gebhart/patrepeval huggingface dataset:
Cloning, sequencing and bioinformatics analysis of adhesin gene babA2 of Helicobacter pylori (2003)

AIM: To obtain DNA of human Helicobacter pylori (Hp) adhesin gene babA2 and the amplified fragment was inserted into plasmid pET-22b (+) for nucleotide sequencing analysis and to carry out bioinformatics analysis. METHODS: The babA2 DNA was amplified by PCR and inserted into the plasmid pET -22b (+) and sequenced. The biological property was analysed by the software ANTHEPROT V4.3c. RESULTS: DNA sequencing analysis showed that the sequence of babA2 DNA was the same as that published by GenBank. ANTHEPROT V4.3c software predicted its relative molecular mass(Mr) was 78 kD and it possessed good antigencity and hydrophobicity.
Best Practices for Operando Battery Experiments: Influences of X-ray Experiment Design on Observed Electrochemical Reactivity (2015)

ADVERTISEMENT RETURN TO ISSUEPREVViewpointNEXTBest Practices for Operando Battery Experiments: Influences of X-ray Experiment Design on Observed Electrochemical ReactivityOlaf J. Borkiewicz, Kamila M. Wiaderek, Peter J. Chupas, and Karena W. Chapman*View Author Information X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States*E-mail: [email protected]. Phone: 1-630-252-0127. Fax: 1-630-252-0365.Cite this: J. Phys. Chem. Lett. 2015, 6, 11, 2081–2085Publication Date (Web):June 4, 2015Publication History Published online4 June 2015Published inissue 4 June 2015https://pubs.acs.org/doi/10.1021/acs.jpclett.5b00891https://doi.org/10.1021/acs.jpclett.5b00891editorialACS PublicationsCopyright © 2015 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views4593Altmetric-Citations77LEARN 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 PDF (1 MB) Get e-AlertscloseSUBJECTS:Electrical conductivity,Electrochemical cells,Electrodes,Reactivity,X-rays Get e-Alerts
A Practical Architecture for an Anycast CDN (2011)

IP Anycast has many attractive features for any service that involve the replication of multiple instances across the Internet. IP Anycast allows multiple instances of the same service to be “naturally” discovered, and requests for this service to be delivered to the closest instance. However, while briefly considered as an enabler for content delivery networks (CDNs) when they first emerged, IP Anycast was deemed infeasible in that environment. The main reasons for this decision were the lack of load awareness of IP Anycast and unwanted side effects of Internet routing changes on the IP Anycast mechanism. In this article we re-evaluate IP Anycast for CDNs by proposing a load-aware IP Anycast CDN architecture. Our architecture is prompted by recent developments in route control technology, as well as better understanding of the behavior of IP Anycast in operational settings. Our architecture makes use of route control mechanisms to take server and network load into account to realize load-aware Anycast. We show that the resulting redirection requirements can be formulated as a Generalized Assignment Problem and present practical algorithms that address these requirements while at the same time limiting connection disruptions that plague regular IP Anycast. We evaluate our algorithms through trace based simulation using traces obtained from a production CDN network.
<title>Microarray-based optical biochip with nanometric resolution</title> (1999)

The choice of metal clusters as signal transducers of molecular binding events is based on their about 1000 times higher extinction coefficients compared to conjugated chromophores. Using cluster based assays it is possible to visualize the binding of biomolecules at a given surface by a bound layer of ligand-modified metal clusters. The success of cluster visualization was mainly based on the significant signal stability contrary to chromophores and especially fluorophores. Cluster probes are not only efficient direct markers but within the past years became the basis of new devices employing cluster resonance, cluster field enhancement, and cluster-cluster interactions. Multilayered highly resonant systems clearly exhibit strong reflection minima induced by the resonant behavior of the metal cluster layer. At least one narrow reflection minimum can be shifted to the red or infra red spectral range and therefore far away from spherical gold colloids to be ready by a 10 micrometer resolution optical scanner type high density device. Even without employing near-field optics spatial resolution is within 100 - 500 nm. The setup enabled us to replace conventional ELISA assays overcoming the various technological limits as there are e.g. multiple incubation steps and spatial resolution. The focus of the development was to provide an optical biochip which allows detection of analytes based on arrays of proteins, DNA and high throughput-screening targets for drug discovery.
Glycerides as prodrugs. 2. 1,3-Dialkanoyl-2-(2-methyl-4-oxo-1,3-benzodioxan-2-yl)glycerides (cyclic aspirin triglycerides) as antiinflammatory agents (1980)

A series of 1,3-dialkanoyl-2-(2-methyl-4-oxo-1,3-benzodioxan-2-yl)glycerides ("cyclic aspirin triglycerides") was synthesized. They demonstrated essentially all the systemic antiinflammatory activity associated with aspirin in the carrageenin-induced rat paw edema test. Examination of the rat stomachs showed that the 1,3-didecanoyl derivative did not cause gastric lesions.
Microsatellite Instability and 8p Allelic Imbalance in Stage B2 and C Colorectal Cancers (1999)

Patients whose tumors exhibited MSI-H had a favorable prognosis, whereas those with 8p allelic imbalance had a poor prognosis; both alterations served as independent prognostic factors. To our knowledge, this is the first report of an association between 8p allelic imbalance and survival in patients with colorectal cancer.
A three stranded β-sheet peptide in aqueous solution containing N-methyl amino acids to prevent aggregation (1997)

A. J. Doig, Chem. Commun., 1997, 2153 DOI: 10.1039/A706167F
Reducing Timing Channels with Fuzzy Time (1992)

This paper describes fuzzy time. This is a collection of techniques that reduces the bandwidths of covert timing channels by making all clocks available to a process noisy. Developed in response to...
Successive approximation tuning of monolithic continuous-time filters (1992)

The Letter proposes the tuning of monolithic continuous-time filters employing a successive approximation algorithm to control the automatic adjustment of a two-integrator loop to its nominal resonant frequency depending on an error signal provided by a digital phase discriminator. This achieves high-precision tunability which does not depend on tight circuit matching.
Transforming Dual Flow Nets into Object Petri Nets (2005)

Abstract This paper summarises two approaches, Dual Flow Nets (DFN) and Object Petri Nets (OPN), and offers a translation mechanism between them. While the DFN model tackles the separation of control and data flow computing aspects, the OPN model has a more generalised structure. The aim of this paper is to show how the modelling based on control/data-flow analysis can benefit from an object-based Petri net approach. Tool support and a translation mechanism that is faithful are pesented, giving an extra dimension (hierarchy) to the existing paradigm of control and data flow interacting in a model. Our methodology provides a comprehensive separation of these two parts, which can be used to feed analysis or synthesis tools, while still being able to reason about both parts through formal methods of verification. 1
A lineage metadata model for the temporal management of a cadastre application (1999)

Nowadays one of the most successful applications of GIS is the management of a land-use cadastre. A lot of corporate GIS databases are in development, they support the legal management and distribution of cadastral maps. However, the management of the propagation of geographical updates toward relevant user databases is still a methodological and technical problem to address in the context of a corporate application. This paper proposes a lineage metadata model that supports the management of geographical changes in the context of a corporate cadastre application. Geographical changes are identified from an analysis of the French cadastre which acts as a case study for the development of our model. The lineage metadata model is based on the application of a filiation tree that permits the management of the evolution of geographical objects and the generation of historical queries. The proposed model is specified and validated with the O/sub 2/ object-oriented database.
Clinical Perspective of Cell-Free DNA Testing for Fetal Aneuploidies (2014)

Cell-free DNA testing in maternal blood provides the most effective method of screening for trisomy 21, with a reported detection rate of 99% and a false positive rate of less than 0.1%. After many years of research, this method is now commercially available and is carried out in an increasing number of patients, and there is an expanding number of conditions that can be screened for. However, the application of these methods in clinical practice requires a careful analysis. Current first-trimester screening strategies are based on a complex combination of tests, aiming at detecting fetal defects and predicting the risk of main pregnancy complications. It is therefore necessary to define the optimal way of combining cell-free DNA testing with current first-trimester screening methods. In this concise review we describe the basis of cell-free DNA testing and discuss the potential approaches for its implementation in combination with current tests in the first trimester.
A Formalism for the Description of Protein Interaction (2010)

The Calculus of Looping Sequences is a formalism for describing evolution of biological systems by means of term rewriting rules.We propose to enrich this calculus by labelling elements of sequences.Since two elements with the same label are considered to be linked, this allows us to represent protein interaction at the domain level.Well-formedness of terms are ensured by both a syntactic constraint and a type system: we discuss the differences between these approaches through the description of a biological system, namely the EGF pathway.
<sup>18</sup>F-Glyco-RGD Peptides for PET Imaging of Integrin Expression: Efficient Radiosynthesis by Click Chemistry and Modulation of Biodistribution by Glycosylation (2013)

Glycosylation frequently improves the biokinetics and clearance properties of macromolecules in vivo and could therefore be used for the design of radiopharmaceuticals for positron emission tomography (PET). Recently, we have developed a click chemistry method for (18)F-fluoroglycosylation of alkyne-bearing RGD-peptides targeting the integrin receptor. To investigate whether this strategy could yield an (18)F-labeled RGD glycopeptide with favorable biokinetics, we generated a series of new RGD glycopeptides, varying the 6-fluoroglycosyl residue from monosaccharide to disaccharide units, which provided the glucosyl ([(19)F]6Glc-RGD, 4b), galactosyl ([(19)F]Gal-RGD, 4c), maltosyl ([(19)F]Mlt-RGD, 4e), and cellobiosyl ([(19)F]Cel-RGD, 4f) conjugated peptides in high yields and purities of >97%. All of these RGD glycopeptides showed high affinity to αvβ3 (11-55 nM), αvβ5 (6-14 nM), and to αvβ3-positive U87MG cells (90-395 nM). (18)F-labeling of the various carbohydrate precursors (1a-f) using cryptate-assisted reaction conditions (CH3CN, 85 °C, 10 min) gave (18)F-labeled glycosyl azides in radiochemical yields (RCYs) of up to 84% ([(18)F]2b). The deacetylation and subsequent click reaction with the alkyne-bearing cyclic RGD peptide proceeded in one-pot reactions with RCYs as high as 81% in 15-20 min at 60 °C, using a minimal amount of peptide precursor (100 nmol). Optimization of the radiosynthesis strategy gave a decay-uncorrected RCY of 16-24% after 70-75 min (based on [(18)F]fluoride). Due to their high-yield radiosyntheses, the glycopeptides [(18)F]6Glc-RGD and [(18)F]Mlt-RGD were chosen for comparative biodistribution studies and dynamic small-animal PET imaging using U87MG tumor-bearing nude mice. [(18)F]6Glc-RGD and [(18)F]Mlt-RGD showed significantly decreased liver and kidney uptake by PET relative to the 2-[(18)F]fluoroglucosyl analog [(18)F]2Glc-RGD, and showed specific tumor uptake in vivo. Notably, [(18)F]Mlt-RGD revealed uptake and retention in the U87MG tumor comparable to that of [(18)F]Galacto-RGD. Both [(18)F]6Glc-RGD and [(18)F]Mlt-RGD were obtained by a reliable and easy click chemistry-based procedure, much more rapidly than was [(18)F]Galacto-RGD. Due to its favorable biodistribution and tissue clearance in vivo, [(18)F]Mlt-RGD represents a viable alternative radiotracer for imaging integrin expression in solid tumors by PET.
A study of classification criteria for a diagnosis of juvenile rheumatoid arthritis (1986)

Criteria for the classification of juvenile rheumatoid arthritis were analyzed in a detailed database of 250 children in order to assess the accuracy of diagnosis and validity of onset types and course subtypes. A number of conclusions have been derived from this study: All definitions of the 1973 criteria for classification of juvenile rheumatoid arthritis should be retained. The addition of onset types to the 1976 revision of the criteria has been validated. The course of the disease after the onset period of 6 months is as important to the outcome of a group of children as is the onset type. The current classification should be broadened to include the course subtypes.
The rat fructose-1,6-bisphosphatase gene. Structure and regulation of expression (1991)

The gene encoding rat fructose-1,6-bisphosphatase was isolated from a rat genomic Charon 4A library by screening with a cDNA to the rat liver enzyme. Southern blotting of rat genomic DNA showed that there is a single copy of the fructose-1,6-bisphosphatase gene. It extends over 23 kilobases and is composed of seven exons and six introns that range in size from 93 to 267 base pairs and from 1,400 to 11,300 base pairs, respectively. The intron/exon boundary sequences conform to consensus acceptor (GTn) and donor (nAG) sequences, and the exons in the gene appear to code for functional protein domains. The transcription start site, determined by 5'-extension sequencing of mRNA, was assigned to a guanine 119 bases 5' to the translation initiation AUG. The sequence of the gene upstream to the cap site contains characteristic RNA polymerase II promoter-binding sites: a putative TATA box at position -29 and a Sp 1 binding site (GGGGCGGAGA) at position -48. A 1,300-base pair fragment of 5'-flanking sequence containing these elements, ligated upstream from a firefly luciferase reporter gene and transfected into cultured normal rat kidney cells, demonstrated strong promoter activity. The accumulation of fructose-1,6-bisphosphatase mRNA in hepatocytes incubated with cAMP suggests that the gene may be cAMP-responsive, which is consistent with the presence of three consensus cAMP regulatory elements at positions -169, -282, and -698 in the 5'-flanking region of the gene. Expression of the fructose-1,6-bisphosphatase promoter-driven luciferaes gene was 2-3-fold activated by the cyclic nucleotide, suggesting that one or more of these elements may be functional. On the other hand, insulin decreased the expression of the endogenous gene in hepatocytes. Thus, expression of the fructose-1,6-bisphosphatase gene is regulated independently by both cAMP and insulin.
Ligation of CD11c during vaccination promotes germinal centre induction and robust humoral responses without adjuvant (2010)

In this study, we investigated the mouse dendritic cell (DC) receptor, complement receptor 4 (CR4; CD11c/CD18), as an immunotarget for triggering humoral immunity. Comparison of antibody titres generated against a panel of 13 anti-antigen-presenting cell receptor monoclonal antibodies, with or without conjugated ovalbumin (OVA), revealed uniquely rapid and robust responses following CR4 targeting, with antibody titres approaching 1 : 100 000 7 days after a single dose of antigen. Furthermore, using just 100 ng OVA conjugated to anti-CD11c Fab', we generated anti-OVA titres greater than those produced by a 100-fold higher dose of OVA in complete Freund's adjuvant at day 28. These anti-OVA antibody titres were sustained and could be boosted further with targeted OVA on day 21. Investigations to explain this vaccine potency showed that, in addition to targeting splenic DC, anti-CDl1c antibodies delivered a powerful adjuvant effect and could boost humoral immunity against OVA even when the OVA was targeted to other molecules on DC, such as major histocompatibility complex class II, CD11a and CD11b. However, interestingly, this adjuvant effect was lost if OVA was targeted to other cells such as B cells via CD21 or CD19. The adjuvant effect was mediated through a marked enhancement of both germinal centre and extrafollicular plasma cell formation in responding spleens. These results demonstrate that anti-CD11c monoclonal antibody can both target antigen and act as a powerful adjuvant for rapid and sustained antibody responses. They also point to an interesting role for CR4 on DC in triggering B cells during humoral immunity.
Plating on Aluminum (1939)

In ordinary electroplating on aluminum, the adhesion of the plate is very poor. To ensure perfect contact, the aluminum surface is accordingly submitted to a new process. The first step comprises an electrolytic anodizing treatment, with alternating current in an aqueous bath containing 30 g./L. of oxalic acid. Ten minutes at 50 volts and a bath temperature of 20° C. are recommended. Then follows a 2 to 15 minute treatment in a 60 g./L. solution of sodium cyanide; and after a thorough water rinse, an electrodeposit of nickel is applied employing one or the other standard nickel baths. On top of the nickel a plate of chromium, copper, iron or other metal can be applied following ordinary commercial procedure for these metals. Letters patent have been granted covering the process.
The p85α Subunit of Class I<sub>A</sub> Phosphatidylinositol 3-Kinase Regulates the Expression of Multiple Genes Involved in Osteoclast Maturation and Migration (2008)

Intracellular signals involved in the maturation and function of osteoclasts are poorly understood. Here, we demonstrate that osteoclasts express multiple regulatory subunits of class I(A) phosphatidylinositol 3-kinase (PI3-K) although the expression of the full-length form of p85alpha is most abundant. In vivo, deficiency of p85alpha results in a significantly greater number of trabeculae and significantly lower spacing between trabeculae as well as increased bone mass in both males and females compared to their sex-matched wild-type controls. Consistently, p85alpha(-/-) osteoclast progenitors show impaired growth and differentiation, which is associated with reduced activation of Akt and mitogen-activated protein kinase extracellular signal-regulated kinase 1 (Erk1)/Erk2 in vitro. Furthermore, a significant reduction in the ability of p85alpha(-/-) osteoclasts to adhere to as well as to migrate via integrin alphavbeta3 was observed, which was associated with reduced bone resorption. Microarray as well as quantitative real-time PCR analysis of p85alpha(-/-) osteoclasts revealed a significant reduction in the expression of several genes associated with the maturation and migration of osteoclasts, including microphathalmia-associated transcription factor, tartrate-resistant acid phosphatase, cathepsin K, and beta3 integrin. Restoring the expression of the full-length form of p85alpha but not the version with a deletion of the Src homology-3 domain restored the maturation of p85alpha(-/-) osteoclasts to wild-type levels. These results highlight the importance of the full-length version of the p85alpha subunit of class I(A) PI3-K in controlling multiple aspects of osteoclast functions.
Sequential degradation of the neuropeptide gonadotropin‐releasing hormone by the 20 S granulosa cell proteasomes (1994)

The decapeptide gonadotropin-releasing hormone (GnRH) is degraded by the 20 S multicatalytic proteinase complex (proteasome EC 3.4.99.46), purified from ovarian granulosa cells, at the Tyr5-Gly6 bond and to a lesser extent at the Gly6-Leu7 bond, when incubated for 2 h at 37 degrees C. Further cleavage, at Trp3-Ser4 and Ser4-Tyr5 bonds of the neurohormone occurs only subsequently to the appearance of the initial N-terminal degradation products, (1-5)GnRH and (1-6)GnRH. Our results suggest that the sequential degradation of GnRH can serve as an important mechanism for the rapid termination of its biological activity in target cells.
Tin(II) Chloride Dihydrate Catalyzed Groebke Condensation: An Efficient Protocol for the Synthesis of 3‐Aminoimidazo[1,2‐<i>a</i>]pyridines (2009)

Abstract The ability of tin(II) chloride dihydrate as a catalyst to promote the three‐component condensation reaction from a diversity of aromatic aldehydes, 2‐aminopyridines and isonitriles at room temperature is described. This methodology affords a number of 3‐aminoimidazo[1,2‐ a ]pyridines in the presence of tin(II) chloride dihydrate as a new and mild Lewis acid catalyst in the multi‐component reaction in reasonable yields and short reaction time without any significant optimization of the reaction conditions.
A Phase 2 Randomized, Double-Blind, Placebo–Controlled Study of the Safety and Efficacy of Talactoferrin in Patients With Severe Sepsis* (2013)

Enteral administration of talactoferrin reduced 28-day all-cause mortality in patients with severe sepsis. This reduction in mortality was sustained at 6 months. Talactoferrin was very well tolerated.
CHiP: A Profiler to Measure the Effect of Cache Contention on Scalability (2013)

Programmers are looking for ways to exploit the multi-core processors which have become commonplace today. One of the options available is to parallelize the existing serial programs using frameworks like OpenMP etc. However, such parallelization does not always yield the speedup expected by the programmer. This is due to various reasons, one of which is the bottleneck presented by the memory system. Carefully optimized serial algorithms fit into most of the cache available, yet these cache optimized serial algorithms might have the worst speedup when parallelized. We present an efficient method to identify such cases and determine whether a serial algorithm's use of shared memory caches will seriously impact its parallel execution. This can help a programmer adjust their program's cache usage. We demonstrate the effect in isolation with a parallelized synthetic micro-benchmark which uses varying fractions of the shared cache. We also present the results of our analysis of the NAS Parallel Benchmark suite and the Rodinia benchmark suite.