gebhart/patrepeval huggingface dataset:
Manipulating trypsin digestion conditions to accelerate proteolysis and simplify digestion workflows in development of protein mass spectrometric assays for the clinical laboratory (2017)

For ease of measurement and accurate identification of proteins by mass spectrometry, protein targets are commonly cleaved into peptides. Protein digestion is a critical step in sample preparation, yielding peptides amenable to both chromatographic separation and mass spectrometric analysis. Trypsin is the most extensively used protease due to its high cleavage specificity; however, it can yield highly variable digestion profiles and is dependent on several factors including digestion buffer, denaturant, trypsin quality selected, and composition/complexity of the sample matrix. Historically, trypsin digestion protocols have relied on lengthy digestion times-which are unsuitable for many clinical applications-to ensure effective proteolysis. Here, we performed an iterative and comprehensive evaluation of digestion conditions for five structurally diverse proteins in plasma and serum: apolipoprotein A-1, retinol-binding protein 4, transthyretin, complement component 9 and C-reactive protein. Conditions were monitored for improvements in signal intensity, reproducibility of digestion profile, and rate of release of proteolytic peptides. This approach yielded an optimized digestion protocol for detection of all five proteins in a single workflow requiring a brief 20 min digestion, without the use of chemical denaturants or reduction/alkylation steps, and only 1 μl of plasma. It is our hope that this data can accelerate the development phase of targeted mass spectrometric protein assays by identifying practical approaches to accelerate and simplify digestion protocols for clinical applications and assist with the selection of tryptic peptides for protein quantitation.
Towards Computational Offloading in Mobile Device Clouds (2013)

Many mobile applications overcome their device limitations in computational, energy, or data resources by offloading computations to the cloud. In this paper, we consider environments in which computational offloading occurs amongst a set of mobile devices. We call such an environment a mobile device cloud (MDC). In this work, we first highlight the gain in computation time and energy consumption that can be achieved by offloading tasks to nearby devices within an MDC compared to a cloud. We then propose and implement an MDC platform that enables the creation and assessment of various offloading algorithms in MDCs. This platform consists of an Android application deployable across MDC devices, and a test bed to measure power being consumed by a mobile device. We utilize this platform to carry out various offloading experiments on an MDC test bed from which we gain interesting insights into the potential for MDC offloading. Results from these experiments show up to 50% gain in time and 26% gain in energy. Finally, we address the off loadee selection problem in MDCs by proposing several social-based algorithms. The potential promise of this approach is shown by evaluating these algorithms using real data sets that include contact traces and social information of mobile devices in a conference setting.
<sup>1</sup>H and <sup>15</sup>N Assignments and Secondary Structure of the Starch‐Binding Domain of Glucoamylase from <i>Aspergillus niger</i> (1995)

1H and 15N NMR resonance assignments of the granular starch-binding domain (SBD) of glucoamylase from Aspergillus niger have been made by multi-dimensional homonuclear and heteronuclear NMR techniques. Secondary structure analysis based on chemical shifts, 1H-1H NOEs, coupling constants and backbone amide exchange data indicates the presence of a well-defined beta-sheet structure. This consists of one parallel and five antiparallel pairs of beta-strands forming two beta-sheets. Cis-trans isomerisation of proline residues and O-glycosylation of threonine residues are observed and compared between the proteolytically derived SBD fragment and the recombinant protein. Structural features of the SBD in solution were compared to the X-ray crystal structure of a homologous domain of cyclodextrin glycosyltransferase from Bacillus circulans. There are some differences in the locations of the start and end of beta-strands but overall the two structures are very similar. This study will form the basis for the structure determination of the granular SBD and of its complexes.
Paper to HTML—an automatic, seamless process for documentation production (1999)

This paper describes how ILOG, a French software company designing C++ and Java class libraries, managed the transition between paper-only documentation and extensive HTML online documentation in less than two years. In this paper, we analyze the underlying reasons for making this change, describe the technological choices that were made, and walk through the various steps of the project from its beginning to final completion.
The Gene 10 (UL49.5) Product of Equine Herpesvirus 1 Is Necessary and Sufficient for Functional Processing of Glycoprotein M (2002)

The functional cooperation of equine herpesvirus 1 (EHV-1) glycoprotein M (gM) and the gene 10 (UL49.5) product was analyzed. Transient-transfection experiments using gM and UL49.5 expression plasmids as well as RK13 cell lines constitutively expressing UL49.5 (RK49.5) or gM (RKgM) demonstrated that the endo-beta-N-acetylglucosaminidase H (endo H)-resistant mature form of gM was detectable only after coexpression of the two proteins. Deletion of the EHV-1 UL49.5-homologous gene 10 in strain KyA resulted in a small-plaque phenotype and up to 190-fold-reduced virus titers. The growth defects of the mutant KyA Delta 49.5 virus, which were very similar to those of a gM-negative KyA virus, could be completely compensated for by growth of the mutant virus on RK49.5 cells or by repairing the deletion of gene 10 in the revertant virus KyA Delta 49.5R. Analysis of cells infected with the UL49.5-negative EHV-1 demonstrated that gM was not transported to the trans-Golgi network in the absence of the UL49.5 product. In contrast, gM was efficiently transported and processed to the endo H-resistant mature form in KyA Delta 49.5-infected RK49.5 cells. Furthermore, radioimmunoprecipitation experiments demonstrated that gM maturation was observed only if a 10,000-M(r) protein was coprecipitated with gM in KyA- or KyA Delta 49.5R-infected cells or virions. This protein was absent in cells infected with Ky Delta 49.5 or KyA Delta gM, suggesting that it was the EHV-1 UL49.5 product. Taken together, our results demonstrate that the expression of the EHV-1 UL49.5 product is necessary and sufficient for gM processing and that it is required for efficient virus replication.
Lipoprotein Metabolism during Acute Inhibition of Hepatic Triglyceride Lipase in the Cynomolgus Monkey (1982)

The role of the enzyme hepatic triglyceride lipase was investigated in a primate model, the cynomolgus monkey. Antisera produced against human postheparin hepatic lipase fully inhibited cynomolgus monkey posttheparin plasma hepatic triglyceride lipase activity. Lipoprotein lipase activity was not inhibited by this antisera. Hepatic triglyceride lipase activity in liver biopsies was decreased by 65-90% after intravenous infusion of this antisera into the cynomolgus monkey. After a 3-h infusion of the antisera, analytic ultracentrifugation revealed an increase in mass of very low density lipoproteins (S(f) 20-400). Very low density lipoprotein triglyceride isolated by isopycnic ultracentrifugation increased by 60-300%. Analytic ultracentrifugation revealed an increase in mass of lipoproteins with flotation greater than S(f) 9 (n = 4). The total mass of intermediate density lipoproteins (S(f) 12-20) approximately doubled during the 3 h of in vivo enzyme inhibition. While more rapidly floating low density lipoproteins (S(f) 9-12) increased, the total mass of low density lipoproteins decreased after infusion of the antibodies. The changes in high density lipoproteins did not differ from those in control experiments. In order to determine whether the increases of plasma concentrations of very low density lipoproteins were due to an increase in the rate of synthesis or a decrease in the rate of clearance of these particles, the metabolism of radiolabeled homologous very low density lipoproteins was studied during intravenous infusion of immunoglobulin G prepared from the antisera against hepatic triglyceride lipase (n = 3) or preimmune goat sera (n = 3). Studies performed in the same animals during saline infusion were used as controls for each immunoglobulin infusion. There was a twofold increase in the apparent half-life of the very low density lipoprotein apolipoprotein-B tracer in animals receiving the antibody, consistent with a decreased catabolism of very low density lipoproteins. Concomitantly, the rise in low density lipoprotein apoprotein-B specific activity was markedly delayed. None of these changes were observed during infusion of preimmune immunoglobulin G.Hepatic triglyceride lipase participates with lipoprotein lipase in the hydrolysis of the lipid in very low density lipoproteins, intermediate density lipoproteins, and the larger low density lipoproteins (S(f) 9-12). Thus, hepatic triglyceride lipase appears to function in a parallel role with lipoprotein lipase in the conversion of very low density and intermediate density lipoproteins to low density lipoproteins (S(f) 0-9).
Abstract 2883: Dectin-2 agonist antibodies reprogram tumor-associated macrophages to drive anti-tumor immunity (2022)

Abstract Tumor-associated macrophages (TAMs), an abundant immune cell population in most cancers, support tumor progression through their immunosuppressive effects. We discovered that TAMs express the pattern recognition receptor Dectin-2 (Clec4n/CLEC6A), an activating C-type lectin receptor (CLR) that binds to high-mannose glycans on fungi and other microbes and stimulates immune responses against infectious disease. Dectin-2 is selectively expressed by myeloid cells, and upon ligation, mediates enhanced phagocytosis, antigen processing and presentation, and proinflammatory cytokine production. Given these properties, we evaluated the therapeutic potential of targeting Dectin-2 to reprogram TAMs using natural ligands as well as our novel agonistic antibodies. We show that Dectin-2 agonists can convert TAMs into immunostimulatory cells in vitro and in vivo, and drive robust anti-tumor immunity. Dectin-2 gene expression is minimal in normal human tissues but elevated across many tumor types, including breast, colon, lung, ovarian, and kidney cancers. We found that Dectin-2 is strongly expressed by macrophages differentiated in vitro and on primary TAMs from various solid tumors. Treatment of tumor-bearing mice with mannan, a natural Dectin-2 ligand derived from S. cerevisiae, mediated tumor regression in multiple syngeneic tumor models, with high rates of tumor clearance in the MB49 bladder cancer model. These effects were Dectin-2 dependent, as efficacy was not observed when a Dectin-2-blocking antibody was co-administered or in knockout mice lacking Dectin-2 signaling components. Depletion of either macrophages or CD8+ T cells impaired efficacy, suggesting that Dectin-2-stimulated TAMs augment anti-tumor CD8+ T cell responses. Based on these data, we developed novel Dectin-2-targeted agonist antibodies capable of activating both in vitro-generated and primary human TAMs to produce an array of proinflammatory cytokines and chemokines akin to tumor-destructive “M1” macrophages. Furthermore, systemically administered Dectin-2 agonist antibodies activated TAMs and mediated anti-tumor effects in immunodeficient mice engrafted with human CD34+ HSCs. The data presented demonstrate the therapeutic potential of Dectin-2 agonist antibodies as a novel pan-cancer approach for myeloid cell-directed tumor immunotherapy. Citation Format: Justin A. Kenkel, Po Y. Ho, Karla A. Henning, Cindy L. Kreder, Jess L. Nolin, Sameera Kongara, Steven J. Chapin, Amreen Husain, Marcin Kowanetz, Edgar G. Engleman, Michael N. Alonso, David Dornan, Shelley E. Ackerman. Dectin-2 agonist antibodies reprogram tumor-associated macrophages to drive anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2883.
Studies on the Mechanism of Action of 2-Formyl-4-pyrrolidinopyridine:  Isolation and Characterization of a Reactive Intermediate (1999)

This paper describes the mechanism of action of 2-formyl-4-pyrrolidinopyridine (FPP, 1a) which is a catalyst for the hydroxyl-directed methanolysis of alpha-hydroxy esters. This species was initially designed to act as a nucleophilic catalyst; however, we have ruled out a nucleophilic mechanism by examining the activity of 6-substituted-FPP derivatives. These compounds are more hindered in the vicinity of the pyridine nitrogen than FPP itself but are also more active catalysts. Furthermore, the presence of p-nitrophenol, a mild acid, was found to accelerate the catalytic reaction. These results are inconsistent with a nucleophilic catalysis mechanism. We provide evidence that the reaction instead proceeds via dioxolanone intermediate 10. Dioxolanone 10 can be obtained by treating either the p-nitrophenyl ester or the pentafluorophenyl ester of glycolic acid with FPP in chloroform in the absence of methanol. It has been isolated, characterized, and shown to be kinetically competent when subjected to the conditions of the catalytic reaction.
BCB contact printing for patterned adhesive full-wafer bonded 0-level packages (2005)

Adhesive wafer bonding with a patterned polymer layer is increasingly attracting attention as cheap and simple 0-level packaging technology for microstructures, because the patterned polymer both fulfills the bonding function and determines the volumes between the two wafers housing the devices to be packaged. To be able to pattern a polymer, it has to be cross-linked to a certain degree which makes the material rigid and less adhesive for the bonding afterward. In this paper, a simple method is presented which combines the advantages of a patterned adhesive layer with the advantages of a liquid polymer phase before the bonding. The pattern in the adhesive layer is "inked" with viscous polymer by pressing the substrate toward an auxiliary wafer with a thin liquid polymer layer. Then, the substrate with the inked pattern is finally bonded to the top wafer. Benzocyclobuene (BCB) was used both for the patterned structures and as the "ink". Tensile bond strength tests were carried out on patterned adhesive bonded samples fabricated with and without this contact printing method. The bonding yield is significantly improved with the contact printing method, the fabrication procedure is more robust and the test results show that the bond strength is at least 2 times higher. An investigation of the samples' failure mechanisms revealed that the bond strength even exceeds the adhesion forces of the BCB to the substrate. Furthermore, the BCB contact printing method was successfully applied for 0-level glass-lid packaging done by full-wafer bonding with a patterned adhesive layer. Here, the encapsulating lids are separated after the bonding by dicing the top wafer independently of the bottom wafer.
Application of PCR: Organismal and Population Biology (1990)

sive analysis of gene structure from a limited number of species, primarily humans, mice, fruit flies, yeast, and the bacterium Escherichia coli. The powerful new molecular biological methods have also led to major discoveries in population biology and the study of organismal evolution. Among the many achievements are a better understanding of the evolutionary relationships among the major groups of microorganisms (Woese 1987) and the discovery that apes and humans had a common ancestor as recently as 5 million years ago (Wilson et al. 1989). Despite the profound nature of such discoveries, little data have been generated by molecular biological methods when the world's total biota is considered. Only a small number of individuals and species have been
Microbial lectins and agglutinins : properties and biological activity (1986)

Introduction to Microbial Lectins and Agglutinins Viruses as Hemagglutinins and Lectins Mannose Specific Bacterial Surface Lectins Glycolipids as Receptors for Escherichia coli Lectins or Adhesions Genetics and Biogenesis of Escherichia coli Adhesions Structure-function Analysis of Gonococcal Pili Adhesions Structure-function Analysis of Gonococcal Pili Adhesions of Vibrio cholerae Fimbrial Lectins of the Oral Actinomyces Myxobacterial Hemagglutinin: A Developmentally Induced Lectin from Myxococcus xanthus Mycoplasmal Adhesions and Lectins Fimbriae, Lectins, and Agglutinins of Nitrogen-fixing Bacteria Lectins of Pseudomonas aeruginosa: Properties, Biological Effects, and Applications Sugar Binding Bacterial Toxins Lectins and Agglutinins in Protozoa Lectins in Etnamoeba histolytica Carbohydrate Recognitions Mediate Attachment of Plasmodium falciparum Malaria to Erythrocytes Lectins from the Cellular Slime Molds Fungal Lectins and Agglutinins The Function of Lectins in Interactions Among Marine Bacteria, Invertebrates, and Algae
Reparameterization Gradients through Acceptance-Rejection Sampling Algorithms (2016)

Variational inference using the reparameterization trick has enabled large-scale approximate Bayesian inference in complex probabilistic models, leveraging stochastic optimization to sidestep intractable expectations. The reparameterization trick is applicable when we can simulate a random variable by applying a differentiable deterministic function on an auxiliary random variable whose distribution is fixed. For many distributions of interest (such as the gamma or Dirichlet), simulation of random variables relies on acceptance-rejection sampling. The discontinuity introduced by the accept-reject step means that standard reparameterization tricks are not applicable. We propose a new method that lets us leverage reparameterization gradients even when variables are outputs of a acceptance-rejection sampling algorithm. Our approach enables reparameterization on a larger class of variational distributions. In several studies of real and synthetic data, we show that the variance of the estimator of the gradient is significantly lower than other state-of-the-art methods. This leads to faster convergence of stochastic gradient variational inference.
REDUCTION OF NITRATE AND NITRITE SALTS UNDER HYDROTHERMAL CONDITIONS (2023)

The feasibility of reducing nitrate/nitrite salts under hydrothermal conditions for the treatment of aqueous mixed wastes stored in the underground tanks at the Department of Energy site at Hanford, Washington was studied. The reduction of nitrate and nitrite salts by reaction with EDTA using a tank waste simulant was examined at temperatures between 623 K and 800 K and pressures between 0.6 and 1.2 kbar. Continuous flow reactors were used to determine kinetics and products of reactions. All reactions were studied under pressures high enough to produce single phase conditions. Above 723 K, the reactions are rapid, go to completion in less than a minute, and produce simple products, such as carbonate, nitrogen, and nitrous oxide gases. The experimental results demonstrate the ability of chemical reactions under hydrothermal conditions to reduce the nitrate and nitrite salts and destroy organic compounds in the waste mixtures.
Risk Evaluation Model for Large Engineering Project Based on Fuzzy Set (2011)

Large projects often face risks from technology, economy, nature, social and other aspects during development and construction. Risk factors are of interdependence and interaction,so they are very difficult to be quantified. This paper describes a risk evaluation method for large projects based on fuzzy set theory which uses respective fuzzy numbers to evaluate the factors. The primary weights of factors and evaluation of alternatives are determined by applying fuzzy numbers. A major advantage of the method is that it allows experts and engineers to express their opinions on project risk evaluation in linguistic variables rather than crisp values. An illustration is presented to demonstrate the application of the method in risk evaluation. The results are consistent with the results calculated by conventional risk evaluation method. The research demonstrates that the method is objective and accurate, and is of an application value in the risk evaluation for large projects.
Tetracycline resistance element of pBR322 mediates potassium transport (1984)

The tetracycline resistance element of plasmid pBR322 partially complements the potassium transport defect of Escherichia coli K-12 mutants having markedly impaired K+ transport. The plasmid increases K+ transport. The Tn10 element does not result in increased transport, demonstrating that the effect is not general for elements that increase resistance to tetracycline.
Preventing self-intersection under free-form deformation (2001)

Free-Form Deformation (FFD) is a versatile and efficient modeling technique which transforms an object by warping the surrounding space. The conventional user-interface is a lattice of movable control points but this tends to be cumbersome and counterintuitive. Directly Manipulated Free-Form Deformation (DMFFD) allows the user to drag object points directly and has proven useful in an interactive sculpting context. A serious shortcoming of both FFD and DMFFD is that some deformations cause self-intersection of the object. This is unrealistic and compromises the object's validity and suitability for later use. An in-built self-intersection test is thus required for FFD and its extensions to be truly robust In this paper, we present the following novel results set of theoretical conditions for preventing self-intersection by ensuring the injectivity (one-to-one mapping) of FFD, an exact. (necessary and sufficient) injectivity test which is accurate but computationally costly, an efficient but approximate injectivity test which is a sufficient condition only, and a new form of DMFFD which acts by composing many small injective deformations. The latter expands the range of possible deformations without sacrificing the speed of the approximate test.
External Representations of Objects of User-Defined Type (1980)

The portable programming language (PPL) is one of a number of recently designed programming languages that enable the user to define new types by giving their representations and operations in terms of those of previously available types. Such provisions for the construction of objects of user-defined type have been discussed elsewhere; this work concerns the related problem of the external representations of such objects, both on input-output media and as written constants within the program text. We introduce an enhancement to the PPL design allowing specification of the external representations of objects of user-defined type. This extension to the PPL design means that objects of user-defined type can be read, written, and used as constants exactly as if their representations had been selected by the writer of the PPL compiler. The implementation and use of the added facilities are also discussed.