MUMAL: multivariate analysis in shotgun proteomics using machine learning techniques.

BACKGROUND: The shotgun strategy (liquid chromatography coupled with tandem mass spectrometry) is widely applied for identification of proteins in complex mixtures. This method gives rise to thousands of spectra in a single run, which are interpreted by computational tools. Such tools normally use a protein database from which peptide sequences are extracted for matching with experimentally derived mass spectral data. After the database search, the correctness of obtained peptide-spectrum matches (PSMs) needs to be evaluated also by algorithms, as a manual curation of these huge datasets would be impractical. The target-decoy database strategy is largely used to perform spectrum evaluation. Nonetheless, this method has been applied without considering sensitivity, i.e., only error estimation is taken into account. A recently proposed method termed MUDE treats the target-decoy analysis as an optimization problem, where sensitivity is maximized. This method demonstrates a significant increase in the retrieved number of PSMs for a fixed error rate. However, the MUDE model is constructed in such a way that linear decision boundaries are established to separate correct from incorrect PSMs. Besides, the described heuristic for solving the optimization problem has to be executed many times to achieve a significant augmentation in sensitivity. RESULTS: Here, we propose a new method, termed MUMAL, for PSM assessment that is based on machine learning techniques. Our method can establish nonlinear decision boundaries, leading to a higher chance to retrieve more true positives. Furthermore, we need few iterations to achieve high sensitivities, strikingly shortening the running time of the whole process. Experiments show that our method achieves a considerably higher number of PSMs compared with standard tools such as MUDE, PeptideProphet, and typical target-decoy approaches. CONCLUSION: Our approach not only enhances the computational performance, and thus the turn around time of MS-based experiments in proteomics, but also improves the information content with benefits of a higher proteome coverage. This improvement, for instance, increases the chance to identify important drug targets or biomarkers for drug development or molecular diagnostics

Miocene sediments from Foz da Fonte and Penedo sections (Lower Tagus basin): clay minerals and isotopic data

Eight depositional sequences (DS) delimited by regional disconformities had been recognized in the Miocene of Lisbon and Setúbal Peninsula areas. In the case of the western coast of the Setúbal Peninsula, outcrops consisting of Lower Burdigalian to Lower Tortonian sediments were studied. The stratigraphic zonography and the environmental considerations are mainly supported on data concerning to foraminifera, ostracoda, vertebrates and palynomorphs. The first mineralogical and geochemical data determined for Foz da Fonte, Penedo Sul and Penedo Norte sedimentary sequences are presented. These analytical data mainly correspond to the sediments' fine fractions. Mineralogical data are based on X-ray diffraction (XRD), carried out on both the less than 38 nm and 2 nm fractions. Qualitative and semi-quantitative determinations of clay and non-clay minerals were obtained for both fractions. The clay minerals assemblages complete the lithostratigraphic and paleoenvironmental data obtained by stratigraphic and palaeontological studies. Some palaeomagnetic and isotopic data are discussed and correlated with the mineralogical data. Multivariate data analysis (Principal Components Analysis) of the mineralogical data was carried out using both R-mode and Q-mode factor analysis

Bronchiectasis: A retrospective study of clinical and aetiological investigation in a general respiratory department

AbstractBackgroundBronchiectasis can result from many diseases, which makes the aetiological investigation a complex process demanding special resources and experience. The aetiological diagnosis has been proven to be useful for the therapeutic approach.ObjectiveEvaluate how accurately and extensive the clinical and aetiological research was for adult bronchiectasis patients in pulmonology outpatient service which were not following a pre-existing protocol.MethodsWe retrospectively reviewed the records of 202 adult patients with bronchiectasis, including the examinations performed to explain the aetiology.ResultsThe mean age of the patients was 54±15 years, there was a predominance of female (63.9%) and non-smoker (70%) patients. Functional evaluation showed a mild airway obstruction.The sputum microbiological examination was available for 168 patients (43.1% had 3 or more sputum examinations during one year). Immunoglobulins and α1-antitrypsin were measured in around 50% of the patients. The sweat test and the CF genotyping test were performed in 18% and 17% of the patients, respectively.The most commonly identified cause was post-infectious (30.3%), mostly tuberculosis (27.2%). No definitive aetiological diagnosis was established in 57.4% of the patients. We achieved a lower aetiological diagnosis if we compare our series with studies in which a diagnostic algorithm was applied prospectively.ConclusionsThe general characteristics of our patients were similar with other series. Detailed investigation of bronchiectasis is not a standard practice in our outpatient service. These results suggest that the use of a predefined protocol, based on current guidelines, could improve the assessment of these patients and facilitate the achievement of a definitive aetiology

Designer solvent ability of alcohols in aqueous biphasic systems composed of deep eutectic solvents and potassium phosphate

Deep eutectic solvents (DES) have been proposed as phase forming components of aqueous biphasic systems (ABS). However, the DES hydrogen bonding complexes are not stable in the high concentrations of water present in this type of systems. Therefore, as previously shown, DES-based ABS should be treated as quaternary systems. This confers DES-based ABS with an extra degree of freedom for the design of separation processes since while one of the DES components acts as a phase forming component, the other could induce the modification of the ABS phase properties and, consequently, the control of the partition of various biomolecules. In this context, the designer solvent effect of the hydrogen bond donor (HBD), using four different alcohols – ethanol, n-propanol 1,2-propanediol and ethylene glycol – mixed at three different molar fractions (2:1; 1:1 and 1:2) with cholinium chloride (the hydrogen bond acceptor, HBA) in quaternary systems composed of K2HPO4 and water, was evaluated in this work. The results show that the presence of the HBD has an impact upon the liquid–liquid equilibrium, and these changes are dependent on the alcohol nature. The NRTL model was correlated to the tie-line experimental data with a low mean deviation. Moreover, several biomolecules (phenolic compounds, alkaloids, and amino acids) were use as molecular probes to evaluate the ability of alcohols to tune the partition in the studied systems. The alcohol presence changes the properties of the ABS’s phases and it is here shown that the HBD of the DES can indeed be used to modulate the partition behavior of target molecules.publishe

Noncommutative massive Thirring model in three-dimensional spacetime

We evaluate the noncommutative Chern-Simons action induced by fermions interacting with an Abelian gauge field in a noncommutative massive Thirring model in (2+1)-dimensional spacetime. This calculation is performed in the Dirac and Majorana representations. We observe that in Majorana representation when $\theta$ goes to zero we do not have induced Chern-Simons term in the dimensional regularization scheme.Comment: Accepted to Phys. Rev. D; 9 pages, Revtex4, no figures, references added, minor improvements, Eq.31 correcte

Protein-olive oil-in-water nanoemulsions as encapsulation materials for curcumin acting as anticancer agent towards MDA-MB-231 cells

The sustainable cellular delivery of the pleiotropic drug curcumin encounters drawbacks related to its fast autoxidation at the physiological pH, cytotoxicity of delivery vehicles and poor cellular uptake. A biomaterial compatible with curcumin and with the appropriate structure to allow the correct curcumin encapsulation considering its poor solubility in water, while maintaining its stability for a safe release was developed. In this work, the biomaterial developed started by the preparation of an oil-in-water nanoemulsion using with a cytocompatible copolymer (Pluronic F 127) coated with a positively charged protein (gelatin), designed as G-Cur-NE, to mitigate the cytotoxicity issue of curcumin. These G-Cur-NE showed excellent capacity to stabilize curcumin, to increase its bio-accessibility, while allowing to arrest its autoxidation during its successful application as an anticancer agent proved by the disintegration of MDA-MB-231 breast cancer cells as a proof of concept

Electrolyte effects on the Amino acid solubility in water: solubilities of Glycine, l-Leucine, l-Phenylalanine, and l-Aspartic acid in salt solutions of (Na+, K+, NH4+)/(Cl–, NO3–)

The solubilities of glycine, L-leucine, L-phenylalanine, and L-aspartic acid in aqueous solutions of the salts composed by combining Na+, K+, and NH4 + cations and Cl− and NO3 − anions were measured up to 2.0 salt molality at 298.2 K by the analytical gravimetric method. Using these data along with a review of literature information, encompassing all amino acids for which solubility is available in the studied aqueous electrolyte solutions, allowed us to interpret the effect of the functional groups of amino acids on their solubility. The four amino acids studied here showed higher solubility in aqueous solutions of salts with the nitrate anion. Except for L-aspartic acid with a polar side chain, amino acids with apolar side chains presented the highest salting-in effect in aqueous salt solutions with NH4 +. The cations Na+ and K+ did not seem to establish relevant interactions with the amino acids and had little impact on their aqueous solubility.This work was developed within the scope of the project CIMO-Mountain Research Center, UIDB/00690/2020 and CICECO-Aveiro Institute of Materials, UIDB/50011/2020 and UIDP/50011/2020, financed by national funds through the Portuguese Foundation for Science and Technology (FCT)/MCTES. Mehriban Aliyeva thanks FCT and European Social Fund (ESF) for her Ph.D. grant (SFRH/BD/139355/2018).info:eu-repo/semantics/publishedVersio