Divergence and Shannon information in genomes

Shannon information (SI) and its special case, divergence, are defined for a DNA sequence in terms of probabilities of chemical words in the sequence and are computed for a set of complete genomes highly diverse in length and composition. We find the following: SI (but not divergence) is inversely proportional to sequence length for a random sequence but is length-independent for genomes; the genomic SI is always greater and, for shorter words and longer sequences, hundreds to thousands times greater than the SI in a random sequence whose length and composition match those of the genome; genomic SIs appear to have word-length dependent universal values. The universality is inferred to be an evolution footprint of a universal mode for genome growth.Comment: 4 pages, 3 tables, 2 figure

“It gave me something big in my life to wonder and think about which took over the space … and not MS”: Managing well-being in multiple sclerosis through art-making

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2014 Informa UK Ltd.Background and aim: Individuals living with Multiple Sclerosis (MS) often face progressive loss of function, uncertainty and disruption to self-image and valued roles. Previous studies show that creative self-expression is valued by some people living with long-term illness, yet its meaning for people living with MS is unclear. This research study explored the meanings of leisure-based visual art-making for people living with MS. Method: This qualitative study followed guidelines for Interpretative Phenomenological Analysis (IPA). Single semi-structured interviews were conducted with five adults (2 males; 3 females; 40–65 years), recruited from MS Ireland. Findings: Participants valued art-making for contributing to a more satisfying way of life; for filling occupational voids and using time well. Deep immersion offered respite from worry about illness. Creative classes offered social camaraderie and opportunities for learning and development. Art-making processes and products were highly affirmative, increasing emotional well-being and promoting self-worth. Most felt that they expressed valued aspects of self through their art. Art-making appeared to assist with identity maintenance, accommodating functional losses associated with MS whilst opening “new doors”. Conclusion: Art-making offered a multi-faceted means of supporting identity and increasing fulfilment in lives that were restricted in many ways by MS

Testing the psychometric properties of Kidscreen-27 with Irish children of low socio-economic status

BACKGROUND: Kidscreen-27 was developed as part of a cross-cultural European Union-funded project to standardise the measurement of children’s health-related quality of life. Yet, research has reported mixed evidence for the hypothesised 5-factor model, and no confirmatory factor analysis (CFA) has been conducted on the instrument with children of low socio-economic status (SES) across Ireland (Northern and Republic). METHOD: The data for this study were collected as part of a clustered randomised controlled trial. A total of 663 (347 male, 315 female) 8–9-year-old children (M = 8.74, SD = .50) of low SES took part. A 5- and modified 7-factor CFA models were specified using the maximum likelihood estimation. A nested Chi-square difference test was conducted to compare the fit of the models. Internal consistency and floor and ceiling effects were also examined. RESULTS: CFA found that the hypothesised 5-factor model was an unacceptable fit. However, the modified 7-factor model was supported. A nested Chi-square difference test confirmed that the fit of the 7-factor model was significantly better than that of the 5-factor model. Internal consistency was unacceptable for just one scale. Ceiling effects were present in all but one of the factors. CONCLUSIONS: Future research should apply the 7-factor model with children of low socio-economic status. Such efforts would help monitor the health status of the population

Kullback-Leibler and Renormalized Entropy: Applications to EEGs of Epilepsy Patients

Recently, renormalized entropy was proposed as a novel measure of relative entropy (P. Saparin et al., Chaos, Solitons & Fractals 4, 1907 (1994)) and applied to several physiological time sequences, including EEGs of patients with epilepsy. We show here that this measure is just a modified Kullback-Leibler (K-L) relative entropy, and it gives similar numerical results to the standard K-L entropy. The latter better distinguishes frequency contents of e.g. seizure and background EEGs than renormalized entropy. We thus propose that renormalized entropy might not be as useful as claimed by its proponents. In passing we also make some critical remarks about the implementation of these methods.Comment: 15 pages, 4 Postscript figures. Submitted to Phys. Rev. E, 199

Fish oil omega-3 fatty acids partially prevent lipid-induced insulin resistance in human skeletal muscle without limiting acylcarnitine accumulation

This is the author accepted manuscript. The final version is available from Portland Press via the DOI in this record Acylcarnitine accumulation in skeletal muscle and plasma has been observed in numerous models of mitochondrial lipid overload and insulin resistance. Fish oil n3PUFA (omega-3 polyunsaturated fatty acids) are thought to protect against lipid-induced insulin resistance. The present study tested the hypothesis that the addition of n3PUFA to an intravenous lipid emulsion would limit muscle acylcarnitine accumulation and reduce the inhibitory effect of lipid overload on insulin action. On three occasions, six healthy young men underwent a 6-h euglycaemic-hyperinsulinaemic clamp accompanied by intravenous infusion of saline (Control), 10% Intralipid® [n6PUFA (omega-6 polyunsaturated fatty acids)] or 10% Intralipid®+10% Omegaven® (2:1; n3PUFA). The decline in insulin-stimulated whole-body glucose infusion rate, muscle PDCa (pyruvate dehydrogenase complex activation) and glycogen storage associated with n6PUFA compared with Control was prevented with n3PUFA. Muscle acetyl-CoA accumulation was greater following n6PUFA compared with Control and n3PUFA, suggesting that mitochondrial lipid overload was responsible for the lower insulin action observed. Despite these favourable metabolic effects of n3PUFA, accumulation of total muscle acylcarnitine was not attenuated when compared with n6PUFA. These findings demonstrate that n3PUFA exert beneficial effects on insulin-stimulated skeletal muscle glucose storage and oxidation independently of total acylcarnitine accumulation, which does not always reflect mitochondrial lipid overload.This research study was funded by The Royal Society [Grant RG100575]

Stereoselective synthesis of 1,2-diamine containing indolines by a conjugate addition nitro-Mannich reaction.

A conjugate addition nitro-Mannich reaction followed by nitro reduction and intramolecular N-arylation gives diastereomerically pure substituted 1,2-diamine containing indolines. Placing the N-arylation cyclisation handle on the imine precursor derived from an ortho-bromine substituted aromatic aldehyde gave the corresponding β-nitroamines in 55-72% yields as single diastereoisomers. Nitro reduction was effected with modified quantities of Zn/HCl and a subsequent Pd(0) catalysed Buchwald Hartwig cyclisation gave indoline products in 40-70% yields as single diastereoisomers

3D-HST: A wide-field grism spectroscopic survey with the Hubble Space Telescope

We present 3D-HST, a near-infrared spectroscopic Treasury program with the Hubble Space Telescope for studying the processes that shape galaxies in the distant Universe. 3D-HST provides rest-frame optical spectra for a sample of ~7000 galaxies at 1<z<3.5, the epoch when 60% of all star formation took place, the number density of quasars peaked, the first galaxies stopped forming stars, and the structural regularity that we see in galaxies today must have emerged. 3D-HST will cover 3/4 (625 sq.arcmin) of the CANDELS survey area with two orbits of primary WFC3/G141 grism coverage and two to four parallel orbits with the ACS/G800L grism. In the IR these exposure times yield a continuum signal-to-noise of ~5 per resolution element at H~23.1 and a 5sigma emission line sensitivity of 5x10-17 erg/s/cm2 for typical objects, improving by a factor of ~2 for compact sources in images with low sky background levels. The WFC3/G141 spectra provide continuous wavelength coverage from 1.1-1.6 um at a spatial resolution of ~0."13, which, combined with their depth, makes them a unique resource for studying galaxy evolution. We present the preliminary reduction and analysis of the grism observations, including emission line and redshift measurements from combined fits to the extracted grism spectra and photometry from ancillary multi-wavelength catalogs. The present analysis yields redshift estimates with a precision of sigma(z)=0.0034(1+z), or sigma(v)~1000 km/s. We illustrate how the generalized nature of the survey yields near-infrared spectra of remarkable quality for many different types of objects, including a quasar at z=4.7, quiescent galaxies at z~2, and the most distant T-type brown dwarf star known. The CANDELS and 3D-HST surveys combined will provide the definitive imaging and spectroscopic dataset for studies of the 1<z<3.5 Universe until the launch of the James Webb Space Telescope.Comment: Replacement reflects version now accepted by ApJS. A preliminary data release intended to provide a general illustration of the WFC3 grism data is available at http://3dhst.research.yale.edu

Epstein-Barr virus transcription factor Zta acts through distal regulatory elements to directly control cellular gene expression

Lytic replication of the human gamma herpes virus Epstein-Barr virus (EBV) is an essential prerequisite for the spread of the virus. Differential regulation of a limited number of cellular genes has been reported in B-cells during the viral lytic replication cycle. We asked whether a viral bZIP transcription factor, Zta (BZLF1, ZEBRA, EB1), drives some of these changes. Using genome-wide chromatin immunoprecipitation coupled to next-generation DNA sequencing (ChIP-seq) we established a map of Zta interactions across the human genome. Using sensitive transcriptome analyses we identified 2263 cellular genes whose expression is significantly changed during the EBV lytic replication cycle. Zta binds 278 of the regulated genes and the distribution of binding sites shows that Zta binds mostly to sites that are distal to transcription start sites. This differs from the prevailing view that Zta activates viral genes by binding exclusively at promoter elements. We show that a synthetic Zta binding element confers Zta regulation at a distance and that distal Zta binding sites from cellular genes can confer Zta-mediated regulation on a heterologous promoter. This leads us to propose that Zta directly reprograms the expression of cellular genes through distal elements

Genomic analysis of shiga toxin-containing Escherichia coli O157:H7 isolated from Argentinean cattle

Cattle are the main reservoir of Enterohemorrhagic Escherichia coli (EHEC), with O157:H7 the distinctive serotype. EHEC is the main causative agent of a severe systemic disease, Hemolytic Uremic Syndrome (HUS). Argentina has the highest pediatric HUS incidence worldwide with 12–14 cases per 100,000 children. Herein, we assessed the genomes of EHEC O157:H7 isolates recovered from cattle in the humid Pampas of Argentina. According to phylogenetic studies, EHEC O157 can be divided into clades. Clade 8 strains that were classified as hypervirulent. Most of the strains of this clade have a Shiga toxin stx2a-stx2c genotype. To better understand the molecular bases related to virulence, pathogenicity and evolution of EHEC O157:H7, we performed a comparative genomic analysis of these isolates through whole genome sequencing. The isolates classified as clade 8 (four strains) and clade 6 (four strains) contained 13 to 16 lambdoid prophages per genome, and the observed variability of prophages was analysed. An inter strain comparison show that while some prophages are highly related and can be grouped into families, other are unique. Prophages encoding for stx2a were highly diverse, while those encoding for stx2c were conserved. A cluster of genes exclusively found in clade 8 contained 13 genes that mostly encoded for DNA binding proteins. In the studied strains, polymorphisms in Q antiterminator, the Q-stx2A intergenic region and the O and P γ alleles of prophage replication proteins are associated with different levels of Stx2a production. As expected, all strains had the pO157 plasmid that was highly conserved, although one strain displayed a transposon interruption in the protease EspP gene. This genomic analysis may contribute to the understanding of the genetic basis of the hypervirulence of EHEC O157:H7 strains circulating in Argentine cattle. This work aligns with other studies of O157 strain variation in other populations that shows key differences in Stx2a-encoding prophages

Information heat engine: converting information to energy by feedback control

In 1929, Leo Szilard invented a feedback protocol in which a hypothetical intelligence called Maxwell's demon pumps heat from an isothermal environment and transduces it to work. After an intense controversy that lasted over eighty years; it was finally clarified that the demon's role does not contradict the second law of thermodynamics, implying that we can convert information to free energy in principle. Nevertheless, experimental demonstration of this information-to-energy conversion has been elusive. Here, we demonstrate that a nonequilibrium feedback manipulation of a Brownian particle based on information about its location achieves a Szilard-type information-energy conversion. Under real-time feedback control, the particle climbs up a spiral-stairs-like potential exerted by an electric field and obtains free energy larger than the amount of work performed on it. This enables us to verify the generalized Jarzynski equality, or a new fundamental principle of "information-heat engine" which converts information to energy by feedback control.Comment: manuscript including 7 pages and 4 figures and supplementary material including 6 pages and 8 figure