The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus

Full-genome sequences have been used to monitor the fine-scale dynamics of epidemics caused by RNA viruses. However, the ability of this approach to confidently reconstruct transmission trees is limited by the knowledge of the genetic diversity of viruses that exist within different epidemiological units. In order to address this question, this study investigated the variability of 45 foot-and-mouth disease virus (FMDV) genome sequences (from 33 animals) that were collected during 2007 from eight premises (10 different herds) in the United Kingdom. Bayesian and statistical parsimony analysis demonstrated that these sequences exhibited clustering which was consistent with a transmission scenario describing herd-to-herd spread of the virus. As an alternative to analysing all of the available samples in future epidemics, the impact of randomly selecting one sequence from each of these herds was used to assess cost-effective methods that might be used to infer transmission trees during FMD outbreaks. Using these approaches, 85% and 91% of the resulting topologies were either identical or differed by only one edge from a reference tree comprising all of the sequences generated within the outbreak. The sequence distances that accrued during sequential transmission events between epidemiological units was estimated to be 4.6 nucleotides, although the genetic variability between viruses recovered from chronic carrier animals was higher than between viruses from animals with acute-stage infection: an observation which poses challenges for the use of simple approaches to infer transmission trees. This study helps to develop strategies for sampling during FMD outbreaks, and provides data that will guide the development of further models to support control policies in the event of virus incursions into FMD free countries

Application of Pade Approximants to Determination of alpha_s(M_Z^2) from Hadronic Event Shape Observables in e+e- Annihilation

We have applied Pade approximants to perturbative QCD calculations of event shape observables in e+e- --> hadrons. We used the exact O(alpha_s^2) prediction and the [0/1] Pade approximant to estimate the O(alpha_s^3) term for 15 observables, and in each case determined alpha_s(M_Z^2) from comparison with hadronic Z^0 decay data from the SLD experiment. We found the scatter among the alpha_s(M_Z^2) values to be significantly reduced compared with the standard O(alpha_s^2) determination, implying that the Pade method provides at least a partial approximation of higher-order perturbative contributions to event shape observables.Comment: 15 pages, 1 EPS figure, Submitted to Physics Letters

Piezomorphic materials

The development of stress-induced morphing materials which are described as piezomorphic materials is reported. The development of a piezomorphic material is achieved by introducing spatial dependency into the compliance matrix describing the elastic response of a material capable of undergoing large strain deformation. In other words, it is necessary to produce an elastically gradient material. This is achieved through modification of the microstructure of the compliant material to display gradient topology. Examples of polymeric (polyurethane) foam and microporous polymer (expanded polytetrafluoroethylene) piezomorphic materials are presented here. These materials open up new morphing applications where dramatic shape changes can be triggered by mechanical stress

Role of KASH domain lengths in the regulation of LINC complexes.

The linker of the nucleoskeleton and cytoskeleton (LINC) complex is formed by the conserved interactions between Sad-1 and UNC-84 (SUN) and Klarsicht, ANC-1, SYNE homology (KASH) domain proteins, providing a physical coupling between the nucleoskeleton and cytoskeleton that mediates the transfer of physical forces across the nuclear envelope. The LINC complex can perform distinct cellular functions by pairing various KASH domain proteins with the same SUN domain protein. For example, in Caenorhabditis elegans, SUN protein UNC-84 binds to two KASH proteins UNC-83 and ANC-1 to mediate nuclear migration and anchorage, respectively. In addition to distinct cytoplasmic domains, the luminal KASH domain also varies among KASH domain proteins of distinct functions. In this study, we combined in vivo C. elegans genetics and in silico molecular dynamics simulations to understand the relation between the length and amino acid composition of the luminal KASH domain, and the function of the SUN-KASH complex. We show that longer KASH domains can withstand and transfer higher forces and interact with the membrane through a conserved membrane proximal EEDY domain that is unique to longer KASH domains. In agreement with our models, our in vivo results show that swapping the KASH domains of ANC-1 and UNC-83, or shortening the KASH domain of ANC-1, both result in a nuclear anchorage defect in C. elegans

Waste Water Force Main Pipe Construction Alternatives to Protect Existing Foundations in the City of Chandler: Case Study

To provide additional wastewater capacity and redundancy in South Chandler, Arizona, a new 28” High Density Polyethylene (HDPE) force main was installed from the upsized Kyrene Lift Station three miles east to tie into an existing 66” transmission sewer line. The force main was installed under the State Route Loop 202 (SR 202L) freeway through existing 48” steel casings constructed ten years prior. Additionally, the force main was constructed through a narrow Arizona Department of Transportation (ADOT) corridor, which required clearance from existing utilities, including overhead 69 kV power poles. Two locations required innovative solutions to both access the existing sleeves and cross the transmission power pole foundations: 1) crossing of the 69 kV power pole required detailed slope stability analysis and location specific trench backfilling; and 2) access to the existing 48” was within 15 feet of an existing ADOT sound wall. Various alternatives for access were analyzed in this paper including temporary shoring, sheet pile installation, and full wall replacement and reconstructing on drilled shafts. Based on the objectives above, the existing power pole does not have sufficient embedment for maximum design loads but is stable with reduced load factors and lower operation wind forces. Also, for construction issue with the existing ADOT sound wall, the temporary shoring and sheet piles used due to the geotechnical conditions and construction costs

Antiviral mechanism change of poly(styrene sulfonate) through gold nanoparticle coating†

Viruses are pathogens capable of causing serious global health problems and therefore the development of interventions against them is of paramount importance. One strategy towards designing broad-spectrum antivirals is through the mimicking of sulfonated glycopolymers on the cell surface so that the virion/cell interaction is inhibited by the antiviral material. A number of natural and synthetic polymers have been investigated, however, most show a virustatic mechanism, which is reversible and non-destructive. Herein we present a facile route to virucidal materials by attaching a previously known virustatic polymer, poly(styrene sulfonate), onto gold nanoparticles. We show that it is possible to alter the polymer's mode of action whilst maintaining its low IC50 by changing the macromolecular architecture

Properties of the Broad-Range Nematic Phase of a Laterally Linked H-Shaped Liquid Crystal Dimer

In search for novel nematic materials, a laterally linked H-shaped liquid crystal dimer have been synthesized and characterized. The distinct feature of the material is a very broad temperature range (about 50 oC) of the nematic phase, which is in contrast with other reported H-dimers that show predominantly smectic phases. The material exhibits interesting textural features at the scale of nanometers (presence of smectic clusters) and at the macroscopic scales. Namely, at a certain temperature, the flat samples of the material show occurrence of domain walls. These domain walls are caused by the surface anchoring transition and separate regions with differently tilted director. Both above and below this transition temperature the material represents a uniaxial nematic, as confirmed by the studies of defects in flat samples and samples with colloidal inclusions, freely suspended drops, X-ray diffraction and transmission electron microscopy.Comment: 30 pages (including Supplementary Information), 7 Figure

The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data.

Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their validity in the subsequent analyses. We introduce the QC system of the Laboratory of Neuro Imaging (LONI): a web-based system featuring a workflow for the assessment of various modality and contrast brain imaging data. The design allows users to anonymously upload imaging data to the LONI-QC system. It then computes an exhaustive set of QC metrics which aids users to perform a standardized QC by generating a range of scalar and vector statistics. These procedures are performed in parallel using a large compute cluster. Finally, the system offers an automated QC procedure for structural MRI, which can flag each QC metric as being 'good' or 'bad.' Validation using various sets of data acquired from a single scanner and from multiple sites demonstrated the reproducibility of our QC metrics, and the sensitivity and specificity of the proposed Auto QC to 'bad' quality images in comparison to visual inspection. To the best of our knowledge, LONI-QC is the first online QC system that uniquely supports the variety of functionality where we compute numerous QC metrics and perform visual/automated image QC of multi-contrast and multi-modal brain imaging data. The LONI-QC system has been used to assess the quality of large neuroimaging datasets acquired as part of various multi-site studies such as the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Study and the Alzheimer's Disease Neuroimaging Initiative (ADNI). LONI-QC's functionality is freely available to users worldwide and its adoption by imaging researchers is likely to contribute substantially to upholding high standards of brain image data quality and to implementing these standards across the neuroimaging community