Dynamical density delay maps: simple, new method for visualising the behaviour of complex systems

Background. Physiologic signals, such as cardiac interbeat intervals, exhibit complex fluctuations. However, capturing important dynamical properties, including nonstationarities may not be feasible from conventional time series graphical representations. Methods. We introduce a simple-to-implement visualisation method, termed dynamical density delay mapping (``D3-Map'' technique) that provides an animated representation of a system's dynamics. The method is based on a generalization of conventional two-dimensional (2D) Poincar� plots, which are scatter plots where each data point, x(n), in a time series is plotted against the adjacent one, x(n+1). First, we divide the original time series, x(n) (n=1,..., N), into a sequence of segments (windows). Next, for each segment, a three-dimensional (3D) Poincar� surface plot of x(n), x(n+1), hx(n),x(n+1) is generated, in which the third dimension, h, represents the relative frequency of occurrence of each (x(n),x(n+1)) point. This 3D Poincar\'e surface is then chromatised by mapping the relative frequency h values onto a colour scheme. We also generate a colourised 2D contour plot from each time series segment using the same colourmap scheme as for the 3D Poincar\'e surface. Finally, the original time series graph, the colourised 3D Poincar\'e surface plot, and its projection as a colourised 2D contour map for each segment, are animated to create the full ``D3-Map.'' Results. We first exemplify the D3-Map method using the cardiac interbeat interval time series from a healthy subject during sleeping hours. The animations uncover complex dynamical changes, such as transitions between states, and the relative amount of time the system spends in each state. We also illustrate the utility of the method in detecting hidden temporal patterns in the heart rate dynamics of a patient with atrial fibrillation. The videos, as well as the source code, are made publicly available. Conclusions. Animations based on density delay maps provide a new way of visualising dynamical properties of complex systems not apparent in time series graphs or standard Poincar\'e plot representations. Trainees in a variety of fields may find the animations useful as illustrations of fundamental but challenging concepts, such as nonstationarity and multistability. For investigators, the method may facilitate data exploration

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016.

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

An interactome-centered protein discovery approach reveals novel components involved in mitosome function and homeostasis in giardia lamblia

Protozoan parasites of the genus Giardia are highly prevalent globally, and infect a wide range of vertebrate hosts including humans, with proliferation and pathology restricted to the small intestine. This narrow ecological specialization entailed extensive structural and functional adaptations during host-parasite co-evolution. An example is the streamlined mitosomal proteome with iron-sulphur protein maturation as the only biochemical pathway clearly associated with this organelle. Here, we applied techniques in microscopy and protein biochemistry to investigate the mitosomal membrane proteome in association to mitosome homeostasis. Live cell imaging revealed a highly immobilized array of 30–40 physically distinct mitosome organelles in trophozoites. We provide direct evidence for the single giardial dynamin-related protein as a contributor to mitosomal morphogenesis and homeostasis. To overcome inherent limitations that have hitherto severely hampered the characterization of these unique organelles we applied a novel interaction-based proteome discovery strategy using forward and reverse protein co-immunoprecipitation. This allowed generation of organelle proteome data strictly in a protein-protein interaction context. We built an initial Tom40-centered outer membrane interactome by co-immunoprecipitation experiments, identifying small GTPases, factors with dual mitosome and endoplasmic reticulum (ER) distribution, as well as novel matrix proteins. Through iterative expansion of this protein-protein interaction network, we were able to i) significantly extend this interaction-based mitosomal proteome to include other membrane-associated proteins with possible roles in mitosome morphogenesis and connection to other subcellular compartments, and ii) identify novel matrix proteins which may shed light on mitosome-associated metabolic functions other than Fe-S cluster biogenesis. Functional analysis also revealed conceptual conservation of protein translocation despite the massive divergence and reduction of protein import machinery in Giardia mitosomes

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Prothymosin alpha: a ubiquitous polypeptide with potential use in cancer diagnosis and therapy

The thymus is a central lymphoid organ with crucial role in generating T cells and maintaining homeostasis of the immune system. More than 30 peptides, initially referred to as “thymic hormones,” are produced by this gland. Although the majority of them have not been proven to be thymus-speciWc, thymic peptides comprise an eVective group of regulators, mediating important immune functions. Thymosin fraction Wve (TFV) was the Wrst thymic extract shown to stimulate lymphocyte proliferation and diVerentiation. Subsequent fractionation of TFV led to the isolation and characterization of a series of immunoactive peptides/polypeptides, members of the thymosin family. Extensive research on prothymosin (proT) and thymosin 1 (T1) showed that they are of clinical signiWcance and potential medical use. They may serve as molecular markers for cancer prognosis and/or as therapeutic agents for treating immunodeWciencies, autoimmune diseases and malignancies. Although the molecular mechanisms underlying their eVect are yet not fully elucidated proT and T1 could be considered as candidates for cancer immunotherapy. In this review, we will focus in principle on the eventual clinical utility of proT, both as a tumor biomarker and in triggering anticancer immune responses. Considering the experience acquired via the use of T1 to treat cancer patients, we will also discuss potential approaches for the future introduction of proT into the clinical setting

An update of the Worldwide Integrated Assessment (WIA) on systemic insecticides. Part 2: impacts on organisms and ecosystems

New information on the lethal and sublethal effects of neonicotinoids and fipronil on organisms is presented in this review, complementing the previous WIA in 2015. The high toxicity of these systemic insecticides to invertebrates has been confirmed and expanded to include more species and compounds. Most of the recent research has focused on bees and the sublethal and ecological impacts these insecticides have on pollinators. Toxic effects on other invertebrate taxa also covered predatory and parasitoid natural enemies and aquatic arthropods. Little, while not much new information has been gathered on soil organisms. The impact on marine coastal ecosystems is still largely uncharted. The chronic lethality of neonicotinoids to insects and crustaceans, and the strengthened evidence that these chemicals also impair the immune system and reproduction, highlights the dangers of this particular insecticidal classneonicotinoids and fipronil. , withContinued large scale – mostly prophylactic – use of these persistent organochlorine pesticides has the potential to greatly decreasecompletely eliminate populations of arthropods in both terrestrial and aquatic environments. Sublethal effects on fish, reptiles, frogs, birds and mammals are also reported, showing a better understanding of the mechanisms of toxicity of these insecticides in vertebrates, and their deleterious impacts on growth, reproduction and neurobehaviour of most of the species tested. This review concludes with a summary of impacts on the ecosystem services and functioning, particularly on pollination, soil biota and aquatic invertebrate communities, thus reinforcing the previous WIA conclusions (van der Sluijs et al. 2015)

Bilingual Learning for Second and Third Generation Children

Throughout the English-speaking world, children from bilingual backgrounds are being educated in mainstream classrooms where they have little or no opportunity to use their mother tongue. Second and third generation children, in particular, are assumed to be learning sufficiently through English only. This study investigated how British Bangladeshi children, learning Bengali in after-school classes but mostly more fluent in English than in their mother tongue, responded when able to use their full language repertoire within the mainstream curriculum. Through action research with mainstream and community language class teachers, bilingual literacy and numeracy tasks were devised and carried out with pupils aged seven to eleven in two East London primary schools. The bilingual activities were videorecorded and analysed qualitatively to identify the strategies used. The following cognitive and cultural benefits of bilingual learning discovered by researchers in other contexts were also found to apply in this particular setting: conceptual transfer, enriched understanding through translation, metalinguistic awareness, bicultural knowledge and building bilingual learner identities. The findings suggest that second and third generation children should be enabled to learn bilingually, and appropriate strategies are put forward for use in the mainstream classroom

Infrared and photoelectron spectroscopy study of vapor phase deposited poly (3-hexylthiophene)

Poly (3-hexylthiophene) (P3HT) was thermally evaporated and deposited in vacuum. Infrared spectroscopy was used to confirm that the thin films were indeed P3HT, and showed that in-situ thermal evaporation provides a viable route for contaminant-free surface/interface analysis of P3HT in an ultrahigh vacuum (UHV) environment. Ultraviolet photoelectron spectroscopy (UPS) as well as X-ray photoelectron spectroscopy (XPS) experiments were carried out to examine the frontier orbitals and core energy levels of P3HT thin films vapor deposited in UHV on clean polycrystalline silver (Ag) surfaces. UPS spectra enable the determination of the vacuum shift at the polymer/metal interface, the valence band maximum (VBM), and the energy of the \Pi-band of the overlayer film. The P3HT vacuum level decreased in contrast to that of the underlying Ag as the film thickness increased. XPS and UPS data confirmed the chemical integrity (stoichiometry) of the polymer at high coverage, as well as the shift of the C 1s and S 2p binding energy peaks and the secondary-electron edge with increasing film thickness, indicating that band bending is present at the P3HT/Ag interface and that the measured onset of the valence band is about 0.8 +- 0.05 eV relative to the Fermi level

An iterative block-shifting approach to retention time alignment that preserves the shape and area of gas chromatography-mass spectrometry peaks

<p>Abstract</p> <p>Background</p> <p>Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector intensity readings, each uniquely addressed along dimensions of <it>time </it>(<it>e.g.</it>, <it>retention time </it>of chemicals on a chromatographic column), a <it>spectral value </it>(<it>e.g., mass-to-charge ratio </it>of ions derived from chemicals), and the <it>analytical run number</it>. They also must rely on data preprocessing techniques. In particular, inter-run variance in the retention time of chemical species poses a significant hurdle that must be cleared before feature extraction, data reduction, and knowledge discovery can ensue. <it>Alignment methods</it>, for calibrating retention reportedly (and in our experience) can misalign matching chemicals, falsely align distinct ones, be unduly sensitive to chosen values of input parameters, and result in distortions of peak shape and area.</p> <p>Results</p> <p>We present an iterative block-shifting approach for retention-time calibration that detects chromatographic features and qualifies them by retention time, spectrum, and the effect of their inclusion on the quality of alignment itself. Mass chromatograms are aligned pairwise to one selected as a reference. In tests using a 45-run GC-MS experiment, block-shifting reduced the absolute deviation of retention by greater than 30-fold. It compared favourably to COW and XCMS with respect to alignment, and was markedly superior in preservation of peak area.</p> <p>Conclusion</p> <p>Iterative block-shifting is an attractive method to align GC-MS mass chromatograms that is also generalizable to other two-dimensional techniques such as HPLC-MS.</p