bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of the Mesoplasma florum W37 Strain
Authors: Baby Vincent , Matteau Dominick , Knight Thomas F. , Rodrigue Sébastien 
Published: November 2013

ABSTRACT

Mesoplasma florum
is a small-genome fast-growing mollicute that is an attractive model for systems and synthetic genomics studies. We report the complete 825,824-bp genome sequence of a second representative of this species,
M. florum
strain W37, which contains 733 predicted open reading frames and 35 stable RNAs.
Draft Genome Sequence of Mycobacterium bovis 04-303, a Highly Virulent Strain from Argentina
Authors: Nishibe Christiane , Canevari Castelão Ana Beatriz , Dalla Costa Ricardo , Pinto Beatriz Jeronimo , Varuzza Leonardo , Cataldi Angel Adrian , Bernardelli Amelia , Bigi Fabiana , Blanco Federico Carlos , Zumárraga Martín José , Almeida Nalvo Franco , Araújo Flábio Ribeiro 
Published: November 2013

ABSTRACT

Mycobacterium bovis
strain 04-303 was isolated from a wild boar living in a free-ranging field in Argentina. This work reports the draft genome sequence of this highly virulent strain and the genomic comparison of its major virulence-related genes with those of
M. bovis
strain AF2122/97 and
Mycobacterium tuberculosis
strain H37Rv.
Whole-Genome Analysis of Influenza B Viruses of Multiple Genotypes Cocirculating in India
Authors: Patil Kunal N. , Bhise Atul B. , Dakhave Minal R. , Kadam Archana A. , Chadha Mandeep S. , Potdar Varsha A. 
Published: November 2013

ABSTRACT
Systematic influenza virus surveillance has been carried out in India since 2004 and has revealed the cocirculation of type B lineages. The genetic diversity of influenza B viruses was observed when full-genome analysis was performed. In 2010, the cocirculation of multiple genotypes was observed.
Complete Genome Sequence of Lactococcus lactis subsp.
lactis
KLDS4.0325
Authors: Yang Xiaochun , Wang Yutang , Huo Guicheng 
Published: November 2013

ABSTRACT

We report the complete genome sequence of
Lactococcus lactis
subsp.
lactis
KLDS4.0325, a probiotic bacterium isolated from homemade koumiss in Xinjiang, China. We have determined the complete genome sequence of strain KLDS4.0325, which consists of a chromosome and three plasmids and reveals genes that are likely to be involved in dairy fermentation and that have probiotic qualities.
Genome Sequences of Five B1 Subcluster Mycobacteriophages
Authors: Breakwell Donald P. , Barrus E. Zane , Benedict Alex B. , Brighton Alicia K. , Fisher Joshua N. B. , Gardner Adam V. , Kartchner Brittany J. , Ladle Kara C. , Lunt Bryce L. , Merrill Bryan D. , Morrell John D. , Burnett Sandra H. , Grose Julianne H. 
Published: November 2013

ABSTRACT

Mycobacteriophages infect members of the
Mycobacterium
genus in the phylum
Actinobacteria
and exhibit remarkable diversity. Genome analysis groups the thousands of known mycobacteriophages into clusters, of which the B1 subcluster is currently the third most populous. We report the complete genome sequences of five additional members of the B1 subcluster.
Complete Genome Sequence of
Carnobacterium gilichinskyi
Strain WN1359
T
(DSM 27470
T
)
Authors: Leonard Michael T. , Panayotova Nedka , Farmerie William G. , Triplett Eric W. , Nicholson Wayne L. 
Published: November 2013

ABSTRACT

We report the complete genome sequence of
Carnobacterium gilichinskyi
strain WN1359, previously isolated from Siberian permafrost and capable of growth under cold (0°C), anoxic, CO
2
-dominated, low-pressure (0.7-kPa) conditions in a simulation of the Mars atmosphere.
Draft Genome Sequence of
Pseudomonas
sp. Strain CMAA 1215, a Plant Growth-Promoting Bacterium Isolated from a Brazilian Mangrove
Authors: Vasconcellos Rafael L. F. , Mendes Rodrigo , Taketani Rodrigo G. , Zucchi Tiago D. , Melo Itamar Soares 
Published: November 2013

ABSTRACT

The aim of this study was to sequence the genome of the plant growth-promoting
Pseudomonas
sp. strain CMAA 1215, an osmotolerant bacterium isolated from mangrove soil.
Complete Genome Sequence of the Solvent Producer Clostridium saccharobutylicum NCP262 (DSM 13864)
Authors: Poehlein Anja , Hartwich Katrin , Krabben Preben , Ehrenreich Armin , Liebl Wolfgang , Dürre Peter , Gottschalk Gerhard , Daniel Rolf 
Published: November 2013

ABSTRACT

Clostridium saccharobutylicum
was employed for the production of acetone and butanol in South Africa until the 1970s. The genome comprises a single replicon (5,107,814 bp) harboring all the genes necessary for solvent production and the degradation of various organic compounds, such as fructose, cellobiose, sucrose, and mannose.
Draft Genome Sequence of Lactobacillus fermentum Strain 3872
Authors: Karlyshev Andrey V. , Raju Kavita , Abramov Vyacheslav M. 
Published: November 2013

ABSTRACT

This report describes a draft genome sequence of
Lactobacillus fermentum
strain 3872. The data revealed remarkable similarity to and dissimilarity with the published genome sequences of other strains of the species. The absence of and variation in structures of some adhesins and the presence of an additional adhesin may reflect adaptation of the bacterium to different host systems and may contribute to specific properties of this strain as a new probiotic.
Pyrosequencing for Rapid Detection of Extensively Drug-Resistant Mycobacterium tuberculosis in Clinical Isolates and Clinical Specimens
Authors: Lin S.-Y. Grace , Rodwell Timothy C. , Victor Thomas C. , Rider Errin C. , Pham Lucy , Catanzaro Antonino , Desmond Edward P. 
Published: November 2013

ABSTRACT

Treating extensively drug-resistant (XDR) tuberculosis (TB) is a serious challenge. Culture-based drug susceptibility testing (DST) may take 4 weeks or longer from specimen collection to the availability of results. We developed a pyrosequencing (PSQ) assay including eight subassays for the rapid identification of
Mycobacterium tuberculosis
complex (MTBC) and concurrent detection of mutations associated with resistance to drugs defining XDR TB. The entire procedure, from DNA extraction to the availability of results, was accomplished within 6 h. The assay was validated for testing clinical isolates and clinical specimens, which improves the turnaround time for molecular DST and maximizes the benefit of using molecular testing. A total of 130 clinical isolates and 129 clinical specimens were studied. The correlations between the PSQ results and the phenotypic DST results were 94.3% for isoniazid, 98.7% for rifampin, 97.6% for quinolones (ofloxacin, levofloxacin, or moxifloxacin), 99.2% for amikacin, 99.2% for capreomycin, and 96.4% for kanamycin. For testing clinical specimens, the PSQ assay yielded a 98.4% sensitivity for detecting MTBC and a 95.8% sensitivity for generating complete sequencing results from all subassays. The PSQ assay was able to rapidly and accurately detect drug resistance mutations with the sequence information provided, which allows further study of the association of drug resistance or susceptibility with each mutation and the accumulation of such knowledge for future interpretation of results. Thus, reporting of false resistance for mutations known not to confer resistance can be prevented, which is a significant benefit of the assay over existing molecular diagnostic methods endorsed by the World Health Organization.
Clinical and Virologic Factors Associated with Reduced Sensitivity of Rapid Influenza Diagnostic Tests in Hospitalized Elderly Patients and Young Children
Authors: Chan Martin C. W. , Lee Nelson , Ngai Karry L. K. , Leung Ting F. , Chan Paul K. S. 
Published: November 2013

ABSTRACTRapid influenza diagnostic tests (RIDTs) are commonly used by clinicians to guide patient management. Data on sensitivities among hospitalized patients are limited. Here, we evaluated the clinical and virologic factors affecting the sensitivities of 2 commercially available RIDTs (BinaxNOW Influenza A&B and QuickVue Influenza A+B) on nasopharyngeal aspirate (NPA) specimens collected from elderly patients and young children hospitalized for influenza. Influenza cases and age-matched negative controls were prospectively enrolled during the 2011-2012 influenza season in Hong Kong. NPA specimens were collected at presentation before antiviral treatment. Real-time reverse transcription-PCR (RT-PCR) results were used as references for the sensitivity analyses. One hundred patients (57 influenza cases and 43 controls) were studied. Both RIDTs had 100% specificities. The sensitivities of the BinaxNOW Influenza A&B and QuickVue Influenza A+B tests were 70% and 82%, respectively. For both tests, the sensitivities were lower in cases with presentation times beyond 2 days of illness onset than for those within this time (50 to 71% versus 85 to 91%, respectively). There were trends toward lower sensitivities for influenza B than for influenza A (66 to 81% versus 76 to 84%, respectively), among young children than among the elderly patients (63 to 78% versus 80 to 88%, respectively), and among cases with pneumonia than those without pneumonia (75% versus 82 to 94%, respectively). The sensitivities of the RIDTs decreased with reduced NPA viral RNA levels (5.6 to 15.0% reduction per 1-log decrease), which declined progressively after illness onset (Spearman's rho, −0.47 [P< 0.05] and −0.66 [P< 0.001] for influenza A and B, respectively). Collectively, late presentation, a low NPA viral load, and probably lower respiratory manifestation are factors associated with reduced sensitivities of RIDTs for diagnosing influenza in hospitalized patients. A negative RIDT result should be interpreted with caution.
Xpert GBS Assay for Rapid Detection of Group B Streptococcus in Gastric Fluid Samples from Newborns
Authors: Jost Christelle , Bercot Béatrice , Jacquier Hervé , Raskine Laurent , Barranger Emmanuel , Mouchnino Geneviève , Cambau Emmanuelle 
Published: November 2013

ABSTRACT
The Xpert GBS real-time PCR assay was applied to gastric fluid samples from 143 newborns, and it detected group B streptococcus (GBS) within 1 h for 16 (11.2%) cases, while microscopic examination detected only 2 cases. The sensitivity and specificity of the Xpert GBS were 80% and 100%, respectively, with regard to 20 cases of GBS colonization or infection. Concordance of Xpert GBS results versus culture was 92.3%. This test detects in a timely manner newborns at risk for invasive GBS disease.
Development of a Loop-Mediated Isothermal Amplification Method for Detection of Histoplasma capsulatum DNA in Clinical Samples
Authors: Scheel Christina M. , Zhou Yitian , Theodoro Raquel C. , Abrams Bethany , Balajee S. Arunmozhi , Litvintseva Anastasia P. 
Published: November 2013

ABSTRACT

Improved methods for the detection of
Histoplasma capsulatum
are needed in regions with limited resources in which the organism is endemic, where delayed diagnosis of progressive disseminated histoplasmosis (PDH) results in high mortality rates. We have investigated the use of a loop-mediated isothermal amplification (LAMP) assay to facilitate rapid inexpensive molecular diagnosis of this disease. Primers for LAMP were designed to amplify the
Hcp100
locus of
H. capsulatum
. The sensitivity and limit of detection were evaluated using DNA extracted from 91 clinical isolates of known geographic subspecies, while the assay specificity was determined using DNA extracted from 50 other fungi and
Mycobacterium tuberculosis
. Urine specimens (
n
= 6) collected from HIV-positive individuals with culture- and antigen-proven histoplasmosis were evaluated using the LAMP assay. Specimens from healthy persons (
n
= 10) without evidence of histoplasmosis were used as assay controls. The
Hcp100
LAMP assay was 100% sensitive and specific when tested with DNA extracted from culture isolates. The median limit of detection was ≤6 genomes (range, 1 to 300 genomes) for all except one geographic subspecies. The LAMP assay detected
Hcp100
in 67% of antigen-positive urine specimens (4/6 specimens), and results were negative for
Hcp100
in all healthy control urine specimens. We have shown that the
Hcp100
LAMP assay is a rapid affordable assay that can be used to expedite culture confirmation of
H. capsulatum
in regions in which PDH is endemic. Further, our results indicate proof of the concept that the assay can be used to detect
Histoplasma
DNA in urine. Further evaluation of this assay using body fluid samples from a larger patient population is warranted.
Economic Evaluation of Laboratory Testing Strategies for Hospital-Associated Clostridium difficile Infection
Authors: Schroeder Lee F. , Robilotti Elizabeth , Peterson Lance R. , Banaei Niaz , Dowdy David W. 
Published: November 2013

ABSTRACT

Clostridium difficile
infection (CDI) is the most common cause of infectious diarrhea in health care settings, and for patients presumed to have CDI, their isolation while awaiting laboratory results is costly. Newer rapid tests for CDI may reduce this burden, but the economic consequences of different testing algorithms remain unexplored. We used decision analysis from the hospital perspective to compare multiple CDI testing algorithms for adult inpatients with suspected CDI, assuming patient management according to laboratory results. CDI testing strategies included combinations of on-demand PCR (odPCR), batch PCR, lateral-flow diagnostics, plate-reader enzyme immunoassay, and direct tissue culture cytotoxicity. In the reference scenario, algorithms incorporating rapid testing were cost-effective relative to nonrapid algorithms. For every 10,000 symptomatic adults, relative to a strategy of treating nobody, lateral-flow glutamate dehydrogenase (GDH)/odPCR generated 831 true-positive results and cost $1,600 per additional true-positive case treated. Stand-alone odPCR was more effective and more expensive, identifying 174 additional true-positive cases at $6,900 per additional case treated. All other testing strategies were dominated by (i.e., more costly and less effective than) stand-alone odPCR or odPCR preceded by lateral-flow screening. A cost-benefit analysis (including estimated costs of missed cases) favored stand-alone odPCR in most settings but favored odPCR preceded by lateral-flow testing if a missed CDI case resulted in less than $5,000 of extended hospital stay costs and <2 transmissions, if lateral-flow GDH diagnostic sensitivity was >93%, or if the symptomatic carrier proportion among the toxigenic culture-positive cases was >80%. These results can aid guideline developers and laboratory directors who are considering rapid testing algorithms for diagnosing CDI.
Differential Inhibitory Effects of Cyanovirin-N, Griffithsin, and Scytovirin on Entry Mediated by Envelopes of Gammaretroviruses and Deltaretroviruses
Authors: Jensen Stig M. R. , Ruscetti Francis W. , Rein Alan , Bertolette Daniel C. , Saucedo Carrie J. , O'Keefe Barry R. , Jones Kathryn S. 
Published: November 2013

ABSTRACT
The antiviral lectins griffithsin (GRFT), cyanovirin-N (CV-N), and scytovirin (SVN), which inhibit several enveloped viruses, including lentiviruses, were examined for their ability to inhibit entry mediated by Env proteins of delta- and gammaretroviruses. The glycoproteins from human T-cell leukemia virus type 1 (HTLV-1) were resistant to the antiviral effects of all three lectins. For gammaretroviruses, CV-N inhibited entry mediated by some but not all of the envelopes examined, whereas GRFT and SVN displayed only little or no effect.
In VivoElectroporation of Minicircle DNA as a Novel Method of Vaccine Delivery To Enhance HIV-1-Specific Immune Responses
Authors: Wang Qingtao , Jiang Wei , Chen Yuhai , Liu Pengyu , Sheng Chunjie , Chen Shuai , Zhang Hui , Pan Changchuan , Gao Shijuan , Huang Wenlin 
Published: November 2013

ABSTRACTDNA vaccines offer advantage over conventional vaccines, as they are safer to use, easier to produce, and able to induce humoral as well cellular immune responses. Unfortunately, no DNA vaccines have been licensed for human use for the difficulties in developing an efficient and safein vivogene delivery system.In vivoelectroporation (EP)-based DNA delivery has attracted great attention for its potency to enhance cellular uptake of DNA vaccines and function as an adjuvant. Minicircle DNA (a new form of DNA containing only a gene expression cassette and lacking a backbone of bacterial plasmid DNA) is a powerful candidate of gene delivery in terms of improving the levels and the duration of transgene expressionin vivo. In this study, as a novel vaccine delivery system, we combinedin vivoEP and the minicircle DNA carrying a codon-optimized HIV-1gaggene (minicircle-gag) to evaluate the immunogenicity of this system. We found that minicircle-gag conferred persistent and high levels of gag expressionin vitroandin vivo. The use of EP delivery further increased minicircle-based gene expression. Moreover, when delivered by EP, minicircle-gag vaccination elicited a 2- to 3-fold increase in cellular immune response and a 1.5- to 3-fold augmentation of humoral immune responses compared with those elicited by a pVAX1-gag positive control. Increased immunogenicity of EP-assisted minicircle-gag may benefit from increasing local antigen expression, upregulating inflammatory genes, and recruiting immune cells. Collectively,in vivoEP of minicircle DNA functions as a novel vaccine platform that can enhance efficacy and immunogenicity of DNA vaccines.
The Rigid Amphipathic Fusion Inhibitor dUY11 Acts through Photosensitization of Viruses
Authors: Vigant Frederic , Hollmann Axel , Lee Jihye , Santos Nuno C. , Jung Michael E. , Lee Benhur 
Published: November 2013

ABSTRACT

Rigid amphipathic fusion inhibitors (RAFIs) are lipophilic inverted-cone-shaped molecules thought to antagonize the membrane curvature transitions that occur during virus-cell fusion and are broad-spectrum antivirals against enveloped viruses (Broad-SAVE). Here, we show that RAFIs act like membrane-binding photosensitizers: their antiviral effect is dependent on light and the generation of singlet oxygen (
1
O
2
), similar to the mechanistic paradigm established for LJ001, a chemically unrelated class of Broad-SAVE. Photosensitization of viral membranes is a common mechanism that underlies these Broad-SAVE.
Joint effects of serum ferritin and body mass index on the risk of coronary artery disease: a case–control study
Authors: Zhou Yunping , Liu Tongtao , Jia Chongqi 
Published: November 2013

ObjectivesSerum ferritin and body mass index (BMI) have been reportedly associated with coronary artery disease (CAD) risk. The aim of the present study was to explore the interaction between serum ferritin and BMI on CAD risk.DesignHospital-based case–control study.SettingPatients with CAD and the controls were recruited from Qilu Hospital, Shandong University.Participants258 CAD cases and 282 healthy controls.MethodsMultiplicative interaction was assessed through a cross-product interaction term in a multivariate logistic regression model. The effect of serum ferritin and BMI were evaluated per 50 µg/L and per 2 kg/m2, respectively. The presence of additive interaction between serum ferritin and BMI was evaluated by calculation of the relative excess risk due to interaction (RERI), attributable proportion due to interaction (AP) and synergy index (S).ResultsThe ORs and 95% CI of the serum ferritin–BMI product term on a multiplicative scale in the univariate and multivariate models were 0.943 (0.904 to 0.984) and 1.004 (0.951 to 1.059), respectively. There was also evidence for interaction on an additive scale; the RERI (95% CI), AP (95% CI) and S (95% CI) in the univariate model were 0.314 (0.026 to 1.506), 0.107 (0.017 to 0.241) and 1.194 (1.053 to 1.406), respectively. After adjusting for the potential confounders, the estimates and 95% CIs for the aforementioned three measures were 0.004 (−0.016 to 0.311), 0.004 (−0.016 to 0.191) and 1.039 (0.774 to 1.285), respectively.ConclusionsSerum ferritin and BMI had an additive interaction on the risk of CAD in Chinese population. Further investigations with big sample size are necessary for confirming this additive interaction.
A descriptive study of access to services in a random sample of Canadian rural emergency departments
Authors: Fleet Richard , Poitras Julien , Maltais-Giguère Julie , Villa Julie , Archambault Patrick 
Published: November 2013

ObjectiveTo examine 24/7 access to services and consultants in a sample of Canadian rural emergency departments (EDs).DesignCross-sectional study—mixed methods (structured interview, survey and government data bases) with random sampling of hospitals.SettingCanadian rural EDs (rural small town (RST) definition—Statistics Canada).Participants28% (95/336) of Canadian rural EDs providing 24/7 physician coverage located in hospitals with acute care hospitalisation beds.Main outcome measuresGeneral characteristics of the rural EDs, information about 24/7 access to consultants, equipment and services, and the proportion of rural hospitals more than 300 km from levels 1 and 2 trauma centres.ResultsOf the 336 rural EDs identified, 122 (36%) were randomly selected and contacted. Overall, 95 EDs participated in the study (participation rate, 78%). Hospitals had, on an average, 23 acute care beds, 7 ED stretchers and 13 500 annual ED visits. The proportion of rural hospitals with local access to the following 24/7 services was paediatrician, 5%; obstetrician, 10%; psychiatrist, 11%; internist, 12%; intensive care unit, 17%; CT scanner, 20%; surgeon, 26%; ultrasound, 28%; basic X-ray, 97% and laboratory services, 99%. Forty-four per cent and 54% of the RST EDs were more than 300 km from a level 1 and level 2 trauma centre, respectively.ConclusionsThis is the first study describing the services available in Canadian rural EDs. Apart from basic laboratory and X-ray services, most rural EDs have limited access to consultants, advanced imaging and critical care services. A detailed study is needed to evaluate the impact of these limited services on patient outcomes, costs and interfacility transport demands.
Urinary bisphenol A concentrations are associated with abnormal liver function in the elderly: a repeated panel study
Authors: Lee Mee-Ri , Park Hyunseung , Bae Sanghyuk , Lim Youn-Hee , Kim Jin Hee , Cho Soo-Hun , Hong Yun-Chul 
Published: November 2013

BackgroundBisphenol A (4,40-isopropylidenediphenol, BPA) is known to adversely affect various organs. The liver is reported to be affected by BPA in animal studies. However, there are few studies in humans on the effects of BPA on the liver. Therefore, we evaluated the relationship between urinary BPA levels and liver function in elderly subjects using repeated measurements.MethodsFrom 2008 to 2010, a total of 560 elderly subjects residing in Seoul were each evaluated up to three times. At the first visit, demographic data, environmental exposure and lifestyle information were obtained from a systemised questionnaire. At each visit, blood and urine samples were collected and stored for analysis. Linear mixed and GLIMMIX model analyses were performed after adjusting for age, sex, Body Mass Index, alcohol consumption, urinary cotinine concentrations, exercise frequency, and low-density lipoprotein cholesterol level.ResultsThe mean urinary BPA concentration was 1.13 μg/g creatinine. Significant relationships were observed between urinary BPA and aspartate aminotransferase, alanine aminotransferase, and gamma-glutamyl transferase after adjusting for potential confounders (p<0.05). When subjects were grouped according to urinary BPA concentrations divided by the median value, higher urinary BPA concentrations were associated with increased abnormal liver function (OR 2.66; 95% CI 1.15 to 5.90).ConclusionsCommunity-level exposure to BPA was associated with abnormal liver function in the elderly, indicating that more stringent control of BPA is necessary to protect susceptible populations.