Nocturnal Flight Periodicity of the Caddisflies (Trichoptera) in Forest and Meadow Habitats of a First Order Michigan Stream

Using ultraviolet light traps, over 5000 caddisfly specimens were collected from a forest and a meadow habitat of Fairbanks Creek in northern Lower Michigan. Samples were collected every 15 minutes, interspersed with 15 minutes of no sampling, from sunset to sunrise during 5 nights from late June to mid-July 2014. Despite having fundamentally different caddisfly assemblages dominated by different species, mean specimen abundance and mean species richness in both habitats exhibited similar trends: peaking between 22:30 and 23:00, decreasing until 02:00 or 02:30, increasing again slightly during the later morning periods, and then decreasing to near zero by 06:00. On average, \u3e90% of species from the forest site were caught by 00:00 and 100% by 02:00, whereas meadow site richness didn’t reach 90% until 01:00 and 100% until 05:00. Species richness per night correlated strongly with dew point for both sites, reflecting consistently warm temperatures throughout the sampling period. Our results suggest that caddisfly flight is controlled by both innate behavior and environmental factors like temperature, and that sampling should continue late into the night to maximize capture, especially in open-canopied areas

) Australian Nuclear Science and Technology Organisation (ANSTO)

ABSTRACT The aim of this work is to model the vibrational behaviour of thin plates joined to a stiff orthogonal side plate using the technique of 'roll swaging'. Swage joints are typically found in plate-type fuel assemblies for nuclear reactors. Since they are potentially liable to flow-induced vibrations, it is crucial to be able to predict their dynamic characteristics. It is shown that the contact between the plates resulting from the swage can be modelled assuming a perfect clamp of all the degrees of freedom but the rotational around the axis parallel to the swage. A modal analysis was performed on different specimens and the values of the first natural frequencies are used to find the equivalent torsional spring stiffness, by matching these frequencies with the results obtained from a finite element model (FEM)

Surface Topographical and Compositional Characterization Using Backscattered Electron Methods

Two pairs of diametrically opposed Schottky surface barrier diodes in a modified scanning electron microscope (SEM) are used to reconstruct surface elevations and composition differences. An empirically determined function of difference of signals from opposing diodes is used to calculate slopes, which are then integrated to elevations by an efficient 2-dimensional Fast Fourier Transform. Composition differences are distinguished by variations in the overall backscattered electron (BSE) intensity estimated by the sum of the four diode signals. Arithmetic average roughness measurements from the BSE device are within 10% of stylus surface tracer measurements when surface slopes average less than 6 degrees and maximum slopes are less than 45°; shadowing effects for rough surfaces, aliasing, and averaging effects from Fourier integration are apparent. Composition measurements show distinction of high contrast phases; phase boundary-slope interactions are noted

Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.

BACKGROUND: There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools. RESULTS: Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and ad hoc analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench. CONCLUSION: Taverna can be used by data analysis experts as a generic tool for composing ad hoc analyses of quantitative data by combining the use of scripts written in the R programming language with tools exposed as services in workflows. When these workflows are shared with colleagues and the wider scientific community, they provide an approach for other scientists wanting to use tools such as R without having to learn the corresponding programming language to analyse their own data.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Brief Report: Sensorimotor Gating in Idiopathic Autism and Autism Associated with Fragile X Syndrome

Prepulse inhibition (PPI) may useful for exploring the proposed shared neurobiology between idiopathic autism and autism caused by FXS. We compared PPI in four groups: typically developing controls (n = 18), FXS and autism (FXS+A; n = 15), FXS without autism spectrum disorder (FXS−A; n = 17), and idiopathic autism (IA; n = 15). Relative to controls, the FXS+A (p < 0.002) and FXS−A (p < 0.003) groups had impaired PPI. The FXS+A (p < 0.01) and FXS−A (p < 0.03) groups had lower PPI than the IA group. Prolonged startle latency was seen in the IA group. The differing PPI profiles seen in the FXS+A and IA indicates these groups may not share a common neurobiological abnormality of sensorimotor gating

TNPO2 variants associate with human developmental delays, neurologic deficits, and dysmorphic features and alter TNPO2 activity in Drosophila

Transportin-2 (TNPO2) mediates multiple pathways including non-classical nucleocytoplasmic shuttling of >60 cargoes, such as developmental and neuronal proteins. We identified 15 individuals carrying de novo coding variants in TNPO2 who presented with global developmental delay (GDD), dysmorphic features, ophthalmologic abnormalities, and neurological features. To assess the nature of these variants, functional studies were performed in Drosophila. We found that fly dTnpo (orthologous to TNPO2) is expressed in a subset of neurons. dTnpo is critical for neuronal maintenance and function as downregulating dTnpo in mature neurons using RNAi disrupts neuronal activity and survival. Altering the activity and expression of dTnpo using mutant alleles or RNAi causes developmental defects, including eye and wing deformities and lethality. These effects are dosage dependent as more severe phenotypes are associated with stronger dTnpo loss. Interestingly, similar phenotypes are observed with dTnpo upregulation and ectopic expression of TNPO2, showing that loss and gain of Transportin activity causes developmental defects. Further, proband-associated variants can cause more or less severe developmental abnormalities compared to wild-type TNPO2 when ectopically expressed. The impact of the variants tested seems to correlate with their position within the protein. Specifically, those that fall within the RAN binding domain cause more severe toxicity and those in the acidic loop are less toxic. Variants within the cargo binding domain show tissue-dependent effects. In summary, dTnpo is an essential gene in flies during development and in neurons. Further, proband-associated de novo variants within TNPO2 disrupt the function of the encoded protein. Hence, TNPO2 variants are causative for neurodevelopmental abnormalities

Peptidylarginine deiminases as drug targets in neonatal hypoxic-ischemic encephalopathy

Oxygen deprivation and infection are major causes of perinatal brain injury leading to cerebral palsy and other neurological disabilities. The identification of novel key factors mediating white and grey matter damage are crucial to allow better understanding of the specific contribution of different cell types to the injury processes and pathways for clinical intervention. Recent studies in the Rice-Vannucci mouse model of neonatal hypoxic ischaemia (HI) have highlighted novel roles for calcium-regulated peptidylarginine deiminases (PADs) and demonstrated neuro-protective effects of pharmacological PAD inhibition following HI and synergistic infection mimicked by LPS stimulation

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Novel genetic loci underlying human intracranial volume identified through genome-wide association

Intracranial volume reflects the maximally attained brain size during development, and remains stable with loss of tissue in late life. It is highly heritable, but the underlying genes remain largely undetermined. In a genome-wide association study of 32,438 adults, we discovered five novel loci for intracranial volume and confirmed two known signals. Four of the loci are also associated with adult human stature, but these remained associated with intracranial volume after adjusting for height. We found a high genetic correlation with child head circumference (ρgenetic=0.748), which indicated a similar genetic background and allowed for the identification of four additional loci through meta-analysis (Ncombined = 37,345). Variants for intracranial volume were also related to childhood and adult cognitive function, Parkinson’s disease, and enriched near genes involved in growth pathways including PI3K–AKT signaling. These findings identify biological underpinnings of intracranial volume and provide genetic support for theories on brain reserve and brain overgrowth