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PubMed2004

Risk factors for the development versus maintenance of posttraumatic stress disorder.

This study examined risk factors for posttraumatic stress disorder (PTSD) in Vietnam veterans: 68 women and 414 men of whom 88 were White, 63 Black, 80 Hispanic, 90 Native Hawaiian, and 93 Japanese American. Continuation ratio logistic regression was used to compare the predictive power of risk factors for the development versus maintenance of full or partial PTSD. The development of PTSD was related to premilitary, military, and postmilitary factors. The maintenance of PTSD was related primarily to military and postmilitary factors. Multivariate analyses identified different models for development and maintenance. We conclude that development of PTSD is related to factors that occur before, during, and after a traumatic event, whereas failure to recover is related primarily to factors that occur during and after the event.

Adult↗

PubMed2006

Multivariate methods in the development of a new tablet formulation: excipient mixtures and principal properties.

A tablet formulation for direct compression has previously been studied using multivariate design. An optimization study of one of the most important tablet properties, disintegration time, revealed that excipients with Principal Properties (PP's) that were predicted as suitable by the model were not represented within the studied material. The feasibility of using mixtures of excipients in the multivariate approach to tablet formulation to solve this problem has been investigated in the present study. By mixing different excipients of the same excipient class, it should be possible to obtain mixtures with the predicted PP's, which in turn should give a formulation with the desired properties. In order to investigate the utility of this approach, separate mixture designs were applied to both binders and fillers (diluents). As reported here, the Partial Least Squares Projections to Latent Structures (PLS) model developed in the previously published screening study has been validated in the sense that the interesting region of the PP space identified in it has been shown to contain excipients, pure or mixed, that give the formulation suitable properties. Formulations with suitable properties were found with the mixture experiments. The local models also offer several alternatives for the composition of the formulation that yield the desired disintegration time.

Chemistry, Pharmaceutical↗

PubMed1995

A mouse homologue of the Xenopus germ cell-specific ribonucleic acid/deoxyribonucleic acid-binding proteins p54/p56 interacts with the protamine 2 promoter.

Recent evidence indicates that a member of the Y box-binding family of transcriptional regulators is identical to p56, a predominant protein of messenger ribonucleoprotein complexes. The p56 protein is highly enriched in oocytes and testis, and a functional RNA binding mouse cytoplasmic homologue has been cloned and partially characterized. Because few potential testis-specific transcriptional regulators have been identified, the testis-enriched Y box-binding proteins represent trans-acting elements of a unique model system for the study of haploid gene expression. The 5' flanking region of the testis-specific, haploid-expressed mouse protamine 2 gene contains an element with a 9-of-12 nucleotide identity with the previously defined Y box consensus sequence. We have investigated the possible role of Y box-binding proteins in transcriptional regulation of protamine 2 using specific antibodies and DNA-protein binding assays. Western blot analyses with two different anti-p54/p56 antibodies demonstrate that a mouse homologue of Xenopus p54/p56 is present in transcriptionally active mouse testis nuclear extracts. Our results further indicate that the Xenopus Y box-binding proteins bind to an element 5' to the mouse protamine 2 gene. Similarly, binding of the mouse testis homologue to the protamine 2 Y box element is demonstrated by gel mobility shift and antibody supershift analyses. The demonstrated interactions between testis-enriched Y box-binding proteins and protamine 2 transcriptional control elements therefore represent a unique system for functional studies to determine the mechanism of regulation of haploid gene expression.

Animals↗

PubMed1994

Characterization of a region of plasmid pBL1 of Brevibacterium lactofermentum involved in replication via the rolling circle model.

The minimal region for autonomous replication of pBL1, a 4.5-kb cryptic plasmid of Brevibacterium lactofermentum ATCC 13869 that has been used to construct a variety of corynebacterium vectors, was shown to be contained on a 1.8-kb HindII-SphI DNA fragment. This region contains two open reading frames (ORFs) (ORF1 and ORF5) which are essential for pBL1 replication in B. lactofermentum. Accumulation of single-strand intermediates in some of the constructions indicates that plasmid pBL1 replicates via the rolling circle replication model; its plus strand and minus strand were identified by hybridization with two synthetic oligonucleotide probes complementary to each pBL1 strand. ORF1 seems to encode the Rep protein and showed partial homology with sequences for Rep proteins from Streptomyces plasmids which replicate via rolling circle replication such as pIJ101, pSB24, and pJV1.

Amino Acid Sequence↗

PubMed1998

Partial-volume Bayesian classification of material mixtures in MR volume data using voxel histograms.

We present a new algorithm for identifying the distribution of different material types in volumetric datasets such as those produced with magnetic resonance imaging (MRI) or computed tomography (CT). Because we allow for mixtures of materials and treat voxels as regions, our technique reduces errors that other classification techniques can create along boundaries between materials and is particularly useful for creating accurate geometric models and renderings from volume data. It also has the potential to make volume measurements more accurately and classifies noisy, low-resolution data well. There are two unusual aspects to our approach. First, we assume that, due to partial-volume effects, or blurring, voxels can contain more than one material, e.g., both muscle and fat; we compute the relative proportion of each material in the voxels. Second, we incorporate information from neighboring voxels into the classification process by reconstructing a continuous function, rho(x), from the samples and then looking at the distribution of values that rho(x) takes on within the region of a voxel. This distribution of values is represented by a histogram taken over the region of the voxel; the mixture of materials that those values measure is identified within the voxel using a probabilistic Bayesian approach that matches the histogram by finding the mixture of materials within each voxel most likely to have created the histogram. The size of regions that we classify is chosen to match the spacing of the samples because the spacing is intrinsically related to the minimum feature size that the reconstructed continuous function can represent.

Algorithms↗

PubMed2004

Sensitivity to curvatures in orientation-based texture segmentation.

Texture segregation has long been attributed to changes in the distribution of elementary features across the visual field [Nature 290 (12) (1981) 91; Biol. Cybernet. 54 (1986) 245]. The study of orientation, a conspicuous feature, has led to models of orientation-based texture segmentation (OBTS) that depend on the magnitude of one or two orientation gradients [Vis. Res. 31 (4) (1991) 679; Vis. Res. 31 (6) (1991) 1073] and influenced further by the relative configuration between the orientation textons and the global orientation edge [Percept. Psychophys. 52 (4) (1992) 255; Vis. Res. 35 (20) (1995) 2863]. Here we show that these models are at best partial and that the notion of orientation gradient has been incompletely used in the study of OBTS. To do so, we first study the behavior of orientation in orientation-defined texture patches. Geometrical analysis identifies two texture curvatures and reveals the incompleteness of previous stimuli. Psychophysical experimentation then demonstrates that segmentation is strongly affected by discontinuities in these curvatures. Importantly, we show that this sensitivity to curvature is independent of the orientation gradients and inconsistent with the simple configural considerations proposed in the past.

Discrimination, Psychological↗

PubMed2004

FMRP and its target RNAs: fishing for the specificity.

Learning and memory difficulties observed in patients with fragile X syndrome, as well as in a mouse model for the syndrome, are partially due to impaired translational regulation of neuronal mRNAs encoding key molecules for the synaptic structure and function. There has been intense interest in characterizing the mRNAs that are regulated by the fragile X mental retardation protein (FMRP) in the neuronal cell. A large number of candidate FMRP-interacting mRNAs has been identified over the last few years and three models have been described so far to explain the specificity of these interactions. Here, we report our vision on how they could work in the same and/or in different pathways and suggest that the three mechanisms may not be mutually exclusive.

Animals↗

PubMed2005

Three-dimensional model of cytochrome P450 human aromatase.

A three-dimensional (3-D) structure of human aromatase (CYP 19) was modeled on the basis of the crystal structure of rabbit CYP2C5, the first solved X-ray structure of an eukaryotic cytochrome P450 and was evaluated by docking S-fadrozole and the steroidal competitive inhibitor (19R)-10-thiiranylestr-4-ene-3,17-dione, into the enzyme active site. According to a previous pharmacophoric hypothesis described in the literature, the cyano group of S-fadrozole partially mimics the steroid backbone C(17) carbonyl group of (19R)-10-thiiranylestr-4-ene-3,17-dione, and was oriented in a favorable position for H-bonding with the newly identified positively charged residues Lys 119 and Arg435. In addition, this model is consistent with the recent combined mutagenesis/modeling studies already published concerning the roles ofAsp309 and His480 in the aromatization of the steroid A ring.

Amino Acid Sequence↗

PubMedDate not supplied

A high dimensional QSAR study on the aldose reductase inhibitory activity of some flavones: topological descriptors in modeling the activity.

The quantitative structure-activity relationships (QSAR) of the Aldose Reductase (AR) inhibitory activity of 48 flavones were studied using Free-Wilson, Combinatorial Protocol in Multiple Linear Regression (CP-MLR), and Partial Least Squares (PLS) procedures. For the latter two procedures 152 Molconn-Z parameters and six indicators corresponding to the hydroxyls of flavones were used as molecular descriptors. Independently, all procedures suggested the significance of hydroxyls in modulating the activity of these compounds. The CP-MLR procedure identified 26 descriptors to model the activity. They suggested that structures rich in aromatic CH fragments, with a limited number of aliphatic fragments such as -CH2-, -CH<, and free hydroxyls at 7-, 3'-, and 4'-positions of the 2-arylbenzpyran-4-one core would be preferred for the activity. The PLS analysis agreed with the information content and the relative significance of the descriptors identified in the CP-MLR for modeling the activity. The study offers the scope to modulate the inhibitory activity of these compounds.

Aldehyde Reductase↗

PubMed1996

Tentative model for the mapping of D epitopes on the RhD polypeptide.

The partial D phenotypes correspond to D-positive individuals that may develop anti-D antibodies following immunization by transfusion or pregnancy, since they lack some of the D epitopes that compose the D antigen. When these red cells are tested with a panel of human monoclonal anti-D, different patterns of reactivity are observed and at least nine distinct epitopes termed epD1 to epD9 can be identified. Molecular analysis of partial D variants have shown that the loss of some D epitopes is associated either with intergenic recombination events between the D and CE genes generating hybrid gene structures D-CE-D or CE-D-CE, or with point mutations of the D gene. Based on these findings, a tentative model that correlates critical amino acid positions and D epitope expression on the D protein was proposed. Although recent studies suggest that the D antigen may be composed of as many as 30 epitopes, the relatively simple model presented here may be useful to serologists as a preliminary approach to understanding the basis of D antigenic variation in terms of structure-activity relationship.

Antibodies, Monoclonal↗

PubMed2005

Probing the beta2 adrenoceptor binding site with catechol reveals differences in binding and activation by agonists and partial agonists.

The beta(2) adrenergic receptor (beta(2)AR) is a prototypical family A G protein-coupled receptor (GPCR) and an excellent model system for studying the mechanism of GPCR activation. The beta(2)AR agonist binding site is well characterized, and there is a wealth of structurally related ligands with functionally diverse properties. In the present study, we use catechol (1,2-benzenediol, a structural component of catecholamine agonists) as a molecular probe to identify mechanistic differences between beta(2)AR activation by catecholamine agonists, such as isoproterenol, and by the structurally related non-catechol partial agonist salbutamol. Using biophysical and pharmacologic approaches, we show that the aromatic ring of salbutamol binds to a different site on the beta(2)AR than the aromatic ring of catecholamines. This difference is important in receptor activation as it has been hypothesized that the aromatic ring of catecholamines plays a role in triggering receptor activation through interactions with a conserved cluster of aromatic residues in the sixth transmembrane segment by a rotamer toggle switch mechanism. Our experiments indicate that the aromatic ring of salbutamol does not activate this mechanism either directly or indirectly. Moreover, the non-catechol ring of partial agonists does not interact optimally with serine residues in the fifth transmembrane helix that have been shown to play an important role in activation by catecholamines. These results demonstrate unexpected differences in binding and activation by structurally similar agonists and partial agonists. Moreover, they provide evidence that activation of a GPCR is a multistep process that can be dissected into its component parts using agonist fragments.

Albuterol↗

PubMed2005

Adenovirus protein VI mediates membrane disruption following capsid disassembly.

In contrast to enveloped viruses, the mechanisms involved in membrane penetration by nonenveloped viruses are not as well understood. In these studies, we determined the relationship between adenovirus (Ad) capsid disassembly and the development of membrane lytic activity. Exposure to low pH or heating induced conformational changes in wild-type Ad but not in temperature-sensitive Ad (ts1) particles that fail to escape the early endosome. Wild-type Ad but not ts1 particles permeabilized model membranes (liposomes) and facilitated the cytosolic delivery of a ribotoxin. Alterations in wild-type Ad capsids were associated with the exposure of a pH-independent membrane lytic factor. Unexpectedly, this factor was identified as protein VI, a 22-kDa cement protein located beneath the peripentonal hexons in the viral capsid. Recombinant protein VI and preprotein VI, but not a deletion mutant lacking an N-terminal amphipathic alpha-helix, possessed membrane lytic activity similar to partially disassembled virions. A new model of Ad entry is proposed based on our present observations of capsid disassembly and membrane penetration.

Adenoviridae↗

PubMed2006

Effect of the glottal source and the vocal tract on the partials amplitude of vibrato in male voices.

In this paper the production of vocal vibrato is investigated. The most relevant features of the acoustical vibrato signal, frequency and amplitude variations of the partials, will be related to the voice production features, glottal source (GS) and vocal tract response (VTR). Unlike previous related works, in this approach, the effect on the amplitude variations of the partials of each one of the above-mentioned voice production features will be identified in recordings of natural singing voice. Moreover, we will take special care of the reliability of the measurements, and, to this aim, a noninteractive vibrato production model will be also proposed in order to describe the vibrato production process and, more importantly, validate the measurements carried out in natural vibrato. Based on this study, it will be shown that during a few vibrato cycles, the glottal pulse characteristics, as well as the VTR, do not significantly change, and only the fundamental frequency of the GS varies. As a result, the pitch variations can be attributed to the GS, and these variations, along with the vocal tract filtering effect, will result in frequency and amplitude variations of the acoustic signal partials.

Auditory Perception↗

PubMed1994

Expression of a growth arrest specific gene (gas-6) during liver regeneration: molecular mechanisms and signalling pathways.

A set of growth arrest-specific (gas) genes negatively regulated by serum has been identified. To define the role of gas genes in a model of cell proliferation in vivo we analyzed the expression of one of these genes (gas-6) during liver regeneration after partial hepatectomy (PH). We found that gas-6 mRNA was down-regulated 4 hours after PH, within the G0 to G1 transition. Later on, gas-6 mRNA increased over the level found in normal liver with a peak at 16 hours, before the onset of DNA synthesis. This surge was probably triggered by an inflammatory response caused by the surgical trauma, because an increase of similar extent occurring with the same time course was present in livers of sham-operated and turpentine-treated rats. Comparison of mRNA steady state levels with nuclear transcription rates indicated that gas-6 expression is post-transcriptionally regulated. As we found that down-regulation of gas-6 expression was prevented by treatment with Actinomycin D, a labile protein might be involved in the determination of gas-6 mRNA stability. To investigate the mitogenic signals controlling gas-6 expression during liver regeneration we treated hepatectomized rats with a specific alpha-1-adrenoceptor blocker (prazosin) as well as with drugs which modify intracellular calcium levels. The decrease of gas-6 mRNA 4 hours after PH was prevented by prazosin and by neomycin, an inhibitor of calcium release from endogenous stores. These findings suggest that down-regulation of gas-6 expression during hepatic regeneration is triggered by catecholamines interaction with alpha-1-adrenergic receptors and by subsequent calcium release. In addition we found that the rise of gas-6 gene expression occurring at 16 hours after PH was not affected by prazosin but was inhibited by trifluoperazine. Therefore, we suggest that up-regulation of gas-6 gene expression is mediated by the interaction of calcium with calmodulin, independently of catecholamines.

Animals↗

PubMed2005

Application of partial least squares discriminant analysis to two-dimensional difference gel studies in expression proteomics.

Two-dimensional difference gel electrophoresis (DIGE) is a tool for measuring changes in protein expression between samples involving pre-electrophoretic labeling ith cyanine dyes. In multi-gel experiments, univariate statistical tests have been used to identify differential expression between sample types by looking for significant changes in spot volume. Multivariate statistical tests, which look for correlated changes between sample types, provide an alternate approach for identifying spots with differential expression. Partial least squares-discriminant analysis (PLS-DA), a multivariate statistical approach, was combined with an iterative threshold process to identify which protein spots had the greatest contribution to the model, and compared to univariate test for three datasets. This included one dataset where no biological difference was expected. The novel multivariate approach, detailed here, represents a method to complement the univariate approach in identification of differentially expressed protein spots. This new approach has the advantages of reduced risk of false-positives and the identification of spots that are significantly altered in terms of correlated expression rather than absolute expression values.

Analysis of Variance↗

PubMed2005

Differential responses of PPARalpha, PPARdelta, and PPARgamma reporter cell lines to selective PPAR synthetic ligands.

To characterize the specificity of synthetic compounds for peroxisome proliferator-activated receptors (PPARs), three stable cell lines expressing the ligand binding domain (LBD) of human PPARalpha, PPARdelta, or PPARgamma fused to the yeast GAL4 DNA binding domain (DBD) were developed. These reporter cell lines were generated by a two-step transfection procedure. First, a stable cell line, HG5LN, expressing the reporter gene was developed. These cells were then transfected with the different receptor genes. With the help of the three PPAR reporter cell lines, we assessed the selectivity and activity of PPAR agonists GW7647, WY-14-643, L-165041, GW501516, BRL49653, ciglitazone, and pioglitazone. GW7647, L-165041, and BRL49653 were the most potent and selective agonists for hPPARalpha, hPPARdelta, and hPPARgamma, respectively. Two PPAR antagonists, GW9662 and BADGE, were also tested. GW9662 was a selective PPARgamma antagonist, whereas BADGE was a low-affinity PPAR ligand. Furthermore, GW9662 was a full antagonist on PPARgamma and PPARdelta, whereas it showed partial agonism on PPARalpha. We conclude that our stable models allow specific and sensitive measurement of PPAR ligand activities and are a high-throughput, cell-based screening tool for identifying and characterizing PPAR ligands.

Anilides↗

PubMed2002

LH receptor defects.

In this article the role of LH receptor gene mutations in patients with aberrant sex differentiation is discussed. In a dominant autosomal familial form of precocious puberty in boys (familial male-limited precocious puberty) LH receptor gene mutations have been identified. These single amino acid changes, mostly found in the sixth transmembrane helix and the third intracellular loop of the transmembrane domain of the LH receptor, cause constitutive activation of LH receptor protein without the hormone present, resulting in precocious production of testosterone by the testicular Leydig cells. The large number of activating LH receptor mutations have allowed more precise molecular modeling of the LH receptor protein. In a rare hereditary form of 46,XY male pseudohermaphroditism known as Leydig cell hypoplasia, LH receptor gene mutations have been identified that completely or partially inactivate the LH receptor protein. Large gene deletions cause complete absence of the LH receptor protein, whereas other, more subtle missense mutations prevent the receptor from assuming an active conformation.

Animals↗

PubMed1976

Stucture of the amino-acid accepting 3'-end of high-molecular-weight eggplant mosaic virus RNA.

The sequence of the first 59 nucleotides from the 3'-OH terminus of high-molecular-weight eggplant mosaic virus RNA has been determined by standard radio-chemical techniques. The fragment was identified among the products of partial T1 RNase digestion by making use of the reverse migration, at pH 2.5, of the 3'-OH terminal oligonucleotide. No abnormal bases were found. A model of secondary structure may be constructed for this fragment, which is known to fix valine in the presence of valyl-tRNA synthetase. Its relation to the structures of genuine tRNAs and to the 3'-OH termini of other viral RNAs that also accept amino acids is discussed.

Amino Acids↗