New approaches to investigating the function of mycelial networks

Fungi play a key role in ecosystem nutrient cycles by scavenging, concentrating, translocating and redistributing nitrogen. To quantify and predict fungal nitrogen redistribution, and assess the importance of the integrity of fungal networks in soil for ecosystem function, we need better understanding of the structures and processes involved. Until recently nitrogen translocation has been experimentally intractable owing to the lack of a suitable radioisotope tracer for nitrogen, and the impossibility of observing nitrogen translocation in real time under realistic conditions. We have developed an imaging method for recording the magnitude and direction of amino acid flow through the whole mycelial network as it captures, assimilates and channels its carbon and nitrogen resources, while growing in realistically heterogeneous soil microcosms. Computer analysis and modeling, based on these digitized video records, can reveal patterns in transport that suggest experimentally testable hypotheses. Experimental approaches that we are developing include genomics and stable isotope NMR to investigate where in the system nitrogen compounds are being acquired and stored, and where they are mobilized for transport or broken down. The results are elucidating the interplay between environment, metabolism, and the development and function of transport networks as mycelium forages in soil. The highly adapted and selected foraging networks of fungi may illuminate fundamental principles applicable to other supply networks

Significant groundwater contribution to Antarctic ice streams hydrologic budget

Satellite observations have revealed active hydrologic systems beneath Antarctic ice streams, but sources and sinks of water within these systems are uncertain. Here we use numerical simulations of ice streams to estimate the generation, flux, and budget of water beneath five ice streams on the Siple Coast. We estimate that 47% of the total hydrologic input (0.98 km3 yr−1) to Whillans (WIS), Mercer (MIS), and Kamb (KIS) ice streams comes from the ice sheet interior and that only 8% forms by local basal melting. The remaining 45% comes from a groundwater reservoir, an overlooked source in which depletion significantly exceeds recharge. Of the total input to Bindschadler (BIS) and MacAyeal (MacIS) ice streams (0.56 km3 yr−1), 72% comes from the interior, 19% from groundwater, and 9% from local melting. This contrasting hydrologic setting modulates the ice streams flow and has important implications for the search for life in subglacial lakes.This work was carried out with support from the Isaac Newton Trust, Cecil H. and Ida M. Green Foundation and Natural Environment Research Council (grant NE/E005950/1 and NE/J005800/1).This is the final version of the article. It was originally published in Geophysical Research Letters and is also available from the Wiley website at http://onlinelibrary.wiley.com/doi/10.1002/2014GL059250/abstract. © American Geophysical Union 201

Fluid and Diffusion Limits for Bike Sharing Systems

Bike sharing systems have rapidly developed around the world, and they are served as a promising strategy to improve urban traffic congestion and to decrease polluting gas emissions. So far performance analysis of bike sharing systems always exists many difficulties and challenges under some more general factors. In this paper, a more general large-scale bike sharing system is discussed by means of heavy traffic approximation of multiclass closed queueing networks with non-exponential factors. Based on this, the fluid scaled equations and the diffusion scaled equations are established by means of the numbers of bikes both at the stations and on the roads, respectively. Furthermore, the scaling processes for the numbers of bikes both at the stations and on the roads are proved to converge in distribution to a semimartingale reflecting Brownian motion (SRBM) in a $N^{2}$-dimensional box, and also the fluid and diffusion limit theorems are obtained. Furthermore, performance analysis of the bike sharing system is provided. Thus the results and methodology of this paper provide new highlight in the study of more general large-scale bike sharing systems.Comment: 34 pages, 1 figure

Reactivation of Kamb Ice Stream tributaries triggers century-scale reorganization of Siple Coast ice flow in West Antarctica

Ongoing, centennial-scale flow variability within the Ross ice streams of West Antarctica suggests that the present-day positive mass balance in this region may reverse in the future. Here, we use a three-dimensional ice-sheet model to simulate ice flow in this region over 250 years. The flow responds to changing basal properties, as a subglacial till layer interacts with water transported in an active subglacial hydrological system. We show that a persistent weak bed beneath the tributaries of the dormant Kamb Ice Stream is a source of internal ice-flow instability, which reorganizes all ice streams in this region, leading to a reduced (positive) mass balance within decades and a net loss of ice within two centuries. This hitherto unaccounted for flow variability could raise sea-level by 5mm this century. Better constraints on future sea-level change from this region will require improved estimates of geothermal heat flux and subglacial water transport.This work was carried out with support from the Isaac Newton trust, Cecil H. and Ida M. Green Foundation and Natural Environment Research Council (grants NE/E005950/1 and NE/J005800/1). SFP was supported by the U.S. Department of Energy Office of Science, Biological and Environmental Research program. ST acknowledges support from National Science Foundation (grant #0338295). SPC was supported by funding from the Cryospheric Sciences program of NASA and HAF was supported by funding from NSF (grant ANT-0838885 (Fricker)). The source code for the results presented can be obtained by contacting the corresponding author directlyThis is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/2015GL06578

Gene induction during differentiation of human monocytes into dendritic cells: an integrated study at the RNA and protein levels

Changes in gene expression occurring during differentiation of human monocytes into dendritic cells were studied at the RNA and protein levels. These studies showed the induction of several gene classes corresponding to various biological functions. These functions encompass antigen processing and presentation, cytoskeleton, cell signalling and signal transduction, but also an increase in mitochondrial function and in the protein synthesis machinery, including some, but not all, chaperones. These changes put in perspective the events occurring during this differentiation process. On a more technical point, it appears that the studies carried out at the RNA and protein levels are highly complementary.Comment: website publisher: http://www.springerlink.com/content/ha0d2c351qhjhjdm

Immune and acute phase markers in exercising adults

Many reports have documented the anti-inflammatory effects of regular exercise in adults. However clinicians and researchers remain uncertain on selecting specific biomarkers that are useful for predicting or monitoring chronic inflammatory states and/or disease. Clearer identification of markers (or clusters of markers) in physically active individuals that vary from established references ranges will indicate the extent of the purported anti-inflammatory effect of regular exercise. Physically active adults were recruited from the community to participate in a prospective study comparing self-reported health outcomes and exercise activity across 150 days of dietary intervention. Of the 450 participants recruited, 64 males (mean age 37.4 y, mean BMI = 25.3) and 59 females (mean age 40.4y, mean BMI= 23.4) agreed to supply a baseline blood sample taken at rest. A total of 187 analytes were measured by standard techniques on these pre-intervention samples including 11 immune markers (cell-types and immunoglobulins) and 11 acute phase reactants (WCC, albumin, haptoglobin, CRP, C3, C4, IGF-1, transferrin, iron, ferritin & ceruloplasmin). We compared baseline values with relevent hospital reference range (RR) values where these are assumed to be more reflective of a much less physically-active community population. A total of 5 out of 11 of the acute phase reactants (Hapt, C3, Fer, Trf (for females), and ceruloplasmin (for males)) had \u3e10% of values below the low ‘cut-off end’ of the relevant RR. Three immune cell-types (CD19, CD8 & CD16/56) had \u3e10% of values below the ‘low-cut-off end’ of the relevant RR. In contrast 25% of subjects had an IgE value that exceeded the RR. Collectively our results support the notion that regular exercise or physical activity exerts an anti-inflammatory affect. The results suggest putative roles for a host of exercise associated adaptive mechanisms beyond the generally accepted role for IL-6 derived from skeletal muscle and\or visceral fat. We conclude that across a host of measures, exercising adults have values for immune and acute phase reactants largely within, but at the non-inflammatory ‘end’ of clinical reference ranges

Advection, diffusion and delivery over a network

Many biological, geophysical and technological systems involve the transport of resource over a network. In this paper we present an algorithm for calculating the exact concentration of resource at any point in space or time, given that the resource in the network is lost or delivered out of the network at a given rate, while being subject to advection and diffusion. We consider the implications of advection, diffusion and delivery for simple models of glucose delivery through a vascular network, and conclude that in certain circumstances, increasing the volume of blood and the number of glucose transporters can actually decrease the total rate of glucose delivery. We also consider the case of empirically determined fungal networks, and analyze the distribution of resource that emerges as such networks grow over time. Fungal growth involves the expansion of fluid filled vessels, which necessarily involves the movement of fluid. In three empirically determined fungal networks we found that the minimum currents consistent with the observed growth would effectively transport resource throughout the network over the time-scale of growth. This suggests that in foraging fungi, the active transport mechanisms observed in the growing tips may not be required for long range transport.Comment: 54 pages including appendix, 10 figure

IoTRec: The IoT Recommender for Smart Parking System

This paper proposes a General Data Protection Regulation (GDPR)-compliant Internet of Things (IoT) Recommender (IoTRec) system, developed in the framework of H2020 EU-KR WISE-IoT (Worldwide Interoperability for Semantic IoT) project, which provides the recommendations of parking spots and routes while protecting users’ privacy. It provides recommendations by exploiting the IoT technology (parking and traffic sensors). The IoTRec provides four-fold functions. Firstly, it helps the user to find a free parking spot based on different metrics (such as the nearest or nearest trusted parking spot). Secondly, it recommends a route (the least crowded or the shortest route) leading to the recommended parking spot from the user’s current location. Thirdly, it provides the real-time provision of expected availability of parking areas (comprised of parking spots organized into groups) in a user-friendly manner. Finally, it provides a GDPR-compliant implementation for operating in a privacy-aware environment. The IoTRec is integrated into the smart parking use case of the WISE-IoT project and is evaluated by the citizens of Santander, Spain through a prototype, but it can be applied to any IoT-enabled locality. The evaluation results show the citizen’s satisfaction with the quality, functionalities, ease of use and reliability of the recommendations/services offered by the IoTRec

Refining Vision Videos

[Context and motivation] Complex software-based systems involve several stakeholders, their activities and interactions with the system. Vision videos are used during the early phases of a project to complement textual representations. They visualize previously abstract visions of the product and its use. By creating, elaborating, and discussing vision videos, stakeholders and developers gain an improved shared understanding of how those abstract visions could translate into concrete scenarios and requirements to which individuals can relate. [Question/problem] In this paper, we investigate two aspects of refining vision videos: (1) Refining the vision by providing alternative answers to previously open issues about the system to be built. (2) A refined understanding of the camera perspective in vision videos. The impact of using a subjective (or "ego") perspective is compared to the usual third-person perspective. [Methodology] We use shopping in rural areas as a real-world application domain for refining vision videos. Both aspects of refining vision videos were investigated in an experiment with 20 participants. [Contribution] Subjects made a significant number of additional contributions when they had received not only video or text but also both - even with very short text and short video clips. Subjective video elements were rated as positive. However, there was no significant preference for either subjective or non-subjective videos in general.Comment: 15 pages, 25th International Working Conference on Requirements Engineering: Foundation for Software Quality 201

Dynamic calcium-mediated stress response and recovery signatures in the fungal pathogen, Candida albicans

Acknowledgements AB conceived the project and wrote the manuscript. CVG conceived the experimental design. SW designed the GCaMP reporter. AM, KL, LV-M, SC and TB constructed strains and optimised imaging. MF developed the image analysis software. CVG and CP carried out the microfluidics experiments and imaging analysis. NG assisted with preparation of the manuscript. PS, SN and DMR developed and undertook the theoretical data analysis and contributed to the interpretation of the results. Funding AB, CG and TB were funded by the Wellcome Trust [Grant number 206412/A/17/Z]. AB and DR were supported by a Wellcome Trust Institutional Strategic Support Award (WT204909/Z/16/Z). CP was funded by a University of Exeter studentship (113516). This work was also supported by a Royal Society URF (UF080611), an MRC NIRG (G0900211/90671) and the MRC-Centre for Medical Mycology at the University of Exeter (MR/N006364/2). DR was funded by the Medical Research Council (MR/P022405/1). SN was supported by the Medical Research Council via the GW4 BioMed2 DTP (MR/W006308/1). MCA was supported by a European Commission ITN ‘FungiBrain’ studentship (607963). LL and SC were funded by a Wellcome Trust Institutional Strategic Support Award to the University of Aberdeen. NG acknowledges support of Wellcome Trust Investigator, Collaborative, Equipment, Strategic and Biomedical Resource awards (101873, 200208, 215599, 224323). NG and AB thank the MRC (MR/M026663/2) for support. This study/research is funded by the National Institute for Health and Care Research (NIHR) Exeter Biomedical Research Centre (BRC). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.Peer reviewedPublisher PD