Biomarker discovery and redundancy reduction towards classification using a multi-factorial MALDI-TOF MS T2DM mouse model dataset

Diabetes like many diseases and biological processes is not mono-causal. On the one hand multifactorial studies with complex experimental design are required for its comprehensive analysis. On the other hand, the data from these studies often include a substantial amount of redundancy such as proteins that are typically represented by a multitude of peptides. Coping simultaneously with both complexities (experimental and technological) makes data analysis a challenge for Bioinformatics

Increasing the Depth of Current Understanding: Sensitivity Testing of Deep-Sea Larval Dispersal Models for Ecologists

Larval dispersal is an important ecological process of great interest to conservation and the establishment of marine protected areas. Increasing numbers of studies are turning to biophysical models to simulate dispersal patterns, including in the deep-sea, but for many ecologists unassisted by a physical oceanographer, a model can present as a black box. Sensitivity testing offers a means to test the models' abilities and limitations and is a starting point for all modelling efforts. The aim of this study is to illustrate a sensitivity testing process for the unassisted ecologist, through a deep-sea case study example, and demonstrate how sensitivity testing can be used to determine optimal model settings, assess model adequacy, and inform ecological interpretation of model outputs. Five input parameters are tested (timestep of particle simulator (TS), horizontal (HS) and vertical separation (VS) of release points, release frequency (RF), and temporal range (TR) of simulations) using a commonly employed pairing of models. The procedures used are relevant to all marine larval dispersal models. It is shown how the results of these tests can inform the future set up and interpretation of ecological studies in this area. For example, an optimal arrangement of release locations spanning a release area could be deduced; the increased depth range spanned in deep-sea studies may necessitate the stratification of dispersal simulations with different numbers of release locations at different depths; no fewer than 52 releases per year should be used unless biologically informed; three years of simulations chosen based on climatic extremes may provide results with 90% similarity to five years of simulation; and this model setup is not appropriate for simulating rare dispersal events. A step-by-step process, summarising advice on the sensitivity testing procedure, is provided to inform all future unassisted ecologists looking to run a larval dispersal simulation

Genetic and neurological foundations of customer orientation: field and experimental evidence

We explore genetic and neurological bases for customer orientation (CO) and contrast them with sales orientation (SO). Study 1 is a field study that establishes that CO, but not SO, leads to greater opportunity recognition. Study 2 examines genetic bases for CO and finds that salespeople with CO are more likely to have the 7R variant of the DRD4 gene. This is consistent with basic research on dopamine receptor activity in the brain that underlies novelty seeking, the reward function, and risk taking. Study 3 examines the neural basis of CO and finds that salespeople with CO, but not SO, experience greater activation of their mirror neuron systems and neural processes associated with empathy. Managerial and research implications are discussed

Physicochemical properties and structural characteristics of whole grain Oryza sativa L. with different treatments

[EN] Physicochemical properties and structural characteristics of whole rice flours with different treatments (soaking, germination and extrusion cooking) were studied. Water solubility, water absorption, crystallinity, adsorption isotherms (BET and GAB models), and glass transition temperature of the samples were determined. Water solubility and water absorption were enhanced by extrusion cooking process (3.17 4.98 vs. 24.1 53.76 g/100 g and 2.77 3.05 vs. 4.46 7.04 ml/g, respectively), but crystallinity was decreased (30 33 vs. 4 16%). Adsorption isotherms showed that extruded samples exhibited higher equilibrium moisture content as compared with their corresponding non-extruded samples (5.0 19.2 vs. 4.0 16.1 g water/g solids). There were no changes in glass transition temperature values in the studied moisture range (3.8 16 g/100 g). These results allow the correct use of whole rice flours with different treatments in foods and also contributed to the knowledge of stabilization of the productsThe author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was partially financed by ANPCYT (PICT 1105) and ERASMUS MUNDUS ACTION 2 ARCOIRIS Fellowship.Albarracin, M.; Talens Oliag, P.; Martínez Navarrete, N.; González, RJ.; Drago, SR. (2016). Physicochemical properties and structural characteristics of whole grain Oryza sativa L. with different treatments. Food Science and Technology International. 22(4):1-10. doi:10.1177/1082013215600078S110224Albarracín, M., José González, R., & Drago, S. R. (2015). Soaking and extrusion effects on physicochemical parameters, phytic acid, nutrient content and mineral bio-accessibility of whole rice grain. International Journal of Food Sciences and Nutrition, 66(2), 210-215. doi:10.3109/09637486.2014.986070Björck, I., & Asp, N.-G. (1983). The effects of extrusion cooking on nutritional value — A literature review. Journal of Food Engineering, 2(4), 281-308. doi:10.1016/0260-8774(83)90016-xBrunauer, S., Deming, L. S., Deming, W. E., & Teller, E. (1940). On a Theory of the van der Waals Adsorption of Gases. Journal of the American Chemical Society, 62(7), 1723-1732. doi:10.1021/ja01864a025Donkor, O. N., Stojanovska, L., Ginn, P., Ashton, J., & Vasiljevic, T. (2012). Germinated grains – Sources of bioactive compounds. Food Chemistry, 135(3), 950-959. doi:10.1016/j.foodchem.2012.05.058Gonzalez, R. J., De Greef, D. M., Torres, R. L., Borras, F. S., & Robutti, J. (2004). Effects of endosperm hardness and extrusion temperature on properties of products obtained with grits from two commercial maize cultivars. LWT - Food Science and Technology, 37(2), 193-198. doi:10.1016/j.lwt.2003.07.004Gonzalez, R., Drago, S., Torres, R., & De Greef, D. (2013). Extrusion Cooking of Cereal-Based Products. Contemporary Food Engineering. doi:10.1201/b15246-13González, R. J., Pastor Cavada, E., Vioque Peña, J., Torres, R. L., De Greef, D. M., & Drago, S. R. (2013). Extrusion Conditions and Amylose Content Affect Physicochemical Properties of Extrudates Obtained from Brown Rice Grains. International Journal of Food Science, 2013, 1-8. doi:10.1155/2013/584148Herawat, H., Kusnandar, F., Adawiyah, D. R., Budijanto, S., & Rahman, M. S. (2014). Thermal characteristics and state diagram of extruded instant artificial rice. Thermochimica Acta, 593, 50-57. doi:10.1016/j.tca.2014.08.017Jones, J. M., & Engleson, J. (2010). Whole Grains: Benefits and Challenges. Annual Review of Food Science and Technology, 1(1), 19-40. doi:10.1146/annurev.food.112408.132746Kim, H. Y., Hwang, I. G., Kim, T. M., Woo, K. S., Park, D. S., Kim, J. H., … Jeong, H. S. (2012). Chemical and functional components in different parts of rough rice (Oryza sativa L.) before and after germination. Food Chemistry, 134(1), 288-293. doi:10.1016/j.foodchem.2012.02.138Lowry, R. R., & Tinsley, I. J. (1976). Rapid colorimetric determination of free fatty acids. Journal of the American Oil Chemists’ Society, 53(7), 470-472. doi:10.1007/bf02636814Matveev, Y. (2000). The plasticizing effect of water on proteins, polysaccharides and their mixtures. Glassy state of biopolymers, food and seeds. Food Hydrocolloids, 14(5), 425-437. doi:10.1016/s0268-005x(00)00020-5Perdon, A., Siebenmorgen, T. J., & Mauromoustakos, A. (2000). Glassy State Transition and Rice Drying: Development of a Brown Rice State Diagram. Cereal Chemistry Journal, 77(6), 708-713. doi:10.1094/cchem.2000.77.6.708ROOS, Y., & KAREL, M. (1991). Plasticizing Effect of Water on Thermal Behavior and Crystallization of Amorphous Food Models. Journal of Food Science, 56(1), 38-43. doi:10.1111/j.1365-2621.1991.tb07970.xRuiz-Ruiz, J., Martínez-Ayala, A., Drago, S., González, R., Betancur-Ancona, D., & Chel-Guerrero, L. (2008). Extrusion of a hard-to-cook bean (Phaseolus vulgaris L.) and quality protein maize (Zea mays L.) flour blend. LWT - Food Science and Technology, 41(10), 1799-1807. doi:10.1016/j.lwt.2008.01.005SIU, G. M., & DRAPER, H. H. (1978). A SURVEY OF THE MALONALDEHYDE CONTENT OF RETAIL MEATS AND FISH. Journal of Food Science, 43(4), 1147-1149. doi:10.1111/j.1365-2621.1978.tb15256.xSun, Z., Yang, W., Siebenmorgen, T., Stelwagen, A., & Cnossen, A. (2002). Thermomechanical Transitions of Rice Kernels. Cereal Chemistry Journal, 79(3), 349-353. doi:10.1094/cchem.2002.79.3.349Timmermann, E. O. (2003). Multilayer sorption parameters: BET or GAB values? Colloids and Surfaces A: Physicochemical and Engineering Aspects, 220(1-3), 235-260. doi:10.1016/s0927-7757(03)00059-1Tovar, J., Bjoerck, I. M., & Asp, N. G. (1990). Starch content and .alpha.-amylolysis rate in precooked legume flours. Journal of Agricultural and Food Chemistry, 38(9), 1818-1823. doi:10.1021/jf00099a00

Racial and Ethnic Differences in Individuals with Sporadic Creutzfeldt-Jakob Disease in the United States of America

BACKGROUND: Little is known about racial and ethnic differences in individuals with sporadic Creutzfeldt-Jakob disease (sCJD). The authors sought to examine potential clinical, diagnostic, genetic, and neuropathological differences in sCJD patients of different races/ethnicities. METHODOLOGY/PRINCIPAL FINDINGS: A retrospective study of 116 definite and probable sCJD cases from Johns Hopkins and the Department of Veterans Affairs Healthcare Systems was conducted that examined differences in demographic, clinical, diagnostic, genetic, and neuropathological characteristics among racial/ethnic groups. Age at disease onset differed among racial/ethnic groups. Non-Hispanic Whites had a significantly older age at disease onset compared to the other groups (65 vs. 60, p = 0.036). Non-Whites were accurately diagnosed more rapidly than Whites (p = 0.008) and non-Hispanic Whites were more likely to have normal appearing basal ganglia on brain magnetic resonance imaging (MRI) compared to minorities (p = 0.02). Whites were also more likely to undergo post-mortem evaluation compared to non-Whites (p = 0.02). CONCLUSIONS/SIGNIFICANCE: Racial/ethnic groups affected by sCJD demonstrated differences in age at disease onset, time to correct diagnosis, clinical presentation, and diagnostic test results. Whites were more likely to undergo autopsy compared to non-Whites. These results have implications in regards to case ascertainment, diagnosis, and surveillance of sCJD and possibly other human prion diseases

Evolution of Parallel Spindles Like genes in plants and highlight of unique domain architecture#

<p>Abstract</p> <p>Background</p> <p>Polyploidy has long been recognized as playing an important role in plant evolution. In flowering plants, the major route of polyploidization is suggested to be sexual through gametes with somatic chromosome number (2<it>n</it>). <it>Parallel Spindle1 </it>gene in <it>Arabidopsis thaliana </it>(<it>AtPS1</it>) was recently demonstrated to control spindle orientation in the 2nd division of meiosis and, when mutated, to induce 2<it>n </it>pollen. Interestingly, <it>AtPS1 </it>encodes a protein with a FHA domain and PINc domain putatively involved in RNA decay (i.e. Nonsense Mediated mRNA Decay). In potato, 2<it>n </it>pollen depending on parallel spindles was described long time ago but the responsible gene has never been isolated. The knowledge derived from <it>AtPS1 </it>as well as the availability of genome sequences makes it possible to isolate potato <it>PSLike </it>(<it>PSL</it>) and to highlight the evolution of <it>PSL </it>family in plants.</p> <p>Results</p> <p>Our work leading to the first characterization of <it>PSLs </it>in potato showed a greater <it>PSL </it>complexity in this species respect to <it>Arabidopsis thaliana</it>. Indeed, a genomic <it>PSL </it>locus and seven cDNAs affected by alternative splicing have been cloned. In addition, the occurrence of at least two other <it>PSL </it>loci in potato was suggested by the sequence comparison of alternatively spliced transcripts.</p> <p>Phylogenetic analysis on 20 <it>Viridaeplantae </it>showed the wide distribution of <it>PSLs </it>throughout the species and the occurrence of multiple copies only in potato and soybean.</p> <p>The analysis of PSL^FHAand PSL^PINcdomains evidenced that, in terms of secondary structure, a major degree of variability occurred in PINc domain respect to FHA. In terms of specific active sites, both domains showed diversification among plant species that could be related to a functional diversification among <it>PSL </it>genes. In addition, some specific active sites were strongly conserved among plants as supported by sequence alignment and by evidence of negative selection evaluated as difference between non-synonymous and synonymous mutations.</p> <p>Conclusions</p> <p>In this study, we highlight the existence of PSLs throughout <it>Viridaeplantae</it>, from mosses to higher plants. We provide evidence that <it>PSLs </it>occur mostly as singleton in the analyzed genomes except in soybean and potato both characterized by a recent whole genome duplication event. In potato, we suggest the candidate <it>PSL </it>gene having a role in 2<it>n </it>pollen that should be deeply investigated.</p> <p>We provide useful insight into evolutionary conservation of FHA and PINc domains throughout plant PSLs which suggest a fundamental role of these domains for PSL function.</p

Dissolved Organic Carbon in the North Atlantic Meridional Overturning Circulation

The quantitative role of the Atlantic Meridional Overturning Circulation (AMOC) in dissolved organic carbon (DOC) export is evaluated by combining DOC measurements with observed water mass transports. In the eastern subpolar North Atlantic, both upper and lower limbs of the AMOC transport high-DOC waters. Deep water formation that connects the two limbs of the AMOC results in a high downward export of non-refractory DOC (197 Tg-C·yr-1). Subsequent remineralization in the lower limb of the AMOC, between subpolar and subtropical latitudes, consumes 72% of the DOC exported by the whole Atlantic Ocean. The contribution of DOC to the carbon sequestration in the North Atlantic Ocean (62 Tg-C·yr-1) is considerable and represents almost a third of the atmospheric CO 2 uptake in the region

Electronic structure, linear, nonlinear optical susceptibilities and birefringence of CuInX2 (X = S, Se, Te) chalcopyrite-structure compounds

The electronic structure, linear and nonlinear optical properties have been calculated for CuInX2 (X=S, Se, Te) chalcopyrite-structure single crystals using the state-of-the-art full potential linear augmented plane wave (FP-LAPW) method. We present results for band structure, density of states, and imaginary part of the frequency-dependent linear and nonlinear optical susceptibilities. We find that these crystals are semiconductors with direct band gaps. We have calculated the birefringence of these crystals. The birefringence is negative for CuInS2 and CuInSe2 while it is positive for CuInTe2 in agreement with the experimental data. Calculations are reported for the frequency-dependent complex second-order non-linear optical susceptibilities . The intra-band and inter-band contributions to the second harmonic generation increase when we replace S by Se and decrease when we replace Se by Te. We find that smaller energy band gap compounds have larger values of in agreement with the experimental data and previous theoretical calculations.Comment: 17 pages, 6 figure

A Requirement for Zic2 in the Regulation of Nodal Expression Underlies the Establishment of Left-Sided Identity

ZIC2 mutation is known to cause holoprosencephaly (HPE). A subset of ZIC2 HPE probands harbour cardiovascular and visceral anomalies suggestive of laterality defects. 3D-imaging of novel mouse Zic2 mutants uncovers, in addition to HPE, laterality defects in lungs, heart, vasculature and viscera. A strong bias towards right isomerism indicates a failure to establish left identity in the lateral plate mesoderm (LPM), a phenotype that cannot be explained simply by the defective ciliogenesis previously noted in Zic2 mutants. Gene expression analysis showed that the left-determining NODAL-dependent signalling cascade fails to be activated in the LPM, and that the expression of Nodal at the node, which normally triggers this event, is itself defective in these embryos. Analysis of ChiP-seq data, in vitro transcriptional assays and mutagenesis reveals a requirement for a low-affinity ZIC2 binding site for the activation of the Nodal enhancer HBE, which is normally active in node precursor cells. These data show that ZIC2 is required for correct Nodal expression at the node and suggest a model in which ZIC2 acts at different levels to establish LR asymmetry, promoting both the production of the signal that induces left side identity and the morphogenesis of the cilia that bias its distribution