bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple Roles for Two Efflux Pumps in the Polycyclic Aromatic Hydrocarbon-Degrading Pseudomonas putida Strain B6-2 (DSM 28064)
Authors: Yao Xuemei , Tao Fei , Zhang Kunzhi , Tang Hongzhi , Xu Ping 
Published: October 2017

ABSTRACT

Microbial bioremediation is a promising approach for the removal of polycyclic aromatic hydrocarbon (PAH) contaminants. Many degraders of PAHs possess efflux pump genes in their genomes; however, their specific roles in the degradation of PAHs have not been clearly elucidated. In this study, two efflux pumps, TtgABC and SrpABC, were systematically investigated to determine their functions in a PAH-degrading
Pseudomonas putida
strain B6-2 (DSM 28064). The disruption of genes
ttgABC
or
srpABC
resulted in a defect in organic solvent tolerance. TtgABC was found to contribute to antibiotic resistance; SrpABC only contributed to antibiotic resistance under an artificial overproduced condition. Moreover, a mutant strain without
srpABC
did not maintain its activity in long-term biphenyl (BP) degradation, which correlated with the loss of cell viability. The expression of SrpABC was significantly upregulated in the course of BP degradation. BP, 2-hydroxybiphenyl, 3-hydroxybiphenyl, and 2,3-dihydroxybiphenyl (2,3-DHBP) were revealed to be the inducers of
srpABC
. 2,3-DHBP was verified to be a substrate of pump SrpABC; SrpABC can enhance the tolerance to 2,3-DHBP by pumping it out. The mutant strain B6-2Δ
srpS
prolonged BP degradation with the increase of
srpABC
expression. These results suggest that the pump SrpABC of strain B6-2 plays a positive role in BP biodegradation by pumping out metabolized toxic substances such as 2,3-DHBP. This study provides insights into the versatile physiological functions of the widely distributed efflux pumps in the biodegradation of PAHs.

IMPORTANCE
Polycyclic aromatic hydrocarbons (PAHs) are notorious for their recalcitrance to degradation in the environment. A high frequency of the occurrence of the efflux pump genes was observed in the genomes of effective PAH degraders; however, their specific roles in the degradation of PAHs are still obscure. The significance of our study is in the identification of the function and mechanism of the efflux pump SrpABC of
Pseudomonas putida
strain B6-2 (DSM 28064) in the biphenyl degradation process. SrpABC is crucial for releasing the toxicity caused by intermediates that are unavoidably produced in PAH degradation, which enables an understanding of how cells maintain the intracellular balance of materials. The findings from this study provide a new perspective on PAH recalcitrance and shed light on enhancing PAH degradation by genetic engineering.
Prevalence and Antimicrobial Resistance of Enterococci Isolated from Retail Meats in the United States, 2002 to 2014
Authors: Tyson Gregory H. , Nyirabahizi Epiphanie , Crarey Emily , Kabera Claudine , Lam Claudia , Rice-Trujillo Crystal , McDermott Patrick F. , Tate Heather 
Published: October 2017

ABSTRACT

Bacteria of the genus
Enterococcus
are important human pathogens that are frequently resistant to a number of clinically important antibiotics. They are also used as markers of animal fecal contamination of human foods and are employed as sentinel organisms for tracking trends in resistance to antimicrobials with Gram-positive activity. As part of the National Antimicrobial Resistance Monitoring System (NARMS), we evaluated several retail meat commodities for the presence of enterococci from 2002 to 2014, and we found 92.0% to be contaminated. The majority of isolates were either
Enterococcus faecalis
(64.0%) or
Enterococcus faecium
(28.6%), and the antimicrobial resistance of each isolate was assessed by broth microdilution. The resistance prevalences for several drugs, including erythromycin and gentamicin, were significantly higher among poultry isolates, compared to retail beef or pork isolates. None of the isolates was resistant to the clinically important human drug vancomycin, only 1 isolate was resistant to linezolid, and resistance to tigecycline was below 1%. In contrast, a majority of both
E. faecalis
(67.5%) and
E. faecium
(53.7%) isolates were resistant to tetracycline. Overall, the robust NARMS testing system employed consistent sampling practices and methods throughout the testing period, with the only significant trend in resistance prevalence being decreased
E. faecium
resistance to penicillin. These data provide excellent baseline levels of resistance that can be used to measure future changes in resistance prevalence that may result from alterations in the use of antimicrobials in food animal production.

IMPORTANCE
Enterococci, including
E. faecalis
and
E. faecium
, are present in the guts of food-producing animals and are used as a measure of fecal contamination of meat. We used the large consistent sampling methods of NARMS to assess the prevalence of
Enterococcus
strains isolated from retail meats, and we found over 90% of meats to be contaminated with enterococci. We also assessed the resistance of the
Enterococcus
strains, commonly used as a measure of resistance to agents with Gram-positive activity, in foods. Resistance prevalence was over 25% for some antimicrobials and sample sources but was less than 1% for several of the most important therapeutic agents used in human medicine.
Aerobic Anoxygenic Photosynthesis Is Commonly Present within the Genus Limnohabitans
Authors: Kasalický Vojtěch , Zeng Yonghui , Piwosz Kasia , Šimek Karel , Kratochvilová Hana , Koblížek Michal 
Published: October 2017

ABSTRACT

The genus
Limnohabitans
(
Comamonadaceae
,
Betaproteobacteria
) is a common and a highly active component of freshwater bacterioplanktonic communities. To date, the genus has been considered to contain only heterotrophic species. In this study, we detected the photosynthesis genes
pufLM
and
bchY
in 28 of 46 strains from three
Limnohabitans
lineages. The
pufM
sequences obtained are very closely related to environmental
pufM
sequences detected in various freshwater habitats, indicating the ubiquity and potential importance of photoheterotrophic
Limnohabitans
in nature. Additionally, we sequenced and analyzed the genomes of 5 potentially photoheterotrophic
Limnohabitans
strains, to gain further insights into their phototrophic capacity. The structure of the photosynthesis gene cluster turned out to be highly conserved within the genus
Limnohabitans
and also among all potentially photosynthetic
Betaproteobacteria
strains. The expression of photosynthetic complexes was detected in a culture of
Limnohabitans planktonicus
II-D5
T
using spectroscopic and pigment analyses. This was further verified by a novel combination of infrared microscopy and fluorescent
in situ
hybridization.

IMPORTANCE
The data presented document that the capacity to perform anoxygenic photosynthesis is common among the members of the genus
Limnohabitans
, indicating that they may have a novel role in freshwater habitats.
Microhomology-Mediated High-Throughput Gene Inactivation Strategy for the Hyperthermophilic Crenarchaeon Sulfolobus islandicus
Authors: Zhang Changyi , Whitaker Rachel J. 
Published: October 2017

ABSTRACT

Sulfolobus islandicus
is rapidly emerging as a model system for studying the biology and evolution within the TACK lineage of the archaeal domain. As the tree of life grows, identifying the cellular functions of genes within this lineage will have significant impacts on our understanding of the evolution of the
l
ast
a
rchaeal
e
ukaryote
c
ommon
a
ncestor (LEACA) and the differentiation of archaea from eukaryotes during the evolution of the modern-day cell. To increase our understanding of this key archaeal organism, we report a novel high-throughput method for targeted gene inactivation in
S. islandicus
through one-step microhomology-directed homologous recombination (HR). We validated the efficacy of this approach by systematically deleting 21 individual toxin-antitoxin gene pairs and its application to delete chromosomal regions as large as 50 kb. Sequence analysis of 96 ArgD
+
transformants showed that
S. islandicus
can effectively incorporate donor markers as short segments through HR in a continuous or discontinuous manner. We determined that the minimal size of homology allowing native
argD
marker replacement was as few as 10 bp, whereas
argD
marker replacement was frequently observed when increasing the size of homology to 30 to 50 bp. The microhomology-mediated gene inactivation system developed here will greatly facilitate isolation of
S. islandicus
gene deletion strains, making generation of a collection of genome-wide targeted mutants feasible and providing a tool to investigate homologous recombination in this organism.

IMPORTANCE
Current procedures for the construction of deletion mutants of
S. islandicus
are still tedious and time-consuming. We developed a novel procedure based on microhomology-mediated HR, allowing for rapid and efficient removal for genetic regions as large as 50 kb. Our work will greatly facilitate functional genomic studies in this promising model organism. Additionally, we developed a quantitative genetic assay to measure HR properties in
S. islandicus
, providing evidence that the ability to incorporate short, mismatched donor DNA into the genome through HR was probably a common trait for members of the
Sulfolobus
genus that are recombinogenic.
Physiological stability in an indigenous sleep device: a randomised controlled trial
Authors: Baddock Sally A , Tipene-Leach David , Williams Sheila M , Tangiora Angeline , Jones Raymond , Mącznik Aleksandra K , Taylor Barry J 
Published: October 2017

ObjectiveTo compare overnight oxygen saturation, heart rate and the thermal environment of infants sleeping in an indigenous sleep device (wahakura) or bassinet to identify potential risks and benefits.DesignRandomised controlled trial.SettingFamily homes in low socio-economic areas in New Zealand.Patients200 mainly Māori mothers and their infants.InterventionsParticipants received a wahakura or bassinet from birth.Main outcome measuresOvernight oximetry, heart rate and temperature at 1 month.ResultsIntention-to-treat analysis for 83 bassinet and 84 wahakura infants showed no significant differences between groups for the mean time oxygen saturation (SpO2) was less than 94% (0.54 min, 95% CI -1.36 to 2.45) or less than 90% (0.22 min, 95% CI -0.56 to 1.00), the mean number of SpO2dips per hour >5% (-0.19, 95% CI -3.07 to 2.69) or >10% (-0.41, 95% CI -1.63 to 0.81), mean heart rate (1.99 beats/min, 95% CI -1.02 to 4.99), or time shin temperature >36°C (risk ratio (RR): 0.63, 95% CI 0.13 to 2.99) or <34°C (RR: 0.89, 95% CI 0.61 to 1.30). A per-protocol analysis of 45 bassinet and 26 wahakura infants and an as-used analysis of 104 infants in a bassinet and 48 in a wahakura found no significant differences between groups for all outcome measures.ConclusionsThis indigenous sleep device is at least as safe as the currently recommended bassinet, which supports its use as a sleep environment that offers an alternative way of bed-sharing.Trial registration numberAustralian New Zealand Clinical Trials Registry: ACTRN12610000993099.
High precompetition injury rate dominates the injury profile at the Rio 2016 Summer Paralympic Games: a prospective cohort study of 51 198 athlete days
Authors: Derman Wayne , Runciman Phoebe , Schwellnus Martin , Jordaan Esme , Blauwet Cheri , Webborn Nick , Lexell Jan , van de Vliet Peter , Tuakli-Wosornu Yetsa , Kissick James , Stomphorst Jaap 
Published: October 2017

ObjectivesTo describe the incidence of injury in the precompetition and competition periods of the Rio 2016 Summer Paralympic Games.MethodsA total of 3657 athletes from 78 countries, representing 83.4% of all athletes at the Games, were monitored on the web-based injury and illness surveillance system over 51 198 athlete days during the Rio 2016 Summer Paralympic Games. Injury data were obtained daily from teams with their own medical support.ResultsA total of 510 injuries were reported during the 14-day Games period, with an injury incidence rate (IR) of 10.0 injuries per 1000 athlete days (12.1% of all athletes surveyed). The highest IRs were reported for football 5-a-side (22.5), judo (15.5) and football 7-a-side (15.3) compared with other sports (p<0.05). Precompetition injuries were significantly higher than in the competition period (risk ratio: 1.40, p<0.05), and acute traumatic injuries were the most common injuries at the Games (IR of 5.5). The shoulder was the most common anatomical area affected by injury (IR of 1.8).ConclusionThe data from this study indicate that (1) IRs were lower than those reported for the London 2012 Summer Paralympic Games, (2) the sports of football 5-a-side, judo and football 7-a-side were independent risk factors for injury, (3) precompetition injuries had a higher IR than competition period injuries, (4) injuries to the shoulder were the most common. These results would allow for comparative data to be collected at future editions of the Games and can be used to inform injury prevention programmes.
Higher BMI is associated with higher expiratory airflow normalised for lung volume (FEF25–75/FVC) in COPD
Authors: Abston Eric , Comellas Alejandro , Reed Robert Michael , Kim Victor , Wise Robert A , Brower Roy , Fortis Spyridon , Beichel Reinhard , Bhatt Surya , Zabner Joseph , Newell John , Hoffman Eric A , Eberlein Michael 
Published: October 2017

IntroductionThe obesity paradox in chronic obstructive pulmonary disease (COPD), whereby patients with higher body mass index (BMI) fare better, is poorly understood. Higher BMIs are associated with lower lung volumes and greater lung elastic recoil, a key determinant of expiratory airflow. The forced expiratory flow (25–75) (FEF25–75)/forced vital capacity (FVC) ratio reflects effort-independent expiratory airflow in the context of lung volume and could be modulated by BMI.MethodsWe analysed data from the COPDGene study, an observational study of 10 192 subjects, with at least a 10 pack-year smoking history. Data were limited to subjects with BMI 20–40 kg/m2(n=9222). Subjects were stratified according to forced expiratory volume in 1 s (FEV1) (%predicted)-quintiles. In regression analyses and Cox proportional hazard models, we analysed the association between BMI, the FEF25–75/FVC ratio, the imaging phenotype, COPD exacerbations, hospitalisations and death.ResultsThere was no correlation between BMI and FEV1(%predicted). However, a higher BMI is correlated with a higher FEF25–75/FVC ratio. In CT scans, a higher BMI was associated with less emphysema and less air trapping. In risk-adjusted models, the quintile with the highest FEF25–75/FVC ratio was associated with a 46% lower risk of COPD exacerbations (OR 0.54, p<0.001) and a 40% lower risk of death (HR 0.60, p=0.02), compared with the lowest quintile. BMI was not independently associated with these outcomes.ConclusionsA higher BMI is associated with lower lung volumes and higher expiratory airflows when normalised for lung volume, as quantified by the FEF25–75/FVC ratio. A higher FEF25–75/FVC ratio is associated with a lower risk of COPD exacerbations and death and might quantify functional aspects of the paradoxical effect of higher BMIs on COPD.
Simulation-based education to improve communication skills: a systematic review and identification of current best practice
Authors: Blackmore Andrew , Kasfiki Eirini Vasileiou , Purva Makani 
Published: October 2017

BackgroundGood communication in healthcare between professionals and between professionals and patients is important in delivering high-quality care. Evidence of translation of technical skills taught through simulation into the clinical environment has been demonstrated, but the evidence for the impact of communication skills is less well known.ObjectivesTo identify and critically appraise the evidence for the impact of communication taught through simulation-based education (SBE) and use this evidence to suggest a model for future SBE interventions for communication skills.Study selectionMEDLINE, CINAHL, EMBASE and PsycINFO were searched for articles pertaining to communication skills taught through simulation. A content expert was consulted to suggest additional studies. 1754 studies were initially screened for eligibility, with 274 abstracts screened further. 147 full-text articles were further assessed for eligibility, with 79 of these excluded. The remaining 68 studies were reviewed and 18 studies were included in the qualitative synthesis as studies designed to show benefits beyond the simulation centre.FindingsThe 18 identified studies with an impact at a Kirkpatrick level of ≥3, are analysed; 4 looking specifically at communication between healthcare professionals and 14 looking at communication between health professionals and patients or relatives.ConclusionsThere is some evidence that the improvements in communication taught through simulation can be translated into benefits measurable beyond the simulation centre, but this evidence is limited due to the way that most of the studies are designed. We suggest a model for SBE aimed at teaching communication skills that is informed by the current evidence and takes into account the need to collect higher-level outcome data.
Outcome of intracerebral haemorrhage related to non-vitamin K antagonists oral anticoagulants versus vitamin K antagonists: a comprehensive systematic review and meta-analysis
Authors: Boulouis Gregoire , Morotti Andrea , Pasi Marco , Goldstein Joshua N , Gurol M Edip , Charidimou Andreas 
Published: October 2017

IntroductionThe characteristics and natural history of acute non-vitamin K antagonists oral anticoagulants (NOAC)-associated intracerebral haemorrhage (ICH) are largely unknown. We performed a comprehensive systematic review and meta-analysis to compare baseline ICH volume, haematoma expansion and clinical outcomes between NOAC-ICH versus vitamin K antagonists-ICH (VKA-ICH).MethodsWe searched PubMed and conference abstracts for observational studies comparing baseline characteristics and outcomes in patients with NOAC-ICH versus VKA-ICH using an appropriate keyword/MeSH term search strategy. Data were extracted following PRISMA and MOOSE guidelines. The main outcome measures were mortality and unfavourable functional outcome (modified Rankin Score: 4–6) at discharge and at 3 months, as well as ICH volumes and haematoma expansion rates in the two groups. Random-effects models with DerSimonian-Laird weights were used for pooled estimates calculation.ResultsTwelve studies including 393 NOAC-ICH and 3482 VKA-ICH were pooled in meta-analysis. There was no difference in mean ICH-volume between the two groups (standard mean difference: −0.24; 95% CI −0.52 to 0.04, p=0.093). The rates of haematoma expansion were comparable in NOAC-ICH versus VKA-ICH (OR: 0.76; 95% CI 0.49 to 1.19, p=0.236). We did not find any difference between patients with NOAC-ICH versus VKA-ICH in all-cause mortality at discharge (OR: 0.66; 95% CI 0.42 to 1.05, p=0.077) and unfavourable functional outcome at discharge (OR: 0.77; 95% CI 0.41 to 1.44, p=0.413). The 3-month outcome was also comparable between the two ICH groups. Moderate-to-substantial statistical heterogeneity was noted.ConclusionOur results confirm that ICH volume, haematoma expansion, mortality and functional outcome appear to be similar for NOAC-ICH versus VKA-ICH. Large prospective cohorts and updated meta-analyses are needed to provide more precise estimates.
Accuracy of clinical diagnosis of dementia with Lewy bodies: a systematic review and meta-analysis
Authors: Rizzo Giovanni , Arcuti Simona , Copetti Massimiliano , Alessandria Maria , Savica Rodolfo , Fontana Andrea , Liguori Rocco , Logroscino Giancarlo 
Published: October 2017

BackgroundThe diagnosis of dementia with Lewy bodies (DLB) is based on diagnostic clinical criteria, which were updated over the years.ObjectiveTo evaluate, through a systematic review, accuracy of the diagnostic criteria, testing a possible improvement over time.MethodsWe searched on MEDLINE and SCOPUS databases for studies reporting diagnostic parameters regarding the clinical diagnosis of DLB until October 2016. We performed meta-analysis, using a Bayesian approach, on those using pathological examination as gold standard, subclassified based on the different diagnostic criteria used.ResultsWe selected 22 studies on 1585 patients. Pooled sensitivity, specificity and accuracy were 60.2%, 93.8%, 79.7%, respectively, for criteria antecedents to McKeith 1996. For McKeith 1996-possible, pooled sensitivity, specificity and accuracy were 65.6%, 80.6%, 77.9% in early stages and 72.3%, 64.3%, 66% in late stages, respectively. For McKeith 1996-probable, pooled sensitivity, specificity and accuracy were 19.4%, 95.1%, 77.7% in early stages and 48.6%, 88%, 79.2% in late stages, respectively. McKeith criteria 2005 were evaluated only in late stages: pooled sensitivity, specificity and accuracy were 91.3%, 66.7% and 81.6%, respectively, for possible diagnosis (only one study) and 88.3%, 80.8%, 90.7% for probable diagnosis, decreasing to 85.6%, 77.1% and 81.7% if only considering clinical settings focused on dementia diagnosis and care.Conclusions and relevanceDiagnostic criteria have become more sensitive and less specific over time, without substantial change in the accuracy. Based on current data, about 20% of DLB diagnosis are incorrect. Future studies are needed to evaluate if the recently released revised consensus criteria will improve the diagnostic accuracy of DLB.
Poor health as a potential risk factor for job loss due to automation: the case of Norway
Authors: Hessel Philipp , Christiansen Solveig , Skirbekk Vegard 
Published: October 2017

ObjectiveThis study aimed to quantify the extent to which health characteristics of workers are related to the potential risk of experiencing job displacement due to automation.MethodsLinking the 2015 Norwegian Statistics on Income and Living Conditions survey (n=6393) with predicted probabilities of automation by occupation, we used Kruskal-Wallis tests and multivariate generalised linear models to assess the association between long-standing illnesses and risk of job automation.ResultsIndividuals with long-standing illnesses face substantially greater risks of losing their job due to automation. Whereas the average risk of job automation is 57% for men and 49% for women with long-standing illnesses, the risk is only 50% for men and 44% for women with limitations (p<0.001). Controlling for age, having a long-standing illness significantly increases the relative risk of facing job automation among men (risk ratio (RR) 1.13, 95% CI 1.09 to 1.19), as well as women (RR 1.11, 95% CI 1.05 to 1.17). While, among men, the association between long-standing illness and risk of job automation remains significant when controlling for education and income, it becomes insignificant among women.ConclusionsIndividuals with poor health are likely to carry the highest burden of technological change in terms of worsening employment prospects because of working in occupations disproportionally more likely to be automated. Although the extent of technology-related job displacement will depend on several factors, given the far-reaching negative consequences of job loss on health and well-being, this process represents a significant challenge for public health and social equity.