A copula-based method for synthetic microarray data generation

In this work, we propose a copula-based method to generate synthetic gene expression data that account for marginal and joint probability distributions features captured from real data. Our method allows us to implant significant genes in the synthetic dataset in a controlled manner, giving the possibility of testing new detection algorithms under more realistic environments.

Synthetic long peptide booster immunization in rhesus macaques primed with replication-competent NYVAC-C-KC induces a balanced CD4/CD8 T-cell and antibody response against the conserved regions of HIV-1.

The Thai trial (RV144) indicates that a prime-boost vaccine combination that induces both T-cell and antibody responses may be desirable for an effective HIV vaccine. We have previously shown that immunization with synthetic long peptides (SLP), covering the conserved parts of SIV, induced strong CD4 T-cell and antibody responses, but only modest CD8 T-cell responses. To generate a more balanced CD4/CD8 T-cell and antibody response, this study evaluated a pox-vector prime/SLP boost strategy in rhesus macaques. Priming with a replication-competent NYVAC, encoding HIV-1 clade C gag, pol and nef, induced modest IFNγ T-cell immune responses, predominantly directed against HIV-1 Gag. Booster immunization with SLP, covering the conserved parts of HIV-1 Gag, Pol and Env, resulted in a more than 10-fold increase in IFNγ ELISpot responses in four of six animals, which were predominantly HIV-1 Pol-specific. The animals showed a balanced polyfunctional CD4 and CD8 T-cell response and high Ab titres.

Sidelobe elimination for generalized synthetic discriminant functions by a two-filter correlation and subsequent postprocessing of the intensity distributions

One of the most important problems in optical pattern recognition by correlation is the appearance of sidelobes in the correlation plane, which causes false alarms. We present a method that eliminate sidelobes of up to a given height if certain conditions are satisfied. The method can be applied to any generalized synthetic discriminant function filter and is capable of rejecting lateral peaks that are even higher than the central correlation. Satisfactory results were obtained in both computer simulations and optical implementation.

Diagnostic and prognostic value of antibodies against chimeric fibrin/filaggrin citrullinated synthetic peptides in rheumatoid arthritis

Introduction: Evidence suggests that citrullinated fibrin(ogen) may be a potential in vivo target of anticitrullinated protein/peptide antibodies (ACPA) in rheumatoid arthritis (RA). We compared the diagnostic yield of three enzyme-linked immunosorbent assay (ELISA) tests by using chimeric fibrin/filaggrin citrullinated synthetic peptides (CFFCP1, CFFCP2, CFFCP3) with a commercial CCP2-based test in RA and analyzed their prognostic values in early RA. Methods: Samples from 307 blood donors and patients with RA (322), psoriatic arthritis (133), systemic lupus erythematosus (119), and hepatitis C infection (84) were assayed by using CFFCP- and CCP2-based tests. Autoantibodies also were analyzed at baseline and during a 2-year follow-up in 98 early RA patients to determine their prognostic value. Results: With cutoffs giving 98% specificity for RA versus blood donors, the sensitivity was 72.1% for CFFCP1, 78.0% for CFFCP2, 71.4% for CFFCP3, and 73.9% for CCP2, with positive predictive values greater than 97% in all cases. CFFCP sensitivity in RA increased to 80.4% without losing specificity when positivity was considered as any positive anti-CFFCP status. Specificity of the three CFFCP tests versus other rheumatic populations was high (> 90%) and similar to those for the CCP2. In early RA, CFFCP1 best identified patients with a poor radiographic outcome. Radiographic progression was faster in the small subgroup of CCP2-negative and CFFCP1-positive patients than in those negative for both autoantibodies. CFFCP antibodies decreased after 1 year, but without any correlation with changes in disease activity. Conclusions: CFFCP-based assays are highly sensitive and specific for RA. Early RA patients with anti-CFFCP1 antibodies, including CCP2-negative patients, show greater radiographic progression.

Regulatable and modulable background expression control in prokaryotic synthetic circuits by auxiliary repressor binding sites.

Expression control in synthetic genetic circuitry, for example, for construction of sensitive biosensors, is hampered by the lack of DNA parts that maintain ultralow background yet achieve high output upon signal integration by the cells. Here, we demonstrate how placement of auxiliary transcription factor binding sites within a regulatable promoter context can yield an important gain in signal-to-noise output ratios from prokaryotic biosensor circuits. As a proof of principle, we use the arsenite-responsive ArsR repressor protein from Escherichia coli and its cognate operator. Additional ArsR operators placed downstream of its target promoter can act as a transcription roadblock in a distance-dependent manner and reduce background expression of downstream-placed reporter genes. We show that the transcription roadblock functions both in cognate and heterologous promoter contexts. Secondary ArsR operators placed upstream of their promoter can also improve signal-to-noise output while maintaining effector dependency. Importantly, background control can be released through the addition of micromolar concentrations of arsenite. The ArsR-operator system thus provides a flexible system for additional gene expression control, which, given the extreme sensitivity to micrograms per liter effector concentrations, could be applicable in more general contexts.

Synthetic long peptide-based vaccine formulations for induction of cell mediated immunity: A comparative study of cationic liposomes and PLGA nanoparticles.

Nanoparticulate formulations for synthetic long peptide (SLP)-cancer vaccines as alternative to clinically used Montanide ISA 51- and squalene-based emulsions are investigated in this study. SLPs were loaded into TLR ligand-adjuvanted cationic liposomes and PLGA nanoparticles (NPs) to potentially induce cell-mediated immune responses. The liposomal and PLGA NP formulations were successfully loaded with up to four different compounds and were able to enhance antigen uptake by dendritic cells (DCs) and subsequent activation of T cells in vitro. Subcutaneous vaccination of mice with the different formulations showed that the SLP-loaded cationic liposomes were the most efficient for the induction of functional antigen-T cells in vivo, followed by PLGA NPs which were as potent as or even more than the Montanide and squalene emulsions. Moreover, after transfer of antigen-specific target cells in immunized mice, liposomes induced the highest in vivo killing capacity. These findings, considering also the inadequate safety profile of the currently clinically used adjuvant Montanide ISA-51, make these two particulate, biodegradable delivery systems promising candidates as delivery platforms for SLP-based immunotherapy of cancer.

Contribuições recentes da reação de hidroformilação na síntese de produtos farmacêuticos: parte II

The hydroformylation reaction represents one of the most important C1-chemistry area in the chemical industry. This catalytic process, which has been developed up to now mainly to the production of commodities chemicals, has shown a remarkable potential for the preparation of several categories of specialty chemicals and in particular pharmaceutical compounds. Arylpropanoic acids, various amines containing aryl groups, and intermediates for the preparation of vitamins, carbocyclic and heterocyclic compounds and many other classes of organic molecules endowed with pharmacological activity are currently accessible in good-to-high yields through hydroformylation of selected olefinic substrates. The asymmetric hydroformylation is going to reach the stage of maturity and hence to contribute in solving many troublesome synthetic problems connected with the preparation of pharmacologically active compounds with very high enantiomeric purity. The present survey emphasizes the usefulness of synthesis gas as a starting material in fine chemistry, which is expected to be important for industry.

Chemistry and light - part 2: light and energy

The conversion of solar energy into more useful forms of energy, such as chemical fuels or electricity, is one of the central problems facing modern science. Progress in photochemistry and chemical synthesis has led to a point where light energy conversion by means of artificial molecular devices can be rationally attempted. In this article, a general approach towards this challenging goal is presented.

Research and training in medicinal chemistry in south and central american countries and sub-saharan Africa

With the proposal to search for universal cooperation in the field of Medicinal Chemistry, the IUPAC group has elaborated a line of work divided into two phases: a- An Awareness of the true situation of Medicinal Chemistry in the different geographic areas of the world; b- A proposal of actions as to achieve more effective cooperation. This first report presents and discusses the actual situation in South and Central America as well as in sub-Saharan Africa.

The chemistry of peroxynitrite, a biological toxin

Oxyradicals play a tole in several diseases. While for several decades the hydroxyl radical - produced via the Fenton reaction - has been considered the species that initiates oxyradical damage, new findings suggest that much of this damage can be ascribed to peroxynitrite, O=NOO-, formed from the reaction of the superoxide anion with nitrogen monoxide near activated macrophages. The rate constant for the reaction of this reaction has been investigated by flash photolysis and was found to be significantly higher than previously described in the literature, 1.9 x 10(10) M-1s-1. Studies of the isomerization to nitrate resulted in the discovery of a complex between peroxynitrite and its protonated form with a stability constant of 1 x 10(4) M-1. Some of the harmful reaction of peroxynitrous acid have been ascribed to the hydroxyl radical as a product of homolysis of the O-O bond during the conversion to nitrate. Kinetics of the isomerization reaction as a function of pressure show that the activation volume is only +1.5+1.0 ml mol-1, which is inconsistent with homolysis. Instead, an intermediate, possibly a distorted trans-isomer of O=NOOH could be responsible for the harmful reactions of peroxynitrite.

Íons nitrênio

This paper reviews the chemistry of nitrenium ions, the nitrogen analogues of the carbenium ions, showing the pioneering studies and some synthetic applications.

The use of mini-projects in an undergraduate laboratory course in chemistry

This paper reports the results of a three-year study of the effectiveness of mini-projects in a first year laboratory course in chemistry at a Scottish university. A mini-project is a short, practical problem which requires for its solution the application of the knowledge and skills developed in previously completed set experiments. A number of recommendations have been made about the most appropriate ways of introducing mini-projects into undergraduate laboratory course. The main hypothesis of this survey was concerned with the value of mini-projects in laboratory courses formulated within the context of Information Processing Theory.