bluuebunny/crossref_metadata_2025_split huggingface dataset:
Untangling the positive genetic correlation between rainbow trout growth and survival
Authors: Vehviläinen Harri , Kause Antti , Kuukka‐Anttila Hanna , Koskinen Heikki , Paananen Tuija 
Published: March 2012

AbstractExplanations for positive and negative genetic correlations between growth and fitness traits are essential for life‐history theory and selective breeding. Here, we test whether growth and survival display genetic trade‐off. Furthermore, we assess the potential of third‐party traits to explain observed genetic associations. First, we estimated genetic correlations of growth and survival of rainbow trout. We then explored whether these associations are explained by genetic correlations with health, body composition and maturity traits. Analysis included 14 traits across life stages and environments. Data were recorded from 249 166 individuals belonging to 10 year classes of a pedigreed population. The results revealed that rapid growth during grow‐out was genetically associated with enhanced survival (mean rG = 0.17). This resulted because genotypes with less nematode caused cataract grew faster and were more likely to survive. Fingerling survival was not genetically related to weight or to grow‐out survival. Instead, rapid fingerling growth made fish prone to deformations (rG = 0.18). Evolutionary genetics provides a theoretical framework to study variation in genetic correlations. This study demonstrates that genetic correlation patterns of growth and survival can be explained by a set of key explanatory traits recorded at different life stages and that these traits can be simultaneously improved by selective breeding.
Prognostic factors in lung cancer in a defined geographical area over two decades with a special emphasis on gender
Authors: Svensson Gunnar , Ewers Sven‐Börje , Ohlsson Ola , Olsson Håkan 
Published: March 2012

AbstractIntroduction:  Many studies over recent decades report an increasing incidence of lung cancer in female patients. Female gender is often reported as a good prognostic factor.Objectives:  The aim of the present study was to investigate prognostic factors with a special emphasis on gender.Methods:  During 1989–2008, 1497 patients in eastern Scania, a part of southern Sweden with 202 000 inhabitants, were referred to one Central Hospital and prospectively registered. All patients were grouped into four 5‐year periods and were analysed for occurrence of lung cancer, patient performance status, types and stages of lung cancer and the relation to gender.Results:  The incidence of lung cancer more than doubled in women. The proportion of adenocarcinomas increased in females and in males to 57% (P = 0.028) and 42% (P = 0.001), respectively, while the frequency of small cell lung carcinomas (SCLCs) decreased in both genders to approximately 14%. Females had significantly more frequent stage 1 (16.6%) and higher surgery rate (23.1%) than males (12% and 18.2%, respectively). Females showed a higher 5‐year survival rate than males (20.1% and 11.5%, respectively; P < 0.001). Patients with non‐small cell lung carcinoma (NSCLC) had a higher 5‐year survival rate than those with SCLC (16.5% and 7.5%, respectively; P < 0.01); however, there was no significant survival difference in females between NSCLC and SCLC.Conclusion:  Female patients exhibited longer survival than males for both NSCLC and SCLC, and this was not explained by a higher frequency of stage 1 or surgery in NSCLC.Please cite this paper as: Svensson G., Ewers S.‐B., Ohlsson O. and Olsson H. Prognostic factors in lung cancer in a defined geographical area over two decades with a special emphasis on gender. Clin Respir J 2013; 7: 91–100.
BASIC REASONS AND FIRST PHILOSOPHY: A COHERENTIST VIEW OF REASONS
Authors: POSTON TED 
Published: March 2012

abstractThis paper develops and defends a coherentist account of reasons. I develop three core ideas for this defense: a distinction between basic reasons and noninferential justification, the plausibility of the neglected argument against first philosophy, and an emergent account of reasons. These three ideas form the backbone for a credible coherentist view of reasons. I work toward this account by formulating and explaining the basic reasons dilemma. This dilemma reveals a wavering attitude that coherentists have had toward basic reasons. More importantly, the basic reasons dilemma focuses our attention on the central problems that afflict coherentist views of basic beliefs. By reflecting on the basic reasons dilemma, I formulate three desiderata that any viable coherentist account of basic beliefs must satisfy. I argue that the account on offer satisfies these desiderata.
Parental interest in comprehensive care for children with attentional concerns
Authors: Banasiewicz Ben , Kemper Kathi J 
Published: March 2012

AbstractMany families seek natural therapies for children. We describe what families want when they seek consultation for natural therapies for children with attention deficit hyperactivity disorder (ADHD). Our objective was to: a) describe the kinds of problems and therapies used by patients presenting with a concern about ADHD; b) assess interest in counselling about health promotion; and c) describe physician recommendations at the initial consultation about conventional and CAM therapies. We reviewed intake forms, physician reports and laboratory studies for new patients seen in an integrative paediatric clinic between January 2010 and June 2011. Of the 75 new patients, 23 (31%) families had concerns about ADHD. Of these, 70% were boys; the average age was 11.2 ± 3.1 years, and 80% received care from specialists. Eleven patients (48%) were taking a prescription medication, but only three (13%) were taking medicine for ADHD; dietary supplements were taken by 12 patients (52%). Most families were interested in health promotion information about diet (87%), exercise (78%), stress management (74%), and sleep (74%). Of 11 patients tested, 82% had low ferritin. Recommendations focused on health promotion (100%), dietary supplements, such as multivitamins/minerals (71%) and omega‐3 fatty acids (82%), and specialist referrals (30%). Families seeking natural therapies for children with ADHD have needs for health promotion and care coordination, which are well addressed using tools and skills already present in the medical home.
Protection against Lethal Leptospirosis after Vaccination with LipL32 Coupled or Coadministered with the B Subunit of Escherichia coli Heat-Labile Enterotoxin
Authors: Grassmann André A. , Félix Samuel R. , Ximendes dos Santos Carolina , Amaral Marta G. , Seixas Neto Amilton C. P. , Fagundes Michel Q. , Seixas Fabiana K. , da Silva Éverton F. , Conceição Fabricio R. , Dellagostin Odir A. 
Published: March 2012

ABSTRACTLeptospirosis, a worldwide zoonosis, lacks an effective, safe, and cross-protective vaccine. LipL32, the most abundant, immunogenic, and conserved surface lipoprotein present in all pathogenic species ofLeptospira, is a promising antigen candidate for a recombinant vaccine. However, several studies have reported a lack of protection when this protein is used as a subunit vaccine. In an attempt to enhance the immune response, we used LipL32 coupled to or coadministered with the B subunit of theEscherichia coliheat-labile enterotoxin (LTB) in a hamster model of leptospirosis. After homologous challenge with 5× the 50% lethal dose (LD50) ofLeptospira interrogans, animals vaccinated with LipL32 coadministered with LTB and LTB::LipL32 had significantly higher survival rates (P< 0.05) than animals from the control group. This is the first report of a protective immune response afforded by a subunit vaccine using LipL32 and represents an important contribution toward the development of improved leptospirosis vaccines.
Prediction System for Rapid Identification of Salmonella Serotypes Based on Pulsed-Field Gel Electrophoresis Fingerprints
Authors: Zou Wen , Lin Wei-Jiun , Hise Kelley B. , Chen Hung-Chia , Keys Christine , Chen James J. 
Published: March 2012

ABSTRACT

A classification model is presented for rapid identification of
Salmonella
serotypes based on pulsed-field gel electrophoresis (PFGE) fingerprints. The classification model was developed using random forest and support vector machine algorithms and was then applied to a database of 45,923 PFGE patterns, randomly selected from all submissions to CDC PulseNet from 2005 to 2010. The patterns selected included the top 20 most frequent serotypes and 12 less frequent serotypes from various sources. The prediction accuracies for the 32 serotypes ranged from 68.8% to 99.9%, with an overall accuracy of 96.0% for the random forest classification, and ranged from 67.8% to 100.0%, with an overall accuracy of 96.1% for the support vector machine classification. The prediction system improves reliability and accuracy and provides a new tool for early and fast screening and source tracking of outbreak isolates. It is especially useful to get serotype information before the conventional methods are done. Additionally, this system also works well for isolates that are serotyped as “unknown” by conventional methods, and it is useful for a laboratory where standard serotyping is not available.
Ultrarapid Detection of
bla
KPC1/2-12
from Perirectal and Nasal Swabs by Use of Real-Time PCR
Authors: Richter Sara N. , Frasson Ilaria , Biasolo Maria Angela , Bartolini Andrea , Cavallaro Antonietta , Palù Giorgio 
Published: March 2012

ABSTRACT

The novel real-time PCR assay developed as described here was able to detect
bla
KPC1/2-12
(
bla
KPC-1/2
to
bla
KPC-12
) from easily available clinical specimens in less than 2 h. The genotypic assay was highly sensitive (100%) and specific (98%). In some cases, it was able to detect
bla
KPC
48 h before positive detection by standard phenotypic assay on patients who were monitored daily. The high sensitivity and rapidity of the molecular method make it the method of choice for KPC surveillance and, thus, containment purposes.
Mixed Tuberculosis Infections in Rural South Vietnam
Authors: Huyen Mai N. T. , Kremer Kristin , Lan Nguyen T. N. , Cobelens Frank G. J. , Buu Tran N. , Dung Nguyen H. , Caws Maxine , Tiemersma Edine W. , van Soolingen Dick 
Published: March 2012

ABSTRACT

Tuberculosis patients may be infected with or have disease caused by more than one
Mycobacterium tuberculosis
strain, usually referred to as “mixed infections.” These have mainly been observed in settings with a very high tuberculosis incidence and/or high HIV prevalence. We assessed the rate of mixed infections in a population-based study in rural Vietnam, where the prevalences of both HIV and tuberculosis are substantially lower than those in previous studies looking at mixed infections. In total, 1,248
M. tuberculosis
isolates from the same number of patients were subjected to IS
6110
restriction fragment length polymorphism (RFLP) typing, spoligotyping, and variable-number-tandem-repeat (VNTR) typing. We compared mixed infections identified by the presence of (i) discrepant RFLP and spoligotype patterns in isolates from the same patient and (ii) double alleles at ≥2 loci by VNTR typing and assessed epidemiological characteristics of these infections. RFLP/spoligotyping and VNTR typing identified 39 (3.1%) and 60 (4.8%) mixed infections, respectively (Cohen's kappa statistic, 0.57). The number of loci with double alleles in the VNTR pattern was strongly associated with the proportion of isolates with mixed infections according to RFLP/spoligotyping (
P
< 0.001). Mixed infections occurred more frequently in newly treated than in previously treated patients, were significantly associated with minor X-ray abnormalities, and were almost significantly associated with lower sputum smear grades. Although the infection pressure in our study area is lower than that in previously studied populations, mixed
M. tuberculosis
infections do occur in rural South Vietnam in at least 3.1% of cases.
Novel Genetic Variation Identified at Fixed Loci in ORF62 of the Oka Varicella Vaccine and in a Case of Vaccine-Associated Herpes Zoster
Authors: Quinlivan Mark L. , Jensen Nancy J. , Radford Kay W. , Schmid D. Scott 
Published: March 2012

ABSTRACT
The live attenuated Oka varicella vaccine (vOka), derived from clade 2 wild-type (wt) virus pOka, is used for routine childhood immunization in several countries, including the United States, which has caused dramatic declines in the incidence of varicella. vOka can cause varicella, establish latency, and reactivate to cause herpes zoster (HZ). Three loci in varicella-zoster virus (VZV) open reading frame 62 (ORF62) (106262, 107252, and 108111) are used to distinguish vOka from wt VZV. A fourth position (105705) is also fixed for the vOka allele in nearly all vaccine batches. These 4 positions and two vOka mutations (106710 and 107599) reportedly absent from Varivax were analyzed on Varivax-derived ORF62 TOPO TA clones. The wt allele was detected at positions 105705 and 107252 on 3% and 2% of clones, respectively, but was absent at positions 106262 and 108111. Position 106710 was fixed for the wt allele, whereas the vOka allele was present on 18.4% of clones at position 107599. We also evaluated the 4 vOka markers in an isolate obtained from a case of vaccine-caused HZ. The isolate carried the vOka allele at positions 105705, 106262, and 108111. However, at position 107252, the wt allele was present. Thus, all of the ORF62 vOka markers previously regarded as fixed occur as the wt allele in a small percentage of vOka strains. Characterization of all four vOka markers in ORF62 and of the clade 2 subtype marker in ORF38 is now necessary to confirm vOka adverse events.
Bacteriophage ϕ6 Nucleocapsid Surface Protein 8 Interacts with Virus-Specific Membrane Vesicles Containing Major Envelope Protein 9
Authors: Sarin L. Peter , Hirvonen Jari J. , Laurinmäki Pasi , Butcher Sarah J. , Bamford Dennis H. , Poranen Minna M. 
Published: March 2012

ABSTRACT

Enveloped double-stranded RNA (dsRNA) bacterial virus
Pseudomonas
phage ϕ6 has been developed into an advanced assembly system where purified virion proteins and genome segments self-assemble into infectious viral particles, inferring the assembly pathway. The most intriguing step is the membrane assembly occurring inside the bacterial cell. Here, we demonstrate that the middle virion shell, made of protein 8, associates with the expanded viral core particle and the virus-specific membrane vesicle.
West Nile Virus Noncoding Subgenomic RNA Contributes to Viral Evasion of the Type I Interferon-Mediated Antiviral Response
Authors: Schuessler Andrea , Funk Anneke , Lazear Helen M. , Cooper Daphne A. , Torres Shessy , Daffis Stephane , Jha Babal Kant , Kumagai Yutaro , Takeuchi Osamu , Hertzog Paul , Silverman Robert , Akira Shizuo , Barton David J. , Diamond Michael S. , Khromykh Alexander A. 
Published: March 2012

ABSTRACT
We previously showed that a noncoding subgenomic flavivirus RNA (sfRNA) is required for viral pathogenicity, as a mutant West Nile virus (WNV) deficient in sfRNA production replicated poorly in wild-type mice. To investigate the possible immunomodulatory or immune evasive functions of sfRNA, we utilized mice and cells deficient in elements of the type I interferon (IFN) response. Replication of the sfRNA mutant WNV was rescued in mice and cells lacking interferon regulatory factor 3 (IRF-3) and IRF-7 and in mice lacking the type I alpha/beta interferon receptor (IFNAR), suggesting a contribution for sfRNA in overcoming the antiviral response mediated by type I IFN. This was confirmed by demonstrating rescue of mutant virus replication in the presence of IFNAR neutralizing antibodies, greater sensitivity of mutant virus replication to IFN-α pretreatment, partial rescue of its infectivity in cells deficient in RNase L, and direct effects of transfected sfRNA on rescuing replication of unrelated Semliki Forest virus in cells pretreated with IFN-α. The results define a novel function of sfRNA in flavivirus pathogenesis via its contribution to viral evasion of the type I interferon response.
The Intertransmembrane Region of Kaposi's Sarcoma-Associated Herpesvirus Modulator of Immune Recognition 2 Contributes to B7-2 Downregulation
Authors: Kajikawa Mizuho , Li Pai-Chi , Goto Eiji , Miyashita Naoyuki , Aoki-Kawasumi Masami , Mito-Yoshida Mari , Ikegaya Mika , Sugita Yuji , Ishido Satoshi 
Published: March 2012

ABSTRACTKaposi's sarcoma-associated herpesvirus (KSHV), a human tumor virus, encodes two homologous membrane-associated E3 ubiquitin ligases, modulator of immune recognition 1 (MIR1) and MIR2, to evade host immunity. Both MIR1 and MIR2 downregulate the surface expression of major histocompatibility complex class I (MHC I) molecules through ubiquitin-mediated endocytosis followed by lysosomal degradation. Since MIR2 additionally downregulates a costimulatory molecule (B7-2) and an integrin ligand (intercellular adhesion molecule 1 [ICAM-1]), MIR2 is thought to be a more important molecule for immune evasion than MIR1; however, the molecular basis of the MIR2 substrate specificity remains unclear. To address this issue, we determined which regions of B7-2 and MIR2 are required for MIR2-mediated B7-2 downregulation. Experiments with chimeras made by swapping domains between human B7-2 and CD8α, a non-MIR2 substrate, and between MIR1 and MIR2 demonstrated a significant contribution of the juxtamembrane (JM) region of B7-2 and the intertransmembrane (ITM) region of MIR2 to MIR2-mediated downregulation. Structure prediction and mutagenesis analyses indicate that Phe119 and Ser120 in the MIR2 ITM region and Asp244 in the B7-2 JM region contribute to the recognition of B7-2 by MIR2. This finding provides new insight into the molecular basis of substrate recognition by MIR family members.
A Role of Template Cleavage in Reduced Excision of Chain-Terminating Nucleotides by Human Immunodeficiency Virus Type 1 Reverse Transcriptase Containing the M184V Mutation
Authors: Acosta-Hoyos Antonio J. , Matsuura Suzanne E. , Meyer Peter R. , Scott Walter A. 
Published: March 2012

ABSTRACTResistance to nucleoside reverse transcriptase (RT) inhibitors is conferred on human immunodeficiency virus type 1 through thymidine analogue resistance mutations (TAMs) that increase the ability of RT to excise chain-terminating nucleotides after they have been incorporated. The RT mutation M184V is a potent suppressor of TAMs. In RT containing TAMs, the addition of M184V suppressed the excision of 3′-deoxy-3′-azidothymidine monophosphate (AZTMP) to a greater extent on an RNA template than on a DNA template with the same sequence. The catalytically inactive RNase H mutation E478Q abolished this difference. The reduction in excision activity was similar with either ATP or pyrophosphate as the acceptor substrate. Decreased excision of AZTMP was associated with increased cleavage of the RNA template at position −7 relative to the primer terminus, which led to increased primer-template dissociation. Whether M184V was present or not, RT did not initially bind at the −7 cleavage site. Cleavage at the initial site was followed by RT dissociation and rebinding at the −7 cleavage site, and the dissociation and rebinding were enhanced when the M184V mutation was present. In contrast to the effect of M184V, the K65R mutation suppressed the excision activity of RT to the same extent on either an RNA or a DNA template and did not alter the RNase H cleavage pattern. Based on these results, we propose that enhanced RNase H cleavage near the primer terminus plays a role in M184V suppression of AZT resistance, while K65R suppression occurs through a different mechanism.
Characterization of Novel Components of the Baculovirus
Per Os
Infectivity Factor Complex
Authors: Peng Ke , van Lent Jan W. M. , Boeren Sjef , Fang Minggang , Theilmann David A. , Erlandson Martin A. , Vlak Just M. , van Oers Monique M. 
Published: March 2012

ABSTRACT

Baculovirus occlusion-derived virus (ODV) infects insect midgut cells under alkaline conditions, a process mediated by highly conserved
per os
infectivity factors (PIFs), P74 (PIF0), PIF1, PIF2, PIF3, PIF4, and PIF5 (ODV-E56). Previously, a multimolecular complex composed of PIF1, PIF2, PIF3, and P74 was identified which was proposed to play an essential role during ODV entry. Recently, more proteins have been identified that play important roles in ODV oral infectivity, including PIF4, PIF5, and SF58, which might work in concert with previously known PIFs to facilitate ODV infection. In order to understand the ODV entry mechanism, the identification of all components of the PIF complex is crucial. Hence, the aim of this study was to identify additional components of the PIF complex. Coimmunoprecipitation (CoIP) combined with proteomic analysis was used to identify the components of the
Autographa californica
multiple nucleopolyhedrovirus (AcMNPV) PIF complex. PIF4 and P95 (AC83) were identified as components of the PIF complex while PIF5 was not, and this was confirmed with blue native PAGE and a second CoIP. Deletion of the
pif4
gene impaired complex formation, but deletion of
pif5
did not. Differentially denaturing SDS-PAGE further revealed that PIF4 forms a stable complex with PIF1, PIF2, and PIF3. P95 and P74 are more loosely associated with this complex. Three other proteins, AC5, AC68, and AC108 (homologue of SF58), were also found by the proteomic analysis to be associated with the PIF complex. Finally the functional significance of the PIF protein interactions is discussed.
Identification of the Target Cells and Sequence of Infection during Experimental Infection of Ovine Fetuses with Cache Valley Virus
Authors: Rodrigues Hoffmann Aline , Welsh Christabel Jane , Varner Patricia Wilcox , de la Concha-Bermejillo Andres , Ball Judith Marchand , Ambrus Andy , Edwards John Francis 
Published: March 2012

ABSTRACTCache Valley virus-induced malformations have been previously reproduced in ovine fetuses; however, no studies have established the course of infection of cells and tissues with Cache Valley virus. To address these questions, ovine fetuses at 35 days of gestation were inoculatedin uterowith Cache Valley virus and euthanized at 7, 10, 14, 21, and 28 days postinfection. On postmortem examination, arthrogryposis and oligohydramnios were observed in some infected fetuses. Morphological studies showed necrosis in the central nervous system and skeletal muscle of infected fetuses evaluated after 7 to 14 days postinfection, and hydrocephalus, micromyelia, and muscular loss were observed in infected fetuses after 21 to 28 days postinfection. Using immunohistochemistry andin situhybridization, intense Cache Valley virus antigen and RNA staining was detected in the brain, spinal cord, skeletal muscle, and, to a lesser degree, in fetal membranes and other tissues of infected fetuses. Viral antigen and RNA staining decreased in targeted and infected tissues with the progression of the infection.
Myxoma Virus M064 Is a Novel Member of the Poxvirus C7L Superfamily of Host Range Factors That Controls the Kinetics of Myxomatosis in European Rabbits
Authors: Liu Jia , Wennier Sonia , Moussatche Nissin , Reinhard Mary , Condit Richard , McFadden Grant 
Published: March 2012

ABSTRACT

The myxoma virus (MYXV) carries three tandem C7L-like host range genes (M062R, M063R, and M064R). However, despite the fact that the sequences of these three genes are similar, they possess very distinctive functions
in vivo
. The role of M064 in MYXV pathogenesis was investigated and compared to the roles of M062 and M063. We report that M064 is a virulence factor that contributes to MYXV pathogenesis but lacks the host range properties associated with M062 and M063.