Simulations Inform Design of Regional Occupancy-Based Monitoring for a Sparsely Distributed, Territorial Species

Sparsely distributed species attract management concern. Insufficient information on population trends, however, challenges conservation and funding prioritization. Occupancybased methods are cost effective and therefore attractive for broad-scale trend monitoring, but appropriate sampling design and inference depend on particulars of the study system. We employed spatially explicit simulations to inform regional occupancy-based monitoring of white-headed woodpeckers (Picoides albolvartus), a sparsely distributed, territorial species threatened by habitat decline and degradation. We incorporated basic knowledge of species ecology into population simulations to compare statistical power and trend estimation error under alternative scenarios. Sampling effort needed to achieve adequate power to observe a long-term population trend (? 80% chance to observe a 2% yearly decline over 20 years) consisted of annually monitoring ? 120 transects using the single-survey approach or ? 90 transects using a repeat-survey approach. The single-survey approach, which employs occupancy as an index of abundance and requires auxiliary information to account for detectability, provided more power for a given level of sampling effort than repeat-survey approaches. Alternate allocation schemes improved statistical power and trend estimates over the baseline (surveying 10 points within all transects annually), including surveying a subset (33%) of transects each year (i.e., a panel design) and surveying fewer points per transect in exchange for a larger spatial sample. Considering this case study, single-survey methods (with separate evaluation of detectability), panel designs, and aligning sampling resolution with home range size could likely benefit broad-scale occupancy-based monitoring of other sparsely distributed and mobile species

Functional Organization of Locomotor Interneurons in the Ventral Lumbar Spinal Cord of the Newborn Rat

Although the mammalian locomotor CPG has been localized to the lumbar spinal cord, the functional-anatomical organization of flexor and extensor interneurons has not been characterized. Here, we tested the hypothesis that flexor and extensor interneuronal networks for walking are physically segregated in the lumbar spinal cord. For this purpose, we performed optical recordings and lesion experiments from a horizontally sectioned lumbar spinal cord isolated from neonate rats. This ventral hemi spinal cord preparation produces well-organized fictive locomotion when superfused with 5-HT/NMDA. The dorsal surface of the preparation was visualized using the Ca2+ indicator fluo-4 AM, while simultaneously monitoring motor output at ventral roots L2 and L5. Using calcium imaging, we provided a general mapping view of the interneurons that maintained a stable phase relationship with motor output. We showed that the dorsal surface of L1 segment contains a higher density of locomotor rhythmic cells than the other segments. Moreover, L1 segment lesioning induced the most important changes in the locomotor activity in comparison with lesions at the T13 or L2 segments. However, no lesions led to selective disruption of either flexor or extensor output. In addition, this study found no evidence of functional parcellation of locomotor interneurons into flexor and extensor pools at the dorsal-ventral midline of the lumbar spinal cord of the rat

Elevated 5hmC levels characterize DNA of the cerebellum in Parkinson’s disease

5-methylcytosine and the oxidation product 5-hydroxymethylcytosine are two prominent epigenetic variants of the cytosine base in nuclear DNA of mammalian brains. We measured levels of 5-methylcytosine and 5-hydroxymethylcytosine by enzyme-linked immunosorbent assay in DNA from post-mortem cerebella of individuals with Parkinson’s disease and age-matched controls. 5-methylcytosine levels showed no significant differences between Parkinson’s disease and control DNA sample sets. In contrast, median 5-hydroxymethylcytosine levels were almost twice as high (p < 0.001) in both male and female Parkinson’s disease individuals compared with controls. The distinct epigenetic profile identified in cerebellar DNA of Parkinson’s disease patients raises the question whether elevated 5-hydroxymethylcytosine levels are a driver or a consequence of Parkinson’s disease

Data-Driven Deterministic Symbolic Regression of Nonlinear Stress-Strain Relation for RANS Turbulence Modelling

This work presents developments towards a deterministic symbolic regression method to derive algebraic Reynolds-stress models for the Reynolds-Averaged Navier-Stokes (RANS) equations. The models are written as tensor polynomials, for which optimal coe cients are found using Bayesian inversion. These coe cient fields are the targets for the symbolic regression. A method is presented based on a regularisation strategy in order to promote sparsity of the inferred models and is applied to high-fidelity data. By being data-driven the method reduces the assumptions commonly made in the process of model development in order to increase the predictive fidelity of algebraic models

A geophysical study of Mesquite Valley: Nevada-California border

This paper reports the results of a geophysical investigation of a sedimentary basin, Mesquite Valley, and its surrounding area in the Basin and Range province of the western United States. Mesquite Valley is located about 40 km south-southwest of Las Vegas, Nevada, and straddles the border between Nevada and California (Figure 1). It is surrounded on three sides by mountains in which Paleozoic sedimentary rocks and Precambrian granites and gneisses crop out (Figure 1) [Burchfiel et al., 1974; Durchfiel and Davis, 1971; Hewett, 1956]. Unlike most basins in the Basin and Range province, however, there are no clearly active, range-bounding normal faults, and, in general, the surrounding topography is more subdued than in the regions farther west or north

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as ‘accidental cell death’ (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. ‘Regulated cell death’ (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death

F.J. Turner’s ‘frontier thesis’: the ruse of American ‘character'

American society was transformed by the expansion of capital Westward and the explosion in opportunities that ensued for land grabbing and agricultural and industrial investment. In Turner’s (1961) frontier thesis this was portrayed as resulting in the emergence of ‘the new man’ i.e. the fulfilment of American character. The frontier thesis is a neo-Darwinian contribution. It posits exceptionalism and transcendence as the keys to American character. The gene pool of the Americans, thriving in a new geographical and social environment, is depicted as achieving a higher level of development than the stratified societies of Old Europe. What the thesis ignores is the importance of orthodox Eurocentric strategies of colonization and land appropriation. Turner portrays pioneer/settler society as a heroic departure, but in many ways, it is a continuation of European precedents. Analogously, the proposition that the push West crystallized American character obscures the role of personality, especially in urban-industrial settings, in establishing the parameters of American life. Turner conceived of character as emerging from a struggle with the spatial frontier. But the struggles of personality with the social frontier of repression and establishment values is no less significant. The paper examines the tensions between character and personality by using some ideas developed by Carl Schmitt on the significance of ‘the opportunity’ in competitive advantage. The importance of the opportunity and personality in developing the American way of life are examined by the vaudeville and celebrity traditions. The exploitation of contingency for personal advantage, the use of melodrama to engineer social impact, the social validation of forthright behaviour are examined in the context of the careers of the film actress Mae West and the comedian Bob Hope

Is music enriching for group-housed captive chimpanzees (Pan troglodytes)?

Many facilities that house captive primates play music for animal enrichment or for caregiver enjoyment. However, the impact on primates is unknown as previous studies have been inconclusive. We conducted three studies with zoo-housed chimpanzees (Pan troglodytes) and one with group-housed chimpanzees at the National Centre for Chimpanzee Care to investigate the effects of classical and pop/rock music on various variables that may be indicative of increased welfare. Study one compared the behaviour and use of space of 18 animals when silence, classical or pop/rock music was played into one of several indoor areas. Overall, chimpanzees did not actively avoid the area when music was playing but were more likely to exit the area when songs with higher beats per minute were broadcast. Chimpanzees showed significantly fewer active social behaviours when music, rather than silence, was playing. They also tended to be more active and engage in less abnormal behaviour during the music but there was no change to either self-grooming or aggression between music and silent conditions. The genre of music had no differential effects on the chimpanzees’ use of space and behaviour. In the second study, continuous focal observations were carried out on three individuals with relatively high levels of abnormal behaviour. No differences in behaviour between music and silence periods were found in any of the individuals. The final two studies used devices that allowed chimpanzees to choose if they wanted to listen to music of various types or silence. Both studies showed that there were no persistent preferences for any type of music or silence. When taken together, our results do not suggest music is enriching for group-housed captive chimpanzees, but they also do not suggest that music has a negative effect on welfare

5-Hydroxymethylcytosine is a predominantly stable DNA modification.

5-Hydroxymethylcytosine (hmC) is an oxidation product of 5-methylcytosine which is present in the deoxyribonucleic acid (DNA) of most mammalian cells. Reduction of hmC levels in DNA is a hallmark of cancers. Elucidating the dynamics of this oxidation reaction and the lifetime of hmC in DNA is fundamental to understanding hmC function. Using stable isotope labelling of cytosine derivatives in the DNA of mammalian cells and ultrasensitive tandem liquid-chromatography mass spectrometry, we show that the majority of hmC is a stable modification, as opposed to a transient intermediate. In contrast with DNA methylation, which occurs immediately during replication, hmC forms slowly during the first 30 hours following DNA synthesis. Isotopic labelling of DNA in mouse tissues confirmed the stability of hmC in vivo and demonstrated a relationship between global levels of hmC and cell proliferation. These insights have important implications for understanding the states of chemically modified DNA bases in health and disease.We would like to acknowledge the CRUK CI Flow Cytometry and Histopathology/ISH core facilities for their contributions, David Oxley, Clive d’Santos and Donna Michelle-Smith for their support with mass spectrometry, Xiangang Zou for his help with mES cells and David Tannahill for critical reading of the manuscript. This work was funded by Cancer Research UK (all authors) and the Wellcome Trust Senior Investigator Award (S.B.).This is the accepted manuscript. The final version is available from Nature Chemistry at http://www.nature.com/nchem/journal/vaop/ncurrent/full/nchem.2064.html

Dual oscillator model of the respiratory neuronal network generating quantal slowing of respiratory rhythm

We developed a dual oscillator model to facilitate the understanding of dynamic interactions between the parafacial respiratory group (pFRG) and the preBötzinger complex (preBötC) neurons in the respiratory rhythm generation. Both neuronal groups were modeled as groups of 81 interconnected pacemaker neurons; the bursting cell model described by Butera and others [model 1 in Butera et al. (J Neurophysiol 81:382–397, 1999a)] were used to model the pacemaker neurons. We assumed (1) both pFRG and preBötC networks are rhythm generators, (2) preBötC receives excitatory inputs from pFRG, and pFRG receives inhibitory inputs from preBötC, and (3) persistent Na+ current conductance and synaptic current conductances are randomly distributed within each population. Our model could reproduce 1:1 coupling of bursting rhythms between pFRG and preBötC with the characteristic biphasic firing pattern of pFRG neurons, i.e., firings during pre-inspiratory and post-inspiratory phases. Compatible with experimental results, the model predicted the changes in firing pattern of pFRG neurons from biphasic expiratory to monophasic inspiratory, synchronous with preBötC neurons. Quantal slowing, a phenomena of prolonged respiratory period that jumps non-deterministically to integer multiples of the control period, was observed when the excitability of preBötC network decreased while strengths of synaptic connections between the two groups remained unchanged, suggesting that, in contrast to the earlier suggestions (Mellen et al., Neuron 37:821–826, 2003; Wittmeier et al., Proc Natl Acad Sci USA 105(46):18000–18005, 2008), quantal slowing could occur without suppressed or stochastic excitatory synaptic transmission. With a reduced excitability of preBötC network, the breakdown of synchronous bursting of preBötC neurons was predicted by simulation. We suggest that quantal slowing could result from a breakdown of synchronized bursting within the preBötC