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This document provides supplemental documentation of how mortality costs and detection costs were derived.

This research focused on drop metrology and the use of camera technology and vibration analysis influence on theoretical and practical tensiography. Drop shape and Tensiography are explained and how they relate to each other. Studies shows a relationship between vibration frequency and surface tension of liquids. However they also reveal the need for a theoretical understanding of the vibration tensiotrace of drops. Camera studies on large diameter dropheads used in tensiography are explored. Various image analysis methods were investigated for determining drop shape from camera images. Examination of the digital image reveals measurement issues. High speed camera images reveal new details of the drop separation process. An examination of drop modelling methods from camera images and the principles of such modelling were undertaken. Camera studies were developed which enabled the practical investigation of edge-detection. The theory developed links the drop shape with the tensiotrace of drops examined. The ray tracing method of the modelling of drop shape would have to be consolidated by establishing a definitive relationship between drop shape and the tensiotrace. This lead to acquiring photo images of real drops to get the profile of its edge or the drop shape. Various methods are used and assumptions are made in finding the edge of a drop from a photo image, in particular to the measurement of length, radii and angles.

This book may be described as a Festschrift—or more accurately a Gedenkschrift, given that it is a posthumous celebration of Gareth Matthews’ (1929-2011) work and career. It consists of a selected anthology of his papers, interspersed with papers by scholars that offer interpretive perspectives on his work . The Matthews papers, which are brilliantly chosen, represent only one dimension of his oeuvre; he was in fact a recognized scholar of ancient and medieval philosophy, particularly Plato, Aristotle and Augustine. The present selection draws from his persistent, oddly related inquiry, pursued over the course of almost 40 years, into the theory and practice of conducting philosophical conversations with children, whether inside or outside the classroom.

Supporting the Simple2 ReproNim paper.

Resting state fMRI with some background musical stimuli.

Comparison of ankle proprioceptive ability and isometric strength, fatigue, VA and recovery of the plantarflexors of PwMS, with healthy controls, to determine if these systems are impaired in PwMS

This file contains a description of our methods for titrating virus filtrate used in experiments and supplemental figures demonstrating virus replication and reproducibility of transmission data.

Supplemental material, sj-docx-5-jop-10.1177_02698811221112933 for The chronic effects of a combination of herbal extracts (Euphytose®) on psychological mood state and response to a laboratory stressor: A randomised, placebo-controlled, double blind study in healthy humans by Fiona Dodd, David Kennedy, Emma Wightman, Julie Khan, Michael Patan, Rian Elcoate and Philippa Jackson in Journal of Psychopharmacology

Supplemental material, sj-docx-2-jop-10.1177_02698811221112933 for The chronic effects of a combination of herbal extracts (Euphytose®) on psychological mood state and response to a laboratory stressor: A randomised, placebo-controlled, double blind study in healthy humans by Fiona Dodd, David Kennedy, Emma Wightman, Julie Khan, Michael Patan, Rian Elcoate and Philippa Jackson in Journal of Psychopharmacology

Supplemental material, sj-docx-5-jop-10.1177_02698811221112933 for The chronic effects of a combination of herbal extracts (Euphytose®) on psychological mood state and response to a laboratory stressor: A randomised, placebo-controlled, double blind study in healthy humans by Fiona Dodd, David Kennedy, Emma Wightman, Julie Khan, Michael Patan, Rian Elcoate and Philippa Jackson in Journal of Psychopharmacology

Supplemental material, sj-docx-6-jop-10.1177_02698811221112933 for The chronic effects of a combination of herbal extracts (Euphytose®) on psychological mood state and response to a laboratory stressor: A randomised, placebo-controlled, double blind study in healthy humans by Fiona Dodd, David Kennedy, Emma Wightman, Julie Khan, Michael Patan, Rian Elcoate and Philippa Jackson in Journal of Psychopharmacology

Supplemental material, sj-docx-3-jop-10.1177_02698811221112933 for The chronic effects of a combination of herbal extracts (Euphytose®) on psychological mood state and response to a laboratory stressor: A randomised, placebo-controlled, double blind study in healthy humans by Fiona Dodd, David Kennedy, Emma Wightman, Julie Khan, Michael Patan, Rian Elcoate and Philippa Jackson in Journal of Psychopharmacology

Supplemental material, sj-pdf-1-cre-10.1177_02692155221091509 for Relaxation and related therapies for people with multiple sclerosis (MS): A systematic review by Ian I. Kneebone, Brooke E. Van Zanden, Diana S. Dorstyn, Rachel M. Roberts, Stephen R. Lord, Dawn Querstret, Alice Theadom, David S. Kennedy, Jay Raman and Roshan das Nair in Clinical Rehabilitation

Supplemental material, sj-doc-1-jop-10.1177_02698811221112933 for The chronic effects of a combination of herbal extracts (Euphytose®) on psychological mood state and response to a laboratory stressor: A randomised, placebo-controlled, double blind study in healthy humans by Fiona Dodd, David Kennedy, Emma Wightman, Julie Khan, Michael Patan, Rian Elcoate and Philippa Jackson in Journal of Psychopharmacology

Supplemental material, sj-docx-4-jop-10.1177_02698811221112933 for The chronic effects of a combination of herbal extracts (Euphytose®) on psychological mood state and response to a laboratory stressor: A randomised, placebo-controlled, double blind study in healthy humans by Fiona Dodd, David Kennedy, Emma Wightman, Julie Khan, Michael Patan, Rian Elcoate and Philippa Jackson in Journal of Psychopharmacology

Supplemental material, sj-docx-2-jop-10.1177_02698811221112933 for The chronic effects of a combination of herbal extracts (Euphytose®) on psychological mood state and response to a laboratory stressor: A randomised, placebo-controlled, double blind study in healthy humans by Fiona Dodd, David Kennedy, Emma Wightman, Julie Khan, Michael Patan, Rian Elcoate and Philippa Jackson in Journal of Psychopharmacology

Anaerobic digestion processes can generate energy in the form of biogas while treating organic wastewater. The efficiency of the treatment, and thus the generation of biogas, is closely linked to the type and design of the reactor, and the technology used. Granular anaerobic digestion technology offers advantages such as a higher loading rate and reduction of the space needed. However, the hydrodynamics inside this type of reactor can be complex due to the presence of solids (granules) and gas (biogas) phases along with the liquid phase (wastewater). This is one of the reasons why the study and optimization of reactors using bench-scale reactors can lead to inaccurate results. A validated computational model would lead to the possibility of performing optimization studies using simulation; however, the validation of these computational models cannot be performed using analytical solutions due to their complexity. In this context, a particle image velocimetry (PIV) experimental setup was validated as part of this work, using computational fluid dynamics (CFD) simulations and data from literature. The experimental results obtained were compared with CFD results from six different models, each using a different turbulence model. The current setup was considered validated, allowing it to be used in the future for obtaining experimental data for the validation of a CFD model of an up-flow anaerobic sludge blanket reactor (UASB).

Supplemental material, sj-docx-4-jop-10.1177_02698811221112933 for The chronic effects of a combination of herbal extracts (Euphytose®) on psychological mood state and response to a laboratory stressor: A randomised, placebo-controlled, double blind study in healthy humans by Fiona Dodd, David Kennedy, Emma Wightman, Julie Khan, Michael Patan, Rian Elcoate and Philippa Jackson in Journal of Psychopharmacology

The transition from Petrol/Diesel and LPG powered vehicles to electric types and hydrogen powered is in progress. The world demand, from China to UK and Tokyo to New York is growing and includes new brands to established companies. Toyota has developed Hybrids on almost all of its Petrol/Diesel models during this transition. The scale of the industry is enormous with experts arguing for and against the performance, sustainability, ethical reasoning, costs and reliability of the technology for now and the future, providing logical answers to support or reject their arguments for success or failure. One in 12 cars sold across the European continent between April and June 2021 operated on batteries and sales of electric cars in Europe have risen from 198,000 in 2018 to 1.17m in 2021. Electric vehicles make up about 1 per cent of the global fleet of passenger cars. However global sales of EV’s are forecast to reach 10.7m by 2025 and then to 28.2m by 2030. It is expected that within four years, one quarter of new cars bought in China and almost 40 per cent of those purchased in Germany will be electric. Given the importance of auto manufacturing to many economies, the disruptive technology in the industry has enormous implications for jobs, urban development and geopolitics. Electric vehicle technology is not new and in some cases the ethical and sustainability of its development is in question, as is the reliability on fossil fuels for transport systems. An opportunity to overhaul the design, mass and functionality of vehicles is lost in the drive to be first to market. For example, the petrol engine has approximately 2,000 moving parts while the electric vehicle (EV) has approximately 20. Batteries store electricity produced typically by coal, uranium, natural gas, or diesel and more recently by PV panels, wind and marine current turbines. Therefore an EV is not a zero-emission vehicle. Rechargeable batteries are typically lithium-ion, nickel-metal oxide, and nickel-cadmium and all are self-discharging. In addition to dry cell batteries, there are also wet cell types used in automobiles, boats, and motorcycles and most are recycled. EV batteries are bulky and heavy and contain large quantities of Lithium, Nickel, Manganese, Cobalt, Copper, Aluminium, steel, and polymers. Some contain up to 6,000 individual lithium-ion cells. Most of these materials comes from mining with poor controls and standards. This paper raises some of the key issues in the development of the electric vehicle and presents some of the design issues for the drive systems, power requirements and distance performance of a range of vehicles on the market.

Supplemental material, sj-pdf-1-cre-10.1177_02692155221091509 for Relaxation and related therapies for people with multiple sclerosis (MS): A systematic review by Ian I. Kneebone, Brooke E. Van Zanden, Diana S. Dorstyn, Rachel M. Roberts, Stephen R. Lord, Dawn Querstret, Alice Theadom, David S. Kennedy, Jay Raman and Roshan das Nair in Clinical Rehabilitation

Supplemental material, sj-docx-3-jop-10.1177_02698811221112933 for The chronic effects of a combination of herbal extracts (Euphytose®) on psychological mood state and response to a laboratory stressor: A randomised, placebo-controlled, double blind study in healthy humans by Fiona Dodd, David Kennedy, Emma Wightman, Julie Khan, Michael Patan, Rian Elcoate and Philippa Jackson in Journal of Psychopharmacology

Supplemental material, sj-docx-6-jop-10.1177_02698811221112933 for The chronic effects of a combination of herbal extracts (Euphytose®) on psychological mood state and response to a laboratory stressor: A randomised, placebo-controlled, double blind study in healthy humans by Fiona Dodd, David Kennedy, Emma Wightman, Julie Khan, Michael Patan, Rian Elcoate and Philippa Jackson in Journal of Psychopharmacology

© 2021 American Neurological Association, Objective: Knowing explicitly where we are is an interpretation of our spatial representations. Reduplicative paramnesia is a disrupting syndrome in which patients present a firm belief of spatial mislocation. Here, we studied the largest sample of patients with delusional misidentifications of space (i.e. reduplicative paramnesia) after stroke to shed light on their neurobiology. Methods: In a prospective, cumulative, case-control study, we screened 400 patients with acute right-hemispheric stroke. We included 64 cases and 233 controls. First, lesions were delimited and normalized. Then, we computed structural and functional disconnection maps using methods of lesion-track and network-mapping. The maps were compared, controlling for confounders. Second, we built a multivariate logistic model including clinical, behavioural and neuroimaging data. Finally, we performed a nested cross-validation of the model with a support-vector machine analysis. Results: The most frequent misidentification subtype was confabulatory mislocation (56%), followed by place reduplication (19%) and chimeric assimilation (13%). Our results indicate that structural disconnection is the strongest predictor of the syndrome and included two distinct streams, connecting right fronto-thalamic and right occipito-temporal structures. In the multivariate model, the independent predictors of reduplicative paramnesia were the structural disconnection map, lesion sparing of right dorsal fronto-parietal regions, age and anosognosia. Good discrimination accuracy was demonstrated (area under the curve = 0.80[0.75-0.85]). Interpretation: Our results localize the anatomical circuits that may have a role in the abnormal spatial-emotional binding and in the defective updating of spatial representations underlying reduplicative paramnesia. This novel data may contribute to better understand the pathophysiology of delusional syndromes after stroke., The authors acknowledge our colleagues from the Department of Neurology and from the Language Research Laboratory for their contribution to patient screening. This work received funding from “PRÉMIO JOÃO LOBO ANTUNES” – SCML (grant to P.N.A.), from “Bolsa de Investigação em Doenças Vasculares Cerebrais 2017”–SPAVC (grant to P.N.A.) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 818521 to M.T.S.).“Data were provided in part bythe Human Connectome Project, WU-Minn Consortium(Principal Investigators: David Van Essen and KamilUgurbil; 1U54 MH091657) funded by the 16 NIH Institutes and Centers that support the NIH Blueprint for Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University.

Background: Unexplained fatigue is a common complaint. When underlying disease causes have been eliminated, lifestyle measures and supplementation can be indicated. Elaborating on clinical findings that G115®, a dry extract from the root of Panax ginseng, combined with vitamins and minerals could alleviate fatigue, this open label study aimed at assessing its effect on perceived fatigue and energy. Methods: Healthy adults self-reporting fatigue (n = 103) completed the Multidimensional Fatigue Inventory questionnaire. They rated their perceptions of mental and physical fatigue, energy, performance, and stress at baseline and 15, 30, 60 and 90 days after a daily intake of 40 mg G115® formulated with vitamins and minerals. Results: Compared with baseline values, mean self-perception of general fatigue was reduced by −7.55 units [95% CI: −8.44; −6.66] (−41.8%, p < 0.0001) at 90 days. All assessed perception ratings (mental and physical fatigue, reduced activity and motivation, performance, and stress) were significantly and steadily improved from two weeks after supplementation up to study's end. Overall satisfaction with the ability of the product to reduce fatigue reached 85% at Day 90. Conclusion: Daily intake with G115® extract formulated with vitamins and minerals suggests an improvement of self-perception of fatigue and energy in a fatigued adult population.

Additional file 1. SPIRIT 2013 checklist.

Supplemental material, Appendices for Proprioceptive impairment in unilateral neglect after stroke: A systematic review by Georgia Fisher, Camila Quel de Oliveira, Arianne Verhagen, Simon Gandevia and David Kennedy in SAGE Open Medicine

One of the most popular methodologies used to predict the wake of a tidal stream turbine (TST) is the RANS turbulence models coupled with the actuator disk method. This methodology has been widely adopted in the in the wind industry, since the mid-1990s, to predict wake development of wind turbines. Moreover, the reason for its popularity is its capability to give accurate results at an affordable computational cost, and the application of 2-dimensional actuator disk approach could further reduce the computational cost. In this paper, a number of RANS turbulence models represented by a porous disk were used to simulate the wake development behind a TST, the findings were compared. The models adopted in this work are the Standard k-ε model, the Standard k-ω model, the RNG (Re-Normalised Group) k-ε model, the SST (Shear Stress Transport) k-ω model and the RSM (Reynold Stress Model). The results are also validated against experimental measurements found in literature, with a key focus on comparing the downstream velocity and turbulence intensity. It has shown that the Standard k-ε model is best at predicting downstream wake velocities while the SST k-ω model is better at predicting downstream wake turbulence intensity. Mesh convergence studies were conducted to optimise the computational efficiency for each turbulence model used.

The Adolescent Brain Cognitive Development (ABCD) Study is an ongoing, nationwide study of the effects of environmental influences on behavioral and brain development in adolescents. The main objective of the study is to recruit and assess over eleven thousand 9-10-year-olds and follow them over the course of 10 years to characterize normative brain and cognitive development, the many factors that influence brain development, and the effects of those factors on mental health and other outcomes. The study employs state-of-the-art multimodal brain imaging, cognitive and clinical assessments, bioassays, and careful assessment of substance use, environment, psychopathological symptoms, and social functioning. The data is a resource of unprecedented scale and depth for studying typical and atypical development. The aim of this manuscript is to describe the baseline neuroimaging processing and subject-level analysis methods used by ABCD. Processing and analyses include modality-specific corrections for distortions and motion, brain segmentation and cortical surface reconstruction derived from structural magnetic resonance imaging (sMRI), analysis of brain microstructure using diffusion MRI (dMRI), task-related analysis of functional MRI (fMRI), and functional connectivity analysis of resting-state fMRI. This manuscript serves as a methodological reference for users of publicly shared neuroimaging data from the ABCD Study.

Malignant peripheral nerve sheath tumors (MPNSTs) are rare sarcomas of the nerve sheath that infrequently involve the head and neck region. The few reports of MPNSTs arising from benign schwannoma precursors typically exhibit epithelioid morphology.

This document provides a simple, generic checklist that authors of academic work (papers, books, conference abstracts, blog posts, etc.) can use to ensure they are following good practice when referencing and citing software they have used, both created by themselves for their research as well as obtained from other sources. It may also be used and adapted by journal editors, publishers and conference chairs as the basis of more specific guidance for their contributors and reviewers.

In Towards a New Architecture, Le Corbusier claims that the field of engineering, through its adherence to the noble fields of Economy and Mathematics, has surpassed the field of architecture in the pursuit of harmonious, meaningful structures. He does not suggest that architects partner with engineers; he only implores architects to cop-opt engineers’ ethic to leverage their own field from its current state of “retrogression”. Gaining expertise then obviates collaboration. Following this, Corbusier laments the glacial unfolding of architecture through incremental developments in structure and ornament, finding impetus for his cross-disciplinary foray in the previous five decades of material development, namely the “conquests” of steel and concrete. (9) This passage, titled ‘Architecture or Revolution’ finds resonance today when ‘steel and concrete’ are replaced by ‘mass timber.’ Superficially anachronistic, this return to timber finds its depth not in the invention of the material, but in its reinvention as a medium under the purview of a variety of disciplines, from architecture and engineering to fabrication and materials science. This transdisciplinary thinking has defined mass timber types by their details, i.e., the ways in which they are assembled and joined with other materials. Mass timber is not borne of a fetishization of wood; it is most viable when its use capitalizes on the intrinsic strengths of steel, concrete, and other extant material systems. (Dangel 108) Unlike dimensional, heavy, or linear engineered wood products, mass timber’s morphology operates as a function of its detail. This paper argues that, if mass timber is an assemblage of details and a fundamentally trans-disciplinary material, the details, or detail, itself is an acute source of trans-disciplinary interaction. An emergent material, mass timber is only entering the adolescent stages of its development. Research and pedagogy surrounding mass timber are best focused on examinations of the intrinsic and extrinsic impacts of its detail. This detail manifests across scales; each scale corresponds to a set of disciplines. The cellular scale finds one in the realm of wood anatomy. Here, detail exists as designed by the growing tree, where the primary program is the express motivation to handle currents flowing through- and along them. (Bejan 130) An anisotropic, cellular solid, wood’s structures and systems at the cellular scale exhibit analogies for mass timber and may provide insight as to how those systems are best assembled. This paper will examine this and a variety of other scales of detail through coursework and exploratory research. Ultimately, it posits methods by which a trans-scalar, trans-disciplinary examination of mass timber’s detail might permit architectural practice, research, and pedagogy that better leverages its latent performance.

The bacterium Clostridium difficile is the most prominent cause of hospital-acquired diarrhoea and disease of the large bowel. Clostridium difficile produces toxins that damage the colonic epithelium, causing inflammatory colitis that may be fatal. The treatment strategy against Clostridium difficile is currently mainly limited to a course of antibiotics metronidazole or the cyclic peptide vancomycin. However, due to emergence of antibiotic resistance, there is a desire for new antibiotics. Host-defence or antimicrobial peptides offer a promising approach to overcoming antibiotic resistance. By interacting selectively with non-specific microbial components, antimicrobial peptidcs evade evolution of microbial resistance. A challenge to the clinical development of therapeutic peptides is site-specific drug delivery. Herein, a novel strategy for the delivery of therapeutic antimicrobial peptides as prodrugs that release active peptide and mutual-drug anti-inflammatory agents upon metabolism by clostridial reductase enzyme for the treatment of Clostridium difficile infection and inflammatory colitis has been developed, whereby antimicrobial peptides are protected at the alpha-amino terminal either by an azo bond to the anti-inflammatory agent 4-aminophenylacetic acid facilitated by an alpha-aminoisobutyric acid linker that increases the antimicrobial potency of the peptides, or by a benzyl carbamate linker bearing either a nitro or azo, bound to anti-inflammatory agent 5-aminosalicylic acid, as a reducible para substituent. The prodrug peptides and antibiotic peptides modified at the amino terminal by alpha-aminoisobutyric acid are prepared and evaluated for antimicrobial susceptibility against pathogenic bactcria Clostridium difficile and Staphylococcus aureus by determination of minimum inhibitory concentrations. The reduction of the prodrug linker containing 5-azosalicylic acid by the presence of Clostridium difficile is demonstrated spectrophotometrically.These results confirm the feasibility of this novel approach to delivery of antimicrobial peptides and anti-inflammatory agents for the treatment of Clostridium difficile infection and associated colitis.

A focus area of phase 3 of 5G PPP is the design and deployment of a 5G end-to-end facility that can demonstrate that the key 5G network KPIs can be met, and which can be accessed and used by vertical industries. This poster paper presents key guidelines to implement such a 5G end-to-end facility.

BACKGROUND:Mitochondrial oxidation is a major source of reactive oxygen species (ROS) and mitochondrial dysfunction plays a central role in development of heart failure (HF). Paraoxonase 2 deficient (PON2-def) mitochondria are impaired in function. In this study, we tested whether PON2-def aggravates HF progression. METHODS AND RESULTS:Using qPCR, immunoblotting and lactonase activity assay, we demonstrate that PON2 activity was significantly decreased in failing hearts despite increased PON2 expression. To determine the cardiac-specific function of PON2, we performed heart transplantations in which PON2-def and wild type (WT) donor hearts were implanted into WT recipient mice. Beating scores of the donor hearts, assessed at 4 weeks post-transplantation, were significantly decreased in PON2-def hearts when compared to WT donor hearts. By using a transverse aortic constriction (TAC) model, we found PON2 deficiency significantly exacerbated left ventricular remodeling and cardiac fibrosis post-TAC. We further demonstrated PON2 deficiency significantly enhanced ROS generation in heart tissues post-TAC. ROS generation was measured through dihydroethidium (DHE) using high-pressure liquid chromatography (HPLC) with a fluorescent detector. By using neonatal cardiomyocytes treated with CoCl2 to mimic hypoxia, we found PON2 deficiency dramatically increased ROS generation in the cardiomyocytes upon CoCl2 treatment. In response to a short CoCl2 exposure, cell viability and succinate dehydrogenase (SDH) activity assessed by MTT assay were significantly diminished in PON2-def cardiomyocytes compared to those in WT cardiomyocytes. PON2-def cardiomyocytes also had lower baseline SDH activity. By using adult mouse cardiomyocytes and mitochondrial ToxGlo assay, we found impaired cellular ATP generation in PON2-def cells compared to that in WT cells, suggesting that PON2 is necessary for proper mitochondrial function. CONCLUSION:Our study suggests a cardioprotective role for PON2 in both experimental and human heart failure, which may be associated with the ability of PON2 to improve mitochondrial function and diminish ROS generation.

This work presents an overview on the potential for generating bioenergy through the anaerobic digestion of the Irish breweries and whiskey distilleries effluents. The results showed that it would be possible to generate 28,210,958 Nm3/year of biogas or 154,846 MWh of thermal heat with 110,715 tonnes of CO2 savings in a year. The electricity generation potential and CO2 savings were also calculated. It was possible to conclude that the anaerobic digestion of the wastewater from the brewery and distillery industries stand out as a feasible option to increase the share of renewable energies in Ireland.

Habitat mapping data are increasingly being recognised for their importance in underpinning marine spatial planning. The ability to collect ultra-high resolution (cm) multibeam echosounder (MBES) data in shallow waters has facilitated understanding of the fine-scale distribution of benthic habitats in these areas that are often prone to human disturbance. Developing quantitative and objective approaches to integrate MBES data with ground observations for predictive modelling is essential for ensuring repeatability and providing confidence measures for habitat mapping products. Whilst supervised classification approaches are becoming more common, users are often faced with a decision whether to implement a pixel based (PB) or an object based (OB) image analysis approach, with often limited understanding of the potential influence of that decision on final map products and relative importance of data inputs to patterns observed. In this study, we apply an ensemble learning approach capable of integrating PB and OB Image Analysis from ultra-high resolution MBES bathymetry and backscatter data for mapping benthic habitats in Refuge Cove, a temperate coastal embayment in south-east Australia. We demonstrate the relative importance of PB and OB seafloor derivatives for the five broad benthic habitats that dominate the site. We found that OB and PB approaches performed well with differences in classification accuracy but not discernible statistically. However, a model incorporating elements of both approaches proved to be significantly more accurate than OB or PB methods alone and demonstrate the benefits of using MBES bathymetry and backscatter combined for class discrimination.

Neuroscientists are now able to acquire data at staggering rates across spatiotemporal scales. However, our ability to capitalize on existing datasets, tools, and intellectual capacities is hampered by technical challenges. The key barriers to accelerating scientific discovery correspond to the FAIR data principles: findability, global access to data, software interoperability, and reproducibility/re-usability. We conducted a hackathon dedicated to making strides in those steps. This manuscript is a technical report summarizing these achievements, and we hope serves as an example of the effectiveness of focused, deliberate hackathons towards the advancement of our quickly-evolving field., Comment: 10 pages, 4 figures, hackathon report

Solar concentrators offer a reasonable alternative to flat-plate collectors for delivering hot air flows at higher temperatures. They are designed to receive solar radiation through an aperture area and direct it towards a smaller absorber area by employing a reflective material. The design and analysis of solar concentrators are mostly based on ray tracing techniques. The aim of this paper is to analyse the optical performance of an Asymmetric Compound Parabolic Concentrator (ACPC) collector with an Inverted Transpired Absorber (ITA) for air heating. It accepts direct solar radiation during the summer period for up to 8 hours a day. The tool used for the optical modelling is the Ray Tracing technique, which consists of an algorithm developed in Matlab® that simulates solar rays entering this collector. The analysis considered the effect of the angle of the lower parabola axis, the glazing inclination and the tertiary section on the direct optical efficiency. Moreover, it also considered the energy distribution on the absorber surface under the effect of the tertiary section. The results show that the glazing optical losses can be reduced by inclining the glass from the vertical aperture as shown in Fig. 2, and that the reflection losses and the reflector material can be reduced by changing the lower parabola axis. The optical efficiency decreases as the tertiary section height increases however the energy distribution becomes more uniform.

Presentation at Mathworks Research Summit 2017

In light of increasing terrestrial carbon (C) transport across aquatic boundaries, the mechanisms governing organic carbon (OC) oxidation along terrestrial-aquatic interfaces are crucial to future climate predictions. Here, we investigate the biochemistry, metabolic pathways, and thermodynamics corresponding to OC oxidation in the Columbia River corridor using ultra-high resolution C characterization. We leverage natural vegetative differences to encompass variation in terrestrial C inputs. Our results suggest that decreases in terrestrial C deposition associated with diminished riparian vegetation induce oxidation of physically-bound OC. We also find that contrasting metabolic pathways oxidize OC in the presence and absence of vegetation and -- in direct conflict with the priming concept -- that inputs of water-soluble and thermodynamically favorable terrestrial OC protects bound-OC from oxidation. In both environments, the most thermodynamically favorable compounds appear to be preferentially oxidized regardless of which OC pool microbiomes metabolize. In turn, we suggest that the extent of riparian vegetation causes sediment microbiomes to locally adapt to oxidize a particular pool of OC, but that common thermodynamic principles govern the oxidation of each pool (i.e., water-soluble or physically-bound). Finally, we propose a mechanistic conceptualization of OC oxidation along terrestrial-aquatic interfaces that can be used to model heterogeneous patterns of OC loss under changing land cover distributions.

Protocol, submissions and scores of the 2017 OHBM Replication Award.

Mathematical framework and schematic of treatment mosaics

Despite their unquestionable value replication studies are hard to find in the literature. Dedicated academic awards have been shown to be an effective way to promote and incentivize replication studies. The purpose of this document is to describe how a replication award can be implemented within academic societies, communities, conferences or university departments. This document outlines a particular way in which such award can be implemented. It might or might not fit any particular organization, but the general principle should be applicable across most scientific fields. If you would like to comment on this white paper or suggest improvements that would benefit other readers please comment on this live version of the creation kit.

Coral reefs are among the world’s most threatened ecosystems. Recent declines in coral reef health are largely attributed to pervasive anthropogenic stressors such as coastal development, overfishing and global change. While the status of tropical reefs is typically assessed through the extent of live coral cover, these ecosystems also support a vast diversity of non-coral invertebrates, the importance of which is often overlooked. This thesis examines the effects of coastal development (e.g. declining water quality, eutrophication), overfishing and global change (e.g. ocean acidification) on tropical Echinodermata in two case studies that present contrasting anthropogenic effects in this taxon. These case studies focus on two phenomena; 1. the expanding population outbreaks of the boom-and-bust crown-of-thorns starfish, Acanthaster cf. planci (herein: A. planci) (Asteroidea), and 2. the contracting populations of the recently listed Vulnerable sea cucumber, Stichopus herrmanni (curryfish) (Holothuroidea), a model species representing overfished tropical bêche-de-mer holothuroids. Predation on corals by high-density populations of A. planci is a major cause of coral reef decline, but the factors behind population outbreaks remain unclear. The ‘enhanced nutrients’ hypothesis posits that increased phytoplankton levels resulting from anthropogenic eutrophication enhance larval survival, with flow-on effects to benthic life stages, leading to population outbreaks. However, outbreaks also occur in regions unaffected by anthropogenic eutrophication, indicating that the larvae of A. planci are resilient to the naturally oligotrophic waters of coral reef ecosystems; the ‘larval resilience’ hypothesis. This thesis addresses the dichotomy between the ‘enhanced nutrients’ and ‘larval resilience’ hypotheses. In targeted experiments, the current paradigm that A. planci outbreaks are linked to terrestrial runoff driving enhanced food for larvae – a premise that has driven management actions for over 30 years – is addressed. To examine whether larval success is associated with particular nutrient (chlorophyll-a) levels, A. planci larvae were reared in a range of food regimes from starvation (no food) to satiation (excess food). Algal concentrations were selected to reflect phytoplankton conditions in nature based on a new online resource for the Great Barrier Reef (GBR), Australia (e-Reefs; Bureau of Meteorology). These included phytoplankton levels in oligotrophic waters (0-0.01 µg chl a L-1), natural background levels determined for the GBR (0.1-1.0 µg chl a L-1), and enhanced eutrophic conditions following runoff events (5.0-10 µg chl a L-1). In a range-finder test, using a four-order of magnitude difference in nutrient conditions (0-10 µg chl a L-1), the response of A. planci larvae was characterised. Phytoplankton levels of 1 µg chl a L-1, close to background levels for some reefs on the GBR and following flood events, were optimal for larval development and survival. Oligotrophic conditions (≤0.1 µg chl a L-1) appeared to be a critical limit, and satiated conditions (10 µg chl a L-1) were deleterious to larval development. To address potential environmental trigger values for larval success, a narrower range of nutrients (0.1-5.0 µg chl a L-1) was investigated. High larval success to the juvenile stage occurred across an order of magnitude of nutrient concentrations (0.5–5.0 µg chl a L-1), suggesting there may not be a narrow trigger value of eutrophication for optimal success of A. planci larvae. Many echinoderm larvae exhibit developmental plasticity, matching their phenotype to environmental conditions (e.g. nutrients). In response to nutrient limitation, echinoderm larvae can grow longer ciliated bands (feeding structures) to increase their ability to capture scarce food particles. To determine whether the larvae of A. planci exhibit phenotypic plasticity, ciliated band length and body allometry were determined for larvae reared in a range of nutrient levels (0-10 µg chl a L-1). Nutrient-limited larvae developed longer ciliated bands relative to their body size, while well-fed larvae had shorter ciliated bands despite their larger body profile. This is the first documentation of nutrient-driven phenotypic plasticity in the larvae of A. planci, a trait that would facilitate larval success in the absence of nutrient enrichment. The larval biology and ecology of A. planci is reviewed. This thesis emphasises that the resilient and opportunistic nature of the larvae of A. planci is key to consider in a management context for this asteroid. Acanthaster planci is more successful in low food conditions than previously appreciated. The initiation of outbreak populations need not require the eutrophic conditions posited by the ‘enhanced nutrients’ hypothesis. The inherent resilience of the larvae of A. planci to oligotrophic conditions is likely to be a critical factor of adult outbreaks and in future population management. Converse to population expansions of A. planci, anthropogenic impacts are driving major population declines of tropical holothuroids. Holothuroids are harvested globally for bêche-de-mer, the dried body wall product, with many species in a perilous state of conservation. Stichopus herrmanni, listed as Vulnerable by the International Union for Conservation of Nature (IUCN), is currently a major fisheries target on the GBR and elsewhere. However, there remains a paucity of data on the biology and ecology of this species to inform management – an issue for bêche-de-mer holothuroids globally. This thesis bridges fundamental knowledge gaps for S. herrmanni, a model species used to represent other exploited tropical holothuroids, providing critical information to their conservation biology. The population biology and recruitment of S. herrmanni was examined across two years on Heron Reef, a protected zone on the GBR. The size class distribution and density of S. herrmanni were documented for six sites across Heron Reef. There was distinct spatial variation in the size and density of S. herrmanni across sites, with no significant difference between the two years. The smallest individuals found (10 cm in length) are some of the only juvenile S. herrmanni documented in nature. Juvenile nurseries of holothuroids are rarely observed in nature, making this an important observation for understanding the recruitment and population biology of this species. The presence of juveniles in the consolidated crustose coralline algal habitat each year in autumn following the summer spawning period, and the absence of small individuals several months later in spring, suggests an ontogenetic migration or displacement of these individuals to adult habitat. The distribution of larger S. herrmanni suggests within-reef connectivity and migration into deeper lagoon areas as they grow. This may be driven by increased food availability in deeper lagoon areas, physical hydrodynamic displacement or increased reproductive success with higher densities of mature adults. Little is known about the ecological roles of large bêche-de-mer holothuroids in lagoon sediment habitats – a vast component of coral reef ecosystems. It is critical to characterise how these species interact with their environment to understand how their removal may impact ecosystem functionality. Seasonal variations in movement, bioturbation, feeding and gonad development of S. herrmanni were investigated over three years at One Tree Reef, which has been a no-take area for decades. The direct influence of the deposit-feeding activity of S. herrmanni on sediment turnover, granulometry, and the abundance of infauna and benthic productivity was determined in the most comprehensive in situ analysis of tropical holothuroid feeding ecology. This species is highly mobile with identifiable individuals exhibiting site fidelity over three years. With the potential to turn over an estimated 64–250 kg ind-1 y-1, S. herrmanni is a major bioturbator. Stichopus herrmanni is a generalist feeder and influences trophic interactions by altering the abundance of infauna and microalgae. Stichopus herrmanni exhibited decreased feeding activity and gonad development in winter, the first documentation of a seasonal disparity in the bioturbation activity of a tropical holothuroid. Given the remarkable contribution of S. herrmanni to sediment bioturbation, the digestive biology of this holothuroid is likely to have an important biogeochemical influence on coral reefs. The gut pH of S. herrmanni was higher when full of sediment (pH 7.04–7.81) compared to empty digestive tracts (pH 6.42–7.77). Dissolution of sediment in the low-pH gut is likely to influence external seawater chemistry when the faecal casts are deposited into the environment. The resulting increases in total alkalinity may benefit local reef calcifiers in the face of ocean acidification. Whether holothuroids have the potential to exacerbate or buffer ocean acidification over diel cycles depends on their relative production of total alkalinity (AT) through the dissolution of ingested calcium carbonate (CaCO3) sediments and release of dissolved inorganic carbon (CT) through respiration and trophic interactions. The potential for S. herrmanni to buffer the impacts of ocean acidification on reef carbonate chemistry was investigated in lagoon sediment mesocosms across diel cycles. Stichopus herrmanni directly reduced the abundance of meiofauna and benthic primary producers through its deposit-feeding activity under present-day and near-future pCO2. These changes in benthic community structure, as well as AT (sediment dissolution) and CT (respiration) production by S. herrmanni, played a significant role in modifying seawater carbonate dynamics night and day. This previously unappreciated role of tropical sea cucumbers, in support of ecosystem resilience in the face of global change, is an important consideration with respect to the bêche-de-mer trade to ensure sea cucumber populations are sustained in a future ocean. The responses of A. planci and bêche-de-mer holothuroids (S. herrmanni) to environmental perturbations due to anthropogenic stressors are indicators of reef health. Due to their ecological importance, these model organisms could be considered as ‘canaries in the coalmine’ for the status of coral reef ecosystems. The results of this thesis provide important new data to inform scientists and policy-makers to develop targeted management strategies to reduce the impacts of anthropogenic stressors on tropical echinoderms. These measures are important in parallel with intensive local management and regulation to reduce the immediate threats facing coral reefs today.

Despite their unquestionable value replication studies are hard to find in the literature. We propose using academic awards to improve this situation and show, using a pilot award in the field of human neuroimaging, that they can be an effective way to promote and incentivize replication studies.

The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC – http://www.nitrc.org) suite of services include a resources registry, image repository and a robust cloud computational environment to meet the needs of the neuroimaging researcher. NITRC provides image-sharing functionality through both the NITRC Resource Registry (NITRC-R), where bulk data files can be released through the file release system (FRS), and the NITRC Image Repository (NITRC-IR), a XNAT-based image data management system. Currently hosting more than 14 projects, 6845 subjects, and 8285 MRI imaging sessions, NITRC-IR provides a large array of structural, diffusion and resting state MRI data. Designed to be flexible about management of data access policy, NITRC provides a simple, free, NIH-funded service to support resource sharing in general, and image sharing in particular. In my talk, I will review these resources and illustrate examples of their use as valuable tools for large-scale brain imaging analysis and inference.