Endocranial Morphology of the Extinct North American Lion (Panthera atrox)

The extinct North American lion (Panthera atrox) is one of the largest felids (Mammalia, Carnivora) to have ever lived, and it is known from a plethora of incredibly well-preserved remains. Despite this abundance of material, there has been little research into its endocranial anatomy. CT scans of a skull of P. atrox from the Pleistocene La Brea Tar pits were used to generate the first virtual endocranium for this species and to elucidate previously unknown details of its brain size and gross structure, cranial nerves, and inner-ear morphology. Results show that its gross brain anatomy is broadly similar to that of other pantherines, although P. atrox displays less cephalic flexure than either extant lions or tigers, instead showing a brain shape that is reminiscent of earlier felids. Despite this unusual reduction in flexure, the estimated absolute brain size for this specimen is one of the largest reported for any felid, living or extinct. Its encephalization quotient (brain size as a fraction of the expected brain mass for a given body mass) is also larger than that of extant lions but similar to that of the other pantherines. The advent of CT scans has allowed nondestructive sampling of anatomy that cannot otherwise be studied in these extinct lions, leading to a more accurate reconstruction of endocranial morphology and its evolution

Metastability of non-reversible mean-field Potts model with three spins

We examine a non-reversible, mean-field Potts model with three spins on a set with $N\uparrow\infty$ points. Without an external field, there are three critical temperatures and five different metastable regimes. The analysis can be extended by a perturbative argument to the case of small external fields. We illustrate the case of large external fields with some phenomena which are not present in the absence of external field.Comment: 34 pages, 12 figure

An assessment of minimum sequence copy thresholds for identifying and reducing the prevalence of artefacts in dietary metabarcoding data

1. Metabarcoding provides a powerful tool for investigating biodiversity and trophic interactions, but the high sensitivity of this methodology makes it vulnerable to errors, resulting in artefacts in the final data. Metabarcoding studies thus often utilise minimum sequence copy thresholds (MSCTs) to remove artefacts that remain in datasets; however, there is no consensus on best practice for the use of MSCTs. 2. To mitigate erroneous reporting of results and inconsistencies, this study discusses and provides guidance for best-practice filtering of metabarcoding data for the ascertainment of conservative and accurate data. Several of the most commonly used MSCTs were applied to example datasets of Eurasian otter Lutra lutra and cereal crop spider (Araneae: Linyphiidae and Lycosidae) diets. 3. Changes in both the method and threshold value considerably affected the resultant data. Of the MSCTs tested, it was concluded that the optimal method for the examples given combined a sample-based threshold with removal of maximum taxon contamination, providing stringent filtering of artefacts while retaining target data. 4. Choice of threshold value differed between datasets due to variation in artefact abundance and sequencing depth, thus studies should employ controls (mock communities, negative controls with no DNA and unused MID tag combinations) to select threshold values appropriate for each individual study

Control of human cytomegalovirus replication by liver resident natural killer cells

Natural killer cells are considered to be important for control of human cytomegalovirus– a major pathogen in immune suppressed transplant patients. Viral infection promotes the development of an adaptive phenotype in circulating natural killer cells that changes their anti-viral function. In contrast, less is understood how natural killer cells that reside in tissue respond to viral infection. Here we show natural killer cells resident in the liver have an altered phenotype in cytomegalovirus infected individuals and display increased anti-viral activity against multiple viruses in vitro and identify and characterise a subset of natural killer cells responsible for control. Crucially, livers containing natural killer cells with better capacity to control cytomegalovirus replication in vitro are less likely to experience viraemia post-transplant. Taken together, these data suggest that virally induced expansion of tissue resident natural killer cells in the donor organ can reduce the chance of viraemia post-transplant

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

CATH version 3.3 (class, architecture, topology, homology) contains 128 688 domains, 2386 homologous superfamilies and 1233 fold groups, and reflects a major focus on classifying structural genomics (SG) structures and transmembrane proteins, both of which are likely to add structural novelty to the database and therefore increase the coverage of protein fold space within CATH. For CATH version 3.4 we have significantly improved the presentation of sequence information and associated functional information for CATH superfamilies. The CATH superfamily pages now reflect both the functional and structural diversity within the superfamily and include structural alignments of close and distant relatives within the superfamily, annotated with functional information and details of conserved residues. A significantly more efficient search function for CATH has been established by implementing the search server Solr (http://lucene.apache.org/solr/). The CATH v3.4 webpages have been built using the Catalyst web framework

Structural and electronic properties of Pb1-xCdxTe and Pb1-xMnxTe ternary alloys

A systematic theoretical study of two PbTe-based ternary alloys, Pb1-xCdxTe and Pb1-xMnxTe, is reported. First, using ab initio methods we study the stability of the crystal structure of CdTe - PbTe solid solutions, to predict the composition for which rock-salt structure of PbTe changes into zinc-blende structure of CdTe. The dependence of the lattice parameter on Cd (Mn) content x in the mixed crystals is studied by the same methods. The obtained decrease of the lattice constant with x agrees with what is observed in both alloys. The band structures of PbTe-based ternary compounds are calculated within a tight-binding approach. To describe correctly the constituent materials new tight-binding parameterizations for PbTe and MnTe bulk crystals as well as a tight-binding description of rock-salt CdTe are proposed. For both studied ternary alloys, the calculated band gap in the L point increases with x, in qualitative agreement with photoluminescence measurements in the infrared. The results show also that in p-type Pb1-xCdxTe and Pb1-xMnxTe mixed crystals an enhancement of thermoelectrical power can be expected.Comment: 10 pages, 13 figures, submitted to Physical Review

Mandibular nerve block in juvenile Nile crocodile: a cadaveric study

Study design Experimental cadaveric study. Animals A group of 16 juvenile Nile crocodile heads. Methods To study the course of the mandibular nerve, one head was dissected. Computed tomography (CT) examination was performed in two heads to identify useful landmarks. Thereafter, a hypodermic needle was inserted through the external mandibular fenestra of 17 hemimandibles (13 heads) and a mixture of methylene blue and iohexol was injected. Injection volumes were 0.5 (n = 7) and 1.0 mL (n = 10) for hemimandibles < 15 and ≥ 15 cm long, respectively. Iohexol spread and nerve staining with methylene blue were assessed with CT and anatomical dissection, respectively. Data were analysed with either one sample t-test or Mann-Whitney Rank Sum test. p < 0.05 Results Both anatomical dissection and imaging confirmed the external mandibular fenestra as a useful anatomical landmark for needle insertion. The CT images acquired after needle positioning confirmed that its tip was located on the medial bony mandibular surface formed by the fusion of the angular and coronoid bone in 100% of the cases. In all the hemimandibles, the rostro-caudal spread of contrast was greater than 23 mm. The length of the stained mandibular nerve in the temporal region and of the stained medial branch of the mandibular nerve, as well as the dorso-ventral and medio-lateral spread of iohexol, was greater in group 1.0 than in group 0.5 (p < 0.001). The caudal spread of iohexol was greater in group 1.0 than in group 0.5 (p = 0.01). Conclusions and clinical relevance The technique developed in this study is feasible. Both injection volumes resulted in staining of the mandibular nerve. The spread of contrast in the anatomical region of interest may result in successful sensory block

Relating neuromuscular control to functional anatomy of limb muscles in extant archosaurs

Electromyography (EMG) is used to understand muscle activity patterns in animals. Understanding how much variation exists in muscle activity patterns in homologous muscles across animal clades during similar behaviours is important for evaluating the evolution of muscle functions and neuromuscular control. We compared muscle activity across a range of archosaurian species and appendicular muscles, including how these EMG patterns varied across ontogeny and phylogeny, to reconstruct the evolutionary history of archosaurian muscle activation during locomotion. EMG electrodes were implanted into the muscles of turkeys, pheasants, quail, guineafowl, emus (three age classes), tinamous and juvenile Nile crocodiles across 13 different appendicular muscles. Subjects walked and ran at a range of speeds both overground and on treadmills during EMG recordings. Anatomically similar muscles such as the lateral gastrocnemius exhibited similar EMG patterns at similar relative speeds across all birds. In the crocodiles, the EMG signals closely matched previously published data for alligators. The timing of lateral gastrocnemius activation was relatively later within a stride cycle for crocodiles compared to birds. This difference may relate to the coordinated knee extension and ankle plantarflexion timing across the swing‐stance transition in Crocodylia, unlike in birds where there is knee flexion and ankle dorsiflexion across swing‐stance. No significant effects were found across the species for ontogeny, or between treadmill and overground locomotion. Our findings strengthen the inference that some muscle EMG patterns remained conservative throughout Archosauria: for example, digital flexors retained similar stance phase activity and M. pectoralis remained an ‘anti‐gravity’ muscle. However, some avian hindlimb muscles evolved divergent activations in tandem with functional changes such as bipedalism and more crouched postures, especially M. iliotrochantericus caudalis switching from swing to stance phase activity and M. iliofibularis adding a novel stance phase burst of activity