bluuebunny/crossref_metadata_2025_split huggingface dataset:
An in‐house HIV genotyping assay for the detection of drug resistance mutations in Southeast Asian patients infected with HIV‐1
Authors: Lee Chun Kiat , Lee Hong Kai , Loh Tze Ping , Sethi Sunil Kumar , Koay Evelyn Siew‐Chuan , Tang Julian Wei‐Tze 
Published: January 2012

AbstractGenotyping for HIV drug resistance is costly and beyond the means for many Southeast Asian patients, who are self‐funded. This prompted the development of a more cost‐effective, in‐house assay for an ethnically diverse, Southeast Asian population at the National University Hospital in Singapore, using Sanger‐based sequencing. Plasma samples from 20 treatment‐failure patients with a broad spectrum of HIV drug resistance mutations were used to validate this assay clinically. Blinded testing gave concordant results for 7/7 (100%) protease drug resistance‐related mutations, including one major and six minor mutations, and 111/116 (95.7%) reverse‐transcriptase (RT) drug resistance‐related mutations, including 65 nucleoside RT inhibitors (NRTI) and 46 non‐nucleoside RT inhibitors (NNRTI) mutations. There were five discordant results, involving three NRTI‐ and two NNRTI‐resistance‐associated mutations. Highly conserved primers designed to have a wide coverage of the HIV pol gene (covering the entire protease and 395 codons of the RT region) enabled efficient multi‐ethnic population‐based genotyping. Reagents for this in‐house test cost around 60% less than those for commercially available assays (SGD150 vs. SGD350 per sample). In addition, this assay also identified mutations located within the C‐terminal domain (codons 312–560) of RT that are beyond the reach of most published and commercial GRTs. Currently, most research on C‐terminal drug‐resistance‐related mutations has been conducted on HIV subtype B infections. Therefore this assay enables further study of these C‐terminal mutations in Southeast Asian populations, where there is a high prevalence of CRF01_AE and other non‐subtype B HIV infections. J. Med. Virol. 84:394–401, 2012. © 2011 Wiley Periodicals, Inc.
Prevalence of hepatitis C virus genotype 1a in Japan and correlation of mutations in the NS5A region and single‐nucleotide polymorphism of interleukin‐28B with the response to combination therapy with pegylated‐interferon‐alpha 2b and ribavirin
Authors: Hayashi Kazuhiko , Katano Yoshiaki , Kuzuya Teiji , Tachi Yoshihiko , Honda Takashi , Ishigami Masatoshi , Itoh Akihiro , Hirooka Yoshiki , Ishikawa Tetsuya , Nakano Isao , Urano Fumihiro , Yoshioka Kentaro , Toyoda Hidenori , Kumada Takashi , Goto Hidemi 
Published: January 2012

AbstractHepatitis C virus (HCV) genotype 1a is rare in Japanese patients and the clinical characteristics of this genotype remain unclear. The interferon (IFN) sensitivity‐determining region (ISDR) and single‐nucleotide polymorphisms (SNPs) of interleukin‐28B (IL28B) among patients with HCV genotype 1b are associated with IFN response, but associations among patients with genotype 1a are largely unknown. This study investigated the clinical characteristics of genotype 1a and examined whether genomic heterogeneity of the ISDR and SNPs of IL28B among patients with HCV genotype 1a affects response to combination therapy with pegylated‐IFN‐α2b and ribavirin. Subjects comprised 977 patients infected with HCV genotype 1, including 574 men and 412 women (mean age, 55.2 ± 10.6 years). HCV was genotyped by direct sequencing of the 5′‐untranslated region and/or core regions and confirmed by direct sequencing of the NS5A region. HCV genotypes 1a (n = 32) and 1b (n = 945) were detected. Twenty‐three (71.9%) of the 32 patients with genotype 1a were patients with hemophilia who had received imported clotting factors. Prevalence of genotype 1a after excluding patients with hemophilia was thus 0.9%. Of the 23 patients with genotype 1a who completed IFN therapy, 11 (47.8%) were defined as achieving sustained virological response. Factors related to sustained virological response by univariate analysis were IL28B and ISDR. In conclusion, HCV genotype 1a is rare in Japan. The presence of IL28B genotype TT, and more than two mutations, in the ISDR are associated with a good response to IFN therapy in patients with HCV genotype 1a. J. Med. Virol. 84:438–444, 2012. © 2011 Wiley Periodicals, Inc.
Human metapneumovirus‐associated hospital admissions over five consecutive epidemic seasons: Evidence for alternating circulation of different genotypes
Authors: Apostoli Paola , Zicari Sonia , Presti Alessandra Lo , Ciccozzi Massimo , Ciotti Marco , Caruso Arnaldo , Fiorentini Simona 
Published: January 2012

AbstractHuman metapneumovirus (hMPV) is a pathogen of the respiratory tract with a worldwide distribution. The purpose of this study was to identify hMPV as the cause of acute respiratory diseases in children admitted at Spedali Civili, a public hospital in Brescia, Italy. Eight hundred forty‐six nasopharyngeal aspirate samples negative for the presence of other common respiratory viruses were tested for the presence of hMPV RNA by reverse transcription‐polymerase chain reaction. Of the 846 samples, 79 (9.3%) were positive for hMPV. Polymerase chain reaction products, obtained by amplification of the partial nucleotide sequence of gene F, were sequenced and compared with sequences deposited in GenBank. All four hMPV subtypes were identified, including the proposed subtype A2 sublineages “A” and “B”. In successive epidemic seasons, large outbreaks of hMPV alternated with small outbreaks in a biannual pattern. This local study provides further evidence that hMPV infection should be considered as a reason for hospital admission for acute respiratory disease in children. J. Med. Virol. 84:511–516, 2012. © 2011 Wiley Periodicals, Inc.
The 40–80 nt region in the 5′‐NCR of genome is a critical target for inactivating poliovirus by chlorine dioxide
Authors: Jin Min , Zhao Zu‐Guo , Wang Xin‐Wei , Shen Zhi‐Qiang , Xu Lu , Yu Yun‐Mei , Qiu Zhi‐Gang , Chen Zhao‐Li , Wang Jing‐Feng , Huang Ai‐Hua , Li Jun‐Wen 
Published: January 2012

AbstractChemical disinfection is the most common method used to inactivate viruses from drinking water throughout the world. In this study, cell culture, ELISA, RT‐PCR, and spot hybridization were employed to investigate the mechanism underlying chlorine dioxide (ClO2)‐induced inactivation of Poliovirus type 1 (PV1), which was also confirmed by recombinant viral genome RNA infection models. The results suggested that ClO2 inactivated PV1 primarily by disrupting the 5′‐non‐coding region (5′‐NCR) of the PV1 genome. Further study revealed that ClO2 degraded specifically the 40–80 nucleotides (nt) region in the 5′‐NCR. Recombinant viral genome RNA infection models confirmed that PV1 RNA lacking this 40–80 nt region was not infectious. This study not only elucidated the mechanism of PV1 inactivation by ClO2, but also defined the critical genetic target for the disinfectant to inactivate Poliovirus. This study also provides a strategy by which rapid, accurate, and molecular methods based on sensitive genetic targets may be established for evaluating the effects of disinfectants on viruses. J. Med. Virol. 84:526–535, 2012. © 2011 Wiley Periodicals, Inc.
Single treatment with ethanol hand rub is ineffective against human rhinovirus—hand washing with soap and water removes the virus efficiently
Authors: Savolainen‐Kopra Carita , Korpela Terttu , Simonen‐Tikka Marja‐Leena , Amiryousefi Ali , Ziegler Thedi , Roivainen Merja , Hovi Tapani 
Published: January 2012

AbstractEthanol‐containing hand rubs are used frequently as a substitute for hand washing with water and soap. However, not all viruses are inactivated by a short term rubbing with alcohol. The capacity of a single round of instructed and controlled hand cleaning with water and soap or ethanol‐containing hand rub, respectively, was tested for removal of human rhinovirus administered onto the skin of healthy volunteers on the back of the hands. Hand washing with soap and water appeared to be much more efficient for removing rhinoviruses from skin than rubbing hands with an ethanol‐containing disinfectant. After washing with soap and water the virus was detected in 3/9 (33.3%) test persons from the left hand and 1/9 (11.1%) cases from the right hand, whereas the virus was detected invariably by real‐time RT‐PCR from both hands after cleaning with alcohol hand rub (P‐value <0.01). Both substances evaluated clinically were also tested in vitro for virucidal efficacy against Human rhinovirus2 (HRV2) using a standardized assay. Both tested substances were poor within the contact time used in the hand‐cleaning test. In conclusion, thorough and conventional hand washing with water and soap can clean efficiently hands contaminated with the virus responsible for an extensive share of common cold episodes. J. Med. Virol. 84:543–547, 2012. © 2011 Wiley Periodicals, Inc.
Case report: Benefits of quantitative polymerase chain reaction in the clinical management of herpes simplex virus 1 infection with prominent hepatitis and unusual secondary progression
Authors: Chaillon Antoine , Schnepf Nathalie , Jonas Maud , Mondon Karl , Orain Isabelle , Lioger Bertrand , Cottier Jean‐Philippe , Hommet Caroline , Goudeau Alain 
Published: January 2012

AbstractHerpes simplex virus (HSV) infection is rarely considered in the differential diagnosis of severe acute hepatitis and disseminated infection in immunocompetent adults. A case of disseminated HSV‐1 infection in an 82‐year‐old woman initially presenting with neurological problems, signs of meningitis and prominent hepatitis was investigated. Initial diagnosis, monitoring, and follow‐up were based on the application of molecular methods to cerebrospinal fluid, serum, and liver tissue samples from this patient. Following an initial full recovery, the patient presented delayed intracerebral haemorrhage and diffuse arthralgia. This atypical case, with delayed secondary progression, highlights the wide range of clinical features of HSV infection and the benefits of monitoring viral load by quantitative real‐time polymerase chain reaction (PCR) during patient management. J. Med. Virol. 84:457–461, 2012. © 2011 Wiley Periodicals, Inc.
A longitudinal study of mentor and protégé outcomes in formal mentoring relationships
Authors: Chun Jae Uk , Sosik John J. , Yun Nam Yi 
Published: January 2012

SummaryThis study examined relationships between mentoring functions offered and transformational leadership as a mentor outcome and affective well‐being and organizational commitment as mutual outcomes for both mentors and protégés. For this examination, we conducted a longitudinal field study by using 111 matched reports from both mentors and protégés collected at three different points in time over seven months in nine Korean companies that administered a standardized formal mentoring program. Study results showed that mentoring functions assessed at Time 2 were positively associated with mentors' and protégés' post‐mentoring outcomes at Time 3 after controlling for pre‐mentoring initial levels of those outcomes at Time 1. Study findings also revealed that relative effects of mentoring on the mentor and protégé outcomes differed by the types of mentoring functions. We discuss the theoretical, practical, and methodological implications from these results. Copyright © 2012 John Wiley & Sons, Ltd.
Negative effects of ADAMTS‐7 and ADAMTS‐12 on endplate cartilage differentiation
Authors: Zhang Qiang , Huang Ming , Wang Xiaolin , Xu Xiaojie , Ni Ming , Wang Yan 
Published: January 2012

AbstractThe roles of ADAMTS‐7 and ADAMTS‐12 in disc degeneration have not been previously examined. The purpose of this study was to examine the expression of ADAMTS‐7 and ADAMTS‐12 in the endplate cells isolated from patients with degenerative disc disease and to see whether they are associated with the pathological change of endplate. Sixty‐four degenerated lumbar endplate specimens were obtained from the patients with degenerative disc disease categorized as type Modic I or II in magnetic resonance imaging (MRI) and 12 nondegenerative specimens as control (vertebra burst fracture patients without degenerative change in MRI) during surgical procedures. The expression of ADAMTS‐7 and ADAMTS‐12 was examined by real‐time PCR and Western blotting. A statistically significant increase in mRNA expression of ADAMTS‐7 and ADAMTS‐12 was observed in the endplate cells in degenerative discs compared with nondegenerative discs. The corresponding protein levels of ADAMTS‐7 and ADAMTS‐12 had the same expression patterns. Moreover, ADAMTS‐7 and ADAMTS‐12 down‐regulated the expression of Col II, Sox9, and Col X the marker genes for chondrogenesis. Our results indicate that ADAMTS‐7 and ADAMTS‐12 appear to be potent negative regulators of endplate cartilage development. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:1238–1243, 2012
Fracture healing in protease‐activated receptor‐2 deficient mice
Authors: O'Neill Kevin R. , Stutz Christopher M. , Mignemi Nicholas A. , Cole Heather , Murry Matthew R. , Nyman Jeffry S. , Hamm Heidi , Schoenecker Jonathan G. 
Published: January 2012

AbstractProtease‐activated receptor‐2 (PAR‐2) provides an important link between extracellular proteases and the cellular initiation of inflammatory responses. The effect of PAR‐2 on fracture healing is unknown. This study investigates the in vivo effect of PAR‐2 deletion on fracture healing by assessing differences between wild‐type (PAR‐2+/+) and knock‐out (PAR‐2−/−) mice. Unilateral mid‐shaft femur fractures were created in 34 PAR‐2+/+ and 28 PAR‐2−/− mice after intramedullary fixation. Histologic assessments were made at 1, 2, and 4 weeks post‐fracture (wpf), and radiographic (plain radiographs, micro‐computed tomography (µCT)) and biomechanical (torsion testing) assessments were made at 7 and 10 wpf. Both the fractured and un‐fractured contralateral femur specimens were evaluated. Polar moment of inertia (pMOI), tissue mineral density (TMD), bone volume fraction (BV/TV) were determined from µCT images, and callus diameter was determined from plain radiographs. Statistically significant differences in callus morphology as assessed by µCT were found between PAR‐2−/− and PAR‐2+/+ mice at both 7 and 10 wpf. However, no significant histologic, plain radiographic, or biomechanical differences were found between the genotypes. The loss of PAR‐2 was found to alter callus morphology as assessed by µCT but was not found to otherwise effect fracture healing in young mice. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:1271–1276, 2012
Hypocholesterolaemic and antioxidant activities of chickpea (Cicer arietinum L.) protein hydrolysates
Authors: Yust María del Mar , Millán‐Linares María del Carmen , Alcaide‐Hidalgo Juan María , Millán Francisco , Pedroche Justo 
Published: January 2012

AbstractBACKGROUND: Some dietary proteins possess biological properties which make them potential ingredients of functional or health‐promoting foods. Many of these properties are attributed to bioactive peptides that can be released by controlled hydrolysis using exogenous proteases. The aim of this work was to test the improvement of hypocholesterolaemic and antioxidant activities of chickpea protein isolate by means of hydrolysis with alcalase and flavourzyme.RESULTS: All hydrolysates tested exhibited better hypocholesterolaemic activity when compared with chickpea protein isolate. The highest cholesterol micellar solubility inhibition (50%) was found after 60 min of treatment with alcalase followed by 30 min of hydrolysis with flavourzyme. To test antioxidant activity of chickpea proteins three methods were used: β‐carotene bleaching method, reducing power and 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) radical‐scavenging effect since antioxidant activity of protein hydrolysates may not be attributed to a single mechanism. Chickpea hydrolysates showed better antioxidant activity in all assays, especially reducing power and DPPH scavenging effect than chickpea protein isolate.CONCLUSION: The results of this study showed the good potential of chickpea protein hydrolysates as bioactive ingredients. The highest bioactive properties could be obtained by selecting the type of proteases and the hydrolysis time. Copyright © 2012 Society of Chemical Industry
Length of Stay: Price and Income Semi‐Elasticities at Different Destinations in Italy
Authors: Salmasi Luca , Celidoni Martina , Procidano Isabella 
Published: January 2012

ABSTRACTIn this paper, we estimate price and income semi‐elasticities of the length of stay at different destinations in Italy using the ‘Multipurpose survey on tourism demand, holidays and trips’ provided by the Italian National Institute of Statistics (ISTAT). We derive the conditional demand function for the length of stay, which depends on tourists' socio‐demographic characteristics, travel characteristics, income and price of touristic services. Since income was not reported in our database, we use the propensity score matching to retrieve this information from the ‘Survey on household income and wealth (SHIW)’, and we use quantile regression to account for the multimodality of the length of stay. Copyright © 2012 John Wiley & Sons, Ltd.
Characterizing North Atlantic weather patterns for climate‐optimal aircraft routing
Authors: Irvine Emma A. , Hoskins Brian J. , Shine Keith P. , Lunnon Robert W. , Froemming Christine 
Published: January 2012

AbstractDaily weather patterns over the North Atlantic are classified into relevant types: typical weather patterns that may characterize the range of climate impacts from aviation in this region, for both summer and winter. The motivation is to provide a set of weather types to facilitate an investigation of climate‐optimal aircraft routing of trans‐Atlantic flights (minimizing the climate impact on a flight‐by‐flight basis). Using the New York to London route as an example, the time‐optimal route times are shown to vary by over 60 min, to take advantage of strong tailwinds or avoid headwinds, and for eastbound routes latitude correlates well with the latitude of the jet stream. The weather patterns are classified by their similarity to the North Atlantic Oscillation and East Atlantic teleconnection patterns. For winter, five types are defined; in summer, when there is less variation in jet latitude, only three types are defined. The types can be characterized by the jet strength and position, and therefore the location of the time‐optimal routes varies by type. Simple proxies for the climate impact of carbon dioxide, ozone, water vapour and contrails are defined, which depend on parameters such as the route time, latitude and season, the time spent flying in the stratosphere, and the distance over which the air is supersaturated with respect to ice. These proxies are then shown to vary between weather types and between eastbound and westbound routes. Copyright © 2012 Royal Meteorological Society
Linear and Nonlinear Support Vector Machine for the Classification of Human 5‐HT1A Ligand Functionality
Authors: Wang Lirong , Ma Chao , Wipf Peter , Xie Xiang‐Qun 
Published: January 2012

AbstractUpon binding to a receptor, agonists and antagonists can induce distinct biological functions and thus lead to significantly different pharmacological responses. Thus, in silico prediction or in vitro characterization of ligand agonistic or antagonistic functionalities is an important step toward identifying specific pharmacological therapeutics. In this study, we investigated the molecular properties of agonists and antagonists of human 5‐hydroxytryptamine receptor subtype 1A (5‐HT1A). Subsequently, intrinsic functions of these ligands (agonists/antagonists) were modeled by support vector machine (SVM), using five 2D molecular fingerprints and the 3D Topomer distance. Five kernel functions, including linear, polynomial, RBF, Tanimoto and a novel Topomer kernel based on Topomer 3D similarity were used to develop linear and nonlinear classifiers. These classifiers were validated through cross‐validation, yielding a classification accuracy ranging from 80.4 % to 92.3 %. The performance of different kernels and fingerprints was analyzed and discussed. Linear and nonlinear models were further interpreted through the illustration of underlying classification mechanism. The computation protocol has been automated and demonstrated through our online service. This study expands the scope and applicability of similarity‐based methods in cheminformatics, which are typically used for the identification of active molecules against a target protein. Our findings provide a good starting point for further systematic classifications of other GPCR ligands and for the data mining of large chemical libraries.
Keyhole chemical exchange saturation transfer
Authors: Varma G. , Lenkinski R. E. , Vinogradov E. 
Published: January 2012

AbstractThe keyhole technique, which involves the acquisition of dynamic data at low resolution in combination with a high‐resolution reference, is developed for the purposes of chemical exchange saturation transfer (CEST) imaging, i.e., Keyhole CEST. Low‐resolution data are acquired with saturation applied at different frequencies for Z‐spectra, along with a high‐resolution reference image taken without saturation. Three methods for high‐resolution reconstruction of Keyhole CEST are evaluated using the values from quantitative high‐resolution CEST maps. In addition, Keyhole CEST is applied for collection of data used for B0 correction. The keyhole approach is evaluated for CEST contrast generation using exchanging protons in hydroxyl groups. First, the techniques are evaluated in vitro using samples of dextrose and chondroitin sulfate. Next, the work is extended in vivo to explore its applicability for gagCEST. Comparable quantitative gagCEST values are found using Keyhole CEST, provided the structure or region of interest is not limited by the low‐resolution dataset. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
Volumetric navigators for real‐time motion correction in diffusion tensor imaging
Authors: Alhamud A. , Tisdall M. Dylan , Hess Aaron T. , Hasan Khader M. , Meintjes Ernesta M. , van der Kouwe André J.W. 
Published: January 2012

AbstractProspective motion correction methods using an optical system, diffusion‐weighted prospective acquisition correction, or a free induction decay navigator have recently been applied to correct for motion in diffusion tensor imaging. These methods have some limitations and drawbacks. This article describes a novel technique using a three‐dimensional‐echo planar imaging navigator, of which the contrast is independent of the b‐value, to perform prospective motion correction in diffusion weighted images, without having to reacquire volumes during which motion occurred, unless motion exceeded some preset thresholds. Water phantom and human brain data were acquired using the standard and navigated diffusion sequences, and the mean and whole brain histogram of the fractional anisotropy and mean diffusivity were analyzed. Our results show that adding the navigator does not influence the diffusion sequence. With head motion, the whole brain histogram‐fractional anisotropy shows a shift toward lower anisotropy with a significant decrease in both the mean fractional anisotropy and the fractional anisotropy histogram peak location (P < 0.01), whereas the whole brain histogram‐mean diffusivity shows a shift toward higher diffusivity with a significant increase in the mean diffusivity (P < 0.01), even after retrospective motion correction. These changes in the mean and the shape of the histograms are recovered substantially in the prospective motion corrected data acquired using the navigated sequence. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.