gebhart/patrepeval huggingface dataset:
Flow-dependent Smad2 phosphorylation and TGIF nuclear localization in human aortic endothelial cells (2011)

Endothelial cells respond to fluid flow stimulation through transient and sustained signal pathway activation. Smad2 is a signaling molecule and transcription factor in the Smad signaling pathway, traditionally associated with TGF-β. Although phosphorylation of Smad2 in the receptor-dependent COOH-terminal region is the most appreciated way Smad2 is activated to affect gene expression, phosphorylation may also occur in the MH1-MH2 linker region (L-psmad2). Here, we show that in human aortic endothelial cells (HAEC), Smad2 was both preferentially phosphorylated in the linker region and localized to the nucleus in a flow-dependent manner. The Smad corepressor transforming growth interacting factor (TGIF) was also found to have flow-dependent nuclear localization. Tissue studies confirmed this L-psmad2 generation trend in rat aorta, indicating likely importance in arterial tissue. HAEC-based inhibitor studies demonstrated that L-psmad2 levels were not related to MAPK phosphorylation, but instead followed the pattern of pAkt(473), both with and without the phosphatidylinositol 3-kinase inhibitor PI-103. Akt and Smad species were also shown to directly interact under flow relative to static controls. To further evaluate impacts of PI-103 treatment, expression profiles for two TGF-β and shear stress-dependent genes were determined and showed that mRNAs were lower from untreated 10 dyn/cm(2) than 2 dyn/cm(2) average shear stress cultures. However, upon exposure to PI-103, this trend was reversed, with a stronger response observed at 10 dyn/cm(2). Taken together, the results of this work suggest that fluid flow exposure may influence endothelial gene expression by a novel mechanism involving Akt, L-psmad2, and TGIF.
Structure of Compstatin in Complex with Complement Component C3c Reveals a New Mechanism of Complement Inhibition (2007)

Undesired complement activation is a major cause of tissue injury in various pathological conditions and contributes to several immune complex diseases. Compstatin, a 13-residue peptide, is an effective inhibitor of the activation of complement component C3 and thus blocks a central and crucial step in the complement cascade. The precise binding site on C3, the structure in the bound form, and the exact mode of action of compstatin are unknown. Here we present the crystal structure of compstatin in complex with C3c, a major proteolytic fragment of C3. The structure reveals that the compstatin-binding site is formed by the macroglobulin (MG) domains 4 and 5. This binding site is part of the structurally stable MG-ring formed by domains MG 1-6 and is far away from any other known binding site on C3. Compstatin does not alter the conformation of C3c, whereas compstatin itself undergoes a large conformational change upon binding. We propose a model in which compstatin sterically hinders the access of the substrate C3 to the convertase complexes, thus blocking complement activation and amplification. These insights are instrumental for further development of compstatin as a potential therapeutic.
SHIP is a negative regulator of growth factor receptor-mediated PKB/Akt activation and myeloid cell survival (1999)

SHIP is an inositol 5' phosphatase that hydrolyzes the PI3'K product PI(3,4,5)P3. We show that SHIP-deficient mice exhibit dramatic chronic hyperplasia of myeloid cells resulting in splenomegaly, lymphadenopathy, and myeloid infiltration of vital organs. Neutrophils and bone marrow-derived mast cells from SHIP-/- mice are less susceptible to programmed cell death induced by various apoptotic stimuli or by growth factor withdrawal. Engagement of IL3-R and GM-CSF-R in these cells leads to increased and prolonged PI3'K-dependent PI(3,4,5)P3 accumulation and PKB activation. These data indicate that SHIP is a negative regulator of growth factor-mediated PKB activation and myeloid cell survival.
Lipid composition: a “key factor” for the rational manipulation of the liposome–protein corona by liposome design (2014)

When liposomes are exposed to biological fluids, a dynamic protein coating immediately covers them forming a ‘protein corona’. Those proteins can interact with receptors (over)expressed on the plasma membrane of target cells bringing the liposomes to their final destination.
RTD/CMOS nanoelectronic circuits: thin-film InP-based resonant tunneling diodes integrated with CMOS circuits (1999)

The combination of resonant tunneling diodes (RTDs) and complementary metal-oxide-semiconductor (CMOS) silicon circuitry can offer substantial improvement in speed, power dissipation, and circuit complexity over CMOS-only circuits. We demonstrate the first integrated resonant tunneling CMOS circuit, a clocked 1-bit comparator with a device count of six, compared with 21 in a comparable all-CMOS design. A hybrid integration process is developed for InP-based RTDs which are transferred and bonded to CMOS chips. The prototype comparator shows sensitivity in excess of 10/sup 6/ VIA, and achieves error-free performance in functionality testing. An optimized integration process, under development, can yield high-speed, low power circuits by lowering the high parasitic capacitance associated with the prototype circuit.
Application development of virtual metrology in semiconductor industry (2005)

Daily wafer fabrication in semiconductor foundry depends on considerable metrology operations for tool-quality and process-quality assurance. The metrology operations required a lot of metrology tools, which increase FAB's investment. Also, these metrology operations will increase cycle time of wafer process. Metrology operations do not bring any value added to wafer but only quality assurance. This article provides a new method denoted virtual metrology (VM) to utilize sensor data collected from 300 mm FAB's tools to forecast quality data of wafers and tools. This proposed method designs key steps to establish a VM control model based on neural networks and to develop and deploy applications following SEMI EDA (equipment data acquisition) standards.
Receptor extracellular domains may contain trafficking information. Studies of the 300-kDa mannose 6-phosphate receptor. (1994)

The 300-kDa mannose 6-phosphate receptor cycles between the trans Golgi network and late endosomes, and between the plasma membrane and early endosomes, to deliver lysosomal enzymes to prelysosomes. Mannose 6-phosphate receptor trafficking requires structural determinants present in the cytoplasmic domain. However, when this domain was joined with the extracellular and transmembrane domains of the epidermal growth factor receptor, it was not sufficient to direct this chimera to late endosomes and the trans Golgi network (Dintzis, S. M., and Pfeffer, S. R. (1990) EMBO J. 9, 77-84). These findings suggested a role for extracellular and/or transmembrane domains in mannose 6-phosphate receptor trafficking. We describe here the construction and expression of chimeric receptors comprised of mannose 6-phosphate receptor extracellular and transmembrane sequences joined with cytoplasmic domain sequences derived from the human epidermal growth factor receptor or the human low density lipoprotein receptor. The chimeras were stable proteins which were efficiently endocytosed and competent to bind a mannose 6-phosphate-containing ligand. Antibody binding assays and indirect immunofluorescence showed that the chimeras containing the mannose 6-phosphate receptor extracellular domain colocalized with mannose 6-phosphate receptors in intracellular compartments. These experiments suggest that the presence of the mannose 6-phosphate receptor extracellular domain may interfere with the rapid recycling of receptors from early endosomes to the cell surface and detain receptors within endosomes.
CellSort: high performance sorting on the cell processor (2007)

In this paper we describe the design and implementation of CellSort − a high performance distributed sort algorithm for the Cell processor. We design CellSort as a distributed bitonic merge with a data-parallel bitonic sorting kernel. In order to best exploit the architecture of the Cell processor and make use of all available forms of parallelism to achieve good scalability, we structure CellSort as a three-tiered sort. The first tier is a SIMD (single-instruction multiple data) optimized bitonic sort, which sorts up to 128KB of items that cat fit into one SPE’s (a co-processor on Cell) local store. We design a comprehensive SIMDization scheme that employs data parallelism even for the most fine-grained steps of the bitonic sorting kernel. Our results show that, SIMDized bitonic sorting kernel is vastly superior to other alternatives on the SPE and performs up to 1.7 times faster compared to quick sort on 3.2GHz Intel Xeon. The second tier is an in-core bitonic merge optimized for cross-SPE data transfers via asynchronous DMAs, and sorts enough number of items that can fit into the cumulative space available on the local stores of the participating SPEs. We design data transfer and synchronization patters that minimize serial sections of the code by taking advantage of the high aggregate cross-SPE bandwidth available on Cell. Results show that, in-core bitonic sort scales well on the Cell processor with increasing number of SPEs, and performs up to 10 times faster with 16 SPEs compared to parallel quick sort on dual-3.2GHz Intel Xeon. The third tier is an out-of-core 1 bitonic merge which sorts large number of items stored in the main memory. Results show that, when properly implemented, distributed out-of-core bitonic sort on Cell can significantly outperform the asymptotically (average case) superior quick sort for large number of memory resident items (up to 4 times faster when sorting 0.5GB of data with 16 SPEs, compared to dual-3.2GHz Intel Xeon). 1 The term “out-of-core ” does not imply a disk-based sort in the context of this paper. However, relation to external sorting is strong (see Sections 2 and 3 for details).
Low-Voltage, Low-Power, Organic Light-Emitting Transistors for Active Matrix Displays (2011)

Intrinsic nonuniformity in the polycrystalline-silicon backplane transistors of active matrix organic light-emitting diode displays severely limits display size. Organic semiconductors might provide an alternative, but their mobility remains too low to be useful in the conventional thin-film transistor design. Here we demonstrate an organic channel light-emitting transistor operating at low voltage, with low power dissipation, and high aperture ratio, in the three primary colors. The high level of performance is enabled by a single-wall carbon nanotube network source electrode that permits integration of the drive transistor and the light emitter into an efficient single stacked device. The performance demonstrated is comparable to that of polycrystalline-silicon backplane transistor-driven display pixels.
Intraneural stimulation elicits an increase in subcutaneous interstitial glycerol levels in humans (1999)

1. The effect of intraneural electrical stimulation of the lateral femoral cutaneous nerve on lipolysis in the innervation territory of the stimulated nerve fascicle was studied in seven healthy women. Lipolysis was evaluated by microdialytic measurement of the interstitial glycerol concentration in subcutaneous adipose tissue. 2. Ten minutes of unilateral intraneural stimulation elicited a 22 +/- 8 % (mean +/- s.e.m.) increase in glycerol levels in the stimulated region (P < 0.05), whereas no change was registered in the corresponding area of the contralateral unstimulated leg. 3. Significantly higher glycerol levels in the stimulated vs. contralateral unstimulated region (47 +/- 13 %, P < 0.05) were already observed at baseline (30 min resting period preceding the 10 min stimulation), in all probability as a consequence of the nerve searching procedure and trial stimulations. After the 10 min stimulation, the overall glycerol increase was 72 +/- 17 % compared with the contralateral leg, illustrating the degree of lipolysis induced by the whole experimental procedure. 4. The sympathetic discharge in the lateral femoral nerve (6 recordings) showed typical characteristics of skin sympathetic activity, and the firing pattern was strikingly similar to simultaneously recorded sympathetic discharge in cutaneous nerve fascicles innervating regions without prominent subcutaneous fat stores (2 double nerve recordings). Thus, no component of cutaneous sympathetic outflow specific for the nerve innervating prominent subcutaneous fat stores could be identified. 5. Our findings suggest that sympathetic nerve fibres travelling in cutaneous nerve fascicles exert a regulatory influence on subcutaneous fat tissue in humans. The combination of intraneural recording/stimulation and subcutaneous microdialysis provides a model for evaluating neural control of human fat metabolism.
Magnetization reversal and domain structure of antiferromagnetically coupled submicron elements (2003)

Switching characteristics and magnetic domain structures in submicron size synthetic antiferromagnets (SyAF), Co90Fe10/Ru/Co90Fe10 have been studied. Submicron size elements with well defined geometry were prepared by electron beam lithography and argon ion milling for SyAFs and Co90Fe10 monolayers deposited by an ultrahigh vacuum sputtering system. Hysteresis loops were obtained by a focused magneto-optic Kerr effect (MOKE) system and magnetic images in the remanent state were observed by magnetic force microscopy (MFM). We found that the MFM images of SyAF exhibit a single domain structure even in the case of aspect ratio of 1, and there is an optimum ferromagnetic film thickness at which SyAF can obtain a single domain structure with such a low aspect ratio. The MOKE results show that the switching field is dependent on the element width and aspect ratio.
WAVE PHENOMENA AND ONE-DIMENSIONAL TWO-PHASE FLOW MODELS. PART I: KINEMATIC WAVES; EXPERIMENTAL RESULTS; THEORY (1997)

This paper describes experimental and analytical work on kinematic wave phenomena in two-phase flows. The main topics are the properties of these waves and the main focus is on the corresponding modeling problems.
Parallel systems in financial information processing (1996)

This paper reports on an ongoing investigation into the applicability of parallel systems in the processing of financial information. For the past five years a wide spectrum of issues has been investigated; this paper attempts to draw together this work as a coherent whole, and discusses past, present and planned activity. A number of case studies applying parallel systems to typical financial applications are described and, where appropriate, results presented. The commonality between the case studies is also discussed.
Enzymatic synthesis of oligodeoxyribonucleotides of defined sequence. (1978)

Procedures for the controlled addition of one or more deoxyribonucleotide residues to the 3' end of an oligodeoxyribonucleotide primer are described. Polynucleotide phosphorylase (EC 2.7.7.8), purified from Escherichia coli B, catalyzes the reaction using a deoxyribonucleoside 5'-diphosphate as substrate, with Mn2+ as cofactor. Reaction occurs rapidly in aqueous solution, and no protecting groups are required, simplifying recovery and purification of the products. The concentrations of sodium chloride and manganous chloride in the incubation mixture are critical to obtaining good yield of the required product. Primers of chain length from 3 to 12 have been extended by up to 9 deoxyribonucleotide residues to obtain oligodeoxyribonucleotides of chain length up to 13. Yields of single addition products varied from 8 to 59%. Factors which influence these yields are discussed. The effects of added polyamines and some organic solvents on the reaction are described. Spermidine or dimethylsulfoxide in the incubation medium tend to favor the addition of several residues of deoxyribonucleotide to the primer.
Differential regulation of the human and murine CD34 genes in hematopoietic stem cells (2002)

Human CD34 (hCD34)-positive cells are used currently as a source for hematopoietic transplantation in humans. However, in steady-state murine hematopoiesis, hematopoietic stem cells (HSCs) with long-term reconstitution activity are found almost exclusively in the murine CD34 (mCD34)-negative to low fraction. To evaluate the possible differences in hCD34 and mCD34 gene expression in hematopoiesis, we made transgenic mouse strains with human genomic P1 artificial chromosome clones spanning the entire hCD34 genomic locus. In all transgenic mouse strains, a vast majority of phenotypic and functional HSC populations including mCD34(-/lo) express the hCD34 transgene. These data strongly support the notion that hCD34(+) human bone marrow cells contain long-term HSCs that can maintain hematopoiesis throughout life.
An automated temporal partitioning and loop fission approach for FPGA based reconfigurable synthesis of DSP applications (1999)

We present an automated temporal partitioning and loop transformation approach for developing dynamically reconfigurable designs starting from behavior level specifications. An Integer Linear Programming (ILP) model is formulated to achieve near-optimal latency designs. We, also present a loop restructuring method to achieve maximum throughput for a class of DSP applications. This restructuring transformation is performed on the temporally partitioned behavior and results in near-optimization of throughput. We discuss eficient memory mapping and address generation techniques for the synthesis of reconfigurable designs. A Case study on the Joint Photographic Experts Group (JPEG) image compression algorithm demonstrates the egectiveness of our approach.
Target Antigen of Monoclonal Reagent S5.7: Comparison with T 3 Antigen (1983)

S5.7 recognizes a 20 kD cell surface protein which is present on T lymphocytes. S5.7 binds to a nonglycosylated protein, which can be labeled by cell-surface radioiodination and by a hydrophobic reagent [125I]-iodo-5-naphthyl-1-azide (INA). As the T-lymphocyte-specific T3 complex was found to contain a nonglycosylated 20 kD species, and since this 20 kD T3 form can be labeled preferentially by INA, a comparison between T3 and S5.7 was made. Isoelectric focusing experiments showed, however, that the two proteins are different. Moreover, the S5.7 monoclonal antibody does not block CML, is not mitogenic, reacts with immature cells of several hemopoietic lineages, and differs in that respect from anti-T3 monoclonal antibodies.
Predicting Fuel Performance for Future HCCI Engines (2012)

Abstract The purpose of this research is to investigate the impact of fuel composition on auto-ignition in homogeneous charge compression ignition (HCCI) engines in order to develop a future metric for predicting fuel performance in future HCCI engine technology. A single-cylinder, variable compression ratio engine operating as an HCCI engine was used to test reference fuels and gasoline blends with octane numbers (ON) ranging from 60 to 88. Correlations between fuel composition, ON, and two existing methods for predicting fuel auto-ignition in HCCI engines (Kalghatgi's octane index and Shibata and Urushihara's HCCI index) are investigated. Results show that octane index and HCCI index poorly predict the impact of fuel composition on auto-ignition for fuels with the same ON. The effect of ethanol in delaying auto-ignition depends on the composition of the original gasoline blend; the same is true for the addition of naphthenes. Low-temperature heat release (LTHR) correlates well with auto-ignition for gasoline fuels exhibiting LTHR. Keywords: Auto-ignitionFuel compositionHomogenous charge compression-ignition (HCCI) ACKNOWLEDGMENTS Research conducted at the University of California, Berkeley, was supported by the Chevron Corporation. The authors also acknowledge the assistance of T. Dillstrom, A. Van Blarigan, and M. Wissink in conducting experimental measurements. Notes a RON and MON were calculated using method described by Morgan et al. (Citation2010). b RON and MON were calculated using bRON and bMON values from Anderson et al. (2010). RON and MON of remaining fuels were assumed. Note. N/A not available. a RON or MON was estimated. b RON or MON was provided by Chevron.
p63: molecular complexity in development and cancer (2004)

Discovery of the p53 homologs p63 and p73 has brought new excitement to the p53 field. Identification of homologous genes coding for several proteins with similar and antagonistic properties towards p53 has been both intriguing and perplexing. A multitude of properties have been attributed to these new homologs and this review will focus on the biochemical and biological aspects of one family member, p63. Although the most ancient member of the p53 family, p63 is the most recently discovered and the least is known about this family member. Unlike p53, whose protein expression is not readily detectable in epithelial cells unless they are exposed to various stress conditions, p63 is expressed in select epithelial cells at high levels under normal conditions. p63 is highly expressed in embryonic ectoderm and in the nuclei of basal regenerative cells of many epithelial tissues in the adult including skin, breast myoepithelium, oral epithelium, prostate and urothelia. In contrast to the tumor suppressive function of p53, over-expression of select p63 splice variants is observed in many squamous carcinomas suggesting that p63 may act as an oncogene. Undoubtedly, the biochemical and biological activities attributed to p63 over the next several years will be diverse and regulation of the p63 gene and its several protein products complex. The use of various model systems and the study of human disease should continue to lead to rapid advances in our understanding of the role of p63 in development, epithelial cell maintenance and tumorigenesis.
Relative Uniform Resource Locators (1995)

A Uniform Resource Locator (URL) is a compact representation of the location and access method for a resource available via the Internet.When embedded within a base document, a URL in its absolute form may contain a great deal of information which is already known from the context of that base document's retrieval, including the scheme, network location, and parts of the url-path.In situations where the base URL is well-defined and known to the parser (human or machine), it is useful to be able to embed URL references which inherit that context rather than re-specifying it in every instance.This document defines the syntax and semantics for such Relative Uniform Resource Locators.