gebhart/patrepeval huggingface dataset:
The primary structure of bovine cellular retinoic acid-binding protein. (1985)

The complete amino acid sequence of bovine adrenal gland cellular retinoic acid-binding protein (CRABP) has been determined. The primary structure was established by analyses of cyanogen bromide fragments and peptides obtained by trypsin and Staphylococcus aureus protease digestions. The polypeptide chain of bovine CRABP comprises 136 amino acid residues. From partial sequence information, CRABP has been shown to be homologous to cellular retinol-binding protein, myelin protein P2, and the fatty acid-binding Z-protein. A comparison of the complete amino acid sequences of the members of this protein family, which also includes the rat intestinal fatty acid-binding protein, shows that CRABP is more similar to cellular retinol-binding protein and protein P2 than to the fatty acid-binding proteins. All five proteins are very similar in their NH2-terminal regions, suggesting that this part is important for a property common to the members of this protein family. This is the first report of a complete amino acid sequence of a CRABP.
A novel leaky wave antenna for the base station in an innovative indoors cellular mobile communication system (2003)

The 8-slot novel leaky wave antenna showing a (34/spl deg//spl times/31/spl deg/) beamwidth at 2400 MHz has been designed and studied experimentally. The radiation patterns of the antenna are similar to that of a travelling wave antenna (Krauss 1988) which agree well with expected results and the directivity is equal to 16 dB. A front-to-back ratio of about 1O dB is realized, showing that the antenna is radiating effectively. The main characteristics of the antenna are low fabrication cost, low profile and it can be mass-produced.
Activation Tagging in Arabidopsis (2000)

Activation tagging using T-DNA vectors that contain multimerized transcriptional enhancers from the cauliflower mosaic virus (CaMV) 35S gene has been applied to Arabidopsis plants. New activation-tagging vectors that confer resistance to the antibiotic kanamycin or the herbicide glufosinate have been used to generate several tens of thousands of transformed plants. From these, over 30 dominant mutants with various phenotypes have been isolated. Analysis of a subset of mutants has shown that overexpressed genes are almost always found immediately adjacent to the inserted CaMV 35S enhancers, at distances ranging from 380 bp to 3.6 kb. In at least one case, the CaMV 35S enhancers led primarily to an enhancement of the endogenous expression pattern rather than to constitutive ectopic expression, suggesting that the CaMV 35S enhancers used here act differently than the complete CaMV 35S promoter. This has important implications for the spectrum of genes that will be discovered by this method.
Measuring the human factor of cyber security (2011)

This paper investigates new methods to measure, quantify and evaluate the security posture of human organizations especially within large corporations and government agencies. Computer security is not just about technology and systems. It is also about the people that use those systems and how their vulnerable behaviors can lead to exploitation. We focus on measuring enterprise-level susceptibility to phishing attacks. Results of experiments conducted at Columbia University and the system used to conduct the experiments are presented that show how the system can also be effective for training users. We include a description of follow-on work that has been proposed to DHS that aims to measure and improve the security posture of government departments and agencies, as well as for comparing security postures of individual agencies against one another.
Development of a Primary Tamarin Hepatocyte Culture System for GB Virus-B: a Surrogate Model for Hepatitis C Virus (2000)

GB virus-B (GBV-B) causes an acute hepatitis in tamarins characterized by increased alanine transaminase levels that quickly return to normal as the virus is cleared. Phylogenetically, GBV-B is the closest relative to hepatitis C virus (HCV), and thus GBV-B infection of tamarins represents a powerful surrogate model system for the study of HCV. In this study, the course of infection of GBV-B in tamarins was followed using a real-time 5' exonuclease (TaqMan) reverse transcription-PCR assay to determine the level of GBV-B in the serum. Peak viremia levels exceeded 10(9) genome equivalents/ml, followed by viral clearance within 14 to 16 weeks. Rechallenge of animals that had cleared infection resulted in viremia that was limited to 1 week, suggestive of a strong protective immune response. A robust tissue culture system for GBV-B was developed using primary cultures of tamarin hepatocytes. Hepatocytes obtained from a GBV-B-infected animal maintained high levels of cell-associated viral RNA and virion secretion for 42 days of culture. In vitro infection of normal hepatocytes resulted in rapid amplification of cell-associated viral RNA and secretion of up to 10(7) genome equivalents/ml of culture supernatant. In addition, infection could be monitored by immunofluorescence staining for GBV-B nonstructural NS3 protein. This model system overcomes many of the current obstacles to HCV research, including low levels of viral replication, lack of a small primate animal model, and lack of a reproducible tissue culture system.
Structural integrity of the nuclear matrix: Differential effects of thiol agents and metal chelators (1986)

Nuclear matrices, associated with over 80% of the chromosomal DNA, could be isolated from BHK nuclei by extraction with 2M-NaCl. The matrices were found to impose at least two levels of structural order upon nuclear DNA. From sedimentation studies it was inferred that metal depletion of the salt-extracted nuclei generated matrix structures, which sedimented at significantly lower rates than control matrices. Fluorescence microscopy revealed that the reduced sedimentation rate is a consequence of the increase in the radius of the DNA halo, i.e. the DNA loops emanating from the residual nucleus. Addition of Cu ions to nuclei prior to salt extraction was found to induce contraction of this DNA halo. These results indicate that Cu ions may play an important role in stabilizing one level of DNA folding. When metal depletion had been brought about by thiol agents, a second effect was observed to occur. Within 15 min, salt-extracted nuclei disintegrated, generating irregularly shaped, slowly sedimenting structures. Disintegration only occurred when the full complement of DNA was still attached to the nuclear matrices. Analysis by sodium dodecyl sulphate-polyacrylamide gel electrophoresis revealed that treatment with thiols did not detectably alter the polypeptide composition of DNA-depleted residual nuclei. Results of these experiments suggest that both metal-protein interactions and disulphide bonds are important in maintaining higher-order structure in the nucleus. A model to account for these observations is discussed.
Immunocytochemical localization of the cystic fibrosis gene product CFTR. (1991)

Antisera against two peptides, corresponding to different domains of the cystic fibrosis gene product CFTR, have been raised and extensively characterized. Both antisera recognize CFTR as a 165-kDa polypeptide in Western analysis of cells transfected with CFTR cDNA as well as in epithelial cell lines. The cell and tissue distribution of CFTR has been studied by immunocytochemistry. CFTR is abundant in epithelial cells, including those lining sweat ducts, small pancreatic ducts, and intestinal crypts. Unexpectedly, the level of CFTR in lung epithelia is relatively low, while it is abundant in the epithelia of kidney tubules. The protein appears to be restricted to the apical, rather than basolateral, regions of epithelial cells and at least a proportion is associated with the plasma membrane. The cell and tissue distributions of CFTR are consistent with a function for this protein as a chloride channel or as a regulator of channel activity.
Extracting delta for incremental data warehouse maintenance (2002)

This paper seeks to highlight an area important to commercial data warehouse deployments that has received limited research attention, namely, the extraction of changes to the data at the source systems. We refer to these changes as deltas. Extracting deltas from source systems is the first step in the incremental maintenance of data warehouses. A common assumption among current incremental maintenance methods is that deltas are somehow made available-normally in the form of differential files. Extraction of deltas from source systems is often not a straight forward process nor an efficient one. In this paper, we analyze how deltas can be extracted from large systems. We analyze delta extraction methods that are currently available, namely, time stamps, differential snapshots, triggers, and archive logs. We point out the strengths and weaknesses of each method through analysis and when appropriate through experimentation. We have been investigating the method called Op-Delta at Boeing that better suits delta extraction from large integrated systems. We discuss the benefits of Op-Delta, discuss how it could be implemented, and present comparative results from our experimentation.
Complement Activation following Optic Nerve Crush in the Adult Rat (2003)

Activation of the complement cascade following peripheral nerve axotomy and following traumatic brain injury has been demonstrated in previous studies. This study investigates the temporal pattern of microglia/macrophages and complement activation following axotomy of sensory CNS neurons, using a standardized experimental crush injury of the optic nerve in adult rats. Numerous ED1-labeled macrophages were found at the lesion site and distal to the injury at 7 days post injury (dpi). Complement C3-mRNA was upregulated 2-28 days post lesion, indicating local synthesis of complement in the optic nerve. Furthermore, increased immunoreactivity (IR) for the end product of the complement cascade, the membrane attack complex (MAC), was detected along disintegrating axons co-labeled with anti-neurofilament distal to the injury. Double-labeling for microglia show MAC-immunoreactivity expressed in their immediate vicinity, indicating a key role of microglia/macrophages in complement activation. The complement regulator Clusterin was upregulated in astrocytes at the lesion site as well as in the distal portion of the injured optic nerve, suggesting activation of a defense response to endogenous complement attack. A crush injury of the optic nerve leads to complement activation at the site of lesion and along the distal portion of the nerve, as well as upregulation of the complement inhibitor Clusterin at least in astrocytes. Reactive microglial cells seem to have a key role in complement activation as a local source of C3. We suggest that the balance between complement activation and their regulators may have impact on axonal degeneration following optic nerve injury.
Engineered antifouling microtopographies – effect of feature size, geometry, and roughness on settlement of zoospores of the green algaUlva (2007)

The effect of feature size, geometry, and roughness on the settlement of zoospores of the ship fouling alga Ulva was evaluated using engineered microtopographies in polydimethylsiloxane elastomer. The topographies studied were designed at a feature spacing of 2 microm and all significantly reduced spore settlement compared to a smooth surface. An indirect correlation between spore settlement and a newly described engineered roughness index (ERI) was identified. ERI is a dimensionless ratio based on Wenzel's roughness factor, depressed surface fraction, and the degree of freedom of spore movement. Uniform surfaces of either 2 mum diameter circular pillars (ERI=5.0) or 2 microm wide ridges (ERI=6.1) reduced settlement by 36% and 31%, respectively. A novel multi-feature topography consisting of 2 mum diameter circular pillars and 10 microm equilateral triangles (ERI=8.7) reduced spore settlement by 58%. The largest reduction in spore settlement, 77%, was obtained with the Sharklet AF topography (ERI=9.5).
Ion-sensitive field-effect transistors in standard CMOS fabricated by post processing (2002)

Highly integrated ion-sensitive field-effect transistor (ISFET) microsystems require the monolithic implementation of ISFETs, CMOS electronics, and additional sensors on the same chip. This paper presents new ISFETs in standard CMOS, fabricated by post-processing of a standard CMOS VLSI chip. Unlike CMOS compatible ISFETs fabricated in a dedicated process, the new sensors are directly combined with state-of-the-art CMOS electronics and are subject to continuous technology upgrading. The ISFETs presented include an intermediate gate formed by one or more conducting layers placed between the gate oxide and the sensing layer. The combination of the highly isolating gate oxide of the MOS with a leaky or conducting sensing layer allows the use of low temperature materials that do not damage the CMOS chip. The operation of ISFETs with an intermediate gate and sensing layers fabricated at low temperature is modeled. ISFETs with a linear pH response and drift as low as 0.3 mV/h are reported.
Strain-induced band gap shrinkage in Ge grown on Si substrate (2003)

Band gap shrinkage induced by tensile strain is shown for Ge directly grown on Si substrate. In Ge-on-Si pin diodes, photons having energy lower than the direct band gap of bulk Ge were efficiently detected. According to photoreflectance measurement, this property is due to band gap shrinkage. The origin of the shrinkage is not the Franz–Keldysh effect but rather tensile strain. It is discussed that the generation of such a tensile strain can be ascribed to the difference of thermal expansion between Ge and Si. Advantages of this tensile Ge for application to photodiode are also discussed.
Influence of External Stent Size on Early Medial and Neointimal Thickening in a Pig Model of Saphenous Vein Bypass Grafting (1996)

External stenting of saphenous vein bypass grafts reduces early intimal and medial hyperplasia. Oversized stents give equally profound suppression of intimal thickening, obviating the need for precise size matching with the graft and greatly simplifying the surgical procedure.
Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis (2002)

Previously, identification of promoters regulated by mammalian transcription factors has relied upon overexpression studies. Here we present the identification of a large set of promoters that are bound by E2F in physiological conditions. Probing a human CpG microarray with chromatin immunoprecipitated using an antibody to E2F4, we have identified 68 unique target loci; 15% are bidirectional promoters and 25% recruit E2F via a mechanism distinct from the defined consensus site. Interestingly, although E2F has been shown previously to regulate genes involved in cell cycle progression, many of the new E2F target genes encode proteins involved in DNA repair or recombination. We suggest that human CpG microarrays, in combination with chromatin immunoprecipitation, will allow rapid identification of target promoters for many mammalian transcription factors.
Phase Behavior and Component Partitioning in Low Water Content Amorphous Carbohydrates and Their Potential Impact on Encapsulation of Flavors (2000)

The compositions at which amorphous ethanol-maltose-water mixtures exhibit liquid-liquid separation have been determined in the temperature range from 20 to 80 degrees C. At water contents below approximately 20% w/w two phases were observed, with the maltose-rich phase slightly richer in water. Partition coefficients of organic nonelectrolytes ranging in hydrophobicity from 1, 2-ethanediol and 1,2-propanediol to benzyl alcohol and propyl acetate have been measured for octanol/sorbitol, benzyl alcohol/sorbitol, and 1-butanol/sorbitol mixtures. Linear correlations were found between the log partition coefficients in the various solvent systems. Replacing water with sorbitol results in more organic partitioning into the octanol. Replacing octanol with benzyl alcohol or 1-butanol also results in more organic partitioning into the hydrophobic phase. The results establish a relationship with partition coefficients for octanol/water mixtures, which are well studied experimentally and for which predictive approaches exist. The implications of these results for flavor retention and encapsulation are discussed.
Development of PCR‐SSOP for the identification of HLA‐A*02 subtypes and determination of HLA‐A*02 frequencies within different ethnic populations (1997)

A PCR-SSOP typing method, involving a single PCR amplification in conjunction with 19 digoxigenin labelled oligonucleotide probes, has been developed for the identification of 17 known HLA-A*02 alleles. The method has been applied to four populations (Northern Ireland, Singapore Chinese, Shetland Island and Mexican) and percentages of HLA-A*02 alleles determined within each population.
Synthesis and Biological Evaluation of Novel 2‐(1H‐Imidazol‐4‐yl)cyclopropane Carboxylic Acids: Key Intermediates for H3 Histamine Receptor Ligands. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Brief History of Antipyretic Therapy (2000)

Both external cooling and pharmacotherapy have been used to treat fever since time immemorial. In the past century such treatments have proliferated at an astonishing rate. The COX-2 inhibitors are the most recent additions to the antipyretic pharmacopoeia. Additional research is needed to determine whether they represent an important new chapter in antipyretic therapy's long history or, for that matter, if the benefits of any currently available treatment for fever outweigh its cost.
Comparative study of seven commercial yeast identification systems. (1999)

Auxacolor and Api Candida appeared to be the most useful systems for identification of germ tube negative yeast isolates in clinical microbiology laboratories, although one should be aware that several germ tube negative Candida species cannot be identified by these systems.
BDNF-induced TrkB activation down-regulates the K+–Cl− cotransporter KCC2 and impairs neuronal Cl− extrusion (2002)

Pathophysiological activity and various kinds of traumatic insults are known to have deleterious long-term effects on neuronal Cl- regulation, which can lead to a suppression of fast postsynaptic GABAergic responses. Brain-derived neurotrophic factor (BDNF) increases neuronal excitability through a conjunction of mechanisms that include regulation of the efficacy of GABAergic transmission. Here, we show that exposure of rat hippocampal slice cultures and acute slices to exogenous BDNF or neurotrophin-4 produces a TrkB-mediated fall in the neuron-specific K+-Cl- cotransporter KCC2 mRNA and protein, as well as a consequent impairment in neuronal Cl- extrusion capacity. After kindling-induced seizures in vivo, the expression of KCC2 is down-regulated in the mouse hippocampus with a spatiotemporal profile complementary to the up-regulation of TrkB and BDNF. The present data demonstrate a novel mechanism whereby BDNF/TrkB signaling suppresses chloride-dependent fast GABAergic inhibition, which most likely contributes to the well-known role of TrkB-activated signaling cascades in the induction and establishment of epileptic activity.
Development of Vascular Lesions in Insulin-treated Animals Fed a Normal Diet (1970)

Experiments were undertaken to study the role of hyperinsulinism in the pathogenesis of atheroma. Chickens injected with long-acting insulin for 19 weeks developed lipid containing lesions in their aortas. This provides further evidence in favour of the hypothesis that insulin and atheroma are causally related.
Conformational HER-2/neu B-cell Epitope Peptide Vaccine Designed to Incorporate Two Native Disulfide Bonds Enhances Tumor Cell Binding and Antitumor Activities (2004)

Cancer vaccines designed to elicit an antibody response that target antigenic sites on a tumor antigen must closely mimic the three-dimensional structure of the corresponding region on the antigen. We have designed a complex immunogen derived from the extracellular domain of human HER-2/neu-(626-649) that represents a three-dimensional epitope. We have successfully introduced two disulfide bonds into this sequence, thereby recapitulating the natural disulfide pairings observed in the native protein. To evaluate the immunogenicity of the doubly cyclized disulfide-linked peptide versus the free uncyclized peptide we examined the induction of antibody responses in both inbred and outbred mice strains, with both constructs eliciting high titered antibodies. The disulfide-paired specific antibodies exhibited enhanced cross-reactivity to HER-2/neu expressed on BT-474 cell line as determined by flow cytometry. The antitumor activities of the disulfidepaired specific antibodies did not improve the in vitro growth inhibition of human breast cancer cells overexpressing HER-2, but showed superior antitumor responses in the context of ADCC and interferon-gamma induction. Inbred mice (FVB/n) vaccinated with the disulfide-paired epitope exhibited a statistically significant reduction in the development of exogenously administered tumors in vivo compared with mice receiving either the free uncyclized or the promiscuous T-cell epitope (MVF) control peptide (p = 0.001). This study demonstrates the feasibility and importance of designing conformational epitopes that mimic the tertiary structure of the native protein for eliciting biologically relevant anti-tumor antibodies. Such approaches are a prerequisite to the design of effective peptide vaccines.
Ferritin and superoxide-dependent lipid peroxidation. (1985)

Ferritin was found to promote the peroxidation of phospholipid liposomes, as evidenced by malondialdehyde formation, when incubated with xanthine oxidase, xanthine, and ADP.Activity was inhibited by superoxide dkmutase but markedly stimulated by the addition of catalase.Xanthine oxidase-dependent iron release from ferritin, measured spectrophotometrically using the ferrous iron chelator 2,2'-dipyridyl, was also inhibited by superoxide dismutase, suggesting that superoxide can mediate the reductive release of iron from ferritin.Potassium superoxide in crown ether also promoted superoxide dismutase-inhibitable release of iron from ferritin.Catalase had little effect on the rate of iron release from ferritin; thus hydrogen peroxide appears to inhibit lipid peroxidation by preventing the formation of an initiating species rather than by inhibiting iron release from ferritin.EPR spin trapping with 5,5-dimethyl-l-pyrroline-N-oxide was used to observe free radical production in this system.Addition of ferritin to the xanthine oxidase system resulted in loss of the superoxide spin trap adduct suggesting an interaction between superoxide and ferritin.The resultant spectrum was that of a hydroxyl radical spin trap adduct which was abolished by the addition of catalase.These data suggest that ferritin may function in vivo as a source of iron for promotion of superoxide-dependent lipid peroxidation.Stimulation of lipid peroxidation but inhibition of hydroxyl radical formation by catalase suggests that, in this system, initiation is not via an iron-catalyzed Haber-Weiss reaction.Cellular damage resulting from ischemia (l), hyperoxia (2), redox cycling (3), and other oxygen-associated toxicities is often attributed to enhanced production of superoxide (0;) with biochemical alterations reported to include peroxidation of membrane phospholipids (4) and DNA degradation (5).However, in aqueous media 0, is relatively unreactive toward most organic compounds (6); thus its proposed deleterious effects may be the result of its participation in reactions leading to other more reactive species.Superoxide-dependent formation of more reactive radicals such as the hydroxyl radical (.OH) requires the presence of transition metal ions such as copper or iron (4).The most widely proposed mech-