bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of species occurrence estimators when basic assumptions are not met: a test using field data where true occupancy status is known
Authors: Miller David A. W. , Bailey Larissa L. , Grant Evan H. Campbell , McClintock Brett T. , Weir Linda A. , Simons Theodore R. 
Published: January 2015

Summary

Populations are rarely censused. Instead, observations are subject to incomplete detection, misclassification and detection heterogeneity that result from human and environmental constraints. Though numerous methods have been developed to deal with observational uncertainty, validation under field conditions is rare because truth is rarely known in these cases.

We present the most comprehensive test of occupancy estimation methods to date, using more than 33 000 auditory call observations collected under standard field conditions and where the true occupancy status of sites was known. Basic occupancy estimation approaches were biased when two key assumptions were not met: that no false positives occur and that no unexplained heterogeneity in detection parameters occurs. The greatest bias occurred for dynamic parameters (i.e. local colonization and extinction), and in many cases, the degree of inaccuracy would render results largely useless.

We examined three approaches to increase adherence or relax these assumptions: modifying the sampling design, employing estimators that account for false‐positive detections and using covariates to account for site‐level heterogeneity in both false‐negative and false‐positive detection probabilities. We demonstrate that bias can be substantially reduced by modifications to sampling methods and by using estimators that simultaneously account for false‐positive detections and site‐level covariates to explain heterogeneity.

Our results demonstrate that even small probabilities of misidentification and among‐site detection heterogeneity can have severe effects on estimator reliability if ignored. We challenge researchers to place greater attention on both heterogeneity and false positives when designing and analysing occupancy studies. We provide 9 specific recommendations for the design, implementation and analysis of occupancy studies to better meet this challenge.
Neurocognitive impairment in a large sample of homeless adults with mental illness
Authors: Stergiopoulos V. , Cusi A. , Bekele T. , Skosireva A. , Latimer E. , Schütz C. , Fernando I. , Rourke S. B. 
Published: January 2015

ObjectiveThis study examines neurocognitive functioning in a large, well‐characterized sample of homeless adults with mental illness and assesses demographic and clinical factors associated with neurocognitive performance.MethodA total of 1500 homeless adults with mental illness enrolled in the At Home Chez Soi study completed neuropsychological measures assessing speed of information processing, memory, and executive functioning. Sociodemographic and clinical data were also collected. Linear regression analyses were conducted to examine factors associated with neurocognitive performance.ResultsApproximately half of our sample met criteria for psychosis, major depressive disorder, and alcohol or substance use disorder, and nearly half had experienced severe traumatic brain injury. Overall, 72% of participants demonstrated cognitive impairment, including deficits in processing speed (48%), verbal learning (71%) and recall (67%), and executive functioning (38%). The overall statistical model explained 19.8% of the variance in the neurocognitive summary score, with reduced neurocognitive performance associated with older age, lower education, first language other than English or French, Black or Other ethnicity, and the presence of psychosis.ConclusionHomeless adults with mental illness experience impairment in multiple neuropsychological domains. Much of the variance in our sample's cognitive performance remains unexplained, highlighting the need for further research in the mechanisms underlying cognitive impairment in this population.
The Intergenerational Continuity of Breastfeeding Intention, Initiation, and Duration: A Systematic Review
Authors: Di Manno Laura , Macdonald Jacqui A. , Knight Tess 
Published: January 2015

AbstractBackgroundIn studies investigating predictors of breastfeeding behaviors, it is not uncommon for researchers to adjust for participants’ having been breastfed as an infant. This assumes an intergenerational effect of breastfeeding continuity. Our aim was to investigate the veracity of that assumption. Specifically, we sought to summarize and evaluate evidence of associations between breastfeeding in one generation and breastfeeding intentions and behaviors in the second generation.MethodsA systematic search of psychological, nursing, and medical databases was conducted for studies examining “having been breastfed” as a factor in breastfeeding intention, initiation, or duration. Quality indicators were assessed and limitations reported. Effects were explored according to outcomes of intention, initiation, and duration.ResultsFifteen papers were found to be eligible for the review. Having been breastfed as an infant was consistently correlated with breastfeeding intention, initiation, and duration. Effect sizes differed depending on methodology. Men's infant‐feeding status was also related to later intentions to support or encourage a partner to breastfeed.ConclusionsRobust evidence for intergenerational breastfeeding continuity is present; however, mechanisms that explain this association were not considered in the studies reviewed and would best be explored within longitudinal cohort studies.
Sacral nerve stimulation for faecal incontinence and constipation: a European consensus statement
Authors: Maeda Y. , O'Connell P. R. , Lehur P.‐A. , Matzel K. E. , Laurberg S. ,   European SNS Bowel Study Group
Published: January 2015

AbstractAimIn Europe during the last decade sacral nerve stimulation (SNS) or sacral neuromodulation (SNM) has been used to treat faecal incontinence (FI) and constipation. Despite this, there is little consensus on baseline investigations, patient selection and operative technique. A modified Delphi process was conducted to seek consensus on the current practice of SNS/SNM for FI and constipation.MethodA systematic literature search of SNS for FI and constipation was conducted using PubMed. A set of questions derived from the search and expert opinion were answered on‐line on two occasions by an international panel of specialists from Europe. A 1‐day face‐to‐face meeting of the experts finalized the discussion.ResultsThree hundred and ninety‐three articles were identified from the literature search, of which 147 fulfilled the inclusion criteria. Twenty‐two specialists in FI and constipation from Europe participated. Agreement was achieved on 43 (86%) of 50 domains including the set‐up of service, patient selection, baseline investigations, operative technique and programming of the device. The median of agreement was 95% (35–100%).ConclusionConsensus was achieved on the majority of domains of SNS/SNM for FI and constipation. This should serve as a benchmark for safe and quality practice of SNS/SNM in Europe.
Myocardial perfusion imaging is an effective screening test for coronary artery disease in liver transplant candidates
Authors: Baker Sally , Chambers Charles , McQuillan Patrick , Janicki Piotr , Kadry Zakiyah , Bowen Daniel , Bezinover Dmitri 
Published: January 2015

AbstractA reliable screening test for coronary artery disease (CAD) in liver transplant (LT) candidates with end‐stage liver disease is essential because a high percentage of perioperative mortality and morbidity is CAD‐related. In this study, the effectiveness of myocardial perfusion imaging (MPI) for identification of significant CAD in LT candidates was evaluated. Records of 244 patients meeting criteria for MPI were evaluated: 74 met inclusion criteria; 40 had a positive MPI and cardiology follow‐up; 27 had a negative MPI and underwent LT; and seven had a negative MPI and then had coronary angiography or a significant cardiac event. A selective MPI interpretation strategy was established where MPI‐positive patients were divided into high, intermediate, and low CAD risk groups. The overall incidence of CAD in this study population was 5.1% and our strategy resulted in PPV 20%, NPV 94%, sensitivity 80%, and specificity 50% for categorizing CAD risk. When applied only to the subset of patients categorized as high CAD risk, the strategy was more effective, with PPV 67%, NPV 97%, sensitivity 80%, and specificity 94%. We determined that renal dysfunction was an independent predictive factor for CAD (p < 0.0001, odds ratio = 8.1), and grades of coronary occlusion correlated significantly with chronic renal dysfunction (p = 0.0079).
Internal biliary stenting during orthotopic liver transplantation: anastomotic complications, post‐transplant biliary interventions, and survival
Authors: Mathur Amit K. , Nadig Satish N. , Kingman Stephanie , Lee Dustin , Kinkade Kathleen , Sonnenday Christopher J. , Welling Theodore H. 
Published: January 2015

AbstractBackgroundBiliary complications are a leading source of surgical morbidity following orthotopic liver transplantation (OLT).MethodsWe examined how prophylactic internal biliary stent placement during OLT affected post‐transplant morbidity and mortality in a single‐center retrospective cohort study of 513 recipients (2006–2012). Recipient and donor covariates were collected. Biliary complications included major and minor anastomotic leaks, strictures, or stenoses. Multivariate regression models were created to estimate how operative biliary stents affected outcomes.ResultsAbout 87.3% (n = 448) of recipients had a duct‐to‐duct biliary anastomosis, and 43.1% (n = 221) had biliary stents placed. The biliary complication rate was <15% at five yr, and 44.8% (n = 230) overall. Stenting was not protective from anastomotic biliary complications (p = 0.06). Stenting was associated with a 74% higher adjusted risk of needing multiple endoscopic retrograde cholangiographies (ERCs; odds ratio [OR] 1.74, p = 0.011), and trended toward a lower adjusted risk for repetitive percutaneous transhepatic cholangiography (PTCs; OR 0.56, p = 0.063). Stenting had no effect on the cumulative freedom from biliary complications (p = 0.94). Biliary complications were associated with mortality (HR 1.86, p = 0.014) and was unaffected by stenting (aHR = 0.72, p = 0.246).ConclusionsBiliary stenting during OLT does not deter biliary complications and is associated with higher risk of multiple invasive biliary interventions, particularly ERCs. Surgeons should evaluate the utility of biliary stents at OLT within this context.
Competency frameworks in diabetes
Authors: Simmons D. , Deakin T. , Walsh N. , Turner B. , Lawrence S. , Priest L. , George S. , Vanterpool G. , McArdle J. , Rylance A. , Terry G. , Little P. 
Published: January 2015

AbstractThe quality, skills and attitudes of staff working in the healthcare system are central to multidisciplinary learning and working, and to the delivery of the quality of care patients expect. Patients want to know that the staff supporting them have the right knowledge and attitudes to work in partnership, particularly for conditions such as diabetes where 95% of all care is delivered by the person with diabetes themselves. With the current changes in the NHS structures in England, and the potential for greater variation in the types of ‘qualified provider’, along with the recent scandal at Mid‐Staffordshire Hospital, staff need to be shown to be competent and named/accredited or recognized as such. This will help to restore faith in an increasingly devolved delivery structure. The education and validation of competency needs to be consistently delivered and assured to ensure standards are maintained for different roles and disciplines across each UK nation. Diabetes UK recommends that all NHS organizations prioritize healthcare professional education, training and competency through the implementation of a National Diabetes Competency Framework and the phased approach to delivery to address this need.
ESCI award lecture: regulation, function and biomarker potential of DNA methylation
Authors: Schübeler Dirk 
Published: January 2015

AbstractMethylation of DNA and modifications of histones have emerged as intricately involved in gene regulation as they cross‐talk and respond in multiple ways to the activity of transcription factors. Measuring these epigenome components has become a powerful tool to identify regulatory principles and biomarkers that predict cellular state during development or disease. Here, I will focus on DNA methylation as a reversible epigenetic modification of DNA that has been studied in great detail at the level of the genome. Recent advances in sequencing have identified unexpected dynamics of this modification, which are tightly linked to gene regulation. Understanding how DNA methylation patterns are read and how they contribute to regulation will be critical to interpret and utilize genomic maps of DNA methylation. As these patterns are dynamic during cellular differentiation and perturbed in disease, they present an opportunity to use DNA methylation as a biomarker.
Living and dead soil organic matter under different land uses on a Mediterranean island
Authors: D'Acqui L. P. , Santi C. A. , Vizza F. , Certini G. 
Published: January 2015

SummarySoil under six different land uses on Pianosa Island, in the Mediterranean Sea, was characterized in terms of microbial activity and organic matter quality, in order to define relationships between living and dead organic matter. Biological measurements and chemical and spectroscopic (13C NMR and FTIR) investigation of the extracted soil organic matter provided clues to the effects of soil management on the reciprocal interactions between living and dead organic matter. In particular, the conversion from the original bushy maquis to other land uses, such as degraded thickets of holm oak, maquis‐invaded groves of olive trees, stands of Aleppo pines and abandoned pastures, implied significant reduction of soil organic carbon (SOC) and its microbial fraction (MBC). Cropland, which is the land use with the greatest perturbation of soil, had the smallest SOC, MBC and soil respiration rate. Significant differences in extractable SOC among land uses occurred, both as total amount and as molecular mass distribution. The relatively good relationship between soil respiration and the extracted SOM‐fraction of 2–50 kDa, expressed on a molecular mass basis, suggests that this size is strongly linked to heterotrophic organisms and that it could be representative of a transitory pool of C in soil.
Using forest growth trajectory modelling to complement BioCondition assessment of mine vegetation rehabilitation
Authors: Ngugi Michael R. , Neldner Victor J. , Kusy Branislav 
Published: January 2015

SummaryThe standard rehabilitation objective for open‐cut mines in Queensland is to establish a self‐sustaining native forest ecosystem. Consequently, mine regulators and managers need tools to project whether sites are likely or not to meet agreed completion criteria and to ensure timely remedial interventions. The Ecosystem Dynamics Simulator (EDS) is such a tool capable of modelling forest dynamics and projecting long‐term growth of woody species only. Here, the model was applied to rehabilitation sites aged between 5 and 22 years in Meandu open‐cut coal mine in southeast Queensland. EDS projected structural characteristics for trees (height, diameter, basal area, foliage projective cover and stem density) and tree species composition as a function of rehabilitation age. Projected stand growth attributes were assessed against BioCondition benchmarks developed from eucalypt (Eucalyptus/Corymbia) remnant forests adjacent to the mine. Growth trajectories indicated that sites with >30% eucalypt basal area composition were more likely to develop into eucalypt‐dominated self‐sustaining ecosystems compared with sites that were initially dominated by acacias (Acacia spp.). Projections suggested that some benchmark attributes such as number of large eucalypt trees would take more than 70 years to be met. The application of EDS provided a framework to support decisions on early remedial intervention and assess the risk associated with lease relinquishment.
Seeding the future – the issues of supply and demand in restoration in Australia
Authors: Broadhurst Linda , Driver Martin , Guja Lydia , North Tom , Vanzella Bindi , Fifield Graham , Bruce Stephen , Taylor David , Bush David 
Published: January 2015

SummaryIt has been almost 15 years since concerns about the limited capacity of remnant native vegetation to supply the volumes of seed required to meet increasing restoration demands were first raised. Since that time little progress has been made towards addressing this constraint with the ongoing decline of native vegetation communities, especially since 2000, further challenging seed supply. We provide examples of the size of this demand for seed, as well as major issues associated with seed sourcing. We also discuss how invoking the concept of market forces to drive seed supply and demand is inappropriate and highlight the need for an industry body to oversee seed collection and utilisation standards. We further propose key actions that are required to secure the seed supply chain within the next 20 years to meet existing and future restoration targets. We argue that concerted, coordinated action at Commonwealth, State and regional levels are required to underpin effective future restoration outcomes.
Twelve years on: Ecological restoration and rehabilitation at Sydney Olympic Park
Authors: O'Meara Jennifer , Darcovich Kerry 
Published: January 2015

When Sydney's 760 ha Homebush Bay industrial site was rezoned for urban renewal and staging the Olympic Games in 2000, massive investment was made to remediate past damage and develop a future public park containing active recreation and natural areas. Since that date, endangered forest and wetland communities, along with threatened fauna species, have received priority treatments to improve the ecological function of the Park's natural areas. Evaluation of progress 12 years on reveals substantial achievements and multiple lessons.
Insulin‐like growth factor‐I and UVB photoprotection in human keratinocytes
Authors: Fernandez Tara Lyn , Van Lonkhuyzen Derek R. , Dawson Rebecca A. , Kimlin Michael G. , Upton Zee 
Published: January 2015

AbstractUltraviolet radiation (UVR), in particular the UVB spectrum, is a risk factor for skin cancer development. The generation and accumulation of UVB‐induced genetic mutations are fundamental premalignant events. Keratinocyte interactions between other cutaneous cell populations and the surrounding microenvironment determine cell fate and acute photoresponses. In this study, the importance of the insulin‐like growth factor (IGF) system, in particular the insulin‐like growth factor‐I (IGF‐I), on influencing key processes in the keratinocyte acute photoresponse was investigated. Exogenous IGF‐I and other growth factors present in dermal fibroblast‐conditioned media (CM) were found to significantly enhance keratinocyte survival following UVB irradiation in vitro. This pretreatment was also shown to cause a shift in the expression levels of various DNA damage response proteins. Consequently, this was associated with accelerated rates of UVB‐induced cyclobutane pyrimidine dimer removal in these samples. Finally, activation of the IGF system influenced cell cycle progression in UVB‐irradiated keratinocytes. Taken together, these results highlight the importance of the IGF signalling network in initiating the repair of potentially mutagenic DNA damage in human keratinocytes. The dysregulation of these processes may therefore have significant implications in the aetiology of skin cancers and other cutaneous diseases.
Temperature and the biogeography of algal stoichiometry
Authors: Yvon‐Durocher Gabriel , Dossena Matteo , Trimmer Mark , Woodward Guy , Allen Andrew P. 
Published: January 2015

AbstractAimThe average carbon‐to‐nitrogen‐to‐phosphorus ratio (C:N:P) of marine algae is known to be tightly coupled to that of the inorganic pools of C, N and P in the ocean interior (i.e. the Redfield ratio), and therefore plays a key role in regulating the C and N cycles in the ocean. The C:N:P ratio of algae also varies substantially, both within and among taxa, in response to variation in the abiotic environment, raising the possibility that biogeochemical controls on the marine C and N cycles may shift as a result of climate change. However, the role of temperature in driving phenotypic variation in stoichiometry within algal taxa, as well as biogeographic variation in particulate C, N and P among oceanic regions, remains largely unresolved.LocationGlobal.MethodsTo assess the extent to which temperature controls algal stoichiometry we performed two complementary meta‐analyses. First, we characterized the global temperature dependence of algal stoichiometry by analysing field data that encompassed 767 estimates of C:N:P from 22 oceanic sites spanning over 130° of latitude. Second, we characterized the within‐species acclimation responses of C:N:P stoichiometry to temperature by analysing data that encompassed 17 experiments, 9 species and 4 taxonomic classes.ResultsThe geographic analyses demonstrated that the N:P and C:P ratios of marine algae were best predicted by latitudinal variation in average sea‐surface temperature, and that both ratios increased 2.6‐fold from 0 to 30 °C. These global‐scale temperature responses, which largely reflect geographic variation in the species compositions of algal assemblages, were of similar magnitude to the average within‐species response of the N:P and C:P ratios to experimental temperature manipulations.Main conclusionsThe congruence between field and experimental observations suggests that temperature‐dependent physiological mechanisms operating at the subcellular level play an important role in determining the stoichiometry of algae in the world's oceans.
A Novel Assay for Easy and Rapid Quantification of Helicobacter pylori Adhesion
Authors: Skindersoe Mette E. , Rasmussen Lone , Andersen Leif P. , Krogfelt Karen A. 
Published: January 2015

AbstractBackgroundReducing adhesion of Helicobacter pylori to gastric epithelial cells could be a new way to counteract infections with this organism. We here present a novel method for quantification of Helicobacter pylori adhesion to cells.MethodsHelicobacter pylori is allowed to adhere to AGS or MKN45g cells in a 96‐well microtiter plate. Then wells are added saponin, which lyses the cells without affecting the bacteria. After addition of alamarBlue® (resazurin) and 1‐ to 2‐hour incubation, fluorescence measurements can be used to quantify the number of adherent bacteria.ResultsBy use of the method, we demonstrate that adhesion of both a sabA and babA deletion mutant of H. pylori is significantly reduced compared to the wild type.ConclusionThe method offers a number of applications and may be used to compare the adherence potential of different strains of H. pylori to either cells or different materials or to screen for potential anti‐adhesive compounds. The results presented here suggest that this easy and reproducible assay is well suited for quantitative investigation of H. pylori adhesion.