gebhart/patrepeval huggingface dataset:
<i>NOD2</i> mediates anti‐inflammatory signals induced by TLR2 ligands: implications for Crohn's disease (2004)

Mutations of the NOD2 gene have been associated with an increased susceptibility to Crohn's disease, but the pathogenetic mechanisms mediated by NOD2 remain elusive. In the present study, we demonstrate that the 3020insC frameshift-mutation in the NOD2 gene associated with Crohn's disease results in defective release of IL-10 from blood mononuclear cells after stimulation with the Toll-like receptor (TLR)2 ligands, peptidoglycan and Pam3Cys-KKKK, but not with bacterial LPS, a TLR4 ligand. The potential pathophysiological significance of this finding in patients with Crohn's disease and who are homozygous for this NOD2 mutation was substantiated by the finding of decreased anti-inflammatory cytokine release when cells from these patients were stimulated with different species of Bacteroides, an enteric microorganism implicated in the pathogenesis of Crohn's disease. In conclusion, defective NOD2 function results in a pro-inflammatory cytokine bias after stimulation of mononuclear cells with TLR2 stimuli, and this could contribute to the overwhelming inflammation seen in Crohn's disease.
Detoxification process for glutaraldehyde-treated bovine pericardium: biological, chemical and mechanical characterization. (1998)

Homocysteic acid treatment effectively reduces toxicity but does not affect the stability of glutaraldehyde cross-linked pericardium.
[Ischemic heart disease--clinical, biochemical and immunobiological parallels]. (1988)

In patients with various forms of ischemic heart disease the following indices were examined by radial immunodiffusion: alpha-1-acid glycoprotein, alpha-1-antitrypsin, haptoglobin, alpha-2-glycoprotein, beta-2-glycoprotein, immunoglobulin, C3 and C4 complement fractions. The changes in the serum glycoproteins during the acute phase of myocardial infarction are pointed out. The changes in the immunoglobulins and the complement fractions in patients with ischemic heart disease are discussed. Their determination in patients with stenocardia and past myocardial infarction is of no diagnostic value.
Highly Dispersed Pd on Co–B Amorphous Alloy: Facile Synthesis via Galvanic Replacement Reaction and Synergetic Effect between Pd and Co (2013)

In this paper, uniform Co–B amorphous alloy nanospheres with an average particle size of 50 nm were synthesized by chemical reduction of cobalt ion with borohydride in aqueous solution containing Bu4PBr and KCl. Then, Pd was introduced into this system by galvanic replacement reaction (GRR) between Co and Na2PdCl4. Pd/Co–B catalysts with different Pd content could be obtained via adjusting the amount of Na2PdCl4 in reaction mixture. The crystal structure, morphology, and surface electronic state of as-prepared catalysts were characterized by XRD, TEM, XPS, and H2-TPD. During the liquid-phase hydrogenation of 2-ethyl-2-hexenaldehyde, the as-prepared Pd/Co–B catalysts exhibited extremely active and more selectivity to 2-ethyl-1-hexanol than the monometallic Pd and Co–B amorphous alloy, showing potential application in industry. The enhanced performances could be attributed to the highly dispersed Pd on the surface of Co–B prepared by GRR and the synergetic effect between Pd and Co.
Update on therapeutic management of idiopathic pulmonary fibrosis (2015)

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive diffuse parenchymal lung disease of unknown origin, with a mortality rate exceeding that of many cancers. The diagnostic process is complex and relies on the clinician integrating clinical, laboratory, radiological, and histological data. In the last decade, major advances in our understanding of the pathogenesis of IPF have shifted the paradigm from a primarily inflammatory process evolving to fibrosis to a condition driven by aberrant wound healing following alveolar epithelial cell injury that results in scarring of the lung, architectural distortion, and irreversible loss of function. Improved understanding of disease pathogenesis has led to the identification of several therapeutic targets and the design of high-quality clinical trials evaluating novel compounds. However, the results of these studies have been mostly disappointing, probably due to the plethora of mediators, growth factors, and signaling pathways involved in the fibrotic process. Most recently, pirfenidone and nintedanib, two compounds with pleiotropic anti-fibrotic properties, have been proven effective in reducing functional decline and disease progression in IPF. This is a major breakthrough. Nevertheless, we still have a long way to go. In fact, neither pirfenidone nor nintedanib is a cure for IPF, and most patients continue to progress despite treatment. As such, comprehensive care of patients with IPF, including management of concomitant conditions and physical debility, as well as timely referral for lung transplantation, remains essential. Several agents with a high potential are currently being tested, and many more are ready for clinical trials. Their completion is critical for achieving the ultimate goal of curing patients with IPF.
Recognition of Base Mismatches in DNA by 5,6-Chrysenequinone Diimine Complexes of Rhodium(III):  A Proposed Mechanism for Preferential Binding in Destabilized Regions of the Double Helix (2000)

5,6-chrysenequinone diimine (chrysi) complexes of rhodium(III) have been shown to be versatile and specific recognition agents for mismatched base pairs in DNA. The design of these compounds was based on the hypothesis that the sterically expansive chrysi ligand, which should be too wide to readily intercalate into B-DNA, would bind preferentially in the destabilized regions of the DNA helix near base mismatches. In this work, this recognition hypothesis is comprehensively explored. Comparison of the recognition patterns of the complex [Rh(bpy)(2)(chrysi)](3+) with a nonsterically demanding analogue, [Rh(bpy)(2)(phi)](3+) (phi = 9,10-phenanthrenequinone diimine), demonstrates that the chrysi ligand does indeed disfavor binding to B-DNA and generate mismatch selectivity. Examination of mismatch recognition by [Rh(bpy)(2)(chrysi)](3+) in both constant and variable sequence contexts using photocleavage assays indicates that the recognition of base mismatches is influenced by the amount that a mismatch thermodynamically destabilizes the DNA helix. Thermodynamic binding constants for the rhodium complex at a range of mismatch sites have been determined by quantitative photocleavage titration and yield values which vary from 1 x 10(6) to 20 x 10(6) M(-)(1). These mismatch-specific binding affinities correlate with independent measurements of thermodynamic destabilization, supporting the hypothesis that helix destabilization is a factor determining the binding affinity of the metal complex for the mismatched site. Although not the only factor involved in the binding of [Rh(bpy)(2)(chrysi)](3+) to mismatch sites, a model is proposed where helix destabilization acts as the "door" which permits access of the sterically demanding intercalator to the base stack.
Java Language Specification, Second Edition: The Java Series (2000)

From the Publisher:
Written by the inventors of the technology, The Java(tm) Language Specification, Second Edition is the definitive technical reference for the Java(tm) programming language. If you want to know the precise meaning of the language's constructs, this is the source for you. 
The book provides complete, accurate, and detailed coverage of the syntax and semantics of the Java programming language. It describes all aspects of the language, including the semantics of all types, statements, and expressions, as well as threads and binary compatibility.
Wave-indices (1997)

In many applications, new data is being generated every day. Often an index of the data of a past window of days is required to answer queries efficiently. For example, in a warehouse one may need an index on the sales records of the last week for efficient data mining, or in a Web service one may provide an index of Netnews articles of the past month. In this paper, we propose a variety of wave indices where the data of a new day can be efficiently added, and old data can be quickly expired, to maintain the required window. We compare these schemes based on several system performance measures, such as storage, query response time, and maintenance work, as well as on their simplicity and ease of coding.
Comparative Evaluation of Tandem MS Search Algorithms Using a Target-Decoy Search Strategy (2007)

Peptide identification of tandem mass spectra by a variety of available search algorithms forms the foundation for much of modern day mass spectrometry-based proteomics. Despite the critical importance of proper evaluation and interpretation of the results generated by these algorithms there is still little consistency in their application or understanding of their similarities and differences. A survey was conducted of four tandem mass spectrometry peptide identification search algorithms, including Mascot, Open Mass Spectrometry Search Algorithm, Sequest, and X! Tandem. The same input data, search parameters, and sequence library were used for the searches. Comparisons were based on commonly used scoring methodologies for each algorithm and on the results of a target-decoy approach to sequence library searching. The results indicated that there is little difference in the output of the algorithms so long as consistent scoring procedures are applied. The results showed that some commonly used scoring procedures may lead to excessive false discovery rates. Finally an alternative method for the determination of an optimal cutoff threshold is proposed.
Functional analyses of GB virus B p13 protein: Development of a recombinant GB virus B hepatitis virus with a p7 protein (2006)

GB virus B (GBV-B), which infects tamarins, is the virus most closely related to hepatitis C virus (HCV). HCV has a protein (p7) that is believed to form an ion channel. It is critical for viability. In vitro studies suggest that GBV-B has an analogous but larger protein (p13). We found that substitutions of the -1 and/or -3 residues of the putative cleavage sites (amino acid 613/614 and 732/733) abolished processing in vitro and rendered an infectious GBV-B clone nonviable in tamarins. Internal cleavage was predicted at two sites (amino acid 669/670 and 681/682), and in vitro analysis indicated processing at both sites, suggesting that p13 is processed into two components (p6 and p7). Mutants with substitution at amino acid 669 or 681 were viable in vivo, but the recovered viruses had changes at amino acid 669 and 681, respectively, which restored cleavage. A mutant lacking amino acid 614-681 (p6 plus part of p7) was nonviable. However, a mutant lacking amino acid 614-669 (p6) produced high titer viremia and acute resolving hepatitis; viruses recovered from both animals lacked the deleted sequence and had no other mutations. Thus, p6 was dispensable but p7 was essential for infectivity. The availability of a recombinant GBV-B virus containing a p7 protein with similarities to the HCV p7 will enhance the relevance of this model and will be of importance for identifying compounds that inhibit p7 function as additional therapeutic agents.
Analysis of DNA double-strand break response and chromatin structure in mitosis using laser microirradiation (2010)

In this study the femtosecond near-IR and nanosecond green lasers are used to induce alterations in mitotic chromosomes. The subsequent double-strand break responses are studied. We show that both lasers are capable of creating comparable chromosomal alterations and that a phase paling observed within 1-2 s of laser exposure is associated with an alteration of chromatin as confirmed by serial section electron microscopy, DAPI, γH2AX and phospho-H3 staining. Additionally, the accumulation of dark material observed using phase contrast light microscopy (indicative of a change in refractive index of the chromatin) ∼ 34 s post-laser exposure corresponds spatially to the accumulation of Nbs1, Ku and ubiquitin. This study demonstrates that chromosomes selectively altered in mitosis initiate the DNA damage response within 30 s and that the accumulation of proteins are visually represented by phase-dark material at the irradiation site, allowing us to determine the fate of the damage as cells enter G1. These results occur with two widely different laser systems, making this approach to study DNA damage responses in the mitotic phase generally available to many different labs. Additionally, we present a summary of most of the published laser studies on chromosomes in order to provide a general guide of the lasers and operating parameters used by other laboratories.
Amplification of the phosphoenol pyruvate carboxylase gene of Brevibacterium lactofermentum to improve amino acid production. (1987)

of Brevibacterium^catalyzes the condensation
A Review of the Rationale and Architectures of PJama: a Durable, Flexible, Evolvable and Scalable Orthogonally Persistent Programming Platform (2000)

A primary goal of research into orthogonal persistence is to simplify significantly the construction, maintenance and operation of applications in order to save software costs, extend the range of applications and improve users ’ experiences. To test such claims we need relevant experiments. To mount such experiments requires an industrial-strength persistent programming platform. The PJama project is an attempt to build such a platform and initiate those experiments. We report our design decisions and their consequences evaluated by four years of experience. We have reached a range of platforms, demonstrated orthogonality and provided durability, schema evolution with instance reformatting, platform migration and recovery. The application programming interface is now close to minimal, while we support open systems through a resumable-programming model. Our architecture is flexible and supports a range of optimisations. Performance measurements and current applications attest to our progress, but it is still possible to identify major research questions, and the experiments to test the utility of orthogonal persistence are still in their early stages.
HERPETIC VIRAL RETINITIS (2013)

Human Herpes Virus (HHV) is a DNA virus and is the most important viral pathogen causing intraocular inflammation. HHV is classified into types 1-8. Among these types, HHV-1, HHV-2, HHV-3 Varicella Zoster Virus (VZV) and HHV-5 Cytomegalovirus (CMV) are known to cause herpetic viral retinitis, including acute retinal necrosis and CMV retinitis. Herpes viral retinitis can be diagnosed from characteristic ocular findings and viral identification by PCR of the aqueous humor. Recently, therapy has become more effective than in the past. Herpes viral retinitis gradually progresses if appropriate treatment is not provided with regard to the patient's immune status. Further advances in diagnostic methods and treatment are required in the future.
Studies on Some Interactions and Reactions of Oligonucleotides in Aqueous Solution<sup>*</sup> (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies on Some Interactions and Reactions of Oligonucleotides in Aqueous Solution*R. Naylor and P. T. GilhamCite this: Biochemistry 1966, 5, 8, 2722–2728Publication Date (Print):August 1, 1966Publication History Published online1 May 2002Published inissue 1 August 1966https://pubs.acs.org/doi/10.1021/bi00872a032https://doi.org/10.1021/bi00872a032research-articleACS PublicationsRequest reuse permissionsArticle Views830Altmetric-Citations182LEARN 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
Scheduling of hydrothermal power systems (1993)

The authors present a method for scheduling hydrothermal power systems based on the Lagrangian relaxation technique. By using Lagrange multipliers to relax system-wide demand and reserve requirements, the problem is decomposed and converted into a two-level optimization problem. Given the sets of Lagrange multipliers, a hydro unit subproblem is solved by a merit order allocation method, and a thermal unit subproblem is solved by using dynamic programming without discretizing generation levels. A subgradient algorithm is used to update the Lagrange multipliers. Numerical results based on Northeast Utilities data show that this algorithm is efficient, and near-optimal solutions are obtained. Compared with previous work where thermal units were scheduled by using the Lagrangian relaxation technique and hydro units by heuristics, the new coordinated hydro and thermal scheduling generates lower total costs and requires less computation time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Transmission line description of optical feedback and injection locking for Fabry-Perot and DFB lasers (1987)

A general theory of semiconductor lasers is presented in which the static and dynamic properties are expressed in terms of the effective left and right reflectivities at a given reference plane in the laser. The theory applies to Fabry-Perot and DFB solitary lasers and to laser configurations with strong optical feedback or strong light injection.
Accelerated coronary MRI with sRAKI: A database-free self-consistent neural network k-space reconstruction for arbitrary undersampling (2020)

sRAKI is a database-free neural network-based reconstruction technique that may further accelerate coronary MRI with arbitrary undersampling patterns, while improving noise resilience over linear parallel imaging and image sharpness over l1 regularization techniques.
Relative Navigation of Air Vehicles (2008)

This paper derives the full equations of motion for relative navigation of air vehicles. An extended Kalman filter is used for estimating the relative position and attitude of two air vehicles designated leader and follower. All leader states are assumed known, whereas the relative states are estimated using line-of-sight measurements between the vehicles along with acceleration and angular rate measurements of the follower. Noise is present on all measurements, whereas biases are present only on the latter two. The global attitude is parameterized using a quaternion, whereas the local attitude error is given by a three-dimensional attitude representation. An application of the new theoretical developments is also given, which involves determining an optimal trajectory to improve the estimation accuracy of the system. A cost function is derived based upon the relative position elements of the estimator covariance. State constraints are appended to the cost function using an exponential term. Results show that minimization of this cost function yields a trajectory that improves accuracy of both the position and attitude state estimates.
An articulated multi-vehicle robot for inspection and testing of pipeline interiors (2002)

The authors describe the construction of an articulated multi-vehicle robot for inspection and testing of pipeline interiors. The robot is capable of traveling inside pipes of radius 520-800 mm diameter over a distance 150 m. Output pressure versus extension characteristics of the two-stage air cylinder, reduction of the wave reflection in a wheel-type ultrasonic probe, an umbilical cable assembly housing optical fibers, air tubes and electric cables are key elements of the robot. The articulated robot was tested in the laboratory to evaluate and the scanning performance. The results of the non-destructive test of a weld bead to the longitudinal direction show that the robot can pick up surrounding color images and transmit them to the ground station's monitor with high precision.
Synthesis and UV/Vis Spectra of J‐Aggregating 5,5′,6,6′‐Tetrachlorobenzimidacarbocyanine Dyes for Artificial Light‐Harvesting Systems and for Asymmetrical Generation of Supramolecular Helices (2003)

Abstract A new class of dyes, in which the self‐assembling property of surfactants is combined with the capability for light energy propagation over long distances in dye J‐aggregates, is described. This has been achieved by the syntheses of achiral 5,5′,6,6′‐tetrachlorobenzimidacarbocyanine dyes 1 , possessing systematically varied hydrophobic and hydrophilic substituents at their nitrogen atoms. These substituents are introduced into the 5,6‐dichlorobenzimidazole precursor 3 by substitution, either firstly by nucleophilic reaction with ψ‐bromoalkylnitriles and secondly by quaternization with alkyl bromides (route II) or firstly by nucleophilic reaction with alkyl bromides and secondly by quaternization with ψ‐bromoalkylnitriles or ψ‐bromoalkyl esters (route III) and subsequent saponification. The UV/Vis spectra of 20 differently substituted dyes containing the same chromophore 1 have been investigated. The spectra of the dye monomers in dimethyl sulfoxide are nearly identical, with no signs of optically activity, whereas in aqueous alkaline solutions quite different spectra are obtained for the dyes, indicating the formation of different aggregates depending on the nitrogen substituents. One of these types of J‐aggregate is optically inactive and displays a single red‐shifted (with respect to the dye monomers) absorption band, resembling the behaviour of J‐aggregates of common cyanine dyes. In the cases of strongly amphiphilic 5,5′,6,6′‐benzimidacarbocyanines 1 with 1,1′‐dialkyl substituents longer than hexyl and 3,3′‐bis(2‐carboxyethyl), 3,3′‐bis(3‐carboxypropyl) or 3,3′‐bis(3‐sulfopropyl) substituents, a new type of J‐aggregate is formed, and is distinguished by a doubly or even triply split J‐absorption band that displays optical activity. A third type of aggregate showing different spectral behaviour occurs when the dyes contain very short 3,3′‐bis(carboxymethyl) substituents or strongly hydrophobic fluorinated octyl groups, or when all four nitrogen atoms are identically substituted by hydrophilic 3‐carboxypropyl groups. The various types of dye aggregates have been characterized through UV/Vis spectroscopic parameters such as the positions and widths of the absorption and fluorescence bands, the Stokes′ shifts, the coupling constants, and the strength of the J‐band splitting. The results provide new prospects for the development of new artificial light‐harvesting systems as well as for the understanding of the evolution of asymmetry in the biosphere. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)