bluuebunny/crossref_metadata_2025_split huggingface dataset:
SYBR Green-Based Real-Time Reverse Transcription-PCR for Typing and Subtyping of All Hemagglutinin and Neuraminidase Genes of Avian Influenza Viruses and Comparison to Standard Serological Subtyping Tests
Authors: Tsukamoto Kenji , Javier Panei Carlos , Shishido Makiko , Noguchi Daigo , Pearce John , Kang Hyun-Mi , Jeong Ok Mi , Lee Youn-Jeong , Nakanishi Koji , Ashizawa Takayoshi 
Published: October 2011

ABSTRACT

Continuing outbreaks of H5N1 highly pathogenic (HP) avian influenza virus (AIV) infections of wild birds and poultry worldwide emphasize the need for global surveillance of wild birds. To support the future surveillance activities, we developed a SYBR green-based, real-time reverse transcriptase PCR (rRT-PCR) for detecting nucleoprotein (NP) genes and subtyping 16 hemagglutinin (HA) and 9 neuraminidase (NA) genes simultaneously. Primers were improved by focusing on Eurasian or North American lineage genes; the number of mixed-base positions per primer was set to five or fewer, and the concentration of each primer set was optimized empirically. Also, 30 cycles of amplification of 1:10 dilutions of cDNAs from cultured viruses effectively reduced minor cross- or nonspecific reactions. Under these conditions, 346 HA and 345 NA genes of 349 AIVs were detected, with average sensitivities of NP, HA, and NA genes of 10
1.5
, 10
2.3
, and 10
3.1
50% egg infective doses, respectively. Utility of rRT-PCR for subtyping AIVs was compared with that of current standard serological tests by using 104 recent migratory duck virus isolates. As a result, all HA genes and 99% of the NA genes were genetically subtyped, while only 45% of HA genes and 74% of NA genes were serologically subtyped. Additionally, direct subtyping of AIVs in fecal samples was possible by 40 cycles of amplification: approximately 70% of HA and NA genes of NP gene-positive samples were successfully subtyped. This validation study indicates that rRT-PCR with optimized primers and reaction conditions is a powerful tool for subtyping varied AIVs in clinical and cultured samples.
Disseminated Mycobacterium chelonae Infection in a Patient Receiving an Epidermal Growth Factor Receptor Inhibitor for Advanced Head and Neck Cancer
Authors: Bark Charles M. , Traboulsi Rana S. , Honda Kord , Starnes Autumn M. , Jacobs Michael R. , Rodriguez Benigno 
Published: October 2011

ABSTRACT

We report a case of disseminated cutaneous
Mycobacterium chelonae
infection in a patient with head and neck cancer on salvage chemotherapy, including the epidermal growth factor receptor inhibitor cetuximab.
Mycobacterium chelonae
should be considered in the differential diagnosis of cutaneous infections in cancer patients receiving epidermal growth factor receptor inhibitors.
Loop-Mediated Isothermal Amplification Assays for Detecting Shiga Toxin-Producing Escherichia coli in Ground Beef and Human Stools
Authors: Wang Fei , Jiang Lin , Ge Beilei 
Published: October 2011

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC), encompassing
E. coli
O157 and non-O157 STEC, is a significant cause of food-borne illnesses and deaths in the United States and worldwide. Shiga toxins (encoded by
stx
) and intimin (encoded by
eae
) are important virulence factors for STEC strains linked to severe human illnesses such as hemorrhagic colitis and hemolytic-uremic syndrome. In this study, the
stx
1
,
stx
2
, and
eae
genes were chosen as targets to design loop-mediated isothermal amplification (LAMP) assays for the rapid, specific, sensitive, and quantitative detection of STEC strains. The assay performances in pure culture and spiked ground beef and human stools were evaluated and compared with those of quantitative PCR (qPCR). No false-positive or false-negative results were observed among 90 bacterial strains used to evaluate assay specificity. The limits of detection for seven STEC strains of various serogroups (O26, O45, O103, O111, O121, O145, and O157) were approximately 1 to 20 CFU/reaction in pure culture and 10
3
to 10
4
CFU/g in spiked ground beef, which were comparable to the results of qPCR. Standard curves generated suggested good linear relationships between STEC cell numbers and LAMP turbidity signals. When applied in ground beef samples spiked with two low levels (1 to 2 and 10 to 20 CFU/25 g) of STEC cultures, the LAMP assays achieved accurate detection after 6 to 8 h enrichment. The assays also consistently detected STEC in human stool specimens spiked with 10
3
or 10
4
CFU/0.5 g stool after 4 h enrichment, while qPCR required 4 to 6 h. In conclusion, the LAMP assays developed in this study may facilitate rapid and reliable identification of STEC contaminations in high-risk food commodities and also facilitate prompt diagnosis of STEC infections in clinical laboratories.
A Vaccinia Virus-Driven Interplay between the MKK4/7-JNK1/2 Pathway and Cytoskeleton Reorganization
Authors: Pereira Anna C. T. C. , Leite Flávia G. G. , Brasil Bruno S. A. F. , Soares-Martins Jamaria A. P. , Torres Alice A. , Pimenta Paulo F. P. , Souto-Padrón Thaïs , Traktman Paula , Ferreira Paulo C. P. , Kroon Erna G. , Bonjardim Cláudio A. 
Published: October 2011

ABSTRACT
Viral manipulation of transduction pathways associated with key cellular functions such as survival, response to microbial infection, and cytoskeleton reorganization can provide the supportive milieu for a productive infection. Here, we demonstrate that vaccinia virus (VACV) infection leads to activation of the stress-activated protein kinase (SAPK)/extracellular signal-regulated kinase (ERK) 4/7 (MKK4/7)–c-Jun N-terminal protein kinase 1/2 (JNK1/2) pathway; further, the stimulation of this pathway requires postpenetration, prereplicative events in the viral replication cycle. Although the formation of intracellular mature virus (IMV) was not affected in MKK4/7- or JNK1/2-knockout (KO) cells, we did note an accentuated deregulation of microtubule and actin network organization in infected JNK1/2-KO cells. This was followed by deregulated viral trafficking to the periphery and enhanced enveloped particle release. Furthermore, VACV infection induced alterations in the cell contractility and morphology, and cell migration was reduced in the JNK-KO cells. In addition, phosphorylation of proteins implicated with early cell contractility and cell migration, such as microtubule-associated protein 1B and paxillin, respectively, was not detected in the VACV-infected KO cells. In sum, our findings uncover a regulatory role played by the MKK4/7-JNK1/2 pathway in cytoskeleton reorganization during VACV infection.
Aminomethylation of BINOL with methyleneiminium salts
Authors: Shustov Gennady , Khlebnikov Vladimir 
Published: October 2011

A new method for synthesizing chiral 3,3′-bis(N,N-dialkylaminomethyl)-1,1′-bi-2-naphthols with high enantiomeric excess is described. The procedure consists of bis-lithiation of diprotected (S)- or (R)-1,1′-bis(2-naphthol) followed by treatment of the intermediate with methyleneiminium salts. Mild reaction conditions prevent racemization and provide 3,3′-bis(N,N-dialkylaminomethyl)-1,1′-bi-2-naphthols or 3-(N,N-dialkylaminomethyl)-1,1′-bi-2-naphthols with an enantiomeric excess >99%.
Feasibility study of hydrogen-bonded nucleic acid base pairs in gas and water phases — A theoretical study
Authors: Arshadi S. , Bekhradnia A.R. , Ebrahimnejad A. 
Published: October 2011

To investigate the base pair binding probabilities for nucleic acid bases, numerous models were studied for contacts between adenine, thymine, guanine, cytosine, and uracil using density functional theory (DFT) in combination with the 6–311G* basis set. We obtained an assessment for the energy given by our calculations in gas and aqueous phases, which showed that it should be incorporated into hydrogen bonding and propeller rotational energies. The 42 complexes of base pairs (5 regular and 37 irregular base pairs) were proposed and their hydrogen-bonding (H-bonding) properties were verified. The hydrogen bonds in some irregular base pairs, including CC, UU, and TT (series 1), were stronger than in regular GC and AT base pairs. Also, the strength of the hydrogen bonds in the proposed base pairs, including CU, GG, GU, and TU (series 2), were similar to regular base pairs from an energetic point of view. The propeller rotations revealed a higher rotational barrier energy (6–7.5 kcal/mol; 1 cal = 4.184 J) for irregular base pairs (series 1 and 2) than regular GC and AT ones (1–3 kcal/mol). Nevertheless, the trend in these affinities of the complex contact probabilities and their biological properties were confirmed by our calculations.
MAPI: towards the integrated exploitation of bioinformatics Web Services
Authors: Ramirez Sergio , Karlsson Johan , Trelles Oswaldo 
Published: October 2011

Abstract

Background
Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity.

Results
To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client.

Conclusions
The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others).
Activation of PI3K/AKT and ERK MAPK signal pathways is required for the induction of lytic cycle replication of Kaposi's Sarcoma-associated herpesvirus by herpes simplex virus type 1
Authors: Qin Di , Feng Ninghan , Fan Weifei , Ma Xinting , Yan Qin , Lv Zhigang , Zeng Yi , Zhu Jianzhong , Lu Chun 
Published: October 2011

AbstractBackgroundKaposi's sarcoma-associated herpesvirus (KSHV) is causally linked to several acquired immunodeficiency syndrome-related malignancies, including Kaposi's sarcoma (KS), primary effusion lymphoma (PEL) and a subset of multicentric Castleman's disease. Regulation of viral lytic replication is critical to the initiation and progression of KS. Recently, we reported that herpes simplex virus type 1 (HSV-1) was an important cofactor that activated lytic cycle replication of KSHV. Here, we further investigated the possible signal pathways involved in HSV-1-induced reactivation of KSHV.ResultsBy transfecting a series of dominant negative mutants and protein expressing constructs and using pharmacologic inhibitors, we found that either Janus kinase 1 (JAK1)/signal transducer and activator of transcription 3 (STAT3) or JAK1/STAT6 signaling failed to regulate HSV-1-induced KSHV replication. However, HSV-1 infection of BCBL-1 cells activated phosphatidylinositol 3-kinase (PI3K)/protein kinase B (PKB, also called AKT) pathway and inactivated phosphatase and tensin homologue deleted on chromosome ten (PTEN) and glycogen synthase kinase-3β (GSK-3β). PTEN/PI3K/AKT/GSK-3β pathway was found to be involved in HSV-1-induced KSHV reactivation. Additionally, extracellular signal-regulated protein kinase (ERK) mitogen-activated protein kinase (MAPK) pathway also partially contributed to HSV-1-induced KSHV replication.ConclusionsHSV-1 infection stimulated PI3K/AKT and ERK MAPK signaling pathways that in turn contributed to KSHV reactivation, which provided further insights into the molecular mechanism controlling KSHV lytic replication, particularly in the context of HSV-1 and KSHV co-infection.
Fixed point theory for cyclic (ϕ - ψ)-contractions
Authors: Karapinar Erdal , Sadarangani Kishin 
Published: October 2011

AbstractIn this article, the concept of cyclic (ϕ - ψ)-contraction and a fixed point theorem for this type of mappings in the context of complete metric spaces have been presented. The results of this study extend some fixed point theorems in literature.2000 Mathematics Subject Classification: 47H10;46T99 54H25.
Lycorine reduces mortality of human enterovirus 71-infected mice by inhibiting virus replication
Authors: Liu Jiangning , Yang Yajun , Xu Yanfeng , Ma Chunmei , Qin Chuan , Zhang Lianfeng 
Published: October 2011

AbstractHuman enterovirus 71 (EV71) infection causes hand, foot and mouth disease in children under 6 years old and this infection occasionally induces severe neurological complications. No vaccines or drugs are clinical available to control EV71 epidemics. In present study, we show that treatment with lycorine reduced the viral cytopathic effect (CPE) on rhabdomyosarcoma (RD) cells by inhibiting virus replication. Analysis of this inhibitory effect of lycorine on viral proteins synthesis suggests that lycorine blocks the elongation of the viral polyprotein during translation. Lycorine treatment of mice challenged with a lethal dose of EV71 resulted in reduction of mortality, clinical scores and pathological changes in the muscles of mice, which were achieved through inhibition of viral replication. When mice were infected with a moderate dose of EV71, lycorine treatment was able to protect them from paralysis. Lycorine may be a potential drug candidate for the clinical treatment of EV71-infected patients.
Quality assurance of sphincterotomy: A prospective single-centre survey
Authors: Sulz Michael , Sagmeister Markus , Schelling Martin , Binek Janek , Borovicka Jan , Ulmer Hanno , Meyenberger Christa 
Published: October 2011

Abstract
Quality assurance becomes an increasingly important part of clinical medicine and of the field of endoscopy. Endoscopic sphincterotomy is associated with a fairly high complication rate. We aimed to assess our quality of sphincterotomy for benchmarking by using a prospective electronic database registry, and to identify potential risk factors for post-interventional complications. Over 2 years, 471 sphincterotomies were performed in a single tertiary referral centre. Patient- and procedure-related variables were prospectively recorded with the support of a multi-centre international sphincterotomy registry. Multivariate analysis was performed. The overall post-interventional complication rate was 9.3%. Pancreatitis happened in 5.5%, bleeding in 2.1%, perforation in 1.3%, and cholangitis in 0.4%. In the multivariate analysis following variables remained highly significant and predictive for complications: ‘papilla only in lateral view’ (p=0.001), antiplatelet therapy (p=0.024), and opacification with contrast up to the pancreatic tail (p=0.001). The primary success rate of sphincterotomy was 95.1%. The rate of post-interventional pancreatitis did not differ significantly regardless of the presence of prophylactic pancreatic stent (p=0.56). The outcome of sphincterotomy in our centre matches with literature data. The extent of pancreatic duct opacification has an influence on the pancreatitis rate. Prevention of pancreatitis by inserting pancreatic stents is not confirmed.
Unexpected Expectations in Critical Values in Anatomic Pathology: Improving Agreement Between Pathologists and Nonpathologists With the Treatable Immediately, Life-Threatening Terminology
Authors: Renshaw Scott A. , Gould Edwin W. , Renshaw Andrew A. 
Published: October 2011

Context.—The degree to which critical values in anatomic pathology are understood in the nonpathology community is not know.
Objective.—To measure the degree of agreement between pathologists and nonpathologists regarding critical values in anatomic pathology.
Design.—A survey containing 15 anatomic pathologic diagnoses was given to a group of pathologists and nonpathologists who were then asked to state whether they should be regarded as critical values.
Results.—Nonpathologists thought that a significantly greater percentage of diagnoses were critical than did pathologists, (49% versus 12%, P &lt; .001). If the term critical value was changed to treatable immediately, life threatening, there was no significant difference between the responses of nonpathologists and pathologists (20% versus 12%, P  =  .06).
Conclusions.—There is considerable disagreement between pathologists and nonpathologists concerning which diagnoses are critical values in anatomic pathology. Use of the term treatable immediately, life threatening significantly improves agreement.
Felty's syndrome autoantibodies bind to deiminated histones and neutrophil extracellular chromatin traps
Authors: Dwivedi Nishant , Upadhyay Jagriti , Neeli Indira , Khan Salar , Pattanaik Debendra , Myers Linda , Kirou Kyriakos A. , Hellmich Bernhard , Knuckley Bryan , Thompson Paul R. , Crow Mary K. , Mikuls Ted R. , Csernok Elena , Radic Marko 
Published: October 2011

AbstractObjectiveTo test the hypothesis that autoantigen modifications by peptidylarginine deiminase type 4 (PAD‐4) increase immunoreactivity.MethodsWe assembled sera from patients with systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), Felty's syndrome (FS), and antineutrophil cytoplasmic antibody–associated vasculitides (AAVs), as well as sera from control subjects without autoimmune diseases. The sera were tested for binding to activated neutrophils, deiminated histones, and neutrophil extracellular chromatin traps (NETs). IgG binding to lipopolysaccharide‐activated neutrophils was assessed with confocal microscopy, and binding to in vitro–deiminated histones was measured using enzyme‐linked immunosorbent assay (ELISA) and Western blotting. In addition, we quantitated histone deimination in freshly isolated neutrophils from the blood of patients and control subjects.ResultsIncreased IgG reactivity with activated neutrophils, particularly binding to NETs, was paralleled by preferential binding to deiminated histones over nondeiminated histones by ELISA in a majority of sera from FS patients but only in a minority of sera from SLE and RA patients. Immunoblotting revealed autoantibody preference for deiminated histones H3, H4, and H2A in most FS patients and in a subset of SLE and RA patients. In patients with AAVs, serum IgG preferentially bound nondeiminated histones over deiminated histones. Increased levels of deiminated histones were detected in neutrophils from RA patients.ConclusionCirculating autoantibodies in FS are preferentially directed against PAD‐4–deiminated histones and bind to activated neutrophils and NETs. Thus, increased reactivity with modified autoantigens in FS implies a direct contribution of neutrophil activation and the production of NET‐associated nuclear autoantigens in the initiation or progression of FS.
Synthesis of Polyisoprene Terpenoid Dendrons and their Applications in Oligo(phenylene ethynylene)s as “Shells”
Authors: Chai Wen‐Yu , Shi Zi‐Fa , An Peng , Wang Wei , Wang Lu‐Feng , Cao Xiao‐Ping 
Published: October 2011

AbstractThe novel double‐stage convergent synthesis of a new class of polyisoprene terpenoid (PIPTP) dendrons is described. PIPTP dendrons bear a highly branched aliphatic hydrocarbon skeleton and a hydrophilic hydroxy focal point functionality. These dendrons have the specific formula C(5×2G+1‐5)H(5×2G+2‐8)O, and each dendritic layer is constructed from an isoprene unit. The key branching steps involve a double alkyl‐metal addition to an ester functionality, followed by deoxygenation of the resulting tertiary alcohol by triethylsilane and trifluoroacetic acid, then hydrogenation or hydrogenolysis. The dendrons were also attached to oligo(phenylene ethynylene)s (OPEs) so as to function as protective shells to allow fine tuning of the nanoscopic environment around the OPE moiety, and to exert precise control of the packing density and intermolecular interaction between the OPE cores. Fluorescence quantum yield data reveal that the OPE core is better encapsulated by the PIPTP dendrons than by Fréchet dendrons.
A Framework for Globally Optimal State Estimation for Systems with Unknown Inputs (II): Untrammeled Approach
Authors: Hsieh Chien‐Shu 
Published: October 2011

AbstractIn this paper, a globally optimal state estimation, in light of unbiased minimum‐variance filtering over all linear unbiased estimators, is addressed. This paper is the second part of a comprehensive extension of original work by Hsieh, with the main aim being to develop an untrammeled filtering framework that does not need any transformations for global unbiased minimum‐variance state estimation (GUMVSE) for systems with unknown inputs that affect both the system and the output. The main contributions of this paper are: (i) a more general derivation of the globally optimal state estimator (GOSE) for the GUMVSE is presented; (ii) a more direct proof, verifying the global optimality of the GOSE by finding the global minimum of the trace of the estimation error covariance, is constructed; and (iii) an application of the proposed result to re‐derive a specific transformation‐based GOSE, i.e., the recursive optimal filter proposed by Cheng et al., is illustrated. The relationship with previously proposed results is also addressed. A simulation example is given to illustrate the usefulness of the proposed results.Copyright © 2011 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society
Degradation and Energy Characteristics of Reactive Amine Solvents during CO2 Absorption/Desorption
Authors: Ewert Günter , Kemper Jasmin , Algayer Yvonne , Meshkova Ana 
Published: October 2011

AbstractFür die Abtrennung von klimarelevantem CO2 aus Rauch‐ und Prozessgasen ist die Reaktivabsorption mit wässrigen Amin‐Lösungen eine technologisch schnell realisierbare Methode. Häufig diskutierte Probleme sind eine kostenmindernde Effizienzsteigerung im Gesamtprozess der CO2‐Absorption und eine energieintensive Lösungsmittelregeneration unter Betriebsbedingungen. Weniger betrachtet wurden dagegen kapazitäts‐ und energieeffizienzreduzierende Degradationsvorgänge der meist eingesetzten Monoethanolamin‐Blends. Die im laufenden Betrieb auftretenden Kapazitätsverminderungen sind insbesondere von der Zeit, der Temperatur und vom O2‐ und SO2‐Gehalt der Rohgase abhängig und sind bei der Auslegung zu berücksichtigen. Durch Zugabe von degradationshemmenden Stoffen kann der Energieaufwand gesenkt werden.
Growth, spectral and thermal studies of ibuprofen crystals
Authors: Ramukutty S. , Ramachandran E. 
Published: October 2011

AbstractRS ‐Ibuprofen was crystallized for the first time in silica gel under suitable pH conditions by reduction of solubility method. The grown crystals were characterized by single crystal X‐ray diffraction and density measurement. The functional groups present in the crystal were identified using Fourier transform infrared spectroscopy. Optical bandgap energy of ibuprofen was estimated as 3.19(3) eV from UV‐Vis spectrum. Thermogravimetric analysis revealed that ibuprofen is thermally stable upto 102.9 °C and the initial loss of mass was due to evaporation only. Morphological study showed that the growth is prominent along b‐axis and the prominent face is {100}. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)