Review of Riemannian Distances and Divergences, Applied to SSVEP-based BCI.

The firstgeneration of brain-computer interfaces (BCI) classifies multi-channel electroencephalographic (EEG) signals, enhanced by optimized spatial filters.The second generation directly classifies covariance matrices estimated on EEG signals, based on straightforward algorithms such as the minimum-distance-to-Riemannian-mean (MDRM). Classification results vary greatly depending on the chosen Riemannian distance or divergence, whose definitions and reference implementations are spread across a wide mathematical literature. This paper reviews all the Riemannian distances and divergences to process covariance matrices, with an implementation compatible with BCI constraints. The impact of using different metrics is assessed on a steady-state visually evoked potentials (SSVEP) dataset, evaluating centers of classes and classification accuracy. Riemannian approaches embed crucial properties to process EEG data. The Riemannian centers of classes outperform Euclidean ones both in offline and online setups. Some Riemannian distances and divergences have better performances in terms of classification accuracy, while others have appealing computational efficiency.

Metabolic Reprogramming in Amyotrophic Lateral Sclerosis.

Mitochondrial dysfunction in the spinal cord is a hallmark of amyotrophic lateral sclerosis (ALS), but the neurometabolic alterations during early stages of the disease remain unknown. Here, we investigated the bioenergetic and proteomic changes in ALS mouse motor neurons and patients' skin fibroblasts. We first observed that SODG93A mice presymptomatic motor neurons display alterations in the coupling efficiency of oxidative phosphorylation, along with fragmentation of the mitochondrial network. The proteome of presymptomatic ALS mice motor neurons also revealed a peculiar metabolic signature with upregulation of most energy-transducing enzymes, including the fatty acid oxidation (FAO) and the ketogenic components HADHA and ACAT2, respectively. Accordingly, FAO inhibition altered cell viability specifically in ALS mice motor neurons, while uncoupling protein 2 (UCP2) inhibition recovered cellular ATP levels and mitochondrial network morphology. These findings suggest a novel hypothesis of ALS bioenergetics linking FAO and UCP2. Lastly, we provide a unique set of data comparing the molecular alterations found in human ALS patients' skin fibroblasts and SODG93A mouse motor neurons, revealing conserved changes in protein translation, folding and assembly, tRNA aminoacylation and cell adhesion processes.

Monitoring the crystallization of starch and lipid components of the cake crumb during staling.

Cake staling is a complex problem which has still not been fully understood. Starch polymers retrogradation, which is linked to biopolymers recrystallisation, is the most important factor affecting cake firmness in addition to water migration and fat crystallization. In this study, the effect of storage temperatures of 4°C and 20°C on starch retrogradation and fat recrystallization was investigated. Starch retrogradation can be tracked through changes in crystalline structure via X-rays diffraction as well as through melting of crystals via calorimetry. These techniques have been coupled to study the different phenomena occurring during staling. The results revealed that the storage of cakes at 20°C for 25 days showed more starch polymer retrogradation and more intense fat recrystallization in the ß form than at 4°C. Consequently, the staling was delayed when a low storage temperature like 4°C was used, which is recommended to retain high quality cakes during storage.

Optimization of gluten-free formulations for French-style breads.

The formulation of gluten-free bread, which will be suitable for patients with coeliac disease, was optimized to provide bread similar to French bread. The effects of the presence of hydrocolloids and the substitution of the flour basis by flour or proteins from different sources were studied. The added ingredients were (1) hydrocolloids (carboxymethylcellulose [CMC], guar gum, hydroxypropylmethylcellulose [HPMC], and xanthan gum), and (2) substitutes (buckwheat flour, whole egg powder, and whey proteins). The bread quality parameters measured were specific volume, dry matter of bread, crust color, crumb hardness, and gas cell size distribution. Specific volume was increased by guar gum and HPMC. Breads with guar gum had color characteristics similar to French bread. Hardness decreased with the addition of hydrocolloids, especially HPMC and guar. Breads with guar gum had the most heterogeneous cell size distribution, and guar gum was therefore selected for further formulations. Bread prepared with buckwheat flour had improved quality: an increased specific volume, a softer texture, color characteristics, and gas-cell size distribution similar to French bread. Bread with 1.9% guar gum (w/w, total flour basis) and 5% buckwheat flour (of all flours and substitutes) mimicked French bread quality attributes.

Long-term humoral and cell-mediated immunity after acellular pertussis vaccination compares favourably with whole-cell vaccines 6 years after booster vaccination in the second year of life.

Humoral and cell-mediated immune responses (CMI) were evaluated in subjects 3 and 6 years after primary and booster vaccination with either three-component acellular (Pa) or whole-cell (Pw) vaccines. Low anti-pertussis toxin (PT) antibody levels confirmed the absence of pertussis disease, consistent with ongoing protection. Anti-pertactin (PRN) antibodies, remained at higher levels in Pa-vaccinated subjects. At year 6, CMI responses continued to be present and were higher in Pa-vaccinated than Pw-vaccinated subjects. Long-term protection with Pa vaccines can be expected to be at least as good as that provided by efficacious Pw vaccines.

Porcine reproductive and respiratory syndrome antibody detection on filter discs.

Two enzyme-linked immunosorbent assay (ELISA) kits were evaluated for detection of porcine reproductive and respiratory syndrome (PRRS) antibodies in pooled sera and filter discs (FDs). Elution and incubation procedures and positive thresholds for both ELISAs were determined using FDs collected from sixty non-infected pigs and five pigs with low PRRS-antibody titres. Eighty paired samples (serum/FD) from infected pigs were titrated using both ELISAs. The authors thus showed that five sera or five FDs could be pooled in one test without significant loss of sensitivity. Compared to individual sera, method sensitivity was found to be 79% and specificity 97.5%, based on data from 200 pools of FDs collected on 15 PRRS-infected farms and 120 pools collected on 71 non-infected farms. To balance loss of sensitivity, two pools of five samples from sows and one pool of five samples from finishing pigs can be tested as an alternative to seven and five single sera, respectively.

Beta-amyloid fibrils activate the C1 complex of complement under physiological conditions: evidence for a binding site for A beta on the C1q globular regions.

Previous studies based on the use of serum as a source of C have shown that fibrils of beta-amyloid peptides that accumulate in the brain of patients with Alzheimer's disease have the ability to bind C1q and activate the classical C pathway. The objective of the present work was to test the ability of fibrils of peptide Abeta1-42 to trigger direct activation of the C1 complex and to carry out further investigations on the site(s) of C1q involved in the interaction with Abeta1-42. Using C1 reconstituted from purified C1q, C1r, and C1s, it was shown that Abeta1-42 fibrils trigger direct C1 activation both in the absence of C1 inhibitor and at C1 inhibitor:C1 ratios up to 8:0, i.e., under conditions consistent with the physiological context in serum. The truncated peptide Abeta12-42 and the double mutant (D7N, E11Q) of Abeta1-42 did not yield C1 activation, providing further evidence that the C1 binding site of beta-amyloid fibrils is located in the acidic N-terminal 1-11 region of the Abeta1-42 peptide. Binding studies performed using a solid phase assay provided strong evidence that C1q interacts with Abeta1-42 fibrils through its C-terminal globular regions. In contrast to previous studies based on a different experimental design, no significant involvement of the C1q collagen-like domain was detected. These findings were confirmed by additional experiments based on C1 activation and C4 consumption assays. These observations provide direct evidence of the ability of beta-amyloid fibrils to trigger activation of the classical C pathway and further support the hypothesis that C activation may be a component of the pathogenesis of Alzheimer's disease.

Induction of porcine cytokine mRNA expression after DNA immunization and pseudorabies virus infection.

Injection of plasmid DNA encoding pseudorabies virus (PRV) glycoprotein into pig muscle has been shown to result in protective immunity against lethal infection. Here, pigs were vaccinated by a single coinjection of three plasmids encoding PRV glycoproteins gB, gC, and gD, with plasmid expressing porcine granulocytemacrophage colony-stimulating factor (GM-CSF) or porcine interferon-alpha (IFN-alpha). DNA immunization induced a primary T cell-mediated response characterized by low rates of IFN-gamma, interleukin-2 (IL-2), and IL4 mRNA in peripheral blood mononuclear cells (PBMC). Very low rates of PRV-specific IgG1 and the absence of IgG2 were obtained. Codelivery of plasmid expressing GM-CSF or IFN-alpha had no effect on cytokine mRNA expression or on B cell response. After a high virulent challenge, high levels of cytokine mRNA, mainly IFN-gamma, and high secondary antibody (Ab) response were induced in all DNA-vaccinated pigs. Codelivery of GMCSF gene significantly increased both Th immune response (i.e., IFN-gamma and IL-4 mRNA expression) and clinical protection but had no effect on secondary B immune response. Codelivery of IFN-alpha gene had no beneficial effect on secondary T and B cell immune responses.

Physicochemical behaviors of sugars, lipids, and gluten in short dough and biscuit.

The structure of short dough and biscuit has been characterized at a macroscopic level (dimensions, bulk structure) and a microscopic level (starch damage, protein aggregates, microstructure) by physical and biochemical methods. The baking process of short dough induces a large decrease of the product bulk density from 1.26 to 0. 42 (+/-0.01) g.cm(-)(3) for final biscuit, leading to a cellular solid with a thin colored surface and a porous inner structure. Proteins appear aggregated in biscuit when compared to short dough, whereas starch granules remain almost intact in biscuits. The components which are involved in the cohesiveness of short dough and biscuit final structure have been identified. They suggest that short dough is a suspension of solid particles in a liquid phase being an emulsion of lipids in a concentrated sugar solution. The role of sugars in biscuit structure suggest that biscuit structure is a composite matrix of protein aggregates, lipids and sugars, embedding starch granules.

Mapping of the interaction between the immunodominant loop of the ectodomain of HIV-1 gp41 and human complement protein C1q.

The human immunodeficiency virus type 1 transmembrane envelope glycoprotein gp41 has been previously shown to activate the C1 complex of human complement through direct interaction with its C1q subunit. The major interaction site has been located within the gp41 immunodominant region (residues 590-620), and a synthetic peptide overlapping residues 601-613 of gp41 (sequence GIWGCSGKLICTT) was shown to inhibit binding of gp41 to C1q in vitro (Thielens, N.M., Bally, I.M., Ebenbichler, C.F., Dierich, M.P. & Arlaud, G.J. (1993) J. Immunol. 151, 6583-6592). The ectodomain of gp41 (s-gp41) was secreted from the methylotrophic yeast Pichia pastoris and purified by immunoaffinity chromatography. Enzymatic deglycosylation of the recombinant s-gp41 was necessary to allow its in vitro interaction with C1q. A solid-phase competition assay was used to monitor the effect of mutant peptides derived from segment 601-613 of gp41 on the binding of deglycosylated s-gp41 to C1q. Whereas mutation of Ser606 had no effect, replacement of Ile602, Trp603, Lys608, Leu609 and Ile610 by Ala abolished the ability of the resulting peptides to inhibit binding of s-gp41 to C1q, suggesting that these residues participate in the interaction between gp41 and C1q. These findings are discussed in the light of a structural model of the immunodominant loop of gp41. It is proposed that the recognition of gp41 by C1q is driven by hydrophobic interactions, and that the sites of gp41 responsible for interaction with gp120 and C1q partly overlap.

Structure and assembly of the catalytic region of human complement protease C1r: a three-dimensional model based on chemical cross-linking and homology modeling.

C1r is the modular serine protease responsible for autocatalytic activation of C1, the first component of the complement classical pathway. Its catalytic region is a noncovalent homodimer of two gamma-B monomers, each comprising two contiguous complement control protein (CCP) modules, IV and V [also known as short consensus repeats (SCRs)], a 15-residue intermediary segment, and the serine protease B domain. With a view to gain insight into domain-domain interactions within this region, fragment C1r (gamma-B)2, obtained by autolytic proteolysis of the active protease, was cross-linked with the water-soluble reagent 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide. Cross-linked species gamma-B intra and gamma-B inter, containing intra- and intermonomer cross-links, respectively, were isolated and then fragmented by CNBr cleavage and trypsin digestion. N-Terminal sequence and mass spectrometry analyses of the resulting cross-linked peptides allowed us to identify one intramonomer cross-link between Lys426 of module V and the C-terminal Asp688 of the serine protease B domain and one intermonomer cross-link between the N-terminal Gly280 of fragment gamma and Glu493 of the B domain. Three-dimensional homology modeling of the CCP modules IV and V and of the B domain was also performed. The complementary information provided by chemical cross-linking and homology modeling studies was used to construct a three-dimensional model of the gamma-B monomer, in which module V interacts with the serine protease on the side opposite to both the active site and the Arg446-Ile447 activation site. Also, a tentative three-dimensional model of the (gamma-B)2 dimer was built, indicating a loose "head to tail" association of the monomers, with the active sites facing opposite directions toward the outside of the dimer. The latter model is compared with available low-resolution structural data, and its functional implications are discussed in terms of the conformational changes occurring during C1r activation.

Identification of the cysteine residues implicated in the formation of alpha 2 and alpha/beta dimers of rat meprin.

Meprin (endopeptidase-24.18; EC 3.4.24.18) is a multisubunit zinc-metallopeptidase found in the brush-border membranes of rodent kidney and human intestine. The alpha and beta subunits of meprin are disulphide-linked to form either soluble alpha 2 homodimers or membrane-associated alpha/beta heterodimers. The aim of the present study was to identify the cysteine residue(s) implicated in the formation of alpha 2 and alpha/beta dimers and to investigate the effects of dimerization on intracellular transport and processing of the alpha subunit. Three cysteine residue candidates for the formation of disulphide bonds in the alpha subunit were selected by hydrophobic cluster analysis. These residues, located at positions 309, 560 and 562, were mutated to serine residues. When the resulting alpha subunit mutants were expressed alone in COS-1 cells, the alpha C560S and alpha C562S mutants were found to be secreted as alpha 2 homodimers whereas the alpha C309S mutant was found as monomers in the culture medium. In double-transfection experiments with the wild-type beta subunit, the alpha C560S and alpha C562S mutants behaved exactly as the wild-type alpha subunit and formed membrane-bound alpha/beta heterodimers. In contrast, the alpha C309S mutant was not retained at the cell surface but rather secreted as monomers in the culture medium, as was found in the simple transfection experiment. These results show that, despite the normal expression level and folding of the protein in a transport-competent from, the alpha C309S mutant is unable to form alpha 2 homodimers or alpha/beta heterodimers. This suggests that Cys309 is the unique residue of the alpha subunit implicated in the alpha 2 and alpha/beta dimerizations. Hydrophobic cluster analysis of the alpha and beta subunit sequences predicts that Cys309 is similar to Cys306 of the beta subunit. We mutated the latter residue to a serine and expressed the beta C306S mutant and the wild-type alpha subunit in the same COS-1 cells. No beta 2 or alpha/beta dimers were observed on immunoblotting, showing that Cys306 of the beta subunit is required for the formation of intermolecular disulphide bonds both in beta 2 homodimers and in alpha/beta heterodimers. Taken together, these results suggest that the alpha/beta heterodimeric form of meprin is held together by a single disulphide bond linking Cys309 in the alpha subunit to Cys306 in the beta subunit.

Proteolytic processing of the alpha-subunit of rat endopeptidase-24.18 by furin.

Endopeptidase-24.18 (EC 3.4.24.18; meprin) is a multisubunit metallopeptidase of the astacin family. It is found in brush-border membranes of rodent kidney and human intestine. The membrane-bound enzyme is composed of alpha/beta dimers. Molecular cloning has shown that both subunits have a similar structural domain organization. Soluble alpha 2 dimers have also been observed in vivo and in transfected cells. The structures of all known alpha-subunits contain, upstream from the transmembrane domain, the sequence RXKR, which corresponds to the RXK/RR consensus sequence for specific cleavage by furin. In order to investigate the involvement of this putative cleavage site in the secretion process of endopeptidase-24,.18 alpha-subunit, we expressed in COS-1 cells rat alpha-subunits in which residues R655 or S656 (within the sequence R652PKRS656) were mutated to valine or leucine respectively. In contrast to the wild-type protein, the alpha R655V and alphaS656L mutants were not secreted in the culture medium. Moreover, when cells expressing the alpha-subunit were infected with a furin-encoding vaccinia virus, immunoblotting showed a shift of the major cell-associated form of endopeptidase-24.18 alpha-subunit from 98 kDa to 85 kDa and an increase in the amounts of secreted alpha-subunit. This shift in molecular mass was not observed with the mutant alpha-subunits. As observed for the 98 kDa species, the 85 kDa cell-associated protein was sensitive to endoglycosidase H treatment, suggesting that the proteolytic cleavage occurred in the endoplasmic reticulum or in an early Golgi compartment. Similar experiments using PACE4 and PC5 instead of furin showed that these enzymes were not able to generate the 85 kDa species. We conclude that furin is most probably the cellular enzyme involved in the proteolysis resulting in secretion of rat endopeptidase-24.18 alpha-subunit.

Characterization of a prolyl endopeptidase from Flavobacterium meningosepticum. Complete sequence and localization of the active-site serine.

A prolyl endopeptidase was purified from Flavobacterium meningosepticum. It was digested with trypsin. Two oligonucleotides, based on tryptic peptide sequences and used in PCR experiments, amplified a 300-base pair (bp) fragment. A 2.4-kilobase EcoRI fragment that hybridized to the 300-bp probe was cloned in lambda ZAP and sequenced from both strands. It contains a reading frame of 2115 bp, encoding the complete protein sequence of 705 amino acids. Ion-spray mass spectrometry experiments demonstrated the presence of an NH2-terminal signal peptide: the periplasmic mature protease is 685 residues in length for a molecular mass of 76784 Da. The prolyl endopeptidase showed no general sequence homology with known protein sequences except with that of porcine brain prolyl endopeptidase. In order to identify the active-site serine, the prolyl endopeptidase was labeled with [3H]diisopropyl fluorophosphate. One labeled peptide was purified and sequenced. The active-site serine was located in position 536 within the sequence GRSNGG. This sequence is different from the active-site sequence of the trypsin (GDSGGP) and subtilisin (GTSMAS) families.