bluuebunny/crossref_metadata_2025 huggingface dataset:
Disentangling seasonal bacterioplankton population dynamics by high‐frequency sampling
Authors: Lindh Markus V. , Sjöstedt Johanna , Andersson Anders F. , Baltar Federico , Hugerth Luisa W. , Lundin Daniel , Muthusamy Saraladevi , Legrand Catherine , Pinhassi Jarone
Published: November 2014

Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta‐diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual populations ranged from 0.23 to 1.79 day−1. Populations that were persistently dominant, transiently abundant or generally rare were found in several major bacterial groups, implying evolution has favoured a similar variety of life strategies within these groups. These findings suggest that high temporal resolution sampling allows constraining the timescales and frequencies at which distinct populations transition between being abundant or rare, thus potentially providing clues about physical, chemical or biological forcing on bacterioplankton community structure.
Bourdieu, Ethics and Symbolic Power
Authors: Pellandini-Simányi Léna
Published: November 2014

This article critically discusses Pierre Bourdieu's views on ethics and normative evaluations. Bourdieu acknowledged that people hold ethical stances, yet sought to show that these stances are – unconsciously – conducive to obtaining symbolic power and legitimizing hierarchy. The first part of the article looks at this argument and charts the shifts it went through particularly in the early 1990s. The second part discusses ontological and empirical critiques of the ethics as ideology argument and suggests the latter to be more salient, as Bourdieu proposed his argument as an empirical rather than as an ontological point. The reason why he nevertheless found the ethics as ideology explanation fitting to nearly all the cases he studied, as the third part argues, is not simply that reality ‘obliged’ him to do so, but his circular definition of symbolic capital as qualities that are worthy of esteem. This definition makes his argument of ethics as ideology unfalsifiable and impedes him from distinguishing between cases when legitimate power is the aim of ethics and between those when it is merely their side effect. The article concludes by suggesting ways in which Bourdieu's work can be fruitfully incorporated into the study of ethics once the tautology is resolved.
The Use of Forensic Tests to Distinguish Blowfly Artifacts from Human Blood, Semen, and Saliva
Authors: Durdle Annalisa , Mitchell R. John , van Oorschot Roland A.H.
Published: November 2014

This study investigated whether routinely used forensic tests can distinguish 3‐day‐old or 2‐week‐old fly artifacts, produced after feeding on human blood, semen, or saliva, from the biological fluid. Hemastix®, Hemident™, and Hemascein™ were unable to distinguish blood from artifacts. Hemastix® returned false positives from negative controls. ABAcard® Hematrace® and Hexagon OBTI could distinguish blood from 3‐day‐old artifacts, but not 2‐week‐old artifacts. Phadebas® and SALIgAE® were unable to distinguish saliva from artifacts. RSID™‐Saliva was able to distinguish saliva from 3‐day‐old artifacts, but not 2‐week‐old artifacts. Semen tests Seminal Acid Phosphatase, RSID™‐Semen, and ABAcard® p30 were all able to distinguish semen from 3‐day‐old artifacts, but not 2‐week‐old artifacts. The tests investigated cannot be relied upon to distinguish artifacts from biological fluids. However, if an artifact is identified by its morphology, a positive result may indicate which biological fluid the fly consumed, and this knowledge may prove useful for investigators searching for DNA.
Intact preservation of environmental samples by freezing under an alternating magnetic field
Authors: Morono Yuki , Terada Takeshi , Yamamoto Yuhji , Xiao Nan , Hirose Takehiro , Sugeno Masaya , Ohwada Norio , Inagaki Fumio
Published: November 2014

The study of environmental samples requires a preservation system that stabilizes the sample structure, including cells and biomolecules. To address this fundamental issue, we tested the cell alive system (CAS)‐freezing technique for subseafloor sediment core samples. In the CAS‐freezing technique, an alternating magnetic field is applied during the freezing process to produce vibration of water molecules and achieve a stable, super‐cooled liquid phase. Upon further cooling, the temperature decreases further, achieving a uniform freezing of sample with minimal ice crystal formation. In this study, samples were preserved using the CAS and conventional freezing techniques at 4, −20, −80 and −196 (liquid nitrogen) °C. After 6 months of storage, microbial cell counts by conventional freezing significantly decreased (down to 10.7% of initial), whereas that by CAS‐freezing resulted in minimal. When Escherichia coli cells were tested under the same freezing conditions and storage for 2.5 months, CAS‐frozen E. coli cells showed higher viability than the other conditions. In addition, an alternating magnetic field does not impact on the direction of remanent magnetization in sediment core samples, although slight partial demagnetization in intensity due to freezing was observed. Consequently, our data indicate that the CAS technique is highly useful for the preservation of environmental samples.
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

Stable 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

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

The 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

Population 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

Background

In 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.

Aims

As 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.

Methods

2501 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.

Results

A 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%).

Conclusions

Identifying 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.
Lessons learned from the clinical development of oral peptides
Authors: Karsdal Morten Asser , Riis Bente Juul , Mehta Nozer , Stern William , Arbit Ehud , Christiansen Claus , Henriksen Kim
Published: November 2014

The oral delivery of peptides and proteins has been hampered by an array of obstacles. However, several promising novel oral delivery systems have been developed. This paper reviews the most advanced oral formulation technologies, and highlights key lessons and implications from studies undertaken to date with these oral formulations. Special interest is given to oral salmon calcitonin (CT), glucagon‐like peptide‐1 (GLP‐1), insulin, PYY‐(3‐36), recombinant human parathyroid hormone (rhPTH(1‐31)‐NH2) and PTH(1‐34), by different technologies. The issues addressed include (i) interaction with water, (ii) interaction with food, (iii) diurnal variation, (iv) inter‐ and intra‐subject variability, (v) correlation between efficacy and exposure and (vi) key deliverables of different technologies. These key lessons may aid research in the development of other oral formulations.
Using mixed methods research designs in health psychology: An illustrated discussion from a pragmatist perspective
Authors: Bishop Felicity L.
Published: November 2014

Purpose

To outline some of the challenges of mixed methods research and illustrate how they can be addressed in health psychology research.

Methods

This 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.

Results

Mixed 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.

Conclusions

Adapting 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.
Learning to Match Auditory and Visual Speech Cues: Social Influences on Acquisition of Phonological Categories
Authors: Altvater‐Mackensen Nicole , Grossmann Tobias
Published: November 2014

Infants' language exposure largely involves face‐to‐face interactions providing acoustic and visual speech cues but also social cues that might foster language learning. Yet, both audiovisual speech information and social information have so far received little attention in research on infants' early language development. Using a preferential looking paradigm, 44 German 6‐month olds' ability to detect mismatches between concurrently presented auditory and visual native vowels was tested. Outcomes were related to mothers' speech style and interactive behavior assessed during free play with their infant, and to infant‐specific factors assessed through a questionnaire. Results show that mothers' and infants' social behavior modulated infants' preference for matching audiovisual speech. Moreover, infants' audiovisual speech perception correlated with later vocabulary size, suggesting a lasting effect on language development.
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

Background

Information 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.

Objective

From 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.

Methods

MSDS 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.

Results

Twenty‐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.

Conclusion

Systematic 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

Aim

Strain 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.

Method

A 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.

Results

Histopathological 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).

Conclusion

This 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.
Primary cutaneous aggressive epidermotropic CD8+ T‐cell lymphoma with KIR3DL2 and NKp46 expression in a human immunodeficiency virus carrier
Authors: Karkouche Raymond , Ingen‐Housz‐Oro Saskia , Le Gouvello Sabine , Charlotte Frédéric , Thomas Marina , Zehou Ouidad , Frenkel Valérie , Boutboul David , Chosidow Olivier , Caumes Eric , Gaulard Philippe , Ortonne Nicolas
Published: November 2014

Primary cutaneous aggressive epidermotropic T‐cell lymphoma (PCAETCL) is a very rare lymphoma characterized by rapidly growing necrotic cutaneous lesions with an epidermotropic CD8+ T‐cell neoplastic infiltrate observed histopathologically. It is associated with a very poor outcome, despite aggressive multi‐agent chemotherapy. We report a 49‐year‐old human immunodeficiency virus (HIV)‐infected patient who developed PCAETCL with associated marked vascular injury leading to diffuse purpuric and necrotic lesions complicated by recalcitrant hemophagocytic activation syndrome. The lymphoma strongly and diffusely expressed CD158k/KIR3DL2 at the protein and transcript level and NKp46 transcripts, in addition to CD8 and cytotoxic proteins. We observed a diffuse CD158k/KIR3DL2 protein expression in another case of PAETCL, not associated with immunodeficiency, which was used as a positive control. PCAETCL can develop in HIV‐infected patients and may present in vasculitis‐like fashion. The possible role of immunosuppression and/or HIV in oncogenesis can be postulated, as patients infected with HIV may develop anti‐HIV cytotoxic CD8+ lymphoproliferations. The frequency of CD158k/KIR3DL2 and NKp46 expression in PCAECL remains to be studied in a series of cases, and may represent interesting targets for future treatments.
Benign lymphangioendothelioma presenting as a giant flank mass
Authors: Schnebelen Alicia M. , Page James , Gardner Jerad M. , Shalin Sara C.
Published: November 2014

Benign lymphangioendothelioma is a rare lesion of controversial etiology and a histopathologic mimic of Kaposi sarcoma and so‐called ‘well‐differentiated’ angiosarcoma. Its most typical clinical presentation is as a slowly expanding, erythematous patch or plaque; it rarely presents as a large mass. We report the second case of a giant benign lymphangioendothelioma, which arose as a serpiginous mass involving most of the flank of an elderly male with no prior radiation exposure and with a remote history of herpes zoster infection. A biopsy revealed numerous anastomosing vascular channels extending from the superficial dermis to the subcutis that were dilated to progressively slit‐like in architecture. The endothelial cells lacked cytologic atypia, hobnailing, or significant mitotic activity, and human herpesvirus‐8 expression was absent. Positivity for podoplanin (D2‐40) was observed in the endothelial cells, supporting a lymphatic phenotype. Furthermore, the lesional cells lacked immunohistochemical expression of Wilms tumor 1, providing further support of a malformative – rather than neoplastic – pathogenesis.
The child and family experience of power mobility: a qualitative synthesis
Authors: Livingstone Roslyn , Field Debra
Published: November 2014

Aim

The 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.

Method

Electronic 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.

Results

Of 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.

Interpretation

This 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

Aim

The 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.

Method

One 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.

Results

At 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).

Interpretation

This 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.
Complex organism–environment feedbacks buffer species diversity against habitat fragmentation
Authors: Zee Peter C. , Fukami Tadashi
Published: November 2014

Understanding the factors that determine the extent of biodiversity loss following habitat destruction is central to ecosystem conservation and management. One potential factor is the ecological feedbacks between organisms and local environmental conditions, which can influence how species affect one another and, consequently, whether or not species persist in fragmented landscapes. We investigated this possibility using a spatially explicit individual‐based model of plant communities. In this model, plant species affected their own and other species’ competitiveness by modifying local environmental conditions. These plant–environment feedbacks were assumed to vary among species pairs in direction and strength to mimic complex feedbacks observed between plants and soil conditions in real communities. We found that complex feedbacks reduced the extent of diversity loss, effectively buffering species against habitat fragmentation. Our analysis suggested that this buffering effect operated via two mechanisms. First, complex feedbacks decreased the likelihood of immediate extinction by making the spatial distribution of each species less clustered and consequently less likely to be eliminated entirely by fragmentation. Second, complex feedbacks decreased the likelihood of additional extinction by generating negative density dependence among surviving species, thereby keeping low‐abundance species from going extinct due to demographic stochasticity and other forces. The buffering effect was particularly strong when species dispersed locally and abiotic environmental conditions varied globally. Our findings highlight the potential importance of organism–environment feedbacks in explaining species extinction by habitat destruction.
Endodontic filling materials
Authors: Ørstavik Dag
Published: November 2014

The principal function of root filling materials is to prevent invasion of bacteria and infection of the root canal system after completed endodontic treatment. This is accomplished by the formation of a tight, permanent seal with the surrounding tooth structure, leaving no space for invasion of or colonization by bacteria. The materials can also have a direct antibacterial effect and kill the microbes when in contact with them. Materials applied onto larger areas of connective tissue, i.e. for retrograde root fillings or perforation repair, should also allow or stimulate complete repair or regeneration. Ideally, the selection of materials for various applications in endodontics should be based on clinical, scientifically valid data. However, most current endodontic practices and choice of materials are based on a convoluted history where data of varying relevance and validity is mixed with experts’ stated opinions and manufacturers’ advertising. In this review, the chemical, physical, and biological properties of different root filling materials are discussed together with their handling characteristics and recommended use in the clinic. Emphasis is placed on evidence generated from clinical practice and research.
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

While 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.
Genome‐wide analysis of long non‐coding RNA in primary nasopharyngeal carcinoma by microarray
Authors: Yang Qing‐Qing , Deng Yan‐Fei
Published: November 2014

Aims

Alterations in the expression of several long non‐coding RNAs (lncRNAs) have been found in primary nasopharyngeal carcinoma (NPC). However, the effect of lncRNA expression on primary NPC as well as the molecular mechanism of lncRNA remains vague. This study was to identify differentially expressed lncRNAs involved in NPC on a genome‐wide scale and predict their potential functions.

Methods and results

Using high‐throughput microarray with 30 586 lncRNA and 26 109 mRNA probes, 856 lncRNAs and 767 mRNAs were expressed differentially between NPC and chronic nasopharyngitis tissues. Bioinformatic analysis (clustering analysis, gene ontology analysis and pathway analysis) was used for further research. Differentially expressed lncRNAs were subgrouped into three types and differentially expressed mRNAs were clustered into 28 pathways. The first coexpression network analysis revealed that 46 lncRNAs interacting with three mRNAs involved the Janus kinase–signal transducer and activator of transcription (JAK–STAT) signalling pathway. Quantitative real‐time polymerase chain reaction (PCR) verified 11 up‐ and down‐regulated lncRNAs and eight mRNAs in NPC. The second coexpression network analysis showed that 23 significantly aberrantly expressed mRNAs interacted with three validated lncRNAs.

Conclusions

This study could provide new insight into the molecular mechanisms of lncRNAs and their potential role in NPC for further study. These differentially expressed lncRNAs may act as novel biomarkers and therapeutic targets for NPC.
Myc protein expression correlates with MYC amplification in small‐cell lung carcinoma
Authors: Hwang David H , Sun Heather , Rodig Scott J , Hornick Jason L , Sholl Lynette M
Published: November 2014

Aims

Myc family members are important contributors to oncogenesis in a variety of tumours. Identification of therapeutic targets is needed in small‐cell lung carcinoma (SCLC), an aggressive disease with limited treatment options. Sequencing studies have identified MYC amplification in 2–7% of SCLCs. This study aims to determine the rate of MYC gene amplification and its correlation with Myc protein overexpression in SCLC.

Methods and results

One hundred and three cases of formalin‐fixed, paraffin‐embedded SCLC were examined. Myc protein expression was scored according to the extent of immunohistochemical staining. MYC copy number (CN) was evaluated with dual‐colour chromogenic in‐situ hybridization (CISH) for the MYC locus and a chromosome 8 (Chr8) centromeric control. Amplification was defined as a MYC/Chr8 ratio of ≥2. Thirty‐eight per cent of SCLCs had some degree of Myc protein expression, and 9% of cases were MYC‐amplified. MYC CN was significantly correlated with the extent of Myc protein expression (Spearman's ρ = 0.57, P < 0.01). There was no significant association between Myc expression or CN and clinicopathological features.

Conclusions

MYC amplification by CISH was identified in 9% of SCLCs, and correlated with protein expression. As novel Myc‐targeted therapies are developed, CISH and IHC should be considered as biomarkers of Myc pathway dysregulation in SCLC.
Alteration in cytochrome P450 3A4 activity as measured by a urine cortisol assay in HIV‐1‐infected pregnant women and relationship to antiretroviral pharmacokinetics
Authors: Aweeka FT , Hu C , Huang L , Best BM , Stek A , Lizak P , Burchett SK , Read JS , Watts H , Mirochnick M , Capparelli EV ,   the International Maternal Pediatric Adolescent AIDS Clinical Trials Group (IMPAACT) P1026s Protocol Team
Published: November 2014

Objectives

Pregnancy results in physiological changes altering the pharmacokinetics of drugs metabolized by cytochrome P450 3A4 (CYP3A4). The urinary ratio of 6‐β hydroxycortisol to cortisol (6βHF : F) is a marker of CYP3A4 induction. We sought to evaluate its change in antiretroviral (ARV)‐treated HIV‐1‐infected women and to relate this change to ARV pharmacokinetics.

Methods

Women receiving various ARVs had pharmacokinetic evaluations during the third trimester of pregnancy (> 30 weeks) and postpartum with determination of 6βHF : F carried out on the same days. The Wilcoxon signed rank test was used to compare the ratio antepartum to postpartum. The relationship between the change in ratio and the change in pharmacokinetics was analysed using Kendall's tau.

Results

6βHF : F ratios were available for 107 women antepartum, with 54 having postpartum values. The ratio was higher antepartum (P = 0.033) (median comparison 1.35; 95% confidence interval 1.01, 1.81). For 71 women taking a protease inhibitor (PI), the antepartum vs. postpartum 6βHF : F comparison was marginally significant (P = 0.058). When the change in the 6βHF : F ratio was related to the change in the dose‐adjusted ARV area under the plasma concentration vs. time curve (AUC) between antepartum and postpartum, the 35 subjects in the lopinavir/ritonavir (LPV/r) arms demonstrated an inverse relationship (P = 0.125), albeit this correlation did not reach statistical significance.

Conclusions

A 35% increase in the urinary 6βHF : F ratio was measured during late pregnancy compared with postpartum, indicating that CYP3A induction occurs during pregnancy. The trend towards an inverse relationship between the change in the 6βHF : F ratio and the change in the LPV AUC antepartum vs. postpartum suggests that CYP3A induction may be one mechanism behind altered LPV exposure during pregnancy.
Assessing the short‐term effects of capture, handling and tagging of sandgrouse
Authors: Casas Fabián , Benítez‐López Ana , García Jesús T. , Martín Carlos A. , Viñuela Javier , Mougeot Francois
Published: November 2014

Capturing and marking free‐living birds permits the study of important aspects of their biology but may have undesirable effects. Bird welfare should be a primary concern, so it is necessary to evaluate and minimize any adverse effects of procedures used. We assess short‐term effects associated with the capture, handling and tagging with backpack‐mounted transmitters of Pin‐tailed Pterocles alchata and Black‐bellied Pterocles orientalis Sandgrouse, steppe birds of conservation concern. There was a significantly higher mortality (15%) during the first week after capture than during the following weeks (< 2.5%) in Pin‐tailed Sandgrouse, but no significant temporal mortality pattern in Black‐bellied Sandgrouse. In Pin‐tailed Sandgrouse, mortality rate during the first week increased with increasing relative transmitter and harness weight regardless of season, and with increasing handling time during the breeding season. There were no significant differences in mortality rate between study areas, type of tag, sex or age or an effect of restraint time. These results suggest the use of lighter transmitters (< 3% of the bird's weight) and a reduction of handling time (< 20 min), particularly during the breeding season, as essential improvements in procedure to reduce the mortality risk associated with the capture, handling and tagging of these vulnerable species.
Creep in Interlaminar Shear of a Nextel™720/aluminosilicate Composite at 1100°C in Air and in Steam
Authors: Ruggles‐Wrenn Marina , Hilburn Skyler
Published: November 2014

Creep in interlaminar shear of an oxide–oxide ceramic composite was evaluated at 1100°C in air and in steam. Composite consists of a porous aluminosilicate matrix reinforced with mullite/alumina (Nextel™720) fibers, has no interface between fibers and matrix, and relies on the porous matrix for flaw tolerance. The interlaminar shear strength was 7.6 MPa. Creep behavior was examined for shear stresses of 2–6 MPa. Creep run‐out of 100 h was not achieved. Larger creep strains and higher creep strain rates were produced in steam. However, steam had a beneficial effect on creep lifetimes. Composite microstructure, damage, and failure mechanisms were investigated.
Treatment and outcomes of metastatic colorectal cancer in Australia: defining differences between public and private practice
Authors: Field K. , Shapiro J. , Wong H.‐L. , Tacey M. , Nott L. , Tran B. , Turner N. , Ananda S. , Richardson G. , Jennens R. , Wong R. , Power J. , Burge M. , Gibbs P.
Published: November 2014

Background

Prior studies have suggested improved outcomes for cancer patients managed in private centres, despite universal healthcare within Australia.

Aims

To compare patient, disease, treatment and survival data for metastatic colorectal cancer (mCRC) managed in private versus public centres.

Methods

Analysis of prospectively collected registry data for consecutive patients with mCRC managed at 16 participating centres from July 2009.

Results

Data for 1065 patients were examined. Age, gender and Charlson comorbidity score were similar for public and private patients. Private patients were more commonly Eastern Cooperative Oncology Group performance score 0–1 (85% vs 78%, P = 0.008), in the highest Index of Relative Socioeconomic Advantage and Disadvantage quintile (57% vs 18%, P < 0.001) or had a single metastatic site (62% vs 54%, P = 0.009). Patients treated in private were more likely to receive chemotherapy (84% vs 70%, P < 0.001), bevacizumab (59% vs 50%, P = 0.008), be treated with curative intent (37% vs 26%, P < 0.001) and undergo metastasectomy (30% vs 22%, P = 0.001). These management differences remained statistically significant after adjusting for baseline characteristics. Management in the private setting was associated with superior overall survival (median 27.9 vs 20 months, hazard ratio 0.7, 95% confidence interval: 0.57 to 0.86, P = 0.001), significant in multivariate analysis adjusting for all baseline covariates.

Conclusions

Significant differences in baseline characteristics were noted for private versus public patients. However, these do not explain the higher rates of treatment delivery in the private setting, which likely contributed towards the observed survival difference. Further studies are required to determine if the increased likelihood of intervention in the private setting is driven by patient, clinician and/or institutional factors.