Bownds, M. D. (1984) J. Gen. Physiol. 84, 251-263) were characterized. Each of these monoclonal antibodies recognizes a different region of T alpha and has a specific effect on the function of transducin. The binding of TF15 is reversibly enhanced by treating T alpha with either 1 M guanidinium chloride or, to a smaller extent, by the removal of bound guanine nucleotide. Its epitope is located in a 12-kDa tryptic fragment containing the binding site for the guanine moiety of GTP. Taken together, these results support previous observations that the conformation of T alpha is modulated by the occupancy of the guanine nucleotide binding site. In contrast to TF15, TF16 recognizes only the native form of T alpha. Its epitope resides within the central portion of the T alpha molecule. While T alpha-bound TF16 does not inhibit either pertussis toxin-catalyzed ADP-ribosylation, rhodopsin binding, or transducin subunit interaction, it blocks both the light-activated uptake of guanosine 5'-O-(3-thiotriphosphate) (GTP gamma S) and the GTP-dependent elution of transducin from photolyzed rhodopsin. These effects are unlikely to be caused by the occupation of the guanine nucleotide binding site by TF16 because this antibody quantitatively precipitates T alpha-GTP gamma S. We propose that bound TF16 locks T alpha in a conformation that prevents the entrance of guanine nucleotide and favors T beta gamma association. In contrast to TF16, the epitope of 4A was mapped to the amino-terminal region of T alpha. This monoclonal antibody blocks pertussis toxin-catalyzed ADP-ribosylation, GTP gamma S uptake, and T alpha-T beta gamma association. Moreover, the binding site for 4A becomes inaccessible when transducin binds to photolyzed rhodopsin. These results suggest that the inhibitory effects of 4A are due to a simultaneous steric blockage of both the interaction of T alpha with T beta gamma and their binding to photolyzed rhodopsin. The results obtained from these studies are correlated with the structure and function of T alpha.
Synthesis and characterization of soluble aromatic polyazomethines from 2,5‐bis(4‐aminophenyl)‐3,4‐diphenylthiophene and aromatic dialdehydes (1984)

Abstract New soluble aromatic polyazomethines with inherent viscosities of 0.4–0.8 dL/g were prepared by the solution polycondensation of 2,5‐bis(4‐aminophenyl)‐3,4‐diphenylthiophene, bis(4‐aminophenyl) ether, and aromatic dialdehydes in o ‐chlorophenol at 20°C. The copolyazomethines are generally soluble in chlorinated hydrocarbons, amide‐type or phenolic solvents. The thermal stability of the polymers, which showed no weight loss up to 400°C in both air and nitrogen atmospheres.