bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flow Cytometric Detection of Mycobacterium avium subsp. paratuberculosis-Specific Antibodies in Experimentally Infected and Naturally Exposed Calves
Authors: Schillinger S. , Bridger P. S. , Bulun H. , Fischer M. , Akineden Ö. , Seeger T. , Barth S. , Henrich M. , Doll K. , Bülte M. , Menge C. , Bauerfeind R. 
Published: July 2013

ABSTRACT

A desirable test to diagnose infections with
Mycobacterium avium
subsp.
paratuberculosis
facilitates identification of infected cattle prior to the state of
M. avium
subsp.
paratuberculosis
shedding. This study aimed at adjusting a flow cytometry (FC)-based assay, using intact
M. avium
subsp.
paratuberculosis
bacteria as the antigen, for diagnosis of
M. avium
subsp.
paratuberculosis
infections in calves. Serum samples were collected from experimentally infected (
n
= 12) and naturally exposed (
n
= 32) calves. Samples from five calves from positive dams were analyzed to determine the dynamics of maternal antibodies. Samples from adult cattle with defined infection status served as the standard (18
M. avium
subsp.
paratuberculosis
shedders, 22
M. avium
subsp.
paratuberculosis
free). After preadsorption with
Mycobacterium phlei
, sera were incubated with
M. avium
subsp.
paratuberculosis
and
M. avium
subsp.
avium
bacterial suspensions, respectively, followed by the separate detection of bovine IgG, IgG1, IgG2, and IgM attached to the bacterial surface.
M. avium
subsp.
paratuberculosis
-specific sample/positive (S/P) ratios were compared to enzyme-linked immunosorbent assay (ELISA) S/P ratios. In adult cattle, the FC assay for IgG1 had a sensitivity of 78% at a specificity of 100%. Maternally acquired antibodies could be detected in calves up to 121 days of life. While all but two sera taken at day 100 ± 10 postnatum from naturally exposed calves tested negative, elevated S/P ratios (IgG and IgG1) became detectable from 44 and 46 weeks postinoculation onwards in two calves infected experimentally. Even with the optimized FC assay,
M. avium
subsp.
paratuberculosis
-specific antibodies can only occasionally be detected in infected calves less than 12 months of age. The failure to detect such antibodies apparently reflects the distinct immunobiology of
M. avium
subsp.
paratuberculosis
infections rather than methodological constraints.
Rapid, Sensitive Recovery of Recombinant Attenuated Salmonella enterica Serovar Typhi Vaccine Strains from Human Blood
Authors: Lottenbach Kathleen R. , Kelly-Aehle Sandra M. , Brenneman Karen E. , Curtiss Roy , Frey Sharon E. 
Published: July 2013

ABSTRACT

Prior to initiating a phase 1 dose escalation trial of the safety and immunogenicity of live, oral, recombinant, attenuated
Salmonella enterica
serovar Typhi vaccine strains in human subjects, the suitability of conventional blood culture procedures to rapidly and reliably detect the organisms in human blood was investigated. Blood culture specimens, with and without added growth supplements, were inoculated with study organism concentrations ranging from approximately 300 to as few as 1 to 2 CFU/10 ml culture and processed in a Bactec 9240 fluorescent series aerobic blood culture system. All cultures seeded with >6 CFU and 93% of cultures seeded with ∼1 to 2 CFU were identified as positive for microbial growth within 44 h of incubation. The results were within the performance standard of ≤5 days to detection that is expected for Gram-negative cultures seeded at 10 to 50 CFU/vial. Recovery of test organisms from blood culture was not improved by the addition of supplements, but cultures with added supplements were identified positive an average of 5 h sooner than those without added supplements. Reliable detection of the investigational vaccine strains at <1 CFU/ml of blood within 2 days in conventional blood culture without added supplements allowed for shortened confinement time of study volunteers without compromising subject safety.
A Single Intraduodenal Administration of Human Adenovirus 40 Vaccine Effectively Prevents Anaphylactic Shock
Authors: Yamasaki Satoshi , Miura Yoshiaki , Davydova Julia , Vickers Selwyn M. , Yamamoto Masato 
Published: July 2013

ABSTRACTVaccine administration into the intestine is known to induce mucosal tolerance most efficiently. Therefore, developing a delivery system that targets the intestinal mucosa is expected to improve the efficiency of immunosuppression. Human enteric adenovirus serotype 40 (Ad40)-based vectors have the advantage of targeting intestinal mucosa, making them prime candidates as mucosal vaccine carriers for immunosuppression. Here, after both oral and intraduodenal administrations, the vector distribution of replication-defective recombinant Ad40 vectors (rAd40) was significantly higher than that of a conventional Ad vector based on human adenovirus 5 (Ad5) in ilea containing Peyer's patches. Single intraduodenal administration of rAd40 induced antigen-specific mucosal immunoreaction mediated by intestinal mucosal and systemic immunity. In ovalbumin-induced allergy mouse models, this approach inhibited antigen-specific delayed-type hypersensitivity reactions, diarrhea occurrence, and systemic anaphylaxis. Thus, a single intraduodenal administration of rAd40 provides a potent method of inducing allergen-specific mucosal tolerance and a new allergen-specific immunotherapy for overcoming problems with current therapies against life-threatening allergic reactions, including anaphylaxis.
Nonsuppurative Encephalomyelitis in a Calf in Japan and Isolation of Japanese Encephalitis Virus Genotype 1 from the Affected Calf
Authors: Katayama Takashi , Saito Sachie , Horiuchi Sanae , Maruta Tetsuya , Kato Tomoko , Yanase Tohru , Yamakawa Makoto , Shirafuji Hiroaki 
Published: July 2013

ABSTRACT
Japanese encephalitis virus (JEV) was isolated from the cerebrum of a calf which showed severe neurological symptoms in late September 2009, and the JEV isolate was revealed to be of genotype 1. This is the first report describing the isolation of genotype 1 JEV from cattle.
Phenotypic and Molecular Characterization of Optochin-Resistant Streptococcus pneumoniae Isolates from Brazil, with Description of Five Novel Mutations in the
atpC
Gene
Authors: Pinto Tatiana C. A. , Souza Aline R. V. , de Pina Sandrine E. C. M. , Costa Natália S. , Borges Neto Armando A. , Neves Felipe P. G. , Merquior Vânia L. C. , Dias Cícero A. G. , Peralta José M. , Teixeira Lúcia M. 
Published: July 2013

ABSTRACT

Optochin (Opt) susceptibility is used largely for the identification of
Streptococcus pneumoniae
in diagnostic laboratories. Opt-resistant (Opt
r
)
S. pneumoniae
isolates have been reported, however, indicating the potential for misidentification of this important pathogen. Point mutations in the
atpC
gene have been associated with the emergence of Opt
r
S. pneumoniae
, but data on the characterization of such atypical variants of
S. pneumoniae
are still limited. The present report describes the results of a polyphasic approach to identifying and characterizing 26 Opt
r
S. pneumoniae
isolates recovered from patients or carriers living in Brazil. Sixteen isolates consisted of heterogeneous populations, and 10 isolates were homogeneously Opt
r
. The isolates had different serotypes and antimicrobial susceptibility profiles. They also presented diverse genetic characteristics, as indicated by pulsed-field gel electrophoresis (PFGE), multilocus variable-number tandem-repeat analysis (MLVA), and
pspA
gene typing. Except for Opt MICs (4- to 64-fold higher among Opt
r
variants), Opt
r
and Opt-susceptible (Opt
s
) subpopulations originating from the same culture had identical characteristics. Sequencing of the
atpC
gene of the Opt
r
variants revealed 13 different nucleotide changes distributed among eight different codons. Changes in codon 49 were the most frequent, suggesting that this might be a hot spot for optochin resistance-conferring mutations. On the other hand, five novel types of mutations in the
atpC
gene (Met13Ile, Gly18Ser, Gly20Ala, Ala31Val, and Ala49Gly) were identified.
In silico
prediction modeling indicated that the
atpC
gene mutations corresponded to alterations in the transmembrane region of the ATPase, leading to a higher hydrophobicity profile in α-helix 1 and to a lower hydrophobicity profile in α-helix 2.
Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection
Authors: Lindsay Brianna , Pop Mihai , Antonio Martin , Walker Alan W. , Mai Volker , Ahmed Dilruba , Oundo Joseph , Tamboura Boubou , Panchalingam Sandra , Levine Myron M. , Kotloff Karen , Li Shan , Magder Laurence S. , Paulson Joseph N. , Liu Bo , Ikumapayi Usman , Ebruke Chinelo , Dione Michel , Adeyemi Mitchell , Rance Richard , Stares Mark D. , Ukhanova Maria , Barnes Bret , Lewis Ian , Ahmed Firoz , Alam Meer Taifur , Amin Ruhul , Siddiqui Sabbir , Ochieng John B. , Ouma Emmanuel , Juma Jane , Mailu Eunice , Omore Richard , O'Reilly Ciara E. , Hannis James , Manalili Sheri , DeLeon Jonna , Yasuda Irene , Blyn Lawrence , Ranken Raymond , Li Feng , Housley Roberta , Ecker David J. , Hossain M. Anowar , Breiman Robert F. , Morris J. Glenn , McDaniel Timothy K. , Parkhill Julian , Saha Debasish , Sampath Rangarajan , Stine O. Colin , Nataro James P. 
Published: July 2013

ABSTRACT

Cultivation-based assays combined with PCR or enzyme-linked immunosorbent assay (ELISA)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. The aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in The Gambia, Mali, Kenya, and Bangladesh. The children were identified, using currently accepted clinical protocols, as either controls or cases with moderate to severe diarrhea. A total of 3,610 stool samples were tested by established clinical culture techniques: 3,179 DNA samples by the Universal Biosensor assay (Ibis Biosciences, Inc.), 1,466 DNA samples by the GoldenGate assay (Illumina), and 1,006 DNA samples by sequencing of 16S rRNA genes. Each method detected different proportions of samples testing positive for each of seven enteric pathogens, enteroaggregative
Escherichia coli
(EAEC), enterotoxigenic
E. coli
(ETEC), enteropathogenic
E. coli
(EPEC),
Shigella
spp.,
Campylobacter jejuni
,
Salmonella enterica
, and
Aeromonas
spp. The comparisons among detection methods included the frequency of positive stool samples and kappa values for making pairwise comparisons. Overall, the standard culture methods detected
Shigella
spp., EPEC, ETEC, and EAEC in smaller proportions of the samples than either of the methods based on detection of the virulence genes from DNA in whole stools. The GoldenGate method revealed the greatest agreement with the other methods. The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens.
Recombination Is Associated with an Outbreak of Novel Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Viruses in China
Authors: Shi Mang , Holmes Edward C. , Brar Manreetpal Singh , Leung Frederick Chi-Ching 
Published: July 2013

ABSTRACT
In 2009 to 2010, there was a marked increase in the number of infections with highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) in China. Through phylogenetic analysis, we show that viruses from this outbreak originated from a single recombination event, illustrating the potential importance of this process for disease emergence.
Morphological and Biochemical Characterization of the Membranous Hepatitis C Virus Replication Compartment
Authors: Paul David , Hoppe Simone , Saher Gesine , Krijnse-Locker Jacomine , Bartenschlager Ralf 
Published: July 2013

ABSTRACT

Like all other positive-strand RNA viruses, hepatitis C virus (HCV) induces rearrangements of intracellular membranes that are thought to serve as a scaffold for the assembly of the viral replicase machinery. The most prominent membranous structures present in HCV-infected cells are double-membrane vesicles (DMVs). However, their composition and role in the HCV replication cycle are poorly understood. To gain further insights into the biochemcial properties of HCV-induced membrane alterations, we generated a functional replicon containing a hemagglutinin (HA) affinity tag in nonstructural protein 4B (NS4B), the supposed scaffold protein of the viral replication complex. By using HA-specific affinity purification we isolated NS4B-containing membranes from stable replicon cells. Complementing biochemical and electron microscopy analyses of purified membranes revealed predominantly DMVs, which contained viral proteins NS3 and NS5A as well as enzymatically active viral replicase capable of
de novo
synthesis of HCV RNA. In addition to viral factors, co-opted cellular proteins, such as vesicle-associated membrane protein-associated protein A (VAP-A) and VAP-B, that are crucial for viral RNA replication, as well as cholesterol, a major structural lipid of detergent-resistant membranes, are highly enriched in DMVs. Here we describe the first isolation and biochemical characterization of HCV-induced DMVs. The results obtained underline their central role in the HCV replication cycle and suggest that DMVs are sites of viral RNA replication. The experimental approach described here is a powerful tool to more precisely define the molecular composition of membranous replication factories induced by other positive-strand RNA viruses, such as picorna-, arteri- and coronaviruses.
Influenza A Virus PB1-F2 Protein Expression Is Regulated in a Strain-Specific Manner by Sequences Located Downstream of the PB1-F2 Initiation Codon
Authors: Buehler Jason , Navi Deepak , Lorusso Alessio , Vincent Amy , Lager Kelly , Miller Cathy L. 
Published: July 2013

ABSTRACT
Translation of influenza A virus PB1-F2 occurs in a second open reading frame (ORF) of the PB1 gene segment. PB1-F2 has been implicated in regulation of polymerase activity, immunopathology, susceptibility to secondary bacterial infection, and induction of apoptosis. Experimental evidence of PB1-F2 molecular function during infection has been collected primarily from human and avian viral isolates. As the 2009 H1N1 (H1N1pdm09) strain highlighted, some swine-derived influenza viruses have the capacity to infect human hosts and emerge as a pandemic. Understanding the impact that virulence factors from swine isolates have on both human and swine health could aid in early identification of viruses with pandemic potential. Studies examining PB1-F2 from swine isolates have focused primarily on H1N1pdm09, which does not encode PB1-F2 but was engineered to carry a full-length PB1-F2 ORF to assess the impact on viral replication and pathogenicity. However, experimental evidence of PB1-F2 protein expression from swine lineage viruses has not been demonstrated. Here, we reveal that during infection, PB1-F2 expression levels are substantially different in swine and human influenza viruses. We provide evidence that PB1-F2 expression is regulated at the translational level, with very low levels of PB1-F2 expression from swine lineage viruses relative to a human isolate PB1-F2. Translational regulation of PB1-F2 expression was partially mapped to two independent regions within the PB1 mRNA, located downstream of the PB1-F2 start site. Our data suggest that carrying a full-length PB1-F2 ORF may not be predictive of PB1-F2 expression in infected cells for all influenza A viruses.
Modulation of the Cellular Distribution of Human Cytomegalovirus Helicase by Cellular Factor Snapin
Authors: Luo Jun , Chen Jun , Yang Edward , Shen Ao , Gong Hao , Pei Zenglin , Xiao Gengfu , Lu Songya , Liu Fenyong 
Published: July 2013

ABSTRACT
Controlled regulation of genomic DNA synthesis is a universally conserved process for all herpesviruses, including human cytomegalovirus (HCMV), and plays a key role in viral pathogenesis, such as persistent infections. HCMV UL105 is believed to encode the helicase of the DNA replication machinery that needs to localize in the nuclei, the site of viral DNA synthesis. No host factors that interact with UL105 have been identified. In this study, we show that UL105 specifically interacts with Snapin, a human protein that is predominantly localized in the cytoplasm and associated with cellular vesicles. UL105 was found to interact with Snapin in both the yeast two-hybrid screen and coimmunoprecipitation experiments in HCMV-infected cells. The nuclear and cytoplasmic levels of UL105 were decreased and increased in cells overexpressing Snapin, respectively, while the levels of UL105 in the nuclei and cytoplasm were increased and decreased in cells in which the expression of Snapin was downregulated with anti-Snapin small interfering RNA (siRNA) molecules, respectively. Furthermore, viral DNA synthesis and progeny production were decreased in cells overexpressing Snapin and increased in the anti-Snapin siRNA-treated cells, respectively. Our results provide the first direct evidence to suggest that Snapin interacts with UL105 and alters its cellular distribution, leading to modulation of viral DNA synthesis and progeny production. Our study further suggests that modulation of the cellular distribution of viral helicase by Snapin may represent a possible mechanism for regulating HCMV genomic DNA synthesis, a key step during herpesvirus lytic and persistent infections.
ORIGIN OF GRANITE
Authors: GROUT FRANK F. 
Published: July 2013

As a result of wide experiences, prolonged study, and many conferences I am convinced that granites, strictly defined, form by cooling of granite magma, by metasomatic replacement of other rocks, and possibly by some intermediate action or mixture of the two processes.
Granite magmas may form from large bodies of basalt magma; or more directly by the melting of part of an earth-zone, characterized by abundant gneisses and granites—a zone that seems to have persisted from early Archean time to the present. The solutions that replace other rocks by granite are partly the granite magmas themselves and partly emanations from such magma; but the suggestion that emanations for this replacement arise from great “unknown depths” throws the discussion into the realm of speculation, which will be unprofitable until we have very strong evidence that large masses of granite result from metasomatism.
The evidences and experiences which have influenced the writer to the views he-now holds are presented in brief.
Suboptimal prescribing of proton-pump inhibitors in low-dose aspirin users: a cohort study in primary care
Authors: de Jong Hilda J I , Korevaar Joke C , van Dijk Liset , Voogd Eef , van Dijk Christel E , van Oijen Martijn G H 
Published: July 2013

ObjectiveDetermine the adherence to recommendations of concomitant proton-pump inhibitor (PPI) treatment in regular low-dose of aspirin (LDASA) users, taking factors associated with the probability of receiving a PPI into account.DesignCohort study.SettingData were obtained from 120 Dutch primary care centres participating in the Netherlands Information Network of Primary Care (LINH).ParticipantsPatients 18 years and older who were regularly prescribed LDASA (30–325 mg) in 2008–2010 were included.Main outcome measuresRegular medication use was defined as receiving each consecutive prescription within 6 months after the previous one. Based on national guidelines, we categorised LDASA users into low and high gastrointestinal (GI) risk. A multilevel multivariable logistic regression analysis was applied to identify patient characteristics that influenced on the probability of regular PPI prescriptions.ResultsWe identified 12 343 patients who started LDASA treatment, of whom 3213 (26%) were at increased risk of GI complications. In this group, concomitant regular use of PPI was 46%, 36% did not receive PPI prescriptions and 18% obtained prescriptions irregularly (p<0.0001). The chance to obtain regularly PPI prescriptions versus no PPI was significantly influenced by, among others, previous GI complications (OR 13.9 (95% CI 11.8 to 16.4)), use of non-steroidal anti-inflammatory drugs (OR 5.2 (4.3 to 6.3)), glucocorticosteroids (6.1 (4.6 to 8.0)), selective serotonin reuptake inhibitors (9.1 (6.7 to 12.2)), drugs for functional GI disorders (2.4 (1.9 to 3.0)) and increased age.ConclusionsPrimary care physicians do not fully adhere to the current recommendations to prescribe PPIs regularly to LDASA users with an increased GI risk. More than 50% of the patients with an increased GI risk are not treated sufficiently with a concomitant PPI, increasing the risk of GI side effects. This finding underlines the necessity to consider merging recommendations into one common, standard and frequently used recommendation by primary care physicians.
Honesty and euthanasia
Authors: Fordyce Peter 
Published: July 2013

THIS series gives readers the opportunity to consider and contribute to discussion of some of the ethical dilemmas that can arise in veterinary practice. Each month, a case scenario is presented, followed by discussion of some of the issues involved. In addition, a possible way forward is suggested; however, there is rarely a cut‐and‐dried answer in such cases, and readers may wish to suggest an alternative approach. This month's dilemma, ‘Honesty and euthanasia’, was submitted and is discussed by Peter Fordyce. Readers with comments to contribute are invited to send them as soon as possible, so that they can be considered for publication in the next issue. Discussion of the dilemma ‘Being a badger's advocate’, which was published in the June issue of In Practice, appears on page 423.The series is being coordinated by Siobhan Mullan, of the University of Bristol. It is hoped it will provide a framework that will help practices find solutions when facing similar dilemmas.
Evaluation of Envisat ASAR IMP imagery for snow mapping at varying spatial resolution (Deception Island, South Shetlands – Antarctica)
Authors: Mora Carla , Vieira Gonçalo , Ramos Miguel 
Published: July 2013

Abstract
Advanced synthetic aperture radar image mode precision (ASAR IMP) scenes of Deception Island from December 2008 to September 2010 have been analysed to assess its potential for snow cover classification. Backscattering was checked against ground truth. Despite the good spatial resolution of the ASAR, its applicability for detecting snow cover, and especially wet snow, was only possible at much lower resolutions, since noise was found to be very high. Scenes with bare ground or with dry snow cover showed highest backscattering, with averages from −10 to −12 dB. Wet snow showed a shift towards lower values, peaking at −15 dB. A threshold of −13 to −14 dB was identified between dry/bare ground and wet snow scenes at Crater Lake. The backscatter difference to a reference snow-free scene usually provided better classification results, and a threshold ranging from −2 to −3 dB was found. Results show that, despite the relative ease of use of C-band ASAR, special care is necessary since the results show significant noise, and it should only be applied to large areas. Large seasonal patterns of snow melt were identified on Deception Island.