Effects of Wind-Hardened Snow on Foraging by Reindeer (Rangifer Tarandus)

Various methods were investigated for assessing the relationship between wind-hardened snow (upsik) and forage availability to reindeer. Mean bottom area of individual craters was not a function of depth, hardness or integrated hardness. Individual crater area was partially dependent on specific cratering time (r2 = .60). Cratering time per active period increased with integrated snow hardness (r2 = .88). Number of craters and total area cratered increased with decreasing site hardness. Reindeer always cratered microsites of lesser depth and hardness than found in the general feeding site. A threefold decrease in snow hardness resulted in a fourfold increase in forage availability.Key words: Rangifer, snow hardness, snow depth, forage availabilityMots clés: Rangifer, dureté de la neige, profondeur de la neige, accessibilité aux plantes fourragère

UMI-tools: Modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy.

Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR-amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalised. In particular, sequencing errors in the UMI sequence are often ignored, or else resolved in an ad-hoc manner. We show that errors in the UMI sequence are common and introduce network based methods to account for these errors when identifying PCR duplicates. Using these methods, we demonstrate improved quantification accuracy both under simulated conditions and real iCLIP and single cell RNA-Seq datasets. Reproducibility between iCLIP replicates and single cell RNA Seq clustering are both improved using our proposed network-based method, demonstrating the value of properly accounting for errors in UMIs. These methods are implemented in the open source UMI-tools software package

Investigation of in vivo measurement of cerebral cytochrome-c-oxidase redox changes using near-infrared spectroscopy in patients with orthostatic hypotension

We have previously used a continuous four wavelength near infrared spectrometer to measure changes in the cerebral concentrations of oxy- (Δ[HbO2] and deoxy- haemoglobin (Δ[HHb]) during head-up tilt in patients with primary autonomic failure. The measured changes in light attenuation also allow calculation of changes in the concentration of oxidised cytochrome c oxidase (Δ[oxCCO]), and this paper analyses the Δ[oxCCO] during the severe episodes of orthostatic hypotension produced by this experimental protocol. We studied 12 patients during a passive change in position from supine to a 60º head-up tilt. The challenge caused a reduction in mean blood pressure of 59.93 (±26.12) mmHg (Mean (±SD), p<0.0001), which was associated with a reduction in the total concentration of haemoglobin (Δ[HbT]= Δ[HbO2]+Δ[HHb]) of 5.02 (±3.81) μM (p<0.0001) and a reduction in the haemoglobin difference concentration (Δ[Hbdiff]= Δ[HbO2]-Δ[HHb]) of 14.4 (±6.73) μM (p<0.0001). We observed a wide range of responses in Δ[oxCCO]. 6 patients demonstrated a drop in Δ[oxCCO] (0.17 ±0.15μM ); 4 patients demonstrated no change (0.01 ±0.12 μM ) and 2 patients showed an increase in Δ[oxCCO] (0.21 ±0.01 μM ). Investigation of the association between the changes in concentrations of haemoglobin species and the Δ[oxCCO] for each patient show a range of relationships. This suggests that a simple mechanism for crosstalk, which might produce artefactual changes in [oxCCO], is not present between the haemoglobin and the oxCCO NIRS signals. Further investigation is required to determine the clinical significance of the changes in [oxCCO]

A model of ant route navigation driven by scene familiarity

In this paper we propose a model of visually guided route navigation in ants that captures the known properties of real behaviour whilst retaining mechanistic simplicity and thus biological plausibility. For an ant, the coupling of movement and viewing direction means that a familiar view specifies a familiar direction of movement. Since the views experienced along a habitual route will be more familiar, route navigation can be re-cast as a search for familiar views. This search can be performed with a simple scanning routine, a behaviour that ants have been observed to perform. We test this proposed route navigation strategy in simulation, by learning a series of routes through visually cluttered environments consisting of objects that are only distinguishable as silhouettes against the sky. In the first instance we determine view familiarity by exhaustive comparison with the set of views experienced during training. In further experiments we train an artificial neural network to perform familiarity discrimination using the training views. Our results indicate that, not only is the approach successful, but also that the routes that are learnt show many of the characteristics of the routes of desert ants. As such, we believe the model represents the only detailed and complete model of insect route guidance to date. What is more, the model provides a general demonstration that visually guided routes can be produced with parsimonious mechanisms that do not specify when or what to learn, nor separate routes into sequences of waypoints

Detection of phospholipase a activity from campylobacter concisus

This was a conference oral presentation at the 2002 ASM Annual Scientific Meeting in Melbourne.<br /

Gender-based Violence Among UK University Students and Staff: A Socio-Ecological Framework

Theories have been used to explain gender-based violence (GBV) in U.S. universities (e.g. Gervais, DiLillo and McChargue, 2014; Tewksbury and Mustaine's, 2001) but they have limited utility in UK universities, as the history, composition, geography, and culture of UK universities differs (Phipps and Smith, 2012; Stenning et al., 2012). Due to these differences, a theoretical framework relevant to UK universities is needed that can guide studies and contextualise findings. As a starting point, this working paper adapted Hagemann-White et al.’s (2010) framework, which was developed for the European Union (EU). To date, this framework is the most researched, demonstrated and wholistic model for the EU. The framework used an ecological model to identify and categorise factors facilitating and scaffolding GBV, including policies, sanctions, redress and implementation of laws, to provide nation states with a framework to guide developing and implementing policies that would more effectively prevent and combat GBV. This working paper aimed to tailor Hagemann-White et al.’s model to UK universities, using a more sophisticated understanding of intersectional (dis)advantage (such as ethnicity, gender, sexuality, disability, class, age), men and masculinities, peer-group support for violence, environmental time-space and power relations, and legal duties in prevention and response

Results of the Mitrofanoff procedure in urinary tract reconstruction in children

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90139/1/j.1464-410X.1997.33724.x.pd

Novel cell types, neurosecretory cells, and body plan of the early-diverging metazoan Trichoplax adhaerens.

BACKGROUND: Trichoplax adhaerens is the best-known member of the phylum Placozoa, one of the earliest-diverging metazoan phyla. It is a small disk-shaped animal that glides on surfaces in warm oceans to feed on algae. Prior anatomical studies of Trichoplax revealed that it has a simple three-layered organization with four somatic cell types. RESULTS: We reinvestigate the cellular organization of Trichoplax using advanced freezing and microscopy techniques to identify localize and count cells. Six somatic cell types are deployed in stereotyped positions. A thick ventral plate, comprising the majority of the cells, includes ciliated epithelial cells, newly identified lipophil cells packed with large lipid granules, and gland cells. Lipophils project deep into the interior, where they alternate with regularly spaced fiber cells whose branches contact all other cell types, including cells of the dorsal and ventral epithelium. Crystal cells, each containing a birefringent crystal, are arrayed around the rim. Gland cells express several proteins typical of neurosecretory cells, and a subset of them, around the rim, also expresses an FMRFamide-like neuropeptide. CONCLUSIONS: Structural analysis of Trichoplax with significantly improved techniques provides an advance in understanding its cell types and their distributions. We find two previously undetected cell types, lipohil and crystal cells, and an organized body plan in which different cell types are arranged in distinct patterns. The composition of gland cells suggests that they are neurosecretory cells and could control locomotor and feeding behavior