gebhart/patrepeval huggingface dataset:
Prediction via Orthogonalized Model Mixing (1996)

Abstract We introduce an approach and algorithms for model mixing in large prediction problems with correlated predictors. We focus on the choice of predictors in linear models, and mix over possible subsets of candidate predictors. Our approach is based on expressing the space of models in terms of an orthogonalization of the design matrix. Advantages are both statistical and computational. Statistically, orthogonalization often leads to a reduction in the number of competing models by eliminating correlations. Computationally, large model spaces cannot be enumerated; recent approaches are based on sampling models with high posterior probability via Markov chains. Based on orthogonalization of the space of candidate predictors, we can approximate the posterior probabilities of models by products of predictor-specific terms. This leads to an importance sampling function for sampling directly from the joint distribution over the model space, without resorting to Markov chains. Compared to the latter, orthogonalized model mixing by importance sampling is faster in sampling models and is also more efficient in finding models that contribute significantly to the prediction. Further advantages are in the speed of convergence and the availability of more reliable convergence diagnostic tools. We illustrate these in practice, using a data set on prediction of crime rates. The model space is small enough so that enumeration of all models is available for comparison and convergence checks. Also, we demonstrate the feasibility of orthogonalized model mixing in a large-size problem, which is very difficult to attack by other methods. The data set is from a designed experiment dealing with predicting protein activity under different storage conditions. The model space is large (the rank of the design matrix is 88) and very difficult to explore if expressed in terms of the original variables. We obtain prediction intervals and a probability distribution of the setting that produces the highest response. Key Words: Bayesian linear modelsImportance samplingModel uncertaintyVariable selection
A modified blockmatching algorithm with vector reliability checking and adaptive smoothing (1989)

The estimation of motion measurement continues to be an important field of investigation with applications in image coding, bandwidth reduction, standards conversion, and display improvements. In picture coding motion estimation is used to exploit redundancy by minimizing the interpolation error. For motion compensating interpolation however, it is more important to estimate the motion correctly. A greater smoothness of the vector field can be accomplished by taking into consideration local dependencies between the vectors. The smoothness in the adaptive algorithm is controlled here according to the reliability of previously estimated vectors.
Protective immunity evoked by oral administration of attenuated aroA Salmonella typhimurium expressing cloned streptococcal M protein. (1988)

Attenuated strains of Salmonella have been used effectively as vaccines against typhoid fever. We have investigated the use of such strains to deliver cloned antiphagocytic virulence determinants of unrelated bacteria. The aroA strain of S. typhimurium SL3261 was transformed with a low-copy plasmid vector pMK207, which contains the cloned gene spm5 encoding streptococcal M protein, the major virulence factor of these organisms. The transformed SL3261 expressed type 5 M protein in the cytoplasmic fraction, and when fed orally to BALB/c mice, evoked both serum and salivary IgA, IgG, and IgM antibodies directed against type 5 M protein. The orally immunized mice were completely protected against both intranasal and intraperitoneal challenge infections with virulent S. typhimurium SL1344 or M5 streptococci. These studies provide evidence that an attenuated strain of Salmonella can be used effectively as a general vaccine vehicle to deliver antiphagocytic virulence determinants of unrelated bacteria.
RK‐682, a potent inhibitor of tyrosine phosphatase, arrested the mammalian cell cycle progression at G1phase (1995)

A specific inhibitor of protein tyrosine phosphatase (PTPase), RK-682 (3-hexadecanoyl-5-hydroxymethyl-tetronic acid) was isolated from microbial metabolites. In vitro, RK-682 inhibited dephosphorylation activity of CD45 and VHR with IC50 54 and 2.0 microM, respectively. In situ, sodium orthovanadate and RK-682 enhanced the phosphotyrosine level of Ball-1 cells, a human B cell leukemia, but not the phosphoserine/threonine level. The PTPase inhibitors, however, had the different arrest point on the cell cycle progression. Sodium orthovanadate inhibited the cell cycle progression at G2/M boundary phase, on the other hand, RK-682 inhibited the G1/S transition.
Evaluating Fluctuations in Human Atrial Fibrillatory Cycle Length Using Monophasic Action Potentials (2006)

AF CL is better estimated by autocorrelation than spectral DF, particularly for bipoles, and stable when measured for >10 seconds. Notably, changes in AF CL preceded reciprocal changes in organization, yet changes in organization did not precede changes in AF CL. These results may help to interpret AF CL fluctuations.
HDX Workbench: Software for the Analysis of H/D Exchange MS Data (2012)

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is an established method for the interrogation of protein conformation and dynamics. While the data analysis challenge of HDX-MS has been addressed by a number of software packages, new computational tools are needed to keep pace with the improved methods and throughput of this technique. To address these needs, we report an integrated desktop program titled HDX Workbench, which facilitates automation, management, visualization, and statistical cross-comparison of large HDX data sets. Using the software, validated data analysis can be achieved at the rate of generation. The application is available at the project home page http://hdx.florida.scripps.edu .
Synthetic peptides of the hamster beta 2‐adrenoceptor as substrates and inhibitors of the beta‐adrenoceptor kinase. (1990)

1. The beta-adrenoceptor is one of a number of G protein-coupled receptors which have been proposed to contain seven transmembrane alpha-helices. The function of this receptor appears to be regulated by phosphorylation by a specific enzyme, the beta-adrenoceptor kinase. Synthetic peptides which comprise each of the proposed intra- and extracellular domains of the beta 2-adrenoceptor have been tested as potential substrates and inhibitors of the beta-adrenoceptor kinase. 2. Two peptides which encompass the middle and terminal portions of the carboxyl tail of the receptor served as substrates by beta-adrenoceptor kinase. The kinetics of the phosphorylation reaction, however, suggest that these peptides are 10(6)-fold poorer substrate than the agonist occupied receptor. 3. A number of synthetic peptides also served as inhibitors of beta 2-adrenoceptor phosphorylation by beta-adrenoceptor kinase. In particular, a peptide which comprised the first intracellular loop of the beta 2-adrenoceptor (amino acids 56-74) inhibited most effectively with an IC50 of 40 microM. 4. These results suggest that multiple intracellular regions of the beta-receptor may serve as potential sites of interaction with beta-adrenoceptor kinase. Moreover, these regions may serve as potential targets for the development of specific inhibitors of beta-adrenoceptor kinase which could be used to block homologous desensitization.
Subretinal implantation of semiconductor-based photodiodes: progress and challenges. (1999)

Retinal diseases that result in photoreceptor degeneration may spare the inner retinal layers. This review concerns a prosthetic approach to restoring visual function through the use of a semiconductor-based microphotodiode array implant, designed to be placed under the neural retina in the subretinal space. The fundamental idea is that current generated by the device in response to light stimulation will alter the membrane potential of overlying neurons and thereby activate the visual system. Initial acute studies indicated that the implant will function in the subretinal space in the absence of an external power supply. More recent and ongoing studies involve chronic subretinal implantations in normal animals. Post-operative studies have demonstrated that implant function will persist for many months. These chronic studies have also assessed the biocompatibility of the implant. Photoreceptors are lost directly overlying the implant, due to the blockade of choroidal circulation to the outer retina by the solid disk device. In comparison, the inner retina maintains its characteristic lamellar structure. Away from the implant site, the retina retains normal anatomy and function. Future studies are needed to determine whether the implant can establish a functional connection to the inner retina and to determine the quality of this connection.
Alicyclobacillus acidocaldariusThermophilic Esterase EST2's Activity in Milk and Cheese Models (2006)

The aim of this work was to investigate the behavior of thermophilic esterase EST2 from Alicyclobacillus acidocaldarius in milk and cheese models. The pure enzyme was used to compare the EST2 hydrolytic activity to the activity of endogenous esterase EstA from Lactococcus lactis. The results indicate that EST2 exhibits 30-fold-higher esterase activity than EstA. As EstA has thioesterase activity, EST2 was assayed for this activity under the optimal conditions determined for EstA (namely, 30 degrees C and pH 7.5). Although it is a thermophilic enzyme, EST2 exhibited eightfold-higher thioesterase activity than EstA with S-methyl thiobutanoate. The abilities of EST2 and EstA to synthesize short-chain fatty acid esters were compared. Two methods were developed to do this. In the first method a spectrophotometric assay was used to monitor the synthesis of esters by the pure enzymes using p-nitrophenol as the alcohol substrate. The synthetic activities were also evaluated under conditions that mimicked those present in milk and/or cheese. The second method involved evaluation of the synthetic abilities of the enzymes when they were directly added to a model cheese matrix. Substantial ester synthesis by EST2 was observed under both conditions. Finally, esterase and thioesterase activities were evaluated in milk using the purified EST2 enzyme and in the model cheese matrix using a strain of L. lactis NZ9000 harboring the EST2 gene and thus overproducing EST2. Both the esterase and thioesterase activities measured in milk and in the cheese matrix were much greater than the activities of the controls.
Identification of Grb2 As a Novel Binding Partner of  Tumor Necrosis Factor (TNF) Receptor I (1999)

Tumor necrosis factor alpha (TNF-alpha) is a proinflammatory cytokine. Its pleiotropic biological properties are signaled through two distinct cell surface receptors: the TNF receptor type I (TNFR-I) and the TNF receptor type II. Neither of the two receptors possesses tyrosine kinase activity. A large majority of TNF-alpha-dependent activities can be mediated by TNFR-I. Recently, c-Raf-1 kinase was identified as an intracellular target of a signal transduction cascade initiated by binding of TNF-alpha to TNFR-I. However, the mechanism engaged in TNF-alpha-dependent activation of c-Raf-1 kinase is still enigmatic. Here we report that the cytosolic adapter protein Grb2 is a novel binding partner of TNFR-I. Grb2 binds with its COOH-terminal SH3 domain to a PLAP motif within TNFR-I and with its NH2-terminal SH3 domain to SOS (son of sevenless). A PLAP deletion mutant of TNFR-I fails to bind Grb2. The TNFR-I/Grb2 interaction is essential for the TNF-alpha-dependent activation of c-Raf-1 kinase; activation of c-Raf-1 kinase by TNF-alpha can be blocked by coexpression of Grb2 mutants harboring inactivating point mutations in the NH2- or COOH-terminal SH3 domain, cell-permeable peptides that disrupt the Grb2/TNFR-I interaction or transdominant negative Ras. Functionality of the TNFR-I/Grb2/SOS/Ras interaction is a prerequisite but not sufficient for TNF-alpha-dependent activation of c-Raf-1 kinase. Inhibition of the TNFR-I/FAN (factor associated with neutral sphingomyelinase) interaction, which is essential for TNF-alpha-dependent activation of the neutral sphingomyelinase, either by cell-permeable peptides or by deletion of the FAN binding domain, prevents activation of c-Raf-1 kinase. In conclusion, binding of the Grb2 adapter protein via its COOH-terminal SH3 domain to the nontyrosine kinase receptor TNFR-I results in activation of a signaling cascade known so far to be initiated, in the case of the tyrosine kinase receptors, by binding of the SH2 domain of Grb2 to phosphotyrosine.
Combined single-electron and coherent-Cooper-pair tunneling in voltage-biased Josephson junctions (1991)

Small-capacitance tunnel junctions show single-electron effects and, in the superconducting state, the coherent tunneling of Cooper pairs. We study these effects in a system of two voltage-biased Josephson junctions in series. Novel features show up in the I-V characteristics, in particular, pronounced structures at subgap voltages. These are due to combined quasiparticle and pair tunneling and to higher-order Cooper-pair tunneling processes. Several of them have been observed in experiments.
Role of meizothrombin and meizothrombin-(Des F1) in the conversion of prothrombin to thrombin by the Echis carinatus venom coagulant (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRole of meizothrombin and meizothrombin-(Des F1) in the conversion of prothrombin to thrombin by the Echis carinatus venom coagulantMoo Jhong Rhee, Sam Morris, and David P. KosowCite this: Biochemistry 1982, 21, 14, 3437–3443Publication Date (Print):July 1, 1982Publication History Published online1 May 2002Published inissue 1 July 1982https://pubs.acs.org/doi/10.1021/bi00257a029https://doi.org/10.1021/bi00257a029research-articleACS PublicationsRequest reuse permissionsArticle Views135Altmetric-Citations30LEARN 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
Capillary electrophoresis for the characterization of the complex dendrimeric contrast agent Gadomer (2006)

A CE method for the characterization of the complex dendrimeric contrast agent Gadomer has been developed and validated. The method was capable of separating the target substance Gadomer 24 from related dendrimers containing amino or carboxyl functions and from impurities of lower molecular weight. The compounds were separated in a fused-silica capillary. The optimized BGE consisted of 15 mM sodium phosphate, pH 6.3, containing 0.5 mM hexadecyltrimethylammonium bromide. The assay was validated with regard to linearity, specificity, accuracy, LOD and LOQ as well as robustness according to the guidelines of the International Conference on Harmonization. The method allows the determination of the purity and stability of the drug substance Gadomer as well as its injectable formulation. On the basis of the present study, a strategy for the quality assurance and quality control of the complex dendrimeric drug candidate Gadomer may be devised. The method may therefore serve as a key component in a set of analytical methodologies designed to assure and control the reproducible quality and safety of this innovative product. To the best of our knowledge, this is the first work reporting a validated method for the characterization, impurity profiling, and stability testing of a dendrimeric agent designed for clinical use.
A training algorithm for optimal margin classifiers (1992)

A training algorithm that maximizes the margin between the training patterns and the decision boundary is presented. The technique is applicable to a wide variety of the classification functions, including Perceptrons, polynomials, and Radial Basis Functions. The effective number of parameters is adjusted automatically to match the complexity of the problem. The solution is expressed as a linear combination of supporting patterns. These are the subset of training patterns that are closest to the decision boundary. Bounds on the generalization performance based on the leave-one-out method and the VC-dimension are given. Experimental results on optical character recognition problems demonstrate the good generalization obtained when compared with other learning algorithms.
Synthesis of Neoglycoproteins Using Oligosaccharide-transfer Activity with Endo-β-N-Acetylglucosaminidase (1995)

We describe a novel method for the enzymatic synthesis of neoglycoproteins. Endo-beta-N-acetylglucosaminidase from Arthrobacter protophormiae (Endo-A) had high levels of transglycosylation activity. The enzyme activity of Endo-A was markedly increased by adding 4-L-aspartyl-glycosylamine (GlcNAc-Asn) to the reaction mixture. Digesting (Man)6(GlcNAc)2 with the enzyme in the presence of GlcNAc-Asn gave a mixture of hydrolytic ((Man)6GlcNAc) and transglycosylic ((Man)6(GlcNAc)2-Asn) products. By means of transglycosylation, (Man)6GlcNAc was transferred en bloc to the partially deglycosylated ovalbumin glycopeptide (EEKYN(GlcNAc)LTSVL) concomitant with the hydrolysis of (Man)6-GlcNAc)2Asn. The structure of the transglycosylation product was designated as (Man)6(GlcNAc)2-peptide by amino acid composition and sequence analysis as well as ion mass spectrometry. The enzyme also transferred oligosaccharide to partially deglycosylated ribonuclease B (GlcNAc-protein) during the hydrolysis of (Man)6-(GlcNAc)2Asn. Native ribonuclease B had (Man)5-9 (GlcNAc)2 as its heterogeneous N-linked sugar chains. High performance liquid chromatography showed that all of the N-linked sugar chains of the synthetic neoribonuclease of the pyridylamino derivatives were modified to (Man)6(GlcNAc)2.
DNA methylation dynamics during ex vivo differentiation and maturation of human dendritic cells (2014)

Our study is the first to map DNA methylation changes during human DC differentiation and maturation in purified cell populations and will greatly enhance the understanding of DC development and maturation and aid in the development of more efficacious DC-based therapeutic strategies.
Autologous Fat Transplantation in the Craniofacial Patient (2012)

Patients with congenital craniofacial malformations present with complex challenges for reconstruction. Successful management requires individualized treatment often involving rebuilding the facial skeleton de novo, as well as correcting the overlying soft-tissue deficiencies in the final stages. At the University of California, Los Angeles (UCLA) Craniofacial Clinic, serial autologous fat transplantation performed during staged reconstruction is the preferred method.A total of 27 patients with a diagnosis of either craniofacial microsomia/Goldenhar (CM) (n = 19) or Treacher Collins syndrome (TC) (n = 8) were treated at the UCLA Craniofacial Clinic by autologous fat transfer between July 1999 and February 2009. Two-dimensional analysis was conducted on standardized preoperative and postoperative photographs to determine facial symmetry for every patient. Results was grouped based on pathology and analyzed by comparing adipocyte donor site (abdomen vs other).The mean ages at the time of first fat transfer were 17 years for the CM group and 15 years for the TC group. The average numbers of fat transfers per patient were 2.05 (CM) and 2.12 (TC). A mean of 3.74 procedures other than fat grafting was performed in each CM patient, whereas 4.38 other procedures were performed in each TC patient. In CM patients, less than 10.5 months between procedures resulted in improved symmetry. There was an average 6.63% improvement in facial symmetry in the CM group, and a 7.67% improvement in the TC group.Based on the UCLA experience, the durability of facial asymmetry and contour correction with fat transplantation is attainable in the craniofacial patient but may also require concomitant skeletal correction in the most severe cases.
Tyr‐426 of the Escherichia coli asparaginyl‐tRNA synthetase, an amino acid in a C‐terminal concerved motif, is involved in ATP binding (1991)

Sequence comparisons of the E. coli asparaginyl-tRNA synthetase (NRSEC) with aminocyl-tRNA synthetase sequences of class II enzymes show significant homologies with aspartyl- and lysyl-tRNA synthetases. Three conserved regions were found, one of which is located in the C-terminal part of the NRSEC sequence. Site-directed mutagenesis was performed in this conserved region. A single point mutation Tyr-426----Ser results in a 15-fold increase in the Km for ATP, while all the other kinetic parameters remain unchanged. The replacement of this Tyr-426 by a Phe does not affect the kinetic behaviour of the enzyme. These data indicate that Tyr-426 is part of the ATP binding site.
Rod Outer Segment Disk Shedding in Rat Retina: Relationship to Cyclic Lighting (1976)

When albino rats are reared in cyclic light, a burst of rod outer segment disk shedding occurs in the retina soon after the onset of light. The number of large packets of outer segment disks (phagosomes) in the pigment epithelium at this time is 2.5 to 5 times greater than at any other time of day or night. The subsequent degradation of large phagosomes to smaller structures within pigment epithelial cells proceeds rapidly. The burst of disk shedding follows a circadian rhythm for at least 3 days, since it occurs in continuous darkness at the same time without the onset of light.
Inhibition of HIV-1 Replication in Cultured Cells with Antisense Oligonucleotides Encapsulated in Immunoliposomes (1993)

Antisense oligonucleotides inhibit HIV replication in vitro, but their activity is limited by their sensitivity to nucleases and low cellular uptake. To see whether these problems could be circumvented, we compared effects of HIV-1 rev and tat gene-specific antisense phosphodiester or phosphorothioate oligonucleotides, either free in solution or encapsulated in antibody-targeted liposomes (immunoliposomes), on acutely or chronically infected cells. Phosphodiester antisense oligonucleotides were inactive in their free form in acutely and chronically infected cells (up to a concentration of 50 microM). When encapsulated in immunoliposomes directed to HLA class I molecules expressed by targeted cells, they inhibited viral replication (at a concentration of 0.5 microM) in acutely infected cells in a sequence-specific manner. The same phosphodiester antisense oligonucleotides in liposomes had no antiviral activity in chronically infected cells. In acutely infected cells, phosphorothioate oligonucleotides free in solution inhibited the replication of HIV without sequence specificity and had slightly greater activity, also nonspecific, when encapsulated in liposomes. Phosphorothioate antisense (anti-rev) oligonucleotides specifically blocked HIV replication in chronically infected cells. When encapsulated in targeted liposomes the efficiency of inhibition for these cells was increased by at least 60-fold relative to the same oligonucleotide free in solution.