gebhart/patrepeval huggingface dataset:
Functional Restoration of BRCA2 Protein by Secondary BRCA2 Mutations in BRCA2 -Mutated Ovarian Carcinoma (2009)

Acquired platinum resistance is a serious problem in the treatment of ovarian carcinomas. However, the mechanism of the drug resistance has not been elucidated. Here, we show functional significance of restoration of BRCA2 protein by secondary BRCA2 mutations in acquired drug resistance of BRCA2-mutated ovarian carcinoma. Three ovarian cancer cell lines (PEO1, PEO4, and PEO6) were derived from a BRCA2 mutation [5193C>G (Y1655X)] carrier with ovarian carcinoma with acquired cisplatin resistance and a secondary BRCA2 mutation [5193C>T (Y1655Y)] that canceled the inherited mutation. PEO1 was BRCA2 deficient and sensitive to cisplatin and a poly(ADP-ribose) polymerase inhibitor, AG14361, whereas PEO4 was resistant. PEO4 and PEO6, derived from ascites at the time of relapse with cisplatin resistance, had the secondary mutation and were BRCA2 proficient. In vitro cisplatin/AG14361 selection of PEO1 led to restoration of BRCA2 due to another secondary BRCA2 mutation. BRCA2 depletion sensitized BRCA2-restored PEO1 clones and PEO4 to cisplatin/AG14361. Thus, restoration of BRCA2 due to secondary BRCA2 mutation is involved in acquired drug resistance of BRCA2-mutated ovarian carcinoma.
High-breakdown-voltage AlSbAs/InAs n-channel field-effect transistors (1992)

InAs channel field-effect transistors of 1- mu m gate length were grown by molecular beam epitaxy and observed to operate at channel electric fields (20 kV/cm) higher than previously demonstrated and several times greater than the threshold for impact ionization in bulk InAs. Voltage gains on the order of 10 were observed with transconductances as high as 414 mS/mm and output conductances as low as 33 mS/mm. These voltage gains are comparable to those of GaAs-based devices and are the highest observed for InAs channel devices. The results demonstrate the potential for practical room-temperature operation of InAs FETs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif‐like domain (2006)

We have determined the crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 at 1.9 A resolution. This protein is a member of the Escherichia coli ygcH sequence family, which contains approximately 15 sequence homologs of bacterial origin. These homologs have a high isoelectric point. The crystal structure reveals that TTHB192 consists of two independently folded domains, and that each domain exhibits a ferredoxin-like fold with a four-stranded antiparallel beta-sheet packed on one side by alpha-helices. These two tandem domains face each other to generate a beta-sheet platform. TTHB192 displays overall structural similarity to Sex-lethal protein and poly(A)-binding protein fragments. These proteins have RNA binding activity which is supported by a beta-sheet platform formed by two tandem repeats of an RNA recognition motif domain with signature sequence motifs on the beta-sheet surface. Although TTHB192 does not have the same signature sequence motif as the RNA recognition motif domain, the presence of an evolutionarily conserved basic patch on the beta-sheet platform could be functionally relevant for nucleic acid-binding. This report shows that TTHB192 and its sequence homologs adopt an RNA recognition motif-like domain and provides the first testable functional hypothesis for this protein family.
Functionally Competent Eosinophils Differentiated Ex Vivo in High Purity from Normal Mouse Bone Marrow (2008)

We have devised an ex vivo culture system which generates large numbers of eosinophils at high purity (>90%) from unselected mouse bone marrow progenitors. In response to 4 days of culture with recombinant mouse FLT3-L and recombinant mouse stem cell factor followed by recombinant mouse IL-5 alone thereafter, the resulting bone marrow-derived eosinophils (bmEos) express immunoreactive major basic protein, Siglec F, IL-5R alpha-chain, and transcripts encoding mouse eosinophil peroxidase, CCR3, the IL-3/IL-5/GM-CSF receptor common beta-chain, and the transcription factor GATA-1. BmEos are functionally competent: they undergo chemotaxis toward mouse eotaxin-1 and produce characteristic cytokines, including IFN-gamma, IL-4, MIP-1alpha, and IL-6. The rodent pathogen pneumonia virus of mice replicates in bmEos and elevated levels of IL-6 are detected in supernatants of bmEos cultures in response to active infection. Finally, differentiating bmEos are readily transfected with lentiviral vectors, suggesting a means for rapid production of genetically manipulated cells.
Aurora‐B phosphorylates Histone H3 at serine28 with regard to the mitotic chromosome condensation (2002)

With regard to mitotic chromosome condensation, Aurora-B directly phosphorylated H3, not only at Ser10 but also at Ser28. The level of Ser28 phosphorylation is diminished to undetectable levels by PP1 phosphatase prior to entry into mitosis.
In vivo dark-field reflection-mode photoacoustic microscopy (2005)

Reflection-mode photoacoustic microscopy with dark-field laser pulse illumination and high-numerical-aperture ultrasonic detection is designed and implemented in noninvasively imaged blood vessels in the skin in vivo. Dark-field optical illumination minimizes the interference caused by strong photoacoustic signals from superficial structures. A high-numerical-aperture acoustic lens provides high lateral resolution, 45-120 microm in this system. A broadband ultrasonic detection system provides high axial resolution, estimated to be approximately 15 microm. The optical illumination and ultrasonic detection are in a coaxial confocal configuration for optimal image quality. The system is capable of imaging optical-absorption contrast as deep as 3 mm in biological tissue.
Fault-tolerant convergence routing (2002)

This paper presents fault-tolerant protocols for fast packet switch networks with convergence routing. The objective is to provide, after a link or a node (switch) failure, fast reconfiguration and continuous host-to-host communication. Convergence routing is a variant of deflection routing, which combines in a dynamic fashion, the on-line routing decision with the traffic load inside the network. Unlike other deflection techniques, convergence routing guarantees that packets will reach or converge to their destinations. This fault-tolerant solution is designed for a switch-based (i.e., arbitrary topology) LAN architecture called MetaNet. The original MetaNet's convergence routing scheme has been modified in order to facilitate the property that the packet header need not be recomputed after a failure and/or a reconfiguration. This is achieved by having, at the network interface, a translator that maps the unique destination address to a virtual address. The virtual addresses are stored at the packet header, and used for convergence routing, with a global sense of direction over (i) a single spanning tree, and (ii) over two edge-disjoint spanning trees, for redundancy (fault tolerance) and greater efficiency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characteristics of an atmospheric microwave-induced plasma generated in ambient air by an argon discharge excited in an open-ended dielectric discharge tube (2002)

Parametric observations on an atmospheric-pressure plasma sustained in ambient air by an argon discharge excited by 2.45 GHz microwaves in an open-ended dielectric discharge tube are reported. Microwave power, discharge tube dimensions, and argon flow rate were the major operating parameters. Three distinctive plasma regions were observed: plasma filaments exiting from the discharge tube, converging point of these filaments, and a plasma flame. At the filament-converging point, argon atom excitation temperature, rotational temperature, and electron density were measured by optical emission spectroscopy (OES) in the operating range of (3.0–5.0) liters per minute of gas flow rate and (650–950) W of microwave power. The measured excitation temperature and rotational temperature were (5000–5800) K and (2800–3400) K, respectively. The electron density obtained by Stark broadening width of the Hβ line showed (5.0–8.0)×1014 cm−3. It was observed that the volume of the plasma flame and the gas temperature were increased with increasing the microwave power. On the other hand, higher gas flow rates increased the electron density. In the plasma flame, the gas temperature measured by a thermocouple and OES was in the range of (1030–2200) K, which showed an exponential decrease in the axial direction away from the converging point.
PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1 (2004)

As the next step towards generating a synthetic biology from artificial genetic information systems, we have examined variants of HIV reverse transcriptase (RT) for their ability to synthesize duplex DNA incorporating the non-standard base pair between 2,4-diaminopyrimidine (pyDAD), a pyrimidine presenting a hydrogen bond 'donor-acceptor-donor' pattern to the complementary base, and xanthine (puADA), a purine presenting a hydrogen bond 'acceptor-donor-acceptor' pattern. This base pair fits the Watson-Crick geometry, but is joined by a pattern of hydrogen bond donor and acceptor groups different from those joining the GC and AT pairs. A variant of HIV-RT where Tyr 188 is replaced by Leu, has emerged from experiments where HIV was challenged to grow in the presence of drugs targeted against the RT, such as L-697639, TIBO and nevirapine. These drugs bind at a site near, but not in, the active site. This variant accepts the pyDAD-puADA base pair significantly better than wild type HIV-RT, and we used this as a starting point. A second mutation, E478Q, was introduced into the Y188L variant, in the event that the residual nuclease activity observed is due to the RT, and not a contaminant. The doubly mutated RT incorporated the non-standard pair with sufficient fidelity that the variant could be used to amplify oligonucleotides containing pyDAD and puADA through several rounds of a polymerase chain reaction (PCR) without losing the non-standard base pair. This is the first time where DNA containing non-standard base pairs with alternative hydrogen bonding patterns has been amplified by a full PCR. This work also illustrates a research strategy that combines in clinico pre-evolution of proteins followed by rational design to obtain an enzyme that meets a particular technological specification.
Challenges in embedded database system administration (1999)

... This paper discusses the database administration challenges posed by embedded systems and describes how Sleepycat Software&amp;apos;s Berkeley DB architecture addresses these challenges.
Phase shift pulse codes with good periodic correlation properties (1961)

A method of generating phase shift pulse codes of arbitrarily long length with zero periodic correlation except for the peak for zero shift is presented. The codes are of length <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p^2</tex> where <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</tex> is any prime number, and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</tex> different phase shifts corresponding to the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</tex> th roots of unity are necessary to generate them. Since <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</tex> different phase shifts are required, these codes are not as easy to generate and process as the binary codes, but this does not seem to be a serious limitation to their usefulness. Application of these codes can be made as interpulse phase modulation for range resolution in pulse Doppler radars or for a method of synchronizing a pulse code communication system.
Isomerization reactions of charcoal-defatted bovine plasma albumin. The N-F transition and acid expansion (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsomerization reactions of charcoal-defatted bovine plasma albumin. The N-F transition and acid expansionMasaru. Sogami and Joseph F. FosterCite this: Biochemistry 1968, 7, 6, 2172–2182Publication Date (Print):June 1, 1968Publication History Published online1 May 2002Published inissue 1 June 1968https://pubs.acs.org/doi/10.1021/bi00846a020https://doi.org/10.1021/bi00846a020research-articleACS PublicationsRequest reuse permissionsArticle Views323Altmetric-Citations142LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Predictive tracking for augmented reality (1995)

Ronald Tadao Azuma. Predictive Tracking for Augmented Reality (Under the direction of T. Gary Bishop.) In Augmented Reality systems, see-through Head-Mounted Displays (HMDs) superimpose virtual three-dimensional objects on the real world. This technology has the potential to enhance a user&amp;apos;s perception of and interaction with the real world. However, many Augmented Reality applications will not be accepted unless virtual objects are accurately registered with their real counterparts. Good registration is difficult, because of the high resolution of the human visual system and its sensitivity to small differences. Registration errors fall into two categories: static errors, which occur even when the user remains still, and dynamic errors caused by system delays when the user moves. Dynamic errors are usually the largest errors. This dissertation demonstrates that predicting future head locations is an effective approach for significantly reducing dynamic errors. This demonstration is performed in real time with an operational Augmented Reality system. First, evaluating the effect of prediction requires robust static registration. Therefore, this system uses a custom optoelectronic head-tracking system and three calibration procedures developed to measure the viewing parameters. Second, the system predicts future head positions and orientations with the aid of inertial sensors. Effective use of these sensors requires accurate estimation of the varying iv prediction intervals, optimization techniques for determining parameters, and a system built to support real-time processes. On average, prediction with inertial sensors is 2 to 3 times more accurate than prediction without inertial sensors and 5 to 10 times more accurate than not doing any prediction at all. Prediction...
Benefit of pattern diversity via two-element array of circular patch antennas in indoor clustered MIMO channels (2006)

In this paper, we analyze a multiple-input multiple-output (MIMO) array consisting of two circular microstrip antennas, designed to exploit pattern diversity. We analytically derive the spatial correlation coefficients of this array as a function of the mode excited, for realistic clustered MIMO channel models. We compare the performance of the circular patch array (CPA) against an array of two spaced dipoles. In particular, we compute a theoretical tradeoff to predict when the pattern diversity provided by the CPA is more effective than space diversity from the uniform linear array (ULA), based on the eigenvalues of the spatial correlation matrix. Through simulations, we show that CPAs yield better performance or satisfy more restrictive size constraints than ULAs in clustered MIMO channels, depending on the element spacing of the ULA. These results make the CPA an attractive solution for miniaturized MIMO arrays for portable devices or access points.
Polymer Gate Dielectric Surface Viscoelasticity Modulates Pentacene Transistor Performance (2007)

Nanoscopically confined polymer films are known to exhibit substantially depressed glass transition temperatures (Lg's) as compared to the corresponding bulk materials. We report here that pentacene thin films grown on polymer gate dielectrics at temperatures well below their bulk Tg's exhibit distinctive and abrupt morphological and microstructural transitions and thin-film transistor (TFT) performance discontinuities at well-defined growth temperatures. The changes reflect the higher chain mobility of the dielectric in its rubbery state and are independent of dielectric film thickness. Optimization of organic TFT performance must recognize this fundamental buried interface viscoelasticity effect, which is detectable in the current-voltage response.
Two-Photon Excitation of Quantum Dot Based Nonradiative Energy Transfer (2006)

We demonstrate nonradiative energy transfer in a two-photon excited system with quantum dot donors and proximal dye acceptors. A prototype nanosensing scheme for maltose is also presented in this excitation mode.
The Complete Nucleotide Sequence of Coxsackievirus B4 and Its Comparison to Other Members of the Picornaviridae (1987)

The genome of the prototype stain of coxsackievirus B4 (J.V.B. Benschoten) has been cloned in Escherichia coli and its complete nucleotide sequence determined. Excluding the poly(A) tract, the RNA genome is 7395 nucleotides in length and appears to encode a single polyprotein of 2183 amino acids. The predicted amino acid sequence of the polyprotein shows close homology (88%) to that of the previously sequenced coxsackievirus B3 and to certain regions of the polyproteins of the polioviruses and human rhinovirus 14. This allows identification of putative polyprotein cleavage signals, antigenic domains and other structural features likely to be important to the biological integrity of the virus.
Evaluation of B cell maturation antigen as a target for antibody drug conjugate mediated cytotoxicity in multiple myeloma (2016)

B-cell maturation antigen (BCMA, also termed TNFRSF17) is an attractive therapeutic target due to its restricted expression on normal and malignant plasma cells (PC). GSK2857916 (or J6M0-MMAF) is a BCMA-specific antibody conjugated to the microtubule-disrupting agent monomethyl auristatin F (MMAF) via a protease-resistant linker. To evaluate the clinical potential of this agent, tumour cells from seventy multiple myeloma (MM) patients were assessed for BCMA expression by immunohistochemistry and flow cytometry. All patients tested expressed BCMA, at varying levels, and both surface and intracellular expression were observed. BCMA expression is maintained through relapse, extramedullary spread and in residual disease post therapy. BCMA levels may also be prognostically useful as higher levels of BCMA were associated with poorer outcomes, even taking into account genetic risk. We observed rapid internalization of surface BCMA and newly expressed protein by 1 h, suggesting a mechanism for J6M0-MMAF activity even with low surface antigen. J6M0-MMAF mediated cytotoxicity of MM cells varied with dose and antigen levels, with clonogenic progenitors killed at lower doses than mature cells. In comparison, J6M0-MMAF killing of primary CD138(+) myeloma cells occurred with slower kinetics. Our observations support BCMA to be a promising therapeutic target in MM for novel therapies such as J6M0-MMAF.
Modern surface pollen from three transects across the Southern Sonoran desert margin, Northwestern Mexico (1998)

Abstract Surface pollen samples collected along three transects that cross the southern margin of the Sonoran Desert east of the Gulf of California reflect regional vegetation gradients but also show strong local variability, notably within the southern desert. Chenopodiaceae‐Amaranthaceae (Cheno‐Am) and Gramineae pollen dominate in tropical deciduous forest; Pinus and Quercus in temperate‐climate vegetation at high elevations; and Gramineae and High‐Spine Compositae in the central Sonoran Desert (>29° N). The ERA group (composed largely of Euphorbiaceae, Rutaceae, Anacardiaceae), Gramineae, Cheno‐Am, and High‐Spine Compositae pollen inter‐vary but dominate as a group in the southern desert; Cheno‐Am here may signal irrigated agriculture. Coastal sites differ from the above, with Cheno‐Am pollen strongly dominant in saline conditions.
Traumatic Brain Injury in the War Zone (2005)

Dr. Susan Okie writes about patients who have received traumatic brain injuries while fighting in the war in Iraq.
High-efficiency photovoltaic devices based on annealed poly(3-hexylthiophene) and 1-(3-methoxycarbonyl)-propyl-1- phenyl-(6,6)C61 blends (2005)

The effects of annealing and fullerene loading in regioregular poly(3-hexylthiophene) (P3HT) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-(6,6)C61 (PCBM) based bulk heterojunction photovoltaics have been investigated. Under specific loading and annealing conditions, a combination of morphological and electronic factors can be brought to play to achieve optimal filling factors, open-circuit voltage (Voc), and short-circuit current density (Jsc). We demonstrate that this occurs at surprisingly low loadings of PCBM and annealing temperatures nearing the melting point of the polymer. Further, we report power conversion efficiencies approaching 5% in the P3HT:PCBM system.
The Activation State of αvβ3Regulates Platelet and Lymphocyte Adhesion to Intact and Thrombin-cleaved Osteopontin (2000)

Cleavage of osteopontin by thrombin has been reported to enhance cell adhesion. We asked whether thrombin could regulate the alpha(v)beta(3)-mediated adhesion of platelets and B lymphocytes to this substrate. Although there was no difference in the extent or the avidity of thrombin- and ADP-stimulated platelet adhesion to intact or thrombin-cleaved human osteopontin, both the extent and avidity of phorbol ester-stimulated B cell adhesion to thrombin-cleaved osteopontin was significantly increased. Thus, these data suggest that the ability of alpha(v)beta(3) to recognize osteopontin can be differentially regulated in a cell-specific manner. To localize the alpha(v)beta(3) binding site on osteopontin, we measured cell adhesion to the two thrombin cleavage products of osteopontin and to a series of nested RGD-containing osteopontin peptides cross-linked to albumin. Whereas ADP-stimulated platelets adhered to the amino-terminal but not the carboxyl-terminal osteopontin fragment and to the osteopontin peptide RGDSVVYGLR, phorbol ester-stimulated B cells did not adhere to this peptide, although they did so in the presence of 1 mm Mn(2+). Thus, our data confirm that thrombin cleavage enhances the accessibility of the binding motif for alpha(v)beta(3) on osteopontin, but this enhancement is also a function of the activation state of alpha(v)beta(3). Moreover, they indicate that the sequence RGDSVVYGLR contains sufficient information to specify activation-dependent alpha(v)beta(3)-mediated platelet and lymphocyte adhesion.