Tractable nonlinear memory functions as a tool to capture and explain dynamical behaviours

Mathematical approaches from dynamical systems theory are used in a range of fields. This includes biology where they are used to describe processes such as protein-protein interaction and gene regulatory networks. As such networks increase in size and complexity, detailed dynamical models become cumbersome, making them difficult to explore and decipher. This necessitates the application of simplifying and coarse graining techniques in order to derive explanatory insight. Here we demonstrate that Zwanzig-Mori projection methods can be used to arbitrarily reduce the dimensionality of dynamical networks while retaining their dynamical properties. We show that a systematic expansion around the quasi-steady state approximation allows an explicit solution for memory functions without prior knowledge of the dynamics. The approach not only preserves the same steady states but also replicates the transients of the original system. The method also correctly predicts the dynamics of multistable systems as well as networks producing sustained and damped oscillations. Applying the approach to a gene regulatory network from the vertebrate neural tube, a well characterised developmental transcriptional network, identifies features of the regulatory network responsible dfor its characteristic transient behaviour. Taken together, our analysis shows that this method is broadly applicable to multistable dynamical systems and offers a powerful and efficient approach for understanding their behaviour.Comment: (8 pages, 8 figures

Real-time environmental Arctic monitoring (R-TEAM) deployment cruise

The R-TEAM mooring was deployed on August 24, 1988 at the coordinates of 79°25'.92N and 06°47'.91 E. This technical report describes the mooring as set and the deployment procedures.Funding was provided by the Office of Naval Research through contract Number N00014-86-C-0135

Tidally generated high-frequency internal wave packets and their effects on plankton in Massachussetts Bay

Tidally generated internal wave packets occur twice a day during late summer in Massachusetts Bay, U.S.A. The packets are formed at Stellwagen Bank and propagate into the Bay at about 60 cm sec—1; they dissipate in shallow water at the western side of the Bay. The dominant waves in packets have lengths of about 300 m, periods of between 8 and 10 min, and amplitudes of up to 30 m. Overturning of the waves has been observed acoustically over Stellwagen Bank, in the deep (80 m) waters in the center of the Bay, and during dissipation in shallow water. The effects of the internal waves on the distribution of plankton were investigated in August 1977 using an instrument package (Longhurst-Hardy Plankton Recorder, in situ fluorometer, CTD) towed either at a constant depth or following an isotherm through wave packets. Phytoplankton and zooplankton appear to be carried passively up and down by the internal waves; the data were insufficient to resolve any active response by zooplankton to vertical displacements by the waves. Vertical distributions of the plankton were altered by overturning of waves and subsequent mixing. Patterns of horizontal distributions of plankton determined by constant-depth tows were dominated by the effects of internal wave vertical displacements. Isotherm-following tows removed much of the variability due to wave displacement, but problems of following rapidly moving isotherms introduced considerable smaller-scale variability. Changes in zooplankton abundance on tow length scales (600-1200 m) were not correlated with temperature, salinity, or density; some significant correlations with chlorophyll fluorescence occurred when internal wave activity was present. Twice a day for several hours or more, phytoplankton were vertically displaced by as much as 30 m, with a period of about 10 min. The light level plant cells experienced varied from 0.1 to 26% of the ambient surface illumination. This rapid change in light should alter fluorescence yields of plant cells and affect continuous in situ measurements of chlorophyll fluorescence. The timing of internal wave packets varies with the semidiurnal tidal cycle and therefore interacts with the day-night cycle to significantly alter the light regime experienced by plant cells over a two-week period. This could affect the primary productivity of the Bay in the area affected by internal wave packets. The sporadic occurrence of internal wave overturning and mixing events in the deep waters of the Bay could enhance primary production by increasing nutrient input to the mixed layer. This effect should be greatly enhanced in the shallow waters where the internal waves dissipate. Comparison of acoustic and plankton recorder data showed that much of the intense acoustic backscattering seen in high-amplitude (10-20 m) internal waves is due to physical structure and processes, and not to the presence of zooplankton

Natural language processing in aid of FlyBase curators.

BACKGROUND: Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. RESULTS: PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article. CONCLUSION: We show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Controlled Porosity in Ferroelectric BaTiO₃ Photoanodes

The use of ferroelectric polarization to promote electron-hole separation has emerged as a promising strategy to improve photocatalytic activity. Although ferroelectric thin films with planar geometry have been largely studied, nanostructured and porous ferroelectric thin films have not been commonly used in photo-electrocatalysis. The inclusion of porosity in ferroelectric thin films would enhance the surface area and reactivity, leading to a potential improvement of the photoelectrochemical (PEC) performance. Herein, the preparation of porous barium titanate (pBTO) thin films by a soft template-assisted sol-gel method is reported, and the control of porosity using different organic/inorganic ratios is verified by the combination of scanning electron microscopy and ellipsometry techniques. Using piezoresponse force microscopy, the switching of ferroelectric domains in pBTO thin films is observed, confirming that the ferroelectric polarization is still retained in the porous structures. In addition, the presence of porosity in pBTO thin films leads to a clear improvement of the PEC response. By electrochemical poling, we also demonstrated the tuning of the PEC performance of pBTO thin films via ferroelectric polarization. Our work offers a simple and low-cost approach to control the morphology optimization of ferroelectric thin films, which could open up the development of materials with great potential for PEC applications

Pseudoscalar and Scalar Meson Photoproduction Interpreted by Regge Phenomenology

We have evaluated pseudoscalar and scalar neutral pion photoproduction in $\vec{\gamma}p\to\pi^0p$ and $\vec{\gamma}p\to a_0^0p$ above the resonance region and within Regge phenomenology. Our fit, including GlueX $\Sigma$ pseudoscalar photoproduction data, shows that previous SLAC $\Sigma$ measurements for $\vec{\gamma}p \to \pi^0p$ above $E_\gamma = 4~\mathrm{GeV}$ are at variance with SLAC data with more recent measurements made by GlueX in vicinity of $E_\gamma = 9~\mathrm{GeV}$. The Regge model predicts that the beam polarization asymmetry $\Sigma$ of the scalar meson is opposite to that of pseudoscalar meson photoproduction, however, the cross sections are similar. While the vector natural parity meson exchange is dominant in both cases, the contribution of the pseudovector unnatural parity meson exchange is very small. Using Regge phenomenology, we predicted high energy behavior for double polarized observables $\mathbb{E}$, $\mathbb{F}$, $\mathbb{G}$, and $\mathbb{H}$ for the reactions $\gamma p\to \pi^0p$ and $\gamma p\to a_0^0p$.Comment: 8 pages, 5 figures, several small glitches were fixe

Using small-angle X-ray scattering to investigate the compaction behaviour of a granulated clay

The compaction behaviour of a commercial granulated clay (magnesium aluminium smectite, gMgSm) was investigated using macroscopic pressure-density measurements, X-ray diffraction (XRD), scanning electron microscopy (SEM), X-ray microtomography (XμT) and small-angle X-ray scattering (SAXS). This material was studied as a potential compaction excipient for pharmaceutical tabletting, but also as a model system demonstrating the capabilities of SAXS for investigating compaction in other situations. Bulk compaction measurements showed that the gMgSm was more difficult to compact than polymeric pharmaceutical excipients such as spheronised microcrystalline cellulose (sMCC), corresponding to harder granules. Moreover, in spite of using lubrication (magnesium stearate) on the tooling surfaces, rather high ejection forces were observed, which may cause problems during commercial tabletting, requiring further amelioration. Although the compacted gMgSm specimens were more porous, however, they still exhibited acceptable cohesive strengths, comparable to sMCC. Hence, there may be scope for using granular clay as one component of a tabletting formulation. Following principles established in previous work, SAXS revealed information concerning the intragranular structure of the gMgSm and its response to compaction. The results showed that little compression of the intragranular morphology occurred below a relative density of 0 · 6, suggesting that granule rearrangements or fragmentation were the dominant mechanisms during this stage. By contrast, granule deformation became considerably more important at higher relative density, which also coincided with a significant increase in the cohesive strength of compacted specimens. Spatially-resolved SAXS data was also used to investigate local variations in compaction behaviour within specimens of different shape. The results revealed the expected patterns of density variations within flat-faced cylindrical specimens. Significant variations in density, the magnitude of compressive strain and principal strain direction were also revealed in the vicinity of a debossed feature (a diametral notch) and within bi-convex specimens. The variations in compaction around the debossed notch, with a small region of high density below and low density along the flanks, appeared to be responsible for extensive cracking, which could also cause problems in commercial tabletting

Oral cannabinoid-rich THC/CBD cannabis extract for secondary prevention of chemotherapy-induced nausea and vomiting : a study protocol for a pilot and definitive randomised double-blind placebo-controlled trial (CannabisCINV)

INTRODUCTION: Chemotherapy-induced nausea and vomiting (CINV) remains an important issue for patients receiving chemotherapy despite guideline-consistent antiemetic therapy. Trials using delta-9-tetrahydrocannabinol-rich (THC) products demonstrate limited antiemetic effect, significant adverse events and flawed study design. Trials using cannabidiol-rich (CBD) products demonstrate improved efficacy and psychological adverse event profile. No definitive trials have been conducted to support the use of cannabinoids for this indication, nor has the potential economic impact of incorporating such regimens into the Australian healthcare system been established. CannabisCINV aims to assess the efficacy, safety and cost-effectiveness of adding TN-TC11M, an oral THC/CBD extract to guideline-consistent antiemetics in the secondary prevention of CINV. METHODS AND ANALYSIS: The current multicentre, 1:1 randomised cross-over, placebo-controlled pilot study will recruit 80 adult patients with any malignancy, experiencing CINV during moderate to highly emetogenic chemotherapy despite guideline-consistent antiemetics. Patients receive oral TN-TC11M (THC 2.5mg/CBD 2.5 mg) capsules or placebo capsules three times a day on day -1 to day 5 of cycle A of chemotherapy, followed by the alternative drug regimen during cycle B of chemotherapy and the preferred drug regimen during cycle C. The primary endpoint is the proportion of subjects attaining a complete response to CINV. Secondary and tertiary endpoints include regimen tolerability, impact on quality of life and health system resource use. The primary assessment tool is patient diaries, which are filled from day -1 to day 5. A subsequent randomised placebo-controlled parallel phase III trial will recruit a further 250 patients. ETHICS AND DISSEMINATION: The protocol was approved by ethics review committees for all participating sites. Results will be disseminated in peer-reviewed journals and at scientific conferences.Tilray. PROTOCOL VERSION: 2.0, 9 June 2017

Low Temperature Geomicrobiology Follows Host Rock Composition Along a Geochemical Gradient in Lau Basin

The East Lau Spreading Center (ELSC) and Valu Fa Ridge (VFR) comprise a ridge segment in the southwest Pacific Ocean where rapid transitions in the underlying mantle chemistry manifest themselves as gradients in seafloor rock geochemistry. We studied the geology and microbial diversity of three silicate rock samples and three inactive sulfide chimney samples collected, from north to south, at the vent fields Kilo Moana, ABE, Tui Malila, and Mariner. This is the first study of microbial populations on basaltic andesite, which was sampled at Mariner vent field. Silicate rock geochemistry exhibits clear latitudinal trends that are mirrored by changes in bacterial community composition. α-proteobacteria, ε-proteobacteria, and Bacteroidetes are most common on a silicate collected from Kilo Moana and their proportions decrease linearly on silicates collected further south. Conversely, a silicate from Mariner vent field hosts high proportions of a unique lineage of Chloroflexi unrelated (<90% sequence similarity) to previously recovered environmental clones or isolates, which decrease at ABE and are absent at Kilo Moana. The exteriors of inactive sulfide structures are dominated by lineages of sulfur oxidizing α-proteobacteria, γ-proteobacteria, and ε-proteobacteria, while the interior of one chimney is dominated by putative sulfur-reducing δ-proteobacteria. A comparison of bacterial communities on inactive sulfides from this and previous studies reveals the presence of a clade of uncultured Bacteroidetes exclusive to sulfidic environments, and a high degree of heterogeneity in bacterial community composition from one sulfide structure to another. In light of the heterogeneous nature of bacterial communities observed here and in previous studies of both active and inactive hydrothermal sulfide structures, the presence of numerous niches may be detected on these structures in the future by finer scale sampling and analysis.Organismic and Evolutionary Biolog