Clustering high-dimensional mixed data to uncover sub-phenotypes: joint analysis of phenotypic and genotypic data.

The LIPGENE-SU.VI.MAX study, like many others, recorded high-dimensional continuous phenotypic data and categorical genotypic data. LIPGENE-SU.VI.MAX focuses on the need to account for both phenotypic and genetic factors when studying the metabolic syndrome (MetS), a complex disorder that can lead to higher risk of type 2 diabetes and cardiovascular disease. Interest lies in clustering the LIPGENE-SU.VI.MAX participants into homogeneous groups or sub-phenotypes, by jointly considering their phenotypic and genotypic data, and in determining which variables are discriminatory. A novel latent variable model that elegantly accommodates high dimensional, mixed data is developed to cluster LIPGENE-SU.VI.MAX participants using a Bayesian finite mixture model. A computationally efficient variable selection algorithm is incorporated, estimation is via a Gibbs sampling algorithm and an approximate BIC-MCMC criterion is developed to select the optimal model. Two clusters or sub-phenotypes ('healthy' and 'at risk') are uncovered. A small subset of variables is deemed discriminatory, which notably includes phenotypic and genotypic variables, highlighting the need to jointly consider both factors. Further, 7 years after the LIPGENE-SU.VI.MAX data were collected, participants underwent further analysis to diagnose presence or absence of the MetS. The two uncovered sub-phenotypes strongly correspond to the 7-year follow-up disease classification, highlighting the role of phenotypic and genotypic factors in the MetS and emphasising the potential utility of the clustering approach in early screening. Additionally, the ability of the proposed approach to define the uncertainty in sub-phenotype membership at the participant level is synonymous with the concepts of precision medicine and nutrition. Copyright © 2017 John Wiley & Sons, Ltd.

A gene variation (rs12691) in the CCAT/enhancer binding protein α modulates glucose metabolism in metabolic syndrome.

BACKGROUND AND AIMS: CCAAT/enhancer-binding protein alpha (CEBPA) is a transcription factor involved in adipogenesis and energy homeostasis. Caloric restriction reduces CEBPA protein expression in patients with metabolic syndrome (MetS). A previous report linked rs12691 SNP in CEBPA to altered concentration of fasting triglycerides. Our objective was to assess the effects of rs12691 in glucose metabolism in Metabolic Syndrome (MetS) patients. METHODS AND RESULTS: Glucose metabolism was assessed by static (glucose, insulin, adiponectin, leptin and resistin plasma concentrations) and dynamic (disposition index, insulin sensitivity index, HOMA-IR and acute insulin response to glucose) indices, performed at baseline and after 12 weeks of 4 dietary interventions (high saturated fatty acid (SFA), high monounsaturated fatty acid (MUFA), low-fat and low-fat-high-n3 polyunsaturated fatty acid (PUFA)) in 486 subjects with MetS. Carriers of the minor A allele of rs12691 had altered disposition index (p = 0.0003), lower acute insulin response (p = 0.005) and a lower insulin sensitivity index (p = 0.025) indicating a lower insulin sensitivity and a lower insulin secretion, at baseline and at the end of the diets. Furthermore, A allele carriers displayed lower HDL concentration. CONCLUSION: The presence of the A allele of rs12691 influences glucose metabolism of MetS patients.

The brainstem localization of gastric preganglionic parasympathetic neurons in the agouti (Dasyprocta leporina).

This study was designed to determine qualitatively, the source of gastric vagal nerve fibres in the Agouti. A total of 18 male and female adult agoutis were used for the present investigation. Following anaesthesia, laparotomy was performed and the stomach exteriorized. Multiple intramuscular injections of wheat germ agglutinin-horseradish peroxidase (WGA-HRP) were then made into different areas of the stomach in the experimental animals. The control animals were divided into four groups of two animals each. The first group had intraperitoneal injection of the tracer, the second had intramuscular injection of normal saline, the third group had injection of tracer into the hepatic portal vein and the last group had injection of the tracer into the gastric walls followed immediately by bilateral vagotomy. Following a survival period of five to seven days, the animals were sacrificed by transcardial perfusion, first with normal saline followed by fixative and finally with 20% buffered sucrose. Following perfusion, the brainstem was extracted from the brain, immersed in 20% buffered sucrose and kept refrigerated overnight for cryoprotection. The brainstems were subsequently sectioned serially, processed for WGA-HRP neurohistochemistry and then analysed under light and dark-field illuminations. The analysis of the sections taken from the experimental animals revealed bilateral presence of WGA-HRP labelled neurons in the dorsal motor nucleus of the vagus nerve (DMNV) and the nucleus ambiguus (nA) of the medulla oblongata. No labelled neurons were seen in any of the sections taken from the control animals. The implications of the findings are discussed.

The organization of the brainstem nuclei associated with the vagus nerve in the Agouti (Dasyprocta leporina). A neurohistological study.

A total of six adult animals were used for the study. Following anaesthesia via intraperitoneal injection of a mixture of ketamin and bombazine in ratio 2:1, thoracotomy was performed to exteriorize the heart for intracardial perfusion. The perfusion canular was inserted into the left ventricle and animal perfused sequentially with normal saline and 10% formal saline. Following perfusion, craniotomy was performed to remove the entire brain along with the upper segments of the spinal cord. The brain specimen was then dehydrated, cleared and infiltrated with paraffin wax. The specimen was then cut in 15 micron thick serial sections. The sections were then processed for neurohistological analyses using a Nikon microscope to which was attached Nikon camera. Analyses of the sections revealed bilateral representation of the dorsal motor nucleus of the vagus nerve in the medulla oblongata. The nucleus ambiguus, nucleus of the tractus solitarius, hypoglossal nucleus and the area postrema were also identified in the medulla oblongata. The implications of our findings are discussed in the text of the article.

The Influence of Different Physical Activity Behaviours on the Gut Microbiota of Older Irish Adults.

OBJECTIVE: A 24-hour day is made up of time spent in a range of physical activity (PA) behaviours, including sleep, sedentary time, standing, light-intensity PA (LIPA) and moderate-to-vigorous PA (MVPA), all of which may have the potential to alter an individual's health through various different pathways and mechanisms. This study aimed to explore the relationship between PA behaviours and the gut microbiome in older adults. DESIGN: Cross-sectional study. SETTINGS AND PARTICIPANTS: Participants (n=100; age 69.0 [3.0] years; 44% female) from the Mitchelstown Cohort Rescreen (MCR) Study (2015-2017). METHODS: Participants provided measures of gut microbiome composition (profiled by sequencing 16S rRNA gene amplicons), and objective measures of PA behaviours (by a 7-day wear protocol using an activPAL3 Micro). RESULTS: Standing time was positively correlated with the abundance of butyrate-producing and anti-inflammatory bacteria, including Ruminococcaceae, Lachnospiraceae and Bifidobacterium, MVPA was positively associated with the abundance of Lachnospiraceae bacteria, while sedentary time was associated with lower abundance of Ruminococcaceae and higher abundance of Streptococcus spp. CONCLUSION: Physical activity behaviours appear to influence gut microbiota composition in older adults, with different PA behaviours having diverging effects on gut microbiota composition.

Differential activation of dendritic cells by Toll-like receptor agonists isolated from the Gram-positive vaccine vector Streptococcus gordonii.

The oral commensal bacterium Streptococcus gordonii has been gathering interest as a candidate live mucosal vaccine delivery vector. S. gordonii has been shown to be capable of activating antigen presenting immune cells in a manner which leads to their activation and maturation, yet the mechanism used by S. gordonii to do so is poorly understood. The aim of this work was to investigate the immunostimulatory components of S. gordonii in inducing murine dendritic cell (DC) activation and maturation. Lipoteichoic acid (LTA), lipoprotein (LP), peptidoglycan (PGN), and DNA were isolated from S. gordonii, and used to stimulate murine DC. Cytokine production and DC surface marker upregulation in response to the bacterial components was quantified by enzyme-linked immunosorbent assay and flow cytometry respectively. The results were contrasted against data obtained from DC derived from MyD88, TRIF [TIR(Toll/Interleukin-1 Receptor)-domain-containing adapter-inducing interferon-beta] or toll-like receptor-2 (TLR-2) knockout mice. The four S. gordonii bacterial components were found to differentially induce cytokine production and surface marker upregulation by murine DC. Activation of DC by both whole S. gordonii cells and the four bacterial components was abrogated in the absence of MyD88, but not in the absence of TRIF. LTA, LP and PGN, but not DNA and whole S. gordonii, required TLR-2 to induce a DC response. The results collectively indicate that S. gordonii activates DC predominantly through a MyD88-dependent and TRIF-independent pathway. This activation can be attributed to multiple immunostimulatory components present within S. gordonii bacterial cells.

Teledermatology and underserved populations.

BACKGROUND: The dermatologic needs of many communities in the United States and worldwide are underserved. Telemedicine enables physicians and non-physician primary care providers to use modern telecommunications devices to gain access to specialist consultations promptly and with much less travel. The independently developed telemedicine programs described herein support 3 traditionally underserved populations: Pacific Islanders, migrant farmworkers, and prison inmates. OBSERVATIONS: In 3 independently designed telemedicine programs, dermatology emerged as the specialty most used by remote practitioners. Patients were presented for both diagnosis and treatment and in the setting of initial evaluation and as part of follow-up care. CONCLUSION: Teledermatology is a useful way to provide dermatologic support to remote or underserved communities.

Do people aggress to improve their mood? Catharsis beliefs, affect regulation opportunity, and aggressive responding.

Do people aggress to make themselves feel better? We adapted a procedure used by G. K. Manucia, D. J. Baumann, and R. B. Cialdini (1984), in which some participants are given a bogus mood-freezing pill that makes affect regulation efforts ineffective. In Study 1, people who had been induced to believe in the value of catharsis and venting anger responded more aggressively than did control participants to insulting criticism, but this aggression was eliminated by the mood-freezing pill. Study 2 showed similar results among people with high anger-out (i.e., expressing and venting anger) tendencies. Studies 3 and 4 provided questionnaire data consistent with these interpretations, and Study 5 replicated the findings of Studies 1 and 2 using measures more directly concerned with affect regulation. Taken together, these results suggest that many people may engage in aggression to regulate (improve) their own affective states.

A new method for monitoring the kinetics of calcium binding to the sarcoplasmic reticulum Ca(2+)-ATPase employing the flash-photolysis of caged-calcium.

The kinetics of Ca2+ binding to the high-affinity sites of the sarcoplasmic reticulum (SR) Ca2(+)-ATPase were directly investigated by continuously monitoring the extravesicular calcium concentration via the metallochromic indicator Arsenazo III following the release of Ca2+ from a photolabile caged-calcium molecule, 1-(2-nitro-4,5-dimethoxyphenyl)-N,N,N',N'-tetrakis [(oxycarbony)methyl]-1,2-ethanediamine (DM-nitrophen), utilizing a pulsed Nd:YAG laser for photolysis. The nature of the binding kinetics is at least biphasic over the first 400 ms for vesicular dispersions of SR. The stoichiometry for calcium binding expressed as Ca:E1 approximately P has been calculated to be approximately 1.4:1 for the pure SR preparation under the reaction conditions employed.

The role of religion in predicting adolescent alcohol use and problem drinking.

OBJECTIVE: There are racial differences in adolescents' propensity to consume alcohol--with white adolescents tending to consume more alcohol than black adolescents--but there is no clear explanation for why such differences exist. The purpose of this study was to examine the relationship between religiosity, a cultural factor that is not well understood currently, and racial differences in adolescent alcohol use. METHOD: Participants were white and black ninth-grade adolescents (N = 899; 54% female, 57.5% white) involved in a 3-year longitudinal study of ways to reduce alcohol use and sexual risk-taking behavior among adolescents in Ohio and Kentucky. RESULTS: Findings indicate that religiosity is differentially associated with alcohol use and problem drinking for white and black adolescents. Religious service attendance was the most significant predictor of alcohol use for black adolescents, whereas religious fundamentalism was most important for white adolescents. In contrast, frequency of prayer was the significant predictor of problem drinking for black adolescents, whereas the level of importance placed on religion was the significant predictor for white adolescents. Important gender differences also emerged in both prediction models and are discussed. CONCLUSIONS: Since there is great heterogeneity among adolescents (in terms of race and gender) in their alcohol use and misuse, the "one-size-fits-all" approach to alcohol treatment and prevention is likely inappropriate. Moreover, conceptualizations of alcohol use and misuse, and its prevention and treatment, should include the consideration of such key cultural factors as religiosity.

Oral lesions in patients with psoriasis: a controlled study.

Stomatitis areata migrans was found in 5.4 percent of patients with psoriasis compared to 1 percent of control patients, while benign migratory glossitis was identified in 10.3 percent of patients with psoriasis and 2.5 percent of control patients. The association of these disorders with psoriasis indicates that they may be manifestations of psoriasis of the oral mucosa.

Pleiotropic effects of TCF7L2 gene variants and its modulation in the metabolic syndrome: from the LIPGENE study.

AIMS/HYPOTHESIS: Variants of the TCF7L2 gene predict the development of type 2 diabetes mellitus (T2DM). We investigated the associations between gene variants of TCF7L2 and clinical features of the metabolic syndrome (MetS) (an entity often preceding T2DM), and their interaction with non-genetic factors, including plasma saturated fatty acids (SFA) concentration and insulin resistance (IR). METHODS: Fasting lipid profiles, insulin sensitivity, insulin secretion, anthropometrics, blood pressure and 10 gene variations of the TCF7L2 gene were determined in 450 subjects with MetS. RESULTS: Several single nucleotide polymorphisms (SNP) showed phenotypic associations independent of SFA or IR. Carriers of the rare T allele of rs7903146, and of three other SNPs in linkage disequilibrium with rs7903146, had lower blood pressure and insulin secretion. High IR and the presence of the T-allele of rs7903146 acted synergistically to define those with reduced insulin secretion. Carriers of the minor allele of rs290481 exhibited an altered lipid profile, with increased plasma levels of apolipoprotein B, non-esterified fatty acids, cholesterol and apolipoprotein B in triglyceride rich lipoproteins, and LDL cholesterol. Carriers of the minor allele of rs11196224 that had higher plasma SFA levels showed elevated procoagulant/proinflammatory biomarkers, impaired insulin secretion and increased IR, whereas carriers of the minor allele of rs17685538 with high plasma SFA levels exhibited higher blood pressure. CONCLUSIONS/INTERPRETATION: SNP in the TCF7L2 gene are associated with differences in insulin secretion, blood pressure, blood lipids and coagulation in MetS patients, and may be modulated by SFA in plasma or IR.

Breast reconstruction after classic radical mastectomy: use of omental pedicled grafts and fascia lata.

The omental pedicle graft is a technic developed to replace tissues removed by classic radical mastectomies in preparation for constructing a new breast. The graft and the reconstruction may be done in one stage. The advantages of the technic are (1) the tissue is readily available, (2) it can be done in one or two stages, and (3) it provides improved esthetic results. During the past eight years, I have used this technic for breast reconstruction in 24 cases.

Ultrafast thermally induced unfolding of RNase A.

A temperature jump (T-jump) method capable of initiating thermally induced processes on the picosecond time scale in aqueous solutions is introduced. Protein solutions are heated by energy from a laser pulse that is absorbed by homogeneously dispersed molecules of the dye crystal violet. These act as transducers by releasing the energy as heat to cause a T-jump of up to 10 K with a time resolution of 70 ps. The method was applied to the unfolding of RNase A. At pH 5.7 and 59 degrees C, a T-jump of 3-6 K induced unfolding which was detected by picosecond transient infrared spectroscopy of the amide I region between 1600 and 1700 cm-1. The difference spectral profile at 3.5 ns closely resembled that found for the equilibrium (native-unfolded) states. The signal at 1633 cm-1, corresponding to the beta-sheet structure, achieved 15 +/- 2% of the decrease found at equilibrium, within 5.5 ns. However, no decrease in absorbance was detected until 1 ns after the T-ump. The disruption of beta-sheet therefore appears to be subject to a delay of approximately 1 ns. Prior to 1 ns after the T-jump, water might be accessing the intact hydrophobic regions.

Efficient optical waveguide coupler.

A new method for high-efficiency interconnection of two planar optical waveguides is described. This technique is based on mode-matched coupling and is particularly useful when the difference between the refractive indices of the individual guides is large. The method consists of etching a deep vertical step in the highindex waveguide followed by the deposition of low-index waveguide on the etched section so that the two guides remain connected end to end. A theoretical treatment for the design of the coupler and for determination of fabricational tolerences is given. Couplers were fabricted using high-index waveguides like GaAs and LiNbO(3) and low-index waveguides made up of glass or solution-deposited (polyurethane or photoresist) films on SiO(2) substrate. It is shown that by controlling the junction profile, efficiencies close to theoretical values can be obtained. Some applications of such a coupler are given.

Reactions of excited triplet states of metal substituted myoglobin with dioxygen and quinone.

The triplet state absorption and phosphorescence of Zn and Pd derivatives of myoglobin were compared. Both metal derivatives exhibit long triplet state lifetimes at room temperature, but whereas the Pd derivative showed exponential decay and an isosbestic point in the transient absorption spectra, the decay of the Zn derivative was nonsingle exponential and the transient absorption spectra showed evidence of more than one excited state species. No difference was seen in triplet quenching by oxygen for either derivative, indicating that differences in the polypeptide chain between the two derivatives are not large enough to affect oxygen penetrability. Quenching was also observed by anthraquinone sulfonate. In this case, the possibility of long-range transfer by an exchange mechanism is considered.

Excited states of tryptophan in cod parvalbumin. Identification of a short-lived emitting triplet state at room temperature.

The fluorescence and phosphorescence spectra of model indole compounds and of cod parvalbumin III, a protein containing a single tryptophan and no tyrosine, were examined in the time scale ranging from subnanoseconds to milliseconds at 25 degrees C in aqueous buffer. For both Ca- bound and Ca-free parvalbumin and for model indole compounds that contained a proton donor, a phosphorescent species emitting at 450 nm with a lifetime of approximately 20-40 ns could be identified. A longer-lived phosphorescence is also apparent; it has approximately the same absorption and emission spectrum as the short-lived triplet molecule. For Ca parvalbumin, the decay of the long-lived triplet tryptophan is roughly exponential with a lifetime of 4.7 ms at 25 degrees C whereas for N-acetyltryptophanamide in aqueous buffer the decay lifetime was 30 microseconds. In contrast, the lifetime of the long-lived tryptophan species is much shorter in the Ca-free protein compared with Ca parvalbumin, and the decay shows complex nonexponential kinetics over the entire time range from 100 ns to 1 ms. It is concluded that the photochemistry of tryptophan must take into account the existence of two excited triplet species and that there are quenching moieties within the protein matrix that decrease the phosphorescence yield in a dynamic manner for the Ca-depleted parvalbumin. In contrast, for Ca parvalbumin, the tryptophan site is rigid on the time scale of milliseconds.

Phenylalanine fluorescence and phosphorescence used as a probe of conformation for cod parvalbumin.

The fluorescence emission and triplet absorption properties of phenylalanine in cod fish parvalbumin type II, a protein that contains no Trp or Tyr, was examined in the time scale ranging from nanoseconds to microseconds at 25°C in aqueous buffer (pH 7.0). In the presence of Ca(II), the decay of fluorescence gave two lifetimes (5.9 and 53 ns) and the triplet lifetime was 425 µs. Upon removal of Ca, the fluorescence intensity decreased to values approaching that for free Phe, while the longest fluorescence decay component was 17 ns. At the same time, the decay of triplet showed complex nonexponential kinetics with decay rates faster than in the presence of Ca. Quenching and denaturation analyses suggest that the Phe's are present in a hydrophobic environment in the Ca-bound protein but that the Ca-free protein is relatively unstructured. It is concluded that Phe luminescence in proteins is sensitive to conformation and that the long lifetime of Phe excited states needs to be considered when studying its photochemistry in proteins.