gebhart/patrepeval huggingface dataset:
Prolonged gene expression and cell survival after infection by a herpes simplex virus mutant defective in the immediate-early genes encoding ICP4, ICP27, and ICP22 (1996)

Very early in infection, herpes simplex virus (HSV) expresses four immediate-early (IE) regulatory proteins, ICP4, ICP0, ICP22, and ICP27. The systematic inactivation of sets of the IE proteins in cis, and the subsequent phenotypic analysis of the resulting mutants, should provide insights into how these proteins function in the HSV life cycle and also into the specific macromolecular events that are altered or perturbed in cells infected with virus strains blocked very early in infection. This approach may also provide a rational basis to assess the efficacy and safety of HSV mutants for use in gene transfer experiments. In this study, we generated and examined the phenotype of an HSV mutant simultaneously mutated in the ICP4, ICP27, and ICP22 genes of HSV. Unlike mutants deficient in ICP4 (d120), ICP4 and ICP27 (d92), and ICP4 and ICP22 (d96), mutants defective in ICP4, ICP27, and ICP22 (d95) were visually much less toxic to Vero and human embryonic lung cells. Cells infected with d95 at a multiplicity of infection of 10 PFU per cell retained a relatively normal morphology and expressed genes from the viral and cellular genomes for at least 3 days postinfection. The other mutant backgrounds were too toxic to allow examination of gene expression past 1 day postinfection. However, when cell survival was measured by the capacity of the infected cells to form colonies, d95 inhibited colony formation similarly to d92. This apparent paradox was reconciled by the observation that host cell DNA synthesis was inhibited in cells infected with d120, d92, d96, and d95. In addition, all of the mutants exhibited pronounced and distinctive alterations in nuclear morphology, as determined by electron microscopy. The appearance of d95-infected cells deviated from that of uninfected cells in that large circular structures formed in the nucleus. d95-infected cells abundantly expressed ICP0, which accumulated in fine punctate structures in the nucleus at early times postinfection and coalesced or grew to the large circular objects that were revealed by electron microscopy. Therefore, while the abundant accumulation of ICPO in the absence of ICP4, ICP22, and ICP27 may allow for prolonged gene expression, cell survival is impaired, in part, as a result of the inhibition of cellular DNA synthesis.
Examination of the potential interactions between herpes simplex virus vectors and replication-competent virus <I>in vitro</I> and <I>in vivo</I> (2003)

Founded in 1683 in Leiden, the Netherlands, Brill is a leading international academic publisher in the Humanities, Social Sciences, International Law, and Biology. With offices in the Netherlands, Germany, Austria, the USA and Asia, Brill today publishes more than 360 journals and 2,000 new books and reference works each year as well as a large number of databases and primary source research collections.
Deep Monocular Video Depth Estimation Using Temporal Attention (2020)

Monocular video depth estimation (MVDE) plays a crucial role in 3D computer vision. In this paper, we propose an end-to-end monocular video depth estimation network based on temporal attention. Our network starts by a motion compensation module where the spatial temporal transformer network (STN) is utilized to warp the input frames using the estimated optical flow. Next, a temporal attention module is used to combine features from the warped frames, while emphasizing the temporal consistency. A monocular depth estimation network is used to estimate the depth from the temporally combined features. Experimental results demonstrate that our proposed framework achieves better performance compared to the state-of-the-art single image depth estimation (SIDE) networks, as well as existing MVDE methods.
Asymmetric Synthesis of (+)-Mequitazine from Quinine (2011)

The first asymmetric synthesis of the antihistaminic drug mequitazine is reported. Our approach started from quinine, a Cinchona alkaloid, whose chiral information was exploited for setting up the stereogenic center of (+)-mequitazine.
HEK293T Cells Are Heterozygous for CCR5 Delta 32 Mutation (2016)

C-C chemokine receptor 5 (CCR5) is a receptor for chemokines and a co-receptor for HIV-1 entry into the target CD4+ cells. CCR5 delta 32 deletion is a loss-of-function mutation, resistant to HIV-1 infection. We tried to induce the CCR5 delta 32 mutation harnessing the genome editing technique, CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR and CRISPR associated protein 9, Cas9) in the commonly used cell line human embryonic kidney HEK 293T cells. Surprisingly, we found that HEK293T cells are heterozygous for CCR5 delta 32 mutation, in contrast to the wild type CCR5 cells, human acute T cell leukemia cell line Jurkat and human breast adenocarcinoma cell line MDA-MB-231 cells. This finding indicates that at least one human cell line is heterozygous for the CCR5 delta 32 mutation. We also found that in PCR amplification, wild type CCR5 DNA and mutant delta 32 DNA can form mismatched heteroduplex and move slowly in gel electrophoresis.
Evaluation of Bidirectional Silicon Carbide Solid-State Circuit Breaker v3.2 (2013)

Abstract : Although solid-state switches can be actuated several orders of magnitude faster than electromechanical ones, most solid-state circuit breakers require some form of sensing, filtering, triggering, latching, and reset capability for control. These functions can contribute to undesirable delays that limit performance. Modifications were made to the design of a small-scale 600-V, 5-A silicon carbide (SiC) junction field-effect transistor (JFET) based bidirectional solid-state circuit breaker (BDSSCB) to reduce self-trigging and reset response times, and increase rated current to 10 A. Additional current rating increases are possible, while maintaining the small-scale BDSSCB footprint area of 32.2 cm2 (5.0 in2), using custom power stage designs. Experimental results are presented for both BDSSCBs evaluated in a pulsed current test circuit.
Features and structure of a cold active N-acetylneuraminate lyase (2019)

N-acetylneuraminate lyases (NALs) are enzymes that catalyze the reversible cleavage and synthesis of sialic acids. They are therefore commonly used for the production of these high-value sugars. This study presents the recombinant production, together with biochemical and structural data, of the NAL from the psychrophilic bacterium Aliivibrio salmonicida LFI1238 (AsNAL). Our characterization shows that AsNAL possesses high activity and stability at alkaline pH. We confirm that these properties allow for the use in a one-pot reaction at alkaline pH for the synthesis of N-acetylneuraminic acid (Neu5Ac, the most common sialic acid) from the inexpensive precursor N-acetylglucosamine. We also show that the enzyme has a cold active nature with an optimum temperature for Neu5Ac synthesis at 20°C. The equilibrium constant for the reaction was calculated at different temperatures, and the formation of Neu5Ac acid is favored at low temperatures, making the cold active enzyme a well-suited candidate for use in such exothermic reactions. The specific activity is high compared to the homologue from Escherichia coli at three tested temperatures, and the enzyme shows a higher catalytic efficiency and turnover number for cleavage at 37°C. Mutational studies reveal that amino acid residue Asn 168 is important for the high kcat. The crystal structure of AsNAL was solved to 1.65 Å resolution and reveals a compact, tetrameric protein similar to other NAL structures. The data presented provides a framework to guide further optimization of its application in sialic acid production and opens the possibility for further design of the enzyme.
Prior image constrained compressed sensing: a quantitative performance evaluation (2012)

The appeal of compressed sensing (CS) in the context of medical imaging is undeniable. In MRI, it could enable shorter acquisition times while in CT, it has the potential to reduce the ionizing radiation dose imparted to patients. However, images reconstructed using a CS-based approach often show an unusual texture and a potential loss in spatial resolution. The prior image constrained compressed sensing (PICCS) algorithm has been shown to enable accurate image reconstruction at lower levels of sampling. This study systematically evaluates an implementation of PICCS applied to myocardial perfusion imaging with respect to two parameters of its objective function. The prior image parameter α was shown here to yield an optimal image quality in the range 0.4 to 0.5. A quantitative evaluation in terms of temporal resolution, spatial resolution, noise level, noise texture, and reconstruction accuracy was performed.
Gain-Cell Embedded DRAM-Based Physical Unclonable Function (2018)

Physical unclonable functions (PUFs) are important elements in hardware-secured systems as they can generate chip identification and encryption keys based on random variables of the manufacturing process. Many previously proposed PUF implementations are based on SRAM memory technology, since it is embedded on-chip and can provide such randomness. Logic-compatible gain-cell embedded DRAM (GC-eDRAM) is a low density, low leakage alternative to traditional SRAM for the implementation of embedded memories that also provide an additional mechanism of randomness by means of the data retention time (DRT) of the bitcells. In this paper, we propose using the DRT of GC-eDRAM arrays as a source for the generation of an intrinsic PUF. We provide an in-depth analysis of the leakage mechanism of GC-eDRAM and demonstrate how it determines the DRT of the bitcell. Based on this analysis, we provide an authentication methodology for enrollment and evaluation of a GC-eDRAM based PUF. Monte Carlo simulations on a 1 kbit array in 28 nm technology demonstrate the high uniqueness of the PUF with an inter-die Hamming distance of 50%. Reliability analysis under a wide voltage range (0.4 V-1 V) and temperature (0 (0 °C-85 °C) variation demonstrate the statistical robustness of the proposed PUF less than a 6% error-rate.
THE RELATIONSHIP BETWEEN THE COMPLEX OF IMMUNOGLOBULIN A AND ALPHA-1-ANTITRYPSIN, ITS CONSTITUENT COMPONENTS AND THE ACUTE-PHASE RESPONSE AS MEASURED BY C-REACTIVE PROTEIN IN RHEUMATOID ARTHRITIS TREATED WITH GOLD OR D-PENICILLAMINE (1987)

Serum levels of immunoglobulin A (IgA), alpha 1-antitrypsin (AT), their complex (IgA-alpha 1AT) and C-reactive protein (CRP) were measured prior to treatment and at 6 months, in 45 rheumatoid arthritis (RA) patients. Twenty-five patients were treated with D-penicillamine (DPA) and 20 patients with gold (sodium aurothiomalate). The level of circulating complex was reduced by both treatments (p less than 0.001). There was a significant correlation between the circulating levels of IgA-alpha 1AT complex and serum IgA (p less than 0.05). No relationship was observed between the level of circulating complex and CRP. These findings suggest that formation of IgA-alpha 1AT complex in RA is dependent on the level of IgA. The complex is reduced by gold and DPA but it does not reflect an acute phase response as measured by CRP.
Trimming the critical current of Josephson junctions (1983)

We have demonstrated the feasibility of trimming the critical current of Josephson tunnel junctions by doping the lead alloy counter electrodes. The critical current may be changed by more than a factor of six, while retaining the quality of the current-voltage characteristics and the critical current uniformity. For junctions with PbSb counter electrodes doped with less than 0.2 nm of Sn, the increase of critical current is stable after proper annealing and depends linearly on the dosage. For dosages heavier than 0.25 nm, the increase of critical current saturates at ∼ 500%. These changes may be explained by the conversion of some oxide at the interface between the counter electrode and the tunneling barrier to the oxide of the dopant. The modification of the height and thickness of the tunneling barrier changes the critical current of the junction.
Load/Unload Systems With Multiple Flying Height States (2004)

In hard disk drives that utilize load/unload technology, the slider loads onto the disk from hundreds of microns away before the slider settles into the designed flying height. Due to the forces acting on the slider after the transition from the unloaded state to the fully loaded state, the resulting flying height of the slider may be about two orders of magnitude higher than the intended nominal flying height. Under certain circumstances, the slider may never reach the nominal flying height required for proper operation of the magnetic recording process. In this paper, the existence of multiple flying heights is demonstrated and verified both by experimentation and simulation. The effect of some of the critical parameters is also identified by both methods. We show that necessary care must be taken to avoid unwanted loading sequences where the system may be unable to store or retrieve data.
The use of a handheld Raman system for virus detection (2012)

The combination of surface enhanced Raman spectroscopy (SERS) with a handheld Raman system would lead to a powerful portable device for defense and security applications. The Thermo Scientific FirstDefender RM instrument is a 785-nm handheld Raman spectrometer intended for rapid field identification of unknown solid and liquid samples. Its sensitivity and effectiveness for SERS-based detection was initially confirmed by evaluating detection of 1,2-di(4- pyridyl)ethylene as a reporter molecule on a silver nanorod (AgNR) substrate, and the results are comparable to those from a confocal Bruker Raman system. As avian influenza A viruses (AIV) are recognized as an important emerging threat to public health, this portable handheld Raman spectrometer is used, for the first time, to detect and identify avian influenza A viruses using a multi-well AgNR SERS chip. The SERS spectra obtained had rich peaks which demonstrated that the instrument can be effectively used for SERS-based influenza virus detection. According to the SERS spectra, these different influenza viruses were distinguished from the negative control via the principal component analysis and by partial least squares-discriminate analysis. Together, these results show that the combination effective SERS substrates when combined with a portable Raman spectrometer provides a powerful field device for chemical and biological sensing.
Piezoelectric micromachined ultrasonic transducers for human-machine interfaces and biometric sensing (2015)

Improvements in thin-film piezoelectric materials such as AlN and PZT enable piezoelectric micromachined transducers that are superior to existing capacitive transducers. This paper presents the basic design equations, equivalent circuit model, and fabrication processes for piezoelectric micromachined ultrasonic transducers (PMUTs) operating in fluid or air. Relative to conventional ultrasonic transducers, PMUTs have the advantages of small size, low cost, low power consumption, and compatibility with integrated circuit manufacturing methods. These advantages enable PMUTs to be used in new applications such as human-machine interfaces and ultrasonic fingerprint sensors.
The Experimental Study on a Bistable Piezoelectric-Electromagnetic Combined Vibration Energy Harvester (2017)

This paper presents an experimental investigation on the bistable piezoelectric electromagnetic combined energy harvester based on vibration. The end of the piezoelectric cantilever beam has a tip magnet. The opposite of the piezoelectric cantilever beam has a coil, a spring and a magnet. The power generation efficiency and dynamic behaviors for three different kinds of the piezoelectric cantilever beam structures are experimentally studied, such as the conventional piezoelectric cantilever beam, the bistable piezoelectric cantilever beam introduced spring and magnet, and the bistable piezoelectric cantilever beam introduced spring, magnet and coil. Experimental results show that the introduction of the spring and magnet improves the maximum output voltage and broaden the effective frequency bandwidth. The power generation efficiency of the system is improved by adding the coil. Complicated nonlinear dynamic behaviors occur in the system, when the spring and the magnet are introduced. These nonlinear dynamic behaviors broaden the effective frequency bandwidth.
Improved Programmable High-Voltage Power Supply (1994)

Improved dc-to-dc converter functions as programmable high-voltage power supply with low-power-dissipation voltage regulator on high-voltage side. Design of power supply overcomes deficiencies of older designs. Voltage regulation with low power dissipation provided on high-voltage side.
Differential-Phase-Shift Quantum Key Distribution Using Single-Photon Detectors (2007)

A novel type of quantum key distribution (QKD) protocol called differential-phase-shift QKD is described. It uses a weak coherent pulse train, and features simple configuration and efficient use of the time domain.
Receptor Binding and Biological Activity of Mammalian Expressed Sensory and Motor Neuron-derived Factor (SMDF) (1999)

Sensory and motor neuron-derived factor (SMDF) is a member of the neuregulin family of proteins. SMDF is structurally characterized by a novel N-terminal domain. Using the signal sequence and N-terminal 28 amino acids (the "epitope") of herpes simplex virus type 1 glycoprotein D (gD), we have expressed SMDF as an epitope-tagged protein (gD-SMDF) in 293 cells, and purified it to > 98% homogeneity on a monoclonal anti-gD column. gD-SMDF stimulates human Schwann cell growth and 3H-thymidine incorporation in MCF-7 and T47D human breast tumor cells in vitro. The biological activity of gD-SMDF is consistent with its ability to compete with 125I-labeled heregulinbeta1 peptide (rHRGbeta1(177-244)) to bind to soluble dimeric ErbB receptor-IgG fusion proteins. gD-SMDF binds with low affinity to homodimeric ErbB3-IgG and ErbB4-IgG but with higher affinity to heterodimeric ErbB2/ErbB3-IgG and ErbB2/ErbB4-IgG. Using a SMDF-IgG(Fc) fusion protein we generated a monoclonal antibody (3G11) which binds SMDF, crossreacts with rHRGbeta1(177-244), and neutralizes the in vitro activities of gD-SMDF and rHRGbeta1(177-244) in human Schwann cells.
Differential protein kinase C ligand regulation detected in vivo by a phenotypic yeast assay (1995)

The molecular dissection of protein kinase C (PKC) action has been based in part on time-consuming functional assays such as the mouse skin model for testing the tumor promoter activity of phorbol esters and related PKC activators. To help overcome the limitations imposed by the complexity of such assays, we developed the yeast Saccharomyces cerevisiae as an alternative, rapid, and simple experimental system. This model has a specific phenotype, an increase in the cell doubling time, that is proportional to the level of enzymatic activity of expressed mammalian PKC isoforms. We used this phenotype to assay and compare the regulation of native bovine PKC alpha and mutants in the conserved regulatory region C1 in vivo by various activators: two diterpenes, the phorbol ester phorbol-12-myristate-13-acetate (PMA) and mezerein, and the indole alkaloid indolactam V. We found that PMA activated PKC mutants lacking either Cys-rich, zinc finger-like repeat of the conserved region C1 to comparably reduced levels, whereas indolactam V activated native PKC alpha but none of the mutants at normal doses. In contrast, mezerein activated native PKC alpha and a mutant lacking the second Cys repeat equally well but mutants lacking the first Cys repeat of C1 at a greatly reduced level. These differential responses were supported by the observed in vitro PKC catalytic activities. Therefore, PMA regulates PKC alpha activity comparably well via either Cys repeat, whereas mezerein regulation predominantly occurs via the first Cys repeat of C1. Indolactam V activation was less potent, it was greatly reduced in the absence of either Cys repeat, and displayed no preference. We introduce this phenotypic assay as a rapid and general screen for the PKC-activating or possibly inhibitory potential of drug candidates and to identify the PKC regulatory sites involved in these interactions.
One-step synthesis of isomalto-oligosaccharide syrups and dextrans of controlled size using engineered dextransucrase (2008)

Isomalto-oligosaccharides and dextrans of controlled molecular weight of about 10 and 40 kDa were produced using a simple one-step process using engineered L. mesenteroides NRRL B-512F dextransucrase variants. Isomalto-oligosaccharides were produced in a 58% yield by the acceptor reaction with glucose, and reached a degree of polymerization of at least 27 glucosyl units. Reaction conditions for optimal synthesis of dextrans of controlled molecular weight were defined, in respect of initial sucrose concentration and reaction temperature. Thus, we achieved synthesis with impressive yields of 69 and 75% for the 40 and 10 kDa dextran species, respectively. These two dextran sizes are particularly suitable for clinical applications, and are of great industrial demand. Compared with the traditional processes based on chemical hydrolysis and fractionation, which achieve only low yields, the new enzymatic methods offer improvement in quantity, quality and efficiency.
ChemInform Abstract: Ester Bio‐Isosters: Synthesis of Oxadiazolyl‐1‐azabicyclo(2.2.1)heptanes as Muscarinic Agonists. (1989)

Abstract Arecoline (I), a muscarinic agonist, undergoes cyclization with acetamidoxime (II) to give the 1,2,4‐oxadiazole (III).
Progress in the development of interpenetrating polymer network hydrogels (2008)

Interpenetrating polymer networks (IPNs) have been the subject of extensive study since their advent in the 1960s. Hydrogel IPN systems have garnered significant attention in the last two decades due to their usefulness in biomedical applications. Of particular interest are the mechanical enhancements observed in "double network" IPN systems which exhibit nonlinear increases in fracture properties despite being composed of otherwise weak polymers. We have built upon pioneering work in this field as well as in responsive IPN systems to develop an IPN system based on end-linked poly-(ethylene glycol) (PEG) and loosely crosslinked poly(acrylic acid) (PAA) with hydrogen bond-reinforced strain-hardening behavior in water and high initial Young's moduli under physiologic buffer conditions through osmotically induced pre-stress. Uniaxial tensile tests and equilibrium swelling measurements were used to study PEG/PAA IPN hydrogels having second networks prepared with varying crosslinking and photoinitiator content, pH, solids content, and comonomers. Studies involving the addition of non-ionic comonomers and neutralization of the second network showed that template polymerization appears to be important in the formation of mechanically enhanced IPNs.
Pulsed coulometric detection with automatic rejection of background signal in surface-oxide-catalyzed anodic detections at gold electrodes in flow-through cells (1988)

A variation of Pulsed Coulometric Detection (PCD) is described in which the detection potential is scanned in a cyclic fashion during current integration to achieve automatic and virtual elimination of baseline drift caused by surface roughening and changes in pH. The technique is examined at a Au electrode for flow-injection determination if thiourea which is typical of numerous sulfur compounds whose anodic reactions are catalyzed by formation of surface oxide. The baseline decays quickly to a near-zero equilibrium value following start-up and is unchanged for a pH step of ca. 2 units. The technique is concluded to be compatible with pH-gradient chromatography.