slfm: An R Package to Evaluate Coherent Patterns in Microarray Data via Factor Analysis

The development of simulation-based methods, such as Markov chain Monte Carlo (MCMC), has contributed to an increased interest in the Bayesian framework as an alternative to deal with factor models. Many studies have used Bayesian factor analysis to explore gene expression data. We are particularly interested in the application of a sparse latent factor model (SLFM) based on sparsity priors (mixtures) to assess the significance of factors. The SLFM measures how strong the observed coherent expression pattern is in the data, which is an important source of information to evaluate gene activity. In the literature, this type of model has shown better results than other approaches intended for identification of patterns and metagene groups related to the underlying biology. However, a full Bayesian factor model relying on MCMC algorithms has an expensive computational cost, which makes it unattractive for general users. In this paper, we present the package slfm which uses C++ implementation via Rcpp to improve the computational performance of the SLFM within the widely used statistical tool R. We investigate real and simulated microarray data related to breast cancer

pexm: A JAGS Module for Applications Involving the Piecewise Exponential Distribution

In this study, we present a new module built for users interested in a programming language similar to BUGS to fit a Bayesian model based on the piecewise exponential (PE) distribution. The module is an extension to the open-source program JAGS by which a Gibbs sampler can be applied without requiring the derivation of complete conditionals and the subsequent implementation of strategies to draw samples from unknown distributions. The PE distribution is widely used in the fields of survival analysis and reliability. Currently, it can only be implemented in JAGS through methods to indirectly specify the likelihood based on the Poisson or Bernoulli probabilities. Our module provides a more straightforward implementation and is thus more attractive to the researchers aiming to spend more time exploring the results from the Bayesian inference rather than implementing the Markov Chain Monte Carlo algorithm. For those interested in extending JAGS, this work can be seen as a tutorial including important information not well investigated or organized in other materials. Here, we describe how to use the module taking advantage of the interface between R and JAGS. A short simulation study is developed to ensure that the module behaves well and a real illustration, involving two PE models, exhibits a context where the module can be used in practice

Improved production of lutein and β-carotene by thermal and light intensity upshifts in the marine microalga Tetraselmis sp. CTP4

The industrial microalga Tetraselmis sp. CTP4 is a promising candidate for aquaculture feed, novel food, cosmeceutical and nutraceutical due to its balanced biochemical profile. To further upgrade its biomass value, carotenogenesis was investigated by testing four environmental factors, namely temperature, light intensity, salinity and nutrient availability over different growth stages. The most important factor for carotenoid induction in this species is a sufficient supply of nitrates leading to an exponential growth of the cells. Furthermore, high temperatures of over 30 degrees C compared to lower temperatures (10 and 20 degrees C) induced the accumulation of carotenoids in this species. Remarkably, the two different branches of carotenoid synthesis were regulated depending on different light intensities. Contents of beta-carotene were 3-fold higher under low light intensities (33 mu mol m(-2) s(-1)) while lutein contents increased 1.5-fold under higher light intensities (170 and 280 mu mol m(-2) s(-1)). Nevertheless, highest contents of carotenoids (8.48 +/- 0.47 mg g(-1) DW) were found upon a thermal upshift from 20 degrees C to 35 degrees C after only two days at a light intensity of 170 mu mol m(-2) s(-1). Under these conditions, high contents of both lutein and beta-carotene were reached accounting for 3.17 +/- 0.18 and 3.21 +/- 0.18 mg g(-1) DW, respectively. This study indicates that Tetraselmis sp. CTP4 could be a sustainable source of lutein and beta-carotene at locations where a robust, euryhaline, thermotolerant microalgal strain is required.Funding Agency Portuguese Foundation for Science and Technology UID/Multi/04326/2019 SFRH/BD/115325/2016 SFRH/BD/140143/2018 SFRH/BD/105541/2014 0055 ALGARED+ 05 INTERREG V-A -Espana Portugal project national Portuguese funding PPBI-POCI-01-0145-FEDER-22122 Nord Universityinfo:eu-repo/semantics/publishedVersio

Impact of Caffeine Consumption on Type 2 Diabetes-Induced Spatial Memory Impairment and Neurochemical Alterations in the Hippocampus

Diabetes affects the morphology and plasticity of the hippocampus, and leads to learning and memory deficits. Caffeine has been proposed to prevent memory impairment upon multiple chronic disorders with neurological involvement. We tested whether long-term caffeine consumption prevents type 2 diabetes (T2D)-induced spatial memory impairment and hippocampal alterations, including synaptic degeneration, astrogliosis, and metabolic modifications. Control Wistar rats and Goto-Kakizaki (GK) rats that develop T2D were treated with caffeine (1 g/L in drinking water) for 4 months. Spatial memory was evaluated in a Y-maze. Hippocampal metabolic profile and glucose homeostasis were investigated by 1H magnetic resonance spectroscopy. The density of neuronal, synaptic, and glial-specific markers was evaluated by Western blot analysis. GK rats displayed reduced Y-maze spontaneous alternation and a lower amplitude of hippocampal long-term potentiation when compared to controls, suggesting impaired hippocampal-dependent spatial memory. Diabetes did not impact the relation of hippocampal to plasma glucose concentrations, but altered the neurochemical profile of the hippocampus, such as increased in levels of the osmolites taurine (P < 0.001) and myo-inositol (P < 0.05). The diabetic hippocampus showed decreased density of the presynaptic proteins synaptophysin (P < 0.05) and SNAP25 (P < 0.05), suggesting synaptic degeneration, and increased GFAP (P < 0.001) and vimentin (P < 0.05) immunoreactivities that are indicative of astrogliosis. The effects of caffeine intake on hippocampal metabolism added to those of T2D, namely reducing myo-inositol levels (P < 0.001) and further increasing taurine levels (P < 0.05). Caffeine prevented T2D-induced alterations of GFAP, vimentin and SNAP25, and improved memory deficits. We conclude that caffeine consumption has beneficial effects counteracting alterations in the hippocampus of GK rats, leading to the improvement of T2D-associated memory impairment

Sphingosine 1-phoshpate receptors are located in synapses and control spontaneous activity of mouse neurons in culture

Sphingosine-1-phosphate (S1P) is best known for its roles as vascular and immune regulator. Besides, it is also present in the central nervous system (CNS) where it can act as neuromodulator via five S1P receptors (S1PRs), and thus control neurotransmitter release. The distribution of S1PRs in the active zone and postsynaptic density of CNS synapses remains unknown. In the current study, we investigated the localization of S1PR1-5 in synapses of the mouse cortex. Cortical nerve terminals purified in a sucrose gradient were endowed with all five S1PRs. Further subcellular fractionation of cortical nerve terminals revealed S1PR2 and S1PR4 immunoreactivity in the active zone of presynaptic nerve terminals. Interestingly, only S1PR2 and S1PR3 immunoreactivity was found in the postsynaptic density. All receptors were present outside the active zone of nerve terminals. Neurons in the mouse cortex and primary neurons in culture showed immunoreactivity against all five S1PRs, and Ca 2+ imaging revealed that S1P inhibits spontaneous neuronal activity in a dose-dependent fashion. When testing selective agonists for each of the receptors, we found that only S1PR1, S1PR2 and S1PR4 control spontaneous neuronal activity. We conclude that S1PR2 and S1PR4 are located in the active zone of nerve terminals and inhibit neuronal activity. Future studies need to test whether these receptors modulate stimulation-induced neurotransmitter release

Neurochemical Modifications in the Hippocampus, Cortex and Hypothalamus of Mice Exposed to Long-Term High-Fat Diet

Metabolic syndrome and diabetes impact brain function and metabolism. While it is well established that rodents exposed to diets rich in saturated fat develop brain dysfunction, contrasting results abound in the literature, likely as result of exposure to different high-fat diet (HFD) compositions and for varied periods of time. In the present study, we investigated alterations of hippocampal-dependent spatial memory by measuring Y-maze spontaneous alternation, metabolic profiles of the hippocampus, cortex and hypothalamus by 1H magnetic resonance spectroscopy (MRS), and levels of proteins specific to synaptic and glial compartments in mice exposed for 6 months to different amounts of fat (10, 45, or 60% of total energy intake). Increasing the dietary amount of fat from 10 to 45% or 60% resulted in obesity accompanied by increased leptin, fasting blood glucose and insulin, and reduced glucose tolerance. In comparison to controls (10%-fat), only mice fed the 60%-fat diet showed increased fed glycemia, as well as plasma corticosterone that has a major impact on brain function. HFD-induced metabolic profile modifications measured by 1H MRS were observed across the three brain areas in mice exposed to 60%- but not 45%-fat diet, while both HFD groups displayed impaired hippocampal-dependent memory. HFD also affected systems involved in neuro- or gliotransmission in the hippocampus. Namely, relative to controls, 60%-fat-fed mice showed reduced SNAP-25, PSD-95 and syntaxin-4 immunoreactivity, while 45%-fat-fed mice showed reduced gephyrin and syntaxin-4 immunoreactivity. For both HFD levels, reductions of the vesicular glutamate transporter vGlut1 and levels of the vesicular GABA transporter were observed in the hippocampus and hypothalamus, relative to controls. Immunoreactivity against GFAP and/or Iba-1 in the hypothalamus was higher in mice exposed to HFD than controls, suggesting occurrence of gliosis. We conclude that different levels of dietary fat result in distinct neurochemical alterations in the brain

Density of sphingosine-1-phosphate receptors is altered in cortical nerve-terminals of insulin-resistant Goto-Kakizaki rats and diet-induced obese mice

Sphingosine-1-phosphate (S1P) is a phosphosphingolipid with pleiotropic biological functions. S1P acts as an intracellular second messenger, as well as extracellular ligand to five G-protein coupled receptors (S1PR1-5). In the brain, S1P regulates neuronal proliferation, apoptosis, synaptic activity and neuroglia activation. Moreover, S1P metabolism alterations have been reported in neurodegenerative disorders. We have previously reported that S1PRs are present in nerve terminals, exhibiting distinct sub-synaptic localization and neuromodulation actions. Since type 2 diabetes (T2D) causes synaptic dysfunction, we hypothesized that S1P signaling is modified in nerve terminals. In this study, we determined the density of S1PRs in cortical synaptosomes from insulin-resistant Goto-Kakizaki (GK) rats and Wistar controls, and from mice fed a high-fat diet (HFD) and low-fat-fed controls. Relative to their controls, GK rats showed similar cortical S1P concentration despite higher S1P levels in plasma, yet lower density of S1PR1, S1PR2 and S1PR4 in nerve-terminal-enriched membranes. HFD-fed mice exhibited increased plasma and cortical concentrations of S1P, and decreased density of S1PR1 and S1PR4. These findings point towards altered S1P signaling in synapses of insulin resistance and diet-induced obesity models, suggesting a role of S1P signaling in T2D-associated synaptic dysfunction

DC-DC power converter for high power solar photovoltaic system

Worldwide there is an enormous dependence on fossil fuels to produce electricity. Burning fossil fuels results in CO2 emission into the atmosphere, causing a negative environmental impact. In order to mitigate these problems, there is a need to integrate renewable energy sources into the power grid, namely solar photovoltaic (PV) energy. Power electronics converter solutions for solar PV module interface are vast and have advantages and disadvantages depending on the purpose. In addition, when the purpose is efficiency, it is important to consider the choice of the most appropriate power semiconductors. This paper presents a study, sizing, and development of a DC-DC power converter for high-power solar PV applications. In this study, a DC-DC boost interleaved power converter with two arms controlled by an incremental conductance Maximum Power Point Tracking (MPPT) control algorithm is proposed. The MPPT is combined with a Proportional-Integral (PI) controller for individual control of the current on each arm and was applied to extract the maximum power available at the solar PV module for different solar radiation and temperature conditions. The digital control system was implemented in a TMS320F28335 microcontroller from Texas Instruments.This work has been supported by FCT – Fundação para a Ciência e Tecnologia within the R&D Units Project Scope: UIDB/00319/2020. This work has been supported by the MEGASOLAR Project POCI-01-0247-FEDER-047220. Mr. Luis A. M. Barros is supported by the doctoral scholarship PD/BD/143006/2018 granted by the Portuguese FCT foundation

How Energy Metabolism Supports Cerebral Function: Insights from 13C Magnetic Resonance Studies In vivo

Cerebral function is associated with exceptionally high metabolic activity, and requires continuous supply of oxygen and nutrients from the blood stream. Since the mid-20th century the idea that brain energy metabolism is coupled to neuronal activity has emerged, and a number of studies supported this hypothesis. Moreover, brain energy metabolism was demonstrated to be compartmentalized in neurons and astrocytes, and astrocytic glycolysis was proposed to serve the energetic demands of glutamatergic activity. Shedding light on the role of astrocytes in brain metabolism, the earlier picture of astrocytes being restricted to a scaffold-associated function in the brain is now out of date. With the development and optimization of non-invasive techniques, such as nuclear magnetic resonance spectroscopy (MRS), several groups have worked on assessing cerebral metabolism in vivo. In this context, 1H MRS has allowed the measurements of energy metabolism-related compounds, whose concentrations can vary under different brain activation states. 1H-[13C] MRS, i.e. indirect detection of signals from 13C-coupled 1H, together with infusion of 13C-enriched glucose has provided insights into the coupling between neurotransmission and glucose oxidation. Although these techniques tackle the coupling between neuronal activity and metabolism, they lack chemical specificity and fail in providing information on neuronal and glial metabolic pathways underlying those processes. Currently, the improvement of detection modalities (i.e. direct detection of 13C isotopomers), the progress in building adequate mathematical models along with the increase in magnetic field strength now available, render possible detailed compartmentalized metabolic flux characterization. In particular, direct 13C MRS offers more detailed dataset acquisitions and provide information on metabolic interactions between neurons and astrocytes, and their role in supporting neurotransmission. Here we review state-of-the-art MR methods to study brain function and metabolism in vivo, and their contribution to the current understanding of how astrocytic energy metabolism supports glutamatergic activity and cerebral function. In this context, recent data suggests that astrocytic metabolism has been underestimated. Namely, the rate of oxidative metabolism in astrocytes is about half of that in neurons, and it can increase as much as the rate of neuronal metabolism in response to somatosensory stimulation

Population distribution of six PCR-amplified loci in Madeira Archipelago (Portugal)

Frequency data of the short tandem repeat (STR) loci HUMTH01, HUMVWA31/A, HUMF13A1, HUMFES/FPS, D12S391 and HUMFIBRA/FGA were determined in blood stains obtained from a population of unrelated individuals from the Madeira Archipelago. The observed genotype distribution showed no significant deviation from the Hardy-Weinberg equilibrium and there was no evidence for association of alleles among the six loci. Population data showed a combined discrimination power of 0.9999998 and a chance of exclusion of 0.99597. The frequencies are similar to those of other compared caucasian populations but significant differences were found between the Madeira population and Japanese, Chinese, Greenland Eskimos and Quechua Amerindians. The six loci studied, together proved to be highly discriminating and valuable for forensic cases.http://www.sciencedirect.com/science/article/B6T6W-3W4GJ8F-8/1/69f0571183c0d939b9244a0841a1802