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PubMed1999

Monte Carlo dynamics in global optimization.

Several very different optimization problems are studied by using the fixed-temperature Monte Carlo dynamics and found to share many common features. The most surprising result is that the cost function of these optimization problems itself is a very good stochastic variable to describe the complicated Monte Carlo processes. A multidimensional problem can therefore be mapped into a one-dimensional diffusion problem. This problem is either solved by direct numerical simulation or by using the Fokker-Planck equations. Above certain temperatures, the first passage time distribution functions of the original Monte Carlo processes are reproduced. At low temperatures, the first passage time has a path dependence and the single-stochastic-variable description is no longer valid. This analysis also provides a simple method to characterize the energy landscapes.

Crystallography, X-Ray↗

PubMed2003

Do sibling and friend relationships share the same temperamental origins? A twin study.

BACKGROUND: Friendship and sibling relationships differ in that there is an element of choice in friendships, whilst the latter represent a fixed and given relationship. The present study set out to investigate the temperamental correlates of friendships and sibling relationships, as well as to examine their genetic and environmental components. METHOD: Two hundred and twelve same-sex twin-pairs (102 MZ and 110 DZ; 104 male pairs and 108 female pairs) aged between 12 and 15, together with their parents, comprised the sample. The twins themselves reported on both negative and positive aspects of the two relationships, and all family members provided reports of the twins' temperament (mothers, fathers, and adolescent self-reports). RESULTS: Analyses revealed that negative aspects of both the sibling relationship and friendship were related to emotionality, while the positive aspects of these relationships were associated with sociability and activity. Genetic influences and the shared environment accounted for variance seen in the sibling relationship. In addition, nonshared environment accounted for a moderate amount of the sibling relationship variability and explained most of the variance for the friendship components. Finally, bivariate analyses of the covariance between temperament and close relationships highlighted the importance of nonshared environmental influences during adolescence. CONCLUSION: Three themes emerged. First, congruent temperamental expressions were seen across these two relationships' contexts. Second, friendship and the sibling relationship have distinct etiological profiles, indicating the child-specific character of adolescent friendships versus the reciprocal nature of the sibling relationship. Finally, the common influences to temperament and relationship quality provided evidence for the validity of adolescents' unique, nonshared experiences.

Adolescent↗

PubMed1994

Analysis of the nucleotide sequence variation of the antigen-binding domain of DR alpha and DQ alpha molecules as related to the evolution of papillomavirus-induced warts in rabbits.

We previously found that regression of skin warts induced by the Shope cottontail rabbit papillomavirus in New Zealand White rabbits, as well as malignant conversion of persistent warts, are linked to a restriction fragment length polymorphism of the major histocompatibility complex class II DR alpha and DQ alpha genes. To find out whether this immunogenetic control could be connected with the antigen binding and presentation function of the alpha 1 domain of class II molecules, we have sequenced the exon 2 of the four DR alpha EcoRI and six of the seven DQ alpha PvuII restriction fragment length polymorphism alleles identified, and deduced the encoded amino acid sequences. We found no amino acid polymorphism among DR alpha alleles, indicating that the alpha 1 domain of the DR alpha chain does not condition wart regression or cancer development. In contrast, 27 of the 82 amino acids of the DQ alpha 1 domain were found variable, defining five amino acid sequence alleles. The restriction fragment length polymorphism allele linked to regression and another allele not linked to regression share the same alpha 1 domain, indicating that wart regression is rather conditioned by a closely linked gene. The most divergent DQ alpha 1 allele, however, was that associated with a higher risk of cancer. Alignment of rabbit and human DQ alpha exon 2 alleles disclosed that amino acid charge variations occur at positions assumed to be important for peptide binding in humans. By modulating the affinity for tumor-specific antigenic peptides, such transitions could affect immune surveillance and, thus, condition the risk for progression to carcinoma of papillomavirus-associated lesions.

Alleles↗

PubMed2004

Genotype of Candida species associated with different conditions of vulvovaginal candidosis.

It is unknown whether strains isolated from recurrent vulvovaginal candidosis (RVVC), vulvovaginal candidosis (VVC) and asymptomatic carriers are varying or not in genotyping. Candida isolates were genotyped to determine whether specific types were associated with RVVC and VVC. A total of 97 Candida isolates from RVVC patients (n = 43), from VVC patients (n = 47) and asymptomatic carriers (n = 7) were identified by germ tube test, chlamydospore test, CHROMagar Candida and API20 system and were genotyped by polymerase chain reaction (PCR) fingerprinting employing random amplification of polymorphic DNA (RAPD) assay with nine random primers screened. The RAPD identified distinct genotypes that were shared among isolates from most different individuals. Most of the 85 C. albicans strains failed to corroborate any obvious differences in the genotypic variability in the VVC, RVVC patient groups and carriers by clustering analysis. Only a few individuals were found to harbor a distinct genotype of C. albicans isolates associated with a specific disease condition.

Candida↗

PubMed2025

Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.

Transposable elements (TEs) significantly influence genomic diversity and gene regulation in plants. Brassica rapa and B. oleracea, with their distinct domestication histories, offer excellent models to explore TE dynamics. Here, we developed a refined TE classification method and systematically analyzed TEs across 12 B. rapa and B. oleracea genomes, identifying 1878 TE families. Approximately half (49.5%) of these TE families were shared between the two species, reflecting a common evolutionary origin, whereas species-specific expansions, particularly among long-terminal repeat (LTR) retrotransposons, underscore their roles in genomic differentiation. We notably characterized a heat-responsive Ty1-copia family (Copia0035) in B. oleracea roots, distinguished by low GC content and the absence of CG and CHG methylation motifs, sharing regulatory similarities with the Arabidopsis heat-induced ONSEN element. Syntenic analyses of gene-TE associations highlighted significant intraspecies TE insertion variability, with more accession-specific insertions in B. rapa and more conserved insertions, often associated with distinct morphotypes in B. oleracea. Gene ontology enrichment indicated TE involvement in developmental, reproductive, and stress response pathways. Transcriptome analysis across diverse accessions revealed that genes proximal to TEs, particularly those regulating floral development and flowering time, exhibit increased expression variability. These findings advance our understanding of TE-mediated genome evolution in Brassica species and underscore their potential utility in breeding and genome engineering strategies for crop improvement.

DNA Transposable Elements↗

PubMed1987

Germline organization of the murine T cell receptor beta-chain genes.

The complete germline organization of the beta-chain genes of the murine T cell receptor was elucidated in order to obtain the structural basis for understanding the mechanisms of somatic DNA rearrangements. Twenty of the 22 known variable (V beta) genes are clustered within 250 kilobases of DNA 5' to the constant region (C beta) genes. These V beta genes share the same transcriptional orientation as the diversity (D beta), joining (J beta), and C beta genes, which implies that chromosomal deletion is the mechanism for most V beta to D beta-J beta rearrangements. Within this V beta cluster, the distance between the most proximal V beta gene and the D beta-J beta-C beta cluster is 320 kilobases, as determined by field-inversion gel electrophoresis. The large distance between V beta and D beta, relative to that between D beta and J beta, may have significant implications for the ordered rearrangement of the T cell receptor beta-chain genes.

Animals↗

PubMed2004

RalA but not RalB enhances polarized delivery of membrane proteins to the basolateral surface of epithelial cells.

RalA and RalB constitute a family of highly similar (85% identity) Ras-related GTPases. Recently, active forms of both RalA and RalB have been shown to bind to the exocyst complex, implicating them in the regulation of cellular secretion. However, we show here that only active RalA enhances the rate of delivery of E-cadherin and other proteins to their site in the basolateral membrane of MDCK cells, consistent with RalA being a regulator of exocyst function. One reason for this difference is that RalA binds more effectively to the exocyst complex than active RalB does both in vivo and in vitro. Another reason is that active RalA localizes to perinuclear recycling endosomes, where regulation of vesicle sorting is thought to take place, while active RalB does not. Strikingly, analysis of chimeras made between RalA and RalB reveals that high-affinity exocyst binding by RalA is due to unique amino acid sequences in RalA that are distal to the common effector-binding domains shared by RalA and RalB. Moreover, these chimeras show that the perinuclear localization of active RalA is due in part to its unique variable domain near the C terminus. This distinct localization appears to be important for RalA effects on secretion because all RalA mutants tested that failed to localize to the perinuclear region also failed to promote basolateral delivery of E-cadherin. Interestingly, one of these inactive mutants maintained binding to the exocyst complex, suggesting that RalA binding to the exocyst is necessary but not sufficient for RalA to promote basolateral delivery of membrane proteins.

Amino Acid Sequence↗

PubMed2001

The C-terminal domain of the Bloom syndrome DNA helicase is essential for genomic stability.

BACKGROUND: Bloom syndrome is a rare cancer-prone disorder in which the cells of affected persons have a high frequency of somatic mutation and genomic instability. Bloom syndrome cells have a distinctive high frequency of sister chromatid exchange and quadriradial formation. BLM, the protein altered in BS, is a member of the RecQ DNA helicase family, whose members share an average of 40% identity in the helicase domain and have divergent N-terminal and C-terminal flanking regions of variable lengths. The BLM DNA helicase has been shown to localize to the ND10 (nuclear domain 10) or PML (promyelocytic leukemia) nuclear bodies, where it associates with TOPIIIalpha, and to the nucleolus. RESULTS: This report demonstrates that the N-terminal domain of BLM is responsible for localization of the protein to the nuclear bodies, while the C-terminal domain directs the protein to the nucleolus. Deletions of the N-terminal domain of BLM have little effect on sister chromatid exchange frequency and chromosome stability as compared to helicase and C-terminal mutations which can increase SCE frequency and chromosome abnormalities. CONCLUSION: The helicase activity and the C-terminal domain of BLM are critical for maintaining genomic stability as measured by the sister chromatid exchange assay. The localization of BLM into the nucleolus by the C-terminal domain appears to be more important to genomic stability than localization in the nuclear bodies.

Adenosine Triphosphatases↗

PubMed1990

A unified hypothesis for the complex genetics of HLA associations with IDDM.

Our understanding of the role of HLA genes associated with insulin-dependent diabetes mellitus (IDDM) is in disarray, despite recent improvements in the definition of specific alleles and haplotypes. Some genes are highly associated with IDDM, other genes are associated with resistance to IDDM, and some highly associated susceptibility genes are markedly influenced by trans-associated synergistic effects (DR3/4 heterozygotes) or protective effects (DR2/4 heterozygotes). This plethora of genetic associations has spawned the notion that there are many contributing susceptibility genes, which, in turn, has led to the search for shared structural features among different genes on IDDM-associated haplotypes. From a more mechanistic point of view, however, the wide range of variable IDDM associations, with both cis- and trans-encoded protective and/or synergistic effects, suggests a different approach. This article proposes a hypothesis in which the different HLA associations with IDDM can be simply explained by a single unifying concept: a hierarchy of affinities determines the interaction between a diabetogenic peptide and different class II molecules, and an individual is susceptible to IDDM if the class II molecule in that individual with the highest affinity for such a peptide is a DQ beta susceptibility gene. The explicit formulation of this proposal and its genetic implications provide an explanation for HLA-encoded dominant "protection" and for some of the more subtle genetic observations related to cis and trans influences in IDDM susceptibility.

Diabetes Mellitus, Type 1↗

PubMedDate not supplied

Executive function and magnetic resonance imaging subcortical hyperintensities in vascular dementia.

OBJECTIVE: To determine the relation between subcortical hyperintensities (SHs) visible on magnetic resonance imaging and executive function among patients with vascular dementia. BACKGROUND: The relation between SHs and executive dysfunction is not well understood, because studies have varied widely in methodology and have produced conflicting results. METHOD: We examined the relation between SHs (expressed as a percentage of total brain volume, not including ventricular volume) and six tests of executive function in a well-defined group of 24 individuals with vascular dementia. Executive tests were divided in two groups: Attention/Speed and Abstraction/Problem Solving. Bivariate correlations were computed between individual neuropsychological variables and SHs. RESULTS: Results showed significant bivariate correlations between SHs and three of the four tests in the Attention/Speed domain. Subcortical hyperintensities shared virtually no association with performance on tests in the Abstraction/Problem-Solving domain. CONCLUSIONS: The finding that SHs are significantly associated with psychomotor slowing and attentional dysfunction is consistent with what is known about the behavioral manifestations of subcortical disease. More detailed investigations of the regional distribution of SHs as well as measures of atrophy, hypoperfusion, and hypometabolism may be necessary to accurately characterize the complex relation between vascular disease and different aspects of executive dysfunction.

Aged↗

PubMed2002

Genes with linkage or association with type 2 diabetes mellitus.

Complex diseases, such as type 2 diabetes mellitus (T2DM), arise from metabolic disruptions with genetic and environmental components. Multiple genes are responsible for the genetic susceptibility to T2DM. The contribution of these genes to the diabetic phenotype may be modest, variable among different populations, and dependent on interactions with other genes and the environment. The methods of genetic dissection based on linkage, allele sharing, and linkage disequilibrium may lack the statistical power to detect weak associations in heterogeneous populations. Nevertheless, genes involved in insulin signaling, insulin secretion, insulin resistance, glucose metabolism, obesity, diabetes comorbidity and the hormone processing protease genes have been associated with T2DM. New research strategies are improving the methods of genetic dissection and include genomic sequence information to characterize profiles of sequence variants that predispose to T2DM.

Chromosome Mapping↗

PubMed2003

[Differential diagnosis of severe acute respiratory syndrome (SARS) in "post-SARS" stage].

The epidemic of severe acute respiratory syndrome (SARS) has now been brought under control and entered the so-called post-SARS stage, with only a very few new cases reported daily throughout China. As an infectious disease spreading through the respiratory tract, SARS is featured by the inconsistency between its clinical representations, physical signs of the lungs and chest imaging findings. It has been shown that atypical pneumonia (AP), with similar clinical features to SARS, has been identified in Guangzhou, China, long before the prevalence of SARS, a fact that urges further understanding of SARS in regard to its incidence and variable clinical courses, for its differential diagnosis with such diseases as AP, influenza-related pneumonia, pulmonary tuberculosis, fungal and cytomegalovirus pneumonia. Information sharing among the medical institutes and training of the first-line medical staff for their better understanding and awareness of SARS and AP is crucial in the clinical practice, to insure timely case identification and avoid "oversensitive" diagnosis. Consultation of particular cases involving experts from multiple medical science fields should be encouraged, which is also an effective measure against newly emerged infectious diseases.

Diagnosis, Differential↗

PubMed1992

Alternaria spore and mycelium sensitivity in allergic patients: in vivo and in vitro studies.

Extracts from Alternaria spores and mycelia were prepared to evaluate their allergenic potencies in allergic patients. Twelve Alternaria-sensitive patients, with histories of rhinitis or asthma, were submitted to skin prick tests and five of 12 patients received nasal challenges with spores and mycelia. In vitro, the allergenic activity of each extract was determined by RAST, basophil histamine-release and RAST-inhibition. All patients demonstrated skin reactivity to both extracts while skin reactivity to mycelia was higher than that induced by the spore extract (P < .005). Of the 12 patients, 11 had positive mycelia-RAST and 9/12 had positive spore-RAST. It was found that mycelium-IgE antibody levels were higher than spore-IgE antibody levels (P < .005). Nine RAST-positive patients had positive histamine release tests (> 50%) and basophils challenged with mycelia appeared 10-fold more sensitive compared to the spore challenge. In four of five patients subjected to nasal provocation tests, immediate-type rhinitis was elicited either after spore or mycelium challenge. The patients exhibited a higher nasal reactivity with the mycelium challenge than with spores. RAST-inhibition studies demonstrated that mycelial extracts shared common allergens with spore. These results indicated that Alternaria spore and mycelium were potent allergens in allergic patients and there was a variability in the pattern of in vivo and in vitro reactions between the patients for each allergen.

Adolescent↗

PubMedDate not supplied

[Developmental and individual differences in delayed response task performance (A-not-B task) in 7- to 12-month-old infant twins].

The purpose of the study was to explore developmental and individual differences in the working memory that was assessed by performance of the A-not-B task in 7- to 12-month-old infant twins. The sample included 150 infant twins participating in genetic project, 18 of them were tested at 8 and 11 months of age. Information concerning birth weight and gestational age was collected from birth records. All infants were tested using Bayley Scales of Mental and Psychomotor Development. The infant's working memory (WM) was tested during A-not-B task performance, which was shown to depend on the maturity of the prefrontal cortex. The behavioral data were analyzed off-line using videotape records. The one-way ANOVA revealed that the AB performance improves with age. A highly significant improvement of the ability to tolerate the delay in A-not-B task was observed between 9 and 10 months of life. There was no longitudinal stability in individual infant performance of A-not-B across the period of 7-12 months of age. The AB delay was significantly correlated with psychomotor and mental development only after the crucial period of the rapid increase in the AB delay (9-10 months). The analysis of intraclass mono- and dizygotic correlations showed that individual differences in the WM (tolerance to AB delay) at 7-9 months and at 10-12 months are of different nature. There was a significant effect of shared environment on AB delay variance in 10-12-month-old group, whereas down to this age no systematic influence on individual variability was observed. These findings suggest that the ability to tolerate the AB delay can be provided by different brain mechanisms in 7-9 and 10-12-month-old infants.

Age Factors↗

PubMedDate not supplied

[Pararenal aortic aneurysms: definition, classification, directions for surgery].

The formidable impact derived by the endovascular correction (Evar) of abdominal aorta aneurysms (AAA), has risen its classification aspects. The topographical criteria has assumed importance in decisional diagnostic-therapeutic strategy especially in cases of so called pararenal aneurysms (PRAA). DEFINITION: PRAA defines aneurysm being involved underenal juxtarenal aorta (JRA), or more rarely, suprarenal aorta with normal aortic diameter at level of celiac (JRA), or more rarely, suprarenal aorta with normal aortic diameter at level of celiac trunk. CLASSIFICATION: The morphologic-topographic aspect is considered in function of selection or eligibility of patients to Evar or standard open surgery, in the need of a suprarenal clamping for the tailoring of proximal anastomosis or anchorage of endoprotesis. Various specific classifications for these aneurysms have been proposed (Schumacher, 1997; Wolf, 2000; Ayari, 2001) that considers: 1. Aneurysm collar: short/long/tortuous, 2. Relations with renal arteries, 3. Relations with the left renal vein. DIRECTIONS FOR SURGICAL TREATMENT: The choice between the technical solution to prefer either open or endovascular surgery will have to consider a series of additional variables to the standard direction common to every AAA based on dimensions and morphology. Priority will have to be given to evaluating, using shared morphologic-topographical classification criteria, real incidence of PRAA-JRA (3%-20% in literature review); greater post opening mortality (1.3%-15.3%); dimensions (AAA with diameter > or = 5.5 cm in operating risk assessment of single patient, in clinical evolution and increase in the time of the lesion); in common occurrence in AAA of steno-obstructive lesions of renal arteries and involvement of same ones in the aneurysm collar in need of reconstruction and suprarenal aortic clamping.

Aortic Aneurysm, Abdominal↗

PubMed2004

[Population genetic structure of Pelophylax nigromaculata in Chinese mainland based on mtDNA control region sequences].

Molecular genetic data were used to investigate population genetic structure and differentiation of Pelophylax nigromaculata (Anura: Ranidae). Frogs were collected from 12 localities across Chinese mainland. Sample sizes of up to 10 frogs per population were assayed for mitochondrial control region sequence variation. The aligned 685 bp of the 5'CR include 111 variable sites. Sixty-seven haplotypes were defined. Most of the haplotypes are unique to local populations, only 7 of the 67 are shared among a few local populations. The overall species haplotype diversity is quite high (h = 0.98 +/- 0.005), and the nucleotide diversity is also high (pi = 0.0303 +/- 0.0029). This is corresponding to huge population size and extensive distribution of Pelophylax nigromaculata throughout Palaearctic and Oriental Regions. Phylogenetic tree of mtDNA control region haplotypes based on maximum parsimony algorithm and reconstructed phylogenetic relationships among the local populations based on neighbor joining algorithm all suggest that the haplotypes of Jiling and Liaoning populations in northeastern China have a sister relationship with 10 local populations in northern, central, southern and southwestern China. The analysis of molecular variance (AMOVA), the pairwise FST values and nucleotide divergence all support significant population subdivision between the Jilin-Liaoning group and multi-population group. The most possible cause of the significant genetic subdivision between the two groups might be referred to the effect of Quaternary glaciation. The possible reasons for the lack of obvious geographic structure on the whole in the multi-population group and the genetic differentiation in some local populations of the multi-population group were also discussed.

Animals↗

PubMed2005

Software model of a machine vision system based on the common house fly.

The vision system of the common house fly has many properties, such as hyperacuity and parallel structure, which would be advantageous in a machine vision system. A software model has been developed which is ultimately intended to be a tool to guide the design of an analog real time vision system. The model starts by laying out cartridges over an image. The cartridges are analogous to the ommatidium of the fly's eye and contain seven photoreceptors each with a Gaussian profile. The spacing between photoreceptors is variable providing for more or less detail as needed. The cartridges provide information on what type of features they see and neighboring cartridges share information to construct a feature map.

Algorithms↗

PubMed1988

Structure and expression of the gene coding for the human serpin hLS2.

We have analyzed genomic clones encoding human leuserpin 2 (hLS2). The gene covers about 14.5 kilobases and consists of 5 exons and 4 introns. The genes coding for hLS2, alpha 1-antitrypsin, alpha 1-antichymotrypsin, and rat angiotensinogen share an equivalent exon-intron structure and therefore constitute a distinct subgroup within the serpin gene family, which otherwise displays a highly variable exon-intron pattern. With the exception of a segment in the second exon, the sequence similarity of the genes coding for hLS2 and alpha 1-antitrypsin extends to all exons including one encoding the 5'-untranslated sequences. The implications of these findings with respect to the genesis of the amino-terminal heterogeneity in the serpin family are discussed.

Amino Acid Sequence↗