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PubMed2005

Focused attention is not enough to activate discontinuities in lines, but scrutiny is.

We distinguish between the roles played by spatial attention and conscious intention in terms of their impact on the processing of segmentation signals, like discontinuities in lines, associated with the act of scrutinizing. We showed previously that the processing of discontinuities in lines can be activated. This is evidenced by an impairment in the detection of a gap between parallel elements when it follows a gap between collinear elements in the same location and orientation. This effect is no longer observed if attention is divided between two gaps in the first stimulus. The results from this study show that focusing attention on a gap between collinear elements is not enough to observe a modulation, consistently with the need to integrate, rather than to separate, collinear elements in usual conditions. The modulation is sensitive to the conscious expectations of subjects, suggesting that an intention can trigger modulations that spatial attention cannot.

Analysis of Variance↗

PubMed2026

Genomic Insights Into the Probiotic and Safety Attributes of Pediococcus acidilactici BC-7 for its Potential Application in Livestock Health.

Pediococcus acidilactici is widely recognized for its health-beneficial aspects and has gained increasing interest for use in livestock industry. It shows strong probiotic efficacy, antimicrobial activity, cholesterol-lowering potential, immune modulation, and other therapeutic attributes. The novel strain from indigenous habitats mainly depicted potent probiotic efficacy and high adaptability. In this study, we evaluated the probiotic characteristics and genomic features of strain BC-7 obtained from a Nili - Ravi buffalo calf raised under domestic conditions using phenotypic assessment, genomic analysis and in vivo studies. The strain BC-7 exhibited key probiotic traits i.e., gut tolerance (70.43% - 97.5%), auto-aggregation (85.24%), co-aggregation (14.33% - 25.88%), hydrophobicity (78.33% - 88%), antioxidant potential (54%), and antibacterial activity (16.47-18 mm). The safety analysis revealed that BC-7 exhibited susceptibility and resistance to various antimicrobial agents and showed no β hemolytic activity. BC-7 was taxonomically classified as Pediococcus acidilactici by 16 S rRNA gene sequencing. Whole genome sequence (WGS) analysis showed that P. acidilactici BC-7 contains a 1.9 Mb genome with 42% GC content. Pediococccus acidilactici BC-7 harbored 1900 genes, which were mainly associated with metabolism and genetic processes. Based on genomic comparison, BC-7 shared 99% average nucleotide identity and strong genomic collinearity with P. acidilactici NARCC1 which is a TYPE strain having potent probiotic potential. Probiotic strain BC-7 shared 1,664 core genes with reference strains and 69 unique genes specific for metabolism and genetic processes. The BC-7 strain contained unique bacteriocins-associated genes and defense-related CAzymes, it harbors only vancomycin resistance genes and lacked true virulence determinants. In vivo trial showed that BC-7 treated mice showed increased growth rate, improved immune modulation, and membrane integrity. These significant findings revealed that BC-7 emerging as a potential probiotic strain with strong functionality and efficacy. Thus, our strain BC-7 could be used as a promising candidate for applications in the animal health industry.

Gastrointestinal tract↗

PubMed1998

Latent structure of EEG sleep variables in depressed and control subjects: descriptions and clinical correlates.

In this study, we aimed to determine the latent structure of multiple EEG sleep variables in patients with major depressive disorder (MDD) and in healthy control subjects and to examine associations between sleep factors and clinical variables. Subjects included 109 women with MDD and 54 healthy control women. EEG sleep data were collected prior to any treatment. Principal components analysis (PCA) was conducted on a set of 24 sleep variables. Separate PCAs were run for patients with MDD, control subjects, and a matched group of patients and controls. Other analyses included correlations, t-tests and MANOVA. Each PCA identified four sleep factors that explained 70% of the total variance in individual sleep variables: slow wave sleep, REM sleep, sleep continuity and REM latency/delta sleep ratio (RL/DSR). Patients with MDD and healthy controls differed on the mean value of the sleep continuity factor, and a multivariate analysis of variance based on the PCA identified MDD-control differences in REM sleep and sleep continuity. In the MDD group, slow wave sleep correlated inversely with age and personality disorder symptoms; sleep continuity correlated with subjective sleep quality and anxiety; and RL/DSR correlated inversely with age. The mean value of the REM factor was higher among treatment non-responders than responders. EEG sleep variables have a similar latent structure in women with MDD and in healthy controls. These sleep factors are supported conceptually and empirically, and correlate with clinical measures in women with MDD. Multivariate statistical techniques decrease the risk of Type I and Type II errors when using a large number of collinear sleep measures, and can clarify conceptual issues related to sleep and depression.

Adult↗

PubMed1996

Comparative mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time.

The model dicotyledonous plant, Arabidopsis thaliana, is closely related to Brassica crop species. It is intended that information concerning the genetic control of basic biological processes in Arabidopsis will be transferable to other species. Genome collinearity and its potential to facilitate the identification of candidate genes in Arabidopsis homologous to genes controlling important agronomic traits in Brassica was investigated. Genetic mapping in B. nigra identified two loci influencing flowering time (FT), with loci on linkage groups 2 and 8 explaining 53% and 12% of the total variation in FT, respectively. The CO gene exerts an important control over FT in A. thaliana, and B. nigra homologues of CO probably also play an important role in regulating FT. B. nigra homologues of CO were identified on linkage groups 2 and 8, the homologue on group 2 was coincident with the major locus controlling FT while the homologue on group 8 was within the 90% confidence interval of the weaker FT gene. The CO homologue on group 2 exhibits abundant allelic variation suggesting that it naturally controls a wide range of flowering times. Fine-scale A. thaliana/B. nigra comparative mapping demonstrated short-range collinearity between the genomes of Arabidopsis and Brassica. Eleven DNA fragments spaced over a 1.5 Mb contig in A. thaliana were used as RFLP probes in B. nigra. Three collinear representations of the A. thaliana contig were identified in B. nigra, with one interrupted by a large chromosomal inversion. Collinearity over this range will allow the resources generated by the Arabidopsis genome project to facilitate map-based cloning in Brassica crops.

Analysis of Variance↗

PubMed2001

Factors affecting the forward shift of posterior corneal surface after laser in situ keratomileusis.

PURPOSE: To evaluate the anteroposterior movement of the corneal back surface after laser in situ keratomileusis (LASIK). DESIGN: Retrospective noncomparative case series. PARTICIPANTS: One hundred ninety-six eyes of 120 subjects with myopic refractive errors of -2.0 to -12.5 diopters. INTERVENTION: LASIK was performed. Corneal topography of the posterior corneal surface was obtained with the scanning slit topography system before and 1 month after surgery. MAIN OUTCOME MEASURES: The amount of forward shift of the posterior corneal surface was determined. Multiple regression analysis was used to assess the factors that affect the forward shift of the posterior corneal surface. RESULTS: After surgery, the posterior corneal surface displayed mean forward shift of 40.9 +/- 24.8 micrometer. Explanatory variables relevant to the forward shift of corneal posterior surface were, in the order of magnitude of influence, the amount of laser ablation (partial regression coefficient B = 0.561, P < 0.0001), preoperative corneal thickness (B = -0.176, P = 0.00096), and preoperative intraocular pressure (B = 1.676, P = 0.0053). Preoperative refraction and achieved myopic correction showed collinearity with the amount of laser ablation. CONCLUSIONS: LASIK induces a forward shift of the cornea. Eyes with thinner corneas, higher intraocular pressure, and higher myopia requiring greater laser ablation are more predisposed to the anterior shift of the cornea.

Adult↗

PubMed1995

Mutational analysis of vaccinia DNA ligase defines residues essential for covalent catalysis.

DNA ligation entails AMP transfer from ATP to the 5' end of DNA to form a DNA-adenylate structure, A(5')pp(5')N. A similar reaction involving GMP transfer occurs during 5' capping of eukaryotic mRNA. In both cases, nucleotidyl transfer occurs through a covalent lysyl-NMP intermediate. There is local sequence conservation among ligases and capping enzymes in the vicinity of the active site lysine (KxDG) and at three other collinear motifs. The role of these motifs in DNA ligation was tested by mutating individual conserved residues in the vaccinia virus DNA ligase. Wild-type and mutated versions of vaccinia ligase were expressed in bacteria as His-tagged fusion proteins and purified by Ni-affinity and phosphocellulose chromatography steps. We found that Ala substitution for Lys-231 (the presumptive active site) abrogated enzyme-adenylate formation and DNA ligation activities. Ala mutations at conserved residues Glu-283, Glu-377, and Lys-397 also resulted in loss of ligation activity, which correlated with a defect in ligase-AMP formation. These results are concordant with mutational studies of yeast RNA capping enzyme and suggest a common structural basis for covalent nucleotidyl transfer.

Amino Acid Sequence↗

PubMed2004

In silico prediction of central nervous system activity of compounds. Identification of potential pharmacophores by the TOPS-MODE approach.

The central nervous system (CNS) activity has been investigated by using a topological substructural molecular approach (TOPS-MODE). A discriminant analysis to classify CNS and non-CNS drugs was developed on a data set (302 compounds) of great structural variability where more than 81% (247/302) were well classified. Randic's orthogonalization procedures was carried out to allow the interpretation of the model and to avoid the collinearity among descriptors. The discriminant model was assessed by a leave-n-out (when n varies from 2 to 20) cross-validation procedure (79.94% of correct classification), an external prediction set composed by 78 CNS/non-CNS drugs (80.77% of correct classification) and a 5-fold full cross-validation (removing 78 compounds in each cycle, 80.00% of good classification). With this methodology was demonstrated that the hydrophobicity increase the CNS activity, while the dipole moment and the polar surface area decrease it; evidencing the capacity of the TOPS-MODE descriptors to estimate CNS activity for new drug candidates. The structural contributions to the CNS activity for two compounds are presented on the basis of fragment contributions. The model has also been able to identify potential structural pharmacophore, showing its possibilities in the lead generation and optimization processes.

Central Nervous System↗

PubMed1993

Mechanistic interpretation of the genotoxicity of nitrofurans (antibacterial agents) using quantitative structure-activity relationships and comparative molecular field analysis.

Quantitative structure-activity relationship (QSAR) and comparative molecular field analysis (CoMFA) have been applied to elucidate the mechanisms of genotoxicity (SOSIP) of nitrofuran derivatives on Escherichia coli PQ37. The following equation was developed: log SOSIP = -33.1qc2 + 1.00 log P - 1.50Isat - 1.19MR - 0.76I5,6 - 3.76; n = 40, r = 0.900, s = 0.475. The QSAR model clearly reveals three important factors, namely, electronic (qc2), hydrophobic (log P) and steric (MR, Isat, I5,6) contributing toward the genotoxic activity of this class of compounds. qc2, the charge on the c2 atom attached to the NO2 group, supports a furan ring opening mechanism in explaining the genotoxicity. The finding of the coefficient of 1 with log P conforms to our previous findings with several different classes of mutagens acting on different systems. CoMFA analysis clearly demonstrates its potential in unraveling the steric features of the molecules through contour maps. The CoMFA cross-validated model also supports the importance of the electronic factor. It could not reveal any hydrophobic influence because the interaction energies of the CH3 and H2O probes are collinear. QSAR (classical) and CoMFA, if used judiciously, may complement each other and enhance the applicability of SAR in drug design.

Escherichia coli↗

PubMed2003

Filling the Radon domain in computed tomography by local convex combination.

Radon data interpolation is a necessary procedure in computed tomography (CT), especially for reconstruction from divergent beam scanning. In a polar-grid representation, the Radon data of a fanbeam projection are populated on an arc, rather on a radial line. Collectively, the Radon data generated from a fanbeam CT system are unevenly populated: The population becomes sparser as the polar distance increases. In CT reconstruction, the Fourier central slice theorem requires a radial scanline full of Radon data. Therefore the vacant entries of a scanline must be filled by interpolation. In addition, interpolation is also required in polar-to-Cartesian conversion. In this paper we propose a practical interpolation technique for filling the vacant entries by local convex combination. It is a linear interpolant that generates a value for a grid point from the available data lying in its neighborhood, by a weighted average, with the weights corresponding to the inverse distances. In fact, the linear convex combination serves as a general flat-smoothing operation in filling a vacancy. Specifically, this technique realizes a variety of linear interpolations, including nearest-neighbor replication, two-point collinear, three-point triangulation, and four-point quadrilateral, and local extrapolation, in a unified framework. Algorithms and a simulation demonstration are provided.

Algorithms↗

PubMed2000

Epidermal permeability-penetrant structure relationships: 4, QSAR of permeant diffusion across human stratum corneum in terms of molecular weight, H-bonding and electronic charge.

Principal components analysis (PCA) and multivariate regression analysis (MRA) are used to assess the predictors of permeant diffusion across human stratum corneum. Log(D/h), was estimated from logk(p)+0.024-0.59 logK(oct), where D=diffusion coefficient (cm(2)/h), h=path length (cm), k(p) permeability coefficient (cm/h), K(oct)=partition coefficient (octanol/water). Molecular weight (MW) with (1) scaled H-bonding parameters alpha and beta, or (2) summed modulus of partial charge from molecular modelling were tested as predictors of (D/h). Charge may be computed for any molecule, whilst alpha and beta values are generally unavailable for molecules of biological interest. PCA suggests a dominant permeation pathway since 93% of data variation is in PC1 of log(D/h), MW and charge and 82% in PC1 of log(D/h), MW, alpha and beta. MRA using MW, alpha and beta is unsatisfactory because of collinearity amongst predictors. The best predictor was the product MW*charge. Similarity of the eigenvectors in PCA and normalised coefficients in MRA indicates that charge and MW are equally important predictors of diffusion.

Data Interpretation, Statistical↗

PubMed2001

Causal models for road accident fatalities in Yemen.

An identification of the causes of road accident fatalities is becoming more important with the growth of technology, population, number of vehicles and the need for their use. Many authors have addressed the problem in the past but no universal findings have been obtained. The problem tends to be different under different environments and for different geographical regions. The aim of this paper is to develop a model for the analysis and forecasting of road accident fatalities in Yemen considering data restrictions. The proposed data has a particular structure of accident occurrence that has not been reported in any existing research using data in other countries. The available data for the period 1978-1995 is used to build models to understand the nature and extent of the causes of fatalities. Part of the data is used for model building and part of it for test purposes. The issues of correlation and causality have been addressed and multiple collinearity is investigated and dealt with. Two alternative models are proposed based on both statistical grounds and that of practicality in viable decision making. The influence of consuming a locally grown stimulant called Qat on road users has been addressed and it is found that it increases the risk of accidents. This is not the common understanding within the authorities in Yemen as growing and consuming Qat is unregulated.

Accidents, Traffic↗

PubMed2006

Complete nucleotide sequence of a P2 family lysogenic bacteriophage, varphiMhaA1-PHL101, from Mannheimia haemolytica serotype A1.

The 34,525 nucleotide sequence of a double-stranded DNA bacteriophage (phiMhaA1-PHL101) from Mannheimia haemolytica serotype A1 has been determined. The phage encodes 50 open reading frames. Twenty-three of the proteins are similar to proteins of the P2 family of phages. Other protein sequences are most similar to possible prophage sequences from the draft genome of Histophilus somni 2336. Fourteen open reading frames encode proteins with no known homolog. The P2 orthologues are collinear in phiMhaA1-PHL101, with the exception of the phage tail protein gene T, which maps in a unique location between the S and V genes. The phage ORFs can be arranged into 17 possible transcriptional units and many of the genes are predicted to be translationally coupled. Southern blot analysis revealed phiMhaA1-PHL101 sequences in other A1 isolates as well as in serotype A5, A6, A9, and A12 strains of M. haemolytica, but not in the related organisms, Mannheimia glucosida or Pasteurella trehalosi.

Bacteriophages↗

PubMed2004

Conditions for noncollinear instabilities of ferromagnetic materials.

Two criteria have been identified here which determine whether a magnetic metal orders in a collinear (e.g., ferromagnet) or noncollinear (e.g., spin-spiral) arrangement. These criteria involve the ratio between the strength of the exchange interaction and the width of the electron bands, as well as Fermi-surface nesting between spin-up and spin-down sheets of the Fermi surface. Based on our analysis we predict that even typical ferromagnetic materials (e.g., Fe, Co, and Ni) should be possible to stabilize in a noncollinear magnetic order in, e.g., high pressure experiments.

Journal Article↗

PubMed2005

Physical organization of the major duplication on Brassica oleracea chromosome O6 revealed through fluorescence in situ hybridization with Arabidopsis and Brassica BAC probes.

The close relationship between Brassica oleracea and Arabidopsis thaliana has been used to explore the genetic and physical collinearity of the two species, focusing on an inverted segmental chromosome duplication within linkage group O6 of B. oleracea. Genetic evidence suggests that these segments share a common origin with a region of Arabidopsis chromosome 1. Brassica oleracea and Arabidopsis bacterial artificial chromosome probes have been used for fluorescence in situ hybridization analysis of B. oleracea pachytene chromosomes to further characterize the inverted duplication. This has been highly effective in increasing the local resolution of the cytogenetic map. We have shown that the physical order of corresponding genetic markers is highly conserved between the duplicated regions in B. oleracea and the physical lengths of the regions at pachytene are similar, while the genetic distances are considerably different. The physical marker order is also well conserved between Arabidopsis and B. oleracea, with only one short inversion identified. Furthermore, the relative physical distances between the markers in one segment of B. oleracea and Arabidopsis have stayed approximately the same. The efficacy of using fluorescence in situ hybridization, together with other forms of physical and genetic mapping, for elucidating such issues relating to synteny is discussed.

Arabidopsis↗

PubMed2001

Genetic and physical characterization of chromosome 4DL in wheat.

The long arm of chromosome 4D in wheat (Triticum aestivum L.) has been shown in previous studies to harbor genes of agronomic importance. A major dominant gene conferring Aluminum (Al) tolerance (Alt2 in 'Chinese Spring' and AltBH in 'BH 1146'), and the Knal locus controlling the K+/Na+ discrimination in saline environments have been mapped to this chromosome arm. However, accurate information on the genetic and physical location of markers related to any of these genes is not available and would be useful for map-based cloning and marker-assisted plant breeding. In the present study, using a population of 91 recombinant inbred lines segregating for Al tolerance, we provide a more extensive genetic linkage map of the chromosome arm 4DL based on RFLP, SSR, and AFLP markers, delimiting the AltBH gene to a 5.9-cM interval between markers Xgdm125 and Xpsr914. In addition, utilizing a set of wheat deletion lines for chromosome arm 4DL, the AltBH gene was physically mapped to the distal region of the chromosome, between deletion breakpoints 0.70 and 0.86, where the kilobase/centimorgan ratio is assumed to be low, making the map-based cloning of the gene a more realistic goal. The polymorphism rates in chromosome arm 4DL for the different types of markers used were extremely low, as confirmed by the physical mapping of AFLPs. Finally, analysis of 1 Mb of contiguous sequence of Arabidopsis chromosome 5 flanking the gene homologous to the BCD1230 clone (a cosegregating marker in our population coding for a ribulose-5-phosphate-3-epimerase gene), revealed a previously identified region of stress-related and disease-resistance genes. This could explain the collinearity observed in comparative mapping studies among different species and the low level of polymorphism detected in the chromosome arm 4DL in hexaploid wheat.

Aluminum↗

PubMed2003

Symmetry considerations and development of pinwheels in visual maps.

Neurons in the visual cortex respond best to rod-like stimuli of given orientation. While the preferred orientation varies continuously across most of the cortex, there are prominent pinwheel centers around which all orientations are present. Oriented segments abound in natural images and tend to be collinear; neurons are also more likely to be connected if their preferred orientations are aligned to their topographic separation. These are indications of a reduced symmetry requiring joint rotations of both orientation preference and the underlying topography. We verify that this requirement extends to cortical maps of monkey and cat by direct statistical analysis. Furthermore, analytical arguments and numerical studies indicate that pinwheels are generically stable in evolving field models that couple orientation and topography.

Animals↗

PubMed2004

Towards an improved measure of the Edinburgh Handedness Inventory: a one-factor congeneric measurement model using confirmatory factor analysis.

The Edinburgh Handedness Inventory was administered to a sample of 203 mentally well adults drawn from the Western Australian Family Study of Schizophrenia (90 men and 113 woman). Confirmatory factor analysis demonstrated that seven out of ten original items of the Edinburgh Handedness Inventory were sufficient to provide an internally consistent and valid measure of hand preference. Exclusion of three problematic items led to a more refined measurement of the latent construct of handedness. The rationale for exclusion was: (1) redundancy stemming from collinearity between writing and drawing, and (2) an unacceptably large measurement error associated with two of the items (use of broom and opening a box-lid). The results suggest that this revision of the Edinburgh Handedness Inventory enhances its measurement properties.

Adult↗

PubMed2004

Cloning the human betaretrovirus proviral genome from patients with primary biliary cirrhosis.

Patients with primary biliary cirrhosis (PBC) have both serologic and tissue evidence of infection. A recently identified human betaretrovirus was originally cloned from the biliary epithelium cDNA library of a patient with PBC. By conducting a BLASTN search, the initial partial pol gene fragment was found to have 95% to 97% nucleotide homology with mouse mammary tumor virus (MMTV) and with retrovirus sequences derived from human breast cancer samples. Using an anti-p27(CA) MMTV antibody, viral proteins were detected in the perihepatic lymph nodes but not in liver tissue samples from patients with PBC, suggesting a higher viral burden in lymphoid tissue. Therefore, in the current study, we used lymph node DNA to clone the proviral genome of the human betaretrovirus from two patients with PBC using a polymerase chain reaction (PCR) walking methodology with conserved primers complementary to MMTV. The human betaretrovirus genome contains five potential open reading frames (ORF) for Gag, protease (Pro), polymerase (Pol), envelope (Env), and superantigen (Sag) proteins that are collinear with their counterparts in MMTV. Alignment studies performed with characterized MMTV and human breast cancer betaretrovirus amino acid sequences revealed a 93% to 99% identity with the p27 capsid proteins, a 93% to 97% identity with the betaretrovirus envelope proteins, and a 76% to 85% identity with the more variable superantigen proteins. Phylogenetic analysis of known betaretrovirus superantigen proteins showed that the human and murine sequences did not cluster as two distinct species. In conclusion, human betaretrovirus nucleic acid sequences have been cloned from patients with PBC. They share marked homology with MMTV and human breast cancer-derived retrovirus sequences.

Amino Acid Sequence↗