gebhart/patrepeval huggingface dataset:
Cellular tropism and cell-to-cell fusion properties of the infectious bronchitis virus spike glycoprotein (2010)

There are numerous vaccines available for the control of infectious bronchitis virus\n(IBV) in poultry, however protection is short-lived and poorly cross-protective\nbetween strains. The vaccines must currently be grown in embryonated eggs, a\ncumbersome and expensive process. The ability to grow vaccines on a cell-line such\nas Vero cells would be highly advantageous.\nThe spike (S) glycoprotein of IBV is comprised of two subunits, S1 and S2, has a\nvital role in virulence in vivo and is responsible for cellular tropism in vitro. This\nproject aims to identify the amino acids present in the S glycoprotein involved in\ndetermination of cellular tropism and cell-to-cell fusion.\nThe IBV Beaudette strain is able to replicate in both primary chick kidney (CK) cells\nand Vero cells, whereas the IBV M41 strain replicates in primary cells only.\nRecombinant IBVs with chimaeric S genes were generated using a reverse genetics\nsystem with the genomic background of Beaudette and part of the S gene from M41.\nTheir growth characteristics and cellular tropism were investigated. The S2 subunit\nof Beaudette was found to be sufficient to confer the ability to grow on Vero cells\nand swapping just three amino acids with corresponding ones from M41 was\nsufficient to remove the ability of the Beaudette S glycoprotein for growth on Vero\ncells.\nBeaudette was further adapted to syncytia formation on Vero cells by serial passage\nand isolates were sequenced to identify amino acid changes between parent and\nVero-adapted viruses that are potentially involved in cell-to-cell fusion.\nUnderstanding the way in which IBV infects host cells is vital in order to rationally\ndesign better vaccination and treatment strategies and help to reduce the prevalence\nof IBV infection in poultry worldwide. Using the IBV reverse genetics system, we\nnow have the potential to grow IBV vaccines on Vero cells.
New heteroisolation stripe-geometry visible-light-emitting lasers (1975)

Visible-light-emitting lasers were fabricated, using a new stripe-geometry double heterostructure. The distinct feature of the geometry is the isolation of the contact stripe electrode to p-GaAs by the use of a layer of n-Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-z</inf> Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z</inf> As epitaxially grown on top of p-GaAs. This geometry results in small internal strain, few crystal imperfections, and low thermal resistance in diodes so that high laser performance can be obtained. Lasing wavelengths as short as 7610 Å and 6680 Å have been attained in CW and pulsed operation, respectively, at room temperature. Various characteristic features of the lasers are described with regard to optical spectra, lasing thresholds, and external quantum efficiencies.
Visual Indicator for Trace Organic Volatiles (2010)

We describe herein a novel approach for visual indication of trace organic vapors. The sensor utilizes a microporous material within a visual thin film transducer to produce changes in color upon exposure to a very wide range of volatile organic compounds. Visual indication at 5 parts per million (ppm) is demonstrated, with optoelectronic detection achieved to below 50 parts per billion (ppb). Through a thoughtful design of the sensor, we are able to avoid interference from water vapor, a critical attribute needed for practical application.
Two microstrip arrays for interferometric SAR applications (1993)

Two types of C-band aircraft interferometric Synthetic Aperture Radar (SAR) are being developed at JPL to measure the ocean wave characteristics. Each type requires two identical antennas with each having a long rectangular aperture to radiate fan-shaped beam(s). One type of these radars requires each of its antennas to radiate a broadside beam that will measure the target's cross-track velocity. The other type, having each of its antennas to radiate two off-broadside pointed beams, will allow the measurement of both the cross-track and the along-track velocities of the target. Because flush mounting of the antenna on the aircraft fuselage is desirable, microstrip patch array is selected for these interferometric SAR antennas. To meet the radar system requirement, each array needs a total of 76 microstrip patches which are arranged in a 38 x 2 rectangular aperture with a physical size of 1.6m x 16.5cm. To minimize the insertion loss and physical real estate of this relatively long array, a combined series/parallel feed technique is used. Techniques to suppress cross-pol radiation and to effectively utilize the RF power are also implemented. Cross-pol level of lower than -30 dB from the co-pol peak and low insertion loss of 0.36 dB have been achieved for both types of arrays. For the type of radar that requires two off-braodside pointed beams, a simple phasing technique is used to achieve this dual-beam capability with adequate antenna gain (20 dBi) and sidelobe level (-14 dB). Both radar arrays have been flight tested on aircraft with excellent antenna performance demonstrated.
Multiemitter BiCMOS logic circuit family (1991)

A new multiemitter BiCMOS circuit using half-micrometer BiCMOS technology with a 3.6-V supply provides 85 % improvement in delay over CMOS design and 40 % improvement over conventional BiCMOS. This benefit is demonstrated in a 64-b carry look-ahead adder where most of the gates have a high number of inputs. A complete logic circuit family based on the multiemitter (ME) concept is proposed in a gate-array structure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Data from A Novel Crizotinib-Resistant Solvent-Front Mutation Responsive to Cabozantinib Therapy in a Patient with <i>ROS1</i>-Rearranged Lung Cancer (2023)

<div>Abstract<p><b>Purpose:</b> Rearranged <i>ROS1</i> is a crizotinib-sensitive oncogenic driver in lung cancer. The development of acquired resistance, however, poses a serious clinical challenge. Consequently, experimental and clinical validation of resistance mechanisms and potential second-line therapies is essential.</p><p><b>Experimental Design:</b> We report the discovery of a novel, solvent-front ROS1<sup>D2033N</sup> mutation in a patient with CD74-<i>ROS1</i>–rearranged lung adenocarcinoma and acquired resistance to crizotinib. Crizotinib resistance of CD74-ROS1<sup>D2033N</sup> was functionally evaluated using cell-based assays and structural modeling.</p><p><b>Results:</b> In biochemical and cell-based assays, the CD74-ROS1<sup>D2033N</sup> mutant demonstrated significantly decreased sensitivity to crizotinib. Molecular dynamics simulation revealed compromised crizotinib binding due to drastic changes in the electrostatic interaction between the D2033 residue and crizotinib and reorientation of neighboring residues. In contrast, cabozantinib binding was unaffected by the D2033N substitution, and inhibitory potency against the mutant was retained. Notably, cabozantinib treatment resulted in a rapid clinical and near-complete radiographic response in this patient.</p><p><b>Conclusions:</b> These results provide the first example of successful therapeutic intervention with targeted therapy to overcome crizotinib resistance in a <i>ROS1</i>-rearranged cancer. <i>Clin Cancer Res; 22(10); 2351–8. ©2015 AACR</i>.</p></div>
Faster ray packets - triangle intersection through vertex culling (2007)

To eliminate unnecessary ray packet-triangle intersection tests, we check for separation of two convex objects: a triangle and a frustum containing intersections of rays with a leaf node of an acceleration structure. We show a performance improvement that is proportional to the ratio of lengths of average leaf edge to triangle edge, which opens new possibilities for creation of better acceleration structures.
Exhaust gas recirculaton control system (1979)

An exhaust gas recirculation (EGR) control system for an internal combustion engine is presented in which an EGR control valve including a vacuum-operated actuator governs the flow of recirculated exhaust gas according to the admission of air into the engine. To accomplish the control with high precision, the control system includes a flow sensor which provides an electrical signal representing the volume flow rate of air in the induction passage and a control circuit for controlling the magnitude of vacuum for the EGR valve through the operation of an electromagnetic valve based on the signal from the flow sensor. Optionally the control system has another flow sensor which provides an electrical signal representing the volume flow rate of recirculated exhaust gas to the control circuit to accomplish a feedback control.
Catalytic asymmetric alkynylation of α-imino ester: A versatile approach to optically active unnatural α-amino acid derivatives (2005)

The catalytic asymmetric introduction of alkynyl functionality to α-amino acid derivatives was realized by the direct addition of terminal alkynes to α-imino ester in the presence of chiral Cu(I) complex under mild reaction conditions. Owing to the rich chemistry to which alkyne can be subjected, the present system provides a remarkably versatile tool for the construction of optically active α-amino acid derivatives. Good yields and enantiomeric excess values were achieved with an array of terminal alkynes and challenging, biologically active, unnatural α-amino acid derivatives could be conveniently obtained.
Estrogenic regulation of polyamine analogue cytotoxicity in human breast cancer cells (2005)

Proc Amer Assoc Cancer Res, Volume 46, 2005

2332 

The polyamine metabolic pathway is an attractive target for therapeutic intervention with manipulation of cellular polyamine levels leading to decreased cell growth in cancer. Synthetic polyamine analogues can act as polyamine antimetabolites that deplete intracellular polyamines, or polyamine mimetics that displace natural polyamines from binding sites, but do not substitute in terms of growth promoting function. Our studies demonstrate that newly designed oligoamine analogues significantly inhibit the key polyamine biosynthesis enzyme, ornithine decarboxylase (ODC), induce the polyamine catabolism enzyme spermidine/spermine N 1-acetyltransferase (SSAT), and effectively inhibit in vitro and in vivo human breast cancer growth via induction of cell cycle arrest and apoptotic cell death. Oligoamines specifically suppress the protein and mRNA expression as well as the ligand-dependent transcriptional activity of the estrogen receptor α (ERα), a principal determinant of breast cell growth and differentiation, in several ER-positive human breast cancer cell lines including MCF-7 and T47D cells. The expressions of ERα-target genes including progesterone receptor (PR) and cyclinD1 are also down-regulated by oligoamines. However, neither ERβ nor other steroid hormonal receptors are affected by analogues. The constitutive expression of a CMV-driven exogenous ERα in ER-negative breast cancer MDA-MB-231 cells was not altered by oligoamines, suggesting that oligoamines specifically suppress transcription of ERα rather than degrade the protein. Simultaneous treatment with spermine reversed oligoamine-induced down-regulation of ERα expression and activity, implying that natural polyamines may play an important role of in maintaining normal ERα function. In ERα promoter deletion/mutation analysis, oligoamines inhibited the ERα promoter element containing the GC and CA rich boxes that have been shown to bind Sp1 transcription factors. Jun NH2-terminal Kinase specific inhibitor SP600125, which blocked oligoamine-induced activation of JNK/c-Jun pathway, inhibited ERα expression, and sensitized tumor cells to oligoamine-induced cell death, indicating that AP-1 transcription factor may positively regulate ERα to protect breast cancer cells against analogue cytotoxicity. Moreover, oligoamines significantly down-regulated the nuclear activity of NF-κB, and down-regulation of NF-κB by oligoamines was prevented by co-treatment of spermine or stably transfected exogenous ERα. These data suggest a possible novel regulation of estrogen signaling by polyamine analogues and interference with the estrogenic signaling pathway by analogues may contribute to polyamine analogue cytotoxicity in human breast cancer. [This work is supported by the grants P50CA88843, CA98454, CA51085, DAMD-17-03-1-0376, and W81XWH-04-1-0457]
Modulation of drug delivery rate by hydrogel-incorporating MEMS devices (2003)

We describe two approaches for modulating fluid flow and drug delivery rate in response to external stimuli using hydrogels incorporated in MEMS devices. The first design, a hydrogel-gated flow controller (HFC), consists of two components, a 3-dimensional crosscut structure and a loaded hydrogel. For a temperature-sensitive HFC, temperature cycling between 25 and 40/spl deg/C results in a flow rate change between 0 and 12 ml/minute, with a 30 second response time. In the second design, a hydrogel-actuated microvalve (HAM) was constructed. In such a device, a hydrogel disc is sandwiched between a porous plate and a flexible silicone rubber membrane. Swelling of the hydrogel produced by diffusion of chemical species through the porous plate, resulting in the deflection of the membrane and closure of the valve intake orifice. A HAM loaded with phenylboronic acid (PBA)-based glucose-sensitive hydrogel was tested. This glucose-sensitive HAM opens and closes in response to changes in glucose concentration and pH. The fastest response time achieved was 16 minutes using a 70 /spl mu/m thick hydrogel and a 60 /spl mu/m porous back plate.
Flaxseed Lignan Complex (FLC) Enriched in Secoisolariciresinol Diglucoside (SDG) Prolongs Survival And Protects Against Radiation‐Induced Pneumonopathy In Mice (2011)

Background Flaxseed (FS), has potent anti-inflammatory and anti-oxidant properties in mouse models of acute and chronic lung injury. It is not known, however, which bioactive ingredient contributes to the protective effects. In this study we tested the lignan component of FS (FLC) consisting mainly of SDG formulated in rodent chow in a murine model of thoracic-radiation induced lung injury. Methods Mice (n=20 per group) were fed an isocaloric control diet or 0.33% or 0.66% FLC corresponding to the lignan content in 10% and 20% wholegrain FS, respectively for 3 weeks. Mice were exposed to a single fraction of 13.5 Gy X-ray thoracic radiation (XRT). Mouse survival, lung inflammation and injury were evaluated 4 months post-XRT in bronchoalveolar lavage. Results Survival increased dose-dependently with FLC diet content (100%, 90% and 44% survival in 0.66%, 0.33% and 0% FLC diets, respectively. Wasting due to radiation also decreased with higher FLC content (12%, 15%, 27% weight loss in 0.66%, 0.33% and 0% FLC). Lung inflammation and injury were also abrogated dose-dependently to levels comparable to those of the wholegrain FS diet. Conclusion The lignan component of FS, mainly consisting of SDG, is protective against radiation pneumonitis in vivo. Funded by: NIH-R01 CA133470-03, NIH-RC1AI081251-01 and the American Institute for Cancer Research #AICR-03B024 (MCS).
Redox‐Active Inorganic Materials for Redox Flow Batteries (2019)

Abstract Continuous growth in utilization of renewable but intermittent energy such as solar and wind will accelerate the demand for grid‐scale energy storage systems. Redox flow batteries (RFBs) have been intensively studied for large‐scale energy storage (MW/MWh), which is particularly attractive when integrated with renewable energy sources. In past decades, extensive efforts have been made to improve electrochemical performance of the RFBs by exploring various active materials, from inorganic redox‐active materials to organic redox‐active molecules. Compared to burgeoning organic RFBs, inorganic RFBs have received extensive research and development in the last several decades. A great deal of efforts has been exerted to commercialize several inorganic RFB systems such as all‐vanadium RFBs and zinc–bromine RFBs. In this article, inorganic redox‐active materials (e.g., metal salts, halides, polysulfides, polyoxometalate (POM), etc.) applied in RFBs are reviewed with a primary focus on their most recent technological advances in aqueous inorganic RFBs. The advantages and limitations of different inorganic RFBs are discussed. Further technological challenges and perspective on inorganic RFBs are also highlighted.
The mechanism of electroforming of metal oxide memristive switches (2009)

Metal and semiconductor oxides are ubiquitous electronic materials. Normally insulating, oxides can change behavior under high electric fields--through 'electroforming' or 'breakdown'--critically affecting CMOS (complementary metal-oxide-semiconductor) logic, DRAM (dynamic random access memory) and flash memory, and tunnel barrier oxides. An initial irreversible electroforming process has been invariably required for obtaining metal oxide resistance switches, which may open urgently needed new avenues for advanced computer memory and logic circuits including ultra-dense non-volatile random access memory (NVRAM) and adaptive neuromorphic logic circuits. This electrical switching arises from the coupled motion of electrons and ions within the oxide material, as one of the first recognized examples of a memristor (memory-resistor) device, the fourth fundamental passive circuit element originally predicted in 1971 by Chua. A lack of device repeatability has limited technological implementation of oxide switches, however. Here we explain the nature of the oxide electroforming as an electro-reduction and vacancy creation process caused by high electric fields and enhanced by electrical Joule heating with direct experimental evidence. Oxygen vacancies are created and drift towards the cathode, forming localized conducting channels in the oxide. Simultaneously, O(2-) ions drift towards the anode where they evolve O(2) gas, causing physical deformation of the junction. The problematic gas eruption and physical deformation are mitigated by shrinking to the nanoscale and controlling the electroforming voltage polarity. Better yet, electroforming problems can be largely eliminated by engineering the device structure to remove 'bulk' oxide effects in favor of interface-controlled electronic switching.
Direct Graphene Growth on Oxides: Interfacial Interactions and Band Gap Formation (2012)

Direct graphene growth on oxides, without a metal catalyst, is a critical step towards the industrial-scale development of graphene devices. Such growth has been accomplished on MgO(111) by physical and chemical vapor deposition, and on Co3O4(111) by molecular beam epitaxy. For MgO(111), there is evidence of significant oxide reconstruction and reaction with the first carbon layer, and a ~ 0.5-1 eV band gap, suggesting a commensurate graphene/oxide interface. For Co3O4(111), growth occurs in a layer-by-layer fashion, with an incommensurate interface. In both cases, there is significant graphene-to-oxide charge transfer. The different results for the two different oxides appear to be due to the relative instability of the O-terminated (111) MgO surface. These results suggest a broad variety of potential electronic/spintronic applications, and indicate feasible routes towards fabrication of graphene devices by industrially practical and scalable methods.
Mutations in the <i>DDR2</i> Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer (2011)

DDR2 mutations are present in 4% of lung SCCs, and DDR2 mutations are associated with sensitivity to dasatinib. These findings provide a rationale for designing clinical trials with the FDA-approved drug dasatinib in patients with lung SCCs.
Neural network aided design of oil production units (2010)

The paper presents a novel neural network based method for predicting the performance of the multi-stage gas/oil separation plants in crude oil production. The developed method can play an important role during planning and operation of oil production facilities. It predicts important oil properties, which are usually obtained from expensive and time-consuming laboratory tests. The prediction is based mainly on the basic oil composition analysis from standard lab tests. The neural networks were trained using data collected from laboratory tests. The objective of these tests is to find the best oil/gas separation stages to minimize the separator gas/oil ratio and to improve the resulting oil specific gravity. The neural networks accept the initial and final pressures and temperatures of each stage and then try to utilize the oil composition information to predict the stage gas/oil ratio. Two neural networks were built, one for the initial stage with difference of pressure over 400 psi, and the second for the separator stages covering the lower range of pressure. The method can also be useful simulation tool in optimizing the oil production operation.
Preclinical Assessment of Mutant Human TRIM5α as an Anti-HIV-1 Transgene (2015)

Current HIV-1 gene therapy approaches aim at stopping the viral life cycle at its earliest steps, such as entry or immediate postentry events. Among the most widely adopted strategies are CCR5 downregulation/knockout and the use of broadly neutralizing antibodies. However, the long-term efficacy and side effects are still unclear. TRIM5α is an interferon-stimulated restriction factor that can intercept incoming retroviruses within one hour of cytosolic entry and potently inhibit the infectivity of restriction-sensitive viruses. The human TRIM5α (TRIM5αhu) generally does not efficiently target HIV-1, but point mutations in its capsid-binding domain can confer anti-HIV-1 activity. Although the mechanisms by which TRIM5αhu mutants inhibit HIV-1 are relatively well understood, their characterization as potential transgenes for gene therapy is lacking. Additionally, previous reports of general immune activation by overexpression of TRIM5α have hindered its broad adoption as a potential transgene. Here we demonstrate the ability of the R332G-R335G TRIM5αhu mutant to efficiently restrict highly divergent HIV-1 strains, including Group O, as well as clinical isolates bearing cytotoxic T lymphocyte escape mutations. R332G-R335G TRIM5αhu efficiently protected human lymphocytes against HIV-1 infection, even when expressed at relatively low levels following lentiviral transduction. Most importantly, under these conditions Rhesus macaque TRIM5α (TRIM5αRh) and TRIM5αhu (wild-type or mutated) had no major effects on the NF-κB pathway. Transgenic TRIM5α did not modulate the kinetics of IκBα, JunB, and TNFAIP3 expression following TNF-α treatment. Finally, we show that human lymphocytes expressing R332G-R335G TRIM5αhu have clear survival advantages over unmodified parental cells in the presence of pathogenic, replication-competent HIV-1. These results support the relevance of R332G-R335G and other mutants of TRIM5αhu as candidate effectors for HIV-1 gene therapy.