Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.

Motivation: Disulfide bonds stabilize protein structures and play relevant roles in their functions. Their formation requires an oxidizing environment and their stability is consequently depending on the redox ambient potential, which may differ according to the subcellular compartment. Several methods are available to predict cysteine-bonding state and connectivity patterns.

Determination of cadmium and lead in beverages after leaching from pewter cups using graphite furnace atomic absorption spectrometry.

Two simple methods have been developed to determine cadmium and lead in different kinds of beverages and vinegar leached from pewter cups produced in Brazil. Leaching experiments have been carried out with different solutions: beer, sugar cane spirit, red and white wine, vinegar and a 3% acetic acid solution. The solutions were kept in cups with and without solder for 24h.

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences.

We introduce BAR-PLUS (BAR(+)), a web server for functional and structural annotation of protein sequences. BAR(+) is based on a large-scale genome cross comparison and a non-hierarchical clustering procedure characterized by a metric that ensures a reliable transfer of features within clusters. In this version, the method takes advantage of a large-scale pairwise sequence comparison of 13,495,736 protein chains also including 988 complete proteomes.

Rotational motion in LiBH4/LiI solid solutions.

We investigated the localized rotational diffusion of the (BH(4))(-) anions in LiBH(4)/LiI solid solutions by means of quasielastic and inelastic neutron scattering. The (BH(4))(-) motions are thermally activated and characterized by activation energies in the order of 40 meV. Typical dwell times between jumps are in the picosecond range at temperatures of about 200 K.

MemPype: a pipeline for the annotation of eukaryotic membrane proteins.

MemPype is a Python-based pipeline including previously published methods for the prediction of signal peptides (SPEP), glycophosphatidylinositol (GPI) anchors (PredGPI), all-alpha membrane topology (ENSEMBLE), and a recent method (MemLoci) that specifically discriminates the localization of eukaryotic membrane proteins in: 'cell membrane', 'internal membranes', 'organelle membranes'. MemLoci scores with accuracy of 70% and generalized correlation coefficient (GCC) of 0.50 on a rigorous homology-unbiased validation set and overpasses other predictors for subcellular localization.

SDHA loss-of-function mutations in KIT-PDGFRA wild-type gastrointestinal stromal tumors identified by massively parallel sequencing.

Approximately 10%-15% of gastrointestinal stromal tumors (GISTs) in adults do not harbor any mutation in the KIT or PDGFRA genes (ie, KIT/PDGFRA wild-type GISTs). Recently, mutations in SDHB and SDHC (which encode succinate dehydrogenase subunits B and C, respectively) but not in SDHA and SDHD (which encode subunits A and D, respectively) were identified in KIT/PDGFRA wild-type GISTs. To search for novel pathogenic mutations, we sequenced the tumor transcriptome of two young adult patients who developed sporadic KIT/PDGFRA wild-type GISTs by using a massively parallel sequencing approach.

GM1 gangliosidosis and Morquio B disease: an update on genetic alterations and clinical findings.

GM1 gangliosidosis and Morquio B syndrome, both arising from beta-galactosidase (GLB1) deficiency, are very rare lysosomal storage diseases with an incidence of about 1:100,000-1:200,000 live births worldwide. Here we report the beta-galactosidase gene (GLB1) mutation analysis of 21 unrelated GM1 gangliosidosis patients, and of 4 Morquio B patients, of whom two are brothers. Clinical features of the patients were collected and compared with those in literature.

MemLoci: predicting subcellular localization of membrane proteins in eukaryotes.

Motivation: Subcellular localization is a key feature in the process of functional annotation of both globular and membrane proteins. In the absence of experimental data, protein localization is inferred on the basis of annotation transfer upon sequence similarity search. However, predictive tools are necessary when the localization of homologs is not known.

One dose of a porcine circovirus 2 subunit vaccine induces humoral and cell-mediated immunity and protects against porcine circovirus-associated disease under field conditions.

This study investigated the efficacy of a one-dose porcine circovirus 2 (PCV2) subunit vaccine based on the PCV2 Cap protein expressed in a baculovirus system on two different farms at which a history of porcine circovirus-associated disease (PCVD) was present. Morbidity, mortality, average daily weight gain, carcass weight, PCV2 load in serum and vaccine immunogenicity were assessed. Serology to porcine reproductive and respiratory syndrome virus (PRRSV) and Mycoplasma hyopneumoniae was performed.

Mobility and dynamics in the complex hydrides LiAlH4 and LiBH4.

The dynamics and bonding of the complex hydrides LiBH4 and LiAlH4 have been investigated by vibrational spectroscopy. The combination of infrared, Raman, and inelastic neutron scattering (INS) spectroscopies on hydrided and deuterided samples reveals a complete picture of the dynamics of the BH4- and AlH4 anions respectively as well as the lattice. The straightforward interpretation of isotope effects facilitates tracer diffusion experiments revealing the diffusion coefficients of hydrogen containing species in LiBH4, and LiAlH4.

Novel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: a proof-of-concept study.

Burkholderia pseudomallei, Burkholderia thailandensis, and the Burkholderia cepacia complex differ greatly in pathogenicity and epidemiology. Yet, they are occasionally misidentified by biochemical profiling, and even 16S rRNA gene sequencing may not offer adequate discrimination between certain species groups. Using the 23 B.

A first comparative map of copy number variations in the sheep genome.

We carried out a cross species cattle-sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Massese, Sarda, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5 Mb of the virtual sheep genome referred to the bovine genome (0.

An initial comparative map of copy number variations in the goat (Capra hircus) genome.

Background: The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species.

[Surgeon dentist's profile inserted in the Strategy of Family Health in cities in the state of Pernambuco, Brazil].

This article intends to approach the incorporation of the oral health to the Family Health Strategy which included the odontology professionals into the primary health care. As the odontology has the work based in a practice of healing with emphasis in restoring activities, the implantation from this new model of attention to the health is questioned in relation to the responsible for the execution of that politics - the human resources. The objective of this article is to characterize the profile of surgeons dentists inserted in the Family Health Strategy in the cities of Pernambuco state connecting it with the specificities of the program.

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.

Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing.

The prediction of protein-protein interacting sites in genome-wide protein interaction networks: the test case of the human cell cycle.

In this paper we aim at investigating possible correlations between the number of putative interaction patches of a given protein, as inferred by an algorithm that we have developed, and its degree (number of edges of the protein node in a protein interaction network). We focus on the human cell cycle that, as compared with other biological processes, comprises the largest number of proteins whose structure is known at atomic resolution both as monomers and as interacting complexes. For predicting interaction patches we specifically develop a HM-SVM based method reaching 71% overall accuracy with a correlation coefficient value equal to 0.

BH4− self-diffusion in liquid LiBH4.

The hydrogen dynamics in solid and in liquid LiBH4 was studied by means of incoherent quasielastic neutron scattering. Rotational jump diffusion of the BH4- subunits on the picosecond scale was observed in solid LiBH4. The characteristic time constant is significantly shortened when the system transforms from the low-temperature phase to the high-temperature phase at 383 K.

[Analysis of oral health attention in the Family Health Strategy of the Sanitary District VI, Recife, Pernambuco State].

The aim of this study was to analyze the work process developed by the oral health teams of the VI Sanitary District of Recife, Pernambuco State, in 2006. It is a descriptive study of qualitative approach in that secondary data were obtained of a previous research accomplished in Recife, where the Sanitary District VI is located. Four semi-structured interviews were accomplished with the oral health coordinator, two surgeon-dentists and a nurse that acted in the Family Health Strategy.

Cytokine expression, glucocorticoid and growth hormone changes after porcine reproductive and respiratory syndrome virus (PRRSV-1) infection in vaccinated and unvaccinated naturally exposed pigs.

The objective of this paper was to study the changes of some cytokines and neuroendocrine hormones in vaccinated and unvaccinated pigs that were naturally infected by a PRRSV-1 (porcine reproductive and respiratory syndrome virus) heterologous field strain. We analyzed gene expression of pro-inflammatory (TNF-α, IL-1β, MCP-1, IL-6), pro-immune (IFN-γ) and anti-inflammatory cytokines (IL-10) in PBMC, as well as hormonal (GH and cortisol) levels in blood samples of pigs obtained in a field trial previously reported [Martelli P, Gozio S, Ferrari L, Rosina S, De Angelis E, Quintavalla C, et al. Efficacy of a modified-live porcine reproductive and respiratory syndrome virus (PRRSV) vaccine in pigs naturally exposed to a heterologous European (Italian cluster) field strain: clinical protection and cell-mediated immunity.

Evaluation of the immune response induced by intradermal vaccination by using a needle-less system in comparison with the intramuscular route in conventional pigs.

The immune response induced by intradermal vaccination using a needle-less device was evaluated in conventional pigs in comparison with the more conventional intramuscular vaccination; to this purpose, vaccination against Aujeszky's Disease (AD) was used as a model of antiviral immunity. Two groups of pigs (n=10 each) were vaccinated 4 weeks apart respectively by the intramuscular (IM group) and intradermal route (ID group; needle-less I.D.

Swine virus-specific cytotoxic cells producing IFNgamma under different conditions of virus antigenic stimulation.

Flow cytometry is a useful tool to determine both the phenotype and function of immune cells during vaccination and viral infection. Since cytokine release is a hallmark of cell activation, detection of intracellular interferon (IFN)gamma in cytotoxic CD8alpha+ cells under physiological conditions and after Aujeszky's Disease Virus (ADV)- or Porcine Circovirus type 2 (PCV2)-swine interaction was carried out. Blood samples were collected from healthy 10-month-old pigs, ADV- or PCV2-vaccinated pigs, and PCV2-infected pigs; the levels of total IFNgamma+ and CD8alpha+IFNgamma+ cells were evaluated after PMA-ionomycin and virus-specific in vitro stimulation.

Gouy phase shift in nondiffracting Bessel beams.

The results of a theoretical and experimental investigation of the Gouy effect in Bessel beams are presented. We point out that the peculiar feature of the Bessel beams of being nondiffracting is related to the accumulation of an extra axial phase shift (i.e.

Impact of time-interleaving on directly-detected 100-Gb/s POLMUX RZ-DQPSK robustness to PDL-induced crosstalk.

The impact of PDL-induced crosstalk on 100-Gb/s POLMUX RZ-DQPSK performance is investigated both experimentally and through numerical simulations in direct detection systems. We found that RZ time-interleaving, contrary to what happens with PMD, features a strong robustness to PDL. The detrimental effect of optical narrow filtering on PDL-induced penalty is also analyzed; RZ time-interleaving still proves the best solution to deal with the PDL issue.

Pharmacokinetic behavior of enrofloxacin in estuarine crocodile (Crocodylus porosus) after single intravenous, intramuscular, and oral doses.

The disposition kinetics of enrofloxacin at a single dose of 5 mg/kg body weight were determined in clinically healthy captive-reared estuarine crocodiles (Crocodylus porosus) after intravenous (i.v.), intramuscular (i.

All-optical wavelength conversion of a 100-Gb/s polarization-multiplexed signal.

We present the results of an in-depth experimental investigation about all-optical wavelength conversion of a 100-Gb/s polarization-multiplexed (POLMUX) signal. Each polarization channel is modulated at 25 Gbaud by differential quadrature phase-shift keying (DQPSK). The conversion is realized exploiting the high nonlinear chi((2)) coefficient of a periodically poled lithium niobate waveguide, in a polarization-independent configuration.