KNeXT: a NetworkX-based topologically relevant KEGG parser

Automating the recreation of gene and mixed gene-compound networks from Kyoto Encyclopedia of Genes and Genomes (KEGG) Markup Language (KGML) files is challenging because the data structure does not preserve the independent or loosely connected neighborhoods in which they were originally derived, referred to here as its topological environment. Identical accession numbers may overlap, causing neighborhoods to artificially collapse based on duplicated identifiers. This causes current parsers to create misleading or erroneous graphical representations when mixed gene networks are converted to gene-only networks. To overcome these challenges we created a python-based KEGG NetworkX Topological (KNeXT) parser that allows users to accurately recapitulate genetic networks and mixed networks from KGML map data. The software, archived as a python package index (PyPI) file to ensure broad application, is designed to ingest KGML files through built-in APIs and dynamically create high-fidelity topological representations. The utilization of NetworkX’s framework to generate tab-separated files additionally ensures that KNeXT results may be imported into other graph frameworks and maintain programmatic access to the original x-y axis positions to each node in the KEGG pathway. KNeXT is a well-described Python 3 package that allows users to rapidly download and aggregate specific KGML files and recreate KEGG pathways based on a range of user-defined settings. KNeXT is platform-independent, distinctive, and it is not written on top of other Python parsers. Furthermore, KNeXT enables users to parse entire local folders or single files through command line scripts and convert the output into NCBI or UniProt IDs. KNeXT provides an ability for researchers to generate pathway visualizations while persevering the original context of a KEGG pathway. Source code is freely available at https://github.com/everest-castaneda/knext

Images of dissipation layers to quantify mixing within a turbulent jet

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/77254/1/AIAA-13435-811.pd

Squirrelpox virus: assessing prevalence, transmission and environmental degradation

Red squirrels (Sciurus vulgaris) declined in Great Britain and Ireland during the last century, due to habitat loss and the introduction of grey squirrels (Sciurus carolinensis), which competitively exclude the red squirrel and act as a reservoir for squirrelpox virus (SQPV). The disease is generally fatal to red squirrels and their ecological replacement by grey squirrels is up to 25 times faster where the virus is present. We aimed to determine: (1) the seropositivity and prevalence of SQPV DNA in the invasive and native species at a regional scale; (2) possible SQPV transmission routes; and, (3) virus degradation rates under differing environmental conditions. Grey (n = 208) and red (n = 40) squirrel blood and tissues were sampled. Enzyme-linked immunosorbent assay (ELISA) and quantitative real-time polymerase chain reaction (qPCR) techniques established seropositivity and viral DNA presence, respectively. Overall 8% of squirrels sampled (both species combined) had evidence of SQPV DNA in their tissues and 22% were in possession of antibodies. SQPV prevalence in sampled red squirrels was 2.5%. Viral loads were typically low in grey squirrels by comparison to red squirrels. There was a trend for a greater number of positive samples in spring and summer than in winter. Possible transmission routes were identified through the presence of viral DNA in faeces (red squirrels only), urine and ectoparasites (both species). Virus degradation analyses suggested that, after 30 days of exposure to six combinations of environments, there were more intact virus particles in scabs kept in warm (25°C) and dry conditions than in cooler (5 and 15°C) or wet conditions. We conclude that SQPV is present at low prevalence in invasive grey squirrel populations with a lower prevalence in native red squirrels. Virus transmission could occur through urine especially during warm dry summer conditions but, more notably, via ectoparasites, which are shared by both species

Physiological responses during ascent to high altitude and the incidence of acute mountain sickness.

Acute mountain sickness (AMS) occurs when there is failure of acclimatisation to high altitude. The aim of this study was to describe the relationship between physiological variables and the incidence of AMS during ascent to 5300 m. A total of 332 lowland-dwelling volunteers followed an identical ascent profile on staggered treks. Self-reported symptoms of AMS were recorded daily using the Lake Louise score (mild 3-4; moderate-severe ≥5), alongside measurements of physiological variables (heart rate, respiratory rate (RR), peripheral oxygen saturation (SpO2 ) and blood pressure) before and after a standardised Xtreme Everest Step-Test (XEST). The overall occurrence of AMS among participants was 73.5% (23.2% mild, 50.3% moderate-severe). There was no difference in gender, age, previous AMS, weight or body mass index between participants who developed AMS and those who did not. Participants who had not previously ascended >5000 m were more likely to get moderate-to-severe AMS. Participants who suffered moderate-to-severe AMS had a lower resting SpO2 at 3500 m (88.5 vs. 89.6%, p = 0.02), while participants who suffered mild or moderate-to-severe AMS had a lower end-exercise SpO2 at 3500 m (82.2 vs. 83.8%, p = 0.027; 81.5 vs. 83.8%, p 5000 m (OR 2.740, p-value 0.003) predicted the development of moderate-to-severe AMS. The Xtreme Everest Step-Test offers a simple, reproducible field test to help predict AMS, albeit with relatively limited predictive precision

On the Isomorphic Description of Chiral Symmetry Breaking by Non-Unitary Lie Groups

It is well-known that chiral symmetry breaking ($\chi$SB) in QCD with $N_{f}=2$ light quark flavours can be described by orthogonal groups as $O(4) \to O(3)$, due to local isomorphisms. Here we discuss the question how specific this property is. We consider generalised forms of $\chi$SB involving an arbitrary number of light flavours of continuum or lattice fermions, in various representations. We search systematically for isomorphic descriptions by non-unitary, compact Lie groups. It turns out that there are a few alternative options in terms of orthogonal groups, while we did not find any description entirely based on symplectic or exceptional Lie groups. If we adapt such an alternative as the symmetry breaking pattern for a generalised Higgs mechanism, we may consider a Higgs particle composed of bound fermions and trace back the mass generation to $\chi$SB. In fact, some of the patterns that we encounter appear in technicolour models. In particular if one observes a Higgs mechanism that can be expressed in terms of orthogonal groups, we specify in which cases it could also represent some kind of $\chi$SB of techniquarks.Comment: 18 pages, to appear in Int. J. Mod. Phys.

Auditing Ranked Voting Elections with Dirichlet-Tree Models: First Steps

Ranked voting systems, such as instant-runo voting (IRV) and single transferable vote (STV), are used in many places around the world. They are more complex than plurality and scoring rules, pre- senting a challenge for auditing their outcomes: there is no known risk- limiting audit (RLA) method for STV other than a full hand count. We present a new approach to auditing ranked systems that uses a sta- tistical model, a Dirichlet-tree, that can cope with high-dimensional pa- rameters in a computationally e cient manner. We demonstrate this ap- proach with a ballot-polling Bayesian audit for IRV elections. Although the technique is not known to be risk-limiting, we suggest some strategies that might allow it to be calibrated to limit risk

Identification of Novel Cetacean Poxviruses in Cetaceans Stranded in South West England

Poxvirus infections in marine mammals have been mainly reported through their clinical lesions and electron microscopy (EM). Poxvirus particles in association with such lesions have been demonstrated by EM and were previously classified as two new viruses, cetacean poxvirus 1 (CePV-1) and cetacean poxvirus 2 (CePV-2). In this study, epidermal pox lesions in cetaceans stranded in South West England (Cornwall) between 2008 and 2012 were investigated by electron microscopy and molecular analysis. PCR and sequencing of a highly conserved region within the viral DNA polymerase gene ruled out both parapoxand orthopoxviruses. Moreover, phylogenetic analysis of the PCR product clustered the sequences with those previously described as cetacean poxviruses. However, taking the close genetic distance of this gene fragment across the family of poxviridae into account, it is reasonable to postulate further, novel cetacean poxvirus species. The nucleotide similarity within each cluster (tentative species) detected ranged from 98.6% to 100%, whilst the similarity between the clusters was no more than 95%. The detection of several species of poxvirus in different cetacean species confirms the likelihood of a heterogeneous cetacean poxvirus genus, comparable to the heterogeneity observed in other poxvirus genera

Adenovirus: an emerging factor in red squirrel Sciurus vulgaris conservation

1. Adenovirus is an emerging threat to red squirrel Sciurus vulgaris conservation, but confirming clinically significant adenovirus infections in red squirrels is challenging. Rapid intestinal autolysis after death in wild animals frequently obscures pathology characteristic of the disease in animals found dead. 2. We review the available literature to determine current understanding of both subclinical and clinically significant adenovirus infections in free-living wild and captive red squirrel populations. 3. Benefits of scientific testing for adenovirus incorporating both transmission electron microscopy (TEM) and polymerase chain reaction (PCR) technologies are compared and contrasted. We favour viral particle detection using TEM in animals exhibiting enteropathy at post-mortem and the use of PCR to detect subclinical cases where no enteric abnormalities are observed. 4. Adenoviral infections associated with re-introduction studies are evaluated by examination of sporadic cases in wild populations and of data from captive collections used to service such studies. 5. The paucity of data available on adenovirus infection in grey squirrel Sciurus carolinensis populations is documented, and we highlight that although subclinical virus presence is recorded in several locations in Great Britain and in Italy, no clinically significant disease cases have been detected in the species thus far. 6. Current speculation about potential interspecific infection between sciurids and other woodland rodents such as wood mice Apodemus sylvaticus is examined. Where subclinical adenovirus presence has been detected in sympatric populations using the same point food sources, husbandry methods may be used to diminish the potential for cross-infection. 7. Our findings highlight the importance of controlling disease in red squirrel populations by using clearly defined scientific methods. In addition, we propose hypothetical conservation benefits of restricting contact rates between red squirrels and sympatric grey squirrels and of limiting competition from other woodland rodent species

Herpesvirus skin disease in free-living common frogs Rana temporaria in Great Britain

Infectious disease is a significant driver of global amphibian declines, yet despite this, relatively little is known about the range of pathogens that affect free-living amphibians. Recent detection of the tentatively named Ranid herpesvirus 3 (RHV3), associated with skin disease in free-living common frogs Rana temporaria in Switzerland, helps to address this paucity in knowledge, but the geographic distribution and epidemiology of the pathogen remains unclear. Syndromic surveillance for ranid herpesvirus skin disease was undertaken throughout Great Britain (GB), January 2014 to December 2016. Reports of common frogs with macroscopic skin lesions with a characteristic grey appearance were solicited from members of the public. Post-mortem examination was conducted on one affected frog found dead in 2015 at a site in England. In addition, archived samples from an incident involving common frogs in England in 1997 with similar macroscopic lesions were further investigated. Transmission electron microscopy identified herpes-like virions in skin lesions from both the 1997 and 2015 incidents. RHV3, or RHV3-like virus, was detected in skin lesions from the 2015 case by PCR and sequencing. Our findings indicate that herpesvirus skin disease is endemic in common frogs in GB, with widespread distribution at apparently low prevalence. Further research into the role of host immunity, virus latency and the significance of infection to host survival is required to better understand the epidemiology and impact of cutaneous herpesvirus infections in amphibian populations

Groundwater : meltwater interaction in a proglacial aquifer

Groundwater plays a significant role in the hydrology of active glacial catchments, with evidence that it may buffer changes in meltwater river flow and partially compensate for glacial loss. However, to date there has been little direct research into the hydrogeology and groundwater dynamics of proglacial aquifers. Here we directly investigate the three dimensional nature of a proglacial sandur (floodplain) aquifer in SE Iceland, using hydrogeological, geophysical, hydrological and stable isotopic techniques, and provide evidence of groundwater-melt water dynamics over three years. We show that the proglacial sandur forms a thick (at least 50-100 m), high permeability (transmissivity up to 2500 m2/day) aquifer, extending over an area of approximately 6 km2. At least 35 million m3 of groundwater is stored in the aquifer, equivalent to ~23-28% of total annual river flow through the catchment. The volume of mean annual groundwater flow through the aquifer is at least 0.1-1 m3/sec, equivalent to ~10-20% of mean annual river flow. Groundwater across the aquifer is actively recharged from local precipitation and strongly influenced by individual rainfall events and seasonal precipitation. Glacial meltwater influence on groundwater also occurs in a zone extending from 20-500 m away from the meltwater river, for at least 3km down-sandur, and to at least 15 m deep. Within this zone summer recharge from the river to groundwater occurs when meltwater river flows are high, maintaining high summer groundwater levels compared to winter levels; and groundwater temperature and chemistry are strongly influenced by meltwater. Beyond this zone there is no substantial meltwater influence on groundwater. From ~2 km down-sandur there is extensive groundwater discharge via springs, supporting semi-perennial streams that form distinct local ecosystems, and providing baseflow to the main meltwater river. This research indicates that predicted continued climate change-related reductions in glacier coverage and increases in precipitation are likely to increase the significance of groundwater storage as a water resource, and of groundwater discharges in maintaining environmental river flows in glacier catchments