bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic resolution of the ‘curse of complexity’ in adaptive evolution of complex traits
Authors: Badyaev Alexander V. 
Published: June 2014

AbstractThe age of most genes exceeds the longevity of their genomic and physiological associations by many orders of magnitude. Such transient contexts modulate the expression of ancient genes to produce currently appropriate and often highly distinct developmental and functional outcomes. The efficacy of such adaptive modulation is diminished by the high dimensionality of complex organisms and associated vast areas of neutrality in their genotypic and developmental networks (and, thus, weak natural selection). Here I explore whether epigenetic effects facilitate adaptive modulation of complex phenotypes by effectively reducing the dimensionality of their deterministic networks and thus delineating their developmental and evolutionary trajectories even under weak selection. Epigenetic effects that link unconnected or widely dispersed elements of genotype space in ecologically relevant time could account for the rapid appearance of functionally integrated adaptive modifications. On an organismal time scale, conceptually similar processes occur during recurrent epigenetic reprogramming of somatic stem cells to produce, recurrently and reversibly, a bewildering array of differentiated and persistent cell lineages, all sharing identical genomic sequences despite strongly distinct phenotypes. I discuss whether close dependency of onset, scope and duration of epigenetic effects on cellular and genomic context in stem cells could provide insights into contingent modulation of conserved genomic material on a much longer evolutionary time scale. I review potential empirical examples of epigenetic bridges that reduce phenotype dimensionality and accomplish rapid adaptive modulation in the evolution of novelties, expression of behavioural types, and stress‐induced ossification schedules.
Non‐coding RNAs as the bridge between epigenetic mechanisms, lineages and domains of life
Authors: Sela Mor , Kloog Yoel , Rechavi Oded 
Published: June 2014

AbstractMany cases of heritable environmental responses have been documented but the underlying mechanisms are largely unknown. Recently, inherited RNA interference has been shown to act as a multigenerational genome surveillance apparatus. We suggest that inheritance of regulatory RNAs is at the root of many other epigenetic phenomena, the trigger that induces other epigenetic mechanisms, such as the depositing of histone modifications and DNA methylation. In addition, we explore the possibility that interacting organisms influence each other's transcriptomes by exchanging heterologous non‐coding RNAs.
Biophysical constraints on the evolution of tissue structure and function
Authors: Hunter P. J. , de Bono B. 
Published: June 2014

Key pointsWe outline an extension of phylogenetic studies of protein interaction networks to take into account biophysical constraints to interaction imposed by tissues regulating these networks and we define these constraints explicitly as a means to track the evolution of tissue structure and function objectively.For biophysical constraints that are associated at the lowest spatial scales with molecular diffusion within and between cells that are less than 100 μm apart, we define a cylinder of 40 μm radius centred on a small vessel as the primary functional tissue unit (pFTU).Molecular transport and communication between distributed or contiguous pFTUs via the endothelial or epithelial vessels is characterised at the level of secondary functional tissue units (sFTUs). sFTUs represent units of physiological function that are replicated multiple times in a whole organ.Non‐dimensional analysis, which expresses the relative importance of biophysical processes, provides the metrics to quantify and compare the function of FTUs for phylogenetic analysis.We lay the ground for a systematic approach to the measurement of tissue structure and function, based on biophysical principles, at the level of primary and secondary FTUs.AbstractPhylogenetic analyses based on models of molecular sequence evolution have driven to industrial scale the generation, cataloguing and modelling of nucleic acid and polypeptide structure. The recent application of these techniques to study the evolution of protein interaction networks extends this analytical rigour to the study of nucleic acid and protein function. Can we further extend phylogenetic analysis of protein networks to the study of tissue structure and function? If the study of tissue phylogeny is to join up with mainstream efforts in the molecular evolution domain, the continuum field description of tissue biophysics must be linked to discrete descriptions of molecular biochemistry. In support of this goal we discuss tissue units, and biophysical constraints to molecular function associated with these units, to present a rationale with which to model tissue evolution. Our rationale combines a multiscale hierarchy of functional tissue units (FTUs) with the corresponding application of physical laws to describe molecular interaction networks and flow processes over continuum fields within these units. Non‐dimensional numbers, derived from the equations governing biophysical processes in FTUs, are proposed as metrics for comparative studies across individuals, species or evolutionary time. We also outline the challenges inherent to the systematic cataloguing and phylogenetic analysis of tissue features relevant to the maintenance and regulation of molecular interaction networks. These features are key to understanding the core biophysical constraints on tissue evolution.
Genome Sequence of Leuconostoc mesenteroides subsp.
cremoris
Strain T26, Isolated from Mesophilic Undefined Cheese Starter
Authors: Pedersen T. B. , Kot W. P. , Hansen L. H. , Sørensen S. J. , Broadbent J. R. , Vogensen F. K. , Ardö Y. 
Published: June 2014

ABSTRACT

Leuconostoc
is the main group of heterofermentative bacteria found in mesophilic dairy starters. They grow in close symbiosis with the
Lactococcus
population and are able to degrade citrate. Here we present a draft genome sequence of
Leuconostoc mesenteroides
subsp.
cremoris
strain T26.
Avian Influenza Virus with Hemagglutinin-Neuraminidase Combination H8N8, Isolated in Russia
Authors: Sivay Mariya V. , Sharshov Kirill A. , Pantin-Jackwood Mary , Muzyka Vladimir V. , Shestopalov Alexander M. 
Published: June 2014

ABSTRACT
We report the genome sequence of an avian influenza virus (AIV) subtype H8N8, isolated in Russia. The genome analysis shows that all genes belong to AIV Eurasian lineages. The PB2 gene was similar to a Mongolian low-pathogenic (LP) AIV H7N1 and a Chinese high-pathogenic (HP) AIV H5N2.
Draft Genome Sequence of Acetobacter aceti Strain 1023, a Vinegar Factory Isolate
Authors: Hung John E. , Mill Christopher P. , Clifton Sandra W. , Magrini Vincent , Bhide Ketaki , Francois Julie A. , Ransome Aaron E. , Fulton Lucinda , Thimmapuram Jyothi , Wilson Richard K. , Kappock T. Joseph 
Published: June 2014

ABSTRACT

The genome sequence of
Acetobacter aceti
1023, an acetic acid bacterium adapted to traditional vinegar fermentation, comprises 3.0 Mb (chromosome plus plasmids).
A. aceti
1023 is closely related to the cocoa fermenter
Acetobacter pasteurianus
386B but possesses many additional insertion sequence elements.
Complete Genome Sequence of a Virulent Strain, Streptococcus iniae ISET0901, Isolated from Diseased Tilapia
Authors: Pridgeon Julia W. , Zhang Dunhua , Zhang Lee 
Published: June 2014

ABSTRACT

Streptococcus iniae
ISET0901 is a virulent strain isolated in 2007 from diseased tilapia. Its full genome is 2,070,856 bp. The availability of this genome will allow comparative genomics to identify virulence genes important for the pathogenesis of streptococcosis caused by
S. iniae
, as well as possible immunogens for vaccine development.
Validation of risk assessment scales and predictors of intentions to quit smoking in Australian Aboriginal and Torres Strait Islander peoples: a cross-sectional survey protocol
Authors: Gould Gillian Sandra , Watt Kerrianne , McEwen Andy , Cadet-James Yvonne , Clough Alan R 
Published: June 2014

IntroductionTobacco smoking is a very significant behavioural risk factor for the health of Australian Aboriginal and Torres Strait Islanders, and is embedded as a social norm. With a focus on women of childbearing age, and men of similar age, this project aims to determine how Aboriginal and Torres Strait Islander smokers assess smoking risks and how these assessments contribute to their intentions to quit. The findings from this pragmatic study should contribute to developing culturally targeted interventions.Methods and analysisA cross-sectional study using quantitative and qualitative data. A total of 120 Aboriginal and Torres Strait Islander community members aged 18–45 years will be recruited at community events and through an Aboriginal Community Controlled Health Service (ACCHS). Participants will be interviewed using a tablet computer or paper survey. The survey instrument uses modified risk behaviour scales, that is, the Risk Behaviour Diagnosis (RBD) scale and the Smoking Risk Assessment Target (SRAT) (adapted from the Risk Acceptance Ladder) to determine whether attitudes of Aboriginal and Torres Strait Islander smokers to health risk messages are predictors of intentions to quit smoking.The questionnaire will be assessed for face and content validity with a panel of Indigenous community members. The internal consistency of the RBD subscales and their patterns of correlation will be explored. Multivariate analyses will examine predictors of intentions to quit. This will include demographics such as age, gender, nicotine dependence, household smoking rules and perceived threat from smoking and efficacy for quitting. The two risk-assessment scales will be examined to see whether participant responses are correlated.Ethics and disseminationThe Aboriginal Health & Medical Research Council Ethics Committee and university ethics committees approved the study. The results will be published in a peer-reviewed journal and a community report will be disseminated by the ACCHS, and at community forums.Note about terminologyWe use the term Aboriginal and Torres Strait Islander peoples, except where previous research has reported findings from only one group for example, Aboriginal people. Indigenous is used here to refer to Indigenous peoples in the international context, and issues, policies or systems, for example, Indigenous health, Indigenous tobacco control.
Use of corticosteroids during pregnancy and risk of asthma in offspring: a nationwide Danish cohort study
Authors: Byrjalsen Anna , Frøslev Trine , Telén Andersen Ane Birgitte , Olsen Morten , Toft Sørensen Henrik 
Published: June 2014

ObjectiveTo examine whether in utero exposure to local and systemic corticosteroids is associated with asthma development in offspring.DesignCohort study.SettingDenmark.ParticipantsWe included all singletons born alive in Denmark between 1996 and 2009. Data on maternal corticosteroid use, asthma in offspring and covariates were obtained from medical registries.Main outcome measuresWe compared asthma risks of children prenatally exposed to corticosteroids and of children of former corticosteroid users with that of unexposed children. We computed absolute risks and used proportional-hazards regression to compute adjusted HRs (aHRs). Using logistic regression we compared exposed children with unexposed siblings in a ‘within-mother-between-pregnancy’ analysis. Adjustment addressed varying length of follow-up.ResultsWe identified 877 778 children, 3.6% of whom were prenatally exposed to systemic (n=5327) or local (n=24 436) corticosteroids. A total of 105 677 children developed asthma during follow-up with a 10-year risk of 18.4% among the exposed and 13.5% among the unexposed. The aHR was 1.54 (95% CI 1.45 to 1.65) for systemic use, 1.45 (95% CI 1.40 to 1.50) for local use and 1.32 (95% CI 1.30 to 1.34) for former use. The adjusted OR of the ‘within-mother-between-pregnancy’ analysis was 1.11 (95% CI 0.98 to 1.25).ConclusionsThese population-based data do not support a strong causal association between maternal corticosteroid use during pregnancy and increased asthma risk in offspring.
Impact of comorbidity on risk of venous thromboembolism in patients with breast cancer: a Danish population-based cohort study
Authors: Ording Anne Gulbech , Horváth-Puhó Erzsébet , Garne Jens Peter , Nyström Petra Witt , Vyberg Mogens , Sørensen Henrik Toft , Lash Timothy L 
Published: June 2014

ObjectivesTo assess the interaction between comorbidity and breast cancer (BC) on the rate of venous thromboembolism (VTE) beyond what can be explained by the independent effects of BC and comorbidity.DesignPopulation-based matched cohort study.SettingDenmark.ParticipantsDanish patients with BC (n=62 376) diagnosed in 1995–2010 and a comparison cohort of women without BC (n=304 803) from the general population were matched to the patients with BC on year of birth in 5-year intervals and on the specific diseases included in the Charlson Comorbidity Index (CCI) and atrial fibrillation and obesity.MeasuresThe rate ratios of VTE per 1000 person-years (PY) were computed by comorbidity levels using the CCI, and interaction contrasts (IC) were calculated as a measure of the excess or deficit VTE rate not explained by the independent effects of BC and comorbidity.ResultsAmong patients with BC with a CCI score of 1, the 0–1 year VTE rate was 12/1000 PY, and interaction accounted for 10% of the rate (IC=3.2, 95% CI 0.5 to 5.9). Among patients with BC with CCI ≥4, the VTE rate was 17, and interaction accounted for 8% of the rate (IC=1.2, 95% CI −1.8 to 4.2). There was no interaction during 2–5 years of follow-up.ConclusionsThere was only little interaction between BC and the CCI score on the rate of VTE.
Parental perceptions of school-based influenza immunisation in Ontario, Canada: a qualitative study
Authors: MacDougall Donna , Crowe Lois , Pereira Jennifer A , Kwong Jeffrey C , Quach Susan , Wormsbecker Anne E , Ramsay Hilary , Salvadori Marina I , Russell Margaret L ,   for the Public Health Agency of Canada/Canadian Institutes of Health Research Influenza Research Network (PCIRN) Program Delivery and Evaluation Group
Published: June 2014

ObjectiveTo understand the perspectives of Ontario parents regarding the advantages and disadvantages of adding influenza immunisation to the currently existing Ontario school-based immunisation programmes.DesignDescriptive qualitative study.ParticipantsParents of school-age children in Ontario, Canada, who were recruited using a variety of electronic strategies (social media, emails and media releases), and identified as eligible (Ontario resident, parent of one or more school-age children, able to read/write English) on the basis of a screening questionnaire. We used stratified purposeful sampling to obtain maximum variation in two groups: parents who had ever immunised at least one child against influenza or who had never done so. We conducted focus groups (teleconference or internet forum) and individual interviews to collect data. Thematic analysis was used to analyse the data.SettingOntario, Canada.ResultsOf the 55 participants, 16 took part in four teleconference focus groups, 35 in 6 internet forum focus groups and four in individual interviews conducted between October 2012 and February 2013. Participants who stated that a school-based influenza immunisation programme would be worthwhile for their child valued its convenience and its potential to reduce influenza transmission without interfering with the family routine. However, most thought that for a programme to be acceptable, it would need to be well designed and voluntary, with adequate parental control and transparent communication between the key stakeholder groups of public health, schools and parents.ConclusionsThese results will benefit decision-makers in the public health and education sectors as they consider the advantages and disadvantages of immunising children in schools as part of a system-wide influenza prevention approach. Further research is needed to assess the perceptions of school board and public health stakeholders.
Improvement of patient satisfaction with the neurosurgery service at a large tertiary care, London-based hospital
Authors: Khan Amad , Naushad Chaudhry Mohammad , Khalid Salema , Nandi Dipankar 
Published: June 2014

AbstractPatient satisfaction is central to healthcare provision and the effective running of any surgical unit. Following on from both formal and informal feedback, we decided to look objectively at patient satisfaction with the neurosurgery service at a large tertiary care hospital in London and identify areas that needed improvement within the unit. Patient satisfaction was looked at with respect to four different aspects of the neurosurgery service: the surgeons, ward doctors, nurses, and hospital services. A questionnaire-based cross-sectional study was conducted and once the data were collected a plan of action to improve service provision was put into place. Data were collected from 150 patients over a 3 month period from September to November 2012. Interventions were made and data re-collected from 150 patients from January to March 2013. With regards to satisfaction with the neurosurgery service, 76.7% (n=115) were satisfied; following implementation of our measures for improvement, which included staff education, meetings and posters, this figure increased to 90.6% (n=136, p<0.001 on Chi-square testing). In conclusion, patient satisfaction should be at the crux of patient care, with a strong focus on effective communication skills, and can be improved by identification of issues by direct patient feedback and subsequent action based on this.
Paediatric ED reattendance rates: comparing nurse practitioners and other clinicians
Authors: Feetham Jane E , Christian Will , Benger Jonathan R , Hoskins Rebecca , Odd David , Lyttle Mark D 
Published: June 2014

ObjectiveThe aim of this project is to establish the unplanned reattendance rate for paediatric emergency nurse practitioners (PENPs) working in a designated paediatric emergency department (PED) while identifying the case mix of patients seen by PENPs compared with their medical counterparts.DesignQuantitative data regarding patient characteristics and reattendance were collected during retrospective review of case notes across two representative 2-week periods.SettingThe study site is a tertiary urban PED with an annual attendance of 32 000 patients aged from birth to 15 years.Main outcome measuresReattendance rates, patient characteristics, triage scores, presenting complaint and numbers of patients discussed with a paediatric emergency medicine consultant were evaluated.ResultsThe results showed that PENPs have a lower reattendance rate (1.75%) when compared with senior and junior doctors in training (4.29%, 5.76%); however, PENPs treat a different population of children. When the odds of PENP reattendance are adjusted for this, the significance of the difference becomes less certain.ConclusionsPENPs work autonomously when seeing children presenting with minor trauma and make a positive contribution in achieving the reattendance Clinical Quality Indicator.
Musculoskeletal symptoms and orthopaedic complications in pregnancy: pathophysiology, diagnostic approaches and modern management
Authors: Bhardwaj Amit , Nagandla Kavitha 
Published: June 2014

AbstractLow back pain is a common musculoskeletal symptom in pregnancy that can present as lumbar pain or pelvic girdle pain, with significant physical and psychosocial implications. Pelvic girdle pain is more prevalent and results in greater disability than lumbar pain. It is possible to distinguish between these two conditions from a detailed history based on the site of the pain, its intensity, disability and pain provocation tests. Management of low back pain in pregnancy is conservative, with physical exercise for lumbar pain and minimising activities that exacerbate pain, analgesics and bed rest for pelvic girdle pain, as well as avoiding abduction beyond the pain-free zone in labour. There is evidence that stabilising exercises in patients with pelvic girdle pain postpartum have a beneficial effect. Other treatment modalities that have been shown to be safe and effective include pelvic belts, transcutaneous electrical nerve stimulation, spinal manipulative therapy, acupuncture and complementary therapy with yoga. Other orthopaedic complications in pregnancy such as carpal tunnel syndrome, pubic symphysis rupture, transient osteoporosis and osteonecrosis are usually self-limiting with a satisfactory outcome. However, a lack of awareness and failure to recognise these complications can result in long-term morbidity. Knowledge of the preoperative diagnostic investigations, surgical approaches and intraoperative positioning of the mother to avoid gravid uterus compression is vital in orthopaedic emergencies such as lumbar disc herniation, cauda equina syndrome, fractures and acute compartment syndrome of the lower limb to ensure a safe maternal and fetal outcome and to prevent serious disability. Pregnancy is not contraindicated in women with pre-existing orthopaedic complications such as kyphoscoliosis and total hip arthroplasty as there is no evidence to suggest increased maternal or fetal risks.
Large testes and brain sizes in odontocetes (order Cetacea, suborder Odontoceti): the influence of mating system on encephalization
Authors: Kelley Trish C. , Higdon Jeff W. , Ferguson Steven H. 
Published: June 2014

Little is known about their mating systems, but odontocetes may utilize the same types of mating systems as terrestrial mammals. Species with relatively large testes are likely to be polygynandrous, while species with smaller testes and greater sexual size dimorphism (SSD) are predicted to be polygynous. The “Machiavellian intelligence or sexual conflict” hypothesis predicts that polygynadrous species also evolved larger brains both to coerce conspecifics to mate and to resist mating attempts by undesirable mates. The “costly tissue” hypothesis predicts that species investing heavily in testes invest less in brain tissue and vice versa to conserve energy. Residual testes and brain mass measurements were used to test the sexual conflict and costly tissue hypotheses in 40 species of odontocetes. Correlations were performed on both raw data and independent contrasts to control for phylogeny. There was a significant positive correlation between residual testes mass and SSD in both data sets, and between residual testes mass and residual brain mass in the non-phylogenetically controlled data set. Results indicate a negative relationship between increased testes masses and SSD in odontocetes. There was no support for the costly tissue hypothesis. Support for Machiavellian intelligence or sexual conflict hypothesis was found only when phylogenetic effects were not considered.