gebhart/patrepeval huggingface dataset:
Interaction of calcitonin-gene-related peptide with its receptors (2002)

The receptor for calcitonin-gene-related peptide (CGRP) is a heterodimer formed by calcitonin-receptor-like receptor (CRLR), a type II (family B) G-protein-coupled receptor, and receptor-activity-modifying protein 1 (RAMP1), a single-membrane-pass protein. It is likely that the first seven or so amino acids of CGRP (which form a disulphide-bonded loop) interact with the transmembrane domain of CRLR to cause receptor activation. The rest of the CGRP molecule falls into three domains. Residues 28-37 and 8-18 are normally required for high-affinity binding, while residues 19-27 form a hinge region. The 28-37 region is almost certainly in direct contact with the receptor; 8-18 may make additional receptor contacts or may stabilize an appropriate conformation of 28-37. It is likely that these regions of CGRP interact both with CRLR and with the extracellular domain of RAMP1.
Functions of the Membrane-Associated and Cytoplasmic Malate Dehydrogenases in the Citric Acid Cycle of Escherichia coli (2000)

Oxidation of malate to oxaloacetate in Escherichia coli can be catalyzed by two enzymes: the well-known NAD-dependent malate dehydrogenase (MDH; EC 1.1.1.37) and the membrane-associated malate:quinone-oxidoreductase (MQO; EC 1.1.99.16), encoded by the gene mqo (previously called yojH). Expression of the mqo gene and, consequently, MQO activity are regulated by carbon and energy source for growth. In batch cultures, MQO activity was highest during exponential growth and decreased sharply after onset of the stationary phase. Experiments with the beta-galactosidase reporter fused to the promoter of the mqo gene indicate that its transcription is regulated by the ArcA-ArcB two-component system. In contrast to earlier reports, MDH did not repress mqo expression. On the contrary, MQO and MDH are active at the same time in E. coli. For Corynebacterium glutamicum, it was found that MQO is the principal enzyme catalyzing the oxidation of malate to oxaloacetate. These observations justified a reinvestigation of the roles of MDH and MQO in the citric acid cycle of E. coli. In this organism, a defined deletion of the mdh gene led to severely decreased rates of growth on several substrates. Deletion of the mqo gene did not produce a distinguishable effect on the growth rate, nor did it affect the fitness of the organism in competition with the wild type. To investigate whether in an mqo mutant the conversion of malate to oxaloacetate could have been taken over by a bypass route via malic enzyme, phosphoenolpyruvate synthase, and phosphenolpyruvate carboxylase, deletion mutants of the malic enzyme genes sfcA and b2463 (coding for EC 1.1.1.38 and EC 1.1.1.40, respectively) and of the phosphoenolpyruvate synthase (EC 2.7.9.2) gene pps were created. They were introduced separately or together with the deletion of mqo. These studies did not reveal a significant role for MQO in malate oxidation in wild-type E. coli. However, comparing growth of the mdh single mutant to that of the double mutant containing mdh and mqo deletions did indicate that MQO partly takes over the function of MDH in an mdh mutant.
Identification of Cell-Active Lysine Specific Demethylase 1-Selective Inhibitors (2009)

Lysine specific demethylase 1 (LSD1) plays a key role in the regulation of gene expression by removing the methyl groups from methylated Lys4 of histone H3 (H3K4). Here we report the identification of the first small-molecule LSD1-selective inhibitors. These inhibitors show in vivo H3K4-methylating activity and antiproliferative activity and should be useful as lead structures for anticancer drugs and as tools for studying the biological roles of LSD1.
FLT4, a novel class III receptor tyrosine kinase in chromosome 5q33-qter. (1992)

The receptors for at least two hematopoietic growth factors, namely the stem cell factor and colony-stimulating factor 1, belong to class III receptor tyrosine kinases. Here we describe cloning of a partial complementary DNA for FLT4, an additional member of this gene family from human leukemia cells. The FLT4 tyrosine kinase domain is 79% homologous with the previously cloned FLT1 (M. Shibuya et al., Oncogene, 5: 519-524, 1990) tyrosine kinase and maps to the chromosomal region 5q33-qter. We have found FLT4 expression in human placenta, lung, heart, and kidney, whereas the pancreas and brain appeared to contain very little if any FLT4 RNA. The results suggest that FLT4 functions in multiple adult tissues.
Autonomous generation of complete 3D object models using next best view manipulation planning (2011)

Recognizing and manipulating objects is an important task for mobile robots performing useful services in everyday environments. In this paper, we develop a system that enables a robot to grasp an object and to move it in front of its depth camera so as to build a 3D surface model of the object. We derive an information gain based variant of the next best view algorithm in order to determine how the manipulator should move the object in front of the camera. By considering occlusions caused by the robot manipulator, our technique also determines when and how the robot should re-grasp the object in order to build a complete model.
SHIELD: Scalable Homomorphic Implementation of Encrypted Data-Classifiers (2015)

Homomorphic encryption (HE) systems enable computations on encrypted data, without decrypting and without knowledge of the secret key. In this work, we describe an optimized Ring Learning With Errors (RLWE) based implementation of a variant of the HE system recently proposed by Gentry, Sahai and Waters (GSW). Although this system was widely believed to be less efficient than its contemporaries, we demonstrate quite the opposite behavior for a large class of applications. We first highlight and carefully exploit the algebraic features of the system to achieve significant speedup over the state-of-the-art HE implementation, namely the IBM homomorphic encryption library (HElib). We introduce several optimizations on top of our HE implementation, and use the resulting scheme to construct a homomorphic Bayesian spam filter, secure multiple keyword search, and a homomorphic evaluator for binary decision trees. Our results show a factor of <inline-formula><tex-math notation="LaTeX">$10\times$</tex-math></inline-formula> improvement in performance (under the same security settings and CPU platforms) compared to IBM HElib for these applications. Our system is built to be easily portable to GPUs (unlike IBM HElib) which results in an additional speedup of up to a factor of <inline-formula> <tex-math notation="LaTeX">$103.5\times$</tex-math></inline-formula> to offer an overall speedup of <inline-formula><tex-math notation="LaTeX"> $1{,}035\times$</tex-math> </inline-formula> .
Migrating a CISC computer family onto RISC via object code translation (1992)

article Free Access Share on Migrating a CISC computer family onto RISC via object code translation Authors: Kristy Andrews View Profile , Duane Sand View Profile Authors Info & Claims ACM SIGPLAN NoticesVolume 27Issue 9Sept. 1992 pp 213–222https://doi.org/10.1145/143371.143520Online:01 September 1992Publication History 44citation937DownloadsMetricsTotal Citations44Total Downloads937Last 12 Months19Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Recombinant Leishmania Hsp90 and Hsp70 are recognized by sera from visceral leishmaniasis patients but not Chagas' disease patients (1992)

Approximately 70% of the cDNA clones identified by immunoscreening Leishmania donovani expression libraries with serum from a patient with visceral leishmaniasis (kala-azar) were found to encode the highly conserved Hsp90 and Hsp70 members of the heat shock protein family. Recombinant fusion proteins containing the C-terminal portions of L. donovani Hsp90 and Hsp70 were used as target antigens in enzyme-linked immunosorbent assays of various sera. Sera from four patients with visceral leishmaniasis recognized recombinant Leishmania Hsp90 and Hsp70, while sera from seven patients with Chagas' disease did not, despite the fact that Trypanosoma cruzi Hsp90 and Hsp70 share more than 80% amino acid identity with their counterparts in Leishmania spp. Thus, Leishmania Hsp90 and Hsp70 elicit strong humoral responses and are potential candidates for specific serodiagnostic assays capable of distinguishing between L. donovani and T. cruzi infections.
Detection of the optic disc in images of the retina using the Hough transform (2008)

We propose a method to locate automatically the optic disc (OD) in fundus images of the retina. Based on the properties of the OD, our proposed method includes edge detection using the Sobel or the Canny method, and detection of circles using the Hough transform. The Hough transform assists in the detection of the center and radius of a circle that approximates the margin of the OD. Based on the feature that the OD is one of the bright areas in a fundus image, potential circles detected by the Hough transform are analyzed using intensity. Forty images of the retina from the DRIVE database were used to evaluate the performance of the proposed method. The success rates including both good and acceptable detections were 92.50% using the Sobel operators and 80% using the Canny edge detector.
Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-Å resolution (1997)

The crystal structure of the tetrameric DNA-binding domain of the single-stranded DNA binding protein from Escherichia coli was determined at a resolution of 2.9 A using multiwavelength anomalous dispersion. Each monomer in the tetramer is topologically similar to an oligomer-binding fold. Two monomers each contribute three beta-strands to a single six-stranded beta-sheet to form a dimer. Two dimer-dimer interfaces are observed within the crystal. One of these stabilizes the tetramer in solution. The other interface promotes a superhelical structure within the crystal that may reflect tetramer-tetramer interactions involved in the positive cooperative binding of the single-stranded DNA-binding protein to single-stranded DNA.
Bulk and Interfacial Studies of a New and Versatile Semifluorinated Lyotropic Liquid Crystalline Polymer (2001)

This study introduces the phase diagram and interfacial characteristics of a novel lyotropic polymeric liquid crystal. The polymer consists of an α-methylstilbene mesogenic group bridged by a low interfacial energy perfluorocyclobutyl ring via flexible aryl ether linkages. The polymer, obtained by thermal cyclopolymerization of trifluorovinyl ether monomers, forms lyotropic lamellar mesophases over a wide range of temperatures and molecular weights. Mesophase behavior probed by optical microscopy, AFM, NMR, and X-ray scattering is detailed. The lamellae consist of longer chains, immersed in a solvent of smaller chains. The interfacial characteristics of these lyomesophases are affected by the low surface energy moiety. At the interface with glass, homeotropic alignment is observed. When cast into thin films, an additional periodicity on the nanometer scale has been detected. Thin films consist of spontaneously oriented bundles with characteristic length scale on 50 nm.
Oral Microbes, Biofilms and Their Role in Periodontal and Peri-Implant Diseases (2018)

Despite many discoveries over the past 20 years regarding the etio-pathogenesis of periodontal and peri-implant diseases, as well as significant advances in our understanding of microbial biofilms, the incidence of these pathologies still continues to rise. This review presents a general overview of the main protagonists and phenomena involved in oral health and disease. A special emphasis on the role of certain keystone pathogens in periodontitis and peri-implantitis is underlined. Their capacity to bring a dysregulation of the homeostasis with their host and the microbial biofilm lifestyle are also discussed. Finally, the current treatment principles of periodontitis and peri-implantitis are presented and their limits exposed. This leads to realize that new strategies must be developed and studied to overcome the shortcomings of existing approaches.
Glycoprotein Nonmetastatic Melanoma Protein B, a Potential Molecular Therapeutic Target in Patients with Glioblastoma Multiforme (2006)

Increased mRNA and protein levels in GBM patient biopsy samples correlated with higher survival risk; as a detectable surface membrane protein in glioma cells, the data indicate that GPNMB is a potentially useful tumor-associated antigen and prognostic predictor for therapeutic approaches with malignant gliomas or any malignant tumor that expresses GPNMB.
Potential antitumor agents. 29. Quantitative structure-activity relationships for the antileukemic bisquaternary ammonium heterocycles (1979)

Quantitative relationships between physicochemical drug properties and antileukemic (L1210) efficacy have been examined for a series of bisquaternary ammonium heterocycles employing multiple variable regression analysis. Three measures of biologic response were examined: ILSmax, the percentage increase in mean life span of leukemic animals at the LD10 dose; D40, the drug dose necessary to provide 40% increase in life span; and CI (=LD 10/D40), the chemotherapeutic index. A cross correlation matrix between these three measures and the LD10 values demonstrates ILSmax and CI to be independent of toxicity. D40 is highly inversely correlated with LD10 and positively correlated with ILSmax, suggesting that this parameter measures a composite of both drug selectivity and toxicity. Superior regression equations resulted at all stages employing ILSmax as a measure of antitumor selectivity. Acceptable equations modeling LD10 could not be obtained. There was a parabolic relationship between agent lipophilic-hydrophilic balance, measured as chromatographic Rm values, and ILSmax. To reduce residual variance in the L1210 screening data, not accepted by this parabolic equation, measures of agent-DNA interaction were investigated as possible indices of site fit. Relative levels of drug-DNA interaction were obtained by spectrofluorimetric quantitation of drug displacement of DNA-bound ethidium. Addition to regression equations of agent C50 values for calf thymus DNA, those micromolar drug concentrations necessary to displace 50% of the ethidium bound to that DNA, provided a significant reduction in the screening data variance. C50 values for drug interactions with poly[d(A-T)] and poly[d(G-C)] were also investigated as possible indicators of drug selectivity towards different DNA sites. Marked differences were observed in the C50 values for the two synthetic nucleic acids, with those for calf thymus DNA and poly[d(G-C)] proving highly covariant. A regression equation containing a positive term in C50[poly[d(G-C)]] and a negative term in C50-[poly[d(A-T)]] provided the greatest acceptance of the variation in the biologic data. The term in C50[poly[d(A-T)]] is the single most important equation term, alone accounting for 35% of the variance in the data. This best equation provides both an adequate summary of the L1210 screening data for the 174 active compounds considered and a physical explanation for the antitumor selectivity for these agents. The major factor influencing antitumor selectivity in these drugs is their ability to distinguish alternating adenine-thymine sequences in DNA.
Robust Salient Motion Detection with Complex Background for Real-Time Video Surveillance (2005)

Moving object detection is very important for video surveillance. In many environments, motion maybe either interesting (salient) motion (e.g., a person) or uninteresting motion (e.g., swaying branches.) In this paper, we propose a new real-time algorithm to detect salient motion in complex environments by combining temporal difference imaging and a temporal filtered motion field. We assume that the object with salient motion moves in a consistent direction for a period of time. No prior knowledge about object size and shape is necessary. Compared to background subtraction methods, our method does NOT need to learn the background model from hundreds of images and can handle quick image variations; e.g., a light being turned on or off. The average speed of our method is about 50fps on images at size 160x120 in 1GB Pentium III machines. The effectiveness of the proposed algorithm to robust detect salient motion is demonstrated for a variety of real environments with distracting motions such as lighting changes, swaying branches, rippling water, waterfall, and fountains.
Microstructured fibers and their applications (2005)

We present an overview of the photonic crystal fiber technology and the current status. We report on the latest fiber developments within respectively large mode area fibers, active double clad fibers, highly nonlinear fibers and hollow core fibers and we present application results with these types of fibers. Special focus is given to active photonic crystal fibers for high power lasers and amplifiers. We describe rod-type fibers for which a record-high power extraction of 250W/m is achieved, high power CW fibers for which a record-high power level of 1525 W is achieved and we present multicore fiber results. Finally, we illustrate how the fibers can be integrated with other fiber components to form an all-fiber, alignment-free, high-power fiber laser subassembly.
Interaction of silver atoms with iridium and with a two-dimensional graphite film on iridium: Adsorption, desorption, and dissolution (2004)

The initial stages in the interaction of silver with the (111)Ir surface and with a two-dimensional graphite film (2D GF) on (111)Ir were studied by high-resolution electron Auger spectroscopy in ultrahigh vacuum. The growth mechanisms of silver films and the desorption fluxes of Ag atoms were determined, and their desorption energies estimated. It was found that the Ag desorption fluxes from a 2D GF on Ir and from a thick silver film on the pure metal are similar and considerably (an order of magnitude) smaller than the sublimation fluxes from bulk silver at the same temperatures. The activation energy for desorption from a submonolayer film varies from 3.2 eV for coverage θ=1 to 3.7 eV at θ ∼ 0. It was shown that silver atoms do not penetrate into the substrate bulk throughout the temperature range covered (300–1800 K).
Nordihydroguairetic Acid, a Lignin, Prevents Oxidative Stress and the Development of Diabetic Nephropathy in Rats (2004)

Recent evidences indicate a pivotal role of reactive oxygen species in etiology of diabetic nephropathy, an important microvascular complication of diabetes mellitus. Moreover, oxidative stress leads to an increased production of lipoxygenase derivatives which also play a role in diabetic nephropathy. The present study was thus designed to examine the effect of an antioxidant and a lipoxygenase inhibitor, nordihydroguairetic acid (NDGA), on renal function and oxidative stress in streptozotocin (STZ)-induced diabetic rats. Diabetes was induced by a single intraperitoneal injection of streptozotocin (65 mg/kg) in rats. After the 4th week of STZ injection, NDGA (5 and 10 mg/kg) was given subcutaneously (s.c.) for another 4 weeks to both control and diabetic rats. At the end of the 8th week, diabetic rats exhibited renal dysfunction as evidenced by reduced creatinine and urea clearance along with enhanced albumin excretion rate as compared with control rats. Biochemical analysis of kidneys revealed a marked increase in oxidative stress demonstrated by increased lipid peroxidation and decreased activities of key antioxidant enzymes, glutathione (GSH), superoxide dismutase (SOD) and catalase in diabetic rats. Chronic treatment with NDGA in diabetic rats significantly prevented both renal dysfunction and oxidative stress as compared with vehicle-treated diabetic rats. The kidneys of diabetic rats showed morphological changes such as hyaline casts, glomerular thickening and moderate interstitial fibrosis and arteriolopathy, whereas NDGA administration in diabetic rats markedly prevented renal morphological alterations. These results emphasize the role of oxidative stress in the pathophysiology of diabetic nephropathy and point towards the potential of NDGA as a complementary therapy for the prevention/treatment of diabetic nephropathy.
Ultrathin polymer coatings by complexation of polyelectrolytes at interfaces: suitable materials, structure and properties (2000)

The article presents the state-of-the-art of alternating physisorption of oppositely charged polyelectrolytes, the so-called “layer-by-layer” method or “electrostatic self-assembly” (ESA), for the preparation of thin polymer coatings. In comparison to other, more established self-organization techniques, this recent method is distinguished by its simplicity, versatility, and speed. In particular, the tendency for self-healing is unique. Emphasis is given to the role of the molecular structure of the polyelectrolytes, and to the nature of the support. Also, various parameters for the preparation of multilayer films are highlighted, which are very important due to the kinetic control of the build-up process. The structure of the resulting coatings, their quality and stability, chemical reactions in the films, and potential applications are discussed.
Clinical Significance of Atypical Glandular Cells on Cervical Cytology (2006)

Histologic diagnosis showed that 29.0% of these Pap tests had findings requiring follow-up or therapeutic intervention, including a 5.2% rate of malignancy. Based on these findings, 99.6% of the diagnoses are within the region of surveillance when AGUS Pap tests are evaluated with colposcopy and directed biopsy, endocervical curettage, an endometrial biopsy in patients with risk factors for endometrial cancer, and pelvic examination.