gebhart/patrepeval huggingface dataset:
Opposite effects of nitric oxide and nitroxyl on postischemic myocardial injury (1999)

Recent experimental evidence suggests that reactive nitrogen oxide species can contribute significantly to postischemic myocardial injury. The aim of the present study was to evaluate the role of two reactive nitrogen oxide species, nitroxyl (NO(-)) and nitric oxide (NO(.)), in myocardial ischemia and reperfusion injury. Rabbits were subjected to 45 min of regional myocardial ischemia followed by 180 min of reperfusion. Vehicle (0.9% NaCl), 1 micromol/kg S-nitrosoglutathione (GSNO) (an NO(.) donor), or 3 micromol/kg Angeli's salt (AS) (a source of NO(-)) were given i.v. 5 min before reperfusion. Treatment with GSNO markedly attenuated reperfusion injury, as evidenced by improved cardiac function, decreased plasma creatine kinase activity, reduced necrotic size, and decreased myocardial myeloperoxidase activity. In contrast, the administration of AS at a hemodynamically equieffective dose not only failed to attenuate but, rather, aggravated reperfusion injury, indicated by an increased left ventricular end diastolic pressure, myocardial creatine kinase release and necrotic size. Decomposed AS was without effect. Co-administration of AS with ferricyanide, a one-electron oxidant that converts NO(-) to NO(.), completely blocked the injurious effects of AS and exerted significant cardioprotective effects similar to those of GSNO. These results demonstrate that, although NO(.) is protective, NO(-) increases the tissue damage that occurs during ischemia/reperfusion and suggest that formation of nitroxyl may contribute to postischemic myocardial injury.
Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires (2019)

High-throughput T cell receptor (TCR) sequencing allows the characterization of an individual's TCR repertoire and directly queries their immune state. However, it remains a non-trivial task to couple these sequenced TCRs to their antigenic targets. In this paper, we present a novel strategy to annotate full TCR sequence repertoires with their epitope specificities. The strategy is based on a machine learning algorithm to learn the TCR patterns common to the recognition of a specific epitope. These results are then combined with a statistical analysis to evaluate the occurrence of specific epitope-reactive TCR sequences per epitope in repertoire data. In this manner, we can directly study the capacity of full TCR repertoires to target specific epitopes of the relevant vaccines or pathogens. We demonstrate the usability of this approach on three independent datasets related to vaccine monitoring and infectious disease diagnostics by independently identifying the epitopes that are targeted by the TCR repertoire. The developed method is freely available as a web tool for academic use at tcrex.biodatamining.be.
Insulin secretion is highly sensitive to desorption of plasma membrane cholesterol (2008)

Cholesterol-rich clusters of SNARE (soluble NSF attachment protein receptor) proteins have been implicated as being important for exocytosis. Here we demonstrate the significance of cholesterol for normal biphasic insulin secretion in mouse beta cells by removal of cholesterol from the plasma membrane using methyl-beta-cyclodextrin (MBCD). Maximal inhibition of insulin secretion in static incubations was achieved using 0.1 mM MBCD. In in situ pancreatic perfusion measurements, both first and second phase insulin secretions were reduced by approximately 50% (P<0.05). This was accompanied by a reduced number of docked large dense core vesicles (LDCVs) (approximately 40%; P<0.01) and a reduced exocytotic response (>50%; P<0.01). Further, subcellular fractionations demonstrated movement of the synaptosomal protein of 25 kDa (SNAP-25) from the plasma membrane to the cytosol after MBCD treatment. The inhibitory actions of MBCD were counteracted by subsequent addition of cholesterol. We hypothesize that desorption of cholesterol leads to the disturbance of a basic exocytotic mechanism partly due to migration of SNAP-25, and we conclude that insulin secretion is highly sensitive to changes in plasma membrane cholesterol.
Insulin growth factor-binding protein 2 is a candidate biomarker for PTEN status and PI3K/Akt pathway activation in glioblastoma and prostate cancer (2007)

PTEN is an important tumor-suppressor gene associated with many cancers. Through expression profiling of glioblastoma tissue samples and prostate cancer xenografts, we identified a molecular signature for loss of the PTEN tumor suppressor in glioblastoma and prostate tumors. The PTEN signature consists of a minimum of nine genes, several of which are involved in various pathways already implicated in tumor formation. Among these signature genes, the most significant was an increase in insulin growth factor-binding protein 2 (IGFBP-2) mRNA. Up-regulation of IGFBP-2 was confirmed at the protein level by Western blot analysis and validated in samples not included in the microarray analysis. The link between IGFBP-2 and PTEN was of particular interest because elevated serum IGFBP-2 levels have been reported in patients with prostate and brain tumors. To further investigate this link, we determined that IGFBP-2 expression is negatively regulated by PTEN and positively regulated by phosphatidylinositol 3-kinase (PI3K) and Akt activation. In addition, Akt-driven transformation is impaired in IGFBP2(-/-) mouse embryo fibroblasts, implicating a functional role for IGFBP-2 in PTEN signaling. Collectively, these studies establish that PTEN and IGFBP-2 expression are inversely correlated in human brain and prostate cancers and implicate serum IGFBP-2 levels as a potential serum biomarker of PTEN status and PI3K Akt pathway activation in cancer patients.
Model-based clustering and data transformations for gene expression data (2001)

http://www.cs.washington.edu/homes/kayee/model.
TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator (2015)

TetGen is a C++ program for generating good quality tetrahedral meshes aimed to support numerical methods and scientific computing. The problem of quality tetrahedral mesh generation is challenged by many theoretical and practical issues. TetGen uses Delaunay-based algorithms which have theoretical guarantee of correctness. It can robustly handle arbitrary complex 3D geometries and is fast in practice. The source code of TetGen is freely available. This article presents the essential algorithms and techniques used to develop TetGen. The intended audience are researchers or developers in mesh generation or other related areas. It describes the key software components of TetGen, including an efficient tetrahedral mesh data structure, a set of enhanced local mesh operations (combination of flips and edge removal), and filtered exact geometric predicates. The essential algorithms include incremental Delaunay algorithms for inserting vertices, constrained Delaunay algorithms for inserting constraints (edges and triangles), a new edge recovery algorithm for recovering constraints, and a new constrained Delaunay refinement algorithm for adaptive quality tetrahedral mesh generation. Experimental examples as well as comparisons with other softwares are presented.
Higher-speed, higher-performance 802.11a wireless LAN via carrier-interferometry orthogonal frequency division multiplexing (2003)

WLANs (wireless local area networks) have emerged as a powerful architecture capable of supporting the requirements of broadband wireless communications. The IEEE 802.11a 5 GHz WLAN standard employs OFDM in its physical layer. This paper introduces carrier interferometry OFDM to the current 802.11a WLAN, and demonstrates that the corresponding small changes to the traditional OFDM scheme lead to notable improvements in probability of error performances and a doubling in throughput. Calling the modified WLAN system pseudo-orthogonal carrier-interferometry WLAN (or PO-CI-WLAN for short), we show that in office buildings, at a bit error rate of 10/sup -3/, PO-CI-WLAN offers a 3 dB performance gain over the IEEE 802.11a 5 GHz WLAN and simultaneously doubles the throughput.
Microwave tunneling current from the resonant interaction of an amplitude modulated laser with a scanning tunneling microscope (1996)

Simulations of the interaction of light with tunneling electrons in a scanning tunneling microscope suggest that there is a resonance in which the tunneling current is markedly increased. If a laser operating near the resonance is amplitude modulated, then the tunneling current will have components at the frequency of modulation and its harmonics, as well as at optical frequencies and dc. It is suggested that this effect should be considered as a new mode for laser-assisted scanning tunneling microscopy. The simulations for the examples were made by solving the one-dimensional time-dependent Schrödinger equation by the numerical procedure of shooting methods, using a planar–planar scanning tunneling microscope model with the exact multiple image potential.
Germ line transmission of yeast artificial chromosomes in transgenic mice (1994)

Several groups have recently reported the successful generation of transgenic mice harbouring yeast artificial chromosomes (YACs). Different methodological approaches have been shown to produce similar results, namely, the faithful expression of the transgenes carried on YAC DNA. In this paper, we compare the reported techniques for obtaining transgenic mice carrying YACs using a 250-kb YAC bearing the mouse tyrosinase gene. These methods include: microinjection of gel-purified YAC DNA into pronuclei of fertilized mouse oocytes, yeast spheroblast fusion with embryonic stem (ES) cells and lipofection of YAC DNA into ES cells. Taken together, these reports show that the delivery of large genomic regions covering a gene of interest (such as those cloned in YAC vectors) is feasible, and will ensure appropriate temporal and spatial expression of the transgene at a level comparable to that of the endogenous counterpart.
A modular microfluid system with an integrated micromixer (1996)

Microsystems are gaining more and more interest in several technological areas. The complete integration of different basic elements like pumps, valves and reaction chambers is possible by the use of microtechnologies. In the field of micro analysis systems a mixing procedure of different solutions is often required. A static micromixer built up in silicon has been developed. The design and fabrication procedures of the micromixer allow the integration of other microcomponents like pumps, valves or sensors. The micromixer consists of two structures silicon wafers. The structured surfaces are bonded together by using a low temperature silicon direct bonding process. The structure of the mixer consists of several identical mixing elements. The size of one element is about . Each element consists of two or more microchannels for different liquids to be mixed. The arrangements of the microchannels in the elements lead to a mixing of the liquids. We found a homogeneous mixing after about 5 mixing elements for mixable liquids. Not mixable liquids will be emulsified after about 16 - 20 mixing elements.
Increased NAD(P)H Oxidase and Reactive Oxygen Species in Coronary Arteries After Balloon Injury (2001)

Reactive oxygen species (ROS), produced by cellular constituents of the arterial wall, provide a signaling mechanism involved in vascular remodeling. Because adventitial fibroblasts are actively involved in coronary remodeling, we examined whether the changes in the redox state affect their phenotypic characteristics. To this end, superoxide anion production and NAD(P)H oxidase activity were measured in porcine coronary arteries in vivo, and the effect of ROS generation on adventitial fibroblast proliferation was examined in vitro. Superoxide production (SOD- and Tiron-inhibitable nitro blue tetrazolium [NBT] reduction) increased significantly within 24 hours after balloon-induced injury, with the product of NBT reduction present predominantly in adventitial fibroblasts. These changes were NAD(P)H oxidase-dependent, because diphenyleneiodonium (DPI) abolished superoxide generation (P<0.001). Furthermore, the injury-induced superoxide production was associated with augmented NAD(P)H oxidase activity and upregulation of p47(phox) and p67(phox) in adventitial fibroblasts (immunohistochemistry). Serum stimulation of isolated adventitial fibroblasts produced time-dependent increases in ROS production (peak 3 to 6 hours). The inhibition of ROS generation with NAD(P)H oxidase inhibitor (DPI) or the removal of ROS with antioxidants (Tiron, catalase) abrogated proliferation of adventitial fibroblasts. These results indicate that vascular NAD(P)H oxidase plays a central role in the upregulation of oxidative stress after coronary injury, providing pivotal growth signals for coronary fibroblasts.
Drug response in a genetically engineered mouse model of multiple myeloma is predictive of clinical efficacy (2012)

The attrition rate for anticancer drugs entering clinical trials is unacceptably high. For multiple myeloma (MM), we postulate that this is because of preclinical models that overemphasize the antiproliferative activity of drugs, and clinical trials performed in refractory end-stage patients. We validate the Vk*MYC transgenic mouse as a faithful model to predict single-agent drug activity in MM with a positive predictive value of 67% (4 of 6) for clinical activity, and a negative predictive value of 86% (6 of 7) for clinical inactivity. We identify 4 novel agents that should be prioritized for evaluation in clinical trials. Transplantation of Vk*MYC tumor cells into congenic mice selected for a more aggressive disease that models end-stage drug-resistant MM and responds only to combinations of drugs with single-agent activity in untreated Vk*MYC MM. We predict that combinations of standard agents, histone deacetylase inhibitors, bromodomain inhibitors, and hypoxia-activated prodrugs will demonstrate efficacy in the treatment of relapsed MM.
High-power disorder-defined coupled stripe AlyGa1−yAs-GaAs-InxGa1−xAs quantum well heterostructure lasers (1989)

Data are presented describing continuous (cw) room-temperature laser operation of AlyGa1−yAs-GaAs-InxGa1−xAs quantum well heterostructure (QWH) phase-locked arrays. The ten-stripe arrays have 3 μm emitters, with emitter to emitter spacing of 4 μm, and are patterned onto the QWH crystal using a self-aligned Si-O impurity-induced layer disordering (IILD) procedure. The IILD process is devised to provide limited layer intermixing to ensure optical coupling (across ∼1 μm). The coupled stripe QWH lasers exhibit narrow twin-lobed far-field patterns that show unambiguously phase locking in the highest order supermode. The cw output power of the lasers (differential quantum efficiency 52%) is shown from threshold (∼75 mA) to over 280 mW (both facets, no optical coatings).
Application of the Synechococcus nirA Promoter To Establish an Inducible Expression System for Engineering the Synechocystis Tocopherol Pathway (2005)

Tocopherols are important antioxidants in lipophilic environments. They are synthesized by plants and some photosynthetic bacteria. Recent efforts to analyze and engineer tocopherol biosynthesis led to the identification of Synechocystis sp. strain PCC 6803 as a well-characterized model system. To facilitate the identification of the rate-limiting step(s) in the tocopherol biosynthetic pathway through the modulation of transgene expression, we established an inducible expression system in Synechocystis sp. strain PCC 6803. The nirA promoter from Synechococcus sp. strain PCC 7942, which is repressed by ammonium and induced by nitrite (S.-I. Maeda et al., J. Bacteriol. 180:4080-4088, 1998), was chosen to drive the expression of Arabidopsis thaliana p-hydroxyphenylpyruvate dioxygenase. The enzyme catalyzes the formation of homogentisic acid from p-hydroxyphenylpyruvate. Expression of this gene under inducing conditions resulted in up to a fivefold increase in total tocopherol levels with up to 20% of tocopherols being accumulated as tocotrienols. The culture supernatant of these cultures exhibited a brown coloration, a finding indicative of homogentisic acid excretion. Enzyme assays, functional complementation, reverse transcription-PCR, and Western blot analysis confirmed transgene expression under inducing conditions only. These data demonstrate that the nirA promoter can be used to control transgene expression in Synechocystis and that homogentisic acid is a limiting factor for tocopherol synthesis in Synechocystis sp. strain PCC 6803.
A programmable NMOS DRAM controller for microcomputer systems with dual-port memory and error checking and correction (1983)

An NMOS DRAM controller for use in microcomputer systems based on the iAPX-86 and iAPX-286 microprocessor families or on the Multibus system bus is described. The controller provides complete support for dual-port memories and memories with error checking and correction. The controller has programmable attributes for configuring it to the particular requirements of the system. The controller uses parallel arbitration to minimize arbitration delay. A memory cycle will start on the same clock edge that samples a command if the cycle has been previously enabled. Novel logic and circuit design techniques have been used to achieve 16 MHz operation, 20 ns input setup time, and 35 ns output delay time.
Transferrin receptor-targeted theranostic gold nanoparticles for photosensitizer delivery in brain tumors (2014)

Therapeutic drug delivery across the blood-brain barrier (BBB) is not only inefficient, but also nonspecific to brain stroma. These are major limitations in the effective treatment of brain cancer. Transferrin peptide (Tfpep) targeted gold nanoparticles (Tfpep-Au NPs) loaded with the photodynamic pro-drug, Pc 4, have been designed and compared with untargeted Au NPs for delivery of the photosensitizer to brain cancer cell lines. In vitro studies of human glioma cancer lines (LN229 and U87) overexpressing the transferrin receptor (TfR) show a significant increase in cellular uptake for targeted conjugates as compared to untargeted particles. Pc 4 delivered from Tfpep-Au NPs clusters within vesicles after targeting with the Tfpep. Pc 4 continues to accumulate over a 4 hour period. Our work suggests that TfR-targeted Au NPs may have important therapeutic implications for delivering brain tumor therapies and/or providing a platform for noninvasive imaging.
Flow tiles (2004)

We present <i>flow tiles</i>, a novel technique for representing and designing velocity fields. Unlike existing procedural flow generators, tiling offers a natural user interface for field design. Tilings can be constructed to meet a wide variety of external and internal boundary conditions, making them suitable for inclusion in larger environments. Tiles offer memory savings through the re-use of prototypical elements. Each flow tile contains a small field and many tiles can be combined to produce large flows. The corners and edges of tiles are constructed to ensure continuity across boundaries between tiles. In addition, all our tiles and the resulting titing are divergence-free and hence suitable for representing a range of effects. We discuss issues that arise in designing flow tiles, algorithms for creating tilings, and three applications: a crowd on city streets, a river flowing between banks, and swirling fog. The first two applications use stationary fields, while the latter demonstrates a dynamic field.
PV Balancers: Concept, Architectures, and Realization (2014)

This paper presents a new concept of module-integrated converters called PV balancers for photovoltaic applications. The proposed concept enables independent maximum power point tracking for each module, and dramatically decreases the requirements in terms of electrical rating, size, and manufacturing cost for power converters. The power rating of a PV balancer is less than 20% of its counterparts, and the manufacturing cost is thus significantly reduced. In this paper, two architectures of PV balancers are proposed, analyzed, realized, and verified through simulation and experimental results. It is anticipated that the proposed approach will be a low-cost solution for future photovoltaic power systems.
e-Commerce Based on ERP for Enterprise by Utilizing DNA and XML (2001)

The developmemnt of the e-commerce must based on the apllication of the enterprise inner management information system(MIS).This paper will discuss the trade mode of e-commerce based on the enterprise resource planning(ERP), and will give the commerce solutions based on ERP for Enterprises by utilizing the DNA and UML.
Niphatenones, Glycerol Ethers from the Sponge Niphates digitalis Block Androgen Receptor Transcriptional Activity in Prostate Cancer Cells: Structure Elucidation, Synthesis, and Biological Activity (2011)

Extracts of the marine sponge Niphates digitalis collected in Dominica showed strong activity in a cell-based assay designed to detect antagonists of the androgen receptor (AR) that could act as lead compounds for the development of a new class of drugs to treat castration recurrent prostate cancer (CRPC). Assay-guided fractionation showed that niphatenones A (3) and B (4), two new glycerol ether lipids, were the active components of the extracts. The structures of 3 and 4 were elucidated by analysis of NMR and MS data and confimed via total synthesis. Biological evaluation of synthetic analogues of the niphatenones has shown that the enantiomers 7 and 8 are more potent than the natural products in the screening assay and defined preliminary SAR for the new AR antagonist pharmacophore, including the finding that the Michael acceptor enone functionality is not required for activity. Niphatenone B (4) and its enantiomer 8 blocked androgen-induced proliferation of LNCaP prostate cancer cells but had no effect on the proliferation of PC3 prostate cancer cells that do not express functional AR, consistent with activity as AR antagonists. Use of the propargyl ether 44 and Click chemistry showed that niphatenone B binds covalently to the activation function-1 (AF1) region of the AR N-terminus domain (NTD).
Identification of Human Papillomavirus Type 18 E6 Polypeptide in Cells Derived from Human Cervical Carcinomas (1987)

We recently reported the expression of human papillomavirus type 18 (HPV-18) E6 protein in bacteria and the production of anti-E6 polyclonal antibodies. This work has now been extended with the production of a panel of monoclonal antibodies against the HPV-18 E6 protein. These antibodies demonstrate that there is little antigenic conservation in the E6 protein between HPV-16 and HPV-18, with only one antibody recognizing a cross-reactive epitope. We have used both the monoclonal and the polyclonal antibodies to look for E6 expression in a number of HPV DNA-containing cell lines. These reagents specifically detected a 16.5K mol. wt. polypeptide in cells derived from a human cervical carcinoma.