gebhart/patrepeval huggingface dataset:
Site-directed mutagenesis (1986)

Research Article| July 01 1986 Site-directed mutagenesis P Carter P Carter Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1986) 237 (1): 1–7. https://doi.org/10.1042/bj2370001 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation P Carter; Site-directed mutagenesis. Biochem J 1 July 1986; 237 (1): 1–7. doi: https://doi.org/10.1042/bj2370001 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 Journal Search Advanced Search This content is only available as a PDF. © 1986 London: The Biochemical Society1986 Article PDF first page preview Close Modal You do not currently have access to this content.
Probing the structure of the V2 domain of human immunodeficiency virus type 1 surface glycoprotein gp120 with a panel of eight monoclonal antibodies: human immune response to the V1 and V2 domains (1993)

We have analyzed a panel of eight murine monoclonal antibodies (MAbs) that depend on the V2 domain for binding to human immunodeficiency virus type 1 (HIV-1) gp120. Each MAb is sensitive to amino acid changes within V2, and some are affected by substitutions elsewhere. With one exception, the MAbs were not reactive with peptides from the V2 region, or only poorly so. Hence their ability to bind recombinant strain IIIB gp120 depended on the preservation of native structure. Three MAbs cross-reacted with strain RF gp120, but only one cross-reacted with MN gp120, and none bound SF-2 gp120. Four MAbs neutralized HIV-1 IIIB with various potencies, and the one able to bind MN gp120 neutralized that virus. Peptide serology indicated that antibodies cross-reactive with the HxB2 V1 and V2 regions are rarely present in HIV-1-positive sera, but the relatively conserved segment between the V1 and V2 loops was recognized by antibodies in a significant fraction of sera. Antibodies able to block the binding of V2 MAbs to IIIB or MN gp120 rarely exist in sera from HIV-1-infected humans; more common in these sera are antibodies that enhance the binding of V2 MAbs to gp120. This enhancement effect of HIV-1-positive sera can be mimicked by several human MAbs to different discontinuous gp120 epitopes. Soluble CD4 enhanced binding of one V2 MAb to oligomeric gp120 but not to monomeric gp120, perhaps by inducing conformational changes in the oligomer.
Total Synthesis and Structural Revision of the Marine Macrolide Neopeltolide (2007)

The total synthesis and structural revision of the marine natural product neopeltolide is reported. The key bond-forming step involves a Lewis acid-catalyzed intramolecular cyclization to install the tetrahydropyran ring and the macrocycle simultaneously. This type of cyclization is the first of its kind and assembles the carbon backbone of the natural product efficiently. The synthesis of the reported structure revealed differences in the data between the natural and synthetic material. After significant investigation, the diastereomeric molecule with the C11 and C13 configurations inverted was synthesized using the initial route. This compound matches the data reported for neopeltolide (1H, 13C, HRMS, IR, NOESY, [alpha]), thereby establishing the correct overall structure for this potent macrolide natural product, including the relative and absolute stereochemistry.
Efficient sensitivity analysis for flow and transport in the Earth's crust and mantle (2006)

This paper focuses on the role of sensitivity analysis in studies of water transport in the environmental and geophysical sciences. Sensitivity analysis is useful in model development to determine how changes in parameter input will affect a model's response. It is also used in data assimilation to incorporate observations into a model. The adjoint method allows an efficient calculation of a model's sensitivity when the number of parameters exceeds the number of observations. In this paper we present studies demonstrating the use of the adjoint method for modelling water transport in both the Earth's crust and mantle.
Nonrigid registration using free-form deformations: application to breast MR images (1999)

In this paper we present a new approach for the nonrigid registration of contrast-enhanced breast MRI. A hierarchical transformation model of the motion of the breast has been developed. The global motion of the breast is modeled by an affine transformation while the local breast motion is described by a free-form deformation (FFD) based on B-splines. Normalized mutual information is used as a voxel-based similarity measure which is insensitive to intensity changes as a result of the contrast enhancement. Registration is achieved by minimizing a cost function, which represents a combination of the cost associated with the smoothness of the transformation and the cost associated with the image similarity. The algorithm has been applied to the fully automated registration of three-dimensional (3-D) breast MRI in volunteers and patients. In particular, we have compared the results of the proposed nonrigid registration algorithm to those obtained using rigid and affine registration techniques. The results clearly indicate that the nonrigid registration algorithm is much better able to recover the motion and deformation of the breast than rigid or affine registration algorithms.
Antigen-driven T cell clones can proliferate in vivo, eradicate disseminated leukemia, and provide specific immunologic memory. (1987)

The aim of the current study was to determine the ability of antigen-driven cloned helper cell independent cytotoxic T lymphocytes (HITc) to proliferate and to survive in vivo and to mediate tumor therapy. The HITc clone utilized (denoted 1.B6) was specifically cytolytic to FBL-3, a syngeneic Friend virus-induced murine leukemia. Activation in vitro (48 hr) with FBL-3 induced secretion of interleukin 2 (IL 2), expression of IL 2 receptors (IL 2R), and in vitro proliferation. These cells could be "rested" for several weeks without stimulation, which resulted in reduced expression of IL 2R; however, restimulation with antigen resulted in reinduction of IL 2R and proliferation. The ability of cloned HITc to proliferate and to survive in vivo was examined in cyclophosphamide (CY) pretreated donor mice congenic for the Thy-1 gene. Adoptively transferred cloned HITc could be found in large numbers, and were widely distributed in vivo 1 wk after transfer. In tumor therapy, 1.B6 cells when injected into a site of tumor (i.p.) and used as an adjunct to CY were effective against disseminated FBL-3. In this circumstance, cloned 1.B6 cells could be recovered from cured mice 125 days after transfer and were shown to specifically lyse tumor and proliferate in vitro in response to FBL-3. Thus as an adjunct to CY, tumor-specific cloned HITc are capable of eradicating disseminated leukemia, persisting long-term in vivo, and providing specific immunologic memory.
High-quality computational imaging through simple lenses (2013)

Modern imaging optics are highly complex systems consisting of up to two dozen individual optical elements. This complexity is required in order to compensate for the geometric and chromatic aberrations of a single lens, including geometric distortion, field curvature, wavelength-dependent blur, and color fringing. In this article, we propose a set of computational photography techniques that remove these artifacts, and thus allow for postcapture correction of images captured through uncompensated, simple optics which are lighter and significantly less expensive. Specifically, we estimate per-channel, spatially varying point spread functions, and perform nonblind deconvolution with a novel cross-channel term that is designed to specifically eliminate color fringing.
Computer-aided design of dither signals for binary display of images (1979)

The quality of binary images displayed using ordered dither is strongly dependent on the spatial arrangement of the thresholds in the dither signal. In the frequency domain, this dependence may be viewed as a consequence of aliasing. A computer-aided approach to the design of dither signals that uses a pairwise exchange algorithm to minimize a measure of susceptibility to aliasing is described. The susceptibility measure may be chosen to take into account many factors that affect perceived image quality. Experimental results are presented that illustrate the potential of the method.
SNPdisk: an efficient para-virtualization snapshot mechanism for virtual disks in private clouds (2011)

Using virtualization techniques, a cloud administrator can consolidate, distribute, and manage computing resources through a network from a central console. Existing open source virtual machine monitors, such as Xen, do not support virtual disk snapshot and rollback, which is important for clouds, especially for virtual cloud storage and computing resource management. Although traditional snapshot technologies may be directly applied to virtual cloud storage, they are inefficient and not fully reliable. Most seriously, the techniques impose limitations on the cloud environments. In this article, we present SNPdisk (snapshot disk), a para-virtualization snapshot mechanism, which uses a novel sparse tree scheme to implement reliable and efficient snapshots. Experiments with a prototype system demonstrate its high performance; it is especially useful for private clouds.
Role of Permanent Pacing to Prevent Atrial Fibrillation (2005)

This advisory summarizes the current database on pacing modalities and algorithms used to prevent and terminate atrial fibrillation (AF). On the basis of the evidence indicating that ventricular pacing is associated with a higher incidence of AF in patients with sinus node dysfunction, a patient who has a history of AF and needs a pacemaker for bradycardia should receive a physiological pacemaker (dual chamber or atrial) rather than a single-chamber ventricular pacemaker. For patients who need a dual-chamber pacemaker, efforts should be made to program the device to minimize the amount of ventricular pacing when atrioventricular conduction is intact. Many pacemakers and implantable defibrillators have features designed to prevent AF and to terminate AF with rapid atrial pacing. The evidence to support their use is limited, although these algorithms appear to be safe and usually add little additional cost. For patients who have a bradycardia indication for pacing and also have AF, no consistent data from large randomized trials support the use of alternative single-site atrial pacing, multisite right atrial pacing, biatrial pacing, overdrive pacing, or antitachycardia atrial pacing. Even fewer data support the use of atrial pacing in the management of AF in patients without symptomatic bradycardia. At present, permanent pacing to prevent AF is not indicated; however, additional studies are ongoing, which will help to clarify the role of permanent pacing for AF.
Grading Of Corneal and Conjunctival Staining in the Context of Other Dry Eye Tests (2003)

The monitoring and assessment of corneal and conjunctival staining can be greatly enhanced by the use of a grading scale, controlled instillation of dyes, and standard evaluation techniques. This is of particular benefit in clinical trials, where ocular surface staining is commonly employed as an outcome measure
Adoptive Cell Therapy for Patients with Melanoma (2011)

Adoptive cell therapy can be an effective treatment for some patients with advanced cancer. This report summarizes clinical trial results from the Surgery Branch, NCI, investigating tumor infiltrating lymphocytes (TIL) and gene engineered peripheral blood T cells for the therapy of patients with melanoma and other solid tumors.
Effects of Moenomycin on Escherichia coli (1987)

The antibiotic moenomycin is a valuable biochemical tool for studying the metabolism of peptidoglycan and the autolytic system in Escherichia coli, since as a specific inhibitor of peptidoglycan polymerases it can efficiently promote cell lysis. In liquid media the bacteriolytic effect on E. coli K12 was dependent on the concentration of moenomycin, on growth phase and on growth rate. Before lysis cells underwent major morphological alterations. In sucrose-containing medium complete transformation to osmotically sensitive spheroplasts was easily achieved by addition of moenomycin. The minimum inhibitory concentration of the antibiotic varied with the strain of E. coli and was highly dependent on the growth medium. A tritiated derivative of moenomycin, [3H]decahydromoenomycin A, was prepared and found to have the same inhibiting efficiency. Its binding to E. coli membranes and membrane proteins was investigated. The absence of irreversible binding suggested that moenomycin might be a competitive inhibitor of the peptidoglycan polymerases. Spontaneous moenomycin resistant variants were isolated at a frequency of about 10(-9).
[Causes of erroneous diagnosis in SOM]. (1994)

During the years of 1988-1990, 230 ears were diagnosed as secretory otitis media (SOM), with intact data, in which 23 ears failed to be diagnosed. Atypical symptom, carelessness in collection of history and in examining the tympanic membrane were considered as one of the important causes of erroneous diagnosis. Analysis of pure tone audiogram should be combined with the age and the former history of patients. "B" type tympanograph has 88% positive rate in diagnosing SOM. So in children, acoustic impedance should be used as a routine audiometric measurements, even if with clear history of receiving ototoxic drug.
Structure and Expression of a Chicken Insulin-Like Growth Factor I Precursor (1989)

Insulin-like growth factor I (IGF-I) is a 70 amino acid growth-promoting polypeptide whose sequence and functions have been highly conserved among mammals. As an initial step in defining the role of IGF-I in other vertebrate species, we have isolated and characterized an IGF-I cDNA from the chicken. This cDNA encodes a 153 amino acid primary translation product which resembles in structure and sequence the IGF-IA protein of mammals. There is strong amino acid conservation between chicken and mammalian IGF-I throughout the entire protein. Sixty of 70 amino acids are identical in mature IGF-I among the chicken, rat, and human peptides, with five differences being localized to the C domain, and two to the D region. A comparable degree of amino acid identity is found in the COOH-terminal extension peptide (28/35 residues). At the NH2-terminus, where there is more amino acid divergence (32/48 identities), the most 5'-AUG codon is the only methionine residue conserved among all three species, suggesting that it functions as the authentic translation initiation site, an observation supported by cell-free studies of biosynthesis and cotranslational proteolytic processing. The pattern of IGF-I gene expression appears to be simpler in chickens than in mammals, since a single predominant mRNA of 2.6 kilobases can be detected in liver polyadenylated RNA on Northern blots. In the chicken, as in rats and humans, IGF-I mRNA is synthesized in multiple tissues, including liver, brain, skeletal muscle, and heart.(ABSTRACT TRUNCATED AT 250 WORDS)
A 0.5 V 900 MHz CMOS Receiver Front End (2006)

A 900 MHz RF receiver front end including an LNA, downconversion mixer and associated LO buffers is presented. All circuits operate from a 0.5 V supply without any internal voltage boosting. The circuit is designed in 0.18 mum standard CMOS. It achieves a conversion gain of 12 dB, an IIP3 of -14 dBm and a noise figure of 9 dB. The circuit, including the LO buffers, dissipates 7.4 mW and occupies an active area of 0.43 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup>
CD44 and Bak Expression in IL-6 or TNF-alpha Gene Knockout Mice After Whole Lung Irradiation (2008)

To understand the molecular mechanisms that underlie radiation pneumonitis, we examined whether knockout of the TNF or the IL-6 gene could give mice an inherent resistance to radiation in the acute phase of alveolar damage after thoracic irradiation. The temporal expression of inflammation (CD44) and apoptosis (Bak) markers in lung after thoracic irradiation was measured to determine the degree of alveolar damage. At 4 weeks post-irradiation (10 Gy), small inflammatory foci were observed in all mice, but there were no obvious histological differences between control (C57BL/6JSlc), TNF-alpha knockout (TNF KO), and IL-6 knockout (IL-6 KO) mice. However, immunohistochemical analysis of CD44 and Bak expression over a time course of 2 weeks highlighted significant differences between the three groups. C57BL/6JSlc and TNF KO mice had increased numbers of both CD44-positive and Bak-positive cells after irradiation, while the IL-6 KO mice showed stable levels of CD44 and Bak. In conclusion, the radioresistant status of IL-6 KO mice in the acute phase of alveolar damage after irradiation suggested an important role for IL-6 in radiation pneumonitis.
Mucosal imbalance of IL-1 and IL-1 receptor antagonist in inflammatory bowel disease. A novel mechanism of chronic intestinal inflammation. (1995)

The etiology and pathogenesis of inflammatory bowel disease (IBD) are unknown. Increasing evidence supports the theory that chronic IBD is the result of dysfunctional immunoregulation manifested by an inappropriate production of mucosal cytokines. The aim of the present study was to test the hypothesis that a specific mucosal imbalance of IL-1 and IL-1 receptor antagonist (IL-1ra) production plays an important role in the perpetuation and chronicity of intestinal inflammation. Total IL-1, IL-1ra, and the IL-1ra/IL-1 ratio were measured in freshly isolated intestinal mucosal cells, as well as in mucosal biopsies obtained from control, Crohn's disease, and ulcerative colitis patients. IL-1 alpha, IL-1 beta, and IL-1 ra were measured by specific non-cross-reacting radioimmunoassays and ELISA. A markedly significant decrease in the intestinal mucosal IL-1ra/IL-1 ratio was found in both Crohn's disease and ulcerative colitis patients when compared with control subjects (p < 0.01). The IL-1ra/IL-1 ratio correlated closely with the clinical severity of disease (r = -0.7846, p < 0.001). Furthermore, the observed decrease in the IL-1ra/IL-1 ratio was specific for IBD because a decreased IL-1ra/IL-1 ratio was not found in patients with self-limiting colitis. These results support the hypothesis that an imbalance between IL-1 and IL-1ra production is of pathogenic importance in chronic inflammatory diseases, including IBD.
Increased plasma soluble fms-like tyrosine kinase 1 and endoglin levels in pregnancies complicated with preeclampsia (2009)

Consistent with previous reports, increased sFlt-1 and Eng levels in maternal plasma is consistent with vascular dysfunction found in gestations complicated with preeclampsia.
Inflammatory cytokines and related genes are induced in the rat hippocampus by limbic status epilepticus (2000)

Limbic status epilepticus was induced in rats by unilateral 60-min electrical stimulation of the CA3 region of the ventral hippocampus. As assessed by RT-PCR followed by Southern blot analysis, transcripts of interleukin-1beta, interleukin-6, interleukin-1 receptor antagonist and inducible nitric oxide synthase were significantly increased 2 h after status epilepticus in the stimulated hippocampus. Induction was maximal at 6 h for interleukin-1beta (445%), interleukin-6 (405%) and tumour necrosis factor-alpha (264%) and at 24 h for interleukin-1 receptor antagonist (494%) and inducible nitric oxide synthase (432%). In rats with spontaneous seizures (60 days after status epilepticus), interleukin-1beta mRNA was still higher than controls (241%). Immunocytochemical staining of interleukin-1beta, interleukin-6 and tumour necrosis factor-alpha was enhanced in glia with a time-course similar to that of the respective transcripts. Sixty days after status epilepticus, interleukin-1beta immunoreactivity was increased exclusively in neurons in one third of the animals. Multiple intracerebroventricular injections of interleukin-1 receptor antagonist (0.5 microg/3 microL) significantly decreased the severity of behavioural convulsions during electrical stimulation and selectively reduced tumour necrosis factor-alpha content in the hippocampus measured 18 h after status epilepticus. Thus, the induction of spontaneously recurring seizures in rats involves the activation of inflammatory cytokines and related pro- and anti-inflammatory genes in the hippocampus. These changes may play an active role in hyperexcitability of the epileptic tissue.
FRET Imaging of Enzyme‐Responsive HPMA Copolymer Conjugate (2016)

Fluorescence resonance energy transfer (FRET) is applied to investigate the enzyme-responsive payload release from a macromolecular therapeutic. The donor Cy5 is attached to the N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer backbone and the acceptor Cy7 is bound to the termini of enzyme-sensitive peptide side chains. Upon exposure to an enzyme, the bond between the peptide and Cy7 is cleaved, thereby leading to the loss of FRET signal. This enzyme response is visualized at the cell, tissue and whole-body levels. The in vitro results demonstrate that high expression of cathepsin B in tumor cells induces effective release of the drug model from conjugates resulting in a high concentration of payload inside tumor cells. The in vivo and ex vivo images show that the conjugate releases drug model faster in the ovarian tumor than in the normal tissues. The information will enhance the understanding of enzyme-responsive polymer carriers and help to shape their design.
Identification of Genes Affecting Lycopene Formation in Escherichia coli Transformed with Carotenoid Biosynthetic Genes: Candidates for Early Genes in Isoprenoid Biosynthesis (1998)

Although isopentenyl diphosphate is a precursor of isoprenoids in Escherichia coli, the genes and enzymes involved in its biosynthesis have not been identified. Thus, we tried to isolate E. coli mutants deficient in the biosynthesis and their complementary genes by use of an artificial phenotypic screening system employing three carotenoid biosynthetic genes, crtE, crtB, and crtI. Cells were mutagenized with ethylmethanesulfonate, then transformed with a plasmid for expression of the carotenogenic genes. Mutants deficient in biosynthesis of isopentenyl diphosphate were expected to form white colonies, because they are unable to produce enough lycopene, whereas wild-type cells form red colonies. Among large numbers of red colonies, we identified 117 white colonies. Next, we transformed each mutant with an E. coli genomic library. Twenty-nine complementary genes that restore red color of host colonies were isolated. A homology search and further complementation study using subcloned genes revealed that the true complementary genes encode isopentenyl diphosphate isomerase, subunits of ATP synthase, enzymes of the Krebs cycle, some aldehyde dehydrogenases, phosphate acetyltransferase, and enzymes which relate to the biosynthesis of ubiquinones and menaquinones. Two unknown genes were also found, designated elb1 and 2, which may be involved in the early steps of isoprenoid biosynthesis.
Protein content and biophysical properties of tracheal aspirates form neonates with respiratory failure1 (2002)

These results suggest in larger newborns a secondary surfactant deficiency due to protein-leakage to play an important role in the pathogenesis of respiratory failure. The increased alveolar-capillary membrane permeability might be caused by inflammatory ARDS-like mechanisms.