gebhart/patrepeval huggingface dataset:
Tissue-Specific Regulation of Human α 1 -Antitrypsin Gene Expression in Transgenic Mice (1989)

The 5'-flanking sequence of the human alpha 1-antitrypsin (AAT) gene contains multiple cis-regulatory elements, including a distal enhancer and proximal sequences essential for its transcription in cultured hepatoma cells. To understand better the promoter specificity of the AAT gene in vivo, transgenic mice harboring the AAT-SV40 hybrid promoter or the natural AAT promoter fused to a reporter gene (CAT) were generated. Examination of CAT activity in various tissues indicated that the CAT gene was expressed primarily in the liver and also, to a lesser extent, in tissues known to express the AAT gene. In addition, the cis-acting elements of the human AAT gene were utilized to drive the transcription of the SV40 T antigen gene in transgenic mice. Hepatocellular malignancy was found in all founder animals examined, while sporadic occurrence of malignancy was also observed in stomach, pancreas, and kidney. These results verify that the 5'-flanking region of the human AAT gene contains cis-regulatory elements sufficient to confer tissue specificity in vivo.
4D Seismic History Matching of a Real Field Case with EnKF: Use of Local Analysis for Model Updating (2010)

Abstract Quantitative incorporation of 4D seismic data into reservoir history matching is an attractive proposition. The use of ensemble Kalman filter (EnKF) in this regard improves overall quality of seismic data matching and estimating reservoir parameters. We performed 4D seismic history matching of a sector model based on a North sea reservoir using real inverted 4D impedance data. Special challenges are involved when we assimilate large amount of in EnKF, and hence, a methodology based on a combination of global and local analysis scheme is used. In history matching process, we have focused on matching the acoustic impedance ratio between two time steps of several years of production. A petro-elastic modeling based on rock physics recipe of North sea reservoir is used. Uncertain reservoir parameters considered are porosity and permeability. Updated dynamic variables (pressure and water saturation) are conditioned to both production and seismic data. The large number of measurements introduced by the integration of 4D seismic data is handled by an efficient EnKF scheme with the possibility to perform localization. Global and local analysis schemes assimilate production data and seismic data respectively. In our implementation of local analysis, we used three significant regions based on flow conditions and seismic data within a given local analysis region is influenced by only variables in the same region. The posterior ensemble of models showed good match to both production data and seismic data. In most of the cases of reservoir characterization, the combined use of 4D seismic with production data improved history matching for the wells and also improved posterior impedance ratio data matching. In addition, 4D seismic data provided more information related to permeability update in the aquifer and in-fill areas. The results indicate that the proposed local analysis-based model updating scheme reduced the amount of spurious correlations and tendencies to ensemble collapse seen with global analysis.
FLIP Prevents Apoptosis Induced by Death Receptors But Not by Perforin/Granzyme B, Chemotherapeutic Drugs, and Gamma Irradiation (1998)

FLICE-inhibitory protein, FLIP (Casper/I-FLICE/FLAME-1/CASH/CLARP/MRIT), which contains two death effector domains and an inactive caspase domain, binds to FADD and caspase-8, and thereby inhibits death receptor-mediated apoptosis. Here, we characterize the inhibitory effect of FLIP on a variety of apoptotic pathways. Human Jurkat T cells undergoing Fas ligand-mediated apoptosis in response to CD3 activation were completely resistant when transfected with FLIP. In contrast, the presence of FLIP did not affect apoptosis induced by granzyme B in combination with adenovirus or perforin. Moreover, the Fas ligand, but not the perforin/granzyme B-dependent lytic pathway of CTL, was inhibited by FLIP. Apoptosis mediated by chemotherapeutic drugs (i.e., doxorubicin, etoposide, and vincristine) and gamma irradiation was not affected by FLIP or the absence of Fas, indicating that these treatments can induce cell death in a Fas-independent and FLIP-insensitive manner.
Expression of hornet genes encoding venom allergen antigen 5 in insects (1993)

Antigen 5, also known as Dol m V, is a major allergen found in the venom of the baldfaced hornet, Dolichovespula maculata. We have inserted the f10 and f17 cDNAs, which encode hornet antigen 5 (HA5) forms 2 (Dol m; VB) and 3 (Dol m VA), respectively, into the genome of the baculovirus, AcMNPV, to produce the recombinant baculovirus gene expression vectors, vEV-HA5f10 and vEV-HA5f17. Insect cells infected with either vEV-HA5f10 or vEV-HA5f17 produce and secrete a novel protein with an electrophoretic mobility which is similar if not identical to authentic mature Dol m V. The gene products also react specifically with a polyclonal antiserum raised to Dol m VB as expected. Dol m V gene products were not acutely toxic when injected into insect larvae. However, infection of fifth instar larvae with vEV-HA5f17 resulted in premature melanization of the larvae and lower weight gain than infection with control virus. Thus, the Dol m V gene product has a subtle, possibly cytotoxic or biochemical effect on insects. The expression systems may prove useful in further structural and functional characterization of these proteins.
Tyrosine-phosphorylated epidermal growth factor receptor and cellular p130 provide high affinity binding substrates to analyze Crk-phosphotyrosine-dependent interactions in vitro. (1992)

The genome of CT10 avian sarcoma virus encodes a 47-kDa fusion protein that consists of viral gag sequences fused to a cell-derived sequence containing SH2 and SH3 domains (v-crk). Genetic and biochemical evidence suggests that v-Crk can induce transformation of chicken embryo fibroblasts by influencing the activity of cellular proteins involved in growth regulation. In this report, we have developed an in vitro microtiter assay to study the binding of bacterially expressed glutathione S-transferase-fusion proteins of v-Crk and its cellular homolog, c-Crk, to the phosphorylated epidermal growth factor receptor (EGFR). Competitive binding data are presented that compare the abilities of heterologous glutathione S-transferase-fusion proteins containing GAPSH2[N], AblSH2, SrcSH2, and PLC-gamma SH2[N] sequences to inhibit Crk binding. Results indicate that both full-length Crk and GAPSH2[N] bind the phosphorylated EGFR with high affinity and can quantitatively compete the binding of each other by competitive enzyme-linked immunosorbent assay. Binding of full-length Crk or the isolated SH2 domains of GAP or Abl resulted in a significant protection of phosphorylated EGFR against dephosphorylation by cellular phosphatase activity, but did not appear to stimulate the intrinsic tyrosine kinase activity of the EGFR. To extend these findings to p130, the major phosphotyrosine-containing protein in CT10-transformed cells, we utilized a nitrocellulose filter binding assay. Results demonstrate high affinity binding of Crk toward denatured p130 and, as is the case for phosphorylated EGFR, Crk binding can partially protect p130 from phosphatase activity. However, no apparent competition of Crk binding was noted with heterologous SH2-containing proteins including GAPSH2[N], suggesting a possible specificity of Crk-p130 binding. These data are consistent with a direct role of SH2 in the modulation of cellular phosphotyrosine status in vivo.
Adverse Metabolic Effect of Omega-3 Fatty Acids in Non-Insulin-Dependent Diabetes Mellitus (1988)

Increased interest in using omega-3 fatty acids led us to examine their metabolic effects in six men with type II (non-insulin-dependent) diabetes mellitus. After 1 month of a diet supplemented with these fatty acids, the patients' fasting glucose rose from 13.1 +/- 1.3 to 15.3 +/- 1.3 mmol/L (P = 0.03) and glucose area during a mixed meal profile rose by 22% (P = 0.04). Basal hepatic glucose output rose from 97 +/- 9 to 122 +/- 8 mg/m2 . min (P = 0.004) but glucose disposal rates measured by euglycemic glucose clamp were unchanged. Fasting insulin levels were similar; peak insulin levels stimulated by meals or intravenous glucagon fell by 30% and 39%, respectively. Plasma and erythrocyte content of omega-3 fatty acid rose significantly. After omega-3 fatty acid withdrawal, fasting glucose returned to baseline. Omega-3 fatty acid treatment in type II diabetes leads to rapid but reversible metabolic deterioration, with elevated basal hepatic glucose output and impaired insulin secretion but unchanged glucose disposal rates. Caution should be used when recommending omega-3 fatty acids in type II diabetic persons.
How partnership works (2009)

Partnerships can achieve results, but they do not develop smoothly. Members must explore their differences before they can perform well together. Some agencies look inwards at their own priorities and expect their partners to follow them. This leads to a blend of co-operation and competition. Other organisations turn outwards and look for partners who can contribute to shared results. They see themselves as others see them. They do not look back to make sure that others are following. This leads to a blend of mutual respect and reciprocity which is as important for success as finely honed memoranda of understanding.
Loran-C Vehicle Tracking in Detroit's Public Safety Dispatch System (1989)

In 1928, the city of Detroit had the distinction of being the first city in the world to introduce police radios and two-way radio police dispatch. Sixty years later, another world first by the City of Detroit Police Department was announced by Mayor Coleman Young: the introduction of emergency vehicle tracking integrated with the “Enhanced 911” emergency dispatch system. This system is the most ambitious undertaking of its kind and incorporates many innovative features, including automatic tracking of the largest fleet of Loran-C equipped vehicles. A complete floor of the Detroit Police Headquarters has been renovated to provide the most advanced facility for public safety dispatch. This paper presents concepts and some details of the Automatic Vehicle Location System developed to complete the elements of the Detroit Public Safety Dispatch System.
A central hydrophobic domain of the hepatitis C virus NS4A protein is necessary and sufficient for the activation of the NS3 protease (1996)

The processing at the NS3/4A, NS4A/4B, NS4B/5A and NS5A/5B junctions in the non-structural region of the hepatitis C virus (HCV) polyprotein is performed by a viral serine protease activity contained within the N-terminal 180 amino acids of the NS3 protein. Full protease activity is only achieved upon the interaction of a region at the N terminus of NS3 with the NS4A protein, this region is also involved in the modulation of the protease activity. Using the rabbit reticulocyte expression system, we have defined the minimal domain of NS4A that is necessary to increase the cleavage efficiency of NS3. A synthetic peptide containing the same region, NS4A amino acids 21 to 32, stimulates the proteolytic activity of NS3 at all the trans-cleavage sites.
Improved seam carving for video retargeting (2008)

Video, like images, should support content aware resizing. We present video retargeting using an improved seam carving operator. Instead of removing 1D seams from 2D images we remove 2D seam manifolds from 3D space-time volumes. To achieve this we replace the dynamic programming method of seam carving with graph cuts that are suitable for 3D volumes. In the new formulation, a seam is given by a minimal cut in the graph and we show how to construct a graph such that the resulting cut is a valid seam. That is, the cut is monotonic and connected. In addition, we present a novel energy criterion that improves the visual quality of the retargeted images and videos. The original seam carving operator is focused on removing seams with the least amount of energy, ignoring energy that is introduced into the images and video by applying the operator. To counter this, the new criterion is looking forward in time - removing seams that introduce the least amount of energy into the retargeted result. We show how to encode the improved criterion into graph cuts (for images and video) as well as dynamic programming (for images). We apply our technique to images and videos and present results of various applications.
Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif (1996)

Relatively limited information about promoter structures in Corynebacterium glutamicum has been available until now. With the aim of isolating and characterizing such transcription initiation signals, random Sau3A fragments of C. glutamicum chromosomal DNA and of the corynebacterial phage phi GA1 were cloned into the promoter probe vector pEKplCm and selected for promoter activity by chloramphenicol resistance of transformed C. glutamicum cells. The nucleotide sequence of ten chromosomal and three phage fragments was determined and the transcriptional start (TS) sites were localized by primer extension analyses. Additionally, the promoters of five previously isolated C. glutamicum genes were cloned and mapped. All of the isolated promoters were also functional in the heterologous host Escherichia coli. A comparative analysis of the newly characterized promoter sequences together with published promoters from C. glutamicum revealed conserved sequences centred about 35 bp (ttGcca) and 10 bp (TA.aaT) upstream of the TS site. The position of these motifs and the motifs themselves are comparable to the -35 and -10 promoter consensus sequences of other Gram-positive and Gram-negative bacteria, indicating that they represent transcription initiation signals in C. glutamicum. However, the C. glutamicum consensus hexamer of the -35 region is much less conserved than in E. coli, Bacillus, Lactobacillus and Streptococcus.
Predominant role of endothelial nitric oxide synthase in vascular endothelial growth factor-induced angiogenesis and vascular permeability (2001)

Nitric oxide (NO) plays a critical role in vascular endothelial growth factor (VEGF)-induced angiogenesis and vascular hyperpermeability. However, the relative contribution of different NO synthase (NOS) isoforms to these processes is not known. Here, we evaluated the relative contributions of endothelial and inducible NOS (eNOS and iNOS, respectively) to angiogenesis and permeability of VEGF-induced angiogenic vessels. The contribution of eNOS was assessed by using an eNOS-deficient mouse, and iNOS contribution was assessed by using a selective inhibitor [l-N(6)-(1-iminoethyl) lysine, l-NIL] and an iNOS-deficient mouse. Angiogenesis was induced by VEGF in type I collagen gels placed in the mouse cranial window. Angiogenesis, vessel diameter, blood flow rate, and vascular permeability were proportional to NO levels measured with microelectrodes: Wild-type (WT) > or = WT with l-NIL or iNOS(-/-) > eNOS(-/-) > or = eNOS(-/-) with l-NIL. The role of NOS in VEGF-induced acute vascular permeability increase in quiescent vessels also was determined by using eNOS- and iNOS-deficient mice. VEGF superfusion significantly increased permeability in both WT and iNOS(-/-) mice but not in eNOS(-/-) mice. These findings suggest that eNOS plays a predominant role in VEGF-induced angiogenesis and vascular permeability. Thus, selective modulation of eNOS activity is a promising strategy for altering angiogenesis and vascular permeability in vivo.
Micron-gap ThermoPhotoVoltaics (MTPV) (2003)

This paper discusses advances made in the field of Micron-gap ThermoPhotoVoltaics (MTPV). Initial modeling has shown that MTPV may enable significant performance improvements relative to conventional far field TPV. These performance improvements include up to a 10x increase in power density, 30% to 35% fractional increase in conversion efficiency, or alternatively, reduced radiator temperature requirements to as low as 550 C. Recent experimental efforts aimed at supporting these predictions have successfully demonstrated that early current and voltage enhancements could be done repeatedly and at higher temperatures. More importantly, these efforts indicated that no unknown energy transfer process occurs reducing the potential utility of MTPV. Progress has been made by running tests with at least one of the following characteristics relative to the MTPV results reported in 2001: Tests at over twice the temperature (900 C); Tests at 50% smaller gaps (0.12 {micro}m); Tests with emitter areas from 4 to 100 times larger (16 mm{sup 2} to 4 cm{sup 2}); and Tests with over 20x reduction in parasitic spacer heat flow. Remaining fundamental challenges to realizing these improvements relative to the recent breakthroughs in conventional far field TPV include reengineering the photovoltaic (PV) diode, filter, and emitter system for MTPV and engineering devices and systems that can achieve submicron vacuum gaps between surfaces with large temperature differences.
The Very Low-density Lipoprotein (VLDL) Receptor: Characterization and Functions as a Peripheral Lipoprotein Receptor (2004)

The very low-density lipoprotein (VLDL) receptor is a member of the low-density lipoprotein (LDL) receptor family. In vitro and in vivo studies have shown that VLDL receptor binds triglyceride (TG)-rich lipoproteins but not LDL, and functions as a peripheral remnant lipoprotein receptor. VLDL receptor is expressed abundantly in fatty acid-active tissues (heart, skeletal muscle and fat), the brain and macrophages. It is likely that VLDL receptor functions in concert with lipoprotein lipase (LPL), which hydrolyses TG in VLDL and chylomicron. In contrast to the LDL receptor, VLDL receptor binds apolipoprotein (apo) E2/2 VLDL particles as well as apoE3/3 VLDL, and the expression is not down-regulated by intracellular lipoproteins. Recently, various functions of the VLDL receptor have been reported in lipoprotein metabolism, metabolic syndrome/atherosclerosis, cardiac fatty acid metabolism, neuronal migration and angiogenesis/tumor growth. Gene therapy of VLDL receptor into the liver showed a benefit effect for lipoprotein metabolism in both LDL receptor knockout and apoE mutant mice. Beyond its function as a peripheral lipoprotein receptor, possibilities of its physiological function have been extended to include signal transduction, angiogenesis and tumor growth.
Insect neuropeptides: Discovery and application in insect management (1993)

New approaches to the development of insect control agents have been revealed through the molecular description of neuropeptides, their biogenesis, action, and degradation. Prerequisite to the exploitation of a neuropeptide as a lead to control agent development is a thorough understanding of the biochemistry of the neuropeptide and appreciation of its physiological impact. Reliable bioassays must be coupled with advanced biochemical and molecular genetic technologies to overcome limitations imposed by the typically low endogenous levels of individual neuropeptides. Purification, amino acid sequencing, and gene cloning provide the molecular tools necessary for studies on neuropeptide synthesis, processing, secretion, receptor binding, and inactivation. Each of these areas consists of a number of amino acid sequence-, and enzyme-dependent steps which may be considered as targets for the development of highly specific control agents. These agents will include antagonist and superagonists, peptidomimetics, recombinant peptides delivered through the baculovirus technology, receptor blockers, and enzyme inhibitors.
Adult Adenovirus Infections: Loss of Orphaned Vaccines Precipitates Military Respiratory Disease Epidemics (2000)

Adenovirus vaccines have greatly reduced military respiratory disease morbidity since the 1970s. However, in 1995, for economic reasons, the sole manufacturer of these vaccines ceased production. A population-based adenovirus surveillance was established among trainees with acute respiratory illness at 4 US military training centers as the last stores of vaccines were depleted. From October 1996 to June 1998, 1814 (53.1%) of 3413 throat cultures for symptomatic trainees (78% men) yielded adenovirus. Adenovirus types 4, 7, 3, and 21 accounted for 57%, 25%, 9%, and 7% of the isolates, respectively. Unvaccinated trainees were much more likely than vaccinated trainees to be positive for types 4 or 7 (odds ratio [OR] p 28.1; 95% CI, 20.2-39.2). Two training centers experienced epidemics of respiratory disease affecting thousands of trainees when vaccines were not available. Until a new manufacturer is identified, the loss of orphaned adenovirus vaccines will result in thousands of additional preventable adenovirus infections.
NEUROGENIC INFLAMMATION AND MIGRAINE: IMPLICATIONS FOR THE THERAPEUTICS (2005)

Significant recent advances in molecular pharmacology have elucidated the molecular pathways involved in neurogenic inflammation (NI). The release of tachykinins and endothelin-3 (ET-3) from trigeminal neurons induces dural vascular permeability and vasodilatation via activation of tachykinin receptor 1 (Tacr1) and endothelin receptor type B (Ednrb) on endothelial cells. Endothelial cell receptor stimulation results in cellular contraction, leading to plasma protein extravasation (PPE), which is the most recognized physiological hallmark of NI, and nitric oxide-induced vasodilatation. By contrast, the release of calcitonin gene-related peptide (CGRP) from trigeminal neurons--also a key physiological component of NI--does not affect vascular permeability but does induce neurogenic vasodilatation (NV) via the direct, (i.e., endothelium-independent) relaxation of vascular smooth muscle. The molecular pharmacology of NI is discussed within the context of migraine research and assesses the putative role of the two key physiological components of NI (i.e., PPE and NV) in migraine pathophysiology. The data indicate that the PPE component of NI plays no significant role in migraine but that NV is likely to be involved in migraine pathophysiology.
anti-Selective Direct Asymmetric Mannich Reactions Catalyzed by Axially Chiral Amino Sulfonamide as an Organocatalyst (2005)

A direct asymmetric Mannich reaction using a novel axially chiral amino trifluoromethanesulfonamide (S)-3 has been developed in highly anti-selective and enantioselective manners. Thus, in the presence of a catalytic amount of (S)-3, the reactions between aldehydes and the alpha-imino ester 4 proceed smoothly to give the functional beta-amino aldehydes with significantly higher anti/syn ratio and enantioselectivity than previously possible.
A power quality monitoring system: a case study in DSP-based solutions for power electronics (2001)

Programmable digital signal processors (DSPs) are emerging as the processors of choice in monitoring and control of high-end power electronics systems. This paper adopts a case study approach to illustrate a development methodology for DSP-based solutions. The unique features of DSP chips that make them ideal for real-time applications are highlighted. Power electronics systems where DSPs have been used are indicated. A case study in which a DSP-based solution was developed for a power quality monitoring application is presented. Through the case study, the issues involved in adopting a system architecture, selecting a DSP, and developing software for an application are discussed. The methodology described in this paper presents broad guidelines which can be intelligently applied to develop DSP-based solutions to meet specific requirements.