bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultra‐high‐sensitivity stable‐isotope probing of rRNA by high‐throughput sequencing of isopycnic centrifugation gradients
Authors: Aoyagi Tomo , Hanada Satoshi , Itoh Hideomi , Sato Yuya , Ogata Atsushi , Friedrich Michael W. , Kikuchi Yoshitomo , Hori Tomoyuki 
Published: November 2014

SummaryStable isotope probing (SIP) of rRNA directly identifies microorganisms assimilating an isotopically labelled substrate. High‐throughput DNA sequencing is available for label screening at high resolution and high sensitivity, yet its effectiveness and validity remain to be clarified. Here, we investigated whether the detection sensitivity of rRNA‐SIP could be improved by using Illumina sequencing in place of terminal restriction fragment length polymorphism (T‐RFLP) analysis. A dilution series of 13C‐labelled RNA from Escherichia coli (1–0.0001%) and unlabelled RNA from Bacillus subtilis was density separated and fractionated. Illumina sequencing of isopycnic centrifugation gradients was able to detect 13C‐labelled RNA in the heaviest fraction with a buoyant density of 1.798 g ml−1 even at the mixing ratio of 0.001%, whereas the detection ability of T‐RFLP was not lower than 0.5%. Quantitative reverse transcription polymerase chain reaction of the density‐separated RNAs showed that 13C‐labelled RNAs at mixing ratios of 0.05–0.001% had definitely accumulated in the heaviest fraction. Consequently, high‐throughput sequencing provided up to 500‐fold higher sensitivity for screening of 13C‐labelled RNA than T‐RFLP. Ultra‐high‐sensitivity rRNA‐SIP represents a clear advance towards a more complete understanding of microbial ecosystem function, including the ecophysiology of rare microorganisms in various natural environments.
Detecting effects of spatial memory and dynamic information on animal movement decisions
Authors: Schlägel Ulrike E. , Lewis Mark A. 
Published: November 2014

Summary

Animals of many species demonstrate movement behaviour in which decisions are based on a variety of information. Effects of resources have been studied widely, often under the assumption that the environment is constant over the course of the study. Much less understood is the role of dynamic information about continuously changing resource availability and past experiences. Such information can be acquired during movement bouts and used for future decisions via memory.

We present a new class of animal movement models, which incorporates a dynamic interplay of movement and information gain processes. Information is contained in a dynamic cognitive map. As an example, we consider time since last visit to locations and how this interacts with environmental information to shape movement patterns. Our models can be fitted to empirical movement trajectories and are therefore amenable to statistical inference (parameter estimation and model selection).

We tested the functionality of our method using simulated data. Parameter estimates were in accordance with true values used in the simulations, and model selection via Bayesian information criterion (BIC) was able to identify true underlying mechanisms of simulated trajectories. Thus, if time since last visit to locations influences movement decisions, our method is able to detect this mechanism.

The use of dynamic information such as the one demonstrated in our example models likely requires cognitive abilities such as spatial memory. Therefore, our method can be used to reveal evidence of spatial memory in empirical movement data. Understanding the components of individual movement decisions and their interactions ultimately helps us to predict how population distribution patterns respond to environmental changes, such as landscape fragmentation and changing climate.
Rapid decline and extinction of a montane frog population in southern Australia follows detection of the amphibian pathogen Batrachochytrium dendrobatidis
Authors: Gillespie G. R. , Hunter D. , Berger L. , Marantelli G. 
Published: November 2014

AbstractThe amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been implicated as a leading agent of amphibian declines. However, few studies have documented the real‐time host/pathogen dynamics during the arrival of Bd and the decline of an amphibian population. Diagnosing population declines is difficult because multiple factors may be involved and data are often inadequate. However, identifying the relative impact among different threatening processes is critical to understanding population declines. We report the decline and extinction of a population of a threatened temperate montane frog species Litoria spenceri in south‐eastern Australia. Unlike most threatened species at the time, its ecology and population demography were well understood, and a monitoring programme was in place, enabling prompt detection of the decline and evaluation of its cause. Histology for Bd on a unique series of phalange samples showed that the decline was strongly linked to the arrival and increased prevalence of Bd, estimated to have emerged in the population within 39 days of first detection. Our study provides the first real‐time observation of a mass die‐off and decline in a temperate Australian species and the first tight estimate of Bd arrival in a declining population in Australia. These findings not only provide further evidence that Bd has contributed to amphibian declines but also demonstrates how Bd may work in concert with other threatening processes, resulting in extinction.
Detecting abundance trends under uncertainty: the influence of budget, observation error and environmental change
Authors: Nuno A. , Milner‐Gulland E. J. , Bunnefeld N. 
Published: November 2014

AbstractPopulation monitoring must robustly detect trends over time in a cost‐effective manner. However, several underlying ecological changes driving population trends may interact differently with observation uncertainty to produce abundance trends that are more or less detectable for a given budget and over a given time period. Errors in detecting these trends include failing to detect declines when they exist (typeII), detecting them when they do not exist (typeI), detecting trends in one direction when they are actually in another direction (typeIII) and incorrectly estimating the shape of the trend. Robust monitoring should be able to avoid each of these error types. Using monitoring of two contrasting ungulate species and multiple scenarios of population change (poaching, climate change and road development) in the Serengeti ecosystem as a case study, we used a ‘virtual ecologist’ approach to investigate monitoring effectiveness under uncertainty. We explored how the prevalence of different types of error varies depending on budgetary, observational and environmental conditions. Higher observation error and conducting surveys less frequently increased the likelihood of not detecting trends and misclassifying the shape of the trend. As monitoring period and frequency increased, observation uncertainty was more important in explaining effectiveness. TypesIandIIIerrors had low prevalence for both ungulate species. Greater investment in monitoring considerably decreased the likelihood of failing to detect significant trends (typeIIerrors). Our results suggest that it is important to understand the effects of monitoring conditions on perceived trends before making inferences about underlying processes. The impacts of specific threats on population abundance and structure feed through into monitoring effectiveness; hence, monitoring programmes must be designed with the underlying processes to be detected in mind. Here we provide an integrated modelling framework that can produce advice on robust monitoring strategies under uncertainty.
Systematic review with meta‐analysis: magnetic resonance enterography signs for the detection of inflammation and intestinal damage in Crohn's disease
Authors: Church P. C. , Turner D. , Feldman B. M. , Walters T. D. , Greer M.‐L. , Amitai M. M. , Griffiths A. M. ,   the ImageKids Study Group
Published: November 2014

SummaryBackgroundIn the treatment of Crohn's disease (CD), mucosal healing has become a major goal, with the hope of avoiding intestinal damage from chronic inflammation. Magnetic resonance enterography (MRE) has emerged as a non‐invasive means of monitoring inflammation and damage.AimsAs part of the development of MRE‐based multi‐item measures of inflammation and damage for paediatric studies, we carried out a systematic review and meta‐analysis to identify MRE variables used to describe these two distinct concepts.Methods2501 studies of MRI and CD were identified. Studies written in any language reporting individual MRE signs for patients diagnosed with CD were included. Two‐hundred‐and‐forty‐four studies were fully reviewed and 62 were included (inflammation, n = 51; damage, n = 24). Sensitivity, specificity and associated confidence intervals were calculated, and hierarchical summary ROC curves were constructed for each MRE sign.ResultsA total of 22 MRE signs were used to reflect inflammation, and 9 to reflect damage. Diagnostic accuracy of MRE signs of inflammation and damage was heterogeneous; however, wall enhancement, mucosal lesions and wall T2 hyperintensity were the most consistently useful for inflammation (most sensitivities >80% and specificities >90%), and detection of abscess and fistula were most consistently useful for damage (most sensitivities >90%, specificities >95%).ConclusionsIdentifying the best MRE variables to reflect inflammation and damage will maximise the utility of this rapidly emerging technique and is the first stage of constructing MRE‐based indices for evaluating inflammation and intestinal damage.
Using mixed methods research designs in health psychology: An illustrated discussion from a pragmatist perspective
Authors: Bishop Felicity L. 
Published: November 2014

PurposeTo outline some of the challenges of mixed methods research and illustrate how they can be addressed in health psychology research.MethodsThis study critically reflects on the author's previously published mixed methods research and discusses the philosophical and technical challenges of mixed methods, grounding the discussion in a brief review of methodological literature.ResultsMixed methods research is characterized as having philosophical and technical challenges; the former can be addressed by drawing on pragmatism, the latter by considering formal mixed methods research designs proposed in a number of design typologies. There are important differences among the design typologies which provide diverse examples of designs that health psychologists can adapt for their own mixed methods research. There are also similarities; in particular, many typologies explicitly orient to the technical challenges of deciding on the respective timing of qualitative and quantitative methods and the relative emphasis placed on each method. Characteristics, strengths, and limitations of different sequential and concurrent designs are identified by reviewing five mixed methods projects each conducted for a different purpose.ConclusionsAdapting formal mixed methods designs can help health psychologists address the technical challenges of mixed methods research and identify the approach that best fits the research questions and purpose. This does not obfuscate the need to address philosophical challenges of mixing qualitative and quantitative methods.
Statement of contribution

What is already known on this subject?

Mixed methods research poses philosophical and technical challenges.

Pragmatism in a popular approach to the philosophical challenges while diverse typologies of mixed methods designs can help address the technical challenges.

Examples of mixed methods research can be hard to locate when component studies from mixed methods projects are published separately.

What does this study add?

Critical reflections on the author's previously published mixed methods research illustrate how a range of different mixed methods designs can be adapted and applied to address health psychology research questions.

The philosophical and technical challenges of mixed methods research should be considered together and in relation to the broader purpose of the research.
Difficulties in using Material Safety Data Sheets to analyse occupational exposures to contact allergens
Authors: Friis Ulrik F. , Menné Torkil , Flyvholm Mari‐Ann , Bonde Jens P. E. , Johansen Jeanne D. 
Published: November 2014

SummaryBackgroundInformation on the occurrence of contact allergens and irritants is crucial for the diagnosis of occupational contact dermatitis. Material Safety Data Sheets (MSDS) are important sources of information concerning exposures in the workplace.ObjectiveFrom a medical viewpoint, to evaluate the information available from MSDSs, and to ascertain whether MSDS are easy to obtain, whether they serve their purpose, and whether they provide sufficient information regarding allergens to enable correct diagnosis.MethodsMSDS and ingredients labelling were collected from consecutive patients and reviewed. If it was suspected that the MSDS were incomplete, the manufacturer, supplier, salesperson or workplace was contacted to gather more information.ResultsTwenty‐five per cent (79/316) of patients provided material for the exposure assessment. One or more shortcomings were found in 18.6% (137/738) of the MSDS. The most frequent shortcoming was ‘Missing R43/H317 while known contact allergen was present’, which was observed in 63.1% (84/137). Other shortcomings were ‘Names of preservatives not included in section 3 despite containing preservatives’, in 48.9% (67/137), and ‘Nothing about allergy in sections 2, 3, 11, 15 or 16 in the MSDS despite the content of allergens’, in 20.4% (28/137). The information retrieved led to additional testing of 21 patients.ConclusionSystematic exposure assessment is time‐consuming. The main shortcomings are errors/omissions in the MSDS.
Endorectal ultrasonography, strain elastography and MRI differentiation of rectal adenomas and adenocarcinomas
Authors: Waage J. E. R. , Leh S. , Røsler C. , Pfeffer F. , Bach S. P. , Havre R. F. , Haldorsen I. S. , Ødegaard S. , Baatrup G. 
Published: November 2014

AbstractAimStrain elastography is a method for recording tissue hardness. Strain in different areas may be compared using strain ratio (SR). The aims of this study were to validate a previously proposed SR cut‐off value of 1.25 for differentiating adenocarcinomas from adenomas and to compare the performance of endorectal ultrasonography (ERUS), strain elastography and MRI in the same patients.MethodA prospective evaluation of 120 consecutive patients with rectal neoplasia, using a predetermined elastography strain ratio cut‐off value, was performed to differentiate adenomas from adenocarcinomas. ERUS and MRI were performed according to standard routine at Haukeland University Hospital, defining T0 as adenomas and T1–T4 as adenocarcinomas. Subsequent histopathology was used as the reference standard.ResultsHistopathological evaluation revealed 21 adenomas and 99 adenocarcinomas. Sensitivity, specificity and accuracy (with 95% CI) were as follows: ERUS: 0.96 (0.90–0.99), 0.62 (0.40–0.80) and 0.90 (0.83–0.94); elastography SR: 0.96 (0.90–0.99), 0.86 (0.66–0.96) and 0.94 (0.88–0.97); and MRI: 0.99 (0.94–1.00), 0.07 (0.00–0.31) and 0.87 (0.80–0.93).ConclusionThis study confirms that the elastography SR assessment accurately differentiates sessile adenomas from adenocarcinomas. SR assessment has a superior ability to differentiate adenomas and adenocarcinomas when compared with ERUS and MRI. MRI examination seems unable to recognize adenomas and should be interpreted with care when early‐stage rectal neoplasia is suspected.
The child and family experience of power mobility: a qualitative synthesis
Authors: Livingstone Roslyn , Field Debra 
Published: November 2014

AimThe aim of this study was to critically synthesize qualitative evidence regarding the child and family experience of power mobility, and to examine how this evidence fits with current theoretical concepts.MethodElectronic database/hand searches were undertaken in September 2012 and updated in February 2014. The searches were restricted to qualitative studies published in English before February 2014 that included at least one child under the age of 19 with a disability and described an outcome related to the use of power mobility. Inclusion criteria were set a priori. Two reviewers independently screened titles, abstracts, and full‐text articles and extracted data. McMaster qualitative review forms were used for quality appraisal.ResultsOf 259 titles, 21 met inclusion criteria. From 143 codes, 15 second‐order themes were developed using constant comparison and analysis. Three overarching themes emerged: power mobility experience promotes developmental change and independent mobility; power mobility enhances social relationships and engagement in meaningful life experiences; and power mobility access and use is influenced by factors in the physical, social, and attitudinal environment.InterpretationThis qualitative research provides rich and rigorous evidence supporting the benefits of power mobility for children and families. Numerous factors, which warrant careful consideration, influence power mobility access and use.
Speech sound disorder at 4 years: prevalence, comorbidities, and predictors in a community cohort of children
Authors: Eadie Patricia , Morgan Angela , Ukoumunne Obioha C , Ttofari Eecen Kyriaki , Wake Melissa , Reilly Sheena 
Published: November 2014

AimThe epidemiology of preschool speech sound disorder is poorly understood. Our aims were to determine: the prevalence of idiopathic speech sound disorder; the comorbidity of speech sound disorder with language and pre‐literacy difficulties; and the factors contributing to speech outcome at 4 years.MethodOne thousand four hundred and ninety‐four participants from an Australian longitudinal cohort completed speech, language, and pre‐literacy assessments at 4 years. Prevalence of speech sound disorder (SSD) was defined by standard score performance of ≤79 on a speech assessment. Logistic regression examined predictors of SSD within four domains: child and family; parent‐reported speech; cognitive‐linguistic; and parent‐reported motor skills.ResultsAt 4 years the prevalence of speech disorder in an Australian cohort was 3.4%. Comorbidity with SSD was 40.8% for language disorder and 20.8% for poor pre‐literacy skills. Sex, maternal vocabulary, socio‐economic status, and family history of speech and language difficulties predicted SSD, as did 2‐year speech, language, and motor skills. Together these variables provided good discrimination of SSD (area under the curve=0.78).InterpretationThis is the first epidemiological study to demonstrate prevalence of SSD at 4 years of age that was consistent with previous clinical studies. Early detection of SSD at 4 years should focus on family variables and speech, language, and motor skills measured at 2 years.
A carboxylated Zn‐phthalocyanine inhibits fibril formation of Alzheimer's amyloid β peptide
Authors: Tabassum Shatera , Sheikh Abdullah M. , Yano Shozo , Ikeue Takafumi , Handa Makoto , Nagai Atsushi 
Published: November 2014

Amyloid β (Aβ), a 39–42 amino acid peptide derived from amyloid precursor protein, is deposited as fibrils in Alzheimer's disease brains, and is considered to play a major role in the pathogenesis of the disease. We have investigated the effects of a water‐soluble Zn‐phthalocyanine, ZnPc(COONa)8, a macrocyclic compound with near‐infrared optical properties, on Aβ fibril formation in vitro. A thioflavin T fluorescence assay showed that ZnPc(COONa)8 significantly inhibited Aβ fibril formation, increasing the lag time and dose‐dependently decreasing the plateau level of fibril formation. Moreover, it destabilized pre‐formed Aβ fibrils, resulting in an increase in low‐molecular‐weight species. After fibril formation in the presence of ZnPc(COONa)8, immunoprecipitation of Aβ1‐42 using Aβ‐specific antibody followed by near‐infrared scanning demonstrated binding of ZnPc(COONa)8 to Aβ1‐42. A study using the hydrophobic fluorescent probe 8‐anilino‐1‐naphthalenesulfonic acid showed that ZnPc(COONa)8 decreased the hydrophobicity during Aβ1‐42 fibril formation. CD spectroscopy showed an increase in the α helix structure and a decrease in the β sheet structure of Aβ1‐40 in fibril‐forming buffer containing ZnPc(COONa)8. SDS/PAGE and a dot‐blot immunoassay showed that ZnPc(COONa)8 delayed the disappearance of low‐molecular‐weight species and the appearance of higher‐molecular‐weight oligomeric species of Aβ1‐42. A cell viability assay showed that ZnPc(COONa)8 was not toxic to a neuronal cell line (A1), but instead protected A1 cells against Aβ1‐42‐induced toxicity. Overall, our results indicate that ZnPc(COONa)8 binds to Aβ and decreases the hydrophobicity, and this change is unfavorable for Aβ oligomerization and fibril formation.
A Comparison of Hyporheic Transport at a Cross‐Vane Structure and Natural Riffle
Authors: Smidt Samuel J. , Cullin Joseph A. , Ward Adam S. , Robinson Jesse , Zimmer Margaret A. , Lautz Laura K. , Endreny Theodore A. 
Published: November 2014

AbstractWhile restoring hyporheic flowpaths has been cited as a benefit to stream restoration structures, little documentation exists confirming that constructed restoration structures induce comparable hyporheic exchange to natural stream features. This study compares a stream restoration structure (cross‐vane) to a natural feature (riffle) concurrently in the same stream reach using time‐lapsed electrical resistivity (ER) tomography. Using this hydrogeophysical approach, we were able to quantify hyporheic extent and transport beneath the cross‐vane structure and the riffle. We interpret from the geophysical data that the cross‐vane and the natural riffle induced spatially and temporally unique hyporheic extent and transport, and the cross‐vane created both spatially larger and temporally longer hyporheic flowpaths than the natural riffle. Tracer from the 4.67‐h injection was detected along flowpaths for 4.6 h at the cross‐vane and 4.2 h at the riffle. The spatial extent of the hyporheic zone at the cross‐vane was 12% larger than that at the riffle. We compare ER results of this study to vertical fluxes calculated from temperature profiles and conclude significant differences in the interpretation of hyporheic transport from these different field techniques. Results of this study demonstrate a high degree of heterogeneity in transport metrics at both the cross‐vane and the riffle and differences between the hyporheic flowpath networks at the two different features. Our results suggest that restoration structures may be capable of creating sufficient exchange flux and timescales of transport to achieve the same ecological functions as natural features, but engineering of the physical and biogeochemical environment may be necessary to realize these benefits.