Determining Principal Component Cardinality through the Principle of Minimum Description Length

PCA (Principal Component Analysis) and its variants areubiquitous techniques for matrix dimension reduction and reduced-dimensionlatent-factor extraction. One significant challenge in using PCA, is thechoice of the number of principal components. The information-theoreticMDL (Minimum Description Length) principle gives objective compression-based criteria for model selection, but it is difficult to analytically applyits modern definition - NML (Normalized Maximum Likelihood) - to theproblem of PCA. This work shows a general reduction of NML prob-lems to lower-dimension problems. Applying this reduction, it boundsthe NML of PCA, by terms of the NML of linear regression, which areknown.Comment: LOD 201

The impact of spectroscopic incompleteness in direct calibration of redshift distributions for weak lensing surveys

Obtaining accurate distributions of galaxy redshifts is a critical aspect of weak lensing cosmology experiments. One of the methods used to estimate and validate redshift distributions is to apply weights to a spectroscopic sample, so that their weighted photometry distribution matches the target sample. In this work, we estimate the selection bias in redshift that is introduced in this procedure. We do so by simulating the process of assembling a spectroscopic sample (including observer-assigned confidence flags) and highlight the impacts of spectroscopic target selection and redshift failures. We use the first year (Y1) weak lensing analysis in Dark Energy Survey (DES) as an example data set but the implications generalize to all similar weak lensing surveys. We find that using colour cuts that are not available to the weak lensing galaxies can introduce biases of up to Δz ∼ 0.04 in the weighted mean redshift of different redshift intervals (Δz ∼ 0.015 in the case most relevant to DES). To assess the impact of incompleteness in spectroscopic samples, we select only objects with high observer-defined confidence flags and compare the weighted mean redshift with the true mean. We find that the mean redshift of the DES Y1 weak lensing sample is typically biased at the Δz = 0.005−0.05 level after the weighting is applied. The bias we uncover can have either sign, depending on the samples and redshift interval considered. For the highest redshift bin, the bias is larger than the uncertainties in the other DES Y1 redshift calibration methods, justifying the decision of not using this method for the redshift estimations. We discuss several methods to mitigate this bias

Freshening of the Mediterranean Salt Giant: controversies and certainties around the terminal (Upper Gypsum and Lago-Mare) phases of the Messinian Salinity Crisis

The late Miocene evolution of the Mediterranean Basin is characterized by major changes in connectivity, climate and tectonic activity resulting in unprecedented environmental and ecological disruptions. During the Messinian Salinity Crisis (MSC, 5.97-5.33 Ma) this culminated in most scenarios first in the precipitation of gypsum around the Mediterranean margins (Stage 1, 5.97-5.60 Ma) and subsequently > 2 km of halite on the basin floor, which formed the so-called Mediterranean Salt Giant (Stage 2, 5.60-5.55 Ma). The final MSC Stage 3, however, was characterized by a "low-salinity crisis", when a second calcium-sulfate unit (Upper Gypsum; substage 3.1, 5.55-5.42 Ma) showing (bio)geochemical evidence of substantial brine dilution and brackish biota-bearing terrigenous sediments (substage 3.2 or Lago-Mare phase, 5.42-5.33 Ma) deposited in a Mediterranean that received relatively large amounts of riverine and Paratethys-derived low-salinity waters. The transition from hypersaline evaporitic (halite) to brackish facies implies a major change in the Mediterranean’s hydrological regime. However, even after nearly 50 years of research, causes and modalities are poorly understood and the original scientific debate between a largely isolated and (partly) desiccated Mediterranean or a fully connected and filled basin is still vibrant. Here we present a comprehensive overview that brings together (chrono)stratigraphic, sedimentological, paleontological, geochemical and seismic data from all over the Mediterranean. We summarize the paleoenvironmental, paleohydrological and paleoconnectivity scenarios that arose from this cross-disciplinary dataset and we discuss arguments in favour of and against each scenario

Sequestration of Highly Expressed mRNAs in Cytoplasmic Granules, P-Bodies, and Stress Granules Enhances Cell Viability

Transcriptome analyses indicate that a core 10%–15% of the yeast genome is modulated by a variety of different stresses. However, not all the induced genes undergo translation, and null mutants of many induced genes do not show elevated sensitivity to the particular stress. Elucidation of the RNA lifecycle reveals accumulation of non-translating mRNAs in cytoplasmic granules, P-bodies, and stress granules for future regulation. P-bodies contain enzymes for mRNA degradation; under stress conditions mRNAs may be transferred to stress granules for storage and return to translation. Protein degradation by the ubiquitin-proteasome system is elevated by stress; and here we analyzed the steady state levels, decay, and subcellular localization of the mRNA of the gene encoding the F-box protein, UFO1, that is induced by stress. Using the MS2L mRNA reporter system UFO1 mRNA was observed in granules that colocalized with P-bodies and stress granules. These P-bodies stored diverse mRNAs. Granules of two mRNAs transported prior to translation, ASH1-MS2L and OXA1-MS2L, docked with P-bodies. HSP12 mRNA that gave rise to highly elevated protein levels was not observed in granules under these stress conditions. ecd3, pat1 double mutants that are defective in P-body formation were sensitive to mRNAs expressed ectopically from strong promoters. These highly expressed mRNAs showed elevated translation compared with wild-type cells, and the viability of the mutants was strongly reduced. ecd3, pat1 mutants also exhibited increased sensitivity to different stresses. Our interpretation is that sequestration of highly expressed mRNAs in P-bodies is essential for viability. Storage of mRNAs for future regulation may contribute to the discrepancy between the steady state levels of many stress-induced mRNAs and their proteins. Sorting of mRNAs for future translation or decay by individual cells could generate potentially different phenotypes in a genetically identical population and enhance its ability to withstand stress

Psychometric evaluation of the Hospital Anxiety and Depression Scale in a large community sample of adolescents in Hong Kong

Purpose: The Hospital Anxiety and Depression Scale (HADS) is widely used in adult populations; however, its usefulness with adolescents has been explored less. This study sought to evaluate the reliability, validity, and factor structure of the Chinese version of HADS in a community sample of adolescents residing in Hong Kong. Methods: A prospective cohort of 5,857 students recruited from 17 secondary schools completed the HADS. Internal consistency and concurrent validity were examined. Confirmatory factor analysis was applied to test the relative fits of six factor structures of the HADS. The best fitting model was further cross-validated by male, female, splithalf samples, and age subgroups. Results: The HADS possessed adequate internal consistency, especially for the anxiety subscale. Significant concurrent intercorrelations with self-reported suicidal thoughts and the Youth Self Report Anxious/Depressed subscale were discovered and found to be stronger for females. The cross-validation supported a two-factor model, where anxiety item 7, "I can sit at ease and feel relaxed", was placed in the depression subscale. Conclusions: The HADS showed satisfactory psychometric properties as a screening instrument in assessing anxious and depressive states as two correlated but distinct factors in adolescents. Study implications and recommendations for future research were discussed.published_or_final_versionSpringer Open Choice, 21 Feb 201

Chronic arthritis in children and adolescents in two Indian health service user populations

BACKGROUND: High prevalence rates for rheumatoid arthritis, spondyloarthopathies, and systemic lupus erythematosus have been described in American Indian and Alaskan Native adults. The impact of these diseases on American Indian children has not been investigated. METHODS: We used International Classification of Diseases-9 (ICD-9) codes to search two Indian Health Service (IHS) patient registration databases over the years 1998–2000, searching for individuals 19 years of age or younger with specific ICD-9-specified diagnoses. Crude estimates for disease prevalence were made based on the number of individuals identified with these diagnoses within the database. RESULTS: Rheumatoid arthritis (RA) / juvenile rheumatoid arthritis (JRA) was the most frequent diagnosis given. The prevalence rate for JRA in the Oklahoma City Area was estimated as 53 per 100,000 individuals at risk, while in the Billings Area, the estimated prevalence was nearly twice that, at 115 per 100,000. These rates are considerably higher than those reported in the most recent European studies. CONCLUSION: Chronic arthritis in childhood represents an important, though unrecognized, chronic health challenge within the American Indian population living in the United States

Protection of Mice against Lethal Challenge with 2009 H1N1 Influenza A Virus by 1918-Like and Classical Swine H1N1 Based Vaccines

The recent 2009 pandemic H1N1 virus infection in humans has resulted in nearly 5,000 deaths worldwide. Early epidemiological findings indicated a low level of infection in the older population (>65 years) with the pandemic virus, and a greater susceptibility in people younger than 35 years of age, a phenomenon correlated with the presence of cross-reactive immunity in the older population. It is unclear what virus(es) might be responsible for this apparent cross-protection against the 2009 pandemic H1N1 virus. We describe a mouse lethal challenge model for the 2009 pandemic H1N1 strain, used together with a panel of inactivated H1N1 virus vaccines and hemagglutinin (HA) monoclonal antibodies to dissect the possible humoral antigenic determinants of pre-existing immunity against this virus in the human population. By hemagglutinination inhibition (HI) assays and vaccination/challenge studies, we demonstrate that the 2009 pandemic H1N1 virus is antigenically similar to human H1N1 viruses that circulated from 1918–1943 and to classical swine H1N1 viruses. Antibodies elicited against 1918-like or classical swine H1N1 vaccines completely protect C57B/6 mice from lethal challenge with the influenza A/Netherlands/602/2009 virus isolate. In contrast, contemporary H1N1 vaccines afforded only partial protection. Passive immunization with cross-reactive monoclonal antibodies (mAbs) raised against either 1918 or A/California/04/2009 HA proteins offered full protection from death. Analysis of mAb antibody escape mutants, generated by selection of 2009 H1N1 virus with these mAbs, indicate that antigenic site Sa is one of the conserved cross-protective epitopes. Our findings in mice agree with serological data showing high prevalence of 2009 H1N1 cross-reactive antibodies only in the older population, indicating that prior infection with 1918-like viruses or vaccination against the 1976 swine H1N1 virus in the USA are likely to provide protection against the 2009 pandemic H1N1 virus. This data provides a mechanistic basis for the protection seen in the older population, and emphasizes a rationale for including vaccination of the younger, naïve population. Our results also support the notion that pigs can act as an animal reservoir where influenza virus HAs become antigenically frozen for long periods of time, facilitating the generation of human pandemic viruses

Gene expression profiles in rat mesenteric lymph nodes upon supplementation with Conjugated Linoleic Acid during gestation and suckling

Background Diet plays a role on the development of the immune system, and polyunsaturated fatty acids can modulate the expression of a variety of genes. Human milk contains conjugated linoleic acid (CLA), a fatty acid that seems to contribute to immune development. Indeed, recent studies carried out in our group in suckling animals have shown that the immune function is enhanced after feeding them with an 80:20 isomer mix composed of c9,t11 and t10,c12 CLA. However, little work has been done on the effects of CLA on gene expression, and even less regarding immune system development in early life. Results The expression profile of mesenteric lymph nodes from animals supplemented with CLA during gestation and suckling through dam's milk (Group A) or by oral gavage (Group B), supplemented just during suckling (Group C) and control animals (Group D) was determined with the aid of the specific GeneChip® Rat Genome 230 2.0 (Affymettrix). Bioinformatics analyses were performed using the GeneSpring GX software package v10.0.2 and lead to the identification of 89 genes differentially expressed in all three dietary approaches. Generation of a biological association network evidenced several genes, such as connective tissue growth factor (Ctgf), tissue inhibitor of metalloproteinase 1 (Timp1), galanin (Gal), synaptotagmin 1 (Syt1), growth factor receptor bound protein 2 (Grb2), actin gamma 2 (Actg2) and smooth muscle alpha actin (Acta2), as highly interconnected nodes of the resulting network. Gene underexpression was confirmed by Real-Time RT-PCR. Conclusions Ctgf, Timp1, Gal and Syt1, among others, are genes modulated by CLA supplementation that may have a role on mucosal immune responses in early life

Gene expression profiles in rat mesenteric lymph nodes upon supplementation with Conjugated Linoleic Acid during gestation and suckling

Background Diet plays a role on the development of the immune system, and polyunsaturated fatty acids can modulate the expression of a variety of genes. Human milk contains conjugated linoleic acid (CLA), a fatty acid that seems to contribute to immune development. Indeed, recent studies carried out in our group in suckling animals have shown that the immune function is enhanced after feeding them with an 80:20 isomer mix composed of c9,t11 and t10,c12 CLA. However, little work has been done on the effects of CLA on gene expression, and even less regarding immune system development in early life. Results The expression profile of mesenteric lymph nodes from animals supplemented with CLA during gestation and suckling through dam's milk (Group A) or by oral gavage (Group B), supplemented just during suckling (Group C) and control animals (Group D) was determined with the aid of the specific GeneChip® Rat Genome 230 2.0 (Affymettrix). Bioinformatics analyses were performed using the GeneSpring GX software package v10.0.2 and lead to the identification of 89 genes differentially expressed in all three dietary approaches. Generation of a biological association network evidenced several genes, such as connective tissue growth factor (Ctgf), tissue inhibitor of metalloproteinase 1 (Timp1), galanin (Gal), synaptotagmin 1 (Syt1), growth factor receptor bound protein 2 (Grb2), actin gamma 2 (Actg2) and smooth muscle alpha actin (Acta2), as highly interconnected nodes of the resulting network. Gene underexpression was confirmed by Real-Time RT-PCR. Conclusions Ctgf, Timp1, Gal and Syt1, among others, are genes modulated by CLA supplementation that may have a role on mucosal immune responses in early life

The intrinsic alignment of red galaxies in DES Y1 redMaPPer galaxy clusters

Clusters of galaxies trace the most non-linear peaks in the cosmic density field. The weak gravitational lensing of background galaxies by clusters can allow us to infer their masses. However, galaxies associated with the local environment of the cluster can also be intrinsically aligned due to the local tidal gradient, contaminating any cosmology derived from the lensing signal. We measure this intrinsic alignment in Dark Energy Survey (DES) Year 1 REDMAPPER clusters. We find evidence of a non-zero mean radial alignment of galaxies within clusters between redshifts 0.1–0.7. We find a significant systematic in the measured ellipticities of cluster satellite galaxies that we attribute to the central galaxy flux and other intracluster light. We attempt to correct this signal, and fit a simple model for intrinsic alignment amplitude (AIA) to the measurement, finding AIA = 0.15 ± 0.04, when excluding data near the edge of the cluster. We find a significantly stronger alignment of the central galaxy with the cluster dark matter halo at low redshift and with higher richness and central galaxy absolute magnitude (proxies for cluster mass). This is an important demonstration of the ability of large photometric data sets like DES to provide direct constraints on the intrinsic alignment of galaxies within clusters. These measurements can inform improvements to small-scale modelling and simulation of the intrinsic alignment of galaxies to help improve the separation of the intrinsic alignment signal in weak lensing studies