bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inactivation of Cellobiose Dehydrogenases Modifies the Cellulose Degradation Mechanism of Podospora anserina
Authors: Tangthirasunun Narumon , Navarro David , Garajova Sona , Chevret Didier , Tong Laetitia Chan Ho , Gautier Valérie , Hyde Kevin D. , Silar Philippe , Berrin Jean-Guy 
Published: November 2016

ABSTRACT

Conversion of biomass into high-value products, including biofuels, is of great interest to developing sustainable biorefineries. Fungi are an inexhaustible source of enzymes to degrade plant biomass. Cellobiose dehydrogenases (CDHs) play an important role in the breakdown through synergistic action with fungal lytic polysaccharide monooxygenases (LPMOs). The three CDH genes of the model fungus
Podospora anserina
were inactivated, resulting in single and multiple CDH mutants. We detected almost no difference in growth and fertility of the mutants on various lignocellulose sources, except on crystalline cellulose, on which a 2-fold decrease in fertility of the mutants lacking
P. anserina CDH1
(
PaCDH1
) and
PaCDH2
was observed. A striking difference between wild-type and mutant secretomes was observed. The secretome of the mutant lacking all CDHs contained five beta-glucosidases, whereas the wild type had only one.
P. anserina
seems to compensate for the lack of CDH with secretion of beta-glucosidases. The addition of
P. anserina
LPMO to either the wild-type or mutant secretome resulted in improvement of cellulose degradation in both cases, suggesting that other redox partners present in the mutant secretome provided electrons to LPMOs. Overall, the data showed that oxidative degradation of cellulosic biomass relies on different types of mechanisms in fungi.

IMPORTANCE
Plant biomass degradation by fungi is a complex process involving dozens of enzymes. The roles of each enzyme or enzyme class are not fully understood, and utilization of a model amenable to genetic analysis should increase the comprehension of how fungi cope with highly recalcitrant biomass. Here, we report that the cellobiose dehydrogenases of the model fungus
Podospora anserina
enable it to consume crystalline cellulose yet seem to play a minor role on actual substrates, such as wood shavings or miscanthus. Analysis of secreted proteins suggests that
Podospora anserina
compensates for the lack of cellobiose dehydrogenase by increasing beta-glucosidase expression and using an alternate electron donor for LPMO.
Waterborne Viruses and F-Specific Coliphages in Mixed-Use Watersheds: Microbial Associations, Host Specificities, and Affinities with Environmental/Land Use Factors
Authors: Jones Tineke H. , Brassard Julie , Topp Edward , Wilkes Graham , Lapen David R. 
Published: November 2016

ABSTRACT

From the years 2008 to 2014, a total of 1,155 water samples were collected (spring to fall) from 24 surface water sampling sites located in a mixed-used but predominantly agricultural (i.e., dairy livestock production) river basin in eastern Ontario, Canada. Water was analyzed for viable F-specific DNA (F-DNA) and F-specific RNA (F-RNA) (genogroup I [GI] to GIV) coliphage and a suite of molecularly detected viruses (norovirus [GI to GIV], torque teno virus [TTV], rotavirus, kobuvirus, adenovirus, astrovirus, hepatitis A, and hepatitis E). F-DNA and F-RNA coliphage were detected in 33 and 28% of the samples at maximum concentrations of 2,000 and 16,300 PFU · 100 ml
−1
, respectively. Animal TTV, human TTV, kobuvirus, astrovirus, and norovirus GIII were the most prevalent viruses, found in 23, 20, 13, 12, and 11% of samples, respectively. Viable F-DNA coliphage was found to be a modest positive indicator of molecularly detected TTV. F-RNA coliphage, unlike F-DNA coliphage, was a modest positive predictor of norovirus and rotavirus. There were, however, a number of significant negative associations among F-specific coliphage and viruses. F-DNA coliphage densities of >142 PFU · 100 ml
−1
delineated conditions when ∼95% of water samples contained some type of virus. Kobuvirus was the virus most strongly related to detection of any other virus. Land use had some associations with virus/F-specific coliphage detection, but season and surface water flow were the variables that were most important for broadly delineating detection. Higher relative levels of detection of human viruses and human F-RNA coliphage were associated with higher relative degrees of upstream human land development in a catchment.

IMPORTANCE
This study is one of the first, to our knowledge, to evaluate relationships among F-specific coliphages and a large suite of enteric viruses in mixed-use but agriculturally dominated surface waters in Canada. This study suggested that relationships between viable F-specific coliphages and molecularly detected viruses do exist, but they are not always positive. Caution should be employed if viable F-specific coliphages are to be used as indicators of virus presence in surface waters. This study elucidates relative effects of agriculture, wildlife, and human activity on virus and F-specific coliphage detection. Seasonal and meteorological attributes play a strong role in the detection of most virus and F-specific coliphage targets.
A System Model for Understanding the Role of Animal Feces as a Route of Contamination of Leafy Greens before Harvest
Authors: Mishra Abhinav , Pang Hao , Buchanan Robert L. , Schaffner Donald W. , Pradhan Abani K. 
Published: November 2016

ABSTRACT

The majority of foodborne outbreaks in the United States associated with the consumption of leafy greens contaminated with
Escherichia coli
O157:H7 have been reported during the period of July to November. A dynamic system model consisting of subsystems and inputs to the system (soil, irrigation, cattle, wild pig, and rainfall) simulating a hypothetical farm was developed. The model assumed two crops of lettuce in a year and simulated planting, irrigation, harvesting, ground preparation for the new crop, contamination of soil and plants, and survival of
E. coli
O157:H7. As predicted by the baseline model for crops harvested in different months from conventional fields, an estimated 13 out of 257 (5.05%) first crops harvested in July would have at least one plant with at least 1 CFU of
E. coli
O157:H7. Predictions indicate that no first crops would be contaminated with at least 1 CFU of
E. coli
O157:H7 for other months (April to June). The maximum
E. coli
O157:H7 concentration in a plant was higher in the second crop (27.10 CFU) than in the first crop (9.82 CFU). For the second crop, the probabilities of having at least one plant with at least 1 CFU of
E. coli
O157:H7 in a crop were predicted as 15/228 (6.6%), 5/333 (1.5%), 14/324 (4.3%), and 6/115 (5.2%) in August, September, October, and November, respectively. For organic fields, the probabilities of having at least one plant with ≥1 CFU of
E. coli
O157:H7 in a crop (3.45%) were predicted to be higher than those for the conventional fields (2.15%).

IMPORTANCE
This study is the first attempt toward developing a mathematical system model to understand the pathway of
E. coli
O157:H7 in the production of leafy greens. Results of the presented system model indicate that the seasonality of outbreaks of
E. coli
O157:H7-associated contamination of leafy greens was in good agreement with the prevalence of this pathogen in cattle and wild pig feces in a major leafy greens-producing region in California. On the basis of comparisons among the results of different scenarios, it can be recommended that the concentration of
E. coli
O157:H7 in leafy greens can be reduced considerably if contamination of soil with wild pig and cattle feces is mitigated.
The Behavior of Staphylococcus aureus Dual-Species Biofilms Treated with Bacteriophage phiIPLA-RODI Depends on the Accompanying Microorganism
Authors: González Silvia , Fernández Lucía , Campelo Ana Belén , Gutiérrez Diana , Martínez Beatriz , Rodríguez Ana , García Pilar 
Published: November 2016

ABSTRACT

The use of bacteriophages as antimicrobials against pathogenic bacteria offers a promising alternative to traditional antibiotics and disinfectants. Significantly, phages may help to remove biofilms, which are notoriously resistant to commonly used eradication methods. However, the successful development of novel antibiofilm strategies must take into account that real-life biofilms usually consist of mixed-species populations. Within this context, this study aimed to explore the effectiveness of bacteriophage-based sanitation procedures for removing polymicrobial biofilms from food industry surfaces. We treated dual-species biofilms formed by the food pathogenic bacterium
Staphylococcus aureus
in combination with
Lactobacillus plantarum
,
Enterococcus faecium
, or
Lactobacillus pentosus
with the staphylococcal phage phiIPLA-RODI. Our results suggest that the impact of bacteriophage treatment on
S. aureus
mixed-species biofilms varies depending on the accompanying species and the infection conditions. For instance, short treatments (4 h) with a phage suspension under nutrient-limiting conditions reduced the number of
S. aureus
cells in 5-h biofilms by ∼1 log unit without releasing the nonsusceptible species. In contrast, longer infection periods (18 h) with no nutrient limitation increased the killing of
S. aureus
cells by the phage (decrease of up to 2.9 log units). However, in some cases, these conditions promoted the growth of the accompanying species. For example, the
L. plantarum
cell count in the treated sample was up to 2.3 log units higher than that in the untreated control. Furthermore, phage propagation inside dual-species biofilms also depended greatly on the accompanying species, with the highest rate detected in biofilms formed by
S. aureus
-
L. pentosus
. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) also showed changes in the three-dimensional structures of the mixed-species biofilms after phage treatment. Altogether, the results presented here highlight the need to study the impact of phage therapy on microbial communities that reflect a more realistic setting.

IMPORTANCE
Biofilms represent a major source of contamination in industrial and hospital settings. Therefore, developing efficient strategies to combat bacterial biofilms is of the utmost importance from medical and economic perspectives. Bacteriophages have shown potential as novel antibiofilm agents, but further research is still required to fully understand the interactions between phages and biofilm-embedded bacteria. The results presented in this study contribute to achieving a better understanding of such interactions in a more realistic context, considering that most biofilms in the environment consist of mixed-species populations.
Genome Sequence of a Potential New Benyvirus Isolated from Mango RNA-seq Data
Authors: Sela Noa , Luria Neta , Yaari Mor , Prusky Dov , Dombrovsky Aviv 
Published: November 2016

ABSTRACT
We report here the sequence of a new benyvirus found through mango cultivar Shelly RNA-seq analysis in Israel. This is the first virus strain reported in mango trees.
One-year outcome after Descemet membrane endothelial keratoplasty (DMEK) comparing sulfur hexafluoride (SF6) 20% versus 100% air for anterior chamber tamponade
Authors: Schaub Friederike , Enders Philip , Snijders Katharina , Schrittenlocher Silvia , Siebelmann Sebastian , Heindl Ludwig M , Bachmann Björn O , Cursiefen Claus 
Published: November 2016

PurposeTo investigate 1-year clinical outcome and complication rates following Descemet membrane endothelial keratoplasty (DMEK) with sulfur hexafluoride 20% (SF620%) anterior chamber tamponade compared with conventionally used 100% air for primary graft attachment during DMEK surgery.MethodsRecords of 1112 consecutive DMEKs were reviewed retrospectively and grouped by anterior chamber tamponade used during DMEK surgery (SF620% vs 100% air). Outcome measures included intraocular pressure (IOP), best spectacle-corrected visual acuity (BSCVA), endothelial cell density (ECD) and central corneal thickness (CCT) at 1, 3, 6 and 12 months after DMEK surgery. Complication rates were assessed, including intraoperative and postoperative complications, and graft detachment rate requiring rebubbling.ResultsA total of 854 cases were included in this study. In 105 cases (12.3%), DMEK was performed with SF620%, and in 749 cases (87.7%) 100% air was used for anterior chamber tamponade. Outcome results for IOP, BSCVA, ECD and CCT at all follow-up time points were comparable for both anterior chamber tamponade groups without statistical significant differences (p≥0.05), but graft detachment rate requiring rebubbling was significantly lower in the SF620% group (p<0.001).ConclusionWhereas SF620% anterior chamber tamponade does not seem to negatively affect the clinical outcome of DMEK surgery within the first postoperative year, use of SF620% significantly reduces the rate of rebubblings.
Hospital-diagnosed atopic dermatitis and long-term risk of myocardial infarction: a population-based follow-up study
Authors: Riis Jette Lindorff , Vestergaard Christian , Hjuler Kasper Fjellhaugen , Iversen Lars , Jakobsen Lars , Deleuran Mette S , Olsen Morten 
Published: November 2016

ObjectiveAtopic dermatitis (AD) is an inflammatory skin disorder with a childhood prevalence reaching 20%. An estimated 50% of patients have a life-long chronic course. The purpose of this study was to estimate the risk of first-time myocardial infarction (MI) in patients with AD compared with a general population cohort.DesignCohort study.SettingDenmark.ParticipantsUsing population-based medical registries, we identified individuals born in Denmark from 1947 to 1983 with at least two hospital-diagnoses of AD following inpatient admissions or hospital-based outpatient visits at any age from 1977 to 2013. Individuals with AD were matched with general population controls (10:1) for birth-year and gender. Unique personal identifiers permitted unambiguous data linkage.Primary outcome measuresFollow-up began on the date of AD diagnosis (index date for general population controls) and continued until death, emigration, MI or the year 2013. We computed the 15-year-cumulative incidence of MI following a diagnosis of AD. Comparing patients with AD with the general population cohort, we computed HRs of MI presented with 95% CIs and adjusted for history of diabetes mellitus, hypertension, hyperlipidaemia or stroke, educational level, birth-year and sex.ResultsWe identified 4814 patients diagnosed with AD. The cumulative incidence of MI was 0.6% for patients with AD and 0.4% for their matched controls. The corresponding adjusted HR was 1.74 (1.21 to 2.49). The HR for patients who were not in need of systemic treatment was 1.58 (1.02 to 2.45) and it was 2.40 (1.27 to 4.45) for those who were treated with azathioprine, methotrexate or cyclosporine.ConclusionsHospital-diagnosed AD was associated with increased risk of MI compared with the general population.
Patient safety events in out-of-hospital paediatric airway management: a medical record review by the CSI-EMS
Authors: Hansen Matthew , Meckler Garth , Lambert William , Dickinson Caitlin , Dickinson Kathryn , Van Otterloo Joshua , Guise Jeanne-Marie 
Published: November 2016

ObjectiveTo describe the frequency and characterise the nature of patient safety events in paediatric out-of-hospital airway management.MethodsWe conducted a retrospective cross-sectional medical record review of all ‘lights and sirens’ emergency medicine services transports from 2008 to 2011 in patients <18 years of age in the Portland Oregon metropolitan area. A chart review tool (see online supplementary appendix) was adapted from landmark patient safety studies and revised after pilot testing. Expert panels of physicians and paramedics performed blinded reviews of each chart, identified safety events and described their nature. The primary outcomes were presence and severity of patient safety events related to airway management including oxygen administration, bag-valve-mask ventilation (BVM), airway adjuncts and endotracheal intubation (ETI).supplementary appendixResultsFrom the 11 328 paediatric transports during the study period, there were 497 ‘lights and sirens’ (code 3) transports (4.4%). 7 transports were excluded due to missing data. Of the 490 transports included in the analysis, 329 had a total of 338 airway management procedures (some had more than 1 procedure): 61.6% were treated with oxygen, 15.3% with BVM, 8.6% with ETI and 2% with airway adjuncts. The frequency of errors was: 21% (71/338) related to oxygen use, 9.8% (33/338) related to BVM, 9.5% (32/338) related to intubation and 0.9% (3/338) related to airway adjunct use. 58% of intubations required 3 or more attempts or failed altogether. Cardiac arrest was associated with higher odds of a severe error.ConclusionsErrors in paediatric out-of-hospital airway management are common, especially in the context of intubations and during cardiac arrest.
Concerns, perceived need and competing priorities: a qualitative exploration of decision-making and non-participation in a population-based flexible sigmoidoscopy screening programme to prevent colorectal cancer
Authors: Hall N , Birt L , Rees C J , Walter F M , Elliot S , Ritchie M , Weller D , Rubin G 
Published: November 2016

ObjectiveOptimising uptake of colorectal cancer (CRC) screening is important to achieve projected health outcomes. Population-based screening by flexible sigmoidoscopy (FS) was introduced in England in 2013 (NHS Bowel scope screening). Little is known about reactions to the invitation to participate in FS screening, as offered within the context of the Bowel scope programme. We aimed to investigate responses to the screening invitation to inform understanding of decision-making, particularly in relation to non-participation in screening.DesignQualitative analysis of semistructured in-depth interviews and written accounts.Participants and settingPeople from 31 general practices in the North East and East of England invited to attend FS screening as part of NHS Bowel scope screening programme were sent invitations to take part in the study. We purposively sampled interviewees to ensure a range of accounts in terms of beliefs, screening attendance, sex and geographical location.Results20 screeners and 25 non-screeners were interviewed. Written responses describing reasons for, and circumstances surrounding, non-participation from a further 28 non-screeners were included in the analysis. Thematic analysis identified a range of reactions to the screening invitation, decision-making processes and barriers to participation. These include a perceived or actual lack of need; inability to attend; anxiety and fear about bowel preparation, procedures or hospital; inability or reluctance to self-administer an enema; beliefs about low susceptibility to bowel cancer or treatment and understanding of harm and benefits. The strength, rather than presence, of concerns about the test and perceived need for reassurance were important in the decision to participate for screeners and non-screeners. Decision-making occurs within the context of previous experiences and day-to-day life.ConclusionsUnderstanding the reasons for non-participation in FS screening can help inform strategies to improve uptake and may be transferable to other screening programmes.
Gabapentinoids for chronic low back pain: a protocol for systematic review and meta-analysis of randomised controlled trials
Authors: Shanthanna Harsha , Gilron Ian , Thabane Lehana , Devereaux Philip J , Bhandari Mohit , AlAmri Rizq , Rajarathinam Manikandan , Kamath Sriganesh 
Published: November 2016

IntroductionChronic low back pain (CLBP) is a common condition and causes significant pain, distress and disability across the world. It is multifactorial in aetiology and is challenging to manage. Although the underlying mechanism of pain is predominantly non-specific, many argue that there is a substantial neuropathic pain element. Neuropathic pain is more severe, with significant disability. Gabapentinoids, including gabapentin and pregabalin, have proven efficacy in some neuropathic pain conditions. Despite no clear evidence, a substantial population of patients with CLBP are treated with gabapentinoids.ObjectivesWe aim to assess whether the use of gabapentinoids is effective and safe in the treatment of predominant CLBP, by conducting a systematic review and meta-analysis of randomised control trials (RCTs).MethodologyWe will search the databases of MEDLINE, EMBASE and Cochrane for RCTs published in English language and have used gabapentinoids for the treatment of CLBP. Study selection and data extraction will be performed independently by paired reviewers using structured electronic forms, piloted between pairs of reviewers. The review outcomes will be guided by Initiative on Methods, Measurement and Pain Assessment in Clinical Trials guidelines, with pain relief as the primary outcome. We propose to carry out meta-analysis if there are three or more studies in a particular outcome domain, using a random effects model. Pooled outcomes will be reported as weighted mean differences or standardised mean differences and risk ratios with their corresponding 95% CIs, for continuous outcomes and dichotomous outcomes, respectively. Rating of quality of evidence will be reported using GRADE summary of findings table.DiscussionThe proposed systematic review will be able to provide valuable evidence to help decision-making in the use of gabapentinoids for the treatment of CLBP. This will help advance patient care and potentially highlight limitations in existing evidence to direct future research.Ethics and disseminationBeing a systematic review, this study would not necessitate ethical review and approval. We plan to report and publish our study findings in a high impact medical journal, with online access.Trial registration numberCRD42016034040.
Sugar, dental caries and the incidence of acute rheumatic fever: a cohort study of Māori and Pacific children
Authors: Thornley Simon , Marshall Roger J , Bach Katie , Koopu Pauline , Reynolds Gary , Sundborn Gerhard , Ei Win Le Shwe Sin 
Published: November 2016

ObjectiveTo determine whether dental caries, as an indicator of cumulative exposure to sugar, is associated with the incidence of acute rheumatic fever and chronic rheumatic heart disease, in Māori and Pacific children aged 5 and 6 years at their first dental visit.Materials and methodsA cohort study was undertaken which linked school dental service records of caries with national hospital discharge and mortality records. Cox models were used to investigate the strength of the association between dental caries and rheumatic fever incidence.ResultsA total of 20 333 children who were free of rheumatic heart disease at enrolment were available for analysis. During a mean follow-up time of 5 years, 96 children developed acute rheumatic fever or chronic rheumatic heart disease. After adjustment for potential confounders, children with five or more primary teeth affected by caries were 57% (95% CI: 20% to 106%) more likely to develop disease during follow-up, compared to children whose primary teeth were caries free. The population attributable to the risk for caries in this cohort was 22%.ConclusionsDental caries is positively associated with the incidence of acute rheumatic fever and chronic rheumatic heart disease in Māori and Pacific children. Sugar intake, an important risk factor for dental caries, is also likely to influence the aetiology of rheumatic fever.