gebhart/patrepeval huggingface dataset:
Identification and Molecular Cloning of a Unique Hyaluronan Synthase from Pasteurella multocida (1998)

Type A Pasteurella multocida, a prevalent animal pathogen, employs a hyaluronan [HA] polysaccharide capsule to avoid host defenses. We utilized transposon insertional mutagenesis to identify the P. multocida HA synthase, the enzyme that polymerizes HA. A DNA fragment from a wild-type genomic library could direct HA production in vivo in Escherichia coli, a bacterium that normally does not produce HA. Analysis of truncated plasmids derived from the original clone indicated that an open reading frame encoding a 972-residue protein was responsible for HA polymerization. This identification was confirmed by expression cloning in E. coli; we observed HA capsule formation in vivo and detected activity in membrane preparations in vitro. The polypeptide size was verified by photoaffinity labeling of the native P. multocida HA synthase with azido-UDP sugar analogs. Overall, the P. multocida sequence is not very similar to the other known HA synthases from streptococci, PBCV-1 virus, or vertebrates. Instead, a portion of the central region of the new enzyme is more homologous to the amino termini of other bacterial glycosyltransferases that produce different capsular polysaccharides or lipopolysaccharides. In summary, we have discovered a unique HA synthase that differs in sequence and predicted topology from the other known enzymes.
Dynamic modeling of the central carbon metabolism of Escherichia coli (2002)

Application of metabolic engineering principles to the rational design of microbial production processes crucially depends on the ability to describe quantitatively the systemic behavior of the central carbon metabolism to redirect carbon fluxes to the product-forming pathways. Despite the importance for several production processes, development of an essential dynamic model for central carbon metabolism of Escherichia coli has been severely hampered by the current lack of kinetic information on the dynamics of the metabolic reactions. Here we present the design and experimental validation of such a dynamic model, which, for the first time, links the sugar transport system (i.e., phosphotransferase system [PTS]) with the reactions of glycolysis and the pentose-phosphate pathway. Experimental observations of intracellular concentrations of metabolites and cometabolites at transient conditions are used to validate the structure of the model and to estimate the kinetic parameters. Further analysis of the detailed characteristics of the system offers the possibility of studying important questions regarding the stability and control of metabolic fluxes.
Targeting of xenografted pancreatic cancer with a new monoclonal antibody, PAM4. (1995)

We have examined the ability of murine monoclonal antibody PAM4, directed against a pancreatic cancer-derived mucin, to target human pancreatic cancers carried as xenografts in athymic nude mice. Four tumor lines were used representing the range of expected differentiation; CaPan1, AsPc1, Hs766T, and BxPc3. In each case tumor uptake of PAM4 (range, 21-48% injected dose/g on day 3) was significantly higher than concomitantly administered, nonspecific, isotype-matched Ag8 antibody (range, 3.6-9.3% injected dose/g on day 3). Based upon the biodistribution data the estimated potential radiation dose delivered to the tumors when normalized to the blood dose as an estimate of dose-limiting myelotoxicity would be 13.1-, 2.2-, 3.4-, and 3.3-fold higher than to blood, respectively. PAM4 showed no evidence of targeting to normal tissues, except within the CaPan1 tumor model, where a small but consistent splenic uptake was observed. Splenic targeting was abolished by use of an increased PAM4 protein dose. Targeting of PAM4 to other normal tissues was not affected by the increased protein dose; however, tumor uptake of PAM4 (percentage of injected dose/g) was significantly increased by as much as 3-fold. The ability of PAM4 to target the CaPan1 tumor compared favorably to that of MN14, an anti-carcinoembryonic antigen murine monoclonal antibody. Tumor uptake of PAM4 was much greater than that for MN14 at days 1 and 3, whereas at later time points equivalent accumulations of activity were noted. Estimates of potential radiation doses to the tumor when normalized to the blood dose were 3.0 for MN14 and 9.6 for PAM4. These studies have shown that PAM4 is able to target pancreatic cancer with high specificity, achieving high concentrations at the tumor site. A rationale exists, then, for the performance of a clinical trial of radiolabeled PAM4 in the detection and localization of pancreatic cancer.
Clean TOCSY for proton spin system identification in macromolecules (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTClean TOCSY for proton spin system identification in macromoleculesC. Griesinger, G. Otting, K. Wuethrich, and Richard R. ErnstCite this: J. Am. Chem. Soc. 1988, 110, 23, 7870–7872Publication Date (Print):November 1, 1988Publication History Published online1 May 2002Published inissue 1 November 1988https://pubs.acs.org/doi/10.1021/ja00231a044https://doi.org/10.1021/ja00231a044research-articleACS PublicationsRequest reuse permissionsArticle Views1158Altmetric-Citations959LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Role of mannose-6-phosphate receptors in herpes simplex virus entry into cells and cell-to-cell transmission (1995)

Herpes simplex virus (HSV) glycoprotein D (gD) is essential for virus entry into cells, is modified with mannose-6-phosphate (M-6-P), and binds to both the 275-kDa M-6-P receptor (MPR) and the 46-kDa MPR (C. R. Brunetti, R. L. Burke, S. Kornfeld, W. Gregory, K. S. Dingwell, F. Masiarz, and D. C. Johnson, J. Biol. Chem. 269:17067-17074, 1994). Since MPRs are found on the surfaces of mammalian cells, we tested the hypothesis that MPRs could serve as receptors for HSV during virus entry into cells. A soluble form of the 275-kDa MPR, derived from fetal bovine serum, inhibited HSV plaques on monkey Vero cells, as did polyclonal rabbit anti-MPR antibodies. In addition, the number and size of HSV plaques were reduced when cells were treated with bovine serum albumin conjugated with pentamannose-phosphate (PM-PO4-BSA), a bulky ligand which can serve as a high-affinity ligand for MPRs. These data imply that HSV can use MPRs to enter cells; however, other molecules must also serve as receptors for HSV because a reasonable fraction of virus could enter cells treated with even the highest concentrations of these inhibitors. Consistent with the possibility that there are other receptors, HSV produced the same number of plaques on MPR-deficient mouse fibroblasts as were produced on normal mouse fibroblasts, but there was no inhibition with PM-PO4-BSA with either of these embryonic mouse cells. Together, these results demonstrate that HSV does not rely solely on MPRs to enter cells, although MPRs apparently play some role in virus entry into some cell types and, perhaps, act as one of a number of cell surface molecules that can facilitate entry. We also found that HSV produced small plaques on human fibroblasts derived from patients with pseudo-Hurler's polydystrophy, cells in which glycoproteins are not modified with M-6-P residues and yet production of infectious HSV particles was not altered in the pseudo-Hurler cells. In addition, HSV plaque size was reduced by PM-PO4-BSA; therefore, it appears that M-6-P residues and MPRs are required for efficient transmission of HSV between cells, a process which differs in some respects from entry of exogenous virus particles.
Extraction of cellular DNA from crude cell lysate with glass (1990)

Journal Article Extraction of cellular DNA from crude cell lysate with glass Get access James D. Thompson, James D. Thompson Hahnemann University, Department of Neoplastic DiseasesPhiladephia, PA 19102, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Kevin K. Cuddy, Kevin K. Cuddy Hahnemann University, Department of Neoplastic DiseasesPhiladephia, PA 19102, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Dale S. Haines, Dale S. Haines Hahnemann University, Department of Neoplastic DiseasesPhiladephia, PA 19102, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar David Gillepsie David Gillepsie Hahnemann University, Department of Neoplastic DiseasesPhiladephia, PA 19102, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 4, 25 February 1990, Page 1074, https://doi.org/10.1093/nar/18.4.1074 Published: 25 February 1990 Article history Received: 04 January 1990 Published: 25 February 1990
Kruppel-like Factor 4 Abrogates Myocardin-induced Activation of Smooth Muscle Gene Expression (2004)

Platelet-derived growth factor BB (PDGF-BB) has been shown to be an extremely potent negative regulator of smooth muscle cell (SMC) differentiation. Moreover, previous studies have demonstrated that the Kruppel-like transcription factor (KLF) 4 potently represses the expression of multiple SMC genes. However, the mechanisms whereby KLF4 suppresses SMC gene expression are not known, nor is it clear whether KLF4 contributes to PDGF-BB-induced down-regulation of SMC genes. The goals of the present studies were to determine the molecular mechanisms by which KLF4 represses expression of SMC genes and whether it contributes to PDGF-BB-induced suppression of these genes. Results demonstrated that KLF4 markedly repressed both myocardin-induced activation of SMC genes and expression of myocardin. KLF4 was rapidly up-regulated in PDGF-BB-treated, cultured SMC, and a small interfering RNA to KLF4 partially blocked PDGF-BB-induced SMC gene repression. Both PDGF-BB and KLF4 markedly reduced serum response factor binding to CArG containing regions within intact chromatin. Finally, KLF4, which is normally not expressed in differentiated SMC in vivo, was rapidly up-regulated in vivo in response to vascular injury. Taken together, results indicate that KLF4 represses SMC genes by both down-regulating myocardin expression and preventing serum response factor/myocardin from associating with SMC gene promoters, and suggest that KLF4 may be a key effector of PDGF-BB and injury-induced phenotypic switching of SMC.
Microglial interaction with β‐amyloid: Implications for the pathogenesis of Alzheimer's disease (2001)

The etiology of Alzheimer's disease (AD) involves a significant inflammatory component as evidenced by the presence of elevated levels of a diverse range of proinflammatory molecules in the AD brain. These inflammatory molecules are produced principally by activated microglia, which are found to be clustered within and adjacent to the senile plaque. Moreover, long-term treatment of patients with non-steroidal anti-inflammatory drugs has been shown to reduce risk and incidence of AD and delay disease progression. The microglia respond to beta-amyloid (Abeta) deposition in the brain through the interaction of fibrillar forms of amyloid with cell surface receptors, leading to the activation of intracellular signal transduction cascades. The activation of multiple independent signaling pathways ultimately leads to the induction of proinflammatory gene expression and production of reactive oxygen and nitrogen species. These microglial inflammatory products act in concert to produce neuronal toxicity and death. Therapeutic approaches focused on inhibition of the microglial-mediated local inflammatory response in the AD brain offer new opportunities to intervene in the disease.
Use of two-photon absorption in a photorefractive crystal for three-dimensional optical memory (1998)

We describe the use of two-photon absorption in a photorefractive crystal for recording bit data in multilayered optical memory. A short-pulse near-infrared laser is used for generating the photorefractive effect by two-photon absorption. We succeeded in recording and reading seven layers of data in a LiNbO(3) crystal with a lateral resolution (distance between bits) of 5microm and an axial resolution (distance between layers) of 20 microm .
Tungsten black absorber for solar light with wide angular operation range (2008)

Using three-dimensional finite-difference time-domain simulations, we designed a structured tungsten slab with subwavelength periodicity that displays near-complete absorptivity throughout the entire solar spectrum over a wide angular range. The structure consists of a square lattice array of pyramids. The parameters of the pyramids are chosen to provide the optimal impedance matching between free space and tungsten, while the period is chosen to be subwavelength in order to generate absorption over an ultrabroad band of wavelengths.
Arginine Racemase of Pseudomonas graveolens (1971)

Arginine racemase has been purified approximately 5400fold and crystallized from an extract of Pseudomonas graveo- lens.The puritication procedure consists of sonic disruption, ammonium sulfate fractionation, treatment with 1-butanol, DEAE-cellulose and DEAE-Sephadex column chromatography, and Sephadex G-150 gel filtration, followed by crystallization.The purit?ed enzyme is homogeneous by the criteria of ultracentrifugation(&,, = 5.2 S) and disc gel electrophoresis.The molecular weight is 167,000, assuming a partial specific volume of 0.74.The enzyme is yellow in solution and exhibits an absorption maximum at 420 mp.The absorption spectrum is shifted neither by varying pH of the enzyme nor by addition of arginine.One mole of pyridoxal 5'-phosphate is tightly bound per 42,000 g of enzyme.The apoenzyme was obtained by dialysis against phenylhydrazine solution.Addition of pyridoxal 5'-phosphate caused return of the 420 rnp absorption peak and reconstitution of activity.Reduction of arginine racemase with sodium borohydride shifted the 420 rnp peak to about 315 mp, and destroyed the racemase activity.The enzyme catalyzes racemization of lysine, arginine, E-N-acetyllysine, ornithine, 2,3 -diaminopropionate, homoarginine, 2,4-diaminobutyrate, ethionine, citrulline, homocitrulline, b-N-acetylornithine, theanine, glutamine, andmethionine in this order, when examined at pH 10.0.Maximum activities for arginine, lysine, theanine, and ornithine are found in the pH regions of 9.0 to 10.6, 7.5 to 10.6, 7.0 to 10.0, and 6.5 to 9.0, respectively.The following Michaelis constants were determined: D-arginine, 1.0 X 10e3 M, and pyridoxal 5'-phosphate, 4.0 x 1O-7 M. The enzyme activity was inhibited by hydroxylamine and D-and L-penicillamine.Ample evidence has been obtained for the occurrence of Damiiio acids in bacteria and animals, and for t,heir presence in
Characterization of a novel photon counting detector for clinical CT: count rate, energy resolution, and noise performance (2009)

We report on a characterization study of a multi-row direct-conversion x-ray detector used to generate the first photon counting clinical x-ray computed tomography (CT) patent images. In order to provide the photon counting detector with adequate performance for low-dose CT applications, we have designed and fabricated a fast application specific integrated circuit (ASIC) for data readout from the pixellated CdTe detectors that comprise the photon counting detector. The cadmium telluride (CdTe) detector has 512 pixels with a 1 mm pitch and is vertically integrated with the ASIC readout so it can be tiled in two dimensions similar to those that are tiled in an arc found in 32-row multi-slice CT systems. We have measured several important detector parameters including the maximum output count rate, energy resolution, and noise performance. Additionally the relationship between the output and input rate has been found to fit a non-paralyzable detector model with a dead time of 160 nsec. A maximum output rate of 6 &times; 10<sup>6</sup> counts per second per pixel has been obtained with a low output x-ray tube for CT operated between 0.01 mA and 6 mA at 140 keV and different source-to-detector distances. All detector noise counts are less that 20 keV which is sufficiently low for clinical CT. The energy resolution measured with the 60 keV photons from a <sup>241</sup>Am source is ~12%. In conclusion, our results demonstrate the potential for the application of the CdTe based photon counting detector to clinical CT systems. Our future plans include further performance improvement by incorporating drift structures to each detector pixel.
Predicting the Uniaxial Compressive Strength and Static Young’s Modulus of Intact Sedimentary Rocks Using the Ultrasonic Test (2009)

The uniaxial compressive strength and static Young’s modulus (Es) of intact rocks are the most important geotechnical parameters for stability analysis of surface and underground structures. These parameters are obtained by the uniaxial compressive test. Although this test is simple, the preparation of the samples, especially of soft rocks, is a hard and time consuming task. By using a nondestructive method such as the ultrasonic test, one can indirectly predict the mentioned parameters. The uniaxial compressive and the ultrasonic tests were carried out on 64 samples of sedimentary rocks and, after regression analysis of the test results; best fit equations for predicting the uniaxial compressive strength and static Young’s modulus of these samples are proposed. Thus, in comparison with other proposed equations, these equations have larger value of accuracy and correlation coefficient (R2) . The equations are practical, simple, and accurate enough to apply and can be used in practice for the prediction purposes with acceptable accuracy.
Propargyl calix[4]arenes and their complexes with silver(I) and gold(I) (1996)

A calix[4]arene 1b has been substituted at the lower rim by reaction with propargyl bromide to give either the 1,3- bis(propargyl) derivative 2b, which is formed regioselectively, or the tetrakis(O-propargyl)calix[4]arene 3 under different reaction conditions. The molecular structure of 2b has been characterized by X-ray analysis (monoclinic, space group P2 1 /c, Z = 4, a = 10.960(1), b = 24.302(3), c = 10.673(1) Å, β = 112.99(8)°, R = 0.0516). The molecules of 2b in the crystal are arranged in a "head-to-head, tail-to-tail" manner with a phenyl substituent of one molecule partly enclosed in the bowlic cavity of another. Since the two OCH 2 C≡CH groups are accessible, 2b can be polymerized by heating to 250 °C and the polymerized propargyl calix[4]arene derivatives are stable up to 460 °C. Compound 3 exists as a mixture of conformers, the ratio of partial cone to 1,3-alternate conformations being 4:1 or 2:1, dependent on the preparative conditions. These propargyl calix[4]arene derivatives can be further derivatized to form silver(I) or gold(I) alkynyl units by reaction with AgNO 3 or [AuCl(SMe 2 )], respectively, and base. Further reaction of these transition metal complexes with phosphines yields calixarene derivatives with two metal-phosphine units at the lower rim of the calix[4]arene bowl. Key words: calix[4]arene, propargyl, gold, silver, polymer.
A dynamically reconfigurable interconnect for array processors (1998)

Reconfigurability of processor arrays is important due to two reasons (1) to efficiently execute different algorithms and (2) to isolate faulty processors. An array processor that is reconfigurable by the user any number of times to yield a different topology or to isolate faults is envisaged in this paper. The system has a host or controller that broadcasts a command to the interconnect to configure itself into a particular fashion. The interconnect uses static-RAM programming technology and can be programmed to different configurations by sending a different set of bits to the configuration random access memory (RAM) in the interconnect. We present three designs reconfigurable into array, ring, mesh, or Illiac mesh topologies. The first design provides no redundancy or fault tolerance. The second design is capable of graceful degradation by bypassing faulty elements. The third design is capable of graceful degradation by rerouting. The details of the interconnect and the configuration RAM contents for typical configurations are illustrated. It is seen that reconfigurable interconnect results in a highly reconfigurable or polymorphic computer.
150 GS/s real-time oscilloscope using a photonic front end (2008)

We demonstrate an optical front end technology that multiplies the sampling rate of a real-time oscilloscope by a factor of three. Our approach uses an optical pre-processor to compress the signal bandwidth of continuous-time high speed RF waveforms. To operate in continuous-time mode, the optical signal, which carries the RF, must be segmented and demultiplexed into an array of N parallel channels. In prior work, large spectral overlap between channels was needed for calibration and this limited the multiplication factor, M, to values far below the maximum value of N, which is limited by the number of back-end digitizers. In this paper, we demonstrate a novel technique using temporal overlap between channels and achieve higher multiplication. The sampling rate of a four-channel 50 GS/s real-time oscilloscope is increased by a factor of 3, enabling us to digitize a 47 GHz tone at 150 GS/s. To our knowledge, this is a record in continuous time RF digitization.
Site-specific incorporation of nonnatural residues during in vitro protein biosynthesis with semi-synthetic aminoacyl-tRNAs (1991)

A method is presented for the incorporation of nonnatural amino acids into proteins during in vitro cell-free translation. A combination of chemical synthesis and run-off transcription was employed to prepare a semisynthetic, nonhypermodified tRNA(Gly) nonsense suppressor acylated with L-3-[125I]iodotyrosine. The presence of this synthetic tRNA during in vitro translation of mRNA containing a nonsense suppression site (e.g., a UAG termination codon) results in the incorporation of the nonnatural amino acid L-3-iodotyrosine into the polypeptide exclusively at the position corresponding to that site. Incorporation of the nonnatural amino acid L-3-[125I]iodotyrosine into the model polypeptide was assessed by quantitative and unambiguous determination of suppression efficiency, read-through, and site specificity of incorporation. Minor modifications of the method employed in this initial experiment also allow the rapid analysis of unlabeled acylated tRNA analogues. Under optimum conditions, the unlabeled amino acid L-3-iodotyrosine was found to be incorporated with a suppression efficiency of 65%. Other nonnatural residues, including N-methylphenylalanine, D-phenylalanine, and phenyllactic acid, were tested in the assay under these same conditions. Suppression efficiencies for this series ranged from 0 to 72% depending on the structure of the residue incorporated. Several other aspects of this methodology, such as tRNA structure and context effects, are briefly discussed.