bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Cover Crop Species and Season on Population Dynamics of Escherichia coli and Listeria innocua in Soil
Authors: Reed-Jones Neiunna L. , Marine Sasha Cahn , Everts Kathryne L. , Micallef Shirley A. 
Published: January 2016

ABSTRACT

Cover crops provide several ecosystem services, but their impact on enteric bacterial survival remains unexplored. The influence of cover cropping on foodborne pathogen indicator bacteria was assessed in five cover crop/green manure systems: cereal rye, hairy vetch, crimson clover, hairy vetch-rye and crimson clover-rye mixtures, and bare ground. Cover crop plots were inoculated with
Escherichia coli
and
Listeria innocua
in the fall of 2013 and 2014 and tilled into the soil in the spring to form green manure. Soil samples were collected and the bacteria enumerated. Time was a factor for all bacterial populations studied in all fields (
P
< 0.001).
E. coli
levels declined when soil temperatures dipped to <5°C and were detected only sporadically the following spring.
L. innocua
diminished somewhat but persisted, independently of season. In an organic field, the cover crop was a factor for
E. coli
in year 1 (
P
= 0.004) and for
L. innocua
in year 2 (
P
= 0.011). In year 1,
E. coli
levels were highest in the rye and hairy vetch-rye plots. In year 2,
L. innocua
levels were higher in hairy vetch-rye (
P
= 0.01) and hairy vetch (
P
= 0.03) plots than in the rye plot. Bacterial populations grew (
P
< 0.05) or remained the same 4 weeks after green manure incorporation, although initial reductions in
L. innocua
numbers were observed after tilling (
P
< 0.05). Green manure type was a factor only for
L. innocua
abundance in a transitional field (
P
< 0.05). Overall, the impacts of cover crops/green manures on bacterial population dynamics in soil varied, being influenced by bacterial species, time from inoculation, soil temperature, rainfall, and tillage; this reveals the need for long-term studies.
Robustness of the Process of Nucleoid Exclusion of Protein Aggregates in Escherichia coli
Authors: Neeli-Venkata Ramakanth , Martikainen Antti , Gupta Abhishekh , Gonçalves Nadia , Fonseca Jose , Ribeiro Andre S. 
Published: January 2016

ABSTRACT

Escherichia coli
segregates protein aggregates to the poles by nucleoid exclusion. Combined with cell divisions, this generates heterogeneous aggregate distributions in subsequent cell generations. We studied the robustness of this process with differing medium richness and antibiotics stress, which affect nucleoid size, using multimodal, time-lapse microscopy of live cells expressing both a fluorescently tagged chaperone (IbpA), which identifies
in vivo
the location of aggregates, and HupA-mCherry, a fluorescent variant of a nucleoid-associated protein. We find that the relative sizes of the nucleoid's major and minor axes change widely, in a positively correlated fashion, with medium richness and antibiotic stress. The aggregate's distribution along the major cell axis also changes between conditions and in agreement with the nucleoid exclusion phenomenon. Consequently, the fraction of aggregates at the midcell region prior to cell division differs between conditions, which will affect the degree of asymmetries in the partitioning of aggregates between cells of future generations. Finally, from the location of the peak of anisotropy in the aggregate displacement distribution, the nucleoid relative size, and the spatiotemporal aggregate distribution, we find that the exclusion of detectable aggregates from midcell is most pronounced in cells with mid-sized nucleoids, which are most common under optimal conditions. We conclude that the aggregate management mechanisms of
E. coli
are significantly robust but are not immune to stresses due to the tangible effect that these have on nucleoid size.

IMPORTANCE
Escherichia coli
segregates protein aggregates to the poles by nucleoid exclusion. From live single-cell microscopy studies of the robustness of this process to various stresses known to affect nucleoid size, we find that nucleoid size and aggregate preferential locations change concordantly between conditions. Also, the degree of influence of the nucleoid on aggregate positioning differs between conditions, causing aggregate numbers at midcell to differ in cell division events, which will affect the degree of asymmetries in the partitioning of aggregates between cells of future generations. Finally, we find that aggregate segregation to the cell poles is most pronounced in cells with mid-sized nucleoids. We conclude that the energy-free process of the midcell exclusion of aggregates partially loses effectiveness under stressful conditions.
The Activity of Escherichia coli Chaperone SurA Is Regulated by Conformational Changes Involving a Parvulin Domain
Authors: Soltes Garner R. , Schwalm Jaclyn , Ricci Dante P. , Silhavy Thomas J. 
Published: January 2016

ABSTRACT

The periplasmic chaperone SurA is critical for the biogenesis of outer membrane proteins (OMPs) and, thus, the maintenance of membrane integrity in
Escherichia coli
. The activity of this modular chaperone has been attributed to a core chaperone module, with only minor importance assigned to the two SurA peptidyl-prolyl isomerase (PPIase) domains. In this work, we used synthetic phenotypes and covalent tethering to demonstrate that the activity of SurA is regulated by its PPIase domains and, furthermore, that its activity is correlated with the conformational state of the chaperone. When combined with mutations in the β-barrel assembly machine (BAM), SurA mutations resulting in deletion of the second parvulin domain (P2) inhibit OMP assembly, suggesting that P2 is involved in the regulation of SurA. The first parvulin domain (P1) potentiates this autoinhibition, as mutations that covalently tether the P1 domain to the core chaperone module severely impair OMP assembly. Furthermore, these inhibitory mutations negate the suppression of and biochemically stabilize the protein specified by a well-characterized gain-of-function mutation in P1, demonstrating that SurA cycles between distinct conformational and functional states during the OMP assembly process.

IMPORTANCE
This work reveals the reversible autoinhibition of the SurA chaperone imposed by a heretofore underappreciated parvulin domain. Many β-barrel-associated outer membrane (OM) virulence factors, including the P-pilus and type I fimbriae, rely on SurA for proper assembly; thus, a mechanistic understanding of SurA function and inhibition may facilitate antibiotic intervention against Gram-negative pathogens, such as uropathogenic
Escherichia coli
,
E. coli
O157:H7,
Shigella
, and
Salmonella
. In addition, SurA is important for the assembly of critical OM biogenesis factors, such as the lipopolysaccharide (LPS) transport machine, suggesting that specific targeting of SurA may provide a useful means to subvert the OM barrier.
Interplay of CodY and ScoC in the Regulation of Major Extracellular Protease Genes of Bacillus subtilis
Authors: Barbieri Giulia , Albertini Alessandra M. , Ferrari Eugenio , Sonenshein Abraham L. , Belitsky Boris R. 
Published: January 2016

ABSTRACT

AprE and NprE are two major extracellular proteases in
Bacillus subtilis
whose expression is directly regulated by several pleiotropic transcriptional factors, including AbrB, DegU, ScoC, and SinR. In cells growing in a rich, complex medium, the
aprE
and
nprE
genes are strongly expressed only during the post-exponential growth phase; mutations in genes encoding the known regulators affect the level of post-exponential-phase gene expression but do not permit high-level expression during the exponential growth phase. Using DNA-binding assays and expression and mutational analyses, we have shown that the genes for both exoproteases are also under strong, direct, negative control by the global transcriptional regulator CodY. However, because CodY also represses
scoC
, little or no derepression of
aprE
and
nprE
was seen in a
codY
null mutant due to overexpression of
scoC
. Thus, CodY is also an indirect positive regulator of these genes by limiting the synthesis of a second repressor. In addition, in cells growing under conditions that activate CodY, a
scoC
null mutation had little effect on
aprE
or
nprE
expression; full effects of
scoC
or
codY
null mutations could be seen only in the absence of the other regulator. However, even the
codY scoC
double mutant did not show high levels of
aprE
and
nprE
gene expression during exponential growth phase in a rich, complex medium. Only a third mutation, in
abrB
, allowed such expression. Thus, three repressors can contribute to reducing exoprotease gene expression during growth in the presence of excess nutrients.

IMPORTANCE
The major
Bacillus subtilis
exoproteases, AprE and NprE, are important metabolic enzymes whose genes are subject to complex regulation by multiple transcription factors. We show here that expression of the
aprE
and
nprE
genes is also controlled, both directly and indirectly, by CodY, a global transcriptional regulator that responds to the intracellular pools of amino acids. Direct CodY-mediated repression explains a long-standing puzzle, that is, why exoproteases are not produced when cells are growing exponentially in a medium containing abundant quantities of proteins or their degradation products. Indirect regulation of
aprE
and
nprE
through CodY-mediated repression of the
scoC
gene, encoding another pleiotropic repressor, serves to maintain a significant level of repression of exoprotease genes when CodY loses activity.
Marital status and risk of dementia: a nationwide population-based prospective study from Sweden
Authors: Sundström Anna , Westerlund Olle , Kotyrlo Elena 
Published: January 2016

ObjectivesTo examine the association between marital status and dementia in a cohort of young-old (50–64) and middle-old (65–74) adults, and also whether this may differ by gender.DesignProspective population-based study with follow-up time of up to 10 years.SettingSwedish national register-based study.Participants2 288 489 individuals, aged 50–74 years, without prior dementia diagnosis at baseline. Dementia was identified using the Swedish National Patient Register and the Cause of Death Register.Outcome measuresThe influence of marital status on dementia was analysed using Cox proportional hazards models, adjusted stepwise for multiple covariates (model 1: adjusted for age and gender; and model 2: additionally adjusted for having adult children, education, income and prior cardiovascular disease).ResultsDuring follow-up, 31 572 individuals in the study were identified as demented. Cox regression showed each non-married subcategory to be associated with a significantly higher risk of dementia than the married group, with the highest risk observed among people in the young-old age group, especially among those who were divorced or single (HRs 1.79 vs 1.71, fully adjusted model). Analyses stratified by gender showed gender differences in the young-old group, with indications of divorced men having a higher relative risk compared with divorced women (HRs 2.1 vs 1.7, only-age adjusted model). However, in the fully adjusted model, these differences were attenuated and there was no longer any significant difference between male and female participants.ConclusionsOur results suggest that those living alone as non-marrieds may be at risk for early-onset and late-onset dementia. Although more research is needed to understand the underlying mechanism by which marital status is associated with dementia, this suggests that social relationships should be taken seriously as a risk factor for dementia and that social-based interventions may provide an opportunity to reduce the overall dementia risk.
A protocol for a randomised clinical trial of the effect of providing feedback on inhaler technique and adherence from an electronic device in patients with poorly controlled severe asthma
Authors: Sulaiman Imran , Mac Hale Elaine , Holmes Martin , Hughes Cian , D'Arcy Shona , Taylor Terrence , Rapcan Viliam , Doyle Frank , Breathnach Aoife , Seheult Jansen , Murphy Desmond , Hunt Eoin , Lane Stephen J , Sahadevan Abhilash , Crispino Gloria , Diette Greg , Killane Isabelle , Reilly Richard B , Costello Richard W 
Published: January 2016

IntroductionIn clinical practice, it is difficult to distinguish between patients with refractory asthma from those with poorly controlled asthma, where symptoms persist due to poor adherence, inadequate inhaler technique or comorbid diseases. We designed an audio recording device which, when attached to an inhaler, objectively identifies the time and technique of inhaler use, thereby assessing both aspects of adherence. This study will test the hypothesis that feedback on these two aspects of adherence when passed on to patients improves adherence and helps clinicians distinguish refractory from difficult-to-control asthma.MethodsThis is a single, blind, prospective, randomised, clinical trial performed at 5 research centres. Patients with partially controlled or uncontrolled severe asthma who have also had at least one severe asthma exacerbation in the prior year are eligible to participate. The effect of two types of nurse-delivered education interventions to promote adherence and inhaler technique will be assessed. The active group will receive feedback on their inhaler technique and adherence from the new device over a 3-month period. The control group will also receive training in inhaler technique and strategies to promote adherence, but no feedback from the device. The primary outcome is the difference in actual adherence, a measure that incorporates time and technique of inhaler use between groups at the end of the third month. Secondary outcomes include the number of patients who remain refractory despite good adherence, and differences in the components of adherence after the intervention. Data will be analysed on an intention-to-treat and a per-protocol basis. The sample size is 220 subjects (110 in each group), and loss to follow-up is estimated at 10% which will allow results to show a 10% difference (0.8 power) in adherence between group means with a type I error probability of 0.05.Trial registration numberNCT01529697; Pre-results.
ESCAPS study protocol: a feasibility randomised controlled trial of ‘Early electrical stimulation to the wrist extensors and wrist flexors to prevent the post-stroke complications of pain and contractures in the paretic arm’
Authors: Fletcher-Smith Joanna C , Walker Dawn-Marie , Sprigg Nikola , James Marilyn , Walker Marion F , Allatt Kate , Mehta Rajnikant , Pandyan Anand D 
Published: January 2016

IntroductionApproximately 70% of patients with stroke experience impaired arm function, which is persistent and disabling for an estimated 40%. Loss of function reduces independence in daily activities and impacts on quality of life. Muscles in those who do not recover functional movement in the stroke affected arm are at risk of atrophy and contractures, which can be established as early as 6 weeks following stroke. Pain is also common. This study aims to evaluate the feasibility of a randomised controlled trial to test the efficacy and cost-effectiveness of delivering early intensive electrical stimulation (ES) to prevent post-stroke complications in the paretic upper limb.Methods and analysisThis is a feasibility randomised controlled trial (n=40) with embedded qualitative studies (patient/carer interviews and therapist focus groups) and feasibility economic evaluation. Patients will be recruited from the Stroke Unit at the Nottingham University Hospitals National Health Service (NHS) Trust within 72 h after stroke. Participants will be randomised to receive usual care or usual care and early ES to the wrist flexors and extensors for 30 min twice a day, 5 days a week for 3 months. The initial treatment(s) will be delivered by an occupational therapist or physiotherapist who will then train the patient and/or their nominated carer to self-manage subsequent treatments.Ethics and disseminationThis study has been granted ethical approval by the National Research Ethics Service, East Midlands Nottingham1 Research Ethics Committee (ref: 15/EM/0006). To our knowledge, this is the first study of its kind of the early application (within 72 h post-stroke) of ES to both the wrist extensors and wrist flexors of stroke survivors with upper limb impairment. The results will inform the design of a definitive randomised controlled trial. Dissemination will include 2 peer-reviewed journal publications and presentations at national conferences.Trial registration numberISRCTN1648908; Pre-results. Clinicaltrials.gov ID:NCT02324634.
Protocol for the China PEACE (Patient-centered Evaluative Assessment of Cardiac Events) Million Persons Project pilot
Authors: Lu Jiapeng , Xuan Si , Downing Nicholas S , Wu Chaoqun , Li Li , Krumholz Harlan M , Jiang Lixin 
Published: January 2016

IntroductionCollection of high-quality data from large populations is considered essential to generate knowledge that is critical to an era of precision medicine. Cardiovascular disease (CVD) is a leading cause of mortality in China and is a suitable focus of an initiative to discover factors that would improve our ability to assess and modify individual risk.Methods and analysisThe pilot phase of China PEACE (Patient-centered Evaluative Assessment of Cardiac Events) Million Persons Project is being conducted during 2014–2015 in four provinces across China to demonstrate the feasibility of a population-based assessment. It is designed to screen 0.4 million community-dwelling residents aged 40–75 years with measurements of blood pressure, height and weight, a lipid blood test, and a questionnaire on cardiovascular-related health status. Participants identified at high risk of CVD receive further health assessments, including ECG, ultrasound scan, blood and urine analysis, and a questionnaire on lifestyle and medical history. Collection of blood and urine samples is used to establish a biobank. High-risk subjects are also counselled with suggestions regarding potential lifestyle changes. In addition, high-risk subjects are followed-up either in a return clinic visit or by telephone interview, with measurement of blood pressure, weight, ECG, and a questionnaire on survival status, hospitalisations and lifestyle. The first 0.1 million participants screened were used to conduct a preliminary analysis, with information on baseline characteristics, health-related behaviours, anthropometric variables, medical history, and prevalence of high-risk subjects.Ethics and disseminationThe central ethics committee at the China National Center for Cardiovascular Disease (NCCD) approved the pilot. Written informed consent is obtained from all participants on entry into the project. Findings will be disseminated in future peer-reviewed papers and will inform strategies aimed at developing precise methods of assessing and modifying risk.Trial registration numberNCT02536456.
Fatal river drowning: the identification of research gaps through a systematic literature review
Authors: Peden Amy E , Franklin Richard C , Leggat Peter A 
Published: January 2016

IntroductionDrowning is a leading cause of unintentional death. Rivers are a common location for drowning. Unlike other location-specific prevention efforts (home swimming pools and beaches), little is known about prevention targeting river drowning deaths.MethodsA systematic literature review was undertaken using English language papers published between 1980 and 2014, exploring gaps in the literature, with a focus on epidemiology, risk factors and prevention strategies for river drowning.ResultsTwenty-nine papers were deemed relevant to the study design including 21 (72.4%) on epidemiology, 18 (62.1%) on risk factors and 10 (34.5%) that proposed strategies for prevention. Risk factors identified included age, falls into water, swimming, using watercraft, sex and alcohol.DiscussionGaps were identified in the published literature. These included a lack of an agreed definition for rivers, rates for fatal river drowning (however, crude rates were calculated for 12 papers, ranging from 0.20 to 1.89 per 100 000 people per annum), and consensus around risk factors, especially age. There was only one paper that explored a prevention programme; the remaining nine outlined proposed prevention activities. There is a need for studies into exposure patterns for rivers and an agreed definition (with consistent coding).ConclusionsThis systematic review has identified that river drowning deaths are an issue in many regions and countries around the world. Further work to address gaps in the published research to date would benefit prevention efforts.
Peritoneal malignant mesothelioma (PMM), and primary peritoneal serous carcinoma (PPSC) and reactive mesothelial hyperplasia (RMH) of the peritoneum. Immunohistochemical and fluorescence in situ hybridisation (FISH) analyses
Authors: Kawai Toshiaki , Tominaga Susumu , Hiroi Sadayuki , Ogata Sho , Nakanishi Kuniaki , Kawahara Kunimitsu , Sonobe Hiroshi , Hiroshima Kenzo 
Published: January 2016

AimsPeritoneal malignant mesothelioma (PMM) is an uncommon tumour, accounting for only 7–9% of all mesotheliomas in Japan. Differential diagnosis between PMM and primary peritoneal serous carcinoma (PPSC), a high-grade serous carcinoma, may be difficult, and separating reactive mesothelial hyperplasia (RMH) from PMM can be even more challenging.MethodsTo help differentiate PMM from PPSC and RMH, we used immunohistochemistry to examine mesothelial-associated markers (calretinin, AE1/AE3, CK5/6, CAM5.2, D2-40, WT-1, HBME1, thrombomodulin), adenocarcinoma-associated markers (CEA, BerEP4, MOC31, ER (estrogen receptor), PgR, TTF-1, Claudin-4, Pax8), and malignant-related and benign-related markers (epithelial membrane antigen (EMA), desmin, GLUT-1, CD146 and IMP3), and FISH to examine for homozygous deletion of 9p21. We used formalin-fixed, paraffin-embedded blocks from 22 PMMs (M:F=18:4; subtypes: 16 epithelioid, 6 biphasic), 11 PPSCs and 23 RMHs.ResultsSeventeen of the mesotheliomas (four PMM from women) were classified as diffuse, while five were localised. Calretinin was 91% positive in PMM, but negative in PPSC (specificity, 100%). BerEP4, Claudin-4 and PAX8 were all 100% positive in PPSC (specificities, 100%, 95% and 95%, respectively, for excluding PMM). For distinguishing PMM and RMH, sensitivity for EMA in mesothelioma was 68%, while for IMP3 and GLUT-1 it was 64% and 50%, respectively, all with high specificities. FISH analysis revealed homozygous deletion of the 9p21 locus in 11/13 PMMs, but in 0/11 RMHs.ConclusionsCalretinin and BerEP4 may be the best positive markers for differentiating PMM from PPSC. EMA, in combination with IMP3 and desmin, is useful, and homozygous deletion of 9p21 may be helpful, for differentiating PMM from RMH.