gebhart/patrepeval huggingface dataset:
Identification of the Epitope for the Epidermal Growth Factor Receptor-specific Monoclonal Antibody 806 Reveals That It Preferentially Recognizes an Untethered Form of the Receptor (2004)

The epidermal growth factor receptor (EGFR) is overexpressed in many epithelial cancers, an observation often correlated with poor clinical outcome. Overexpression of the EGFR is commonly caused by EGFR gene amplification and is sometimes associated with expression of a variant EGFR (de2-7 EGFR or EGFRvIII) bearing an internal deletion in its extracellular domain. Monoclonal antibody (mAb) 806 is a novel EGFR antibody with significant antitumor activity that recognizes both the de2-7 EGFR and a subset of the wild type (wt) EGFR when overexpressed but does not bind the wt EGFR expressed in normal tissues. Despite only binding to a low proportion of the wt EGFR expressed in A431 tumor cells (approximately 10%), mAb 806 displays robust antitumor activity against A431 xenografts grown in nude mice. To elucidate the mechanism leading to its unique specificity and mode of antitumor activity, we have determined the EGFR binding epitope of mAb 806. Analysis of mAb 806 binding to EGFR fragments expressed either on the surface of yeast or in an immunoblot format identified a disulfide-bonded loop (amino acids 287-302) that contains the mAb 806 epitope. Indeed, mAb 806 binds with apparent high affinity (approximately 30 nm) to a synthetic EGFR peptide corresponding to these amino acids. Analysis of EGFR structures indicates that the epitope is fully exposed only in the transitional form of the receptor that occurs because EGFR changes from the inactive tethered conformation to a ligand-bound active form. It would seem that mAb 806 binds this small proportion of transient receptors, preventing their activation, which in turn generates a strong antitumor effect. Finally, our observations suggest that the generation of antibodies to transitional forms of growth factor receptors may represent a novel way of reducing normal tissue targeting yet retaining antitumor activity.
Molecular basis for the herbicide resistance of Roundup Ready crops (2006)

The engineering of transgenic crops resistant to the broad-spectrum herbicide glyphosate has greatly improved agricultural efficiency worldwide. Glyphosate-based herbicides, such as Roundup, target the shikimate pathway enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, the functionality of which is absolutely required for the survival of plants. Roundup Ready plants carry the gene coding for a glyphosate-insensitive form of this enzyme, obtained from Agrobacterium sp. strain CP4. Once incorporated into the plant genome, the gene product, CP4 EPSP synthase, confers crop resistance to glyphosate. Although widely used, the molecular basis for this glyphosate-resistance has remained obscure. We generated a synthetic gene coding for CP4 EPSP synthase and characterized the enzyme using kinetics and crystallography. The CP4 enzyme has unexpected kinetic and structural properties that render it unique among the known EPSP synthases. Glyphosate binds to the CP4 EPSP synthase in a condensed, noninhibitory conformation. Glyphosate sensitivity can be restored through a single-site mutation in the active site (Ala-100-Gly), allowing glyphosate to bind in its extended, inhibitory conformation.
A model for the regulation of the calmodulin-dependent enzymes erythrocyte Ca2+-transport ATPase and brain phosphodiesterase by activators and inhibitors (1982)

Acidic phospholipids, unsaturated fatty acids and limited proteolysis mimic the activating effect of calmodulin on erythrocyte Ca2+-transport ATPase and on brain cyclic nucleotide phosphodiesterase, as has been reported previously in several studies. Three different antagonists of calmodulin-induced activation of these enzymes were tested for their inhibitory potency on the stimulation produced by the other activators. Trifluoperazine and penfluridol were found to antagonize all the above mentioned types of activation of Ca2+-transport ATPase in the same concentration range. Both inhibitors also can reverse the activation of phosphodiesterase by oleic acid, phosphatidylserine and calmodulin at similar concentrations. However, in contrast with erythrocyte Ca2+-transport ATPase, activation of phosphodiesterase by limited tryptic digestion cannot be antagonized by penfluridol and trifluoperazine. Calmidazolium, formerly referred to as compound R 24571, was found to be a relatively specific inhibitor of calmodulin-induced activation of phosphodiesterase and Ca2+-transport ATPase, since antagonism of the other activators required much higher concentrations of the drug. The results suggest that the investigated drugs exert their inhibitory effect on calmodulin-regulated enzymes not solely via their binding to calmodulin but may also interfere directly with the calmodulin effector enzyme. In addition, a general mechanism of activation and inhibition of calmodulin-dependent enzymes is derived from our results.
Identification and characterization of a selenoprotein family containing a diselenide bond in a redox motif (2007)

Selenocysteine (Sec, U) insertion into proteins is directed by translational recoding of specific UGA codons located upstream of a stem-loop structure known as Sec insertion sequence (SECIS) element. Selenoproteins with known functions are oxidoreductases containing a single redox-active Sec in their active sites. In this work, we identified a family of selenoproteins, designated SelL, containing two Sec separated by two other residues to form a UxxU motif. SelL proteins show an unusual occurrence, being present in diverse aquatic organisms, including fish, invertebrates, and marine bacteria. Both eukaryotic and bacterial SelL genes use single SECIS elements for insertion of two Sec. In eukaryotes, the SECIS is located in the 3' UTR, whereas the bacterial SelL SECIS is within a coding region and positioned at a distance that supports the insertion of either of the two Sec or both of these residues. SelL proteins possess a thioredoxin-like fold wherein the UxxU motif corresponds to the catalytic CxxC motif in thioredoxins, suggesting a redox function of SelL proteins. Distantly related SelL-like proteins were also identified in a variety of organisms that had either one or both Sec replaced with Cys. Danio rerio SelL, transiently expressed in mammalian cells, incorporated two Sec and localized to the cytosol. In these cells, it occurred in an oxidized form and was not reducible by DTT. In a bacterial expression system, we directly demonstrated the formation of a diselenide bond between the two Sec, establishing it as the first diselenide bond found in a natural protein.
p53- specific CD8~+ T- cell responses in individuals with cutaneous squamous cell carcinoma (2006)

Background: Systemic immunosuppression is a significant risk factor for cutaneous squamous cell carcinoma (SCC). p53 is mutated and overexpressed in up to 90% of cutaneous SCC lesions. Despite considerable evidence that the immune response is important in the control of cutaneous SCC, there are no studies documenting potential tumour- associated antigens. Objectives: We tested the hypothesis that individualswith cutaneous SCC have functional circulating CD8+ T cells specific for p53. Methods: Interferon- γ immunosorbent assays were used to screen peripheral blood mononuclear cells for reactivity to six p53- derived HLA- A 0201- restricted epitopes from HLA- A 0201- positive patients and controls. Results: We observed significantly elevated frequencies of p53- specific CD8+ T cells in seven of 26 individuals with cutaneous SCC and in one of 10 controls. The degree of lymphocytic infiltrate significantly correlated with the frequency of CD8+ T cells specific for p53 epitopes, but not with control epitopes. Conclusions: Overall, these data suggest that p53 may represent a target for CD8+ T cells in a proportion of individuals with cutaneous SCC.
Project synopsis (1997)

Ths paper describes preliminary efforts at evaluating the performance of the Stanford real-time information processor (STRIP v2.0). We de~ribe a benchmm'k for active real-time aat~es based on a program trading application and report STRIP's performance on this benchmark.
Basic Processes Underlying Agrobacterium-Mediated DNA Transfer To Plant Cells (1988)

REVIEWSAgrobacterium chromosome.Three chromosomal virulence loci, chvA and chvB (23, 24) and pscA (89), encode products involved in the binding of Agrobacterium to plant cells during the infection process.The chvA and chvB are located on a 15.5 kbp segment of the Agrobacterium chromosome.The 8.5 kbp chvB portion encodes a membrane protein of approximately 235 kilodaltons (kd) that acts an an intermediate in the synthesis of cyclic /3-1,2glucan (77, 115) , and chvA may encode a transport function (E.Nester,
Unraveling the Molecular Mechanisms of Photoacidity (2003)

Distinct class of photoinduced hydrogen-atom-transfer processes: phototautomerizations in molecules with no intramolecular hydrogen bond in the structure,
Disappearance kinetics of solutes from synovial fluid after intra‐ articular injection. (1994)

1. Five rheumatoid patients with a knee joint effusion participated in the study. An aqueous solution (0.1 to 0.2 ml) containing paracetamol, salicylate, diclofenac and [125I]-albumin was injected into a given joint to yield target concentrations of approximately 20 micrograms ml-1 for diclofenac, salicylate and paracetamol and 10(8) counts ml-1 for [125I]-albumin. 2. Paracetamol, salicylate and diclofenac were analysed in synovial fluid by h.p.l.c. [125I]-albumin was analysed using gamma counting. 3. The clearances (+/- s.d.) obtained for the solutes were [125I]-albumin (0.0053 +/- 0.0019 l h-1), diclofenac (0.0096 +/- 0.0061 l h-1), salicylate (0.024 +/- 0.022 l h-1) and paracetamol (0.055 +/- 0.041 l h-1). The corresponding fractions unbound of these solutes in synovial fluid were 0.0, < or = 0.01, 0.34 +/- 0.09 and 0.85 +/- 0.10, respectively. 4. Diffusion of unbound solute through the synovium is estimated to account for (+/- s.d.) 0.52 +/- 0.08, 0.87 +/- 0.06 and 0.99 +/- 0.01 of the total clearance of diclofenac, salicylate and paracetamol from the joint space, respectively. The remaining proportion of clearance is accounted for by efflux of solute bound to albumin. 5. An expression for the ratio of synovial fluid to total plasma concentrations after systemic administration was developed to include both diffusion of unbound solute and albumin flux. Most solutes appear to satisfy the conditions in which this expression reduces to the limiting case where the unbound concentration of the solute is identical in the synovial fluid and plasma under steady state conditions.
Production of biallelic CMP-Neu5Ac hydroxylase knock-out pigs (2013)

After the knock-out (KO) of α1,3 galactosyltransfease (Gal-T), the Hanganutziu-Deicher antigen became a major antigen of the "non-Gal antigen" that is implicated in subsequent xenograft rejection. For deletion of non-Gal antigen, we successfully produced zinc finger nuclease (ZFN)-mediated monoallelic/biallelic male and female CMP-N-acetylneuraminic acid hydroxylase (CMAH) KO miniature pigs: the efficiency of the gene targeting (41.7%) was higher when donor DNA was used with the ZFN than those of ZFN alone (9.1%). Monoallelic KO pigs had no integration of exogenous DNA into their genome, indicating that this technique would provide a new avenue to reduce the risk of antibiotics resistance when organs from genetically modified pigs are transplanted into patients. Until now, both monoallelic and biallelic CMAH KO pigs are healthy and show no sign of abnormality and off-target mutations. Therefore, these CMAH null pigs on the Gal-T KO background could serve as an important model for the xenotransplantation.
Stability of yellow fever vaccine. (1996)

Yellow fever, an acute mosquito-borne viral haemorrhagic fever, is preventable by use of the live, attenuated 17D vaccine. The vaccine is used principally in tropical climates and is subject to potentially adverse conditions. Lyophilized vaccine without stabilizers deteriorates rapidly when exposed to temperatures above -20 degrees C. In 1987, the WHO recommended that each lot of vaccine meet the following stability test: maintenance of potency (> 1,000 mouse i.c.LD50/human dose) with mean loss of titre < 1.0 log10 after being held at 37 degrees C for 14 days. In 1987, only 5 out of 12 yellow fever vaccines produced worldwide met the stability standards. To improve stability of the vaccine, a number of additives have been systematically investigated. A successful formulation, now used by a number of manufacturers, employs sugars, amino acids, and divalent cations [lactose (4%), sorbitol (2%), histidine (0.01 M), alanine (0.01 M), in phosphate buffered saline with Ca2+ and Mg2+]. As opposed to vaccine produced without stabilizers, which loses 1.5-2.5 log10/dose, stabilized vaccines lose only 0.3-0.5 log10 after being held at 37 degrees C for 14 days. The vaccine is stable after storage for > or = two years at 4 degrees C and 22 degrees C, and has a stability profile as good or better than many other live and inactivated vaccines currently used in the EPI, including measles, pertussis, oral and inactivated poliomyelitis vaccines. WHO is taking steps to enssure that all 11 current YF vaccine manufacturers produce vaccines that meet accepted stability standards. The principal rationale for increasing 17D vaccine stability beyond that achieved with the present stabilizers would be the improvement in stability of other EPI vaccines, to the point where yellow fever vaccine was the most sensitive vaccine among those deployed. The acceptable characteristics of current stabilized 17D vaccines and the high cost of changing and validating new vaccine formulations precludes a major investment at this time. Despite its stability when freeze dried, yellow fever 17D vaccine is quite unstable after reconstitution and must be discarded after one hour. Improvement in vaccine stability after reconstitution would thus reduce cost, stretch supplies of vaccine, and ensure against vaccine failures due to use of degraded vaccine. This is an area for future research.
<title>Uniaxis rangefinder using contrast detection of a projected pattern</title> (2001)

12 Many methods have been proposed for range finding systems to know the distance of the targets. We try to capture profiles of objects in addition to the distance of objects using optical principle. When a grating pattern is projected on to the object to be measured, the projected pattern is sharply observed on a focused plane. And the pattern blurs due to defocusing except on this focused plane. We detect contrast variation of the projected grating pattern and calculate the distance to the object and captures its shapes at the same time. This method features in using merely one optical axis in range finding system.
DESIGN OF AN EFFICIENT AND RAPID CHEMICAL VAPOR INFILTRATION (CVI) RE-CIRCULATION SYSTEM (2013)

Carbon-carbon (C/C, carbon fiber reinforced carbon matrix) composites are widely used in the aerospace industry because of the material's high temperature capability and structural properties. C/C maintains its mechanical and friction properties during extreme conditions so it is used extensively for high energy brakes, clutches, nosecones and leading edges of aircraft/spacecraft. Manufacturing C/C is expensive, requires high temperatures (approx. 1000°C) and typically requires rough vacuum environments (5-225 Torr). There are 5 general types of chemical vapor infiltration (CVI) systems and each type has a standard configuration in terms of a vacuum plumbing circuit. Standard CVI systems have a total carbon deposition efficiency of 5-30% using a reaction zone filled with carbon fiber preforms. Total processing time varies from 50 to 2000 hours depending on the type of system and its temperature, pressure and residence time. Unused hydrocarbon reaction exhaust (effluent) gases are either burned off or used to power something externally adding more CO2 and CO to the environment. A reduction of processing time and waste is needed to reduce the cost of production and the emissions of greenhouse gases. A new method can be added to 4 of the general types of CVI that decreases the residence time by re-circulating a controlled amount of the effluent gases through a separate in-situ isobaric semi-closed loop circuit which also allows for more carbon to be deposited per liter of virgin precursor gas in the reaction zone. An electric potential is also applied to compare the effect on carbon deposition to standard techniques. Re-circulating a portion of effluent gases through the reaction zone decreases the residence time with minimal effect on the desired matrix microstructure. Decreasing the residence time and re-circulating a portion of effluent gases increases the deposition rate and total carbon deposition efficiency. This re-circulating loop can be added to any CVI system to enhance the process, lower production costs and reduce greenhouse emissions.
Multilayer Hybrid Microfluidics: A Digital-to-Channel Interface for Sample Processing and Separations (2010)

Microchannels can separate analytes faster with higher resolution, higher efficiency and with lower reagent consumption than typical column techniques. Unfortunately, an impediment in the path toward fully integrated microchannel-based laboratories-on-a-chip is the integration of preseparation sample processing. In contrast, the alternative format of digital microfluidics (DMF), in which discrete droplets are manipulated on an array of electrodes, is well-suited for carrying out sequential chemical reactions such as those commonly employed in proteomic sample preparation. We recently reported a new paradigm of "hybrid microfluidics," integrating DMF with microchannels for in-line sample processing and separations. Here, we build on our initial efforts, introducing a second-generation hybrid microfluidic device architecture. In the new multilayer design, droplets are manipulated by DMF in the two-plate format, an improvement that facilitates dispensing samples from reservoirs, as well as droplet splitting and storage for subsequent analysis. To demonstrate the capabilities of the new method, we implemented an on-chip serial dilution experiment, as well as multistep enzymatic digestion. Given the myriad applications requiring preprocessing and chemical separations, the hybrid digital-channel format has the potential to become a powerful new tool for micro total analysis systems.
A retrospective study of direct pulp capping with calcium hydroxide compounds (1985)

Abstract Direct pulp capping with calcium hydroxide compounds was performed on 510 human teeth. Pulp had been exposed as a result of cavity preparation in 70% of cases, and by removal of carious dentine in 15%. For the remaining 15% of the cases no information on the cause of exposure was available. The teeth were clinically and radiographically controlled 1, 3, 6 and 12 months after treatment and at the stopping date. 245 cases were available for clinical examination. Information on the remaining cases was obtained from the records. Using the life table method, the trial time was calculated for each case as the time from dale of treatment to the date of failure, the date of last contact or the stopping date. The data were analyzed according to cause of perforation, age of patient and type of tooth. Five‐year survival was 82% No significant difference in survival was observed between non‐carious and small carious exposures. Young teeth and molars showed a higher survival rate when the longer observation periods were considered.
Whither Goest NTIA? The Fate of a Federal Telecommunications Agency (1996)

In the past year, Congress has sealed the fate of the National Telecommunications and Information Administration (NTIA). Although President Clinton has pledged to veto any action that abolishes the Commerce Department, in which the NTIA is located, Congress will ultimately dismantle the NTIA. Thus, the question becomes what entity will shoulder NTIA's workload, which includes among other responsibilities managing federal use of the radio frequency spectrum, developing executive branch telecommunications policy, and administering the Federal Grants Program. Although the Federal Communications Commission (FCC) appears to many a natural successor to the NTIA's varied responsibilities, the Authors suggest other agencies are more appropriate. For instance, relocation of NTIA's spectrum management functions are better suited to the General Services Administration (GSA), Office of Management and Budget (OMB), or the Treasury Department. The Authors indicate that these agencies are in a more neutral position than the FCC because they do not have a relationship with the private sector which makes balancing the needs of competing groups difficult. Moreover, the NTIA's policy-making functions should remain with an executive branch agency in order to provide the president the ability to take independent positions on telecommunications issues.
Risk Factors For Nosocomial Legionella Pneumophila Pneumonia (1994)

Over a 5-yr period, from January 1985 to January 1990, we prospectively studied 300 episodes of nosocomial pneumonia in a 1,000-bed teaching hospital. All cases had an accurate bacteriologic diagnosis obtained by means of highly reliable techniques. Legionella pneumophila caused a total of 36 episodes; 22 were endemic and 14 occurred during an epidemic outbreak. No patient with Legionella pneumonia had been intubated before infection. To identify risk factors for nosocomial L. pneumophila pneumonia, we compared the 22 endemic cases of nosocomial pneumonia due to L. pneumophila with the 264 cases due to other bacteria. After adjusting for other variables by means of logistic regression analysis, cytotoxic chemotherapy (OR = 5.2; 95% CI, 1.5 to 17.9) and use of corticosteroids (OR = 4.6; 95% CI, 1.5 to 14.1) were positively associated with L. pneumophila pneumonia, whereas previous antibiotic therapy (OR = 0.2; 95% CI, 0.1 to 0.8) and lowered consciousness (OR = 0.2; 95% CI, 0.07 to 0.8) were negatively associated. The major risk factors for Legionella pneumonia delineated in this study should be considered in the clinical approach to and empiric therapy of patients with suspected nosocomial pneumonia.
Decomposed eigenface for face recognition under various lighting conditions (2005)

Face recognition under various lighting condition's is discussed to cover cases when too few images are available for registration. This paper proposes decomposition of an eigenface into two orthogonal eigenspaces for realizing robust face recognition under such conditions. The decomposed eigenfaces consisting of two eigenspaces are constructed for each person even if only one image is available. A universal eigenspace called the canonical space (CS) plays an important role in creating the eigenspaces by way of decomposition, where CS is constructed a priori by principal component analysis (PCA) over face images of many people under many lighting conditions. In the registration stage, an input face image is decomposed to a projection image in CS and the residual of the projection. Then two eigenspaces are created independently in CS and in the orthogonal complement CS/sup /spl perp//. Some refinements of the two eigenspaces are also discussed. By combining the two eigenspaces, we can easily realize face identification that is robust to illumination change, even when too few images are registered. Through experiments, we show the effectiveness of the decomposed eigenfaces as compared with conventional methods.