gebhart/patrepeval huggingface dataset:
Identification of a cysteine-rich receptor for fibroblast growth factors. (1992)

The fibroblast growth factor (FGF) family consists of seven members whose activities are thought to be mediated by multiple receptors. Here we describe the cDNA cloning, expression, and characterization of a cysteine-rich FGF receptor (CFR) that is distinct from previously identified FGF receptors. The deduced amino acid sequence for CFR suggests that it is an integral membrane protein containing a large extracellular domain comprising 16 cysteine-rich repeated units and an intracellular domain of 13 amino acids. No reported sequences exhibit significant homologies to either the repeated extracellular motif or to the entire CFR amino acid sequence. Several CFR transcripts are present in embryonic chick tissue, suggesting that CFR undergoes alternate mRNA splicing or that related genes are present. Chinese hamster ovary cells transfected with the CFR cDNA express a 150-kDa polypeptide that binds FGF-1, FGF-2, and FGF-4 but does not bind several non-FGF family members. The high degree of evolutionary conservation among vertebrate CFRs and its ability to bind three different FGFs with high affinity suggest that this unique receptor plays an important role in FGF biology.
Ser67Asp and His68Asp Substitutions in Candida parapsilosis Carbonyl Reductase Alter the Coenzyme Specificity and Enantioselectivity of Ketone Reduction (2009)

A short-chain carbonyl reductase (SCR) from Candida parapsilosis catalyzes an anti-Prelog reduction of 2-hydroxyacetophenone to (S)-1-phenyl-1,2-ethanediol (PED) and exhibits coenzyme specificity for NADPH over NADH. By using site-directed mutagenesis, the mutants were designed with different combinations of Ser67Asp, His68Asp, and Pro69Asp substitutions inside or adjacent to the coenzyme binding pocket. All mutations caused a significant shift of enantioselectivity toward the (R)-configuration during 2-hydroxyacetophenone reduction. The S67D/H68D mutant produced (R)-PED with high optical purity and yield in the NADH-linked reaction. By kinetic analysis, the S67D/H68D mutant resulted in a nearly 10-fold increase and a 20-fold decrease in the k(cat)/K(m) value when NADH and NADPH were used as the cofactors, respectively, but maintaining a k(cat) value essentially the same with respect to wild-type SCR. The ratio of K(d) (dissociation constant) values between NADH and NADPH for the S67D/H68D mutant and SCR were 0.28 and 1.9 respectively, which indicates that the S67D/H68D mutant has a stronger preference for NADH and weaker binding for NADPH. Moreover, the S67D/H68D enzyme exhibited a secondary structure and melting temperature similar to the wild-type form. It was also found that NADH provided maximal protection against thermal and urea denaturation for S67D/H68D, in contrast to the effective protection by NADP(H) for the wild-type enzyme. Thus, the double point mutation S67D/H68D successfully converted the coenzyme specificity of SCR from NADP(H) to NAD(H) as well as the product enantioselectivity without disturbing enzyme stability. This work provides a protein engineering approach to modify the coenzyme specificity and enantioselectivity of ketone reduction for short-chain reductases.
Real time aircraft simulation using J-MASS (2002)

McDonnell Douglas Aerospace (MDA) has developed a six degree-of-freedom (DOF) aircraft model that is suitable for use at various levels of simulation, from manned to interactive to all digital. The model is based on the performance of the aircraft being simulated and is used for development of flying qualities criteria or for existing simulations where high angle of attack, take-off's and landings are not required. The model is ideal for use in air combat studies where the exact performance of the model is known and real time operation is required (20 Hertz update rate). The original aircraft model was written in FORTRAN and is still in use. When a manned simulation is not needed, digital pilot logic provides stick and throttle inputs to the model. Available maneuvers include lever flight, sustained turns, waypoint following and others. This model has been rewritten in Ada and re-engineered to add additional capabilities. The model has become more object oriented, and still updates in real-time. In addition, an Ada interface has been added to the model so it is compliant with the Joint Modeling and Simulation System (J-MASS).
Truncating mutation of theDFNB59gene causes cochlear hearing impairment and central vestibular dysfunction (2007)

We have identified a consanguineous family from Morocco segregating autosomal recessive congenital progressive hearing loss (ARNSHL) and retinal degeneration. Detailed clinical investigation of the six siblings revealed combined severe cone-rod dystrophy (CORD) and severe/profound hearing impairment in two of them, while there is isolated CORD in three and nonsyndromic profound hearing loss in one. We therefore assumed a partial overlap of two nonsyndromic autosomal recessive conditions instead of a monogenic syndrome and performed genomewide linkage analysis. The disease loci were mapped to chromosome 2q31.1-2q32.1 for ARNSHL and to 2q13-2q14.1 for CORD, respectively. The retinal phenotype was shown to be due to homozygosity for a novel splice site mutation, c.2189+1G>T, in the retinitis pigmentosa gene MERTK. The ARNSHL interval comprised the DFNB59 locus. The DFNB59 gene has been identified recently, and two missense mutations (p.R183W and p.T54I) have been shown to cause auditory neuropathy in both humans and transgenic mice. Mutation screening in the DFNB59 gene in our family revealed homozygosity for a 1-bp insertion in exon 2 (c.113_114insT), predicting a truncated protein of 47 amino acids, in all three hearing impaired subjects. This is the first description of biallelic putative loss-of-function of the DFNB59 gene. Detailed audiological investigation clearly indicated hair cell dysfunction and, in contrast to cases reported previously, excluded auditory neuropathy. We show that besides otoferlin (OTOF), DFNB59 is the second known gene in which mutations can result in these two distinct forms of hearing impairment. Moreover, all patients in our family with homozygosity for the DFNB59 mutation display central vestibular dysfunction.
Heparin kinetics determined by three assay methods (1982)

Heparin kinetics were determined in four normal subjects, each of whom received three different doses (25, 50, and 75 units/kg body weight) by intravenous injection. Multiple blood samples were collected after each dose and each plasma sample was assayed for heparin activity using three different assay methods. Two of these assays are based on coagulation tests, i.e., activated partial thromboplastin time and thrombin time, while the third is based on chemical neutralization of heparin using hexadimethrine bromide. Heparin kinetics showed pronounced dose-dependent changes, irrespective of the assay method used, which were characterized by increasing biologic half-life and decreasing total clearance (Cl) with increasing dose. No changes were noted in apparent volume of distribution (Vd). This data also showed that there were differences in kinetic parameters of heparin depending on the assay method. In general, values for total Cl and apparent Vd based on chemical neutralization were approximately 1.5 to 2.0 times these parameters based on coagulation tests. We conclude that the immediate mechanism of the dose-dependent heparin kinetics is decreasing total clearance with increasing dose and suggest that in vivo activation of the anticoagulant properties of heparin may explain the assay-dependent kinetics.
A Sterile α-Motif Domain in NafY Targets Apo-NifDK for Iron-Molybdenum Cofactor Delivery via a Tethered Domain (2010)

NafY participates in the final steps of nitrogenase maturation, having a dual role as iron-molybdenum cofactor (FeMo-co) carrier and as chaperone to the FeMo-co-deficient apo-NifDK (apo-dinitrogenase). NafY contains an N-terminal domain of unknown function (n-NafY) and a C-terminal domain (core-NafY) necessary for FeMo-co binding. We show here that n-NafY and core-NafY have very weak interactions in intact NafY. The NMR structure of n-NafY reveals that it belongs to the sterile α-motif (SAM) family of domains, which are frequently involved in protein-protein interactions. The presence of a SAM domain in NafY was unexpected and could not be inferred from its amino acid sequence. Although SAM domains are very commonly found in eukaryotic proteins, they have rarely been identified in prokaryotes. The n-NafY SAM domain binds apo-NifDK. As opposed to full-length NafY, n-NafY impaired FeMo-co insertion when present in molar excess relative to FeMo-co and apo-NifDK. The implications of these observations are discussed to offer a plausible mechanism of FeMo-co insertion. NafY domain structure, molecular tumbling, and interdomain motion, as well as NafY interaction with apo-NifDK are consistent with the function of NafY in FeMo-co delivery to apo-NifDK.
Preparation of biologically active platelet‐derived growth factor isoforms AA and AB (1990)

We have expressed the mature platelet-derived growth factor (PDGF) A chain within a fusion protein of the cro repressor and beta-galactosidase in Escherichia coli. Monomeric PDGF-A was excised from this fusion protein by CNBr cleavage. After protection of thiols by S-sulfonation, this fragment was purified by gel permeation chromatography and reversed-phase high-performance liquid chromatography. The monomeric protein was dimerized in the presence of a mixture of reduced and oxidized glutathione to yield biologically active recombinant AA dimer (rPDGF-AA) with an overall yield of about 0.2 mg/l culture. When monomeric rPDGF-A and rPDGF-B were reacted at stoichiometric concentrations in the presence of glutathione, almost exclusively hetero-dimers of type AB were formed. Heterodimers AB stimulated [3H]thymidine incorporation into AKR-2B fibroblasts half-maximally at about 2 ng/ml. AA homodimers were fivefold less active. About 60,000 binding sites were found for rPDGF-AB, 30,000 for rPDGF-AA and 45,000 for rPDGF-BB on AKR-2B fibroblasts.
Droplet-trace-based array partitioning and a pin assignment algorithm for the automated design of digital microfluidic biochips (2006)

Microfluidics-based biochips combine electronics with biology to open new application areas such as point-of-care medical diagnostics, on-chip DNA analysis, and automated drug discovery. Bioassays are mapped to microfluidic arrays using synthesis tools, and they are executed through the manipulation of sample and reagent droplets by electrical means. Most prior work on CAD for biochips has assumed independent control of electrodes using a large number of (electrical) input pins. Such solutions are not feasible for low-cost disposable biochips that are envisaged for many field applications. A more promising design strategy is to divide the microfluidic array into smaller partitions and use a small number of electrodes to control the electrodes in each partition. We propose a partitioning algorithm based on the concept of "droplet trace", which is extracted from the scheduling and droplet routing results produced by a synthesis tool. An efficient pin assignment method, referred to as the "Connect-5 algorithm", is combined with the array partitioning technique based on droplet traces. The array partitioning and pin assignment methods are evaluated using a set of multiplexed bioassays.
Clinical Validation Study of Percutaneous Cochlear Access Using Patient-Customized Microstereotactic Frames (2009)

These results demonstrate the feasibility of PCI access using customized microstereotactic frames.
Chemometric Quantitation of the Active Substance (Containing C≡N) in a Pharmaceutical Tablet Using Near-Infrared (NIR) Transmittance and NIR FT-Raman Spectra (2002)

In this study, near-infrared (NIR) transmittance and Raman spectroscopy chemometric calibrations of the active substance content of a pharmaceutical tablet were developed using partial least-squares regression (PLS). Although the active substance contained the strongly Raman active C≡N functional group, the best results were obtained with NIR transmittance, which highlights the difference between (microscopic) surface sampling and whole tablet diffuse transmittance sampling. The tablets exist in four dosages with only two different concentrations of active substance (5 mg (5.6% w/w), and 10, 15, and 20 mg (8.0% w/w) active substance per tablet). A calibration on all four dosages resulted in a prediction error expressed as the root mean squared error of cross-validation (RMSECV) of 0.30% w/w for the NIR transmittance calibration. The corresponding error when using Raman spectra was 0.56% w/w. Specially prepared calibration batches covering the range 85–115% of the nominal content for each dosage were added to the first sample set, and NIR transmittance calibrations on this set—containing coated as well as uncoated tablets—gave a further reduction in prediction errors to 0.21–0.289% w/w. This corresponds to relative prediction errors (RMSECV/y nom ) of 2.6–3.7%. This is a reasonably low error when compared to the error of the chromatographic reference method, which was estimated to 3.5%.
Embedding speech in Web interfaces (2002)

We describe work in progress at the MITRE Corporation on embedding speech enabled interfaces in Web browsers. This research is part of our work to establish the infrastructure to create Web hosted versions of prototype multimodal interfaces, both intelligent and otherwise. Like many others, we believe that the Web is the best potential delivery and distribution vehicle for complex software applications, and that the functionality of these Web hosted applications should match the functionality available in standalone applications. We discuss our approach to several aspects of this goal.
Immunological response in Stevens–Johnson syndrome and toxic epidermal necrolysis (2014)

Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are life-threatening cutaneous adverse drug reactions that induce widespread epidermal necrosis. Recent advances in pharmacogenomic studies have provided evidence of genetic predispositions to SJS/TEN. Several concepts have been proposed to explain the pathogenesis of severe cutaneous adverse drug reactions. In the hapten concept, small molecules called haptens elicit an immune response only when attached to proteins. The "p-i" concept postulates that the causative drugs can stimulate cells by binding directly and reversibly to immune receptors. In addition, there is the idea that drugs alter the antigen by binding to the human leukocyte antigen pocket. With regard to keratinocyte death, several cell death mediators, such as FasL, granulysin and annexin A1, have been proposed as playing a role in SJS/TEN pathogenesis. A subset of T lymphocytes, including regulatory T cells, also may play a role in SJS/TEN.
Airway epithelial cell expression of interleukin-6 in transgenic mice. Uncoupling of airway inflammation and bronchial hyperreactivity. (1994)

We produced transgenic mice which overexpress human IL-6 in the airway epithelial cells. Transgenic mice develop a mononuclear cell infiltrate adjacent to large and mid-sized airways. Immunohistochemistry reveals these cells to be predominantly CD4+ cells, MHC class II+ cells, and B220+ cells. Transgenic mice and nontransgenic mice had similar baseline respiratory system resistance (0.47 +/- 0.06 vs 0.43 +/- 0.04 cmH2O/ml per s at 9 wk of age, P = NS and 0.45 +/- 0.07 vs 0.43 +/- 0.09 cmH2O/ml per s at 17 wk of age, P = NS). Transgenic mice, however, required a significantly higher log dose of methacholine to produce a 100% increase in respiratory system resistance as compared with non-transgenic littermates (1.34 +/- 0.24 vs 0.34 +/- 0.05 mg/ml, P < or = 0.01). We conclude that the expression of human IL-6 in the airways of transgenic mice results in a CD4+, MHC class II+, B220+ lymphocytic infiltrate surrounding large and mid-sized airways that does not alter basal respiratory resistance, but does diminish airway reactivity to methacholine. These findings demonstrate an uncoupling of IL-6-induced airway lymphocytic inflammation and airway hyperresponsiveness and suggest that some forms of airway inflammation may serve to restore altered airway physiology.
A novel class of unconventional myosins from Toxoplasma gondii (1997)

Here, we describe the complete deduced amino acid sequence of three unconventional myosins identified in the protozoan parasite Toxoplasma gondii. Phylogenetic analysis reveals that the three myosins represent a novel, highly-divergent class addition to the myosin superfamily. Toxoplasma gondii myosin-A (TgM-A) is a remarkably small approximately 93 kDa myosin that shows a striking departure from typical myosin heavy chain structure in having a head and tail domain but no discernible neck domain. In other myosins, the neck is defined by one or more IQ motifs that serve as potential light chain binding domains. No IQ motifs are apparent in TgM-A. The tail domain of TgM-A encompasses only 57 amino acid residues and is characterized by its highly basic charge (pI = 10.8). The other two Toxoplasma myosins, TgM-B and TgM-C appear to be the product of differential RNA splicing with TgM-B yielding a protein of approximately 114 kDa and TgM-C a protein of approximately 125 kDa. These two myosins are identical throughout their head domain and neck domain which contains a single IQ motif. TgM-B and C share the proximal 245 residues of their tail domain and then diverge in their tail structure distally. The tails, like that of TgM-A, share no homology to any other myosin tails apart from a highly basic charge. The identification of yet another class of unconventional myosins, including a myosin as novel in structure as the 93 kDa TgM-A, continues to underscore the diversity of this family of molecular motors.
Effect of femoral head size on wear of the polyethylene acetabular component. (1990)

A technique was developed to determine the wear of the acetabular component of a total hip replacement by examination of standardized initial and follow-up radiographs. Three hundred and eighty-five hips were followed for at least 9.5 years after replacement. The least amount and rate of linear wear were associated with use of a femoral head that had a diameter of twenty-eight millimeters (p less than 0.001). The greatest amount and mean rate of linear wear occurred with twenty-two-millimeter components, but these differences were not statistically significant. The greatest volumetric wear and mean rate rate of volumetric wear were seen with thirty-two-millimeter components (p less than 0.001). A wider radiolucent line in acetabular Zone 1 was associated with use of the thirty-two-millimeter head. The amounts of resorption of the proximal part of the femoral neck and of lysis of the proximal part of the femur both correlated positively with the extent of linear and volumetric wear; this suggests an association between the amount of debris from wear and these changes in the femoral neck and proximal part of the femur.
On the role and fate of LPS-dephosphorylating activity in the rat liver (2005)

Gut-derived lipopolysaccharide (LPS) plays a role in the pathogenesis of liver diseases like fibrosis. The enzyme alkaline phosphatase (AP) is present in, among others, the intestinal wall and liver and has been previously shown to dephosphorylate LPS. Therefore, we investigated the effect of LPS on hepatic AP expression and the effect of AP on LPS-induced hepatocyte responses. LPS-dephosphorylating activity was expressed at the hepatocyte canalicular membrane in normal and fibrotic animals. In addition to this, fibrotic animals also displayed high LPS-dephosphorylating activity around bile ducts. The enzyme was shown to dephosphorylate LPS from several bacterial species. LPS itself rapidly enhanced the intrahepatic mRNA levels for this enzyme within 2 h by a factor of seven. Furthermore, in vitro and in vivo studies showed that exogenous intestinal AP quickly bound to the asialoglycoprotein receptor on hepatocytes. This intestinal isoform significantly attenuated LPS-induced hepatic tumor necrosis factor-alpha and nitric oxide (nitrite and nitrate) responses in vitro. The enzyme also reduced LPS-induced hepatic glycogenolysis in vivo. This study shows that LPS enhances AP expression in hepatocytes and that intestinal AP is rapidly taken up by these same cells, leading to an attenuation of LPS-induced responses in vivo. Gut-derived LPS-dephosphorylating activity or enzyme upregulation within hepatocytes by LPS may therefore be a protective mechanism within the liver.
Bone marrow transplantation in the treatment of alpha-mannosidosis. (1987)

Bone marrow transplantation was performed in a patient with alpha-mannosidosis. To our knowledge this is the first time such treatment has been attempted. The patient died 18 weeks after successful grafting and specimens of tissues were obtained at necropsy. Alpha-mannosidase activity in spleen and liver was just below normal (spleen 102 mumol/g/hour, control 113-330; liver 29 mumol/g/hour, control 30-131). Splenic alpha-mannosidase activity was indistinguishable from the control enzyme with respect to the Michaelis constant, heat stability, and inhibition by cobalt ions, as was 86% of the liver enzyme. In brain tissue alpha-mannosidase activity was 7% of controls, and less than one third had the properties of the normal enzyme. Oligosaccharides were present only in small amounts in liver and spleen, whereas they were greatly increased in brain tissue. Electron microscopic pictures of liver and spleen tissue showed normal morphology, but brain tissue showed definite vacuolation. These findings suggest that transplantation reversed the somatic changes of alpha-mannosidosis but did not affect lysosomal storage within brain tissue. It is concluded that marrow transplantation may not be a suitable treatment for alpha-mannosidosis.
Role of Phospholipase Cγ-induced Activation of Protein Kinase Cϵ (PKCϵ) and PKCβI in Epidermal Growth Factor-mediated Protection of Tight Junctions from Acetaldehyde in Caco-2 Cell Monolayers (2007)

Epidermal growth factor (EGF) protects the intestinal epithelial tight junctions from acetaldehyde-induced insult. The role of phospholipase Cgamma (PLCgamma) and protein kinase C (PKC) isoforms in the mechanism of EGF-mediated protection of tight junction from acetaldehyde was evaluated in Caco-2 cell monolayers. EGF-mediated prevention of acetaldehyde-induced decrease in transepithelial electrical resistance and an increase in inulin permeability, and subcellular redistribution of occludin and ZO-1 was attenuated by reduced expression of PLCgamma1 by short hairpin RNA. EGF induced a rapid activation of PLCgamma1 and PLC-dependent membrane translocation of PKCepsilon and PKCbetaI. Inhibition of PKC activity or selective interference of membrane translocation of PKCepsilon and PKCbetaI by RACK interference peptides attenuated EGF-mediated prevention of acetaldehyde-induced increase in inulin permeability and redistribution of occludin and ZO-1. BAPTA-AM and thapsigargin blocked EGF-induced membrane translocation of PKCbetaI and attenuated EGF-mediated prevention of acetaldehyde-induced disruption of tight junctions. EGF-induced translocation of PKCepsilon and PKCbetaI was associated with organization of F-actin near the perijunctional region. This study shows that PLCgamma-mediated activation of PKCepsilon and PKCbetaI and intracellular calcium is involved in EGF-mediated protection of tight junctions from acetaldehyde-induced insult.