bluuebunny/crossref_metadata_2025_split huggingface dataset:
Original Article: Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs
Authors: Slomka Marek J. , Densham Anstice L. E. , Coward Vivien J. , Essen Steve , Brookes Sharon M. , Irvine Richard M. , Spackman Erica , Ridgeon Jonathan , Gardner Rebecca , Hanna Amanda , Suarez David L. , Brown Ian H. 
Published: August 2010

Please cite this paper as: Slomka et al. (2010) Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs. Influenza and Other Respiratory Viruses 4(5), 277–293.Background  There is a requirement to detect and differentiate pandemic (H1N1) 2009 (H1N1v) and established swine influenza A viruses (SIVs) by real time reverse transcription (RRT) PCR methods.Objectives  First, modify an existing matrix (M) gene RRT PCR for sensitive generic detection of H1N1v and other European SIVs. Second, design an H1 RRT PCR to specifically detect H1N1v infections.Methods  RRT PCR assays were used to test laboratory isolates of SIV (n = 51; 37 European and 14 North American), H1N1v (n = 5) and avian influenza virus (AIV; n = 43). Diagnostic sensitivity and specificity were calculated for swabs (n = 133) and tissues (n = 116) collected from field cases and pigs infected experimentally with SIVs and H1N1v.Results  The “perfect match” M gene RRT PCR was the most sensitive variant of this test for detection of established European SIVs and H1N1v. H1 RRT PCR specifically detected H1N1v but not European SIVs. Validation with clinical specimens included comparison with virus isolation (VI) as a “gold standard”, while field infection with H1N1v in swine was independently confirmed by sequencing H1N1v amplified by conventional RT PCR. “Perfect match” M gene RRT PCR had 100% sensitivity and 95·2% specificity for swabs, 93·6% and 98·6% for tissues. H1 RRT PCR demonstrated sensitivity and specificity of 100% and 99·1%, respectively, for the swabs, and 100% and 100% for the tissues.Conclusions  Two RRT PCRs for the purposes of (i) generic detection of SIV and H1N1v infection in European pigs, and for (ii) specific detection of H1N1v (pandemic influenza) infection were validated.
Cross‐protection between antigenically distinct H1N1 swine influenza viruses from Europe and North America
Authors: De Vleeschauwer Annebel R. , Van Poucke Sjouke G. , Karasin Alexander I. , Olsen Christopher W. , Van Reeth Kristien 
Published: August 2010

Please cite this paper as: De Vleeschauwer et al. (2011) Cross‐protection between antigenically distinct H1N1 swine influenza viruses from Europe and North America. Influenza and Other Respiratory Viruses 5(2), 115–122.Background  An avian‐like H1N1 swine influenza virus (SIV) is enzootic in swine populations of Western Europe. The virus is antigenically distinct from H1N1 SIVs in North America that have a classical swine virus‐lineage H1 hemagglutinin, as does the pandemic (H1N1) 2009 virus. However, the significance of this antigenic difference for cross‐protection among pigs remains unknown.Objectives  We examined protection against infection with a North American triple reassortant H1N1 SIV [A/swine/Iowa/H04YS2/04 (sw/IA/04)] in pigs infected with a European avian‐like SIV [A/swine/Belgium/1/98 (sw/B/98)] 4 weeks earlier. We also examined the genetic relationships and serologic cross‐reactivity between both SIVs and with a pandemic (H1N1) 2009 virus [A/California/04/09 (Calif/09)].Results  After intranasal inoculation with sw/IA/04, all previously uninfected control pigs showed nasal virus excretion, high virus titers in the entire respiratory tract at 4 days post‐challenge (DPCh) and macroscopic lung lesions. Most pigs previously infected with sw/B/98 tested negative for sw/IA/04 in nasal swabs and respiratory tissues, and none had lung lesions. At challenge, these pigs had low levels of cross‐reactive virus neutralizing and neuraminidase inhibiting (NI) antibodies to sw/IA/04, but no hemagglutination‐inhibiting antibodies. They showed similar antibody profiles when tested against Calif/09, but NI antibody titers were higher against Calif/09 than sw/IA/04, reflecting the higher genetic homology of the sw/B/98 neuraminidase with Calif/09.Conclusions  Our data indicate that immunity induced by infection with European avian‐like H1N1 SIV affords protection for pigs against North American H1N1 SIVs with a classical H1, and they suggest cross‐protection against the pandemic (H1N1) 2009 virus.
The Statistical Interpretation of Forensic Glass Evidence
Authors: Curran James M. 
Published: August 2010

Summary When examining a sample of glass fragments recovered from a suspect in a forensic case, many questions arise: “Did this man break that window?”, “Are these fragments from the crime scene source?”, “Do the fragments recovered from the suspect come from more than one source?”, “How common is it to find glass on someone unrelated with crime?” etc. Such questions are usually answered with the help of statistical methods. This paper reviews some of the statistical solutions and problems encountered in the interpretation and evaluation of forensic glass evidence.
Stratification of Skewed Populations: A review
Authors: Horgan Jane M. 
Published: August 2010

SummaryWhen Dalenius provided a set of equations for the determination of stratum boundaries of a single auxiliary variable, that minimise the variance of the Horvitz–Thompson estimator of the mean or total under Neyman allocation for a fixed sample size, he pointed out that, though mathematically correct, those equations are troublesome to solve. Since then there has been a proliferation of approximations of an iterative nature, or otherwise cumbersome, tendered for this problem; many of these approximations assume a uniform distribution within strata, and, in the case of skewed populations, that all strata have the same relative variation. What seems to have been missed is that the combination of these two assumptions offers a much simpler and equally effective method of subdivision for skewed populations; take the stratum boundaries in geometric progression.
The Rational and the Irrational in Nationalism
Authors: Kecmanovic Dusan 
Published: August 2010

AbstractIn comparison to other questions related to nationalism (for example, is nationalism more a pre‐modern or modern phenomenon? Is it more of a political or ethno‐cultural nature?), relatively little attention has been devoted to the question of whether nationalism is more rational or irrational. Weber's definition of instrumentally rational and value‐rational action has been used in this analysis to determine to what extent nationalism is rational or irrational. The analysis has focused mainly on those concepts of nationalism and those phenomena associated with nationalism that are predominantly irrational or extra‐rational. Some psychological and anthropological constants constitute the irrational (extra‐rational) side of nationalism. Nationalism as a Janus‐faced phenomenon comprises the irrational (extra‐rational) and the rational. The rational and irrational overlap quite profoundly in numerous manifestations of nationalist behaviour.
National Identity and the Geo‐Soul: Spiritually Mapping Siam
Authors: Ricks Jacob I. 
Published: August 2010

AbstractThis paper investigates the re‐centring of religious identity within the geo‐body in the developing world through the case study of Thailand, formerly Siam. Although by 1932, monarchic rule and colonial powers had demarcated the ‘geo‐body’ of Siam, the national soul was not yet fully cultivated. After the fall of the absolute monarchy, Prime Minister Phibunsongkhram sought to mould the religio‐national identity of Thailand until the religious community's borders coincided with those of the nation‐state. One focus of nationalist leaders' efforts was the adaptation and promotion of Buddhist temples throughout the state. These temples became markers of both geographic and cosmological space, serving to infuse the geographic body with a religio‐national soul. Thus, the nationalism that developed embraced the fusion of the religious identity with the national identity.
Validation of swabs as a non‐destructive and relatively non‐invasive DNA sampling method in fish
Authors: LE VIN A. L. , ADAM A. , TEDDER A. , ARNOLD K. E. , MABLE B. K. 
Published: August 2010

AbstractNon‐destructive methods of collecting DNA from small fish species can be problematic, as fin clips can potentially affect behaviour or survivorship in the wild. Swabbing body mucus may provide a less invasive method of DNA collection. However, risk of contamination from other individuals in high density groups could give erroneous genotyping results. We compared multilocus microsatellite genotypes from the same individuals when collected at low and high density and compared this with fin clips. We found no differences between these categories, with a genotyping error rate of 0.42%, validating the use of body mucus swabbing for DNA collection in fish.
Introgression of B-genome chromosomes in a doubled haploid population ofBrassica napus ×B. carinata
Authors: Navabi Z. K. , Parkin I. A.P. , Pires J. C. , Xiong Z. , Thiagarajah M. R. , Good A. G. , Rahman M. H. 
Published: August 2010

The Brassica B-genome species possess many valuable agronomic and disease resistance traits. To transfer traits from the B genome of B. carinata into B. napus , an interspecific cross between B. napus and B. carinata was performed and a doubled haploid (DH) population was generated from the BC2S3generation. Successful production of interspecific DH lines as identified using B-genome microsatellite markers is reported. Five percent of DH lines carry either intact B-genome chromosomes or chromosomes that have deletions. All of the DH lines have linkage group J13/B7 in common. This was further confirmed using B. nigra genomic DNA in a fluorescent in situ hybridization assay where the B-genome chromosomes were visualized and distinguished from the A- and C-genome chromosomes. The 60 DH lines were also evaluated for morphological traits in the field for two seasons and were tested for resistance to blackleg, caused by Leptosphaeria maculans , under greenhouse conditions. Variation in the DH population followed a normal distribution for several agronomic traits and response to blackleg. The lines with B-genome chromosomes were significantly different (p < 0.01) from the lines without B-genome chromosomes for both morphological and seed quality traits such as days to flowering, days to maturity, and erucic acid content.
Do neuromuscular adaptations occur in endurance-trained boys and men?
Authors: Cohen Rotem , Mitchell Cam , Dotan Raffy , Gabriel David , Klentrou Panagiota , Falk Bareket 
Published: August 2010

Most research on the effects of endurance training has focused on endurance training's health-related benefits and metabolic effects in both children and adults. The purpose of this study was to examine the neuromuscular effects of endurance training and to investigate whether they differ in children (9.0–12.9 years) and adults (18.4–35.6 years). Maximal isometric torque, rate of torque development (RTD), rate of muscle activation (Q30), electromechanical delay (EMD), and time to peak torque and peak RTD were determined by isokinetic dynamometry and surface electromyography (EMG) in elbow and knee flexion and extension. The subjects were 12 endurance-trained and 16 untrained boys, and 15 endurance-trained and 20 untrained men. The adults displayed consistently higher peak torque, RTD, and Q30, in both absolute and normalized values, whereas the boys had longer EMD (64.7 ± 17.1 vs. 56.6 ± 15.4 ms) and time to peak RTD (98.5 ± 32.1 vs. 80.4 ± 15.0 ms for boys and men, respectively). Q30, normalized for peak EMG amplitude, was the only observed training effect (1.95 ± 1.16 vs. 1.10 ± 0.67 ms for trained and untrained men, respectively). This effect could not be shown in the boys. The findings show normalized muscle strength and rate of activation to be lower in children compared with adults, regardless of training status. Because the observed higher Q30values were not matched by corresponding higher performance measures in the trained men, the functional and discriminatory significance of Q30remains unclear. Endurance training does not appear to affect muscle strength or rate of force development in either men or boys.
Plasma prekallikrein levels are positively associated with circulating lipid levels and the metabolic syndrome in children
Authors: MacKenzie James A. , Roosa Kristen A. , Gump Brooks B. , Dumas Amy K. , Bendinskas Kestutis G. 
Published: August 2010

Plasma prekallikrein (PK) has been shown to be associated with cardiovascular disease (CVD) and its risk factors, but these associations have not been investigated in children. The present study examined PK activity in relation to well-established cardiovascular risk factors in a cohort of children aged 9–11 years (N = 97). We found a significant and positive association between PK and fasting levels of total cholesterol (p < 0.01), non-high-density lipoprotein cholesterol (p < 0.01), and triglycerides (p < 0.001). In addition, there was a significant association between PK activity and the metabolic syndrome, a clustering of risk factors considered to have an impact on atherosclerosis and CVD mortality. Finally, we found that children with a family history of CVD had significantly elevated PK activity. These novel findings warrant further investigations into the relationship between circulating PK levels and CVD risk factors because PK may be involved in the progression of the disease state.
Postprandial insulin sensitivity and thermogenesis in frail elderly women
Authors: Goulet Eric D.B. , Khursigara Zareen , Gougeon Réjeanne , Morais José A. 
Published: August 2010

The frailty syndrome is associated with inflammation, hypercortisolemia, and cardiovascular diseases, all of which are linked with insulin resistance. But whether frailty is characterized by insulin resistance is unclear, especially in the postprandial state. The prevalence of underweight with frailty is high. We wondered whether hypermetabolism associated with inflammation and hypercortisolemia could increase the thermic effect of food (TEF) and contribute to the frailty-associated body weight loss. In this study, we determined whether insulin sensitivity and TEF responses differ between frail and healthy elderly persons following a meal. Ten healthy and 13 frail elderly women were recruited and studied during the 5 h following the ingestion of a standardized liquid mixed-meal test. Areas under the curve (AUC) for glucose and insulin, and the product of AUC glucose × AUC insulin × 10−6(PGI) were used as indices of insulin sensitivity. TEF was measured by indirect calorimetry. Following the meal, glucose and insulin AUCs and PGI were significantly higher in frail than in healthy elderly women and, except for the insulin AUC; these differences remained significant after adjustment for age, body weight, and physical activity. Physical activity, determined by questionnaire, was the single best predictor of PGI, explaining 27% of its variance. There was no difference in TEF between groups, and it did not correlate with any significant variable measured. Our results suggest that postprandial insulin resistance is higher in frail than in healthy elderly women, and TEF is similar, indicating that both processes do not contribute to the propensity for body weight loss.
Shear strength of disturbed regions with corroded stirrups in reinforced concrete beams
Authors: Suffern Christopher , El-Sayed Ahmed , Soudki Khaled 
Published: August 2010

This paper reports experimental data on the structural performance of disturbed regions in reinforced concrete beams with corrosion damage to the embedded steel stirrups. A total of 15 reinforced concrete beams were constructed and tested. The test beams were 350 mm deep, 125 mm wide, and 1850 mm long. The beams were tested in three-point bending under a simply supported span of 1500 mm. Nine beams had the embedded stirrups subjected to accelerated corrosion. The test variables were the corrosion damage level and the shear span-to-depth ratio. The test results indicated that the corroded beams exhibited reduced shear strength in comparison to the uncorroded control specimens. The shear strength reduction was up to 53%. Furthermore, the reduction in shear strength due to the corrosion was found to be greater at smaller shear span-to-depth ratios.
Prototypical arsine–triel adducts (R3AsEX3 for E = B, Al, and Ga)
Authors: Conrad Eamonn , Pickup Janet , Burford Neil , McDonald Robert , Ferguson Michael J. 
Published: August 2010

Complexes of arsine ligands (R3As, R = Me, Et, Ph) and Lewis acids of group-13 elements of the form EX3 (E = B, X = Ph, C6F5; E = Al, X = Cl, Br, I; E = Ga, X = Cl) have been isolated and characterized by X-ray crystallography, infrared spectroscopy, 1H, 13C{1H}, 11B{1H}, and 27Al NMR spectroscopy. The compounds are compared with rare arsine–triel adducts.
A DFT study on the catalytic mechanism of UDP-glucose dehydrogenase
Authors: Huang WenJuan , Llano Jorge , Gauld James W. 
Published: August 2010

Uridine 5′-diphosphate glucuronic acid (UDPGlcUA) is a key intermediary metabolite in many species, including pathogenic bacteria and humans. It is biosynthesized from UDP-glucose (UDPGlc) by uridine diphosphate glucose dehydrogenase (UDPGlcDH) via a twofold two-electron–one-proton oxidation that successively transforms the 6-hydroxymethyl of glucopyranose into a formyl, and the latter into the final carboxylic function. The catalytic mechanism of UDPGlcDH was investigated using a large enzyme active-site model in combination with the B3LYP method and the polarizable continuum model (IEF-PCM) self-consistent reaction field. The latter was used to correct for the long-range electrostatic effect of the protein environment. The overall mechanism consists of four catalytic steps: (i) NAD+-dependent oxidation of glucose to glucuronaldehyde, (ii) nucleophilic addition of Cys260–SH to glucuronaldehyde to form a 6-thiohemiacetal intermediate, (iii) NAD+-dependent oxidation of the 6-thiohemiacetal to form a 6-thioester intermediate, and finally, (iv) hydrolysis of the 6-thioester to give glucuronic acid. In addition, this study also provides insight into the debated roles of Lys204 and Asp264, and the most likely protonation state of a reactive Michaelis complex of UDPGlcDH.
The assessment of density functionals for DNA–protein stacked and T-shaped complexes
Authors: Rutledge Lesley R. , Wetmore Stacey D. 
Published: August 2010

The present work uses 129 nucleobase – amino acid CCSD(T)/CBS stacking and T-shaped interaction energies as reference data to test the ability of various density functionals with double-zeta quality basis sets, as well as some semi-empirical and molecular mechanics methods, to accurately describe noncovalent DNA–protein π–π and π+–π interactions. The goal of this work is to identify methods that can be used in hybrid approaches (QM/MM, ONIOM) for large-scale modeling of enzymatic systems involving active-site (substrate) π–π contacts. Our results indicate that AMBER is a more appropriate choice for the lower-level method in hybrid techniques than popular semi-empirical methods (AM1, PM3), and suggest that AMBER accurately describes the π–π interactions found throughout DNA–protein complexes. The M06–2X and PBE-D density functionals were found to provide very promising descriptions of the 129 nucleobase – amino acid interaction energies, which suggests that these may be the most suitable methods for describing high-level regions. Therefore, M06–2X and PBE-D with both the 6–31G(d) and 6–31+G(d,p) basis sets were further examined through potential-energy surface scans to better understand how these techniques describe DNA–protein π–π interactions in both minimum and nonminimum regions of the potential-energy surfaces, which is critical information when modeling enzymatic reaction pathways. Our results suggest that studies of stacked nucleobase – amino acid systems should implement the PBE-D/6–31+G(d,p) method. However, if T-shaped contacts are involved and (or) smaller basis sets must be considered due to limitations in computational resources, then M06–2X/6–31G(d) provides an overall excellent description of both nucleobase – amino acid stacking and T-shaped interactions for a range of DNA–protein π–π and π+–π interactions.
Dynamics of antimicrobial resistance and virulence genes in Enterococcus faecalis during swine manure storage
Authors: Mangalappalli-Illathu Anil , Duriez Patrick , Masson Luke , Diarra Moussa Sory , Scott Andrew , Tien Yuan-Ching , Zhang Yun , Topp Edward 
Published: August 2010

In this study we used 2 experimental approaches to evaluate the stability of antimicrobial resistance (AMR) phenotypes, selected AMR genes, and selected virulence genes in Enterococcus faecalis during manure storage on a commercial swine farm. Isolates of E. faecalis were obtained directly from fresh fecal material (n = 120) and from the manure storage facility (n = 85) and compared. Tetracycline resistance and the virulence genes cob, esp, eep, and ccf were detected at lower frequency in manure isolates than in fecal isolates. A second approach consisted of immersing in diffusion chambers pure cultures of E. faecalis that varied in their AMR phenotypes and virulence genotypes in the swine manure storage facility for 8 weeks, sampling periodically, and evaluating the recovered strains for changes in their genotypic or phenotypic characteristics. Enterococcus faecalis populations declined exponentially, with rate constants ranging from 0.011 to 0.022 h–1. Among the AMR and virulence genes examined, 1 AMR gene (sat4) and 7 virulence genes (agrBfs, cob, cpd, cylB, efaAfs, enlA, and esp) were lost at low frequencies in the recovered strains. The AMR phenotypes were stable during the incubation, with minimal loss (P > 0.05) of the streptomycin-resistance phenotype. Overall, these results suggest that some attributes of public health significance in populations of E. faecalis decrease in frequency during manure storage.
Endothelin-1-mediated cerebrovascular remodeling is not associated with increased ischemic brain injury in diabetesThis article is one of a selection of papers published in the two-part special issue entitled 20 Years of Endothelin Research.
Authors: Li Weiguo , Kelly-Cobbs Aisha I. , Mezzetti Erin M. , Fagan Susan C. , Ergul Adviye 
Published: August 2010

Diabetes increases the risk of as well as poor outcome after stroke. Matrix metalloprotease (MMP) activation disrupts blood–brain barrier integrity after cerebral ischemia. We have previously shown that type 2 diabetes promotes remodeling of middle cerebral arteries (MCA) characterized by increased media/lumen (M/L) ratio and MMP activity in an endothelin (ET)-1-dependent manner in the Goto–Kakizaki (GK) rat model. In the present study, we examined the effects of ET-1-mediated vascular remodeling on neurovascular damage following cerebral ischemic injury in GK rats 5 and 12 weeks after the onset of diabetes. The MCA structure, cerebral perfusion as well as infarct size, and hemorrhage were measured in control and diabetic rats subjected to transient MCA occlusion. M/L ratio was increased after 12 but not 5 weeks of diabetes. The baseline cerebral perfusion was lower and the infarct volume smaller in diabetic rats in both age groups. The incidence of hemorrhagic transformation was higher after 5 weeks of diabetes as compared to that after 12 weeks or in the control groups. These findings provide evidence that ET-1-mediated cerebrovascular remodeling does not worsen the neurovascular damage of ischemic brain injury in diabetes. It is possible that this early remodeling response is compensatory in nature to regulate vascular tone and integrity, especially when ischemia is layered on diabetic vascular disease.