Global environmental drivers of marine fish egg size

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.All data, R packages, and code (data manipulation, analyses, figures andtables) can be downloaded from our GitHub repositories (www.github.com/dbarneche/noaaErddap; www.github.com/dbarneche/envPred;https://github.com/dbarneche/fishEggSize)Aim To test long‐standing theory on the role of environmental conditions (both mean and predictability) in shaping global patterns in the egg sizes of marine fishes. Location Global (50° S to 50° N). Time period 1880 to 2015. Major taxa studied Marine fish. Methods We compiled the largest geo‐located dataset of marine fish egg size (diameter) to date (n = 1,078 observations; 192 studies; 288 species; 242 localities). We decomposed sea surface temperature (SST) and chlorophyll‐a time series into mean and predictability (seasonality and colour of environmental noise – i.e. how predictable the environment is between consecutive time steps), and used these as predictors of egg size in a Bayesian phylogenetic hierarchical model. We test four specific hypotheses based on the classic discussion by Rass (1941), as well as contemporary life‐history theory, and the conceptual model of Winemiller and Rose (1992). Results Both environmental mean and predictability correlated with egg size. Our parsimonious model indicated that egg size decreases by c. 2.0‐fold moving from 1 to 30 °C. Environments that were more seasonal with respect to temperature were associated with larger eggs. Increasing mean chlorophyll‐a, from 0.1 to 1 mg/m3, was associated with a c. 1.3‐fold decrease in egg size. Lower chlorophyll‐a seasonality and reddened noise were also associated with larger egg sizes – aseasonal but more temporally autocorrelated resource regimes favoured larger eggs. Main conclusions Our findings support results from Rass (1941) and some predictions from Winemiller and Rose (1992). The effects of environmental means and predictability on marine fish egg size are largely consistent with those observed in marine invertebrates with feeding larvae, suggesting that there are important commonalities in how ectotherm egg size responds to environmental change. Our results further suggest that anthropogenically mediated changes in the environment will have profound effects on the distribution of marine life histories.Centre for Geometric Biolog

A Big Fan of Signals? Exploring Autogenic and Allogenic Process and Product In a Numerical Stratigraphic Forward Model of Submarine-Fan Development

Distinguishing an allogenic signal from trends and patterns produced by autogenic processes is a critical element in interpreting, understanding, and predicting strata. Lobyte3D is a new reduced-complexity model of dispersive flow over an evolving topography on fan systems that produces surprisingly complex potentially hierarchical strata despite a simple formulation. Two submarine-fan model scenarios are run, one with constant sediment input, and one with a sinusoidal variation in sediment input with an oscillation period of 25 ky and a peak-to-trough 80% volume change. Both model scenarios show that flows cluster to produce lobes which migrate and can rapidly switch location. Runs tests that can detect thickening and thinning bed trends and spectral analysis that detects the frequency of any signal present suggest that strata can be ordered even in the absence of any allogenic signal, with cycles and trends in bed thickness, but no single characteristic frequency. In the oscillating-supply scenario, an allogenic signal is present in places, particularly in the axial mid fan, but may be difficult to distinguish from the autogenic signal with only limited outcrop data, and without knowing a priori how the allogenic signal is likely to be preserved in complex and incomplete strata. Based on these limited model results we hypothesize that analysis of mid-fan vertical sections, using simple power-spectrum analysis and counting of the significant peaks present across a range of frequencies, may allow identification of a “signal bump” that could be evidence of the presence and nature of allocyclic forcing. Further Lobyte3D modeling work will explore if and how the “signal bump” is preserved with input signals across a range of frequencies and amplitudes, to guide further data collection and interpretation in outcrop and subsurface strata

An adaptive non-raster scanning method in atomic force microscopy for simple sample shapes

It is a significant challenge to reduce the scanning time in atomic force microscopy while retaining imaging quality. In this paper, a novel non-raster scanning method for high-speed imaging is presented. The method proposed here is developed for a specimen with the simple shape of a cell. The image is obtained by scanning the boundary of the specimen at successively increasing heights, creating a set of contours. The scanning speed is increased by employing a combined prediction algorithm, using a weighted prediction from the contours scanned earlier, and from the currently scanned contour. In addition, an adaptive change in the height step after each contour scan is suggested. A rigorous simulation test bed recreates the x-y specimen stage dynamics and the cantilever height control dynamics, so that a detailed parametric comparison of the scanning algorithms is possible. The data from different scanning algorithms are compared after the application of an image interpolation algorithm (the Delaunay interpolation algorithm), which can also run on-line.We would like to acknowledge the support of the Engineering and Physical Sciences Research Council (EPSRC) (grant nos. EP/I034882/1 & EP/I034831/1)

Genotype-Dependent Tumor Regression in Marek’s Disease Mediated at the Level of Tumor Immunity

Marek’s disease (MD) of chickens is a unique natural model of Hodgkin’s and Non Hodgkin’s lymphomas in which the neoplastically-transformed cells over-express CD30 (CD30hi) antigen. All chicken genotypes can be infected with MD virus and develop microscopic lymphomas. From 21 days post infection (dpi) microscopic lymphomas regress in resistant chickens but, in contrast, they progress to gross lymphomas in susceptible chickens. Here we test our hypothesis that in resistant chickens at 21 dpi the tissue microenvironment is pro T-helper (Th)-1 and compatible with cytotoxic T lymphocyte (CTL) immunity but in susceptible lines it is pro Th-2 or pro T-regulatory (T-reg) and antagonistic to CTL immunity. We used the B2, non-MHC-associated, MD resistance/susceptibility system (line [L]61/line [L]72) and quantified the levels of key mRNAs that can be used to define Th-1 (IL-2, IL-12, IL-18, IFNγ), Th-2 (IL-4, IL-10) and T-reg (TGFβ, GPR-83, CTLA-4, SMAD-7) lymphocyte phenotypes. We measured gene expression in both whole tissues (represents tissue microenvironment and tumor microenvironment) and in the lymphoma lesions (tumor microenvironment) themselves. Gene ontology-based modeling of our results shows that the dominant phenotype in whole tissue as well as in microscopic lymphoma lesions, is pro T-reg in both L61 and L72 but a minor pro Th-1 and anti Th-2 tissue microenvironment exists in L61 whereas there is an anti Th-1 and pro Th-2 tissue microenvironment in L72. The tumor microenvironment per se is pro T-reg, anti Th-1 and pro Th-2 in both L61 and L72. Together our data suggests that the neoplastic transformation is essentially the same in both L61 and L72 and that resistance/susceptibility is mediated at the level of tumor immunity in the tissues

A Multi-mode Transverse Dynamic Force Microscope - Design, Identification and Control

This is the author accepted manuscript. The final version is available from IEEE via the DOI in this record.The transverse dynamic force microscope (TDFM) and its shear force sensing principle permit true non-contact force detection in contrast to typical atomic force microscopes. The two TDFM measurement signals for the cantilever allow, in principle, two different scanning modes of which, in particular, the second presented here permits a full-scale non-contact scan. Previous research mainly focused on developing the sensing mechanism, whereas this work investigates the vertical axis dynamics for advanced robust closed-loop control. This paper presents a new TDFM digital control solution, built on field-programmable gate array (FPGA) equipment running at high implementation frequencies. The integrated control system allows the implementation of online customizable controllers, and raster-scans in two modes at very high detection bandwidth and nano-precision. Robust control algorithms are designed, implemented, and practically assessed. The two realized scanning modes are experimentally evaluated by imaging nano-spheres with known dimensions in wet conditions.Engineering and Physical Sciences Research Council (EPSRC

Optimisation of a nano-positioning stage for a Transverse Dynamic Force Microscope

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.This paper describes the optimisation of a nano-positioning stage for a Transverse Dynamic Force Microscope (TDFM). The nano-precision stage is required to move a specimen dish within a horizontal region of 1 μm × 1 μm and with a resolution of 0.3 nm. The design objective was to maximise positional accuracy during high speed actuation. This was achieved by minimising out-of-plane distortions and vibrations during actuation. Optimal performance was achieved through maximising out-of-plane stiffness through shape and material selection as well optimisation of the anchoring system. Several shape parameters were optimised including the shape of flexural beams and the shape of the dish holder. Physical prototype testing was an essential part of the design process to confirm the accuracy of modelling and also to reveal issues with manufacturing tolerances. An overall resonant frequency of 6 kHz was achieved allowing for a closed loop-control frequency of 1.73 kHz for precise horizontal motion control. This resonance represented a 12-fold increase from the original 500 Hz of a commercially available positioning stage. Experimental maximum out-of-plane distortions below the first resonance frequency were reduced from 0.3 μm for the first prototype to less than 0.05 μm for the final practical prototype

Real-time sliding mode observer scheme for shear force estimation in a transverse dynamic force microscope

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.This paper describes a sliding mode observer scheme for estimation of the shear force affecting the cantilever in a Transverse Dynamic Force Microscope (TDFM). The vertically oriented cantilever is oscillated in proximity to the specimen under investigation. The amplitude of oscillation of the cantilever tip is affected by these shear forces. They are created by the ordered-water layer above the specimen. The oscillation amplitude is therefore a measure of distance between the tip and the surface of the specimen. Consequently, the estimation of the shear forces provides useful information about the specimen characteristics. For estimating the shear forces, an approximate finite dimensional model of the cantilever is created using the method of lines. This model is subsequently reduced for its model order. An unknown input sliding mode observer has been used to reconstruct the unknown shear forces using only tip position measurements and the cantilever excitation. This paper describes the development of the sliding mode scheme and presents experimental results from the TDFM set up at the Centre for Nanoscience and Quantum Information (NSQI) at Bristol University

Biomimetic knee design to improve joint torque and life for bipedal robotics

© Springer International Publishing AG, part of Springer Nature 2018. This paper details the design, construction, and performance analysis of a biologically inspired knee joint for use in bipedal robotics. The design copies the condylar surfaces of the distal end of the femur and utilizes the same crossed four-bar linkage design the human knee uses. The joint includes a changing center of rotation, a screw-home mechanism, and patella; these are characteristics of the knee that are desirable to copy for bipedal robotics. The design was calculated to have an average sliding to rolling ratio of 0.079, a maximum moment arm of 2.7 in and a range of motion of 151°. This should reduce wear and perform similar to the human knee. Prototypes of the joint have been created to test these predicted properties