gebhart/patrepeval huggingface dataset:
Solubilization and Iterative Saturation Mutagenesis of α1,3‐fucosyltransferase from <i>Helicobacter pylori</i> to enhance its catalytic efficiency (2016)

α1,3-Fucosyltransferase (α1,3-FucT) is essential for the biosynthesis of biologically active α1,3-fucosyloligosacchairdes (3-FOs) from human milk oligosaccharides (HMO), particularly 3-fucosyllactose (3-FL) trisaccharide. α1,3-FucT from Helicobacter pylori 26695 (FutA) accepts lactose and LacNAc as glycan acceptors and has a very low level of expression in Escherichia coli, and it shows a low catalytic activity for lactose in the large-scale synthesis of 3-FL. To overcome the poor solubility of FutA, codon optimization, and systematic truncation of the protein at the C-terminus with only one heptad repeat remaining (Δ52 FutA) were conducted to yield 150-200 mg/L of soluble protein of FutA and resulting in more than an 18-fold increase in the 3-FL yield. To improve the low level of enzyme catalytic activity for lactose, focused directed evolution was attempted using a semi-rational approach that combines structure-guided computational analysis and subsequent iterative saturation mutagenesis (ISM). In order to select the functional residues in active site/substrate binding site, docking simulation was used together with HotSpot Wizard to target evolutionarily variable amino acid positions. A128 site was selected from the key residue located in the active site, and A128N mutant displayed a 3.4-fold higher catalytic activity than wild-type Δ52 FutA. Considering that the A128N mutation is located in the deep cleft of the lactose binding site, the residues within the substrate binding sites, especially on the two α-helices for lactose and one α-helix for GDP-fucose, were subjected to structure-guided ISM. The selected residues from each helix were clustered, and ISM was performed for each cluster in parallel. In particular, the mutant with triple mutations (A128N/H129E/Y132I) located on the α5 helix exhibited a 9.6-fold improvement in specific activity when compared to wild-type Δ52 FutA. When such clustered mutations on two α-helices (α5 and α2/loop) were combined, mutants with triple (A128N/H129E/S46F) and quadruple mutations (A128N/H129E/Y132I/S46F) were generated, which showed the synergistic effects, that is 14.5- and 15.5-fold improvement in specific activity relative to wild-type Δ52 FutA, respectively. The mutations increased their binding affinity for lactose and kcat values for lactose and GDP-fucose. The Δ52 FutA quadruple mutant (A128N/H129E/Y132I/S46F) was successfully applied to in vitro synthesis of 3-FL with an improved yield and productivity (>96% yield based on 5 mM of GDP-Fuc within 1 h). Biotechnol. Bioeng. 2016;113: 1666-1675. © 2016 Wiley Periodicals, Inc.
Two-dimensional near-field and far-field imaging of a Ne-like Ar capillary discharge table-top soft-x-ray laser (1998)

We have performed systematic measurements and numerical modeling of the divergence and exit beam size of a 46.9 nm Ne-like Ar capillary discharge pumped soft-x-ray amplifier. Two-dimensional near-field and far-field measurements were obtained over a wide range of discharge parameters. The spot size and divergence of the laser beam were observed to increase significantly with decreasing discharge pressure. Simultaneously, the beam intensity distribution changed from a single peak pattern to an annular profile. These effects are shown to be the result of increased refraction of the soft-x-ray beam, caused by larger density gradients in the plasma columns of the lower pressure discharges. The spatial images are nearly cylindrically symmetric, and have less structure than those reported in the literature for laser-driven soft-x-ray lasers. Beam profiles synthesized by model calculations are found to be in good agreement with the recorded images. The obtained images in combination with the model computations clarify the origin of the different beam patterns that are observed in capillary discharge soft-x-ray laser experiments.
Progress in the growth of nonpolar gallium nitride (2007)

Abstract The active regions of conventional c ‐plane (Al,In,Ga)N optoelectronic devices suffer from deleterious polarization effects. These polarization effects can be eliminated by growing devices on alternative GaN planes, such as {1 $ \bar 1 $ 00} m ‐plane or {11 $ \bar 2 $ 0} a ‐plane films. Previous attempts to grow nonpolar GaN by vapor phase and molecular beam epitaxy methods yielded rough and faceted surfaces that were unsuitable for device use. Beginning with Waltereit et al.'s work [Nature 406 , 865 (2000)], significant progress has been made in improving nonpolar GaN structural quality and morphology. This paper reviews the structural and morphological characteristics of planar, nonpolar a ‐plane and m ‐plane GaN films grown by vapor phase and molecular beam epitaxy techniques. Defect reduction via lateral epitaxial overgrowth, and the influence of extended defects on surface morphology will be further discussed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Toward the Next Generation of Multiperiod Optimal Power Flow Solvers (2018)

Distributed energy storage devices are commonly employed as an effective approach for addressing operational challenges introduced by the large scale integration of renewables. However, the modeling of storage devices results in intertemporal coupling of the individual optimal power flow (OPF) problems defined at each subdivision of the time period of interest. The resulting multiperiod optimal power flow (MPOPF) problem becomes intractable prohibiting, forecasting, and planning over long time periods. Interior point (IP) methods have been extensively employed for the solution of OPF and MPOPF problems. This work proposes an efficient IP algorithm, BELTISTOS, particularly designed for MPOPF problems. The structure of the linear system associated with the Karush-Kuhn-Tucker conditions is revisited, and a Schur-complement-based approach tailored to its structure is proposed. Through benchmark cases involving power-grid models of increasing complexity, the BELTISTOS algorithm is demonstrated to provide several orders of magnitude faster solution times than standard optimization methods, such as IPOPT, MIPS, and KNITRO, using significantly less memory.
Arithmetic coding-based continuous error detection for efficient ARQ-based image transmission (2000)

Block cyclic redundancy check (CRC) codes are typically used to perform error detection in automatic repeat request (ARQ) protocols for data communications. Although efficient, CRCs can detect errors only after an entire block of data has been received and processed. We propose a new "continuous" error detection scheme using arithmetic coding that provides a novel tradeoff between the amount of added redundancy and the amount of time needed to detect an error once it occurs. This method of error detection, first introduced by Bell, Witten, and Cleary (1990), is achieved through the use of an arithmetic codec, and has the attractive feature that it can be combined physically with arithmetic source coding, which is widely used in state of-the-art image coders. We analytically optimize the tradeoff between added redundancy and error-detection time, achieving significant gains in bit rate throughput over conventional ARQ schemes for binary symmetric channel models for all probabilities of error.
Nicotine‐evoked transmitter release from synaptosomes: functional association of specific presynaptic acetylcholine receptors and voltage‐gated calcium channels (2001)

It has previously been shown that nicotine-evoked dopamine release from rat striatal synaptosomes and nicotine-evoked norepinephrine release from hippocampal synaptosomes are mediated by distinct nicotinic acetylcholine receptor (nAChR) subtypes. In the present study, the functional association of these nicotinic receptors with specific subtypes of voltage-gated calcium channels was examined. Cd(2+) (200 microM), as well as omega-conotoxin MVIIC (5 microM), blocks approximately 85% of nicotine-evoked dopamine release from striatal synaptosomes, indicating a major involvement of calcium channels. Furthermore, the toxin-susceptibility suggests that these calcium channels contain alpha(1A) and/or alpha(1B) subunits. Inhibition of nicotine-evoked dopamine release by conotoxins alpha-MII and omega-GVIA is additive and indicates that presynaptic alpha3beta2 nAChRs are functionally coupled to alpha(1A), but not alpha(1B), calcium channel subtypes. Conversely, insensitivity to alpha-AuIB and sensitivity to omega-MVIIC indicate that non-alpha3beta2/alpha3beta4-containing nAChRs are functionally coupled to alpha(1B)-containing calcium channels. In contrast, Cd(2+) blocks only 65% of nicotine-evoked norepinephrine release from hippocampal synaptosomes, indicating that a substantial fraction of this release occurs through mechanisms not involving calcium channels. This Cd(2+)-insensitive component of release is blocked by alpha-AuIB and therefore appears to be triggered by Ca(2+) flowing directly through the channels of presynaptic alpha3beta4 nAChRs. Thus, these data indicate that different presynaptic termini can have distinctive functional associations of specific nAChRs and voltage-gated calcium channels.
SURVEYING THE EXTRACTION OF CESIUM NITRATE BY 1,3-ALTERNATECALIX[4]ARENE CROWN-6 ETHERS IN 1,2-DICHLOROETHANE (1999)

ABSTRACT The extraction of cesium nitrate from a mixture of alkali metal nitrates by calix7lsqb;4]arene crown-6 ethers in 1,2-dichloroethane diluent has been surveyed at 25 °C. The results reveal that smaller substituents (but larger than C2,) at the phenolic positions of the calixarene opposite the crown ether increase both the extraction efficiency and the cesium selectivity. Benzo substituents on the crown ether tend to decrease extraction strength while increasing cesium-to-sodium selectivity. Conversely, a cyclohexano group on the crown ether has a negative impact on both extraction strength and selectivity.
Effects of acoustic parameters on bubble cloud dynamics in ultrasound tissue erosion (histotripsy) (2007)

High intensity pulsed ultrasound can produce significant mechanical tissue fractionation with sharp boundaries ("histotripsy"). At a tissue-fluid interface, histotripsy produces clearly demarcated tissue erosion and the erosion efficiency depends on pulse parameters. Acoustic cavitation is believed to be the primary mechanism for the histotripsy process. To investigate the physical basis of the dependence of tissue erosion on pulse parameters, an optical method was used to monitor the effects of pulse parameters on the cavitating bubble cloud generated by histotripsy pulses at a tissue-water interface. The pulse parameters studied include pulse duration, peak rarefactional pressure, and pulse repetition frequency (PRF). Results show that the duration of growth and collapse (collapse cycle) of the bubble cloud increased with increasing pulse duration, peak rarefactional pressure, and PRF when the next pulse arrived after the collapse of the previous bubble cloud. When the PRF was too high such that the next pulse arrived before the collapse of the previous bubble cloud, only a portion of histotripsy pulses could effectively create and collapse the bubble cloud. The collapse cycle of the bubble cloud also increased with increasing gas concentration. These results may explain previous in vitro results on effects of pulse parameters on tissue erosion.
Enhanced VIP Algorithms for Forwarding, Caching, and Congestion Control in Named Data Networks (2016)

Emerging Information-Centric Networking (ICN) architectures seek to optimally utilize both bandwidth and storage for efficient content distribution over the network. The Virtual Interest Packet (VIP) framework has been proposed to enable joint design of forwarding, caching, and congestion control strategies within the Named Data Networking (NDN) architecture. While the existing VIP algorithms exhibit good performance, they are primarily focused on maximizing network throughput and utility, and do not explicitly consider user delay. In this paper, we develop a new class of enhanced algorithms for joint dynamic forwarding, caching and congestion control within the VIP framework. These enhanced VIP algorithms adaptively stabilize the network and maximize network utility, while improving the delay performance by intelligently making use of VIP information beyond one hop. Generalizing Lyapunov drift techniques, we prove the throughput optimality and characterize the utility-delay tradeoff of the enhanced VIP algorithms. Numerical experiments demonstrate the superior performance of the resulting enhanced algorithms for handling Interest Packets and Data Packets within the actual plane, in terms of low network delay and high network utility.
Study the Antifungal and Ocular Permeation of Ketoconazole from Ophthalmic Formulations Containing Trans-Ethosomes Nanoparticles (2021)

Ketoconazole (KET), a synthetic imidazole broad-spectrum antifungal agent, is characterized by its poor aqueous solubility and high molecular weight, which might hamper its corneal permeation. The aim was to develop an ophthalmic formulation loaded with optimized trans-ethosomal vesicles to enhance KET ocular permeation, antifungal activity, rapid drug drainage, and short elimination half-life. Four formulation factors affecting the vesicles' size, zeta potential, entrapment efficiency, and flexibility of the trans-ethosomes formulations were optimized. The optimum formulation was characterized, and their morphological and antifungal activity were studied. Different ophthalmic formulations loaded with the optimized vesicles were prepared and characterized. The ocular irritation and in vivo corneal permeation were investigated. Results revealed that the drug-to-phospholipid-molar ratio, the percentage of edge activator, the percentage of ethanol, and the percentage of stearyl amine significantly affect the characteristics of the vesicles. The optimized vesicles were spherical and showed an average size of 151.34 ± 8.73 nm, a zeta potential value of +34.82 ± 2.64 mV, an entrapment efficiency of 94.97 ± 5.41%, and flexibility of 95.44 ± 4.33%. The antifungal activity of KET was significantly improved following treatment with the optimized vesicles. The developed in situ gel formulations were found to be nonirritating to the cornea. The trans-ethosomes vesicles were able to penetrate deeper into the posterior eye segment without any toxic effects. Accordingly, the in situ developed gel formulation loaded with KET trans-ethosomes vesicles represents a promising ocular delivery system for the treatment of deep fungal eye infections.
Pilot Contamination Reduction in Multi-User TDD Systems (2010)

This paper considers the problem of interference mitigation in multi-cell multi-antenna time division duplex (TDD) wireless systems for downlink transmission. An efficient way to obtain channel state information (CSI) at the base station is by using uplink pilots and reciprocity of the downlink channel. At the same time, it has been shown that pilots from different cells contaminate each other, resulting in corruption of precoding matrices used by base stations, and high inter-cell interference. This paper studies the effects of shifting the location of pilots in time frames used in neighboring cells, and its effectiveness in obtaining better channel estimates, and, thereby, inter-cell interference reduction.
Key exploration & development technologies and engineering practice of continental shale oil: A case study of Member 2 of Paleogene Kongdian Formation in Cangdong Sag, Bohai Bay Basin, East China (2020)

Based on detailed core description and systematic joint test data, enrichment laws of continental shale oil have been examined deeply. Key technologies such as the identification and quantitative evaluation method for sweet spot, precise design and tracking of horizontal well trajectory, and the low-cost horizontal well volume fracturing technology of the whole process “slick water + quartz sand” for continental shale oil have been formed. The research results show that the enrichment of pure continental shale oil of the Paleogene Kong 2 Member in Cangdong Sag is controlled by predominant fabric facies and cross-over effect of retained hydrocarbons jointly; and there are four modes of shale oil enrichment, i.e. laminar felsic, laminar mixed, thin-layer limy dolomitic, and thick-layer limy dolomitic shales. The identification and evaluation method for shale oil sweet spots can predict sweet spots accurately. The precise trajectory design for sweet spot layer and tracking-trajectory optimization while drilling by considering geological and engineering factors have been proved effective by field application, with drilling rate of sweet spots reaching 100% and drilling rate of type I sweet spots reaching over 75%. The whole process “slick water + quartz sand” low cost volume fracturing has been proved effective in creating multi-stage fracture network in the horizontal section, and improved productivity greatly. It can lower the comprehensive engineering cost by 26.4%.
The Demands On The a-Si FET As A Pixel Switch For Liquid Crystal Displays (1986)

The matrix-addressed liquid crystal display (LCD) has attracted considerable attention in the past few years as an alternative to the cathode ray tube (CRT). This type of display has been demonstrated to have stable performance over a long life as well as the attractive features of small volume, light weight, low power, good brightness and full color. Amor-phous silicon (a-Si) is currently the preferred material for switch devices and plasma enhanced chemical vapor deposition (PECVD)is the preferred deposition technology since the process can be carried out at low temperature, yields material with a low density of defect states and affords good step coverage. The electrical requirements for an a-Si field effect transistor (FET) used as a pixel switch for a LCD include switching time, on current and off current. These parameters depend on the instrinsic characteristics of the amorphous materi-als used, the overall display structure and the device geometry. Present and potential material and geometry limitations will be discussed for different display systems of current interest.
[99mTc]Tc-PSMA-T4—Novel SPECT Tracer for Metastatic PCa: From Bench to Clinic (2022)

Despite significant advances in nuclear medicine for diagnosing and treating prostate cancer (PCa), research into new ligands with increasingly better biological properties is still ongoing. Prostate-specific membrane antigen (PSMA) ligands show great potential as radioisotope carriers for the diagnosis and therapy of patients with metastatic PCa. PSMA is expressed in most types of prostate cancer, and its expression is increased in poorly differentiated, metastatic, and hormone-refractory cancers; therefore, it may be a valuable target for the development of radiopharmaceuticals and radioligands, such as urea PSMA inhibitors, for the precise diagnosis, staging, and treatment of prostate cancer. Four developed PSMA-HYNIC inhibitors for technetium-99m labeling and subsequent diagnosis were subjected to preclinical in vitro and in vivo studies to evaluate and compare their diagnostic properties. Among the studied compounds, the PSMA-T4 (Glu-CO-Lys-L-Trp-4-Amc-HYNIC) inhibitor showed the best biological properties for the diagnosis of PCa metastases. [<sup>99m</sup>Tc]Tc-PSMA-T4 also showed effectiveness in single-photon emission computed tomography (SPECT) studies in humans, and soon, its usefulness will be extensively evaluated in phase 2/3 clinical trials.
Toward Detection and Monitoring of Gait Pathology using Inertial Sensors under Rotation, Scale, and Offset Invariant Dynamic Time Warping (2015)

Walking ability can be degraded by a number of pathologies, including movement disorders, stroke, and injury. Personal activity tracking devices gather inertial data needed to measure walking quality, but the required algorithmic methods are an active area of study. To detect changes in walking ability, the similarity between a person’s current gait cycles and their known baseline gait cycles may be measured on an ongoing basis. This strategy requires a similarity measure robust to variability encountered in an outpatient scenario, including changes in walking surface, walking speed, and sensor orientation. Here we propose rotation, scale, and offset invariant dynamic time warping (RSOI-DTW), a variant of the well-known dynamic time warping (DTW) algorithm, as a generalization of DTW appropriate for three-dimensional inertial data. RSOI-DTW is invariant under rotation, scaling, and offset, yet it preserves the salient features of gait cycles required for gait monitoring. To support this claim, gait cycles from 21 subjects walking with four different styles were compared using both DTW and RSOI-DTW. The data show that RSOI-DTW converges quickly and achieves rotation, scale, and offset invariance. Both algorithms distinguish persons and detect abnormal walking, but only RSOI-DTW does so in the presence of sensor rotation. Variations in walking speed pose a challenge for both algorithms, but performance is improved by collecting baseline information at a variety of speeds.
Tolerances of a Page-Based Holographic Data Storage System (2007)

The media tilt and position tolerances of a high Numerical aperture (NA) holographic data storage system are examined experimentally. The sources for these tolerances are explained and techniques for optimizing the drive tolerances are described.
Synthesis and biological screening of 3-chloro-2-piperazinylmethyl-N-aryl sulfonamide indole derivatives as 5-HT6 receptor ligands: Part III (2012)

In continuation to our earlier work and to improve upon the potentency of 2-piperazinylmethyl-N-aryl sulfonamide indole derivatives, a new series of compounds were taken up for synthesis by inserting halo group at 3rd position of indole. The critical intermediate 3-halo-2-formyl indole was achieved through the Vilsmerier reaction, which on further reductive amination followed by sulfonylation gave 3-chloro-2-piperazinylmethyl-N-aryl sulfonamide indole derivatives as a targeted series of compounds. The design, synthesis and their in-vitro affinity towards the 5-HT6 receptor is discussed in this communication.
Dynamic rate control scheduling for ATM switches (2002)

High-speed networks of the future must be able to support traffic with a wide range of characteristics and quality-of-service (QoS) requirements. In an ATM switch, the order in which buffered cells are served plays a crucial role in determining QoS. This paper proposes a new approach to cell scheduling in an ATM switch based on dynamic rate control. Dynamic rate control scheduling provides minimum rate guarantees, flexible distribution of unused bandwidth and internal switch congestion control in a switch with multiple bottleneck points. The paper develops the principles of dynamic rate control scheduling and discusses its application to ATM switches.