gebhart/patrepeval huggingface dataset:
Sequence-specific interaction between S1F, a spinach nuclear factor, and a negative cis-element conserved in plastid-related genes. (1992)

The nuclear gene rps1 coding for the spinach plastid ribosomal protein CS1 exhibits both a constitutive and leaf-specific expression pattern. In contrast to other chloroplast-related genes like rbcS and cab, the leaf induction of rps1 expression is light-independent. These unique features of rps1 expression provide good models to study the mechanisms regulating plastid development and differentiation in higher plants. We report on the identification of a spinach leaf nuclear factor, designated S1F, interacting with the rps1 promoter. The S1F binding site is conserved in the promoter region of many plastid-related genes, including rbcS, cab, and rpl21. A binding activity similar to S1F was detected in nuclear extract from dark-grown de-differentiated soybean suspension cells. Through site-specific mutagenesis and transient expression in soybean cell protoplasts, we show that the S1F binding site is a negative element down-regulating the promoter activity of rps1. A ligated tetramer of S1F site was able to repress activity of the cauliflower mosaic virus 35 S promoter extending the negative function of the S1F binding site on promoter activity.
Ionized physical vapor deposition of titanium nitride: Plasma and film characterization (2002)

The ionized physical vapor deposition of titanium nitride is experimentally investigated in terms of both plasma characteristics and TiN material properties. The vibrational and translational gas temperatures of N2 molecules are determined using optical emission spectroscopy by fitting the intensities of vibrational transitions to the nonequilibrium Treanor distribution. The gas temperature is typically 720 K at 15 mTorr. The dissociation of nitrogen is determined using mass spectrometry and found to increase with plasma power from 10% to 30% as the power is increased from 750 to 1500 W. From this data, it is calculated that the density of atomic nitrogen in the inductively coupled plasma source is the order of 1012 cm−3. Langmuir probe measurements indicate that the electron temperature is 1.6–2.0 eV and the ion density is (2–6)×1011 cm−3. Rutherford backscattering spectroscopy (RBS) shows that the TiNx films have increasing nitrogen composition (0.26&amp;lt;x&amp;lt;1.5) as the nitrogen content increases from 2% to 9% in the Ar/N2 plasma. The flux of nitrogen atoms from the plasma, as determined from the measured gas temperature and dissociation, is compared with the flux of nitrogen that is incorporated in the film according to RBS. The ratio of these two fluxes gives an upper-bound for the sticking coefficient of atomic N on TiNx, which is ∼0.1 for titanium-rich films and ∼0.003 for nitrogen-rich films.
The Cys-Rich Region of Hepatitis A Virus Cellular Receptor 1 Is Required for Binding of Hepatitis A Virus and Protective Monoclonal Antibody 190/4 (1998)

The hepatitis A virus cellular receptor 1 (HAVcr-1) cDNA codes for a class I integral membrane glycoprotein, termed havcr-1, of unknown natural function which serves as an African green monkey kidney (AGMK) cell receptor for HAV. The extracellular domain of havcr-1 has an N-terminal Cys-rich region that displays homology with sequences of members of the immunoglobulin superfamily, followed by a Thr/Ser/Pro (TSP)-rich region characteristic of mucin-like O-glycosylated proteins. The havcr-1 glycoprotein contains four putative N-glycosylation sites, two in the Cys-rich region and two in the TSP-rich region. To characterize havcr-1 and define region(s) involved in HAV receptor function, we expressed the TSP-rich region in Escherichia coli fused to glutathione S-transferase and generated antibodies (Ab) in rabbits (anti-GST2 Ab). Western blot analysis with anti-GST2 Ab detected 62- and 65-kDa bands in AGMK cells and 59-, 62-, and 65-kDa bands in dog cells transfected with the HAVcr-1 cDNA (cr5 cells) but not in dog cells transfected with the vector alone (DR2 cells). Treatment of AGMK and cr5 cell extracts with peptide-N-glycosidase F resulted in the collapse of the havcr-1-specific bands into a single band of 56 kDa, which indicated that different N-glycosylated forms of havcr-1 were expressed in these cells. Treatment of AGMK and cr5 cells with tunicamycin reduced binding of protective monoclonal Ab (MAb) 190/4, which suggested that N-glycans are required for binding of MAb 190/4 to havcr-1. To test this hypothesis, havcr-1 mutants lacking the N-glycosylation motif at the first site (mut1), second site (mut2), and both (mut3) sites were constructed and transfected into dog cells. Binding of MAb 190/4 and HAV to mut1 and mut3 cells was highly reduced, while binding to mut2 cells was not affected and binding to dog cells expressing an havcr-1 construct containing a deletion of the Cys-rich region (d1- cells) was undetectable. HAV-infected cr5 and mut2 cells but not mut1, mut3, d1-, and DR2 cells developed the characteristic cytoplasmic granular fluorescence of HAV-infected cells. These results indicate that the Cys-rich region of havcr-1 and its first N-glycosylation site are required for binding of protective MAb 190/4 and HAV receptor function.
Cyclin D dysregulation: an early and unifying pathogenic event in multiple myeloma (2005)

Two oncogenic pathways have been hypothesized for multiple myeloma (MM) and premalignant monoclonal gammopathy of undetermined significance (MGUS) tumors: a nonhyperdiploid pathway associated with a high prevalence of IgH translocations and a hyperdiploid pathway associated with multiple trisomies of 8 chromosomes. Cyclin D1, D2, or D3 expression appears to be increased and/or dysregulated in virtually all MM tumors despite their low proliferative capacity. Translocations can directly dysregulate CCND1 (11q13) or CCND3 (6p21), or MAF (16q23) or MAFB (20q11) transcription factors that target CCND2. Biallelic dysregulation of CCND1 occurs in nearly 40% of tumors, most of which are hyperdiploid. Other tumors express increased CCND2, either with or without a t(4;14) translocation. Using gene expression profiling to identify 5 recurrent translocations, specific trisomies, and expression of cyclin D genes, MM tumors can be divided into 8 TC (translocation/cyclin D) groups (11q13, 6p21, 4p16, maf, D1, D1+D2, D2, and none) that appear to be defined by early, and perhaps initiating, oncogenic events. However, despite subsequent progression events, these groups have differing gene expression profiles and also significant differences in the prevalence of bone disease, frequency at relapse, and progression to extramedullary tumor.
The Hapsburg Commercial System (1997)

ORIGINS Although historians continue to debate and differ over the perhaps insoluble issue of when the medieval world ended and modern history began, virtually all are agreed that the expansion of European trade beyond the Mediterranean and the North Atlantic—first with Portuguese expansion down the coast of Africa throughout the fifteenth century, and, from 1492, with the initiation of Spanish expansion in the Caribbean, into the American hemisphere—was crucial in the transition from an essentially inward-looking Europe to a truly global economy, albeit one which European powers would continue to dominate until the twentieth century. The dramatic expansion after 1500 of the lines of maritime and commercial communication—with both Spain and Portugal looking, at least in theory in the case of the former and in practice in that of the latter, beyond America and Africa to the fabulous Orient—also extended both the scope for the sources of international conflict to manifest themselves beyond Europe, and, increasingly in the seventeenth and eighteenth centuries, for the threats of war between European powers to be located, at least in part, beyond the geographical confines of the Old World. In so far as Portuguese trade with Brazil was concerned, the relatively low-value (in relation to volume) cargoes of dye-woods which began to flow to Europe in increasing quantities by the middle of the sixteenth century attracted few predators. Cargoes of sugar, too, were generally unattractive to intruders.
Indentation Creep of Na 2 O · 3SiO 2 Glasses with Various Water Contents (1990)

Time‐dependent deformation behavior induced by an indentation, called indentation creep, was investigated for Na 2 O · 3SiO 2 glasses with various water contents by measuring the indentation depth as a function of time using a conical indenter. It was found that the indentation creep behavior of the glasses could be best explained as steady‐state inhomogeneous (non‐Newtonian viscous) flow. Water in the glasses appeared to reduce the stress (or yield stress) needed to cause this flow. Crack initiation of the glasses was promoted by water through this inhomogeneous flow.
Cytochromes P450: Metabolic and Toxicological Aspects (1996)

Foreword, R.L. Smith General Considerations Cytochrome P450: From a Single Protein to a Family of Proteins-With Some Personal Reflections, R.W. Estabrook Role of Metabolism in Chemical Toxicity, N.P.E. Vermeulen The Chemistry of Cytochrome P450 Reactions, F.P. Guengerich Cytochrome P450 Families/Subfamilies The CYP1 Family, K. Kawajiri and S-.I. Hayashi The CYP2A Subfamily, T.H.K. Chang and D.J. Waxman The CYP2B Subfamily, R.W. Nims and R.A. Lubet The CYP2C Subfamily, T.H. Richardson and E.F. Johnson The CYP2D Subfamily, F.J. Gonzalez The CYP2E Subfamily, M.J.J. Ronis, K.O. Lindros, and M. Ingelman-Sundberg The CYP3A Family, P. Maurel The CYP4 Family, B.G. Lake and D.F.V. Lewis Current Issues Expression of Cytochrome P450 Proteins in Disease, C. Ioannides, C.R. Barnett, A. Irizar, and P.R. Flatt Cytochromes P450 and Immunotoxicity, M. Pirmohamed and B.K. Park Molecular Modeling of Mammalian Cytochromes P450, D.F.V. Lewis Index
Infiltration of CD4+ lymphocytes into the brain contributes to neurodegeneration in a mouse model of Parkinson disease (2008)

Parkinson disease (PD) is a neurodegenerative disorder characterized by a loss of dopamine-containing neurons. Mounting evidence suggests that dopaminergic cell death is influenced by the innate immune system. However, the pathogenic role of the adaptive immune system in PD remains enigmatic. Here we showed that CD8+ and CD4+ T cells but not B cells had invaded the brain in both postmortem human PD specimens and in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of PD during the course of neuronal degeneration. We further demonstrated that MPTP-induced dopaminergic cell death was markedly attenuated in the absence of mature T lymphocytes in 2 different immunodeficient mouse strains (Rag1-/- and Tcrb-/- mice). Importantly, similar attenuation of MPTP-induced dopaminergic cell death was seen in mice lacking CD4 as well as in Rag1-/- mice reconstituted with FasL-deficient splenocytes. However, mice lacking CD8 and Rag1-/- mice reconstituted with IFN-gamma-deficient splenocytes were not protected. These data indicate that T cell-mediated dopaminergic toxicity is almost exclusively arbitrated by CD4+ T cells and requires the expression of FasL but not IFNgamma. Further, our data may provide a rationale for targeting the adaptive arm of the immune system as a therapeutic strategy in PD.
Immunogenicity of hepatitis B virus vaccine (Heptavax-B)--response of healthy adults. (1984)

We vaccinated 30 healthy adults who were susceptible to hepatitis B virus with 20 mug of Merck Sharp & Dohme vaccine at zero, one and six months and measured their antibody (anti-HBs) response weekly for four weeks and monthly for at least seven months. A month following the first dose 40% had antibodies and 90% were positive for anti-HBs a month following the second dose. The third dose raised the response rate to 93.3% but its major effect was to substantially raise the titer of virtually all of the vaccinees. Two persons had no antibody response to vaccination and four others were hyporesponders. No complications or significant side effects were observed.
Data Fusion towards building roof reconstruction based on CSR approach (2009)

3D building modeling has emerged as a focus of research as well as development for many urban planning and geo-information related applications. To its most abstract form on geometric level, 3D building roofs are regarded as the fundamental elements to present outlines of 3D building models. The emphasis of this study is to demonstrate a novel algorithm of building roof reconstruction, termed CSR (Construct-Shape-Refine). The proposed algorithm aims at reconstructing building roof models purely by employing 3D line features or integrating 3D and 2D line features from existing data. In particular, the latter integration involving fusion from multiple data sources strengthens the reliability as well as the precision of 3D building roofs. The CSR approach is characterized through three stages. Geometric inferences are imposed at the stage of Construct where topological relationship of the 3D line features is established while 3D coordinates of roof corners are adjusted and estimated through Shape processes, apart from compensating the hidden boundaries, if any. The efficiencies of two fusion streams, including fusion of 3D line features that result from different sources or fusing 3D line features with photogrammetric line features, are gained as promoting the building roof quality via Refine workflow. Experiments of the Construct-Shape stages show that the proposed method is independent of building roof types, however constrained in polygons under current consideration, as well as whether 3D line features are complete for both successful and efficient performance of building roof reconstruction on a 3D line feature basis. Moreover, the Refine stage offers more up-to-date and satisfactory building roof reconstruction results as compared to the situation when only one single data set is considered.
Environmental stress, ageing and glial cell senescence: a novel mechanistic link to Parkinson's disease? (2013)

Exposure to environmental toxins is associated with a variety of age-related diseases including cancer and neurodegeneration. For example, in Parkinson's disease (PD), chronic environmental exposure to certain toxins has been linked to the age-related development of neuropathology. Neuronal damage is believed to involve the induction of neuroinflammatory events as a consequence of glial cell activation. Cellular senescence is a potent anti-cancer mechanism that occurs in a number of proliferative cell types and causes the arrest of proliferation of cells at risk of malignant transformation following exposure to potentially oncogenic stimuli. With age, senescent cells accumulate and express a senescence-associated secretory phenotype (SASP; that is the robust secretion of many inflammatory cytokines, growth factors and proteases). Whereas cell senescence in peripheral tissues has been causally linked to a number of age-related pathologies, little is known about the induction of cellular senescence and the SASP in the brain. On the basis of recently reported findings, we propose that environmental stressors associated with PD may act in part by eliciting senescence and the SASP within non neuronal glial cells in the ageing brain, thus contributing to the characteristic decline in neuronal integrity that occurs in this disorder.
Immunocytochemical localization of Fe‐SOD in different cells of Anabaena cylindrica Lemm. grown at two different photon irradiances (1993)

SUMMARY Superoxide dismutase (SOD) converts superoxide radicals into hydrogen peroxide and molecular oxygen and therefore represents the primary defence against oxygen damage. Using antibodies against Anabaena cylindrica Lemm. iron‐SOD, the isoenzyme was localized by immunogold labelling in vegetative cells, heterocysts and akinetes of the cyanobacterium Anabaena cylindrica grown at different light intensities. At a low photon irradiance (25 μmol photons m −2 s −1 ), the density of iron‐SOD labelling was similar in vegetative cells and in heterocysts, whereas in akinetes only 60 % of the gold particles were present as compared with the other cell types. At a higher photon irradiance (140 μmol photons m −2 S −1 ), iron‐SOD labelling increased by 100% in both vegetative cells and in heterocysts but did not change in akinetes. The cultures grown at the photon irradiance of 140 μmol photons m −2 s −1 showed a rate of photosynthetic oxygen evolution 40 % higher than that of cultures grown at the lower photon irradiance. The increase of SOD labelling in vegetative cells is in line with the increased photosynthetic oxygen evolution induced by light. The unchanged SOD labelling observed in the akinetes suggests that light intensity does not seem to affect the oxidative metabolism due to respiratory activity.
Mosquito hearing: sound-induced antennal vibrations in male and female Aedes aegypti (1999)

Male mosquitoes are attracted by the flight sounds of conspecific females. In males only, the antennal flagellum bears a large number of long hairs and is therefore said to be plumose. As early as 1855, it was proposed that this remarkable antennal anatomy served as a sound-receiving structure. In the present study, the sound-induced vibrations of the antennal flagellum in male and female Aedes aegypti were compared, and the functional significance of the flagellar hairs for audition was examined. In both males and females, the antennae are resonantly tuned mechanical systems that move as simple forced damped harmonic oscillators when acoustically stimulated. The best frequency of the female antenna is around 230 Hz; that of the male is around 380 Hz, which corresponds approximately to the fundamental frequency of female flight sounds. The antennal hairs of males are resonantly tuned to frequencies between approximately 2600 and 3100 Hz and are therefore stiffly coupled to, and move together with, the flagellar shaft when stimulated at biologically relevant frequencies around 380 Hz. Because of this stiff coupling, forces acting on the hairs can be transmitted to the shaft and thus to the auditory sensory organ at the base of the flagellum, a process that is proposed to improve acoustic sensitivity. Indeed, the mechanical sensitivity of the male antenna not only exceeds the sensitivity of the female antenna but also those of all other arthropod movement receivers studied so far.
Interaction of polyamic acids and polyamic esters with copper and substituted polysilsesquioxane copolymers (1992)

Abstract The interactions of biphenyldianhydride– p ‐phenylenediamine (BPDA–PDA) polyamic acid and ester polymers with copper and copper‐treated surfaces containing polysilsesquioxanes formed from 3‐aminopropyltriethoxysilane (APS) (or copolymers of APS and phenyltriethoxysilane) were compared by grazing‐incidence infrared spectroscopy. This investigation of a flexible dianhydride–stiff diamine copolymer compliments earlier work using the stiff dianhydride–flexible diamine polyamic acid and ester of pyromellitic dianhydride–oxydianiline (PMDA–ODA). Results support earlier findings that amic acids form thermally labile salts on copper but esters do not. Further, while APS forms a copper‐interactive film that insulates amic acid/metal interaction, APS–phenylsilsesquioxane copolymers create an interfacial region interactive with both copper and overlying polyamic acid.
Intelligent Anticipated Exploration of Web Sites (2001)

In this paper we describe a web search agent, called Global Search Agent (hereafter GSA for short). GSA integrates and enhances several search techniques in order to achieve significant improvements in the user-perceived quality of delivered information as compared to usual web search engines. GSA features intelligent merging of relevant documents from different search engines, anticipated selective exploration and evaluation of links from the current result set, automated derivation of refined queries based on user relevance feedback. System architecture as well as experimental accounts are also illustrated.
Caveolin 1 Expression Independently Predicts Shorter Survival in Oligodendrogliomas (2009)

Caveolin 1 (cav-1) is the basic component of the flask-shaped membrane microdomains known as caveolae that are involved in various cell functions. Caveolin 1 can be overexpressed in tumors,suggesting a proneoplastic role, or it can be downregulated. We previously reported that cav-1 expression increases with tumor grade in astrocytomas. Here, we studied cav-1 immunoreactivity in brain umors with an oligodendroglial component to determine the prognostic value of cav-1 expression and to correlate it with 1p/19q deletions. Fifty-four oligodendrogliomas, 26 mixed oligoastrocytomas,and 7 glioblastomas with an oligodendroglial component were assessed for cav-1 expression by immunohistochemistry and for 1p/19q status by fluorescence in situ hybridization. Caveolin-1 was detected in a minority of cases (22%) and was associated mostly with Grade III mixed oligoastrocytomas and glioblastomas with anoligodendroglial component; cav-1 expression was significantly correlated with the absence of a 1p/19q deletion (p = 0.0002). In the 63 cases in which survival data were available, cav-1 expression was also significantly associated with shorter survivals, whereas 1p/19q deletion was associated with longer survivals. Among high-grade tumors, cav-1 expression was the only factor that retained a statistical significance after multivariate analysis for the prediction ofa short survival (p G 0.015). These data are the first evidence that cav-1 immunohistochemistry is an independent prognostic marker in tumors with an oligodendroglial component regardless of the 1p/19q status.
Use of Pertussis Toxin Encoded by ptx Genes from Bordetella bronchiseptica To Model the Effects of Antigenic Drift of Pertussis Toxin on Antibody Neutralization (2000)

Recently, concern has been voiced about the potential effect that antigenic divergence of circulating strains of Bordetella pertussis might have on the efficacy of pertussis vaccines. In order to model antigenic drift of pertussis toxin, a critical component of many pertussis vaccines, and to examine the effects of such drift on antibody neutralization, we engineered a strain of B. pertussis to produce a variant pertussis toxin molecule that contains many of the amino acid changes found in the toxin encoded by Bordetella bronchiseptica ptx genes. This altered form of the toxin, which is efficiently secreted by B. pertussis and which displays significant biological activity, was found to be neutralized by antibodies induced by vaccination as readily as toxin produced by wild-type B. pertussis. These findings suggest that significant amino acid changes in the pertussis toxin sequence can occur without drastically altering the ability of antibodies to recognize and neutralize the toxin molecule.
Improved approximation algorithms for maximum cut and satisfiability problems using semidefinite programming (1995)

We present randomized approximation algorithms for the maximum cut (MAX CUT) and maximum 2-satisfiability (MAX 2SAT) problems that always deliver solutions of expected value at least .87856 times the optimal value. These algorithms use a simple and elegant technique that randomly rounds the solution to a nonlinear programming relaxation. This relaxation can be interpreted both as a semidefinite program and as an eigenvalue minimization problem. The best previously known approximation algorithms for these problems had perfc~rmance guarantees of ~for MAX CUT and ~for MAX 2SAT. Slight extensions of our analysis lead to a .79607-approximation algorithm for the maximum directed cut problem (MAX DICUT) and a .758-approximation algorithm for MAX SAT, where the best previously known approxim ation algorithms had performance guarantees of ~and ~, respectively. Our algorithm gives the first substantial progress in approximating MAX CUT in nearly twenty years, and represents the first use of :semidefinite programming in the design of approximation algorithms.