bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulated rRNA/DNA Ratios Show Potential To Misclassify Active Populations as Dormant
Authors: Steven Blaire , Hesse Cedar , Soghigian John , Gallegos-Graves La Verne , Dunbar John 
Published: April 2017

ABSTRACT

The use of rRNA/DNA ratios derived from surveys of rRNA sequences in RNA and DNA extracts is an appealing but poorly validated approach to infer the activity status of environmental microbes. To improve the interpretation of rRNA/DNA ratios, we performed simulations to investigate the effects of community structure, rRNA amplification, and sampling depth on the accuracy of rRNA/DNA ratios in classifying bacterial populations as “active” or “dormant.” Community structure was an insignificant factor. In contrast, the extent of rRNA amplification that occurs as cells transition from dormant to growing had a significant effect (
P
< 0.0001) on classification accuracy, with misclassification errors ranging from 16 to 28%, depending on the rRNA amplification model. The error rate increased to 47% when communities included a mixture of rRNA amplification models, but most of the inflated error was false negatives (i.e., active populations misclassified as dormant). Sampling depth also affected error rates (
P
< 0.001). Inadequate sampling depth produced various artifacts that are characteristic of rRNA/DNA ratios generated from real communities. These data show important constraints on the use of rRNA/DNA ratios to infer activity status. Whereas classification of populations as active based on rRNA/DNA ratios appears generally valid, classification of populations as dormant is potentially far less accurate.

IMPORTANCE
The rRNA/DNA ratio approach is appealing because it extracts an extra layer of information from high-throughput DNA sequencing data, offering a means to determine not only the seedbank of taxa present in communities but also the subset of taxa that are metabolically active. This study provides crucial insights into the use of rRNA/DNA ratios to infer the activity status of microbial taxa in complex communities. Our study shows that the approach may not be as robust as previously supposed, particularly in complex communities composed of populations employing different growth strategies, and identifies factors that inflate the erroneous classification of active populations as dormant.
Contamination of Fresh Produce by Microbial Indicators on Farms and in Packing Facilities: Elucidation of Environmental Routes
Authors: Bartz Faith E. , Lickness Jacquelyn Sunshine , Heredia Norma , Fabiszewski de Aceituno Anna , Newman Kira L. , Hodge Domonique Watson , Jaykus Lee-Ann , García Santos , Leon Juan S. 
Published: April 2017

ABSTRACT

To improve food safety on farms, it is critical to quantify the impact of environmental microbial contamination sources on fresh produce. However, studies are hampered by difficulties achieving study designs with powered sample sizes to elucidate relationships between environmental and produce contamination. Our goal was to quantify, in the agricultural production environment, the relationship between microbial contamination on hands, soil, and water and contamination on fresh produce. In 11 farms and packing facilities in northern Mexico, we applied a matched study design: composite samples (
n
= 636, equivalent to 11,046 units) of produce rinses were matched to water, soil, and worker hand rinses during two growing seasons. Microbial indicators (coliforms,
Escherichia coli
,
Enterococcus
spp., and somatic coliphage) were quantified from composite samples. Statistical measures of association and correlations were calculated through Spearman's correlation, linear regression, and logistic regression models. The concentrations of all microbial indicators were positively correlated between produce and hands (ρ range, 0.41 to 0.75;
P
< 0.01). When
E. coli
was present on hands, the handled produce was nine times more likely to contain
E. coli
(
P
< 0.05). Similarly, when coliphage was present on hands, the handled produce was eight times more likely to contain coliphage (
P
< 0.05). There were relatively low concentrations of indicators in soil and water samples, and a few sporadic significant associations were observed between contamination of soil and water and contamination of produce. This methodology provides a foundation for future field studies, and results highlight the need for interventions surrounding farmworker hygiene and sanitation to reduce microbial contamination of farmworkers' hands.

IMPORTANCE
This study of the relationships between microbes on produce and in the farm environment can be used to support the design of targeted interventions to prevent or reduce microbial contamination of fresh produce with associated reductions in foodborne illness.
The PerR-Regulated P
1B-4
-Type ATPase (PmtA) Acts as a Ferrous Iron Efflux Pump in Streptococcus pyogenes
Authors: Turner Andrew G. , Ong Cheryl-lynn Y. , Djoko Karrera Y. , West Nicholas P. , Davies Mark R. , McEwan Alastair G. , Walker Mark J. 
Published: April 2017

ABSTRACT

Streptococcus pyogenes
(group A
Streptococcus
[GAS]) is an obligate human pathogen responsible for a broad spectrum of human disease. GAS has a requirement for metal homeostasis within the human host and, as such, tightly modulates metal uptake and efflux during infection. Metal acquisition systems are required to combat metal sequestration by the host, while metal efflux systems are essential to protect against metal overload poisoning. Here, we investigated the function of PmtA (
P
erR-regulated
m
etal
t
ransporter
A
), a P
1B-4
-type ATPase efflux pump, in invasive GAS M1T1 strain 5448. We reveal that PmtA functions as a ferrous iron [Fe(II)] efflux system. In the presence of high Fe(II) concentrations, the 5448Δ
pmtA
deletion mutant exhibited diminished growth and accumulated 5-fold-higher levels of intracellular Fe(II) than did the wild type and the complemented mutant. The 5448Δ
pmtA
deletion mutant also showed enhanced susceptibility to killing by the Fe-dependent antibiotic streptonigrin as well as increased sensitivity to hydrogen peroxide and superoxide. We suggest that the PerR-mediated control of Fe(II) efflux by PmtA is important for bacterial defense against oxidative stress. PmtA represents an exemplar for an Fe(II) efflux system in a host-adapted Gram-positive bacterial pathogen.
The Agr-Like Quorum Sensing System Is Required for Pathogenesis of Necrotic Enteritis Caused by Clostridium perfringens in Poultry
Authors: Yu Qiang , Lepp Dion , Mehdizadeh Gohari Iman , Wu Tao , Zhou Hongzhuan , Yin Xianhua , Yu Hai , Prescott John F. , Nie Shao-Ping , Xie Ming-Yong , Gong Joshua 
Published: April 2017

ABSTRACTClostridium perfringensencodes at least two different quorum sensing (QS) systems, the Agr-like and LuxS, and recent studies have highlighted their importance in the regulation of toxin production and virulence. The role of QS in the pathogenesis of necrotic enteritis (NE) in poultry and the regulation of NetB, the key toxin involved, has not yet been investigated. We have generated isogenicagrB-null and complemented strains from parent strain CP1 and demonstrated that the virulence of theagrB-null mutant was strongly attenuated in a chicken NE model system and restored by complementation. The production of NetB, a key NE-associated toxin, was dramatically reduced in theagrBmutant at both the transcriptional and protein levels, though not in aluxSmutant. Transwell assays confirmed that the Agr-like QS system controls NetB production through a diffusible signal. Global gene expression analysis of theagrBmutant identified additional genes modulated by Agr-like QS, including operons related to phospholipid metabolism and adherence, which may also play a role in NE pathogenesis. This study provides the first evidence that the Agr-like QS system is critical for NE pathogenesis and identifies a number of Agr-regulated genes, most notablynetB, that are potentially involved in mediating its effects. The Agr-like QS system thus may serve as a target for developing novel interventions to prevent NE in chickens.
The Variable Internal Structure of the Mycoplasma penetrans Attachment Organelle Revealed by Biochemical and Microscopic Analyses: Implications for Attachment Organelle Mechanism and Evolution
Authors: Distelhorst Steven L. , Jurkovic Dominika A. , Shi Jian , Jensen Grant J. , Balish Mitchell F. 
Published: April 2017

ABSTRACT

Although mycoplasmas have small genomes, many of them, including the HIV-associated opportunist
Mycoplasma penetrans
, construct a polar attachment organelle (AO) that is used for both adherence to host cells and gliding motility. However, the irregular phylogenetic distribution of similar structures within the mycoplasmas, as well as compositional and ultrastructural differences among these AOs, suggests that AOs have arisen several times through convergent evolution. We investigated the ultrastructure and protein composition of the cytoskeleton-like material of the
M. penetrans
AO with several forms of microscopy and biochemical analysis, to determine whether the
M. penetrans
AO was constructed at the molecular level on principles similar to those of other mycoplasmas, such as
Mycoplasma pneumoniae
and
Mycoplasma mobile
. We found that the
M. penetrans
AO interior was generally dissimilar from that of other mycoplasmas, in that it exhibited considerable heterogeneity in size and shape, suggesting a gel-like nature. In contrast, several of the 12 potential protein components identified by mass spectrometry of
M. penetrans
detergent-insoluble proteins shared certain distinctive biochemical characteristics with
M. pneumoniae
AO proteins, although not with
M. mobile
proteins. We conclude that convergence between
M. penetrans
and
M. pneumoniae
AOs extends to the molecular level, leading to the possibility that the less organized material in both
M. pneumoniae
and
M. penetrans
is the substance principally responsible for the organization and function of the AO.

IMPORTANCE
Mycoplasma penetrans
is a bacterium that infects HIV-positive patients and may contribute to the progression of AIDS. It attaches to host cells through a structure called an AO, but it is not clear how it builds this structure. Our research is significant not only because it identifies the novel protein components that make up the material within the AO that give it its structure but also because we find that the
M. penetrans
AO is organized unlike AOs from other mycoplasmas, suggesting that similar structures have evolved multiple times. From this work, we derive some basic principles by which mycoplasmas, and potentially all organisms, build structures at the subcellular level.
Electrical and structural adaptations of the paediatric athlete’s heart: a systematic review with meta-analysis
Authors: McClean Gavin , Riding Nathan R , Ardern Clare L , Farooq Abdulaziz , Pieles Guido E , Watt Victoria , Adamuz Carmen , George Keith P , Oxborough David , Wilson Mathew G 
Published: April 2017

AimTo describe the electrocardiographic (ECG) and echocardiographic manifestations of the paediatric athlete’s heart, and examine the impact of age, race and sex on cardiac remodelling responses to competitive sport.DesignSystematic review with meta-analysis.Data sourcesSix electronic databases were searched to May 2016: MEDLINE, PubMed, EMBASE, Web of Science, CINAHL and SPORTDiscus.Inclusion criteria(1) Male and/or female competitive athletes, (2) participants aged 6–18 years, (3) original research article published in English language.ResultsData from 14 278 athletes and 1668 non-athletes were included for qualitative (43 articles) and quantitative synthesis (40 articles). Paediatric athletes demonstrated a greater prevalence of training-related and training-unrelated ECG changes than non-athletes. Athletes ≥14 years were 15.8 times more likely to have inferolateral T-wave inversion than athletes <14 years. Paediatric black athletes had significantly more training-related and training-unrelated ECG changes than Caucasian athletes. Age was a positive predictor of left ventricular (LV) internal diameter during diastole, interventricular septum thickness during diastole, relative wall thickness and LV mass. When age was accounted for, these parameters remained significantly larger in athletes than non-athletes. Paediatric black athletes presented larger posterior wall thickness during diastole (PWTd) than Caucasian athletes. Paediatric male athletes also presented larger PWTd than females.ConclusionsThe paediatric athlete’s heart undergoes significant remodelling both before and during ‘maturational years’. Paediatric athletes have a greater prevalence of training related and training-unrelated ECG changes than non-athletes, with age, race and sex mediating factors on cardiac electrical and LV structural remodelling.
Analysis of CTG repeat length variation in theDMPKgene in the general population and the molecular diagnosis of myotonic dystrophy type 1 in Malaysia
Authors: Ambrose Kathlin K , Ishak Taufik , Lian Lay-Hoong , Goh Khean-Jin , Wong Kum-Thong , Ahmad-Annuar Azlina , Thong Meow-Keong 
Published: April 2017

ObjectiveThe lack of epidemiological data and molecular diagnostic services in Malaysia has hampered the setting-up of a comprehensive management plan for patients with myotonic dystrophy type 1 (DM1), leading to delayed diagnosis, treatment and support for patients and families. The aim of this study was to estimate the prevalence of DM1 in the 3 major ethnic groups in Malaysia and evaluate the feasibility of a single tube triplet-primed PCR (TP-PCR) method for diagnosis of DM1 in Malaysia.Design, setting and participantsWe used PCR to determine the size of CTG repeats in 377 individuals not known to be affected by DM and 11 DM1 suspected patients, recruited from a tertiary hospital in Kuala Lumpur. TP-PCR was performed on selected samples, followed by Southern blot hybridisation of PCR amplified fragments to confirm and estimate the size of CTG expansion.Outcome measuresThe number of individuals not known to be affected by DM with (CTG)>18was determined according to ethnic group and as a whole population. The χ2test was performed to compare the distribution of (CTG)>18with 12 other populations. Additionally, the accuracy of TP-PCR in detecting CTG expansion in 11 patients with DM1 was determined by comparing the results with that from Southern blot hybridisation.ResultsOf the 754 chromosomes studied, (CTG)>18frequency of 3.60%, 1.57% and 4.00% in the Malay, Chinese and Indian subpopulations, respectively, was detected, showing similarities to data from Thai, Taiwanese and Kuwaiti populations. We also successfully detected CTG expansions in 9 patients using the TP-PCR method followed by the estimation of CTG expansion size via Southern blot hybridisation.ConclusionsThe results show a low DM1 prevalence in Malaysia with the possibility of underdiagnosis and demonstrates the feasibility of using a clinical and TP-PCR-based approach for rapid and cost-effective DM1 diagnosis in developing countries.
Impact of changes in pill appearance in the adherence to angiotensin receptor blockers and in the blood pressure levels: a retrospective cohort study
Authors: Lumbreras B , López-Pintor E 
Published: April 2017

ObjectiveTo assess the level of adherence to angiotensin receptor blockers (ARBs) in patients regularly attending a community pharmacy and the influence of a change in patients' adherence to pharmacological treatment.DesignRetrospective cohort study of a random sample of consecutive patients collecting their medication.Setting40 community pharmacies in Alicante (Southeast Spain).Participants602 consecutive ≥18 years old patients following treatment with ARBs at least 3 previous refills were included.Main outcome measuresPrevalence of uncontrolled blood pressure (BP) and adherence to prescribed pharmacological treatment (measured through both the Batalla and the Morisky-Green tests). A multivariate Poisson regression model was used to estimate the adjusted risk ratio (RRa) for non-adherence to pharmacological treatment by the presence of a change in patient's adherence and other significant variables.Results161/602 (13.7%) patients presented uncontrolled BP. According to the Morisky test, 410/602 (68.2%) patients were considered adherent to pharmacological treatment and 231/602 (38.4%) patients according to the Batalla test. According to the Morisky-Green test, in the multivariable analysis, patients with a previous change in pill appearance were less likely to be adherent than those patients with no change in their pharmacological treatment (RRa 0.45; CI 95% 0.22 to 0.90; p=0.024). Systolic BP was higher in patients with a change in pill appearance in the previous 3 refills (median BP 142 mm Hg; IQR 136–148) than in those who did not have a change (median BP 127 mm Hg; IQR 118–135; p<0.001).ConclusionsThere was a low percentage of adherence and nearly 15% of uncontrolled BP in patients who regularly collected their medication. Switching between pills of different appearances was associated with lower patient adherence to pharmacological treatment and a higher uncontrolled BP than no change in pharmacological treatment or change only in package but not in pill appearance.
Evidence of potential bias in a comparison of β blockers and calcium channel blockers in patients with chronic obstructive pulmonary disease and acute coronary syndrome: results of a multinational study
Authors: Dong Yaa-Hui , Alcusky Matthew , Maio Vittorio , Liu Jun , Liu Mengdan , Wu Li-Chiu , Chang Chia-Hsuin , Lai Mei-Shu , Gagne Joshua J 
Published: April 2017

ObjectivesA number of observational studies have reported that, in patients with chronic obstructive pulmonary disease (COPD), β blockers (BBs) decrease risk of mortality and COPD exacerbations. To address important methodological concerns of these studies, we compared the effectiveness and safety of cardioselective BBs versus non-dihydropyridine calcium channel blockers (non-DHP CCBs) in patients with COPD and acute coronary syndromes (ACS) using a propensity score (PS)-matched, active comparator, new user design. We also assessed for potential unmeasured confounding by examining a short-term COPD hospitalisation outcome.Setting and participantsWe identified 22 985 patients with COPD and ACS starting cardioselective BBs or non-DHP CCBs across 5 claims databases from the USA, Italy and Taiwan.Primary and secondary outcome measuresStratified Cox regression models were used to estimate HRs for mortality, cardiovascular (CV) hospitalisations and COPD hospitalisations in each database after variable-ratio PS matching. Results were combined with random-effects meta-analyses.ResultsCardioselective BBs were not associated with reduced risk of mortality (HR, 0.90; 95% CI 0.78 to 1.02) or CV hospitalisations (HR, 1.06; 95% CI 0.91 to 1.23), although statistical heterogeneity was observed across databases. In contrast, a consistent, inverse association for COPD hospitalisations was identified across databases (HR, 0.54; 95% CI 0.47 to 0.61), which persisted even within the first 30 days of follow-up (HR, 0.55; 95% CI 0.37 to 0.82). Results were similar across a variety of sensitivity analyses, including PS trimming, high dimensional-PS matching and restricting to high-risk patients.ConclusionsThis multinational study found a large inverse association between cardioselective BBs and short-term COPD hospitalisations. The persistence of this bias despite state-of-the-art pharmacoepidemiologic methods calls into question the ability of claims data to address confounding in studies of BBs in patients with COPD.
Awareness and attitudes of the Lebanese population with regard to physician–pharmaceutical company interaction: a survey study
Authors: Ammous Ahmad , Bou Zein Eddine Savo , Dani Alia , Dbaibou Jana , El-Asmar Jose M , Sadder Liane , Akl Elie A 
Published: April 2017

ObjectiveTo assess the awareness and attitudes of the general public in Lebanon regarding the interactions between physicians and pharmaceutical companies.SettingPrimary healthcare clinics and shopping malls in the Greater Beirut Area.Participants263 participants completed the questionnaire, of whom 62% were female and 38% were male. Eligible participants were Arabic-speaking or English-speaking adults (age≥18 years) residing in Lebanon for at least 5 years.Primary and secondary outcome measuresAwareness, attitudes and beliefs of the general public.Results263 out of 295 invited individuals (89% completion rate) completed the questionnaire. While the majority of participants were aware of pharmaceutical company presence (or absence) in physicians' offices (range of 71–76% across questions), smaller percentages were aware of gift-related practices of physicians (range of 26–69% across questions). 40% thought that the acceptance of small gifts or meals by physicians is wrong/unethical. The percentage of participants reporting lower trust in physicians due to their participation in various pharmaceutical company-related activities ranged from 12% to 45% (the highest percentage being for large gifts). Participants who reported receiving free medication samples were significantly more likely to consider physicians' acceptance of small gifts as ‘not a problem’ than ‘unethical’ (OR=1.53; p=0.044).ConclusionsParticipants in our survey were generally more aware of pharmaceutical company presence (or absence) in physicians' offices than of gift-related practices of physicians. While the level of trust was not affected for the majority of participants for various types of interactions, it was affected the most for accepting large gifts.
Interactive web-based pulmonary rehabilitation programme: a randomised controlled feasibility trial
Authors: Chaplin Emma , Hewitt Stacey , Apps Lindsay , Bankart John , Pulikottil-Jacob Ruth , Boyce Sally , Morgan Mike , Williams Johanna , Singh Sally 
Published: April 2017

ObjectivesThe aim of this study was to determine if an interactive web-based pulmonary rehabilitation (PR) programme is a feasible alternative to conventional PR.DesignRandomised controlled feasibility trial.SettingParticipants with a diagnosis of chronic obstructive pulmonary disease were recruited from PR assessments, primary care and community rehabilitation programmes. Patients randomised to conventional rehabilitation started the programme according to the standard care at their referred site on the next available date.Participants103 patients were recruited to the study and randomised: 52 to conventional rehabilitation (mean (±SD) age 66 (±8) years, Medical Research Council (MRC) 3 (IQR2–4)); 51 to the web arm (mean (±SD) age 66 (±10) years, MRC 3 (IQR2–4)). Participants had to be willing to participate in either arm of the trial, have internet access and be web literate.InterventionsPatients randomised to the web-based programme worked through the website, exercising and recording their progress as well as reading educational material. Conventional PR consisted of twice weekly, 2 hourly sessions (an hour for exercise training and an hour for education).Outcome measuresRecruitment rates, eligibility, patient preference and dropout and completion rates for both programmes were collected. Standard outcomes for a PR assessment including measures of exercise capacity and quality of life questionnaires were also evaluated.ResultsA statistically significant improvement (p≤0.01) was observed within each group in the endurance shuttle walk test (WEB: mean change 189±211.1; PR classes: mean change 184.5±247.4 s) and Chronic Respiratory disease Questionnaire-Dyspnoea (CRQ-D; WEB: mean change 0.7±1.2; PR classes: mean change 0.8±1.0). However, there were no significant differences between the groups in any outcome. Dropout rates were higher in the web-based programme (57% vs 23%).ConclusionsAn interactive web-based PR programme is feasible and acceptable when compared with conventional PR. Future trials maybe around choice-based PR programmes for select patients enabling stratification of patient care.Trial registration numberISRCTN03142263; Results.