gebhart/patrepeval huggingface dataset:
Receptor for hyaluronan-mediated motility (RHAMM), a hyaladherin that regulates cell responses to growth factors (1999)

Conference Article| February 01 1999 Receptor for hyaluronan-mediated motility (RHAMM), a hyaladherin that regulates cell responses to growth factors W.-F. Cheung; W.-F. Cheung *Mount Sinai Hospital, Connective Tissue Research Group, Toronto, ON M5G 1X5, Canada Search for other works by this author on: This Site PubMed Google Scholar T. F. Cruz; T. F. Cruz *Mount Sinai Hospital, Connective Tissue Research Group, Toronto, ON M5G 1X5, Canada Search for other works by this author on: This Site PubMed Google Scholar E. A. Turley E. A. Turley 1 †The Hospital for Sick Children, Research Institute, Division of Cardiovascular Research, Toronto, ON M5G 1X8, Canada 1To whom correspondence should be addressed Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1999) 27 (2): 135–141. https://doi.org/10.1042/bst0270135 Article history Received: September 23 1998 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share MailTo Twitter LinkedIn Cite Icon Cite Get Permissions Citation W.-F. Cheung, T. F. Cruz, E. A. Turley; Receptor for hyaluronan-mediated motility (RHAMM), a hyaladherin that regulates cell responses to growth factors. Biochem Soc Trans 1 February 1999; 27 (2): 135–141. doi: https://doi.org/10.1042/bst0270135 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: AP-1, activator protein-1, ERK, extracellular signal-regulated kinase, HA, hyaluronan, IHABP, intracellular hyaluronic-acid-binding protein, MAP, mitogen-activated protein, MEK, MAP kinase kinase, PDGF, platelet-derived growth factor, RACE, rapid amplification of cDNA ends, RHAMM, receptor for HA-mediated motility, RT, reverse transcriptase This content is only available as a PDF. © 1999 Biochemical Society1999 Article PDF first page preview Close Modal You do not currently have access to this content.
Concepts for Modelling Configurable Products (1998)

The effect of 1,2-cyclohexylene-aminotetraacetic acid (CDTA), diethylenetriaminepentaacetis acid (DTPA) and 2,3-dimercaptol-1-propanesulphonic acid, sodium salt (DMPS) on Mn distribution and excretion in rats was examined after 1 hr exposure to 54MnCl2 (approximately 0.1 microgram Mn/m3). All complexing agents were injected i.p., 0.32 mM/kg/day, for 7 days, starting either immediately after exposure (day 0, group I), or 1 week after exposure (day 7, group II). The controls were injected i.p. with 4 ml/kg of 0.9% saline. Activity of 54Mn was determined in lung, liver, kidney, and brain, 24 hrs after the last treatment and in urine and feces collected for 24 hrs on days 1-7 and 8-14 respectively. CDTA and DTPA administered immediately after Mn exposure appeared to be most effective, resulting in a two-fold decrease of 54Mn in brain and kidney, and a statistically significant decrease in lung (DTPA) and liver (CDTA). In group II a two-fold decrease of 54Mn in kidney and liver was observed with CDTA. There was also a decrease after DTPA administration. DMPS was not effective in these experiments. On the first day after exposure, 54Mn levels in urine were more than 15 and 25 times higher for CDTA and DTPA, respectively than for saline, in the early treatment group. Excretion of Mn in feces was not affected. Our data show that the effectiveness of removing inhaled Mn depends both on the complexing agent and the time of its administration.
Catalytic-rate improvement of a thermostable malate dehydrogenase by a subtle alteration in cofactor binding (1995)

The nucleotide-binding fold of many NAD(+)-dependent dehydrogenases contains a conserved acidic amino acid residue which hydrogen-bonds with the 2'- and 3'-hydroxy groups of the adenine-ribose of the cofactor. This residue is highly conserved as aspartate in malate dehydrogenases, except in the thermophilic enzyme from Thermus aquaticus B (TaqMDH), which has glutamic acid-41 in the equivalent position. The catalytic mechanism was dissected to investigate the functional significance of this difference in TaqMDH with respect to a mutant enzyme where glutamic acid-41 was replaced by aspartic acid. The mutant enzyme was found to retain a high degree of protein structural stability to both thermal and chemical denaturation. When compared with the wild-type enzyme the mutant had a higher Km and Kd for both reduced and oxidized cofactors (NADH and NAD+) and a 2-3-fold increase in steady-state kcat in both assay directions. The rate-determining step for the reduction of oxaloacetate by wild-type TaqMDH was shown to be the rate of NAD+ release, which was about 2.5-fold higher for the mutant enzyme. This correlates well with the 1.8-fold higher steady-state kcat of the mutant enzyme and represents an improvement in the steady-state kcat of a thermophilic enzyme at moderate temperature by a conservative amino acid substitution which increases the rate of product release.
Differentiation of avian keratinocytes. Characterization and relations of the keratin proteins of adult and embryonic feathers and scales (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDifferentiation of avian keratinocytes. Characterization and relations of the keratin proteins of adult and embryonic feathers and scalesD. J. Kemp and G. E. RogersCite this: Biochemistry 1972, 11, 6, 969–975Publication Date (Print):March 1, 1972Publication History Published online1 May 2002Published inissue 1 March 1972https://doi.org/10.1021/bi00756a005Request reuse permissionsArticle Views188Altmetric-Citations72LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (3 MB) Get e-Alertsclose Get e-Alerts
Streptococcus pneumoniaeAntigen Test Using Positive Blood Culture Bottles as an Alternative Method To Diagnose Pneumococcal Bacteremia (2005)

Recovery of Streptococcus pneumoniae from positive blood culture bottles may be difficult due to autolysis of pneumococci. Therefore, we evaluated the performance of the Binax NOW S. pneumoniae antigen test with samples from positive blood culture bottles and defined the duration of detectable pneumococcal antigen in these bottles. Use of the S. pneumoniae antigen test is an alternative method for identifying S. pneumoniae from positive blood culture bottles and may enable a diagnosis of pneumococcal bacteremia despite negative subcultures.
Conditional genome alteration in mice (1998)

The recent ability to inactivate specific genes in mice has significantly accelerated our understanding of molecular, cellular, and even behavioral aspects of normal and disease processes. However, this ability has also demonstrated the extreme complexity of genetic determination in mammals, in particular, that genes in the same family or pathway can be functionally redundant and that a given gene often has multiple roles. Thus, inactivation of a gene often does not indicate its complete spectrum of functions. To circumvent this problem, many new tools and novel applications of classic techniques have been developed to place spatial and temporal restrictions on the genomic alterations. These approaches include chimera and mosaic studies, organ transplantation, complementation assays, dominant negative mutants, conditional gene knockouts, and lineage-specific gene rescue. Not only has this opened up more sophisticated ways to make genomic alterations, but it has provided the opportunity to create animal models for sporadic human genetic diseases.
Gender Differences in Human Immunodeficiency Virus Type 1-Specific CD8 Responses in the Reproductive Tract and Colon following Nasal Peptide Priming and Modified Vaccinia Virus Ankara Boosting (2004)

Induction of mucosal anti-human immunodeficiency virus type 1 (HIV-1) T-cell responses in males and females will be important for the development of a successful HIV-1 vaccine. An HIV-1 envelope peptide, DNA plasmid, and recombinant modified vaccinia virus Ankara (rMVA) expressing the H-2D(d)-restricted cytotoxic T lymphocyte P18 epitope were used as immunogens to test for their ability to prime and boost anti-HIV-1 T-cell responses at mucosal and systemic sites in BALB/c mice. We found of all prime-boost combinations tested, an HIV-1 Env peptide subunit mucosal prime followed by systemic (intradermal) boosting with rMVA yielded the maximal induction of gamma interferon (IFN-gamma) spot-forming cells in the female genital tract and colon. However, this mucosal prime-systemic rMVA boost regimen was minimally immunogenic for the induction of genital, colon, or lung anti-HIV-1 T-cell responses in male mice. We determined that a mucosal Env subunit immunization could optimally prime an rMVA boost in female but not male mice, as determined by the magnitude of antigen-specific IFN-gamma responses in the reproductive tracts, colon, and lung. Defective mucosal priming in male mice could not be overcome by multiple mucosal immunizations. However, rMVA priming followed by an rMVA boost was the optimal prime-boost strategy for male mice as determined by the magnitude of antigen-specific IFN-gamma responses in the reproductive tract and lung. Thus, prime-boost immunization strategies able to induce mucosal antigen-specific IFN-gamma responses were identified for male and female mice. Understanding the cellular and molecular basis of gender-determined immune responses will be important for optimizing induction of anti-HIV-1 mucosal immune responses in both males and females.
Gaussian Process Optimization in the Bandit Setting: No Regret and Experimental Design (2009)

Many applications require optimizing an unknown, noisy function that is expensive to evaluate. We formalize this task as a multi-armed bandit problem, where the payoff function is either sampled from a Gaussian process (GP) or has low RKHS norm. We resolve the important open problem of deriving regret bounds for this setting, which imply novel convergence rates for GP optimization. We analyze GP-UCB, an intuitive upper-confidence based algorithm, and bound its cumulative regret in terms of maximal information gain, establishing a novel connection between GP optimization and experimental design. Moreover, by bounding the latter in terms of operator spectra, we obtain explicit sublinear regret bounds for many commonly used covariance functions. In some important cases, our bounds have surprisingly weak dependence on the dimensionality. In our experiments on real sensor data, GP-UCB compares favorably with other heuristical GP optimization approaches.
High-level expression of EPHB6, EFNB2, and EFNB3 is associated with low tumor stage and high TrkA expression in human neuroblastomas. (1999)

Neuroblastoma (NB) is a common pediatric tumor of neural crest origin that is biologically and clinically heterogeneous. EPH family receptor tyrosine kinases and ephrin ligands play fundamental roles in neurodevelopmental processes. Recently, we found that NB cell lines expressed several EPHB and EFNB transcripts, which encode EPHB subgroup receptors and ephrin-B subgroup ligands, respectively. To explore the role of EPHB receptors and ephrin-B ligands in the biology of NB, we examined the expression of EPHB and EFNB transcripts in 47 primary NB specimens. Multiple EPHB and EFNB transcripts were expressed in all of the NB tumors examined, suggesting the involvement of these transcripts in modulating the biological behavior of NB. Higher levels of EPHB6, EFNB2, and EFNB3 expression were found in low-stage tumors (stage 1, 2, and 4S) than in advanced-stage tumors (stage 3 and 4; P = 0.0013, P = 0.0048, and P = 0.027, respectively). Expression of TrkA, a well-established prognostic marker of favorable NB, was positively correlated with EPHB6, EFNB2, and EFNB3 expression (P < 0.0001, P = 0.0019, and P = 0.0001, respectively). MYCN-amplified tumors expressed lower levels of EPHB6, EFNB2, EFNB3, and TrkA transcripts compared to nonamplified tumors (P = 0.0006, P = 0.0023, P = 0.0048, and P = 0.0001, respectively). These data suggest that high-level expression of EPHB6, EFNB2, and EFNB3 is associated with favorable NB and that low-level expression of EPHB6, EFNB2, and EFNB3 correlates with aggressive MYCN-amplified NB. Thus, EPHB6, EFNB2, and EFNB3 may have biological relevance in NB. Further investigation on the biology of these genes may help provide insight into the treatment of NB.
In Vivo Imaging in Cancer (2010)

Imaging has become an indispensable tool in the study of cancer biology and in clinical prognosis and treatment. The rapid advances in high resolution fluorescent imaging at single cell level and MR/PET/CT image registration, combined with new molecular probes of cell types and metabolic states, will allow the physical scales imaged by each to be bridged. This holds the promise of translation of basic science insights at the single cell level to clinical application. In this article, we describe the recent advances in imaging at the macro- and micro-scale and how these advances are synergistic with new imaging agents, reporters, and labeling schemes. Examples of new insights derived from the different scales of imaging and relevant probes are discussed in the context of cancer progression and metastasis.
Trapping HIV-1 Reverse Transcriptase Before and After Translocation on DNA (2003)

A disulfide cross-linking strategy was used to covalently trap as a stable complex (complex N) a short-lived, kinetic intermediate in DNA polymerization. This intermediate corresponds to the product of polymerization prior to translocation. We also prepared the trapped complex that corresponds to the product of polymerization after translocation (complex P). The cross-linking method that we used is a variation of a technique developed by the Verdine and Harrison laboratories. It involves disulfide interchange between an engineered sulfhydryl group of the protein (Q258C mutation) and a disulfide-containing tether attached at the N(2) amino group of a modified dG in either the template or the primer strand of the nucleic acid. We report here a highly efficient synthesis of the precursor, bis(3-aminopropyl)disulfide dihydrochloride, used to introduce this substituent into the oligonucleotide. Efficient cross-linking takes place when the base pair containing the substituent is positioned seven registers from the dNTP-binding site (N site) and the N site is occupied. Complex N, but not complex P, is a substrate for the ATP-based excision reaction that unblocks nucleoside reverse transcriptase inhibitor (NRTI)-terminated primers and causes resistance to several NRTIs, confirming predictions that the excision reaction takes place only when the 3'-end of the primer is bound at the N site. These techniques can be used for biochemical and structural studies of the mechanism of DNA polymerization, translocation, and excision-based resistance of RT to NRTIs. They may also be useful in studying other DNA or RNA polymerases or other enzymes.
Sol−Gel Synthesis of Layered Birnessite-Type Manganese Oxides (1997)

Layered birnessite-type manganese oxides have been synthesized by sol−gel reactions involving KMnO4 or NaMnO4 with glucose. These microporous manganese oxides are designated as octahedral layer materials, K-OL-1 and Na-OL-1, because their layered structure consists of edge-shared MnO6 octahedra. The interlayer regions are occupied by alkali metal cations and water molecules. K-OL-1 and Na-OL-1 have been characterized by elemental analysis, powder X-ray diffraction, scanning electron microscopy, FT-IR spectroscopy, and Auger electron spectroscopy. The empirical formula of K-OL-1 has been determined to be K0.28MnO1.96(H2O)0.19. An interlayer spacing of 7 Å, typical of natural and synthetic birnessites, has been measured by X-ray diffraction. The sol−gel synthesis of K-OL-1 is carried out with concentrated aqueous solutions of glucose and KMnO4 in a 1.5:1 mole ratio. Diluted reaction mixtures produce flocculent gels or precipitates which yield other manganese oxide phases such as cryptomelane and Mn2O3. The synthesis appears to be general for reactions of KMnO4 with a variety of sugars as well as other polyalcohols such as ethylene glycol, glycerol, and poly(vinyl alcohol). Reactions between NaMnO4 and glucose yield two related Na-OL-1 products. A procedure analogous to the K-OL-1 synthesis generates layered sodium birnessite materials with 5.5 and 7 Å interlayer distances. The 7 Å Na-OL-1 is obtained exclusively by hydrating the mixture of products. The 5.5 Å Na-OL-1 is prepared by calcining the Na-OL-1 xerogel at 800 °C instead of the typical 400 °C temperature. Both K-OL-1 and Na-OL-1 undergo significant yet incomplete cation extraction and ion exchange with monovalent and divalent cations.
High quality Nb-based tunnel junctions for high frequency and digital applications (2003)

A number of new fabrication techniques are developed and optimized in order to fit the requirements of contemporary superconducting electronics. To achieve ultimate performance of integrated submm receivers with operational frequency of 1 THz, tunnel junctions with AlN tunnel barrier having a R/sub n/S value as low as 1 /spl Omega//spl mu/m/sup 2/ have been developed. High quality characteristics of Nb/AlN/Nb tunnel junctions with R/sub j//R/sub n/=16 and R/sub n/S=10 /spl Omega//spl mu/m/sup 2/ have been demonstrated. Electron Beam Lithography (EBL) in combination with Chemical Mechanical Polishing (CMP) has been incorporated to produce Nb/AlN/Nb junctions with 0.03 /spl mu/m/sup 2/ area. A new approach to obtain overdamped Nb/AlO/sub x//Nb tunnel junctions has been proposed and realized. The dependencies of the main parameters of novel junctions on the current density and circuit geometry have been studied. These junctions may have a good potential in Josephson junction arrays and Single-Flux-Quantum applications (RSFQ).
Comparison of the Effects of Apo(a) Kringle IV-10 and Plasminogen Kringles on the Interactions of Lipoprotein(a) with Regulatory Molecules (1999)

Lipoprotein(a) [Lp(a)] is associated with atherosclerosis and with disease processes involving thrombosis. Lp(a) contains apoprotein (a) [apo(a)], which has a sequence highly homologous to plasminogen. Hence, Lp(a) binds directly to extracellular matrix, cellular plasminogen receptors and fibrin(ogen) and competes for the binding of plasminogen to these regulatory surfaces. These interactions may contribute to the proatherothrombogenic consequences of high Lp(a) levels. These interactions are mediated by lysine binding sites (LBS). Therefore, we examined the role of apo(a) kringle IV-10 [the only apo(a) kringle demonstrated to exhibit lysine binding activity in the intact lipoprotein] in the interaction of Lp(a) with these regulatory molecules. We have compared directly apo(a) KIV-10 with plasminogen K4 to examine whether these highly structurally homologous kringle modules are also functionally homologous. Futhermore, because the plasminogen K5-protease domain (K5-PD) binds directly to fibrin, we have also examined the ability of this plasminogen fragment to inhibit the interaction of Lp(a) with these regulatory molecules and with extracellular matrix. Apo(a) KIV-10 competed effectively for the binding of 125I-Lp(a) to these surfaces but was less effective than either intact Lp(a), plasminogen K4 or plasminogen. Plasminogen KS-PD was a better competitor than apo(a) KIV-10 for 125I-Lp(a) binding to the representative extracellular matrix, Matrigel, and to plasmin-treated fibrinogen. In contrast, plasminogen K5-PD did not compete for the interaction of Lp(a) with cells, although it effectively competed for plasminogen binding. These results suggest that Lp(a) recognizes sites in all of the regulatory molecules that are also recognized by apo(a) KIV-10 and that Lp(a) recognizes sites in extracellular matrix and in plasmin-modified fibrinogen that also are recognized by plasminogen K5-PD. Thus, the interaction of Lp(a) with cells is clearly distinct from that with extracellular matrix and with plasmin-treated fibrinogen and the recognition sites within Lp(a) and plasminogen for these regulatory molecules are not identical.
cDNA cloning and functional expression in yeast Saccharomyces cerevisiae of β‐naphthoflavone‐induced rabbit liver P‐450 LM4 and LM6 (1988)

A cDNA library was constructed from liver mRNA of a β‐naphthoflavone‐induced rabbit. Two clones pLM4‐1 and pLM6‐1 containaing 2.2‐kbp inserts that hybridized at low stringincy with a mouse P1 P ‐450 probe were selected. The clone pLM4‐1 was fully sequenced and found to contain a full‐length cDNA coding for cytochrome P ‐450 LM4. Partial sequence and restriction mapping made it possible to identify pLM6‐1 as coding for the major part of cytochrome P ‐450 LM6. Cloned LM4‐1 cDNA was reformed by deletion of the 5′ and 3′ non‐coding regions before insertion into yeast expression vectors PYe DP1/10. A similar operation was performed on pLM6–1 cDNA after replacement of the missing N‐terminus‐coding sequences by homologous sequences form the pLM4–1 clone resulting in a chimeric cytochrome P ‐450 coding sequence. Expression of cloned rabbit cytochrome P ‐450 into transformed yeast was optimized by studying the effect of the nature of the DNA sequence just preceding the initiation codon on the level of cytochrome P ‐450 production. Yeast synthesized cytochromes P ‐450 were characterized by immunoblotting, spectra and catalytic activity determinations. Cloned cytochrome P ‐450 LM4 was found by all criteria to be identical to the authentic rabbit one. The chimeric cytochrome P ‐450 that contains the 143 N‐terminal amino acids of cytochrome P ‐450 LM4 and the remaining 375 amino acids of cytochrome P ‐450 LM6 was found to exhibit most of the authentic cytochrome P ‐450 LM6 catalytic properties. Enzymatic and evolutionary implications of these results are discussed.
Independent navigation of multiple mobile robots with hybrid reciprocal velocity obstacles (2009)

We present an approach for smooth and collision-free navigation of multiple mobile robots amongst each other. Each robot senses its surroundings and acts independently without central coordination or communication with other robots. Our approach uses both the current position and the velocity of other robots to predict their future trajectory in order to avoid collisions. Moreover, our approach is reciprocal and avoids oscillations by explicitly taking into account that the other robots also sense their surroundings and change their trajectories accordingly. We build on prior work related to velocity obstacles and reciprocal velocity obstacles and introduce the concept of hybrid reciprocal velocity obstacles for collision avoidance that takes into account the kinematics of the robots and uncertainty in sensor data. We apply our approach to a set of iRobot Create robots using centralized sensing and show natural, direct, and collision-free navigation in several challenging scenarios.