A surrogate forelimb: Evolution, function and development of the avian cervical spine

The neck is a critical portion of the avian spine, one that works in tandem with the beak to act as a surrogate forelimb and allows birds to manipulate their surroundings despite the lack of a grasping capable hand. Birds display an incredible amount of diversity in neck morphology across multiple anatomical scales—from varying cervical counts down to intricate adaptations of individual vertebrae. Despite this morphofunctional disparity, little is known about the drivers of this enormous variation, nor how neck evolution has shaped avian macroevolution. To promote interest in this system, I review the development, function and evolution of the avian cervical spine. The musculoskeletal anatomy, basic kinematics and development of the avian neck are all documented, but focus primarily upon commercially available taxa. In addition, recent work has quantified the drivers of extant morphological variation across the avian neck, as well as patterns of integration between the neck and other skeletal elements. However, the evolutionary history of the avian cervical spine, and its contribution to the diversification and success of modern birds is currently unknown. Future work should aim to broaden our understanding of the cervical anatomy, development and kinematics to include a more diverse selection of extant birds, while also considering the macroevolutionary drivers and consequences of this important section of the avian spine

The neck as a keystone structure in avian macroevolution and mosaicism

BACKGROUND: The origin of birds from non-avian theropod dinosaur ancestors required a comprehensive restructuring of the body plan to enable the evolution of powered flight. One of the proposed key mechanisms that allowed birds to acquire flight and modify the associated anatomical structures into diverse forms is mosaic evolution, which describes the parcelization of phenotypic traits into separate modules that evolve with heterogeneous tempo and mode. Avian mosaicism has been investigated with a focus on the cranial and appendicular skeleton, and as such, we do not understand the role of the axial column in avian macroevolution. The long, flexible neck of extant birds lies between the cranial and pectoral modules and represents an opportunity to study the contribution of the axial skeleton to avian mosaicism. RESULTS: Here, we use 3D geometric morphometrics in tandem with phylogenetic comparative methods to provide, to our knowledge, the first integrative analysis of avian neck evolution in context with the head and wing and to interrogate how the interactions between these anatomical systems have influenced macroevolutionary trends across a broad sample of extant birds. We find that the neck is integrated with both the head and the forelimb. These patterns of integration are variable across clades, and only specific ecological groups exhibit either head-neck or neck-forelimb integration. Finally, we find that ecological groups that display head-neck and neck-forelimb integration tend to display significant shifts in the rate of neck morphological evolution. CONCLUSIONS: Combined, these results suggest that the interaction between trophic ecology and head-neck-forelimb mosaicism influences the evolutionary variance of the avian neck. By linking together the biomechanical functions of these distinct anatomical systems, the cervical vertebral column serves as a keystone structure in avian mosaicism and macroevolution

Transcritical generation of nonlinear internal waves in the presence of background shear flow

While the occurrence of large amplitude internal waves in the Earth\u27s natural bodies of water is widely documented, the generation of these waves remains an active area of exploration. We discuss numerical simulations of transcritical flows of a density stratified fluid with a dual focus on the role of a background shear current and transitions of the background current from super to subcritical. We demonstrate that the presence of a background shear can lead to the formation of large quasi-trapped regions of high vorticity over the downstream slope of the topography, but that this vorticity leads to only moderate perturbations of the underlying pycnocline, and hence that a wave and instability can co-exist for long times. Subsequently, we demonstrate the existence of hysteresis in the wave amplitude when the current is accelerated to supercritical then decelerated to subcritical, as opposed to accelerated to the subcritical value from rest. Finally, we explore situations in which the background shear is strong enough to preclude the formation of solitary-like waves, and discuss possible implications for the coastal ocean

The Surrogate Arm: Functional Morphology of the Avian Cervical Column

The avian neck allows the head to perform a variety of tasks that would be carried out by the forelimbs in other vertebrates, as the forelimbs are primarily adapted for flight in birds. This has created a strong additional selection pressure on the cervical column and has resulted in the evolution of a vast array of neck morphologies throughout extant birds. This diversity is most evident in the large variation observed in vertebral counts of the neck, and the lack of known homology between species with differing cervical counts has hindered research into morphological variation of the avian cervical spine. The lack of quantitative assessment of this variation has stunted our understanding of how the neck became such an integral component of avian biology. Recent work has shown that Hox gene patterning is conserved within the neck across Aves and that five cervical regions exist within the avian spine, and homologous interspecific comparisons can now be made by comparing aspects of regional morphology. Iterating on previous work, this thesis uses 3D geometric morphometrics as a proxy to delineate and analyse these cervical regions within extant birds. Here I use a holistic approach to understand functional and ecological drivers in avian neck shape and length in a diverse selection of 52 specimens (46 species) of modern birds by combining three-dimensional geometric morphometrics with multivariate statistics and quantitative dissection as part of the following four objectives. The first objective sought to determine if patterns of cervical regionalisation exist within extant Aves by assessing the variation in regional vertebral counts and by using Phenotypic Trajectory Analysis to examine factors that affect morphological variation across the entire cervical spine. Results indicated that increases to cervical counts are not responsible for neck elongation in birds and that few ecological factors have a significant correlation with regional vertebral counts. Vertebral morphology across the entire cervical column only displays significant variation in birds with extreme cervical kinematics, such as carnivores. The second objective was to quantify the relationship between neck length, head mass, and body mass across extant birds. Neck length and head mass scale according to isometry. The relationship between neck length and head mass is also isometric and this indicates that neck length in birds is not as tightly constrained by head mass when compared to other vertebrates. Relative neck lengths are shorter in birds that locomote using powered flight and head mass is lower in terrestrial birds. This may indicate that powered flight is a constraint on cervical morphological variation. The third objective was to quantify factors affecting variation in the morphology and length of individual regions. Region lengths strongly correlated with neck length and this suggests that avian neck elongation is a product of increases to vertebral length rather than increases to vertebral counts, and that regions 2 and 5 are responsible for this elongation. Body mass and neck length were revealed to have the strongest correlation with morphological variation in regions across 4 out of 5 cervical regions. Only ecological factors associated with specialised cervical kinematics, i.e. adaptations to carnivory or aquatic foraging, displayed significant variation in regional vertebral morphology. The final objective was to quantify variation in avian muscle architecture and I found that muscle architecture and mass scaled predominantly according to positive allometry. Ecology has a weak correlation with muscle architecture and mass variation and may accommodate fast head strikes and adaptations to underwater foraging in certain taxa. Cranial muscles that support the head appear to be more morpho-functionally restricted, whilst caudal muscles display much more variation in architecture and mass. This thesis has shown that across multiple aspects of morphology, the avian cervical column is a generalised musculoskeletal system, only adapting to specialised patterns of cervical kinematics. The avian cervical column is often referred to as a surrogate arm due to its role in positioning the head to manipulate the environment in the stead of the forelimbs which are heavily adapted for flight and the generalised pattern of morphological variation recovered here supports the hypothesis that the avian neck is a surrogate arm. Future work is needed to be done in the wake of this thesis to ensure that more birds are sampled for their variation in muscle architecture, as well as undertaking projects that seek to quantify variation in avian cervical kinematics and patterns of intervertebral flexion

Patent Thickets Identification

Patent thickets have been identified by various citations-based techniques, such as Graevenitz et al (2011) and Clarkson (2005). An alternative direct measurement is based on expert opinion. We use natural language processing techniques to measure pairwise semantic similarity of patents identified as thicket members by experts to create a semantic network. We compare the semantic similarity scores for patents in different expert-identified thickets: those within the same thicket, those in different thickets, and those not in thickets. We show that patents within the same thicket are significantly more semantically similar than other pairs of patents. We then present a statistical model to assess the probability of a newly added patent belonging to a thicket based on semantic networks as well as other measures from the existing thicket literature (the triples of Graevenitz and Clarkson’s density ratio). We conclude that combining information from semantic distance with other sources can be helpful to isolate the patents that are likely to be members of thickets

Feature Identification in Time Series Data Sets

We present a computationally inexpensive, flexible feature identification method which uses a comparison of time series to identify a rank-ordered set of features in geophysically-sourced data sets. Many physical phenomena perturb multiple physical variables nearly simultaneously, and so features are identified as time periods in which there are local maxima of absolute deviation in all time series. Unlike other available methods, this method allows the analyst to tune the method using their knowledge of the physical context. The method is applied to a data set from a moored array of instruments deployed in the coastal environment of Monterey Bay, California, and a data set from sensors placed within the submerged Yax Chen Cave System in Tulum, Quintana Roo, Mexico. These example data sets demonstrate that the method allows for the automated identification of features which are worthy of further study

A high-throughput method for isolation of salicylic acid metabolic mutants

<p>Abstract</p> <p>Background</p> <p>Salicylic acid (SA) is a key defense signal molecule against biotrophic pathogens in plants. Quantification of SA levels in plants is critical for dissecting the SA-mediated immune response. Although HPLC and GC/MS are routinely used to determine SA concentrations, they are expensive and time-consuming. We recently described a rapid method for a bacterial biosensor <it>Acinetobacter </it>sp. ADPWH_<it>lux</it>-based SA quantification, which enables high-throughput analysis. In this study we describe an improved method for fast sample preparation, and present a high-throughput strategy for isolation of SA metabolic mutants.</p> <p>Results</p> <p>On the basis of the previously described biosensor-based method, we simplified the tissue collection and the SA extraction procedure. Leaf discs were collected and boiled in Luria-Bertani (LB), and then the released SA was measured with the biosensor. The time-consuming steps of weighing samples, grinding tissues and centrifugation were avoided. The direct boiling protocol detected similar differences in SA levels among pathogen-infected wild-type, <it>npr1 </it>(nonexpressor of pathogenesis-related genes), and <it>sid2 </it>(SA induction-deficient) plants as did the previously described biosensor-based method and an HPLC-based approach, demonstrating the efficacy of the protocol presented here. We adapted this protocol to a high-throughput format and identified six <it>npr1 </it>suppressors that accumulated lower levels of SA than <it>npr1 </it>upon pathogen infection. Two of the suppressors were found to be allelic to the previously identified <it>eds5 </it>mutant. The other four are more susceptible than <it>npr1 </it>to the bacterial pathogen <it>Pseudomonas syringae </it>pv. <it>maculicola </it>ES4326 and their identity merits further investigation.</p> <p>Conclusions</p> <p>The rapid SA extraction method by direct boiling of leaf discs further reduced the cost and time required for the biosensor <it>Acinetobacter </it>sp. ADPWH_<it>lux</it>-based SA estimation, and allowed the screening for <it>npr1 </it>suppressors that accumulated less SA than <it>npr1 </it>after pathogen infection in a high-throughput manner. The highly efficacious SA estimation protocol can be applied in genetic screen for SA metabolic mutants and characterization of enzymes involved in SA metabolism. The mutants isolated in this study may help identify new components in the SA-related signaling pathways.</p

Continuing professional development requirements for UK health professionals: a scoping review

Abstract Objectives This paper sets out to establish the numbers and titles of regulated healthcare professionals in the UK and uses a review of how continuing professional development (CPD) for health professionals is described internationally to characterise the postqualification training required of UK professions by their regulators. It compares these standards across the professions and considers them against the best practice evidence and current definitions of CPD. Design A scoping review. Search strategy We conducted a search of UK health and social care regulators’ websites to establish a list of regulated professional titles, obtain numbers of registrants and identify documents detailing CPD policy. We searched Applied Social Sciences Index and Abstracs (ASSIA), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Medline, EMCare and Scopus Life Sciences, Health Sciences, Physical Sciences and Social Sciences & Humanities databases to identify a list of common features used to describe CPD systems internationally and these were used to organise the review of CPD requirements for each profession. Results CPD is now mandatory for the approximately 1.5 million individuals registered to work under 32 regulated titles in the UK. Eight of the nine regulators do not mandate modes of CPD and there is little requirement to conduct interprofessional CPD. Overall 81% of those registered are required to engage in some form of reflection on their learning but only 35% are required to use a personal development plan while 26% have no requirement to engage in peer-to-peer learning. Conclusions Our review highlights the wide variation in the required characteristics of CPD being undertaken by UK health professionals and raises the possibility that CPD schemes are not fully incorporating the best practice