Bioaccumulation modelling and sensitivity analysis for discovering key players in contaminated food webs: the case study of PCBs in the Adriatic Sea

Modelling bioaccumulation processes at the food web level is the main step to analyse the effects of pollutants at the global ecosystem level. A crucial question is understanding which species play a key role in the trophic transfer of contaminants to disclose the contribution of feeding linkages and the importance of trophic dependencies in bioaccumulation dynamics. In this work we present a computational framework to model the bioaccumulation of organic chemicals in aquatic food webs, and to discover key species in polluted ecosystems. As a result, we reconstruct the first PCBs bioaccumulation model of the Adriatic food web, estimated after an extensive review of published concentration data. We define a novel index aimed to identify the key species in contaminated networks, Sensitivity Centrality, and based on sensitivity analysis. The index is computed from a dynamic ODE model parametrised from the estimated PCBs bioaccumulation model and compared with a set of established trophic indices of centrality. Results evidence the occurrence of PCBs biomagnification in the Adriatic food web, and highlight the dependence of bioaccumulation on trophic dynamics and external factors like fishing activity. We demonstrate the effectiveness of the introduced Sensitivity Centrality in identifying the set of species with the highest impact on the total contaminant flows and on the efficiency of contaminant transport within the food web

Circulating tumour cells: insights into tumour heterogeneity

Tumour heterogeneity is a major barrier to cure breast cancer. It can exist between patients with different intrinsic subtypes of breast cancer or within an individual patient with breast cancer. In the latter case, heterogeneity has been observed between different metastatic sites, between metastatic sites and the original primary tumour, and even within a single tumour at either a metastatic or a primary site. Tumour heterogeneity is a function of two separate, although linked, processes. First, genetic instability is a hallmark of malignancy, and results in ‘fixed’ genetic changes that are almost certainly carried forward through progression of the cancer over time, with increasingly complex additional genetic changes in new metastases as they arise. The second type of heterogeneity is due to differential but ‘plastic’ expression of various genes important in the biology and response to various therapies. Together, these processes result in highly variable cancers with differential response, and resistance, to both targeted (e.g. endocrine or anti‐human epithelial growth receptor type 2 ( HER 2) agents) and nontargeted therapies (e.g. chemotherapy). Ideally, tumour heterogeneity would be monitored over time, especially in relation to therapeutic strategies. However, biopsies of metastases require invasive and costly procedures, and biopsies of multiple metastases, or serially over time, are impractical. Circulating tumour cells ( CTC s) represent a potential surrogate for tissue‐based cancer and therefore might provide the opportunity to monitor serial changes in tumour biology. Recent advances have enabled accurate and reliable quantification and molecular characterization of CTC s with regard to a number of important biomarkers including oestrogen receptor alpha and HER 2. Preliminary data have demonstrated that expression of these markers between CTC s in individual patients with metastatic breast cancer reflects the heterogeneity of the underlying tumours. Future studies are designed to determine the clinical utility of these novel technologies in either research or routine clinical settings.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/99056/1/joim12047.pd

Local trace formulae and scaling asymptotics in Toeplitz quantization, II

In the spectral theory of positive elliptic operators, an important role is played by certain smoothing kernels, related to the Fourier transform of the trace of a wave operator, which may be heuristically interpreted as smoothed spectral projectors asymptotically drifting to the right of the spectrum. In the setting of Toeplitz quantization, we consider analogues of these, where the wave operator is replaced by the Hardy space compression of a linearized Hamiltonian flow, possibly composed with a family of zeroth order Toeplitz operators. We study the local asymptotics of these smoothing kernels, and specifically how they concentrate on the fixed loci of the linearized dynamics.Comment: Typos corrected. Slight expository change

Improved CMB anisotropy constraints on primordial magnetic fields from the post-recombination ionization history

We investigate the impact of a stochastic background of Primordial Magnetic Fields (PMF) generated before recombination on the ionization history of the Universe and on the Cosmic Microwave Background radiation (CMB). Pre-recombination PMFs are dissipated during recombination and reionization via decaying MHD turbulence and ambipolar diffusion. This modifies the local matter and electron temperatures and thus affects the ionization history and Thomson visibility function. We use this effect to constrain PMFs described by a spectrum of power-law type, extending our previous study (based on a scale-invariant spectrum) to arbitrary spectral index. We derive upper bounds on the integrated amplitude of PMFs due to the separate effect of ambipolar diffusion and MHD decaying turbulence and their combination. We show that ambipolar diffusion is relevant for $n_{\rm B}>0$ whereas for $n_{\rm B}<0$ MHD turbulence is more important. The bound marginalized over the spectral index on the integrated amplitude of PMFs with a sharp cut-off is $\sqrt{\langle B^2 \rangle}<0.83$ nG. We discuss the quantitative relevance of the assumptions on the damping mechanism and the comparison with previous bounds.Comment: 11 pages, 21 figures. Minor updates to match the published versio

No more time to stay ‘single’ in the detection of Anisakis pegreffii, A. simplex (s. s.) and hybridization events between them: a multi-marker nuclear genotyping approach

A multi-marker nuclear genotyping approach was performed on larval and adult specimens of Anisakis spp. (N = 689) collected from fish and cetaceans in allopatric and sympatric areas of the two species Anisakis pegreffii and Anisakis simplex (s. s.), in order to: (1) identify specimens belonging to the parental taxa by using nuclear markers (allozymes loci) and sequence analysis of a new diagnostic nuclear DNA locus (i.e. partial sequence of the EF1 α−1 nDNA region) and (2) recognize hybrid categories. According to the Bayesian clustering algorithms, based on those markers, most of the individuals (N = 678) were identified as the parental species [i.e. A. pegreffii or A. simplex (s. s.)], whereas a smaller portion (N = 11) were recognized as F1 hybrids. Discordant results were obtained when using the polymerase chain reaction–restriction fragment length polymorphisms (PCR–RFLPs) of the internal transcribed spacer (ITS) ribosomal DNA (rDNA) on the same specimens, which indicated the occurrence of a large number of ‘hybrids’ both in sympatry and allopatry. These findings raise the question of possible misidentification of specimens belonging to the two parental Anisakis and their hybrid categories derived from the application of that single marker (i.e. PCR–RFLPs analysis of the ITS of rDNA). Finally, Bayesian clustering, using allozymes and EF1 α−1 nDNA markers, has demonstrated that hybridization between A. pegreffii and A. simplex (s. s.) is a contemporary phenomenon in sympatric areas, while no introgressive hybridization takes place between the two species

Explicit characterization of the identity configuration in an Abelian Sandpile Model

Since the work of Creutz, identifying the group identities for the Abelian Sandpile Model (ASM) on a given lattice is a puzzling issue: on rectangular portions of Z^2 complex quasi-self-similar structures arise. We study the ASM on the square lattice, in different geometries, and a variant with directed edges. Cylinders, through their extra symmetry, allow an easy determination of the identity, which is a homogeneous function. The directed variant on square geometry shows a remarkable exact structure, asymptotically self-similar.Comment: 11 pages, 8 figure

Identification of the het-r vegetative incompatibility gene of Podospora anserina as a member of the fast evolving HNWD gene family

In fungi, vegetative incompatibility is a conspecific non-self recognition mechanism that restricts formation of viable heterokaryons when incompatible alleles of specific het loci interact. In Podospora anserina, three non-allelic incompatibility systems have been genetically defined involving interactions between het-c and het-d, het-c and het-e, het-r and het-v. het-d and het-e are paralogues belonging to the HNWD gene family that encode proteins of the STAND class. HET-D and HET-E proteins comprise an N-terminal HET effector domain, a central GTP binding site and a C-terminal WD repeat domain constituted of tandem repeats of highly conserved WD40 repeat units that define the specificity of alleles during incompatibility. The WD40 repeat units of the members of this HNWD family are undergoing concerted evolution. By combining genetic analysis and gain of function experiments, we demonstrate that an additional member of this family, HNWD2, corresponds to the het-r non-allelic incompatibility gene. As for het-d and het-e, allele specificity at the het-r locus is determined by the WD repeat domain. Natural isolates show allelic variation for het-

Measurement of angular momentum transport in turbulent flow between independently rotating cylinders

We present measurements of the angular momentum flux (torque) in Taylor-Couette flow of water between independently rotating cylinders for all regions of the \(\Omega_1, \Omega_2\) parameter space at high Reynolds numbers, where $\Omega_1$ \(\Omega_2\) is the inner (outer) cylinder angular velocity. We find that the Rossby number Ro = \(\Omega_1 - \Omega_2\)/\Omega_2 fully determines the state and torque $G$ as compared to G(Ro = \infty) \equiv \Gi. The ratio G/\Gi is a linear function of $Ro^{-1}$ in four sections of the parameter space. For flows with radially-increasing angular momentum, our measured torques greatly exceed those of previous experiments [Ji \textit{et al.}, Nature, \textbf{444}, 343 (2006)], but agree with the analysis of Richard and Zahn [Astron. Astrophys., \textbf{347}, 734 (1999)].Comment: 4 pages, 4 figures, to appear in Physical Review Letter