bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct Observation is a Valid Criterion for Estimating Physical Activity and Sedentary Behavior
Authors: Lyden Kate , Petruski Natalia , Mix Stephanie , Staudenmayer John , Freedson Patty 
Published: July 2014

Background:Physical activity and sedentary behavior measurement tools need to be validated in free-living settings. Direct observation (DO) may be an appropriate criterion for these studies. However, it is not known if trained observers can correctly judge the absolute intensity of free-living activities.Purpose:To compare DO estimates of total MET-hours and time in activity intensity categories to a criterion measure from indirect calorimetry (IC).Methods:Fifteen participants were directly observed on three separate days for two hours each day. During this time participants wore an Oxycon Mobile indirect calorimeter and performed any activity of their choice within the reception area of the wireless metabolic equipment. Participants were provided with a desk for sedentary activities (writing, reading, computer use) and had access to exercise equipment (treadmill, bike).Results:DO accurately and precisely estimated MET-hours [% bias (95% CI) = –12.7% (–16.4, –7.3), ICC = 0.98], time in low intensity activity [% bias (95% CI) = 2.1% (1.1, 3.2), ICC = 1.00] and time in moderate to vigorous intensity activity [% bias (95% CI) –4.9% (–7.4, –2.5), ICC = 1.00].Conclusion:This study provides evidence that DO can be used as a criterion measure of absolute intensity in free-living validation studies.
Dietary Rice Bran Protects against Rotavirus Diarrhea and Promotes Th1-Type Immune Responses to Human Rotavirus Vaccine in Gnotobiotic Pigs
Authors: Yang Xingdong , Wen Ke , Tin Christine , Li Guohua , Wang Haifeng , Kocher Jacob , Pelzer Kevin , Ryan Elizabeth , Yuan Lijuan 
Published: July 2014

ABSTRACT

Rice bran (RB) contains a distinct stoichiometry of phytochemicals that can promote gut mucosal immune responses against enteric pathogens. The effects of RB on rotavirus diarrhea and immunogenicity of an attenuated human rotavirus (HRV) vaccine were evaluated in gnotobiotic pigs. The four treatment groups studied were RB plus vaccine, vaccine only, RB only, and mock control. Pigs in the RB groups were fed the amount of RB that replaced 10% of the pigs' total daily calorie intake from milk starting from 5 days of age until they were euthanized. Pigs in the vaccine groups were orally inoculated with two doses of the attenuated HRV vaccine. A subset of pigs from each group was orally challenged with the homologous virulent HRV on postinoculation day 28. Diarrhea and virus shedding were monitored daily from postchallenge day 0 to day 7. RB feeding significantly protected against diarrhea upon virulent HRV challenge and enhanced the protective rate of the vaccine against rotavirus diarrhea. Consistent with protection, RB significantly increased gamma interferon (IFN-γ)-producing CD4
+
and CD8
+
T cell responses in intestinal and systemic lymphoid tissues. Furthermore, RB also increased the number of total IgM- and IgA-secreting cells, total serum IgM, IgG, and IgA titers, and HRV-specific IgA titers in intestinal contents. RB reduced the numbers of intestinal and systemic HRV-specific IgA and IgG antibody-secreting cells and reduced serum HRV-specific IgA and IgG antibody titers before the challenge. These results demonstrate clear beneficial effects of RB in protection against rotavirus diarrhea and stimulation of nonspecific and HRV-specific immune responses, as well as its biased Th1-type adjuvant effect for the vaccine.
Recombinant Mycobacterium bovis Bacillus Calmette-Guérin Vectors Prime for Strong Cellular Responses to Simian Immunodeficiency Virus Gag in Rhesus Macaques
Authors: Sixsmith Jaimie D. , Panas Michael W. , Lee Sunhee , Gillard Geoffrey O. , White KeriAnn , Lifton Michelle A. , Balachandran Harikrishnan , Mach Linh , Miller John P. , Lavine Christy , DeMarco C. Todd , Tomaras Georgia D. , Gee Connie , Porcelli Steven A. , Larsen Michelle H. , Frothingham Richard , Schmitz Joern E. , Jacobs William R. , Haynes Barton F. , Letvin Norman L. , Korioth-Schmitz Birgit 
Published: July 2014

ABSTRACTLive attenuated nonpathogenicMycobacterium bovisbacillus Calmette-Guérin (BCG) mediates long-lasting immune responses, has been safely administered as a tuberculosis vaccine to billions of humans, and is affordable to produce as a vaccine vector. These characteristics make it very attractive as a human immunodeficiency virus (HIV) vaccine vector candidate. Here, we assessed the immunogenicity of recombinant BCG (rBCG) constructs with different simian immunodeficiency virus (SIV)gagexpression cassettes as priming agents followed by a recombinant replication-incompetent New York vaccinia virus (NYVAC) boost in rhesus macaques. Unmutated rBCG constructs were used in comparison to mutants with gene deletions identified in anin vitroscreen for augmented immunogenicity. We demonstrated that BCG-SIVgagis able to elicit robust transgene-specific priming responses, resulting in strong SIV epitope-specific cellular immune responses. While enhanced immunogenicity was sustained at moderate levels for >1 year following the heterologous boost vaccination, we were unable to demonstrate a protective effect after repeated rectal mucosal challenges with pathogenic SIVmac251. Our findings highlight the potential for rBCG vaccines to stimulate effective cross-priming and enhanced major histocompatibility complex class I presentation, suggesting that combining this approach with other immunogens may contribute to the development of effective vaccine regimens against HIV.
Group A Streptococcus Expresses a Trio of Surface Proteins Containing Protective Epitopes
Authors: Niedermeyer Shannon E. , Penfound Thomas A. , Hohn Claudia , Li Yi , Homayouni Ramin , Zhao Jingnan , Dale James B. 
Published: July 2014

ABSTRACTGroup A streptococci (GAS) (Streptococcus pyogenes) are common causes of infections in humans for which there is no licensed vaccine. Decades of work has focused on the role of the surface M protein in eliciting type-specific protective immunity. Recent studies have identified additional surface proteins of GAS that contain opsonic epitopes. In the present study, we describe a serotype M65 GAS originally isolated during an epidemiologic study in Bamako, Mali, which simultaneously expressed M, M-related protein (Mrp), and streptococcal protective antigen (Spa) on the bacterial surface. Theemm,mrp, andspagenes were sequenced from PCR amplicons derived from the M65 chromosome. Rabbit antisera raised against synthetic peptides copying the N-terminal regions of M, Mrp, and Spa were highly specific for each peptide, reacted with the surface of M65 GAS, and promoted bactericidal activity against the organism. A mixture of antisera against all three peptides was most effective in the bactericidal assays. Immunofluorescence microscopy revealed that the M, Mrp, and Spa antisera bound to the bacterial surface in the presence of human plasma proteins and resulted in the deposition of complement. Five additionalspagenes were identified in the Mrp-positive GAS serotypes, and their sequences were determined. Our results indicate that there are multiple antigens on the surface of GAS that evoke antibodies that promote bacterial killing. A more complete understanding of the relative contributions of M, Mrp, and Spa in eliciting protective immunity may aid in the development of GAS vaccines with enhanced coverage and efficacy.
Analysis of Culture-Dependent versus Culture-Independent Techniques for Identification of Bacteria in Clinically Obtained Bronchoalveolar Lavage Fluid
Authors: Dickson Robert P. , Erb-Downward John R. , Prescott Hallie C. , Martinez Fernando J. , Curtis Jeffrey L. , Lama Vibha N. , Huffnagle Gary B. 
Published: July 2014

ABSTRACT

The diagnosis and management of pneumonia are limited by the use of culture-based techniques of microbial identification, which may fail to identify unculturable, fastidious, and metabolically active viable but unculturable bacteria. Novel high-throughput culture-independent techniques hold promise but have not been systematically compared to conventional culture. We analyzed 46 clinically obtained bronchoalveolar lavage (BAL) fluid specimens from symptomatic and asymptomatic lung transplant recipients both by culture (using a clinical microbiology laboratory protocol) and by bacterial 16S rRNA gene pyrosequencing. Bacteria were identified in 44 of 46 (95.7%) BAL fluid specimens by culture-independent sequencing, significantly more than the number of specimens in which bacteria were detected (37 of 46, 80.4%,
P
≤ 0.05) or “pathogen” species reported (18 of 46, 39.1%,
P
≤ 0.0001) via culture. Identification of bacteria by culture was positively associated with culture-independent indices of infection (total bacterial DNA burden and low bacterial community diversity) (
P
≤ 0.01). In BAL fluid specimens with no culture growth, the amount of bacterial DNA was greater than that in reagent and rinse controls, and communities were markedly dominated by select
Gammaproteobacteria
, notably
Escherichia
species and
Pseudomonas fluorescens
. Culture growth above the threshold of 10
4
CFU/ml was correlated with increased bacterial DNA burden (
P
< 0.01), decreased community diversity (
P
< 0.05), and increased relative abundance of
Pseudomonas aeruginosa
(
P
< 0.001). We present two case studies in which culture-independent techniques identified a respiratory pathogen missed by culture and clarified whether a cultured “oral flora” species represented a state of acute infection. In summary, we found that bacterial culture of BAL fluid is largely effective in discriminating acute infection from its absence and identified some specific limitations of BAL fluid culture in the diagnosis of pneumonia. We report the first correlation of quantitative BAL fluid culture results with culture-independent evidence of infection.
Endotracheal Aspirate and Bronchoalveolar Lavage Fluid Analysis: Interchangeable Diagnostic Modalities in Suspected Ventilator-Associated Pneumonia?
Authors: Scholte Johannes B. J. , van Dessel Helke A. , Linssen Catharina F. M. , Bergmans Dennis C. J. J. , Savelkoul Paul H. M. , Roekaerts Paul M. H. J. , van Mook Walther N. K. A. 
Published: July 2014

ABSTRACTAuthoritative guidelines state that the diagnosis of ventilator-associated pneumonia (VAP) can be established using either endotracheal aspirate (ETA) or bronchoalveolar lavage fluid (BALF) analysis, thereby suggesting that their results are considered to be in accordance. Therefore, the results of ETA Gram staining and semiquantitative cultures were compared to the results from a paired ETA-BALF analysis. Different thresholds for the positivity of ETAs were assessed. This was a prospective study of all patients who underwent bronchoalveolar lavage for suspected VAP in a 27-bed university intensive care unit during an 8-year period. VAP was diagnosed when ≥2% of the BALF cells contained intracellular organisms and/or when BALF quantitative culture revealed ≥104CFU/ml of potentially pathogenic microorganisms. ETA Gram staining and semiquantitative cultures were compared to the results from paired BALF analysis by Cohen's kappa coefficients. VAP was suspected in 311 patients and diagnosed in 122 (39%) patients. In 288 (93%) patients, the results from the ETA analysis were available for comparison. Depending on the threshold used and the diagnostic modality, VAP incidences varied from 15% to 68%. For the diagnosis of VAP, the most accurate threshold for positivity of ETA semiquantitative cultures was moderate or heavy growth, whereas the optimal threshold for BALF Gram staining was ≥1 microorganisms per high power field. The Cohen's kappa coefficients were 0.22, 0.31, and 0.60 for ETA and paired BALF Gram stains, cultures, and BALF Gram stains, respectively. Since the ETA and BALF Gram stains and cultures agreed only fairly, they are probably not interchangeable for diagnosing VAP.
Cryptic and Rare Aspergillus Species in Brazil: Prevalence in Clinical Samples and
In Vitro
Susceptibility to Triazoles
Authors: Negri C. E. , Gonçalves S. S. , Xafranski H. , Bergamasco M. D. , Aquino V. R. , Castro P. T. O. , Colombo A. L. 
Published: July 2014

ABSTRACT

Aspergillus
spp. are among the most common causes of opportunistic invasive fungal infections in tertiary care hospitals. Little is known about the prevalence and
in vitro
susceptibility of
Aspergillus
species in Latin America, because there are few medical centers able to perform accurate identification at the species level. The purpose of this study was to analyze the distribution of cryptic and rare
Aspergillus
species among clinical samples from 133 patients with suspected aspergillosis admitted in 12 medical centers in Brazil and to analyze the
in vitro
activity of different antifungal drugs. The identification of
Aspergillus
species was performed based on a polyphasic approach, as well as sequencing analysis of the internal transcribed spacer (ITS) region, calmodulin, and β-tubulin genes and phylogenetic analysis when necessary. The
in vitro
susceptibility tests with voriconazole, posaconazole, and itraconazole were performed according to the CLSI M38-A2 document (2008). We demonstrated a high prevalence of cryptic species causing human infection. Only three isolates, representing the species
Aspergillus thermomutatus
,
A. ochraceus
, and
A. calidoustus
, showed less
in vitro
susceptibility to at least one of the triazoles tested. Accurate identifications of
Aspergillus
at the species level and with
in vitro
susceptibility tests are important because some species may present unique resistance patterns against specific antifungal drugs.
Rapid Inactivation of Mycobacterium and Nocardia Species before Identification Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Dunne W. Michael , Doing Kirk , Miller Elizabeth , Miller Eric , Moreno Erik , Baghli Mehdi , Mailler Sandrine , Girard Victoria , van Belkum Alex , Deol Parampal 
Published: July 2014

ABSTRACT

The identification of mycobacteria outside biocontainment facilities requires that the organisms first be rendered inactive. Exposure to 70% ethanol (EtOH) either before or after mechanical disruption was evaluated in order to establish a safe, effective, and rapid inactivation protocol that is compatible with identification of
Mycobacterium
and
Nocardia
species using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). A combination of 5 min of bead beating in 70% EtOH followed by a 10-min room temperature incubation period was found to be rapidly bactericidal and provided high-quality spectra compared to spectra obtained directly from growth on solid media. The age of the culture, the stability of the refrigerated or frozen lysates, and freeze-thaw cycles did not adversely impact the quality of the spectra or the identification obtained.
Engineering Recombinant Orsay Virus Directly in the Metazoan Host Caenorhabditis elegans
Authors: Jiang Hongbing , Franz Carl J. , Wang David 
Published: July 2014

ABSTRACT

The recent identification of Orsay virus, the first virus that is capable of naturally infecting
Caenorhabditis elegans
, provides a unique opportunity to explore host-virus interaction studies in this invaluable model organism. A key feature of this system is the robust genetic tractability of the host,
C. elegans
, which would ideally be complemented by the ability to genetically manipulate Orsay virus in parallel. To this end, we developed a plasmid-based reverse genetics system for Orsay virus by creating transgenic
C. elegans
strains harboring Orsay virus cDNAs. Both wild-type and mutant Orsay viruses, including a FLAG epitope-tagged recombinant Orsay virus, were generated by use of the reverse genetics system. This is the first plasmid-based virus reverse genetics system in the metazoan
C. elegans
. The Orsay virus reverse genetics we established will serve as a fundamental tool in host-virus interaction studies in the model organism
C. elegans
.

IMPORTANCE
To date, Orsay virus is the first and the only identified virus capable of naturally infecting
Caenorhabditis elegans
.
C. elegans
is a simple multicellular model organism that mimics many fundamental features of human biology and has been used to define many biological properties conserved through evolution. Thus, the Orsay virus-
C. elegans
infection system provides a unique opportunity to study host-virus interactions. In order to take maximal advantage of this system, the ability to genetically engineer mutant forms of Orsay virus would be highly desirable. Most efforts to engineer viruses have been done with cultured cells. Here we describe the creation of mutant viruses directly in the multicellular organism
C. elegans
without the use of cell culture. We engineered a virus expressing a genetically tagged protein that could be detected in
C. elegans
. This provides proof of concept for modifying Orsay virus, which will greatly facilitate studies in this experimental system.
Cross-sectional association between cigarette smoking and abdominal obesity among Austrian bank employees
Authors: de Oliveira Fontes Gasperin Lizia , Neuberger Manfred , Tichy Alexander , Moshammer Hans 
Published: July 2014

ObjectivesThere is increasing evidence that smoking is associated with abdominal obesity and other risk factors for the metabolic syndrome. The aim of this study is to investigate these associations in a sample of healthy Austrian adults.Setting and participantsData of 986 employees of an Austrian company (405 men and 581 women; participation rate approximately 80%) obtained during their annual medical check-up at the workplace were analysed.Primary and secondary outcome measuresInformation on smoking status, education level, physical activity, diet, body weight, height, body mass index (BMI), waist circumference and biochemical parameters was obtained. The influence of smoking on health and anthropometric measures was investigated.ResultsNo differences in total body fat and/or body fat distribution were found between non-smokers, smokers and former smokers; however, among daily smokers, the number of cigarettes smoked per day was significantly associated with higher body weight (p=0.001) and BMI (p=0.009). Male and female smokers had significantly higher white cell count than non-smokers and former smokers. Heavy smokers also had an unhealthier lipid profile (lower high-density lipoprotein cholesterol) and higher fasting glucose levels even after controlling for physical activity and calorie intake.ConclusionsContrary to the beliefs of many smokers, heavy smoking is associated with higher body weight and unfavourable metabolic changes.
Assessment of the quality of reporting in randomised controlled trials of acupuncture in the Korean literature using the CONSORT statement and STRICTA guidelines
Authors: Kim Kun Hyung , Kang Jung Won , Lee Myeong Soo , Lee Jae-Dong 
Published: July 2014

ObjectivesThis study aims to assess the completeness of reporting of randomised controlled trials (RCTs) of acupuncture in the Korean literature.DesignSystematic review.MethodsWe searched 12 Korean databases and 7 Korean journals to identify eligible RCTs of acupuncture published from 1996 to July 2011. We used the Consolidated Standards of Reporting Trials (CONSORT) checklist for parallel RCTs and the revised STandards for Reporting Interventions in Clinical Trials of Acupuncture (STRICTA) to assess the quality of reporting in Korean RCTs. We compared the completeness of reporting of CONSORT and STRICTA items in RCTs published in two time periods (1996–2004 referred to as the early period and 2005–2011 referred to as the late period).ResultsWe analysed 146 eligible RCTs using the CONSORT statement concerning RCTs of both needling and non-needling acupuncture and the STRICTA guidelines for 90 trials of needling acupuncture. Among the 103 RCTs in the late period, the proportion of RCTs that completely reported the CONSORT items of outcome definition (15.5%), sample size calculation (2.9%), randomisation (56%), allocation concealment (5.8%), implementation of allocation (11.7%), outcome assessor blinding (20.3%), flow of participants (25.2%), number of participants analysed (19.4%), ancillary analyses (0.0%), adverse events (24.3%), generalisability of findings (1.9%) and overall evidence (32.0%) remained small. Among the 61 RCTs of needling acupuncture in the late period, the STRICTA items of setting/context (24.6%) and practitioner background (27.9%) showed incomplete reporting. The completeness of reporting improved over time in several CONSORT and STRICTA items.ConclusionsThe completeness of reporting of Korean RCTs of acupuncture was suboptimal according to the CONSORT and revised STRICTA statements. Trial authors and journal editors should use the CONSORT statement and STRICTA guidelines for transparent reporting in Korean RCTs of acupuncture. The endorsement of the CONSORT and revised STRICTA statements in author instructions is also required.
Cost-effectiveness of ranibizumab and bevacizumab for age-related macular degeneration: 2-year findings from the IVAN randomised trial
Authors: Dakin Helen A , Wordsworth Sarah , Rogers Chris A , Abangma Giselle , Raftery James , Harding Simon P , Lotery Andrew J , Downes Susan M , Chakravarthy Usha , Reeves Barnaby C ,   on behalf of the IVAN Study Investigators
Published: July 2014

ObjectiveTo assess the incremental cost and cost-effectiveness of continuous and discontinuous regimens of bevacizumab (Avastin) and ranibizumab (Lucentis) for neovascular age-related macular degeneration (nAMD) from a UK National Health Service (NHS) perspective.DesignA within-trial cost-utility analysis with a 2-year time horizon, based on a multicentre factorial, non-inferiority randomised controlled trial.Setting23 hospital ophthalmology clinics.Participants610 patients aged ≥50 years with untreated nAMD in the study eye.Interventions0.5 mg ranibizumab or 1.25 mg bevacizumab given continuously (monthly) or discontinuously (as-needed) for 2 years.Main outcome measuresQuality-adjusted life-years (QALYs).ResultsTotal 2-year costs ranged from £3002/patient ($4700; 95% CI £2601 to £3403) for discontinuous bevacizumab to £18 590/patient ($29 106; 95% CI £18 258 to £18 922) for continuous ranibizumab. Ranibizumab was significantly more costly than bevacizumab for both continuous (+£14 989/patient ($23 468); 95% CI £14 522 to £15 456; p<0.001) and discontinuous treatment (+£8498 ($13 305); 95% CI £7700 to £9295; p<0.001), with negligible difference in QALYs. Continuous ranibizumab would only be cost-effective compared with continuous bevacizumab if the NHS were willing to pay £3.5 million ($5.5 million) per additional QALY gained. Patients receiving continuous bevacizumab accrued higher total costs (+£599 ($938); 95% CI £91 to £1107; p=0.021) than those receiving discontinuous bevacizumab, but also accrued non-significantly more QALYs (+0.020; 95% CI −0.032 to 0.071; p=0.452). Continuous bevacizumab therefore cost £30 220 ($47 316) per QALY gained versus discontinuous bevacizumab. However, bootstrapping demonstrated that if the NHS is willing to pay £20 000/QALY gained, there is a 37% chance that continuous bevacizumab is cost-effective versus discontinuous bevacizumab.ConclusionsRanibizumab is not cost-effective compared with bevacizumab, being substantially more costly and producing little or no QALY gain. Discontinuous bevacizumab is likely to be the most cost-effective of the four treatment strategies evaluated in this UK trial, although there is a 37% chance that continuous bevacizumab is cost-effective.Trial registration numberISRCTN92166560.