gebhart/patrepeval huggingface dataset:
Pickling State in the Java System. (1996)

The Java^TM 1 system (hereafter referred to simply as &amp;quot;Java&amp;quot;) inherently supports the transmission of stateless computation in the form of object classes. In this paper we address the related task of capturing the state of a Java object in a serialized form for the purposes of transmission or storage, to be used later in reconstituting an equivalent object. This is accomplished by a mechanism known as pickling[2][3][5]. Pickling is the process of creating a serialized representation of objects. Pickling defines the serialized form to include meta information that identifies the type of each object and the relationships between objects within a stream. Values and types are serialized with enough information to insure that the equivalent typed object and the objects to which it refers can be recreated. Unpickling is the complementary process of recreating objects from the serialized representation. Pickling and unpickling extract from the Java Virtual machine, at runtime, any meta in...
Comprehensive molecular characterization of gastric adenocarcinoma (2014)

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein-Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies.
Is Ca2+ ‐Calmodulin‐Dependent Protein Phosphorylation in Rat Brain Modulated by Carboxylmethylation? (1985)

Calmodulin stimulation of protein kinase activity in calmodulin-depleted preparations of rat brain cytosol or synaptosomal membranes was attenuated by prior carboxylmethylation of the enzyme source with purified protein-O-carboxylmethyltransferase. Similarly, calmodulin stimulation of highly purified Ca2+-calmodulin-dependent protein kinase was reduced if the kinase was exposed to methylating conditions prior to addition of calmodulin. Biochemical and acidic sodium dodecyl sulfate-gel electrophoretic analyses indicated that all sources of protein kinase activity were substrates for methylation. The specific activity of methyl group incorporation into protein kinase increased with increasing purity of the preparation, reaching values of 1.72 pmol CH3/micrograms protein or 0.15-1.12 mol CH3/mol of holoenzyme. Analysis of ATP binding in cytosol with the use of the photoaffinity probe [32P]8-azido-ATP indicated that carboxylmethylation reduced ATP binding. These results suggest that carboxylmethylation of Ca2+-calmodulin protein kinase may modulate the activity of this enzyme in rat brain.
Purine nucleoside synthesis: an efficient method employing nucleoside phosphorylases (1981)

An improved method for the enzymatic synthesis of purine nucleosides is described. Pyrimidine nucleosides were used as pentosyl donors and two phosphorylases were used as catalysts. One of the enzymes, either uridine phosphorylase (Urd Pase) or thymidine phosphorylase (dThd Pase), catalyzed the phosphorolysis of the pentosyl donor. The other enzyme, purine nucleoside phosphorylase (PN Pase), catalyzed the synthesis of the product nucleoside by utilizing the pentose 1-phosphate ester generated from the phosphorolysis of the pyrimidine nucleoside. Urd Pase, dThd Pase, and PN Pase were separated from each other in extracts of Escherichia coli by titration with calcium phosphate gel. Each enzyme was further purified by ion-exchange chromatography. Factors that affect the stability of these catalysts were studied. The pH optima for the stability of Urd Pase, dThd Pase, and PN Pase were 7.6, 6.5, and 7.4, respectively. The order of relative heat stability was Urd Pase greater than PN Pase greater than dThd Pase. The stability of each enzyme increased with increasing enzyme concentration. This dependence was strongest with dThd Pase and weakest with Urd Pase. Of the substrates tested, the most potent stabilizers of Urd Pase, dThd Pase, and PN Pase were uridine, 2'-deoxyribose 1-phosphate, and ribose 1-phosphate, respectively. Some general guidelines for optimization of yields are given. In a model reaction, optimal product formation was obtained at low phosphate concentrations. As examples of the efficiency of the method, the 2'-deoxyribonucleoside of 6-(dimethylamino)purine and the ribonucleoside of 2-amino-6-chloropurine were prepared in yields of 81 and 76%, respectively.
Digital Protein Analysis: Technologies for Protein Diagnostics and Proteomics through Single-Molecule Detection (2011)

Protein quantification tools are valuable in biological and biomedical research and in clinical applications because they enable measurements that elucidate physiological states, including disease states. Protein biomarker detection is likely to play a major role in patient health and aid in the personalization of medicine. However, protein detection has lagged behind other bio-analytical methods due to intrinsic properties of proteins as well as the complexity of biological fluids, such as blood. This thesis describes the design, development, and testing of several technologies for the advancement of protein detection in clinical and research settings. A common thread through these technologies is the isolation of millions of protein molecules on a solid surface, the interrogation of those molecules by fluorescently-labeled antibodies, and the identification and quantification of those molecules by single molecule resolution imaging. By systematically investigating the parameters that have prevented single-molecule quantification of surface-immobilized proteins, we achieved technologies that can digitally quantify biomarkers in single-plex and multi-plex formats and be used to detect protein-protein interactions. Additionally we characterized a surface coating method that will be of benefit to a wide array of biophysical studies. Finally, we conducted proof-of-principle experiments and computer simulations for the development of a high-throughput proteomics technology that relies on only a small set of probes: 8 to 50) to analyze each of the approximately 23,000 human proteins.
Asymmetric Dimethylarginine Concentration and Early Recurrence of Atrial Fibrillation after Electrical Cardioversion (2008)

Our data suggest that high levels of ADMA are associated with an increased risk of AF recurrence within 1 month after electrical CV, supporting the hypothesis that ADMA might participate in the process of atrial remodeling.
Role of Tetrabenazine for Huntington's Disease-Associated Chorea (2010)

Tetrabenazine can provide significant benefit in the treatment of chorea associated with HD. Given the potential adverse effects of tetrabenazine, health-care providers need to screen patients carefully prior to initiating treatment with this medication. In the future, additional long-term and comparative studies would be useful for further clarification of the role of tetrabenazine in the treatment of HD-associated chorea.
Cloned alpha and beta C-protein antigens of group B streptococci elicit protective immunity (1991)

Streptococcus agalactiae (group B streptococci [GBS]) is the leading cause of neonatal sepsis and meningitis in the United States. The surface-associated C proteins of GBS play a role in immunity, but their number, size, structure, function, and virulence properties have not been well characterized. A recombinant library of DNA fragments from GBS strain A909 (type Ia/C) was prepared in the plasmid pUX12, a specially constructed Escherichia coli expression vector. The library was screened with a rabbit antiserum shown to be protective for passive immunity to GBS infection in a mouse lethality model. Clones were divided into two distinct groups on the basis of DNA-DNA cross-hybridization, restriction enzyme analysis, and the expression of antigenic proteins in E. coli. A characteristic clone from each group was chosen for further study. Clone pJMS23 expresses gene products that biochemically and immunologically correspond to the trypsin-resistant, C-protein alpha antigen. Clone pJMS1 expresses a gene product that binds to immunoglobulin A and is similar to the trypsin-sensitive, C-protein beta antigen. Antisera raised in rabbits against E. coli containing each of the plasmid clones were able to elicit protective immunity in mice challenged by GBS strains carrying the C proteins but not by non-C-protein-bearing strains. Southern blot analysis shows no DNA homology between the clones, and there is no immunological cross-reactivity between the antigens they express. Therefore, pJMS23 and pJMS1 encode two different C proteins that define unique protective epitopes.
Quorum sensing Escherichia coli regulators B and C (QseBC): a novel two‐component regulatory system involved in the regulation of flagella and motility by quorum sensing in E. coli (2002)

Quorum sensing is a cell-to-cell signalling mechanism in which bacteria secrete hormone-like compounds called autoinducers. When these auto-inducers reach a certain threshold concentration, they interact with bacterial transcriptional regulators, thereby regulating gene expression. Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 as well as E. coli K-12 produces the autoinducer-2 (AI-2), which is synthesized by the product of the luxS gene, and previous work from our laboratory has shown that genes encoding the EHEC type III secretion system were activated by quorum sensing. Recently, by hybridizing an E. coli K-12 gene array with cDNA synthesized from RNA extracted from EHEC strain 86-24 and its isogenic luxS mutant, we observed that other potential virulence-associated factors, such as genes encoding the expression and assembly of flagella, motility and chemotaxis, were also activated by quorum sensing. The array data also indicated that several genes encoding putative E. coli regulators were controlled by quorum sensing. In this report, we describe a two-component system regulated by quorum sensing that shares homology with Salmonella typhimurium PmrAB, which we have named quorum sensing E. coli regulator B and C (QseBC). The qseBC genes, previously identified only as open reading frames b3025 and b3026, are organized in an operon in the E. coli chromosome, with qseB encoding the response regulator and qseC the sensor kinase. We confirmed the regulation of qseBC by quorum sensing using qseB::lacZ transcriptional fusions and characterized the phenotypes of an isogenic qseC mutation in EHEC. This mutant expressed less flagellin and had reduced motility compared with the wild-type and complemented strains. Transcription of flhD, fliA, motA and fliC::lacZ fusions was decreased in the qseC mutant, suggesting that qseBC is a transcriptional regulator of flagella genes. A qseC mutant was also generated in E. coli K-12 strain MC1000 that showed the same phenotypes as the EHEC mutant, indicating that qseBC regulates flagella and motility by quorum sensing in both EHEC and K-12. QseBC activates transcription of flhDC, which is the master regulator for the flagella and motility genes and, in the absence of flhD, QseBC failed to activate the transcription of fliA. Motility of a luxS, but not of a qseC, mutant can be restored by providing AI-2 exogenously as preconditioned media, suggesting that the qseC mutant is unable to respond to AI-2. However, QseC has no effect on the expression of other quorum sensing-controlled genes such as those encoding for the type III secretion system. These data indicate that QseBC is one component of the quorum-sensing regulatory cascade in both EHEC and K-12 that is involved in the regulation of flagella and motility genes, but that additional regulators in this cascade remain to be characterized.
Phosphorylated Proteins and Control over Apatite Nucleation, Crystal Growth, and Inhibition (2008)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTPhosphorylated Proteins and Control over Apatite Nucleation, Crystal Growth, and InhibitionAnne George*† and Arthur Veis‡View Author Information Department of Oral Biology, Brodie Tooth Development Genetics and Regenerative Medicine Research Laboratory, University of Illinois at Chicago, Chicago, Illinois 60612, and Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611* Corresponding author. Phone: (312) 413-0738. Fax: (312) 996-6044. E-mail: [email protected]†University of Illinois at Chicago.‡Northwestern University.Cite this: Chem. Rev. 2008, 108, 11, 4670–4693Publication Date (Web):October 3, 2008Publication History Received10 January 2008Published online3 October 2008Published inissue 12 November 2008https://pubs.acs.org/doi/10.1021/cr0782729https://doi.org/10.1021/cr0782729review-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views6514Altmetric-Citations587LEARN 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 SUBJECTS:Biopolymers,Differential pulse voltammetry,Mineralization,Peptides and proteins,Post-translational modification Get e-Alerts
Analysis of the Gene Expression Profile Activated by the CC Chemokine Ligand 5/RANTES and by Lipopolysaccharide in Human Monocytes (2002)

The gene expression profile induced by the CC chemokine ligand (CCL) 5/RANTES in human monocytes was examined using the oligonucleotide array technology. Of 5600 transcripts examined, 42 were consistently induced by CCL5, and none were suppressed. Chemokine-inducible transcripts could be clustered in functional groups, including selected cytokines and receptors (e.g., IL-1beta, CCL2/monocyte chemotactic protein-1, and the CCL5 receptor CCR1) and molecules involved in extracellular matrix recognition and digestion (e.g., CD44 splice transcripts, urokinase-type plasminogen activator receptor, matrix metalloprotease (MMP)-9, and MMP-19). Transcript expression, confirmed by quantitative real-time PCR analysis for selected genes, was associated with protein induction for some (e.g., CCL2), but not all (e.g., IL-1beta), transcripts examined. The chemokine-induced gene profile was distinct from that activated by LPS, a prototypic phagocyte activator. Although certain transcripts were stimulated by both agonists (e.g., IL-1beta and CCL2), others were induced only by either LPS (e.g., TNF-alpha and IL-6) or CCL5 (e.g., MMP-19) or were divergently regulated (e.g., CCR1). Thus, CCL5, a prototypic CC inflammatory chemokine, activates a restricted transcriptional program in monocytes distinct from that induced by the prototypic pathogen-derived proinflammatory stimulant LPS. Chemokine-induced chemokines production could represent a novel amplification loop of leukocyte recruitment, while a subset of chemokine-inducible transcripts could be involved in monocyte extravasation and tissue invasion.
Low-power-consumption short-length and high-modulation-depth silicon electrooptic modulator (2003)

We propose and analyze a novel compact electrooptic modulator on a silicon-on-insulator (SOI) rib waveguide. The device confines both optical field and charge carriers in a micron-size region. The optical field is confined by using a planar Fabry-Perot microcavity with deep Si/SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Bragg reflectors. Carriers are laterally confined in the cavity region by employing deep-etched trenches. The refractive index of the cavity is varied by using the free-carrier dispersion effect produced by a p-i-n diode. The device has been designed and analyzed using electrical and optical simulations. Our calculations predict, for a 20-μm-long device, a modulation depth of around 80% and a transmittance of 86% at an operating wavelength of 1.55 μm by using an electrical power under dc conditions on the order of 25 μW.
Signal-dependent activation of the MEF2 transcription factor by dissociation from histone deacetylases (2000)

Myocyte enhancer factor-2 (MEF2) transcription factors control muscle-specific and growth factor-inducible genes. We show that hypertrophic growth of cardiomyocytes in response to phenylephrine and serum is accompanied by activation of MEF2 through a posttranslational mechanism mediated by calcium, calmodulin-dependent protein kinase (CaMK), and mitogen-activated protein kinase (MAPK) signaling. CaMK stimulates MEF2 activity by dissociating class II histone deacetylases (HDACs) from the DNA-binding domain. MAPKs, which activate MEF2 by phosphorylation of the transcription activation domain, maximally stimulate MEF2 activity only when repression by HDACs is relieved by CaMK signaling to the DNA-binding domain. These findings identify MEF2 as an endpoint for hypertrophic stimuli in cardiomyocytes and demonstrate that MEF2 mediates synergistic transcriptional responses to the CaMK and MAPK signaling pathways by signal-dependent dissociation from HDACs.
Microbes and the gut‐brain axis (2012)

The strongest evidence for a role of microbes as signaling components in the gut-brain axis currently arises from animal studies and indicate that mechanisms of communication are likely to be multiple. There is need for the concepts generated in animal models to be translated to the human in the future.
Structure-dependent immunostimulatory effect of CpG oligodeoxynucleotides and their delivery system (2012)

Unmethylated cytosine-phosphate-guanosine (CpG) oligodeoxynucleotides (ODNs) are recognized by Toll-like receptor 9 (TLR9) found in antigen-presenting cells and B cells and can activate the immune system. Using CpG ODNs as an adjuvant has been found to be effective for treating infectious diseases, cancers, and allergies. Because natural ODNs with only a phosphodiester backbone are easily degraded by nuclease (deoxyribonuclease [DNase]) in serum, CpG ODNs with a phosphorothioate backbone have been studied for clinical application. CpG ODNs with a phosphorothioate backbone have raised concern regarding undesirable side effects; however, several CpG ODNs with only a phosphodiester backbone have been reported to be stable in serum and to show an immunostimulatory effect. In recent years, research has been conducted on delivery systems for CpG ODNs using nanoparticles (NPs). The advantages of NP-based delivery of CpG ODN include (1) it can protect CpG ODN from DNase, (2) it can retain CpG ODN inside the body for a long period of time, (3) it can improve the cellular uptake efficiency of CpG ODN, and (4) it can deliver CpG ODN to the target tissues. Because the target cells of CpG ODN are cells of the immune system and TLR9, the receptor of CpG ODN is localized in endolysosomes, CpG ODN delivery systems are required to have qualities different from other nucleic acid drugs such as antisense DNA and small interfering RNA. Studies until now have reported various NPs as carriers for CpG ODN delivery. This review presents DNase-resistant CpG ODNs with various structures and their immunostimulatory effects and also focuses on delivery systems of CpG ODNs that utilize NPs. Because CpG ODNs interact with TLR9 and activate both the innate and the adaptive immune system, the application of CpG ODNs for the treatment of cancers, infectious diseases, and allergies holds great promise.
Berührungslose Prüfung von Kunststoffen mittels photothermischer Wärmewellenanalyse (1984)

Abstract Nach einer Einführung in die Grundlagen von Wärmewellen werden die photoakustischen Meßmethoden (Gaszelle, Piezokeramik) den photothermischen Meßmöglichkeiten (Frontseiten‐ und Rückseitenmethode) erläuternd gegenübergestellt. Kunststoffbezogene Problemstellungen wurden bisher nahezu ausschließlich mit photoakustischen Methoden bearbeitet. Die Vorteile der photothermischen Messungen – berührungslose und zerstörungsfreie Prüfung – konnten bisher an Metallen verdeutlicht werden. Der experimentelle Teil dieser Arbeit zeigt in ersten Schritten auf, daß auch bei Kunststoffen folgende Problemstellungen mit der Methode der photothermischen Wärmewellenanalyse bearbeitet werden können. Dickenmessung dünner Schichten; äußere und innere Fehlstellen; Haftungsfehler bei Verklebungen oder Beschichtungen; Vernetzungsreaktionen; Glasfaseranteil; Glasfaser‐ und Molekülorientierungen; Alterungsvorgänge. Die bisherigen Ergebnisse lassen sich in die zerstörungsfreie Qualitätssicherung dünner Schichten und Folien übertragen. Die zerstörungsfreie Prüfung von dickwandigen Bauteilen bedarf einer methodischen Weiterentwicklung.
Topoisomerase I Inhibitors (1997)

Topoisomerase I inhibitors are a new class of anticancer agents with a mechanism of action aimed at interrupting DNA replication in cancer cells, the result of which is cell death. Most if not all Topoisomerase I inhibitors are derivatives of the plant extract camptothecin. Irinotecan (CPT-11), a semi-synthetic derivative of camptothecin, is approved in the United States for the treatment of colorectal cancer. Ongoing clinical trials with CPT-11 show a 13% to 32% response rate when it is used singly or in combination with other chemotherapeutic agents such as 5-fluorouracil. The major dose-limiting toxicities of CPT-11 are myelosuppression and a dual phase diarrhea. Topotecan is another semi-synthetic analogue of camptothecin. It is approved for use in the United States for the treatment of cisplatin refractory ovarian carcinoma. Current clinical trials suggest antitumor activity against a variety of human tumor types. There is significant interindividual variability in the plasma disposition of this drug. The main dose-limiting toxicity is myelosuppression. There are other derivatives of camptothecin, as well as new formulations of the parent plant extract, that are in various stages of clinical trials. Some of these clinical trials are aimed at increasing the therapeutic benefits of the agents when used singly or in combination with other chemotherapeutic agent(s) or treatment modalities. The dose-limiting toxicity observed in most of these clinical trials is myelosuppression.