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Anaerobic gut fungal community in ostriches ( Struthio camelus )
Anaerobic gut fungi (AGF; Neocallimastigomycota) are crucial for the degradation of plant biomass in herbivores. While extensively studied in mammals, information regarding their occurrence, diversity, and community structure in nonmammalian hosts remains sparse. Here, we report on the AGF community in fecal samples of 13 domesticated ostriches. The ostrich (Struthio camelus) is an herbivorous, flightless, hindgut-fermenting member of the class Aves (birds). Illumina-based metabarcoding targeting the D2 region of the large ribosomal subunit (28S rRNA) revealed a uniform AGF community with low alpha diversity in the fecal samples. The community was mostly comprised of sequences potentially representing two novel species in the genus Piromyces, and a novel genus in the Neocallimastigomycota. Sequences affiliated with these novel taxa were absent or extremely rare in datasets derived from mammalian and tortoise samples, indicating a strong pattern of AGF-host association. One Piromyces strain (strain Ost1) was successfully isolated. Transcriptomics-enabled molecular dating analysis suggested a divergence time of ≈ 30Mya, a time frame in line with current estimates for ostrich evolution. Comparative gene content analysis between strain Ost1 and other Piromyces species from mammalian sources revealed a high degree of similarity. Our findings expand the range of AGF animal hosts to include members of the birds (class Aves), highlight a unique AGF community in the ostrich alimentary tract, and document the occurrence of a strong pattern of fungal–host association in ostriches, similar to previously observed patterns in AGF canonical mammalian hosts.
Journal Article
Creating an isotopically similar Earth–Moon system with correct angular momentum from a giant impact
The giant impact hypothesis is the dominant theory explaining the formation of our Moon. However, the inability to produce an isotopically similar Earth–Moon system with correct angular momentum has cast a shadow on its validity. Computer-generated impacts have been successful in producing virtual systems that possess many of the observed physical properties. However, addressing the isotopic similarities between the Earth and Moon coupled with correct angular momentum has proven to be challenging. Equilibration and evection resonance have been proposed as means of reconciling the models. In the summer of 2013, the Royal Society called a meeting solely to discuss the formation of the Moon. In this meeting, evection resonance and equilibration were both questioned as viable means of removing the deficiencies from giant impact models. The main concerns were that models were multi-staged and too complex. We present here initial impact conditions that produce an isotopically similar Earth–Moon system with correct angular momentum. This is done in a single-staged simulation. The initial parameters are straightforward and the results evolve solely from the impact. This was accomplished by colliding two roughly half-Earth-sized impactors, rotating in approximately the same plane in a high-energy, off-centered impact, where both impactors spin into the collision.
Journal Article
eDiscovery is here to stay: is your medical practice prepared for its risks and costs?
The adoption of electronic medical records technology in medical practices is helping to improve quality and decrease costs. While electronic records can increase practice efficiencies, this stored digital information is also playing an increasingly central role in the discovery phase of lawsuits. The sheer volume of electronic files that may be subject to a search and review during the electronic discovery phase (eDiscovery or e-discovery) can be overwhelming to produce. This phase of litigation is costly, too--the average eDiscovery project can run into the hundreds of thousands of dollars. A medical practice can reduce the number of procedural headaches and unnecessary legal costs by designing and implementing an eDiscovery strategy and process to reduce their legal and financial risk.
Journal Article
Performance of the LHCb RICH detector at the LHC
The LHCb experiment has been taking data at the Large Hadron Collider (LHC) at CERN since the end of 2009. One of its key detector components is the Ring-Imaging Cherenkov (RICH) system. This provides charged particle identification over a wide momentum range, from 2–100 GeV/
c
. The operation and control, software, and online monitoring of the RICH system are described. The particle identification performance is presented, as measured using data from the LHC. Excellent separation of hadronic particle types (
π
, K, p) is achieved.
Journal Article
The anaerobic gut fungal community in ostriches ( Struthio camelus )
Anaerobic gut fungi (AGF;
) are essential for plant biomass degradation in herbivores. While extensively studied in mammals, information regarding their occurrence, diversity, and community structure in non-mammalian hosts remains sparse. Here, we report on the AGF community in ostriches (
), herbivorous, flightless, hindgut fermenting members of the class
(birds). Culture-independent diversity surveys of fecal samples targeting the D2 region of the large ribosomal subunit (28S rRNA) revealed a uniform community with low alpha diversity. The community was mostly comprised of sequences potentially representing two novel species in the genus
, and a novel genus in the
. Sequences affiliated with these novel taxa were absent or extremely rare in datasets derived from mammalian and tortoise samples, indicating a strong pattern of AGF-host association. One
strain (strain Ost1) was successfully isolated. Transcriptomics-enabled molecular dating analysis suggested a divergence time of ≈ 30 Mya, a time frame in line with current estimates for ostrich evolution. Comparative gene content analysis between strain Ost1 and other
species from mammalian sources revealed a high degree of similarity. Our findings expand the range of AGF animal hosts to include members of the birds (class
), highlight a unique AGF community adapted to the ostrich alimentary tract, and demonstrate that - like mammals - coevolutionary phylosymbiosis (i.e. concurrent evolution of AGF and their animal hosts) plays a central role in explaining current AGF distribution patterns in
.
Journal Article
Cedar: a Dimensionally Adaptive Flow Solver for Cylindrical Combustors
This thesis discusses the application, evaluation, and extension of dimensionally adaptive meshing to the numerical solution of velocity and pressure fields inside cylindrical reactors. Due to the high length to diameter ratios of many cylindrical reactor vessels the flow field can become axisymmetric, allowing for simplification of the governing equations and significant reduction in computational time required for solution.A fully 3D solver is developed from existing computational tools at BYU and validated against theoretical velocity profiles for pipe flow at various Reynolds numbers, as well as with experimental data for an axial-fired center jet with recirculating flow. Dimensionally adaptive meshing is then incorporated into the validated 3D solver. The boundary conditions and assumptions at the dimensional boundary are discussed. The flow information is passed across the boundary through spatial mass-weighted averaging. The 3D and axisymmetric computational domains are decoupled from one another so information can only be passed from the 3D domain downstream to the axisymmetric domain. The dimensional boundary placement must meet two main requirements, the flow must be one-way and axisymmetric. It is found that the flow becomes axisymmetric early on in the reactor (~0.3-0.4 m), but recirculation exists farther downstream (until ~0.61 m) and thus governs the placement of the dimensional boundary.The resulting computational tool capable of running simulations using dimensionally adaptive meshes is called CEDAR (Computationally Efficient Dimensionally Adaptive Recirculating flow solver). Several studies are then undertaken to examine CEDAR’s ability to reproduce exit velocity profiles comparable to those produced by a fully 3D mesh, including variations in pressure, firing rate, and geometry. It is found that the flow structure inside the reactor is self-similar over a wide range of operating parameters as long as the burner jets are turbulent. This observation is supported by free and confined jet theory. These theories also provide a method for placing the dimensional boundary, which is a linear function of the confining geometry diameter only (assuming that the jet diameter is less than 1/10 the diameter of the confining geometry). All exit velocity profiles produced by CEDAR are on average within 5% of the fully 3D profiles. Timing studies reveal an average 5.16 times speedup in computational time over fully 3D computations.
Dissertation
Test-beam demonstration of a TORCH prototype module
The TORCH time-of-flight detector is designed to provide a 15 ps timing resolution for charged particles, resulting in π /K particle identification up to 10 GeV/c momentum over a 10 m flight path. Cherenkov photons, produced in a quartz plate of 10 mm thickness, are focused onto an array of micro-channel plate photomultipliers (MCP-PMTs) which measure the photon arrival times and spatial positions. A half-scale (660 × 1250 × 10 mm 3 ) TORCH demonstrator module has been tested in an 8 GeV/c mixed proton-pion beam at CERN. Customised square MCP-PMTs of active area 53 × 53 mm 2 and granularity 64 × 64 pixels have been employed, which have been developed in collaboration with an industrial partner. The single-photon timing performance and photon yields have been measured as a function of beam position in the radiator, giving measurements which are consistent with expectations. The expected performance of TORCH for high luminosity running of the LHCb Upgrade II has been simulated.
Journal Article
Earthworms and pH affect communities of nematodes and enchytraeids in forest soil
In northern boreal forests the occurrence of endogeic and anecic earthworms is determined by soil pH. Increasing evidence suggests that large detritivorous soil animals such as earthworms can influence the other components of the decomposer community. To study the effects of earthworms and pH on soil nematode and enchytraeid communities, a factorially designed experiment was conducted with Lumbricus rubellus and/or Aporrectodea caliginosa. Earthworms were added to \"mesocosms\" containing unlimed (pH 4.8) or limed (pH 6.1) coniferous mor humus with their natural biota of micro-organisms. In the absence of earthworms, nematodes were significantly more abundant in limed than in unlimed humus. Earthworms markedly decreased the numbers of nematodes both in unlimed and limed soils. Earthworm activities eliminated enchytraeids in unlimed soil, but liming improved the survival of some species. It was concluded that liming of soil, either alone or mediated by the earthworm populations, is likely to affect soil nematode and enchytraeid community and mineralisation.[PUBLICATION ABSTRACT]
Journal Article