Thin Animals

Lattice animals provide a discretized model for the theta transition displayed by branched polymers in solvent. Exact graph enumeration studies have given some indications that the phase diagram of such lattice animals may contain two collapsed phases as well as an extended phase. This has not been confirmed by studies using other means. We use the exact correspondence between the q --> 1 limit of an extended Potts model and lattice animals to investigate the phase diagram of lattice animals on phi-cubed random graphs of arbitrary topology (``thin'' random graphs). We find that only a two phase structure exists -- there is no sign of a second collapsed phase. The random graph model is solved in the thermodynamic limit by saddle point methods. We observe that the ratio of these saddle point equations give precisely the fixed points of the recursion relations that appear in the solution of the model on the Bethe lattice by Henkel and Seno. This explains the equality of non-universal quantities such as the critical lines for the Bethe lattice and random graph ensembles.Comment: Latex, 10 pages plus 6 ps/eps figure

Multivariate Granger Causality and Generalized Variance

Granger causality analysis is a popular method for inference on directed interactions in complex systems of many variables. A shortcoming of the standard framework for Granger causality is that it only allows for examination of interactions between single (univariate) variables within a system, perhaps conditioned on other variables. However, interactions do not necessarily take place between single variables, but may occur among groups, or "ensembles", of variables. In this study we establish a principled framework for Granger causality in the context of causal interactions among two or more multivariate sets of variables. Building on Geweke's seminal 1982 work, we offer new justifications for one particular form of multivariate Granger causality based on the generalized variances of residual errors. Taken together, our results support a comprehensive and theoretically consistent extension of Granger causality to the multivariate case. Treated individually, they highlight several specific advantages of the generalized variance measure, which we illustrate using applications in neuroscience as an example. We further show how the measure can be used to define "partial" Granger causality in the multivariate context and we also motivate reformulations of "causal density" and "Granger autonomy". Our results are directly applicable to experimental data and promise to reveal new types of functional relations in complex systems, neural and otherwise.Comment: added 1 reference, minor change to discussion, typos corrected; 28 pages, 3 figures, 1 table, LaTe

Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts

A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/ Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts

Stalking influenza by vaccination with pre-fusion headless HA mini-stem.

Inaccuracies in prediction of circulating viral strain genotypes and the possibility of novel reassortants causing a pandemic outbreak necessitate the development of an anti-influenza vaccine with increased breadth of protection and potential for rapid production and deployment. The hemagglutinin (HA) stem is a promising target for universal influenza vaccine as stem-specific antibodies have the potential to be broadly cross-reactive towards different HA subtypes. Here, we report the design of a bacterially expressed polypeptide that mimics a H5 HA stem by protein minimization to focus the antibody response towards the HA stem. The HA mini-stem folds as a trimer mimicking the HA prefusion conformation. It is resistant to thermal/chemical stress, and it binds to conformation-specific, HA stem-directed broadly neutralizing antibodies with high affinity. Mice vaccinated with the group 1 HA mini-stems are protected from morbidity and mortality against lethal challenge by both group 1 (H5 and H1) and group 2 (H3) influenza viruses, the first report of cross-group protection. Passive transfer of immune serum demonstrates the protection is mediated by stem-specific antibodies. Furthermore, antibodies indudced by these HA stems have broad HA reactivity, yet they do not have antibody-dependent enhancement activity

Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models

Accurate identification of sparse heterozygous single-nucleotide variants (SNVs) is a critical challenge for identifying the causative mutations in mouse genetic screens, human genetic diseases and cancer. When seeking to identify causal DNA variants that occur at such low rates, they are overwhelmed by false-positive calls that arise from a range of technical and biological sources. We describe a strategy using whole-exome capture, massively parallel DNA sequencing and computational analysis, which identifies with a low false-positive rate the majority of heterozygous and homozygous SNVs arising de novo with a frequency of one nucleotide substitution per megabase in progeny of N-ethyl-N-nitrosourea (ENU)-mutated C57BL/6j mice. We found that by applying a strategy of filtering raw SNV calls against known and platform-specific variants we could call true SNVs with a false-positive rate of 19.4 per cent and an estimated false-negative rate of 21.3 per cent. These error rates are small enough to enable calling a causative mutation from both homozygous and heterozygous candidate mutation lists with little or no further experimental validation. The efficacy of this approach is demonstrated by identifying the causative mutation in the Ptprc gene in a lymphocyte-deficient strain and in 11 other strains with immune disorders or obesity, without the need for meiotic mapping. Exome sequencing of first-generation mutant mice revealed hundreds of unphenotyped protein-changing mutations, 52 per cent of which are predicted to be deleterious, which now become available for breeding and experimental analysis. We show that exome sequencing data alone are sufficient to identify induced mutations. This approach transforms genetic screens in mice, establishes a general strategy for analysing rare DNA variants and opens up a large new source for experimental models of human disease

A ROSAT HRI survey of bright nearby galaxies

We use the extensive public archive of ROSAT High Resolution Imager (HRI) observations to carry out a statistical investigation of the X-ray properties of nearby galaxies. Specifically we focus on the sample of 486 bright (B_T < 12.5) northern galaxies studied by Ho, Filippenko and Sargent (HFS) in the context of their exploration of the optical spectroscopic properties of nearby galactic nuclei. Over 20% of HFS galaxies are encompassed in ROSAT HRI fields of reasonable (> 10ks) exposure. The X-ray sources detected within the optical extent of each galaxy are categorised as either nuclear or non-nuclear depending on whether the source is positioned within or outside of a 25 arcsecond radius circle centred on the optical nucleus. A nuclear X-ray source is detected in over 70% of the galaxies harbouring either a Seyfert or LINER nucleus compared to a detection rate of only ~40% in less active systems. The correlation of the H alpha luminosity with nuclear X-ray luminosity previously observed in QSOs and bright Seyfert 1 galaxies appears to extend down into the regime of ultra-low luminosity (L(x)~10^38 - 10^40 erg/s) active galactic nuclei (AGN). The inferred accretion rates for this sample of low-luminosity AGN are significantly sub-Eddington. In total 142 non-nuclear sources were detected. In combination with published data for M31 this leads to a luminosity distribution (normalised to an optical blue luminosity of L(B) = 10^10 L(solar)) for the discrete X-ray source population in spiral galaxies of the form dN/dL38 = 1.0 +/- 0.2 L38^-1.8, where L38 is the X-ray luminosity in units of 10^38 erg/s. The implied L(x)/L(B) ratio is ~1.1 x 10^39 erg/s/(10^10 L(solar)). The nature of the substantial number of ``super-luminous'' non-nuclear objects detected in the survey is discussed.Comment: 20 pages, 7 figures, accepted for publication in MNRAS. Also available from http://www.star.le.ac.uk/~tro/papers/xhfs.p

An introductory survey of probability density function control

YesProbability density function (PDF) control strategy investigates the controller design approaches where the random variables for the stochastic processes were adjusted to follow the desirable distributions. In other words, the shape of the system PDF can be regulated by controller design.Different from the existing stochastic optimization and control methods, the most important problem of PDF control is to establish the evolution of the PDF expressions of the system variables. Once the relationship between the control input and the output PDF is formulated, the control objective can be described as obtaining the control input signals which would adjust the system output PDFs to follow the pre-specified target PDFs. Motivated by the development of data-driven control and the state of the art PDF-based applications, this paper summarizes the recent research results of the PDF control while the controller design approaches can be categorized into three groups: (1) system model-based direct evolution PDF control; (2) model-based distribution-transformation PDF control methods and (3) data-based PDF control. In addition, minimum entropy control, PDF-based filter design, fault diagnosis and probabilistic decoupling design are also introduced briefly as extended applications in theory sense.De Montfort University - DMU HEIF’18 project, Natural Science Foundation of Shanxi Province [grant number 201701D221112], National Natural Science Foundation of China [grant numbers 61503271 and 61603136

Interactions among mitochondrial proteins altered in glioblastoma

Mitochondrial dysfunction is putatively central to glioblastoma (GBM) pathophysiology but there has been no systematic analysis in GBM of the proteins which are integral to mitochondrial function. Alterations in proteins in mitochondrial enriched fractions from patients with GBM were defined with label-free liquid chromatography mass spectrometry. 256 mitochondrially-associated proteins were identified in mitochondrial enriched fractions and 117 of these mitochondrial proteins were markedly (fold-change &#8805;2) and significantly altered in GBM (p &#8804; 0.05). Proteins associated with oxidative damage (including catalase, superoxide dismutase 2, peroxiredoxin 1 and peroxiredoxin 4) were increased in GBM. Protein–protein interaction analysis highlighted a reduction in multiple proteins coupled to energy metabolism (in particular respiratory chain proteins, including 23 complex-I proteins). Qualitative ultrastructural analysis in GBM with electron microscopy showed a notably higher prevalence of mitochondria with cristolysis in GBM. This study highlights the complex mitochondrial proteomic adjustments which occur in GBM pathophysiology

Influence of a Conductive Material and Different Anaerobic Inocula on Biochemical Methane Potential of Substrates from Alcoholic Beverage Production

The impact of a conductive material as powdered activated carbon (PAC) on the biochemical methane potential of whisky pot ale (PA) and brewery spent yeast (SY) was investigated. The test was carried out with three different types of anaerobic inocula: manure inoculum (MI), sewage sludge (SS) and granular sludge (GR). Brewery spent yeast produced partial (in sewage and granular sludge) and total (in manure inoculum) methanogenesis inhibition due to the toxicity of some of its constituents (hops extract). The inhibition was overcome by the supplementation of PAC, that improved significantly the anaerobic digestion process for SY, allowing to reach biochemical methane potential values between 657-699 L CH4 kg-1 VS and it reduced redox potential from 369 to 398 mV. The activated carbon did not improve the methane yields from whisky PA since microorganisms did not have difficulties to process this substrate; in fact, the redox potential slightly increased from 355 to 330 mV