metaXCMS: second-order analysis of untargeted metabolomics data

Mass spectrometry-based untargeted metabolomics often results in the observation of hundreds to thousands of features that are differentially regulated between sample classes. A major challenge in interpreting the data is distinguishing metabolites that are causally associated with the phenotype of interest from those that are unrelated but altered in downstream pathways as an effect. To facilitate this distinction, here we describe new software called metaXCMS for performing second-order ("meta") analysis of untargeted metabolomics data from multiple sample groups representing different models of the same phenotype. While the original version of XCMS was designed for the direct comparison of two sample groups, metaXCMS enables meta-analysis of an unlimited number of sample classes to facilitate prioritization of the data and increase the probability of identifying metabolites causally related to the phenotype of interest. metaXCMS is used to import XCMS results that are subsequently filtered, realigned, and ultimately compared to identify shared metabolites that are up- or down-regulated across all sample groups. We demonstrate the software's utility by identifying histamine as a metabolite that is commonly altered in three different models of pain. metaXCMS is freely available at http://metlin.scripps.edu/metaxcms/.     

Automated iterative MS/MS acquisition: a tool for improving efficiency of protein identification using a LC-MALDI MS workflow

We have developed an information-dependent, iterative MS/MS acquisition (IMMA) tool for improving MS/MS efficiency, increasing proteome coverage, and shortening analysis time for high-throughput proteomics applications based on the LC-MALDI MS/MS platform. The underlying principle of IMMA is to limit MS/MS analyses to a subset of molecular ions that are likely to identify a maximum number of proteins. IMMA reduces redundancy of MS/MS analyses by excluding from the precursor ion peak lists proteotypic peptides derived from the already identified proteins and uses a retention time prediction algorithm to limit the degree of false exclusions. It also increases the utilization rate of MS/MS spectra by removing "low value" unidentifiable targets like nonpeptides and peptides carrying large loads of modifications, which are flagged by their "nonpeptide" excess-to-nominal mass ratios. For some samples, IMMA increases the number of identified proteins by ～20-40% when compared to the data dependent methods. IMMA terminates an MS/MS run at the operator-defined point when "costs" (e.g., time of analysis) start to overrun "benefits" (e.g., number of identified proteins), without prior knowledge of sample contents and complexity. To facilitate analysis of closely related samples, IMMA's inclusion list functionality is currently under development.     

Evaluation of sensory attributes of coffee brews from robusta coffee roasted under different conditions

Robusta coffee beans with a different initial moisture of 5, 7.5 and 10% were convectively roasted at 230 °C, microwaved at 700 W, and roasted by the coupled convective-microwave method. Sensory attributes of brews prepared from these coffee samples were evaluated. Final temperature of microwaved coffee beans was lower than that of the beans processed by the two other methods, which resulted in a higher content of volatile aroma compounds and a lesser degree of charring of their surface. Lower initial humidity of coffee beans shortened the time of roasting. However, the aroma developed upon roasting of the moistest beans was the most intense and pleasant. Modification of roasting conditions increased shifting of the overall acceptability of coffee infusions by 2 points in a 10-point hedonic scale, which implies that, if roasting conditions are adequate to the type of coffee, its sensory characteristics can be improved. Thus, optimization of roasting parameters can increase the share of robusta in well-accepted commercial coffee blends, a convenient fact because of the significant difference in price between the latter and arabica coffee.     

Development and Comprehensive Characteristics of Thermosensitive Liquid Suppositories of Metoprolol Based on Poly(lactide-co-glycolide) Nanoparticles

Thermosensitive liquid suppositories (LSs) carrying the model antihypertensive drug metoprolol tartrate (MT) were developed and evaluated. The fundamental purpose of this work was to produce, for the first time, liquid MT suppositories based on biodegradable nanoparticles and optimize their rheological and mechanical properties for prospective rectal administration. The nanoparticle system was based on a biodegradable copolymer synthesized by ring opening polymerization (ROP) of glycolide (GL) and L,L-lactide (LLA). Biodegradable nanoparticles loaded with the model drug were produced by the o/o method at the first stage of the investigation. Depending on the concentration of the drug in the sample, from 66 to 91% of MT was released over 12 h, according to first-order kinetics. Then, thermosensitive LSs with MT-loaded biodegradable nanoparticles were obtained by a cold method and their mechanical and rheological properties were evaluated. To adjust the thermogelling and mucoadhesive properties for rectal administration, the amounts of major formulation components such as poloxamers (P407, P188), Tween 80, hydroxypropylcellulose (HPC), polyvinylpyrrolidone (PVP), and sodium alginate were optimized. The in vitro release results revealed that more than 80% of the MT was released after 12 h, following also first-order kinetics. It was discovered that the diffusion process was dominant. The drug release profile was mainly governed by the rheological and mechanical properties of the developed formulation. Such a novel, thermosensitive formulation might be an effective alternative to hypertension treatment, particularly for unconscious patients, patients with mental illnesses, geriatric patients, and children.     

The Heart as a Target of Vasopressin and Other Cardiovascular Peptides in Health and Cardiovascular Diseases

The automatism of cardiac pacemaker cells, which is tuned, is regulated by the autonomic nervous system (ANS) and multiple endocrine and paracrine factors, including cardiovascular peptides. The cardiovascular peptides (CPs) form a group of essential paracrine factors affecting the function of the heart and vessels. They may also be produced in other organs and penetrate to the heart via systemic circulation. The present review draws attention to the role of vasopressin (AVP) and some other cardiovascular peptides (angiotensins, oxytocin, cytokines) in the regulation of the cardiovascular system in health and cardiovascular diseases, especially in post-infarct heart failure, hypertension and cerebrovascular strokes. Vasopressin is synthesized mostly by the neuroendocrine cells of the hypothalamus. There is also evidence that it may be produced in the heart and lungs. The secretion of AVP and other CPs is markedly influenced by changes in blood volume and pressure, as well as by other disturbances, frequently occurring in cardiovascular diseases (hypoxia, pain, stress, inflammation). Myocardial infarction, hypertension and cardiovascular shock are associated with an increased secretion of AVP and altered responsiveness of the cardiovascular system to its action. The majority of experimental studies show that the administration of vasopressin during ventricular fibrillation and cardiac arrest improves resuscitation, however, the clinical studies do not present consisting results. Vasopressin cooperates with the autonomic nervous system (ANS), angiotensins, oxytocin and cytokines in the regulation of the cardiovascular system and its interaction with these regulators is altered during heart failure and hypertension. It is likely that the differences in interactions of AVP with ANS and other CPs have a significant impact on the responsiveness of the cardiovascular system to vasopressin in specific cardiovascular disorders.     

Modulation of Muscarinic Signalling in the Central Nervous System by Steroid Hormones and Neurosteroids

Muscarinic acetylcholine receptors expressed in the central nervous system mediate various functions, including cognition, memory, or reward. Therefore, muscarinic receptors represent potential pharmacological targets for various diseases and conditions, such as Alzheimer’s disease, schizophrenia, addiction, epilepsy, or depression. Muscarinic receptors are allosterically modulated by neurosteroids and steroid hormones at physiologically relevant concentrations. In this review, we focus on the modulation of muscarinic receptors by neurosteroids and steroid hormones in the context of diseases and disorders of the central nervous system. Further, we propose the potential use of neuroactive steroids in the development of pharmacotherapeutics for these diseases and conditions.     

Age- and Lifespan-Dependent Differences in GO Caused DNA Damage in Acheta domesticus

The rising applicability of graphene oxide (GO) should be preceded by detailed tests confirming its safety and lack of toxicity. Sensitivity to GO of immature, or with different survival strategy, individuals has not been studied so far. Therefore, in the present research, we focused on the GO genotoxic effects, examining selected parameters of DNA damage (total DNA damage, double-strand breaks—DSB, 8-hydroxy-2′-deoxyguanosine-8-OHdG, abasic site—AP sites), DNA damage response parameters, and global methylation in the model organism Acheta domesticus. Special attention was paid to various life stages and lifespans, using wild (H), and selected for longevity (D) strains. DNA damage was significantly affected by stage and/or strain and GO exposure. Larvae and young imago were generally more sensitive than adults, revealing more severe DNA damage. Especially in the earlier life stages, the D strain reacted more intensely/inversely than the H strain. In contrast, DNA damage response parameters were not significantly related to stage and/or strain and GO exposure. Stage-dependent DNA damage, especially DSB and 8-OHdG, with the simultaneous lack or subtle activation of DNA damage response parameters, may result from the general life strategy of insects. Predominantly fast-living and fast-breeding organisms can minimize energy-demanding repair mechanisms.     

Daily Treatment of Mice with Type 2 Diabetes with Adropin for Four Weeks Improves Glucolipid Profile,Reduces Hepatic Lipid Content and Restores Elevated Hepatic Enzymes in Serum

Adropin is a peptide hormone encoded by Energy Homeostasis Associated gene. Adropin modulates energy homeostasis and metabolism of lipids and carbohydrates. There is growing evidence demonstrating that adropin enhances insulin sensitivity and lowers hyperlipidemia in obese mice. The aim of this study was to investigate the effects of daily administration of adropin for four weeks in mice with experimentally induced type 2 diabetes (T2D). Adropin improved glucose control without modulating insulin sensitivity. Adropin reduced body weight, size of adipocytes, blood levels of triacylglycerol and cholesterol in T2D mice. T2D mice treated with adropin had lower liver mass, reduced hepatic content of triacylglycerol and cholesterol. Furthermore, adropin attenuated elevated blood levels of hepatic enzymes (ALT, AST, GGT and ALP) in T2D mice. In T2D mice, adropin increased the circulating adiponectin level. Adropin had no effects on circulating insulin and glucagon levels and did not alter pancreatic islets morphology. These results suggest that adropin improves glucose control, lipid metabolism and liver functions in T2D. In conjunction with reduced lipid content in hepatocytes, these results render adropin as an interesting candidate in therapy of T2D.     

Detecting anomalous packets in network transfers: investigations using PCA,autoencoder and isolation forest in TCP

Machine Learning - Large-scale scientific workflows rely heavily on high-performance file transfers. These transfers require strict quality parameters such as guaranteed bandwidth, no packet loss...     

Monomer/modified nanosilica systems: Photopolymerization kinetics and composite characterization

The article describes the influence of the amount and type of organically modified nanosilica (surface and structure modified Aerosil 7200 and surface-modified Aerosil R711) on the photopolymerization kinetics of tetraethylene glycol dimethacrylate and on the physical properties of nanosilica dispersions in the monomer and the polymer matrix. Kinetic measurements showed that silica addition can accelerate or retard the polymerization depending on the silica content; the magnitude of this affect depends on the type of silica modification and can be associated with stability of silica dispersion (as measured by Zeta potential value). The highest reactivity showed compositions containing 4-5 wt.-% of silica and acceleration of the polymerization seems to result mainly from the increase in the propagation rate coefficient. The composites obtained show a uniform dispersion of nanoparticles within the polymer matrix for the silica content at least several wt.-%. The size of aggregates covered with the polymer layer is between 50 and 150 nm for Aerosil R7200 and 75-300 nm for Aerosil R711.