gebhart/patrepeval huggingface dataset:
Herpes Simplex Virus Type 1 Thymidine Kinase Sequence Fused to the <i>lacZ</i> Gene Increases Levels of β-Galactosidase Activity per Genome of High-Capacity but Not First-Generation Adenoviral Vectors In Vitro and In Vivo (2008)

Increased transgene expression per vector genome is an important goal in the optimization of viral vectors for gene therapy. Herein we demonstrate that herpes simplex virus type 1 (HSV1) thymidine kinase (TK) gene sequences (1,131 bp) fused to the 3' end of lacZ increase transgene expression from high-capacity adenoviral vectors (HCAd), but not from first-generation (Ad) vectors. The woodchuck hepatitis virus posttranscriptional regulatory element (WPRE), in contrast, increased transgene expression levels from Ad but not HCAd vectors. The differential activity of the HSV1 TK gene and WPRE sequences was detected both in vitro and in vivo and suggests potentially different mechanisms of action or the interaction of these elements with vector genomic sequences.
A Simple Modification Method to Obtain Anisotropic and Porous 3D Microfibrillar Scaffolds for Surgical and Biomedical Applications (2017)

In native tissues, cellular organization is predominantly anisotropic. Yet, it remains a challenge to engineer anisotropic scaffolds that promote anisotropic cellular organization at macroscopic length scales. To overcome this challenge, an innovative, cheap and easy method to align clinically approved non-woven surgical microfibrillar scaffolds is presented. The method involves a three-step process of coating, unidirectional stretching of scaffolds after heating them above glass transition temperature, and cooling back to room temperature. Briefly, a polymer coating is applied to a non-woven mesh that results in a partial welding of randomly oriented microfibers at their intersection points. The coated scaffold is then heated above the glass transition temperature of the coating and the scaffold polymer. Subsequently, the coated scaffold is stretched to produce aligned and three dimentional (3D) porous fibrillar scaffolds. In a proof of concept study, a polyglycolic acid (PGA) micro-fibrillar scaffold was coated with poly(4-hydroxybutirate) (P4HB) acid and subsequently aligned. Fibroblasts were cultured in vitro within the scaffold and results showed an increase in cellular alignment along the direction of the PGA fibers. This method can be scaled up easily for industrial production of polymeric meshes or directly applied to small pieces of scaffolds at the point of care.
High-performance nanomaterials formed by rigid yet extensible cyclic β-peptide polymers (2018)

Organisms have evolved biomaterials with an extraordinary convergence of high mechanical strength, toughness, and elasticity. In contrast, synthetic materials excel in stiffness or extensibility, and a combination of the two is necessary to exceed the performance of natural biomaterials. We bridge this materials property gap through the side-chain-to-side-chain polymerization of cyclic β-peptide rings. Due to their strong dipole moments, the rings self-assemble into rigid nanorods, stabilized by hydrogen bonds. Displayed amines serve as functionalization sites, or, if protonated, force the polymer to adopt an unfolded conformation. This molecular design enhances the processability and extensibility of the biopolymer. Molecular dynamics simulations predict stick-slip deformations dissipate energy at large strains, thereby, yielding toughness values greater than natural silks. Moreover, the synthesis route can be adapted to alter the dimensions and displayed chemistries of nanomaterials with mechanical properties that rival nature.
Discovery of ML323 as a Novel Inhibitor of the USP1/UAF1 Deubiquitinase Complex (2014)

Advances in pharmacological approaches to target the ubiquitin–proteasome system have revealed several potential new molecular targets within the ubiquitin machinery. Likewise, the functional consequences of ubiquitination and deubiquitination have recently been linked to a wide variety of critical biological processes well beyond just protein disposal [1]. For example, the deubiquitining enzyme, ubiquitin-specific protease 1 (USP1), in association with its WD40 binding partner, UAF1 (USP1-associated factor 1), is a known regulator of DNA damage response and has been suggested as a promising target to improve the efficacy of the commonly used DNA damaging drugs by modulating the cancer cells' ability to repair or tolerate DNA lesions [2-7]. To further evaluate the therapeutic potential of targeting the USP1/UAF1 deubiquitinase complex, we conducted a quantitative high-throughput screen and a subsequent medicinal chemistry optimization campaign in pursuit of small molecules that inhibit USP1/UAF1. Herein, we describe the discovery and optimization of ML323, a probe molecule that displays reversible, nanomolar inhibitory activity and excellent selectivity toward USP1/UAF1. In addition, ML323 potentiates the cytotoxicity of cisplatin and increases endogenous monoubiquitination levels of both PCNA and FANCD2, two known cellular targets of USP1/UAF1 [8]. Lastly, ML323 possesses a promising in vitro ADME profile, suggesting its suitability for further testing in PK/PD studies.
A Conserved Domain in the Leader Proteinase of Foot-and-Mouth Disease Virus Is Required for Proper Subcellular Localization and Function (2008)

The leader proteinase (L(pro)) of foot-and-mouth disease virus (FMDV) is involved in antagonizing the innate immune response by blocking the expression of interferon (IFN) and by reducing the immediate-early induction of IFN-beta mRNA and IFN-stimulated genes. In addition to its role in shutting off cap-dependent host mRNA translation, L(pro) is associated with the degradation of the p65/RelA subunit of nuclear factor kappaB (NF-kappaB). Bioinformatics analysis suggests that L(pro) contains a SAP (for SAF-A/B, Acinus, and PIAS) domain, a protein structure associated in some cases with the nuclear retention of molecules involved in transcriptional control. We have introduced a single or a double mutation in conserved amino acid residues contained within this domain of L(pro). Although three stable mutant viruses were obtained, only the double mutant displayed an attenuated phenotype in cell culture. Indirect immunofluorescence analysis showed that L(pro) subcellular distribution is altered in cells infected with the double mutant virus. Interestingly, nuclear p65/RelA staining disappeared from wild-type (WT) FMDV-infected cells but not from double mutant virus-infected cells. Consistent with these results, NF-kappaB-dependent transcription was not inhibited in cells infected with double mutant virus in contrast to cells infected with WT virus. However, degradation of the translation initiation factor eIF-4G was very similar for both the WT and the double mutant viruses. Since L(pro) catalytic activity was demonstrated to be a requirement for p65/RelA degradation, our results indicate that mutation of the SAP domain reveals a novel separation-of-function activity for FMDV L(pro).
Device and method for altering the acoustic signature of an internal combustion engine (1992)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Paul A. Hayes, Thomas E. Reinhart, Terrence M. Shaw; Device and method for altering the acoustic signature of an internal combustion engine. J. Acoust. Soc. Am. 1 August 1992; 92 (2): 1198. https://doi.org/10.1121/1.404026 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAcoustical Society of AmericaThe Journal of the Acoustical Society of America Search Advanced Search |Citation Search
NOVEL READOUT SCHEME FOR MEMS VIBRATORY GYROSCOPES BASED ON SIGNAL PHASE SHIFT (2012)

This paper introduces and demonstrates experimentally a new readout scheme for MEMS vibratory gyroscopes that relies on signal phase instead of signal amplitude to measure the rotation rate. When the drive and sense resonance modes of the gyroscope are both excited by forces of equal intensity and 90 phase difference, the Coriolis force induces a phase shift in the gyroscope response that is proportional to the gyroscope rotation rate. This effect is predicted by theoretical analysis and has been verified through simulation and measurement of two different gyroscopes, a high-frequency bulk acoustic wave (BAW) disk gyroscope, and a low-frequency mode-matched tuning fork gyroscope (M 2 -TFG). The two gyroscopes report a measured phase sensitivity of 0.597 mV//s and 0.148 mV//s, respectively.
ChemInform Abstract: Hydrogen Sulfide (H<sub>2</sub>S) Releasing Agents: Chemistry and Biological Applications (2014)

Abstract Review: [156 refs.
BrightBrainer feasibility study in a medical adult day program (2015)

Purpose: To determine the feasibility of BrightBrainer training of elderly with dementia attending a Medical Adult Day Program. Method: BrightBrainer brain training games were played by 10 participants who sat in front of a projector screen and interacted through a bimanual game controller. The custom games targeted several cognitive domains such as focus, problem solving, short term memory, working memory, and language comprehension. Participants had a choice of what games to play among those available, and the difficulty adjusted automatically based on individual past performance. The system underwent feasibility trials spanning 16 sessions over 8 weeks. Participants were evaluated pre-intervention, post-intervention, and at 8 week follow up using standardized neuropsychological measures. Computerized measures of movement repetitions, task performance, session duration, games played and game scores were stored on a remote server. Results: Group analysis showed improvement in the cognitive domain of 1.4 points on Mini Mental Status Exam (MMSE) between pre-training and follow-up. One participant who started with MC1 ended with normal cognition (max scores on MMSE and Brief Interview of Mental Status - BIMS). Caregiver feedback noted participants' increased ability to follow one-step directions, to perform activities of daily living and increased desire to attend the Adult Day Program. Most participants enjoyed the computerized training.
Multiplexed sensing using optical low-coherence reflectometry (1995)

A novel multiplexed optical sensor permitting absolute length measurement in remote reflective sensor arrays is proposed. Based on optical low-coherence reflectometry, this technique has been used to demonstrate length measurements to within 10 μm for 6-m sensor cables situated 70 km from the receiver.
The Predictive Cruise Control – A System to Reduce Fuel Consumption of Heavy Duty Trucks (2004)

<div class="htmlview paragraph">Predictive Cruise Control (PCC) is a system that enhances and works in combination with the existing Conventional Cruise Control. Based on elevation information captured in a 3D map and a predictive algorithm, PCC allows the vehicle speed to vary around the cruise control set speed within a defined speed band in an effort to reduce fuel consumption. As fuel consumption is a major portion of a truck's life cycle costs (LCC) and cruise control is used extensively in the United States and Canada, PCC can significantly reduce the truck's LCC.</div>
Sapphire: copying garbage collection without stopping the world (2003)

Abstract The growing use in concurrent systems of languages that require garbage collection (GC), such as Java, is raising practical interest in concurrent GC. Sapphire is a new algorithm for concurrent copying GC for Java. It stresses minimizing the amount of time any given application thread may need to block to support the collector. In particular, Sapphire is intended to work well in the presence of a large number of application threads, on small‐ to medium‐scale shared memory multiprocessors. Sapphire extends previous concurrent copying algorithms, and is most closely related to replicating copying collection, a GC technique in which application threads observe and update primarily the old copies of objects. The key innovations of Sapphire are: (1) the ability to ‘flip’ one thread at a time (changing the thread's view from the old copies of objects to the new copies), as opposed to needing to stop all threads and flip them at the same time; (2) exploiting Java semantics and assuming any data races occur on volatile fields, to avoid a barrier on reads of non‐volatile fields; and (3) working in concert with virtually any underlying (non‐concurrent) copying collection algorithm. Copyright © 2003 John Wiley & Sons, Ltd.
Analysis and comparison of genome editing using CRISPResso2 (2018)

Abstract Genome editing technologies are rapidly evolving, and analysis of deep sequencing data from target or off-target regions is necessary for measuring editing efficiency and evaluating safety. However, no software exists to analyze base editors, perform allele-specific quantification or that incorporates biologically-informed and scalable alignment approaches. Here, we present CRISPResso2 to fill this gap and illustrate its functionality by experimentally measuring and analyzing the editing properties of six genome editing agents.
High-speed all-semiconductor optically addressed spatial light modulator (1997)

We report a monolithically grown optically addressed multiple-quantum-well spatial light modulator with high-frame rate operation (&gt;44 kHz) and large sensitivity (&lt;1 μJ/cm2). The separated-detector-modulator device operates in the reflection mode and can provide a modulation gain of 35 with 60% modulation depth. We also show that higher modulation gains (&gt;50) can be achieved at the expense of modulation depth. In addition, by using a voltage pulse, we reduce the recovery time of the device from 90 ms to 1 μs such that high-frame rate operation can be achieved. We demonstrate 60% modulation of the reflected readout beam at 44 kHz by only using 43 mW/cm2 cw writing illumination.
Elevated apoptotic cell population in patients with chronic fatigue syndrome: the pivotal role of protein Kinase RNA (1997)

PKR-mediated apoptosis in CFS individuals may contribute to the pathogenesis and the fatigue symptomatology associated with CFS.
Method for Measuring Thermal Conductivity of Small Samples Having Very Low Thermal Conductivity (2013)

This paper describes the development of a hot plate method capable of using air as a standard reference material for the steady-state measurement of the thermal conductivity of very small test samples having thermal conductivity on the order of air. As with other approaches, care is taken to ensure that the heat flow through the test sample is essentially one-dimensional. However, unlike other approaches, no attempt is made to use heated guards to block the flow of heat from the hot plate to the surroundings. It is argued that since large correction factors must be applied to account for guard imperfections when sample dimensions are small, it may be preferable to simply measure and correct for the heat that flows from the heater disc to directions other than into the sample. Experimental measurements taken in a prototype apparatus, combined with extensive computational modeling of the heat transfer in the apparatus, show that sufficiently accurate measurements can be obtained to allow determination of the thermal conductivity of low thermal conductivity materials. Suggestions are made for further improvements in the method based on results from regression analyses of the generated data.
Video stabilization and rolling shutter distortion reduction (2010)

This paper presents an algorithm that stabilizes video and reduces rolling shutter distortions using a six-parameter affine model that explicitly contains parameters for translation, rotation, scaling, and skew to describe transformations between frames. Rolling shutter distortions, including wobble, skew and vertical scaling distortions, together with both translational and rotational jitter are corrected by estimating the parameters of the model and performing compensating transformations based on those estimates. The results show the benefits of the proposed algorithm quantified by the Interframe Transformation Fidelity (ITF) metric.
An SRAM PUF with 2 Independent Bits/Cell in 65nm (2019)

An SRAM Physical Unclonable Function (PUF) cell is fabricated and reported, which has two bits per cell. The Decision Voltage of the cell is analyzed and the cell is designed such that only the NMOS devices in the latch configuration contribute to the cell response. Either one of two pairs of NMOS devices is selected, such that two independent bits are generated. The cell was fabricated and measured in TSMC 65nm technology with a highly competitive area of 1420F <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> per bit.
Abstract 1843: Overexpression of polyisoprenylated methylated protein methyl esterase in triple negative breast cancer (2012)

Abstract Lack of targeted, more effective therapies for triple negative breast cancer (TNBC) has necessitated the continuous search for protein biomarkers and targets for novel therapeutic development. Polyisoprenylated monomeric G-proteins such as Ras and Rab are hyperactive in about 30% of cancers and have profound effects on cell growth. Inhibition of polyisoprenylated methylated protein methyl esterase (PMPMEase) causes the death of cancer cells thus suggesting that hyperactivity of PMPMEase may result in cancers. The current studies were to address the hypothesis that PMPMEase activity is elevated in breast cancer. PMPMEase activity was determined in breast tumors and normal adjacent tissues (NAT) in snap-frozen tissues from 10 breast cancer cases. Five- to over 20-fold increases in PMPMEase activity compared to the respective NATs were detected in 8 of the 10 cases. Specific activities ranging from 0.25 ± 0.02 to 1.58 ± 0.07 nmol/h/mg were detected in the tumors compared to 0.09 nmol/h/mg or less in the NATs. Breast cancer tissue microarrays (TMAs) consisting of 125 independent breast cancer cases and NATs were analyzed for PMPMEase expression by immunohistochemistry and scored for their immunoreactive staining intensities. Intermediate to very strong immunoreactivities were detected in the breast cancer TMA core slices compared to only trace staining in those of the NATs. The mean scores ± SEM ranged from 310 ± 21, 290 ± 7, 350 ± 15, 360 ± 18, 390 ± 14, 360 ± 29, 390 ± 13, 275 ± 10 to 65 ± 10 for TNBC, ER(+), ER(+)PR(+), ER(+)HER2(+), ER(+)PR(+)HER2(+), PR(+)HER2(+), HER2(+), PR(+) and NATs, respectively. These results show that PMPMEase overexpression in breast cancer may explain the increased enzymatic activity in the tumors. PMPMEase enzymatic activity and/or immunoreactivity may serve as diagnostic procedures for breast cancer. PMPMEase may also serve as valid target for anticancer drug development. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1843. doi:1538-7445.AM2012-1843
Analysis of two-cavity gyroklystron (1981)

Abstract Small signal analytical analysis and large signal numerical calculations are presented for a gyroklystron in which a low order (TE011) mode in the bunching cavity is coupled by the electron beam to a high order (TE041) mode in the output cavity. A drift region separates the two cavities. We demonstrate that the probunching of the beam before entering the output cavity not only enhances the interaction efficiency of the TE041 mode but also improves the mode stability by suppressing the TE241 mode. The gyroklystron may be operated either as an oscillator or as an amplifier by a small variation of the applied magnetic field. The effect of the beam velocity spread on the efficiency is also investigated. It is found that the operation of the gyroklystron is more sensitive to beam velocity spread than that of a gyromonotron. Optimum conditions for a cold beam are not necessarily those for a wam beam.
Inhibition of Na+,K+ pump affects nucleic acid synthesis and smooth muscle cell proliferation via elevation of the [Na+]i/[K+]i ratio: possible implication in vascular remodelling (2001)

Elevation of the [Na+]i/[K+]i ratio caused by Na+,K+ pump inhibition markedly enhances nucleic acid synthesis in quiescent VSMC and blocks cell cycle progression in serum-supplied VSMC. The relative contribution of this phenomenon as well as the anti-apoptotic action of increased [Na+]i/[K+]i ratio to vascular remodelling under augmented content of endogenous Na+,K+ pump inhibitors, seen in volume-expanded hypertension, should be investigated by in-vivo studies.
WebGuard: A System for Web Content Protection. (2001)

In this paper, we present WebGuard, a content protection system for Web documents. WebGuard allows content owners to exercise control over usage conditions governing access to their content. We first introduce the concept of transparent digital rights management, and then show how WebGuard realizes it, using existing Web browsers.
Flexible beam delivery for material processing laser power through a fiber optic cable (1983)

A neodymium: yttrium-aluminum-garnet (Nd:YAG) laser used in a pulsed mode is coupled to and passed through a single quartz fiber optic cable at peak power levels required for laser material processing. This flexible fiber permits laser cutting, drilling, and welding of metals with a robot. Metals in excess of 2 mm (0.080 inches) thick have been laser cut.
Development of a Human Monoclonal Antibody for Potential Therapy of CD27-Expressing Lymphoma and Leukemia (2012)

Collectively, the data suggest that the human mAb 1F5, which has recently entered clinical development under the name CDX-1127, may provide direct antitumor activity against CD27-expressing lymphoma or leukemia, independent of its potential to enhance immunity through its agonistic properties.
Hourglass Worm Gears Designed to Concentrate Surface Normals (1994)

To avoid the influence of small displacement of gear axes under load, the authors propose that all contact normals of a tooth surface should be at right angles to the direction of the small displacement induced at each contact point under load. On the basis of this state of surface normals, a few methods of tooth surface generation have been devised for realizing the concept. In this research, an hourglass worm gear was made using one of the generating methods, and tested experimentally. As a result, the validity of this designing concept was substantiated.