Identification, release and olfactory detection of bile salts in the intestinal fluid of the Senegalese sole (Solea senegalensis)

Olfactory sensitivity to bile salts is wide-spread in teleosts; however, which bile salts are released in suYcient quantities to be detected is unclear. The current study identiWed bile salts in the intestinal and bile Xuids of Solea senegalensis by mass spectrometry–liquid chromatography and assessed their olfactory potency by the electro-olfactogram

Mass Transfer and Volume Changes in French Fries During Air Frying

An erratum to this article can be found at http://dx.doi.org/10.1007/s11947-012-0904-8 (The graph located in the left upper corner of Fig. 2 is incorrect)The production of healthier fried foods requires the adaptation of industrial processes. In this context, air frying is an alternative to deep oil frying to obtain French fries with lower fat content. Kinetic analysis of compositional changes and main fluxes involved in air frying were carried out, and the results were compared to those obtained for deep oil frying. The influence of the type of sample (unpretreated, frozen, or blanched potatoes) was also analyzed. The results showed that oil uptake is much lower in air frying although a much longer processing time is required. Also, water loss and thus the loss of volume were much higher in air frying compared to the conventional process.The authors would like to thank the Universitat Politecnica de Valencia (PAID-06-09-2876) for the financial support given to this investigation.Andrés Grau, AM.; Argüelles Foix, AL.; Castelló Gómez, ML.; Heredia Gutiérrez, AB. (2013). Mass Transfer and Volume Changes in French Fries During Air Frying. Food and Bioprocess Technology. 6(8):1917-1924. https://doi.org/10.1007/s11947-012-0861-2S1917192468Aguilar, C. N., Anzaldúa-Morales, R., Talamás, R., & Gastélum, G. (1997). Low-temperature blanch improves textural quality of French-fries. Journal of Food Science, 62, 568–571.AOAC. (1980). Official methods of analysis (12th ed.). Washington, D.C., USA: Association of Official Analytical Chemists.Califano, A. N., & Calvelo, A. (1987). Adjustment of surface concentration of reducing sugars before frying of potato strips. Journal of Food Processing and Preservation, 12, 1–9.Clark, J. P. (2003). Happy birthday, potato chip! And other snack developments. Food Technology, 57(5), 89–92.Debnath, S., Bhat, K. K., & Rastogi, N. K. (2003). Effect of pre-drying on kinetics of moisture loss and oil uptake during deep fat frying of chickpea flour-based snack food. LWT—Food Science and Technology, 36, 91–98.Du Pont, M. S., Kirby, A. B., & Smith, A. C. (1992). Instrumental and sensory tests of cooked frozen French fries. International Journal of Food Science and Technology, 27, 285–295.Dueik, V., Robert, P., & Bouchon, P. (2010). Vacuum frying reduces oil uptake and improves the quality parameters of carrot crisps. Food Chemistry, 119(3), 1143–1149.Hubbard, L. J., & Farkas, B. E. (2000). Influence of oil temperature on convective heat transfer during immersion frying. Journal of Food Processing and Preservation, 24(2), 143–162.Krokida, M. K., Oreopoulou, V., & Maroulis, Z. B. (2000). Water loss and oil uptake as a function of frying time. Journal of Food Engineering, 44, 39–46.Mestdagh, F., De Wilde, T., Fraselle, S., Govaert, Y., Ooghe, W., Degroodt, J. M., Verhé, R., Van Peteghem, C., & De Meulenaer, B. (2008). Optimization of the blanching process to reduce acrylamide in fried potatoes. LWT- Food Science and Technology, 41(9), 1648–1654.Mohsenin, N. M. (1986). Physical properties of plant and animal materials. Nueva York: Gordon and Breach.Moyano, P. C., & Pedreschi, F. (2006). Kinetics of oil uptake during frying of potato slices: effect of pre-treatments. LWT- Food Science and Technology, 39, 285–291.Ngadi, M. O., Wang, Y., Adedeji, A. A., & Raghavan, G. S. V. (2009). Effect of microwave pretreatment on mass transfer during deep-fat frying of chicken nugget. LWT- Food Science and Technology, 42(1), 438–440.Pedreschi, F., & Moyano, P. (2005). Oil uptake and texture development in fried potato slices. Journal of Food Engineering, 70(4), 557–563.Saguy, S., & Dana, D. (2003). Integrated approach to deep fat frying: engineering, nutrition, health and consumer aspects. Journal of Food Engineering, 56, 143–152.Troncoso, E., & Pedreschi, F. (2009). Modeling water loss and oil uptake during vacuum frying of pre-treated potato slices. LWT- Food Science and Technology, 42(6), 1164–1173

Two-Particle-Self-Consistent Approach for the Hubbard Model

Even at weak to intermediate coupling, the Hubbard model poses a formidable challenge. In two dimensions in particular, standard methods such as the Random Phase Approximation are no longer valid since they predict a finite temperature antiferromagnetic phase transition prohibited by the Mermin-Wagner theorem. The Two-Particle-Self-Consistent (TPSC) approach satisfies that theorem as well as particle conservation, the Pauli principle, the local moment and local charge sum rules. The self-energy formula does not assume a Migdal theorem. There is consistency between one- and two-particle quantities. Internal accuracy checks allow one to test the limits of validity of TPSC. Here I present a pedagogical review of TPSC along with a short summary of existing results and two case studies: a) the opening of a pseudogap in two dimensions when the correlation length is larger than the thermal de Broglie wavelength, and b) the conditions for the appearance of d-wave superconductivity in the two-dimensional Hubbard model.Comment: Chapter in "Theoretical methods for Strongly Correlated Systems", Edited by A. Avella and F. Mancini, Springer Verlag, (2011) 55 pages. Misprint in Eq.(23) corrected (thanks D. Bergeron

Characterising and Predicting Haploinsufficiency in the Human Genome

Haploinsufficiency, wherein a single functional copy of a gene is insufficient to maintain normal function, is a major cause of dominant disease. Human disease studies have identified several hundred haploinsufficient (HI) genes. We have compiled a map of 1,079 haplosufficient (HS) genes by systematic identification of genes unambiguously and repeatedly compromised by copy number variation among 8,458 apparently healthy individuals and contrasted the genomic, evolutionary, functional, and network properties between these HS genes and known HI genes. We found that HI genes are typically longer and have more conserved coding sequences and promoters than HS genes. HI genes exhibit higher levels of expression during early development and greater tissue specificity. Moreover, within a probabilistic human functional interaction network HI genes have more interaction partners and greater network proximity to other known HI genes. We built a predictive model on the basis of these differences and annotated 12,443 genes with their predicted probability of being haploinsufficient. We validated these predictions of haploinsufficiency by demonstrating that genes with a high predicted probability of exhibiting haploinsufficiency are enriched among genes implicated in human dominant diseases and among genes causing abnormal phenotypes in heterozygous knockout mice. We have transformed these gene-based haploinsufficiency predictions into haploinsufficiency scores for genic deletions, which we demonstrate to better discriminate between pathogenic and benign deletions than consideration of the deletion size or numbers of genes deleted. These robust predictions of haploinsufficiency support clinical interpretation of novel loss-of-function variants and prioritization of variants and genes for follow-up studies

LD-Spline: Mapping SNPs on genotyping platforms to genomic regions using patterns of linkage disequilibrium

<p>Abstract</p> <p>Background</p> <p>Gene-centric analysis tools for genome-wide association study data are being developed both to annotate single locus statistics and to prioritize or group single nucleotide polymorphisms (SNPs) prior to analysis. These approaches require knowledge about the relationships between SNPs on a genotyping platform and genes in the human genome. SNPs in the genome can represent broader genomic regions via linkage disequilibrium (LD), and population-specific patterns of LD can be exploited to generate a data-driven map of SNPs to genes.</p> <p>Methods</p> <p>In this study, we implemented LD-Spline, a database routine that defines the genomic boundaries a particular SNP represents using linkage disequilibrium statistics from the International HapMap Project. We compared the LD-Spline haplotype block partitioning approach to that of the four gamete rule and the Gabriel et al. approach using simulated data; in addition, we processed two commonly used genome-wide association study platforms.</p> <p>Results</p> <p>We illustrate that LD-Spline performs comparably to the four-gamete rule and the Gabriel et al. approach; however as a SNP-centric approach LD-Spline has the added benefit of systematically identifying a genomic boundary for each SNP, where the global block partitioning approaches may falter due to sampling variation in LD statistics.</p> <p>Conclusion</p> <p>LD-Spline is an integrated database routine that quickly and effectively defines the genomic region marked by a SNP using linkage disequilibrium, with a SNP-centric block definition algorithm.</p

Evolutionary Patterns and Selective Pressures of Odorant/Pheromone Receptor Gene Families in Teleost Fishes

BACKGROUND: Teleost fishes do not have a vomeronasal organ (VNO), and their vomeronasal receptors (V1Rs, V2Rs) are expressed in the main olfactory epithelium (MOE), as are odorant receptors (ORs) and trace amine-associated receptors (TAARs). In this study, to obtain insights into the functional distinction among the four chemosensory receptor families in teleost fishes, their evolutionary patterns were examined in zebrafish, medaka, stickleback, fugu, and spotted green pufferfish. METHODOLOGY/PRINCIPAL FINDINGS: Phylogenetic analysis revealed that many lineage-specific gene gains and losses occurred in the teleost fish TAARs, whereas only a few gene gains and losses have taken place in the teleost fish vomeronasal receptors. In addition, synonymous and nonsynonymous nucleotide substitution rate ratios (K(A)/K(S)) in TAARs tended to be higher than those in ORs and V2Rs. CONCLUSIONS/SIGNIFICANCE: Frequent gene gains/losses and high K(A)/K(S) in teleost TAARs suggest that receptors in this family are used for detecting some species-specific chemicals such as pheromones. Conversely, conserved repertoires of V1R and V2R families in teleost fishes may imply that receptors in these families perceive common odorants for teleosts, such as amino acids. Teleost ORs showed intermediate evolutionary pattern between TAARs and vomeronasal receptors. Many teleost ORs seem to be used for common odorants, but some ORs may have evolved to recognize lineage-specific odors

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

<p>Abstract</p> <p>Background</p> <p>Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome.</p> <p>Results</p> <p>We have developed <it>ChIPpeakAnno </it>as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with <it>ChIPpeakAnno </it>can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes.</p> <p>Conclusions</p> <p><it>ChIPpeakAnno </it>enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such as a different Chromatin immunoprecipitation (ChIP) preparation and a dataset from literature, or existing annotation packages, such as <it>GenomicFeatures </it>and <it>BSgenom</it>e, provides flexibility. Tight integration to the <it>biomaRt </it>package enables up-to-date annotation retrieval from the BioMart database.</p

Hospital-level associations with 30-day patient mortality after cardiac surgery: a tutorial on the application and interpretation of marginal and multilevel logistic regression

Background: Marginal and multilevel logistic regression methods can estimate associations between hospital-level factors and patient-level 30-day mortality outcomes after cardiac surgery. However, it is not widely understood how the interpretation of hospital-level effects differs between these methods. Methods. The Australasian Society of Cardiac and Thoracic Surgeons (ASCTS) registry provided data on 32,354 patients undergoing cardiac surgery in 18 hospitals from 2001 to 2009. The logistic regression methods related 30-day mortality after surgery to hospital characteristics with concurrent adjustment for patient characteristics. Results: Hospital-level mortality rates varied from 1.0% to 4.1% of patients. Ordinary, marginal and multilevel regression methods differed with regard to point estimates and conclusions on statistical significance for hospital-level risk factors; ordinary logistic regression giving inappropriately narrow confidence intervals. The median odds ratio, MOR, from the multilevel model was 1.2 whereas ORs for most patient-level characteristics were of greater magnitude suggesting that unexplained between-hospital variation was not as relevant as patient-level characteristics for understanding mortality rates. For hospital-level characteristics in the multilevel model, 80% interval ORs, IOR-80%, supplemented the usual ORs from the logistic regression. The IOR-80% was (0.8 to 1.8) for academic affiliation and (0.6 to 1.3) for the median annual number of cardiac surgery procedures. The width of these intervals reflected the unexplained variation between hospitals in mortality rates; the inclusion of one in each interval suggested an inability to add meaningfully to explaining variation in mortality rates. Conclusions: Marginal and multilevel models take different approaches to account for correlation between patients within hospitals and they lead to different interpretations for hospital-level odds ratios. © 2012 Sanagou et al; licensee BioMed Central Ltd