Optimization of multi-classifiers for computational biology: application to gene finding and expression

Genomes of many organisms have been sequenced over the last few years. However, transforming such raw sequence data into knowledge remains a hard task. A great number of prediction programs have been developed to address part of this problem: the location of genes along a genome and their expression. We propose a multi-objective methodology to combine state-of-the-art algorithms into an aggregation scheme in order to obtain optimal methods’ aggregations. The results obtained show a major improvement in sensitivity when our methodology is compared to the performance of individual methods for gene finding and gene expression problems. The methodology proposed here is an automatic method generator, and a step forward to exploit all already existing methods, by providing alternative optimal methods’ aggregations to answer concrete queries for a certain biological problem with a maximized accuracy of the prediction. As more approaches are integrated for each of the presented problems, de novo accuracy can be expected to improve further.     

Novel saccharinate-bridged palladium complexes for efficient C-O bond activation displaying promising luminescence properties

The synthesis of mono- and dinuclear cyclometallated palladium(II) complexes with deprotonated saccharinate ligands displaying different coordination modes is described. The new compounds were prepared by direct reaction between saccharine and the corresponding hydroxo-complexes [{Pd(μ-OH)(C^N)}(2)] (C^N = 2-(2-pyridyl)phenyl (Phpy) I; = 7,8-benzoquinolyl (Bzq) II), showing a general formula [{Pd(μ-sac)(C^N)}(2)] with saccharinate 1 displaying a bridging -NCO-coordination mode. Bridge splitting with neutral ligands (L = pyridine (py) 2, quinoline (quinol) 3 or acridine (acrid) 4) yielded new mononuclear derivatives with saccharinate acting as an N-monodentated ligand. Structural characterization by X-ray diffraction of complexes I1, I2 and II2 confirmed the proposed formulae. All complexes emit in the solution and solid state at room temperature. Emission features between 640-680 nm in the solid state for complexes I1 and II1 are significantly red-shifted if compared to the emission in solution. These broad emissions are consistent with the simultaneous presence of (3)ππ* and (3)MMLCT transitions indicating the existence of a strong intramolecular Pd-Pd ground state interaction. The dimeric complexes have also shown to catalyze Suzuki-Miyaura cross-coupling of coumaryl tosylate and aryl boronic acids under phosphine-free conditions. Initial studies suggest the involvement of palladium nanoparticles, which has been further investigated using mercury-drop test and poisoning experiments.     

Chemoselective aromatic C-H insertion of α-diazo-β-ketoesters catalyzed by dirhodium(II) carboxylates

The ability of α-diazo-β-ketoesters bearing a substituent on the benzylic position to undergo aromatic C-H insertion is described. Good to excellent yields of the aromatic C-H insertion products were observed with Rh(2)(tpa)(4) or Rh(2)(esp)(2) catalysts. This is an attractive strategy to prepare tetralins carrying a methyl group on the benzylic position, a structural motif found in several types of natural products.     

Development of an ionic‐liquid‐based dispersive liquid–liquid microextraction method for the determination of antichagasic drugs in human breast milk: Optimization by central composite design

Chagas disease constitutes a major public health problem in Latin America. Human breast milk is a biological sample of great importance for the analysis of therapeutic drugs, as unwanted exposure through breast milk could result in pharmacological effects in the nursing infant. Thus, the goal of breast milk drug analysis is to inquire to which extent a neonate may be exposed to a drug during lactation. In this work, we developed an analytical technique to quantify benznidazole and nifurtimox (the two antichagasic drugs currently available for medical treatment) in human breast milk, with a simple sample pretreatment followed by an ionic‐liquid‐based dispersive liquid–liquid microextraction combined with high‐performance liquid chromatography and UV detection. For this technique, the ionic liquid 1‐octyl‐3‐methylimidazolium hexafluorophosphate has been used as the “extraction solvent.” A central composite design was used to find the optimum values for the significant variables affecting the extraction process: volume of ionic liquid, volume of dispersant solvent, ionic strength, and pH. At the optimum working conditions, the average recoveries were 77.5 and 89.7%, the limits of detection were 0.06 and 0.09 μg/mL and the interday reproducibilities were 6.25 and 5.77% for benznidazole and nifurtimox, respectively. The proposed methodology can be considered sensitive, simple, robust, accurate, and green.     

Aggregation phenomena on the ternary ionic-nonionic surfactant system: didodecyldimethylammonium bromide/octyl-beta-D-glucopyranoside/water. Mixed microaggregates, vesicles, and micelles

The formation of a variety of mixed colloidal aggregates has been investigated on a ternary ionic-nonionic system constituted by (i) a double-chain cationic surfactant with a 12-carbon atom hydrophobic tail, didodecyldimethylammonium bromide (di-C(12)DMAB), (ii) a nonionic single-chain surfactant, octyl-beta-D-glucopyranoside (OBG), and (iii) water. The study has been carried out by means of conductivity, zeta-potential, transmission electron microscopy (TEM), and cryogenic transmission electron microscopy (cryo-TEM) experiments on the highly diluted, very diluted, and moderately diluted regions. The formation of mixed microaggregates, prior to the appearance of mixed vesicles, has been undoubtly confirmed by conductivity, TEM, and zeta-potential results. The concentrations at which these mixed colloidal aggregates form, i.e., the mixed critical microaggregate concentration (CAC), the mixed critical vesicle concentration (CVC), and the mixed critical micelle concentration (CMC), have been determined from conductivity data, while the zeta-potential experiments allow for the characterization of the aggregate/solution interface. The shape and size of the microaggregates and vesicles have been evaluated from TEM and cryo-TEM micrographs, respectively. All of the experimental evidence has been also analyzed in terms of the theoretical packing parameter, P.     

Effects of pH and ionic strength on the adsorption of phosphate and arsenate at the goethite-water interface

The surface properties of a well-crystallized synthetic goethite have been studied by acid-base potentiometric titrations, electrophoresis, and phosphate and arsenate adsorption isotherms at different pH and electrolyte concentrations. The PZC and IEP of the studied goethite were 9.3+/-0.1 and 9.3+/-0.2, respectively. Phosphate and arsenate adsorption decrease as the pH increases in either 0.1 or 0.01 M KNO(3) solutions. Phosphate adsorption is more sensitive to changes in pH and ionic strength than that of arsenate. The combined effects of pH and ionic strength result in higher phosphate adsorption in acidic media at most ionic strengths, but result in lower phosphate adsorption in basic media and low ionic strengths. The CD-MUSIC model yields rather good fit of the experimental data. For phosphate it was necessary to postulate the presence of three inner-sphere surface complexes (monodentate nonprotonated, bidentate nonprotonated, and bidentate protonated). In contrast, arsenate could be well described by postulating only the presence of the two bidenate species. A small improvement of the arsenate adsorption data could be achieved by assuming the presence of a monodentate protonated species. Model predictions are in agreement with spectroscopic evidence, which suggest, especially for the case of arsenate, that mainly bidentate inner-sphere complexes are formed at the goethite-water interface.     

A Highly Active Bifunctional Iridium Complex with an Alcohol/Alkoxide‐Tethered N‐Heterocyclic Carbene for Alkylation of Amines with Alcohols

A series of new iridium(III) complexes containing bidentate N‐heterocyclic carbenes (NHC) functionalized with an alcohol or ether group (NHC? OR, R=H, Me) were prepared. The complexes catalyzed the alkylation of anilines with alcohols as latent electrophiles. In particular, biscationic Ir^III complexes of the type [Cp*(NHC‐OH)Ir(MeCN)]²⁺2[BF₄^?] afforded higher‐order amine products with very high efficiency; up to >99 % yield using a 1:1 ratio of reactants and 1–2.5 mol % of Ir, in short reaction times (2–16 h) and under base‐free conditions. Quantitative yields were also obtained at 50 °C, although longer reaction times (48–60 h) were needed. A large variety of aromatic amines have been alkylated with primary and secondary alcohols. The reactivity of structurally related iridium(III) complexes was also compared to obtain insights into the mechanism and into the structure of possible catalytic intermediates. The Ir^III complexes were stable towards oxygen and moisture, and were characterized by NMR, HRMS, single‐crystal X‐ray diffraction, and elemental analyses.     

A naphthodithiophene-diketopyrrolopyrrole donor molecule for efficient solution-processed solar cells

We report the synthesis, characterization, and first implementation of a naphtho[2,3-b:6,7-b']dithiophene (NDT)-based donor molecule in highly efficient organic photovoltaics (OPVs). When NDT(TDPP)(2) (TDPP = thiophene-capped diketopyrrolopyrrole) is combined with the electron acceptor PC(61)BM, a power conversion efficiency (PCE) of 4.06 ± 0.06% is achieved-a record for a PC(61)BM-based small-molecule OPV. The substantial PCE is attributed to the broad, high oscillator strength visible absorption, the ordered molecular packing, and an exceptional hole mobility of NDT(TDPP)(2).     

Gold-catalyzed bis-cyclization of 1,2-diol- or acetonide-tethered alkynes. Synthesis of β-lactam-bridged acetals: a combined experimental and theoretical study

2-Azetidinone-tethered alkyn-1,2-diols or alkynyl acetonides, readily prepared from imines of (R)-2,3-O-isopropylideneglyceraldehyde, were used as starting materials for the regio- and diastereospecific catalytic bis-oxycyclization reaction in the presence of a gold/acid binary system. Interestingly, in contrast to the gold-catalyzed reactions of N-tethered terminal alkynes, which lead to the corresponding 6,8-dioxabicyclo[3.2.1]octane derivatives (proximal adduct), the reactions of substituted alkynic diols and acetonides under identical conditions gave the 7,9-dioxabicyclo[4.2.1]nonane derivatives (distal adducts) as the sole products, through exclusive 7-endo/5-exo bis-oxycyclizations by initial attack of the oxygen atom to the external alkyne carbon. Moreover, the mildness of the method allowed the incorporation of a 1,3-diyne moiety as reactive partner, displaying exquisite chemoselectivity toward the internal alkynic moiety. In order to confirm the mechanistic proposal, labeling studies with deuterium oxide have been performed. Besides, density functional calculations were performed to gain insight into the mechanisms of the bis-oxycyclization reactions.