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PubMed1999

Highly resistant regression and object matching.

In many disciplines, it is of great importance to match objects. Procrustes analysis is a popular method for comparing labeled point configurations based on a least squares criterion. We consider alternative procedures that are highly resistant to outlier points, and we describe an application in electrophoretic gel matching. We consider procedures based on S estimators, least median of squares, and least quartile difference estimators. Practical implementation issues are discussed, including random subset selection and intelligent subset selection (where subsets with small size or near collinear subsets are ignored). The relative performances of the resistant and Procrustes methods are examined in a simulation study.

Algorithms↗

PubMed1999

Clonal evolution of B cells in transformation from low- to high-grade lymphoma.

An outcome of low-grade B cell non-Hodgkins's lymphomas is the transformation to high-grade diffuse large B cell lymphomas (DLBL). To investigate the mechanisms of clonal evolution in the transformation to DLBL, we performed longitudinal molecular analyses of immunoglobulin (Ig), V(H)DJ(H) gene sequences expressed in cases of chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL), and follicular lymphoma (FL) that transformed to DLBL. Among the neoplastic CLL and SLL cells and their respective high-grade transformants, there was no evidence for a clonotypic shift or acquired mutations in the expressed Ig V(H)DJ(H) gene segments, as further confirmed by a specific and sensitive PCR-single strand polymorphism analysis. In contrast, among the FL cells there was a high degree of intraclonal diversification with highly divergent V(H)DJ(H) gene sequences. Despite this intraclonal heterogeneity, the related DLBL expressed a collinear but unique V(H)DJ(H) gene sequence. The intraclonal genealogical tree for the FL case demonstrated that the DLBL emerged in association with unique V(H)DJ(H) gene mutational events. Among the intraclonal FL and related DLBL transformants, the nature and distribution of the Ig V(H)DJ(H) gene mutations were consistent with antigenic selection. Thus, clonal evolution in the transformation from low- to high-grade B cell lymphoma may involve distinct pathways which vary according to the cellular origin and the type of the progenitor B cell tumor.

Amino Acid Sequence↗

PubMed1996

Characterization of the human forkhead gene FREAC-4. Evidence for regulation by Wilms' tumor suppressor gene (WT-1) and p53.

We describe the cloning and sequence analysis of a nearly full-length cDNA as well as a corresponding 5.2-kilobase pair genomic fragment encoding FREAC-4, a member of the forkhead family of transcription factors. The cDNA is collinear with respect to the coding region of the intronless genomic clone. The conceptual translation product predicts a protein of 465 amino acids with a hyperacidic amino-terminal end, a DNA binding forkhead domain and a carboxyl-terminal part that is rich in homopolymeric runs of prolines and alanines. The transcription start is identified using an RNase protection assay. A 2.7-kilobase pair genomic DNA fragment, located immediately upstream of the translation start, was fused to a luciferase reporter gene. Significant levels of luciferase activity were detected when this construct was transfected into two kidney-derived cell lines, 293 and COS-7 cells, whereas only background reporter gene expression was observed in a cell line of nonkidney origin. Cotransfections with plasmids expressing WT-1, WTAR (a mutated form of WT-1), p53, and a mutated form of p53 revealed a complex pattern of regulation with a 3-fold induction with WT-1, a 7-fold induction with mutated p53, and a 4-fold repression with wild-type p53. A 5'-promoter deletion series delimits a DNA fragment necessary for WT-1 inducibility in cotransfection experiments. This fragment is shown to contain at least one cis-element that is capable of interacting with recombinant WT-1.

Amino Acid Sequence↗

PubMed2005

[Classification of terpenes and terpene oxides in volatile oil of Fruit of Acanthopanax senticosus (Rupr. Et Maxim) Harms with gas chromatographic retention parameters].

Gas chromatographic (GC) retention parameters (A and B values) for 24 volatile compounds in volatile oil of Acanthopanax senticosus (Rupr. Et Maxim) Harms were obtained from the retention times under five temperature-programming conditions with self-developed GC_AB software based on Levenberg-Marquardt method. The correlation analysis between A and B parameters of terpene and its oxides was carried out. Good linear relationships between A and B parameters were built for seven monoterpenes (C10H16) , nine sesquiterpenes (C15H24), three monoterpene oxides (C10HnO) and three sesquiterpene oxides (C15HnOx) at the same carbon number, respectively. But poor A-B linearity was built for the group formed from monoterpenes and monoterpene oxides or that formed from sesquiterpenes and sesquiterpene oxides at the same carbon number. At the same time the A-B relationships for monoterpenes, sesquiterpenes and their oxides are not collinear. Therefore, this discipline is applied in the assistant identification for terpenes with different carbon numbers and in the classification between terpenes and their oxides. It shows that GC retention parameters calculated from retention times under several temperature-programming conditions are useful for the classification of monoterpenes, sesquiterpenes and their oxides in the analysis of volatile oils from traditional Chinese herbs.

Chromatography, Gas↗

PubMed2005

Comparative analysis of local spin definitions.

This work provides a survey of the definition of electron spin as a local property and its dependence on several parameters in actual calculations. We analyze one-determinant wave functions constructed from Hartree-Fock and, in particular, from Kohn-Sham orbitals within the collinear approach to electron spin. The scalar total spin operators S2 and Sz are partitioned by projection operators, as introduced by Clark and Davidson, in order to obtain local spin operators SASB and SzA, respectively. To complement the work of Davidson and co-workers, we analyze some features of local spins which have not yet been discussed in sufficient depth. The dependence of local spin on the choice of basis set, density functional, and projector is studied. We also discuss the results of Sz partitioning and show that SzA values depend less on these parameters than SASB values. Furthermore, we demonstrate that for small organic test molecules, a partitioning of Sz with preorthogonalized Lowdin projectors yields nearly the same results as one obtains using atoms-in-molecules projectors. In addition, the physical significance of nonzero SASB values for closed-shell molecules is investigated. It is shown that due to this problem, SASB values are useful for calculations of relative spin values, but not for absolute local spins, where SzA values appear to be better suited.

Journal Article↗

PubMed1991

Regression and cluster analysis of the acute toxicity of 267 chemicals to six species of biota and the octanol/water partition coefficient.

The acute toxicities of 267 compounds to six aquatic and one terrestrial species were investigated with correlation, principal component and cluster analysis techniques for relationships with each other and with the compounds' octanol/water partition coefficient. Selection of the investigated chemicals was based on the availability of at least three of the following measured parameters: acute (24-h to 96-h) lethal concentrations (LC50) to the fish fathead minnow (Pimephales promelas), the fish goldorfe (Leuciscus idus melanotus), the zooplankter Daphnia magna, the ciliate Tetrahymena pyriformis, and the algae Scenedesmus quadricauda; the (30-min) inhibitory concentrations (EC50) to the luminescent marine bacterium Photobacterium phosphoreum (the Microtox test); the acute oral dose (LD50) for the common Norway rat and the octanol/water partition coefficient (log P or log Kow). The results indicate highly significant correlations between the fathead minnow, goldorfe and Daphnia LC50 and the Photobacterium EC50 concentrations. The cluster and principal components analyses did not detect any clearly defined groups of compounds. The toxicities were also highly collinear with the octanol/water partition coefficients for all species except the rat, where two relationships are indicated, with the division at log P = 2.00.

Animals↗

PubMed1976

Grouping of multiple ambiguous contours: towards an understanding of surface perception.

Coplanar lines of different orientations rotating in depth and viewed in parallel projection may appear to rotate in different directions and reverse independently of each other, or they may appear coplanar and all reverse together. The frequency of the latter "grouped" appearance for lines with an orientation range of 30 degrees was a function of the number of lines in a given space. Grouping was greater for lines converging to an implicit vanishing point and for lines with collinear edges regardless of their orientations. Line length, and by inference, interline separation also had effect of the nature of the response.

Analysis of Variance↗

PubMed2004

Comparative analysis of the Borrelia garinii genome.

Three members of the genus Borrelia (B.burgdorferi, B.garinii, B.afzelii) cause tick-borne borreliosis. Depending on the Borrelia species involved, the borreliosis differs in its clinical symptoms. Comparative genomics opens up a way to elucidate the underlying differences in Borrelia species. We analysed a low redundancy whole-genome shotgun (WGS) assembly of a B.garinii strain isolated from a patient with neuroborreliosis in comparison to the B.burgdorferi genome. This analysis reveals that most of the chromosome is conserved (92.7% identity on DNA as well as on amino acid level) in the two species, and no chromosomal rearrangement or larger insertions/deletions could be observed. Furthermore, two collinear plasmids (lp54 and cp26) seem to belong to the basic genome inventory of Borrelia species. These three collinear parts of the Borrelia genome encode 861 genes, which are orthologous in the two species examined. The majority of the genetic information of the other plasmids of B.burgdorferii is also present in B.garinii although orthology is not easy to define due to a high redundancy of the plasmid fraction. Yet, we did not find counterparts of the B.burgdorferi plasmids lp36 and lp38 or their respective gene repertoire in the B.garinii genome. Thus, phenotypic differences between the two species could be attributable to the presence or absence of these two plasmids as well as to the potentially positively selected genes.

Borrelia burgdorferi↗

PubMed2004

Electron localization-delocalization transitions in dissociation of the C4- anion: a large-D analysis.

We present a study, employing high level ab initio methods, of electron localization-delocalization transitions along the dissociation path of the C4- anion to C2 and C2-. We find that at the equilibrium geometry, the symmetrical and nonsymmetrical configurations of the linear C4- anion are almost isoenergetic. However, along a collinear dissociation path, the dipole moment drops abruptly to zero when the separation between the two middle carbon nuclei reaches about R = 2.15 angstroms. The dipole moment remains zero until about R = 2.78 angstroms, and then continuously increases as dissociation proceeds. This behavior is analogous to critical phenomena: The abrupt drop to zero of the dipole moment resembles a first-order phase transition, the later steady rise resembles a continuous phase transition. We show that a simple sub-Hamiltonian model, corresponding to the large-dimension limit for an electron in the field of four collinear carbon atoms, exhibits both kinds of phase transitions along the dissociation path.

Journal Article↗

PubMed2002

Through a genome, darkly: comparative analysis of plant chromosomal DNA.

Plant nuclear genomes encompass a wide range of variation in size and nucleotide composition with diverse arrangements of chromosomal segments, repetitive sequences and distribution of genes. Comparative genomic analysis may be undertaken at different levels of organisation, which are reflected in this review, together with a focus on the genetic and functional significance of the observed variation. Patterns of genome organisation have been revealed which reflect the different underlying mechanisms and constraints driving change. Thus comparative issues of genome size, nucleotide sequence composition and genome heterogeneity are provided as a background to understanding the different levels of segmental and repetitive sequence duplication and distribution of genes. The extent of synteny and collinearity revealed by recent genetic and sequence comparisons is discussed, together with a consideration of problems associated with such analyses. The possible origins and mechanisms of variation in genome size and organisation are covered, including the prevalence of duplication at different levels of organisation. The likely genetic, functional and adaptive consequences of replicated loci are discussed with evidence from comparative studies. The scope for comparative analysis of epigenetic plant genome variation is considered. Finally, opportunities for applying comparative genomics to isolating genes and understanding complex crop genomes are addressed.

DNA, Plant↗

PubMed2005

Photocatalytic degradation-excitation-emission matrix fluorescence for increasing the selectivity of polycyclic aromatic hydrocarbon analyses.

The application of photocatalysis enhancement to calibration of fluorescence excitation-emission matrixes (EEMs) with parallel factor (PARAFAC) analysis is described. In this study, three- and four-way PARAFAC analysis was employed to extract the fluorescent species' spectra from overlapping EEMs. Time-dependent photocatalysis degradation of the polycyclic aromatic hydrocarbons (PAHs) was employed to create an additional dimension for analysis. The consequent four-dimension degradation-EEM data cubes have greater selectivity for each PAH than do three-dimension EEM data cubes alone. On a scale of 0 to 1, with 0 being completely collinear spectra and 1 being orthogonal spectra, including the time-dependent measurements increased the selectivity an average of 21%, from 0.73 to 0.87.

Catalysis↗

PubMed1997

IgA nephropathy: prognostic classification of end-stage renal failure. L'Association des Néphrologues de l'Est.

BACKGROUND: As yet, no clinical or morphological prognostic classification of IgA nephropathy (IgAN) has been generally accepted. The objective of our study was to quantify the risk of developing end-stage renal failure (ESRF) in IgAN. METHODS: We report a prospective longitudinal study of 210 patients with IgAN confirmed by biopsy between 1987 and 1991. Thirty-two (15.2%) patients were lost to follow-up. Mean follow-up after renal biopsy was 5.6 (SD = 2.6) years. The variables included age, gender, illnesses prior to discovery of IgAN, clinical features at IgAN discovery, 24-h proteinuria, serum creatinine, IgA level, and antihypertensive drugs taken at the time of renal biopsy. Sixty-six renal biopsies were classified by light-microscopy according to Lee's morphological classification. The end-point was ESRF. Survival was analysed by a backward and forward stepwise procedure using the Cox model. The most accurate determination of relative risk was obtained by assessing collinearity of the variables. RESULTS: Thirty-three patients (15.7%) (31 men) developed ESRF. The five univariately significant variables: gender, gross haematuria, 24-h proteinuria (24-P), serum creatinine (SC), and antihypertensive treatment, were candidates for multivariate analysis. The final model used SC (< or = 100, 100-150, > 150 mumol/l), 24-P (< 1, > or = 1 g/day) and gender (female vs male) as independent variables (relative risk and 95% confidence interval were 3.5 (2.1, 5.9) for SC; 5.1 (1.9, 13.6) for 24-P; and 3.5 (0.9, 15) for gender). These estimates were used to construct a prognostic classification of ERSF for men with IgAN: stage 1 (SC < or = 150 mumol/l and 24-P < 1 g/day), stage 2 ((SC > 150 mumol/l and 24-P < 1 g/day) or (SC < or = 150 mumol/l and 24-P > or = 1 g/day)); stage 3 (SC > 150 mumol/l and 24-P > or = 1 g/day). The ESRF-free survival was estimated with Kaplan-Meier analysis. It was 98.5% for stage 1, 86.6% for stage 2, 21.3% for stage 3 (P < 0.001), 7 years after histological diagnosis. The validity of Lee's prognostic classification was confirmed using an independent sample. CONCLUSIONS: These classifications identify groups at high risk of ESRF. Therapeutic studies should focus on these groups.

Adult↗

PubMed2004

Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm).

This article describes the applicability of multivariate projection techniques, such as principal-component analysis (PCA) and partial least-squares (PLS) projections to latent structures, to the large-volume high-density data structures obtained within genomics, proteomics, and metabonomics. PCA and PLS, and their extensions, derive their usefulness from their ability to analyze data with many, noisy, collinear, and even incomplete variables in both X and Y. Three examples are used as illustrations: the first example is a genomics data set and involves modeling of microarray data of cell cycle-regulated genes in the microorganism Saccharomyces cerevisiae. The second example contains NMR-metabonomics data, measured on urine samples of male rats treated with either of the drugs chloroquine or amiodarone. The third and last data set describes sequence-function classification studies in a set of G-protein-coupled receptors using hierarchical PCA.

Animals↗

PubMed2004

The reading frame BPLF1 of Epstein-Barr virus: a homologue of herpes simplex virus protein VP16.

The open reading frame BPLF1 of Epstein-Barr virus (EBV) shows homology to the Herpes simplex virus 1 (HSV1) protein VP16. This protein is a structural tegument component playing a pivotal role for HSV replication as trans-activator of viral immediate-early genes. An EBV gene with a comparable function has not been described so far. However, computer analysis indicated that BPLF1 may be a tegument protein homologous to VP16. This is the first report on the characterisation of the BPLF1 gene, its transcription, and expression of its gene product in vitro and in vivo. Using RT-PCR and Northern blot assays we demonstrated that the BPLF1 gene belongs to the class of late lytic cycle genes of EBV. Besides a full length transcript of 9.5 kb also a polyadenylated transcript of approximately 3 kb is synthesised. However, no consensus splice sites could be identified. Northern blot experiments using partially overlapping probes and sequencing of a BPLF1-specific cDNA revealed 1,550 nucleotides of the BPLF1 transcript, collinear in sequence with the viral genome from position 64547 to 66097. A recombinant Western blot assay detected BPLF1-specific antibodies in seropositive individuals, in particular in cases with elevated viral replication like infectious mononucleosis, chronic active infection, and nasopharyngeal carcinoma. This demonstrated expression of the BPLF1 protein in vivo. Thus, experimental data and computer analysis strongly support the hypothesis of BPLF1 being a tegument protein of the EBV homologous to VP16 of HSV1 and ORF22 of Varicella zoster virus.

Animals↗

PubMed2003

Comparative analysis of the genomes of Rachiplusia ou and Autographa californica multiple nucleopolyhedroviruses.

The Rachiplusia ou multiple nucleopolyhedrovirus (RoMNPV) is a variant of Autographa californica MNPV (AcMNPV) but is significantly more virulent against several major agricultural pests. The genome sequence of the R1 strain of RoMNPV was determined and compared to that of AcMNPV strain C6. The RoMNPV genome is approximately 131.5 kbp with a G+C content of 39.1 %. The homologous repeat regions (hrs) described for AcMNPV-C6 are present in RoMNPV-R1 but the hrs of RoMNPV have fewer palindromic repeats. The RoMNPV-R1 nucleotide sequence is almost completely collinear with the sequence of AcMNPV-C6 and contains homologues of 150 of the 155 ORFs described for AcMNPV-C6. Deletions, insertions and substitutions have resulted in the loss of homologues for AcMNPV ORFs ac2 (bro), ac3 (ctl), ac97, ac121 and ac140 from the RoMNPV genome. The average amino acid sequence identity between RoMNPV and AcMNPV ORFs is 96.1 % and there are differences in promoter motif composition for 23 of these ORFs. Maximum-likelihood analysis of selection pressures on AcMNPV and RoMNPV ORFs indicate that ORFs ro18/ac20-ac21 (arif-1) and ro135/ac143 (odv-e18) have undergone positive selection.

Animals↗

PubMed2004

Neural mechanisms for the robust representation of junctions.

Junctions provide important cues in various perceptual tasks, such as the determination of occlusion relationships for figure-ground separation, transparency perception, and object recognition, among others. In computer vision, junctions are used in a number of tasks, like point matching for image tracking or correspondence analysis. We propose a biologically motivated approach to junction representation in which junctions are implicitly characterized by high activity for multiple orientations within a cortical hypercolumn. A local measure of circular variance is suggested to extract junction points from this distributed representation. Initial orientation measurements are often fragmented and noisy. A coherent contour representation can be generated by a model of V1 utilizing mechanisms of collinear long-range integration and recurrent interaction. In the model, local oriented contrast estimates that are consistent within a more global context are enhanced while inconsistent activities are suppressed. In a series of computational experiments, we compare junction detection based on the new recurrent model with a feedforward model of complex cells. We show that localization accuracy and positive correctness in the detection of generic junction configurations such as L- and T-junctions is improved by the recurrent long-range interaction. Further, receiver operating characteristics analysis is used to evaluate the detection performance on both synthetic and camera images, showing the superior performance of the new approach. Overall, we propose that nonlocal interactions implemented by known mechanisms within V1 play an important role in detecting higher-order features such as corners and junctions.

Models, Neurological↗

PubMed2004

Structure and solvation of melittin in hexafluoroacetone/water.

Intermolecular (1)H[(19)F] and (1)H[(1)H] nuclear Overhauser effects have been used to explore interaction of solvent components with melittin dissolved in 50% hexafluoroacetone trihydrate (HFA)/water. Standard nuclear Overhauser effect experiments and an analysis of C(alpha)H proton chemical shifts confirm that the conformation of the peptide in this solvent is alpha-helical from residues Ala4 to Thr11 and from Leu13 to Arg24. The two helical regions are not collinear; the interhelix angle (144 +/- 20 degrees ) found in this work is near that observed in the solid state and previous NMR studies. Intermolecular NOEs arising from interactions between spins of the solvent and the solute indicate that both fluoroalcohol and water molecules are strongly enough bound to the peptide that solvent-solute complexes persist for > or =2 ns. Preferential interactions of HFA with many hydrophobic side chains of the peptide are apparent while water molecules appear to be localized near hydrophilic side chains. These results indicate that interactions of both HFA and water are qualitatively different from those present when the peptide is dissolved in 35% hexafluoro-2-propanol/water, a chemically similar helix-supporting solvent system.

Acetone↗

PubMed2006

A comparative study of ulnar-shortening osteotomy by the freehand technique versus the Rayhack technique.

PURPOSE: To compare the results of ulnar shortening by the traditional freehand method with those achieved by the Rayhack technique. METHODS: A historical cohort of 95 patients (97 ulnas) who had ulnar shortening for the treatment of ulnar-impaction syndrome was evaluated. Forty-three patients (45 ulnas) were treated by the freehand technique and 52 patients (52 ulnas) by the Rayhack technique. Both groups were well matched in terms of age, gender, prior history of trauma, and associated injuries. The following variables were compared: duration of surgery, relief of pain, return to work, postoperative complications, time elapsed between surgery and return to work, union of the osteotomy, collinear alignment of the ulnar shaft, and alignment of the plate against the bone. These variables were compared by using the independent-groups t test, chi-square test, and Fisher exact test, as appropriate. RESULTS: Statistical analysis of the compared parameters: duration of surgery, relief of pain, return to work, postoperative complications, time elapsed between surgery and return to work, and union of the osteotomy, showed that none was significant. There were no cases of malalignment of the ulnar shaft or malalignment of the plate against bone in either group. Our calculations show that one would need a cohort of at least 300 patients in each group to show meaningful differences between the groups provided the same proportions held true. CONCLUSIONS: There was a trend toward a higher incidence of nonunion in patients who had the freehand technique although we were unable to show a statistical difference. TYPE OF STUDY/LEVEL OF EVIDENCE: Therapeutic, Level III.

Adolescent↗