Estimating total horizontal aeolian flux within shrub-invaded groundwater-dependent meadows using empirical and mechanistic models

Wind erosion is a significant environmental problem that removes soil resources from sensitive ecosystems and contributes to air pollution. In regions of shallow groundwater, friable (puffy) soils are maintained through capillary action, surface evaporation of solute-rich soil moisture, and protection from mobilization by groundwater-dependent grasses and shrubs. When a reduction in vegetation cover occurs through any disturbance process, there is potential for aeolian transport and dust emission. We find that as mean gap size between vegetation elements scaled by vegetation height increases, total horizontal aeolian sediment flux increases and explains 58% of the variation in total horizontal aeolian sediment flux. We also test a probabilistic model of wind erosion based on gap size between vegetation elements scaled by vegetation height (the Okin model), which predicts measured total horizontal aeolian sediment flux more closely than another commonly used model based on the average plant area observed in profile (Raupach model). The threshold shear velocity of bare soil appears to increase as gap size between vegetation elements scaled by vegetation height increases, reflecting either surface armoring or reduced interaction between the groundwater capillary zone and surface sediments. This work advances understanding of the importance of measuring gap size between vegetation elements scaled by vegetation height for empirically estimating Q and for structuring process-based models of desert wind erosion in groundwater-dependent vegetation

Validation and calibration of next-generation sequencing to identify Epstein-Barr virus-positive gastric cancer in The Cancer Genome Atlas

The Epstein-Barr virus (EBV)-positive subtype of gastric adenocarcinoma is conventionally identified by in situ hybridization (ISH) for viral nucleic acids, but next-generation sequencing represents a potential alternative. We therefore determined normalized EBV read counts by whole genome, whole exome, mRNA and miRNA sequencing for 295 fresh-frozen gastric tumor samples. Formalin-fixed, paraffin-embedded tissue sections were retrieved for ISH confirmation of 13 high-EBV and 11 low-EBV cases. In pairwise comparisons, individual samples were either concordantly high or concordantly low by all genomic methods for which data were available. Empiric cut-offs of sequencing counts identified 26 (9%) tumors as EBV-positive. EBV-positivity or negativity by molecular testing was confirmed by EBER-ISH in all but one tumor evaluated by both approaches (kappa=0.91). EBV-positive gastric tumors may be accurately identified by quantifying viral sequences in genomic data. Simultaneous analyses of human and viral DNA, mRNA and miRNA could streamline tumor profiling for clinical care and research

Explorations of object and location memory using fMRI

Content-specific sub-systems of visual working memory (VWM) have been explored in many neuroimaging studies with inconsistent findings and procedures across experiments. The present study employed functional magnetic resonance imaging (fMRI) and a change detection task using a high number of trials and matched stimulus displays across object and location change (what vs. where) conditions. Furthermore, individual task periods were studied independently across conditions to identify differences corresponding to each task period. Importantly, this combination of task controls has not previously been described in the fMRI literature. Composite results revealed differential frontoparietal activation during each task period. A separation of object and location conditions yielded a distributed system of dorsal and ventral streams during the encoding of information corresponding to bilateral inferior parietal lobule (IPL) and lingual gyrus activation, respectively. Differential activity was also shown during the maintenance of information in middle frontal structures bilaterally for objects and the right IPL and left insula for locations. Together, these results reflect a domain-specific dissociation spanning several cortices and task periods. Furthermore, differential activations suggest a general caudal-rostral separation corresponding to object and location memory, respectively

Acrylamide-forming potential of potatoes grown at different locations, and the ratio of free asparagine to reducing sugars at which free asparagine becomes a limiting factor for acrylamide formation

Acrylamide is produced from free asparagine and reducing sugars during high-temperature cooking and food processing, and potato products are major contributors to dietary acrylamide intake. The present study analysed twenty varieties of potatoes grown at two sites (Doncaster and Woburn) in the United Kingdom to assess the effect of location of cultivation on acrylamide-forming potential. Analysis of variance revealed a full site by variety nested within type (French fry, boiling and crisping) by storage interaction for acrylamide (p < 0.003, F-test), reducing sugars and total sugars (p < 0.001, F-test). There was much greater free asparagine in potatoes grown at the Doncaster site compared with the Woburn site. Modelling of the relationship between the ratio of free asparagine to reducing sugars and the levels of acrylamide identified a value of 2.257 ± 0.149 as the tipping point in the ratio below which free asparagine concentration could affect acrylamide formation

Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species.

Meningitis is commonly caused by infection with a variety of bacterial or viral pathogens. Acute bacterial meningitis (ABM) can cause severe disease, which can progress rapidly to a critical life-threatening condition. Rapid diagnosis of ABM is critical, as this is most commonly associated with severe sequelae with associated high mortality and morbidity rates compared to viral meningitis, which is less severe and self-limiting. We have designed a microarray for detection and diagnosis of ABM. This has been validated using randomly amplified DNA targets (RADT), comparing buffers with or without formamide, in glass slide format or on the Alere ArrayTubeTM (Alere Technologies GmbH) microarray platform. Pathogen-specific signals were observed using purified bacterial nucleic acids and to a lesser extent using patient cerebral spinal fluid (CSF) samples, with some technical issues observed using RADT and glass slides. Repurposing the array onto the Alere ArrayTubeTM platform and using a targeted amplification system increased specific and reduced nonspecific hybridization signals using both pathogen nucleic and patient CSF DNA targets, better revealing pathogen-specific signals although sensitivity was still reduced in the latter. This diagnostic microarray is useful as a laboratory diagnostic tool for species and strain designation for ABM, rather than for primary diagnosis

Acrylamide in potato crisps prepared from 20 UK-grown varieties: effects of variety and tuber storage time

Twenty varieties of field-grown potato were stored for 2 months and 6 months at 8 °C. Mean acrylamide contents in crisps prepared from all varieties at both storage times ranged from 131 μg per kg in Verdi to 5360 μg per kg in Pentland Dell. In contrast to previous studies, the longer storage period did not affect acrylamide formation significantly for most varieties, the exceptions being Innovator, where acrylamide formation increased, and Saturna, where it decreased. Four of the five varieties designated as suitable for crisping produced crisps with acrylamide levels below the European Commission indicative value of 1000 μg per kg (Saturna, Lady Rosetta, Lady Claire, and Verdi); the exception was Hermes. Two varieties more often used for French fries, Markies and Fontane, also produced crisps with less than 1000 μg per kg acrylamide. Correlations between acrylamide, its precursors and crisp colour are described, and the implications of the results for production of potato crisps are discussed

The inter-observer agreement of examining pre-school children with acute cough: a nested study

BACKGROUND: The presence of clinical signs have implications for diagnosis, prognosis and treatment. Therefore, the aim of this study was to examine the inter-observer agreement of clinical signs in pre-school children presenting to primary care. METHODS: A nested study comparing two clinical assessments within a prospective cohort of 256 pre-school children with acute cough recruited from eight general practices in Leicestershire, UK. We examined agreement (using kappa statistics) between unstandardised and standardised clinical assessments of tachypnoea, chest signs and fever. RESULTS: Kappa values were poor or fair for all clinical signs (range 0.12 to 0.39) with chest signs the most reliable. CONCLUSIONS: Primary care clinicians should be aware that clinical signs may be unreliable when making diagnosis, prognosis and treatment decisions in pre-school children with cough. Future research should aim to further our understanding of how best to identify abnormal clinical signs

A theoretical framework for the ecological role of three-dimensional structural diversity

The three-dimensional (3D) physical aspects of ecosystems are intrinsically linked to ecological processes. Here, we describe structural diversity as the volumetric capacity, physical arrangement, and identity/traits of biotic components in an ecosystem. Despite being recognized in earlier ecological studies, structural diversity has been largely overlooked due to an absence of not only a theoretical foundation but also effective measurement tools. We present a framework for conceptualizing structural diversity and suggest how to facilitate its broader incorporation into ecological theory and practice. We also discuss how the interplay of genetic and environmental factors underpin structural diversity, allowing for a potentially unique synthetic approach to explain ecosystem function. A practical approach is then proposed in which scientists can test the ecological role of structural diversity at biotic–environmental interfaces, along with examples of structural diversity research and future directions for integrating structural diversity into ecological theory and management across scales