gebhart/patrepeval huggingface dataset:
Relationship of arachidonic acid metabolizing enzyme expression in epithelial cancer cell lines to the growth effect of selective biochemical inhibitors. (1999)

Arachidonic acid (AA) metabolizing enzymes are emerging as significant mediators of growth stimulation for epithelial cells. The relative contribution of the various family members of AA metabolizing enzymes to epithelial cancer cell growth is not known. To study this question, we first analyzed a series of epithelial cancer cells to establish the relative frequency of expression for the various enzymes. We analyzed the expression of five AA metabolizing enzymes as well as 5-lipoxygenase activating protein (FLAP) in a panel of human epithelial cancer cell lines (n = 20) using reverse transcription-PCR. From this analysis, we found that cyclooxygenase-1 (COX-1), 5-lipoxygenase (5-LOX), and FLAP were universally expressed in all cancer cell lines tested. For the remaining enzymes, the expression of COX-2, 12-LOX, and 15-LOX varied among cell lines, 60, 35, and 90%, respectively. Although the pattern of expression varied among the different cell types, all of the enzymes were expressed in all major cancer histologies. Using a panel of selective biochemical AA metabolizing enzyme inhibitors, we then evaluated the effect of these agents on cell lines with known expression status for the AA metabolizing enzymes. For the enzymes that were not universally expressed, growth inhibition by selective biochemical inhibitors did not closely correlate with the expression status of specific enzymes (P > 0.05). For the universally expressed enzymes, the LOX inhibitors were more potent growth inhibitors than the COX inhibitors. The frequent expression of the AA metabolizing enzymes suggests that AA metabolism pathway may be modulated in response to xenobiotic exposure during carcinogenesis. Although establishing a priori AA metabolizing enzyme status was not consistently informative about what AA metabolizing enzyme inhibition would be most growth inhibitory, the frequent inhibition of many epithelial cancers by these biochemical inhibitors opens a new avenue for cancer therapy and intervention in carcinogenesis.
ChemInform Abstract: The First Analogues of LNA (Locked Nucleic Acids): Phosphorothioate‐LNA and 2′‐Thio‐LNA (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Characterization of Apolipoprotein J-Alzheimer's Aβ Interaction (1995)

The main component of Alzheimer's amyloid deposits, A beta, has been found also as a soluble (sA beta) normal constituent of biological fluids and cell culture supernatants. Whether or not sA beta is the immediate precursor of A beta, it is clear that peptides with the same amino acid sequence can have both fibrillar and non-fibrillar conformations. The interconversion mechanism from one form to another is presently under intensive investigation. We have previously described that (i) a synthetic peptide A beta 1-40 immobilized on affinity matrices was able to retrieve apolipoprotein J (apoJ) from plasma and cerebrospinal fluid; and (ii) the interaction of sA beta with apoJ occurs in vivo, as demonstrated by the ability of anti-apoJ to co-precipitate sA beta from normal cerebrospinal fluid. We have characterized the binding between A beta 1-40 and apoJ and found that the interaction is saturable, specific, and reversible. The dissociation constant of 2 x 10(-9) M is indicative of high affinity binding. The stoichiometry of the reaction is 1:1; apoJ has five times more affinity for fresh A beta 1-40 than for the aggregated peptide. Competitive inhibition studies carried out with apolipoprotein E (isoforms E2, E3, and E4), transthyretin, vitronectin, and alpha 1-antichymotrypsin indicate that the complex apoJ.A beta 1-40 cannot be dissociated by any of these competitors at physiologic concentrations. The data strongly suggest that apoJ plays an important role as a carrier protein for sA beta.
The Human Complement System in Health and Disease (1998)

Introduction and Historical Notes, Michael M. Frank Molecular Architecture Overview of the Complement System, John E. Volanakis Clq and Mannose-Binding Lectin, Kenneth B. M. Reid Complement Enzymes, John E. Volanakis and Gerard J. Arlaud The Chemistry and Biology of C3, C4, and C5, John D. Lambris, Arvind Sahu, and Rick A. Wetsel Proteins of the Membrane Attack Complex, Mnason E. Plumb and James M. Sodetz Regulatory Proteins of Complement, M. Kathryn Liszewski and John P. Atkinson Complement Receptors, Joseph M. Ahearn and Ariella M. Rosengard Phylogeny of the Complement System, Masaru Nonaka Regulation of Complement Protein Gene Expression, Harvey R. Colten and Gerard Garnier Biology Characterization of Complement Anaphylatoxins and Their Biological Responses, Julia A. Ember, Mark A. Jagels, and Tony E. Hugli Complement-Mediated Phagocytosis, Melvin Berger Cellular Responses to the Membrane Attack Complex, Carolyn Mold Regulation by Complement of Acquired Immunity, Michael C. Carroll and Douglas T. Fearon Endothelial Cell Responses to Complement Activation, Soheyla Saadi and Jeffrey L. Platt The Complement System in Reproduction, Teresa J. Oglesby Bacteria and Complement, Franz Petry and Michael Loos Complement and Viruses, Neil R. Cooper Complement and Disease Complement Deficiencies and Infection, Peter Densen Processing and Clearance of Immune Complexes by Complement and the Role of Complement in Immune Complex Diseases, Kevin A. Davies and Mark J. Walport C1 Inhibitor Gene and Hereditary Angioedema, Alvin E. Davis III Paroxysmal Nocturnal Hemoglobinuria and Complement, Wendell F. Rosse Complement in Central Nervous System Disorders, Moon L. Shin, Horea Rus, and Florin Niculescu Development of Clinically Useful Agents to Control Complement-Mediated Tissue Damage, Eric Wagner and Michael M. Frank Autoimmune Hemolytic Anemia, Alan D. Schreiber Complement and Glomerular Diseases, Clark West Role of Complement in Diseased and Normal Human Skin, Kim B. Yancey and Thomas J. Lawley Complement and Neuromuscular Diseases, Milan Basta and Marinos C. Dalakas
Direct electrophysiological measurement of human default network areas (2009)

Neuroimaging-based investigations in humans have established the existence of brain regions that are selectively metabolically active while resting. We report a population-scale neurophysiological measurement of activity in regions of this "default network," by recording high-frequency power (76-200 Hz) electrical potentials directly from these regions in three human subjects. A selective increase observed during only resting, when compared with activity, firmly establishes a neuronal origin for default network phenomena.
Decreased Resistance to Bacterial Infection and Granulocyte Defects in IAP-Deficient Mice (1996)

Granulocyte [polymorphonuclear leucocyte (PMN)] migration to sites of infection and subsequent activation is essential for host defense. Gene-targeted mice deficient for integrin-associated protein (IAP, also termed CD47) succumbed to Escherichia coli peritonitis at inoccula survived by heterozygous littermates. In vivo, they had an early defect in PMN accumulation at the site of infection. In vitro, IAP-/- PMNs were deficient in beta3 integrin-dependent ligand binding, activation of an oxidative burst, and Fc receptor-mediated phagocytosis. Thus, IAP plays a key role in host defense by participating both in PMN migration in response to bacterial infection and in PMN activation at extravascular sites.
Protein Kinase D2 Mediates Activation of Nuclear Factor κB by Bcr-Abl in Bcr-Abl+ Human Myeloid Leukemia Cells (2004)

The Bcr-Abl tyrosine kinase activates various signaling pathways including nuclear factor kappaB that mediate proliferation, transformation, and apoptosis resistance in Bcr-Abl(+) myeloid leukemia cells. Here we report that protein kinase (PK) D2, a serine threonine kinase of the PKD family, is a novel substrate of Bcr-Abl. PKD2 was found to be the major isoform of the PKD family expressed in chronic myeloid leukemia cells and is tyrosine phosphorylated by Bcr-Abl in its pleckstrin homology domain. A mutant that mimicks tyrosine phosphorylation of PKD2 in the pleckstrin homology domain activates nuclear factor kappaB independently of its catalytic activity. Furthermore, our data show that Bcr-Abl-induced activation of the nuclear factor kappaB cascade in LAMA84 cells is largely mediated by tyrosine-phosphorylated PKD2. These data present a novel mechanism of Bcr-Abl-induced nuclear factor kappaB activation in myeloid leukemia. Targeting PKD2 tyrosine phosphorylation, not its kinase activity, could be a novel therapeutic approach for the treatment of Bcr-Abl(+) myeloid leukemia.
Recombinant chimeric OKT3 scFv IgM antibodies mediate immune suppression while reducing T cell activationin vitro (2001)

OKT3, a mouse anti-human CD3 monoclonal antibody (mAb), is a potent immunosuppressive agent used in clinical transplantation to treat allograft rejection. Two major drawbacks of this therapy are the systemic release of several cytokines due to cross-linking mediated by the mAb between T cells and FcgammaR-bearing cells and the human anti-mouse antibody (HAMA) response. To overcome these side effects, three chimeric OKT3 single chain variable fragment (scFv) IgM antibodies, scOKT3-gamma DeltaIgM wt, scOKT3-gamma DeltaIgM C575S and scOKT3-gamma DeltaIgM VAEVD, were generated. They consist of the light and heavy variable binding domains of OKT3 mAb as well as the CH3 and CH4 domains of different human IgM variants linked with a human IgG3 hinge region to provide more flexibility and stability. Like the native IgM, scOKT3-gamma DeltaIgM antibodies are able to form polymeric structures, which lead to an increase in binding affinity and immunosuppressive potential compared with the parental OKT3 mAb. However, independently of their polymerization, all scOKT3-gamma DeltaIgM constructs do not induce any significant T cell proliferation or cytokine release (IL-2, TNF-alpha and IFN-gamma) in in vitro assays, while their CD3-modulating properties are retained. These results suggest that the use of scOKT3-gamma DeltaIgM antibodies may offer significant advantages over the OKT3 mAb in improving clinical immunosuppressive treatment.
Multispectral iris recognition analysis: Techniques and evaluation (2006)

This thesis explores the benefits of using multispectral iris information acquired using a narrow-band multispectral imaging system. Commercial iris recognition systems typically sense the iridal reflection pertaining to the near-infrared (IR) range of the electromagnetic spectrum. While near-infrared imaging does give a very reasonable image of the iris texture, it only exploits a narrow band of spectral information. By incorporating other wavelength ranges (infrared, red, green, blue) in iris recognition systems, the reflectance and absorbance properties of the iris tissue can be exploited to enhance recognition performance. Furthermore, the impact of eye color on iris matching performance can be determined. In this work, a multispectral iris image acquisition system was assembled in order to procure data from human subjects. Multispectral images pertaining to 70 different eyes (35 subjects) were acquired using this setup. Three different iris localization algorithms were developed in order to isolate the iris information from the acquired images. While the first technique relied on the evidence presented by a single spectral channel (viz., near-infrared), the other two techniques exploited the information represented in multiple channels. Experimental results confirm the benefits of utilizing multiple channel information for iris segmentation. Next, an image enhancement technique using the CIE L*a*b* histogram equalization method was designed to improve the quality of the multispectral images. Further, a novel encoding method based on normalized pixel intensities was developed to represent the segmented iris images. The proposed encoding algorithm, when used in conjunction with the traditional texture-based scheme, was observed to result in very good matching performance. The work also explored the matching interoperability of iris images across multiple channels. This thesis clearly asserts the benefits of multispectral iris processing, and provides a foundation for further research in this topic.
The GORE-TEX™ Expanded Polytetrafluoroethylene Prosthetic Ligament (1985)

For assessment of the accelerated in vitro and in vivo performance of the GORE-TEXTM Prosthetic Ligament, mechanical testing included cyclic creep and bending fatigue. Elongation of less than 3% after 20,000,000 cycles under load conditions was used to simulate the functioning human anterior cruciate ligament (ACL). Device tensile strength was 4830 N± 280 N. The device was tested in 17 sheep as an ACL replacement. No immobilization was used postoperation. Implant time ranged from 0 to 369 days. Joint stability was maintained in all animals. Fixation strength resulting from osseous ingrowth reached an average of 1380 N at a mean implant duration of 218 days. Clinical trials are underway at 15 centers in the United States. The indication for polytetrafluoroethylene (PTFE) reconstruction is chronic insufficiency of the ACL in knees worthy of salvage. The following evaluation of 130 patients at IS months or less shows improved stability in 129. Two grafts have been removed—one secondary to infection and the other as a result of improper placement.
Enhancement of Escherichia coli recA protein enzymic function by dATP (1989)

The Escherichia coli recA protein has been shown to hydrolyze several nucleoside triphosphates in the presence of ssDNA. The substitution of dATP for rATP has significant effects on various recA protein biochemical properties. In the presence of dATP, recA protein can invade more secondary structure in native ssDNA than it can in the presence of rATP. The dATP-recA protein complex can compete more effectively with the E. coli ssDNA binding protein (SSB) for ssDNA binding sites compared with the rATP-recA protein complex. Finally, the rate of dATP hydrolysis stimulated by dsDNA is greater than the rate of rATP hydrolysis. These effects, in turn, are observed as alterations in the recA protein catalyzed DNA strand exchange reaction. In the absence of SSB protein, the rate of joint molecule and product formation in the DNA strand exchange reaction is greater in the presence of dATP than in the presence of rATP. The rate of product formation in the dATP-dependent reaction is also faster than the rATP-dependent reaction when SSB protein is added to the ssDNA before recA protein; the rate of rATP-dependent product formation is inhibited 10-fold under these conditions. This nucleotide, dATP, was previously shown to induce an apparent affinity of recA protein for ssDNA which is higher than any other NTP. These results suggest that the observed enhancement of enzymatic activity may be related to the steady-state properties of the high-affinity ssDNA binding state of recA protein. In addition, the data suggest that recA protein functions in NTP hydrolysis as a dimer of protein filaments and that the binding of ssDNA to only one of the recA filaments is sufficient to activate all recA protein molecules in the dimeric filament. The implications of this finding to the enzymatic function of recA protein are discussed.
The GAMYB protein from barley interacts with the DOF transcription factor BPBF and activates endosperm‐specific genes during seed development (2002)

HvGAMYB, a MYB transcription factor previously shown to be expressed in barley aleurone cells in response to gibberellin during germination, also has an important role in gene regulation during endosperm development. The mRNA was detected early (10 DAF) in the seeds where it accumulates, not only in the aleurone layer, starchy endosperm, nucellar projection and vascular tissue, but also in the immature embryo as shown by in situ hybridization analysis. The HvGAMYB protein, expressed in bacteria, binds to oligonucleotides containing the 5'-TAACAAC-3' or 5'-CAACTAAC-3' sequences, derived from the promoter regions of the endosperm-specific genes Hor2 and Itr1, encoding a B-hordein and trypsin-inhibitor BTI-CMe, respectively. Binding is prevented when these motifs are mutated to 5'-TgACAAg-3' and 5'-CgACTgAC-3'. Transient expression experiments in co-bombarded developing endosperms demonstrate that HvGAMYB trans-activates transcription from native Hor2 and Itr1 promoters through binding to the intact motifs described above. Trans-activation of the Hor2 promoter also requires an intact prolamine box (PB). This suggests that HvGAMYB interacts in developing barley endosperms with the PB-binding factor BPBF, an endosperm-specific DOF transcriptional activator of the Hor2 gene. The in vivo interaction experiment between HvGAMYB and BPBF was done in the yeast two-hybrid system, where HvGAMYB potentiates the BPBF trans-activation capacity through interaction with its C-terminal domain.
The α3 laminin subunit, α6β4 and α3β1 integrin coordinately regulate wound healing in cultured epithelial cells and in the skin (1999)

Previously, we demonstrated that proteolytic processing within the globular domain of the alpha3 subunit of laminin-5 (LN5) converts LN5 from a cell motility-inducing factor to a protein complex that can trigger the formation of hemidesmosomes, certain cell-matrix attachment sites found in epithelial cells. We have prepared a monoclonal antibody (12C4) whose epitope is located toward the carboxy terminus of the globular domain of the alpha3 laminin subunit. This epitope is lost from the alpha3 subunit as a consequence of proteolytic processing. Antibody 12C4 stains throughout the matrix of cells that fail to process the alpha3 laminin subunit, but does not recognize the matrix of confluent cultures of MCF-10A cells, which efficiently process their alpha3 laminin chain. In subconfluent populations of MCF-10A cells, 12C4 only stains matrix deposited at the outer edges of cell colonies. In these cells, integrin alpha3beta1 occasionally colocalizes with the staining generated by the 12C4 antibody but alpha6beta4 integrin does not. In wounded MCF-10A cell cultures, the 12C4 antibody stains the extracellular matrix beneath those cells at the very edge of the cellular sheet that moves to cover the wound site. A similar phenomenon is observed in human skin wounds, since we also detect expression of the unprocessed alpha3 laminin subunit at the leading tip of the sheet of epidermal cells that epithelializes skin wounds in vivo. In addition, using alpha3 laminin subunit and integrin function-inhibiting antibodies, we provide evidence that LN5 and its two integrin receptors (alpha6beta4 and alpha3beta1) appear necessary for wound healing to occur in MCF-10A cell culture wounds. We propose a model for healing of wounded epithelial tissues based on these results.
The Development of Synthetic Vaccines (1981)

Technology is now available for synthesis of vaccines derived from short amino acid sequences on the surface of a virus or other pathogen. Such small peptide sequences are capable of “recognizing” the entire pathogen and of stimulating effective antibody production. These synthetic vaccines are potentially “medically ideal” agents, whose clinical applicability is now being explored.
Secure fuzzy vault based fingerprint verification system (2005)

This paper describes a secure fingerprint verification system based on the fuzzy vault scheme, where the sensitive biometric template is not stored, but a transformed version. We propose an adaptive alignment technique to reach the most reliable reference point, and a methodology to construct a set of rotation and shifting invariant features, acting as the lock set for the fuzzy vault. We investigate the parameters of the fuzzy vault and the number of the templates needed to obtain a reliable reference point, such that a high unlock complexity for attackers with an acceptable unlock rate for the legal users is achieved.
EVALUATION OF SYNTHETIC INORGANIC ION EXCHANGERS FOR CESIUM AND STRONTIUM REMOVAL FROM CONTAMINATED GROUNDWATER AND WASTEWATER (1997)

ABSTRACT The ion exchange testing of 30 synthetic adsorbents including layered and framework polyvalent metal silicates and phosphates, as well as amorphous exchangers was carried out. Their selectivity to alkali and alkaline earth metal cations in individual and complex solutions was determined. Several exchangers were found to have high selectivity for cesium and strontium. These exchangers are sodium phlogopite, layered sodium titanium silicate Na2TiSi2O7·2H2O, framework niobium (Na2Nb4Si2O15·4H2O, tentative formula), zirconium (Na2ZrSi3O9·H2O) and titanium (Na2Ti2SiO7·2H2O) silicates, and a layered δ-tin phosphate (Sn(HPO4)·2H2O). For all these materials cesium and strontium ion exchange capacities as a function of pH were determined. The effect of sodium, magnesium and calcium on Cs− and Sr2− ions sorption was also studied over the concentration range 0.005 M - 1 0 M and the explanations for the phenomena observed were proposed based on the knowledge of the crystal structure of the exchangers. Testing of the most promising exchangers for selective cesium and strontium recovery from ground water simulant in batch regime was carried out.
Algorithmic design of self-folding polyhedra (2011)

Self-assembly has emerged as a paradigm for highly parallel fabrication of complex three-dimensional structures. However, there are few principles that guide a priori design, yield, and defect tolerance of self-assembling structures. We examine with experiment and theory the geometric principles that underlie self-folding of submillimeter-scale higher polyhedra from two-dimensional nets. In particular, we computationally search for nets within a large set of possibilities and then test these nets experimentally. Our main findings are that (i) compactness is a simple and effective design principle for maximizing the yield of self-folding polyhedra; and (ii) shortest paths from 2D nets to 3D polyhedra in the configuration space are important for rationalizing experimentally observed folding pathways. Our work provides a model problem amenable to experimental and theoretical analysis of design principles and pathways in self-assembly.
Isolation and Characterization of the Saccharomyces cerevisiae DPP1 Gene Encoding Diacylglycerol Pyrophosphate Phosphatase (1998)

Diacylglycerol pyrophosphate (DGPP) is involved in a putative novel lipid signaling pathway. DGPP phosphatase (DGPP phosphohydrolase) is a membrane-associated 34-kDa enzyme from Saccharomyces cerevisiae which catalyzes the dephosphorylation of DGPP to yield phosphatidate (PA) and then catalyzes the dephosphorylation of PA to yield diacylglycerol. Amino acid sequence information derived from DGPP phosphatase was used to identify and isolate the DPP1 (diacylglycerol pyrophosphate phosphatase) gene encoding the enzyme. Multicopy plasmids containing the DPP1 gene directed a 10-fold overexpression of DGPP phosphatase activity in S. cerevisiae. The heterologous expression of the S. cerevisiae DPP1 gene in Sf-9 insect cells resulted in a 500-fold overexpression of DGPP phosphatase activity over that expressed in wild-type S. cerevisiae. DGPP phosphatase possesses a Mg2+-independent PA phosphatase activity, and its expression correlated with the overexpression of DGPP phosphatase activity in S. cerevisiae and in insect cells. DGPP phosphatase was predicted to be an integral membrane protein with six transmembrane-spanning domains. The enzyme contains a novel phosphatase sequence motif found in a superfamily of phosphatases. A dpp1Delta mutant was constructed by deletion of the chromosomal copy of the DPP1 gene. The dpp1Delta mutant was viable and did not exhibit any obvious growth defects. The mutant was devoid of DGPP phosphatase activity and accumulated (4-fold) DGPP. Analysis of the mutant showed that the DPP1 gene was not responsible for all of the Mg2+-independent PA phosphatase activity in S. cerevisiae.