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PubMed2003

Zea mays ontology--a database of international terms.

Data retrieval, comprehension and sharing within and between plant-based databases are essential to exploit comparative genomic information to elucidate functional aspects of plant biology and to conduct studies of synteny and homology. However, the functionality is often hampered by the variability of terms used to describe comparable objects. The Zea mays Plant Structure Ontology database is designed to overcome this problem via the provision of a controlled vocabulary that facilitates knowledge sharing. It comprises international botanical terms, references, synonyms, and phylogenetic information and is open-source.

Databases, Factual↗

PubMed2000

Low variability in a Y-linked plant gene and its implications for Y-chromosome evolution.

Sex chromosomes have evolved independently in several different groups of organisms, but they share common features, including genetic degeneration of the Y chromosome. Suppression of recombination between ancestral proto-X and proto-Y chromosomes is thought to have led to their gradual divergence, and to degeneration of the Y chromosome, but the evolutionary forces responsible are unknown. In non-recombining Y chromosomes, deleterious mutations may be carried to fixation by linked advantageous mutations ("selective sweeps"). Occurrence of deleterious mutations may drive "Muller's ratchet" (stochastic loss of chromosomes with the fewest mutations). Selective elimination of deleterious mutations, causing "background selection" may accelerate stochastic fixation of mildly detrimental mutations. All these processes lower effective population sizes, and therefore reduce variability of genes in evolving Y chromosomes. We have studied DNA diversity and divergence in a recently described X- and Y-linked gene pair (SLX-1 and SLY-1) of the plant Silene latifolia to obtain evidence about the early stages of Y degeneration. Here we show that DNA polymorphism in SLY-1 is 20-fold lower than in SLX-1, but the pattern of polymorphism does not suggest a selective sweep.

Animals↗

PubMed2004

Resource effects of training general practitioners in risk communication skills and shared decision making competences.

RATIONALE, AIMS AND OBJECTIVES: Involving patients more in decisions about their own care requires doctors to be trained in effective ways of communicating information and in developing competences to negotiate levels of patient involvement which are most appropriate for each case. The aim of this study was to determine the cost of such training and identify which service resource variables are subsequently affected. METHODS: An explanatory cluster randomized crossover trial was carried out which involved training general practitioners (GPs) in the use of risk communication (RC) tools, shared decision making (SDM) competences or both. Continuing care by GPs of patients with one of four chronic conditions (menopausal symptoms, menorrhagia, atrial fibrillation, prostatism) was reviewed before and after training. Cost of training was assessed by prospective monitoring of resources used. Data on prescribing, referrals and investigations were collected via questionnaires to participating practitioners. Data on follow-up GP consultations were extracted from medical records. Three two-level logistic models were performed to investigate the probability of training having an effect on prescribing, referrals and investigations ordered at the review consultation. RESULTS: Training cost pound 1218 per practitioner which increased the cost of a consultation by pound 2.89. Training in SDM or combined with RC significantly affected the probability of a prescription being issued to women with menopausal symptoms and menorrhagia (although RC on its own had no effect) but did not significantly affect prescribing for patients with prostatism or atrial fibrillation. It did not significantly affect the probability of investigations, referrals or follow-up GP visits for any of the conditions. CONCLUSION: Unless training has a major influence on consultation length, it is unlikely to have any major impacts on cost.

Chronic Disease↗

PubMed2003

Race, ancestry, and genes: implications for defining disease risk.

Geneticists are interested in finding genes associated with disease. Because of widespread health disparities, race is a variable that is often said to be relevant in this context. The idea is that members of a preconceived "race" share common ancestry that may include genetic risk factors. Human variation has been shaped by the long-term processes of population history, and population samples that reflect that history carry statistical information about shared genetic variation or "ancestry." But race is an elusive concept and a term difficult even to define rigorously. Unfortunately, these problems are neither new nor related to recent genetic knowledge. Race is also one of the most politically charged subjects in American life because its associated sociocultural component has notoriously led to categorical treatment that has been misleading and politically misused. There are ways in which the concept of race (whether or not the term is used) can be a legitimate tool in the search for disease-associated genes. But in that context race reflects deeply confounded cultural as well as biological factors, and a careful distinction must be made between race as a statistical risk factor and causal genetic variables.

Genetic Predisposition to Disease↗

PubMed2004

Genomes of the parapoxviruses ORF virus and bovine papular stomatitis virus.

Bovine papular stomatitis virus (BPSV) and orf virus (ORFV), members of the genus Parapoxvirus of the Poxviridae, are etiologic agents of worldwide diseases affecting cattle and small ruminants, respectively. Here we report the genomic sequences and comparative analysis of BPSV strain BV-AR02 and ORFV strains OV-SA00, isolated from a goat, and OV-IA82, isolated from a sheep. Parapoxvirus (PPV) BV-AR02, OV-SA00, and OV-IA82 genomes range in size from 134 to 139 kbp, with an average nucleotide composition of 64% G+C. BPSV and ORFV genomes contain 131 and 130 putative genes, respectively, and share colinearity over 127 genes, 88 of which are conserved in all characterized chordopoxviruses. BPSV and ORFV contain 15 and 16 open reading frames (ORFs), respectively, which lack similarity to other poxvirus or cellular proteins. All genes with putative roles in pathogenesis, including a vascular endothelial growth factor (VEGF)-like gene, are present in both viruses; however, BPSV contains two extra ankyrin repeat genes absent in ORFV. Interspecies sequence variability is observed in all functional classes of genes but is highest in putative virulence/host range genes, including genes unique to PPV. At the amino acid level, OV-SA00 is 94% identical to OV-IA82 and 71% identical to BV-AR02. Notably, ORFV 006/132, 103, 109, 110, and 116 genes (VEGF, homologues of vaccinia virus A26L, A33R, and A34R, and a novel PPV ORF) show an unusual degree of intraspecies variability. These genomic differences are consistent with the classification of BPSV and ORFV as two PPV species. Compared to other mammalian chordopoxviruses, PPV shares unique genomic features with molluscum contagiosum virus, including a G+C-rich nucleotide composition, three orthologous genes, and a paucity of nucleotide metabolism genes. Together, these data provide a comparative view of PPV genomics.

Animals↗

PubMed1983

Relation of cell surface antigens on methylcholanthrene-induced fibrosarcomas to immunoglobulin heavy chain complex variable region-linked T cell interaction molecules.

For optimal activation, T suppressor cells must receive a signal froma specialized inducer cell. The activating signal is delivered by a molecular complex that is composed, in part, of polymorphic gene products that are controlled by the immunoglobulin heavy chain complex (Igh) and that map to the variable region (Igh-V) of the complex. Consequently, if suppressor/inducer cells and their acceptor cells do not share Igh-V-encoded polymorphisms, the inducer molecules fail to activate the suppressor cells. Other polymorphic gene products (those that act as transplantation antigens on methylcholanthrene-induced fibrosarcomas) have been shown to be encoded by a gene(s) that maps to the same general region of chromosome 12 as does the Igh complex. Therefore, we tested the hypothesis that polymorphic gene products expressed by the T suppressor/inducer cell and its biologically active product were related to the transplantation antigens on these fibrosarcomas. We have found that isoantisera directed to a number of BALB/c methylcholanthrene-induced tumors block the induction of T suppressor cells but they do so only if the inducer or acceptor T cell (or both) expresses BALB/c Igh-linked polymorphisms. All other BALB/c gene products are irrelevant. These findings suggest that "transformation related antigens" on some sarcoma cells are variants of, or are otherwise related to, the cell interaction molecules that T cell subsets use to communicate with one another under normal circumstances. Furthermore, the findings that (a) multiple methylcholanthrene-induced tumors express serologically related antigens (as well as the unique ones that have been previously demonstrated by transplantation tests) and (b) these serologically related antigens can be found on Igh-V-controlled T cell communication molecules raise the intriguing possibility that, like certain viruses, methylcholanthrene reacts with specific regions of cellular DNA that either directly or indirectly regulate the expression of other specific genes (in this particular case the genes that encode the T cell communication molecules).

Animals↗

PubMed2006

Recurrent replacement of mtDNA and cryptic hybridization between two sibling bat species Myotis myotis and Myotis blythii.

The two sibling bat species Myotis myotis and Myotis blythii occur in sympatry over wide areas of Southern and Central Europe. Morphological, ecological and previous genetic evidence supported the view that the two species constitute two well-differentiated groups, but recent phylogenetic analyses have shown that the two species share some mtDNA haplotypes when they occur in sympatry. In order to see whether some genetic exchange has occurred between the two species, we sequenced a highly variable segment of the mitochondrial control region in both species living in sympatry and in allopatry. We also analysed the nuclear diversity of 160 individuals of both species found in two mixed nursery colonies located north and south of the Alps. MtDNA analysis confirmed that European M. blythii share multiple, identical or very similar haplotypes with M. myotis. Since allopatric Asian M. blythii presents mtDNA sequences that are very divergent from those of the two species found in Europe, we postulate that the mitochondrial genome of the European M. blythii has been replaced by that of M. myotis. The analysis of nuclear diversity shows a strikingly different pattern, as both species are well differentiated within mixed nursery colonies (F(ST) = 0.18). However, a Bayesian analysis of admixture reveals that the hybrids can be frequently observed, as about 25% of sampled M. blythii show introgressed genes of M. myotis origin. In contrast, less than 4% of the M. myotis analysed were classified as non-parental genotypes, revealing an asymmetry in the pattern of hybridization between the two species. These results show that the two species can interbreed and that the hybridization is still ongoing in the areas of sympatry. The persistence of well-differentiated nuclear gene pools, in spite of an apparent replacement of mitochondrial genome in European M. blythii by that of M. myotis, is best explained by a series of introgression events having occurred repeatedly during the recent colonization of Europe by M. blythii from Asia. The sharp contrast obtained from the analysis of mitochondrial and nuclear markers further points to the need to cautiously interpret results based on a single class of genetic markers.

Animals↗

PubMedDate not supplied

Representing clinical guidelines in GLIF: individual and collaborative expertise.

OBJECTIVE: An evaluation of the cognitive processes used in the translation of a clinical guideline from text into an encoded form so that it can be shared among medical institutions. DESIGN: A comparative study at three sites regarding the generation of individual and collaborative representations of a guideline for the management of encephalopathy using the GuideLine Interchange Format (GLIF) developed by members of the InterMed Collaboratory. MEASUREMENTS: Using theories and methods of cognitive science, the study involves a detailed analysis of the cognitive processes used in generating representations in GLIF. The resulting process-outcome measures are used to compare subjects with various types of computer science or clinical expertise and from different institutions. RESULTS: Consistent with prior studies of text comprehension and expertise, the variability in strategies was found to be dependent on the degree of prior experience and knowledge of the domain. Differing both in content and structure, the representations developed by physicians were found to have additional information and organization not explicitly stated in the guidelines, reflecting the physicians' understanding of the underlying pathophysiology. The computer scientists developed more literal representations of the guidelines; addition were mostly limited to specifications mandated by the logic of GLIF itself. Collaboration between physicians and computer scientists resulted in consistent representations that were more than the sum of the separate parts, in that both domain-specific knowledge of medicine and generic knowledge of guideline structure were seamlessly integrated. CONCLUSION: Because of the variable construction of guideline representations, understanding the processes and limitations involved in their generation is important in developing strategies to construct shared representations that are both accurate and efficient. The encoded guidelines developed by teams that include both clinicians and experts in computer-based representations are preferable to those developed by individuals of either type working alone.

Brain Diseases↗

PubMed1992

Suppression of chaos and other dynamical transitions induced by intercellular coupling in a model for cyclic AMP signaling in Dictyostelium cells.

The effect of intercellular coupling on the switching between periodic behavior and chaos is investigated in a model for cAMP oscillations in Dictyostelium cells. We first analyze the dynamic behavior of a homogeneous cell population which is governed by a three-variable differential system for which bifurcation diagrams are obtained as a function of two control parameters. We then consider the mixing of two populations behaving in a chaotic and periodic manner, respectively. Cells are coupled through the sharing of a common chemical intermediate, extracellular cAMP, which controls its production and release by the cells into the extracellular medium; the dynamics of the mixed suspension is governed by a five-variable differential system. When the two cell populations differ by the value of a single parameter which measures the activity of the enzyme that degrades extracellular cAMP, the bifurcation diagram established for the three-variable homogeneous population can be used to predict the dynamic behavior of the mixed suspension. The analysis shows that a small proportion of periodic cells can suppress chaos in the mixed suspension. Such a fragility of chaos originates from the relative smallness of the domain of aperiodic oscillations in parameter space. The bifurcation diagram is used to obtain the minimum fraction of periodic cells suppressing chaos. These results are related to the suppression of chaos by the small-amplitude periodic forcing of a strange attractor. Numerical simulations further show how the coupling of periodic cells with chaotic cells can produce chaos, bursting, simple periodic oscillations, or a stable steady state; the coupling between two populations at steady state can produce similar modes of dynamic behavior.

Journal Article↗

PubMedDate not supplied

[Whether variable cleavage of Enoplida (Nematoda) is primitive? Notes to D.A. Voronov article "Comparative embryology of Nematoda and the law of embryologic similarity].

The early embryonic development of Nematoda proceeds by three ways, which strictly correspond to three phylogenetic lineages. Under the first way the endodermal precursor is localized in the posterior blastomere at the two-cells stage (such a determination is the peculiarity of all the Chromadoria, including Secernentea and Caenorhabditis elegans). Under the second way the endodermal precursor is localized in the anterior blastomere of the egg. This feature is very unusual for Metazoa, but it is the only way of entoderm determination in all the Dorylaimia orders (Mononchida, Mermithida, Trichinellida, Dioctophymida, Dorylaimida). The third way described for the sea Enoplida is characterized with variable location of blastomers and changeable localization of endodermal precursor before eight-cells stage. It is still unknown of these three variants was typical the most recent common ancestor of present Nematoda. D.A. Voronov (2001) produced argument in favour of variable cleavage as primitive one for Nematoda. This opinion is rejected because of the similarity in development between sea Enoplida and C. elegans. Both of them share such features as low-cell gastrula and neurula, identical phylotypic lima bean stage of embryogenesis, identity of some geometrical figures 4 or 8 blastomers, isolating of the endodermal precursor at the eight-cells stage, the lack in development of any plesiomorphous features, which are widely distributed outside Nematoda (under the variable cleavage of Enoplida there are no such locations of blastomers, which are typical for spiral or radial cleavage, there are no embryonic leaves as well). One can see the homology of separate cells at adult Enoplida and Rhabditia. Cell lineage of Triplonchida as far as it is described at Tobrilus gracilis doesn't exclude the hypothesis on their origin from the cleavage similar to one of present Dorylaimia with localization of the endodermal precursor in the anterior blastomere. In view of all the considerations mentioned above one should interpret variable cleavage of Enoplida as derivation from invariant cleavage.

Animals↗

PubMed2002

Ductal carcinoma in situ of the breast: a new phenotype classification system and its relation to prognosis.

In a study of invasive breast cancer, multiple correspondence analysis (MCA) revealed clustering of eight pathobiological variables. Two different phenotypes were distinguished by an index calculated on the basis of the variables (histologic grade, necrosis, lymphoid infiltration, number of mitosis and expression of c-erbB-2, p53, progesterone receptor and Bcl-2). Phenotype A lesions share most of the features of normal breast tissue. Phenotype B looks more malignant, has a higher early recurrence rate and is more frequently seen in younger patients. Our aim was to see if ductal breast carcinoma in situ (DCIS) could be divided into the same phenotypes. One hundred and eighty DCIS were investigated. Association between the eight variables was studied in 2 x 2 models. The phenotype index was calculated by summing weights for the variables in the MCA. All variables were associated, except Bcl-2. DCIS was divided in two phenotypes. Thirty-three tumours were Phenotype A and 147 Phenotype B. The mean age at diagnosis was 65.5 and 58.4 years for Phenotypes A and B, respectively (p = 0.0012). No difference regarding local relapse free survival was seen. Two phenotypes were distinguished in DCIS, similar to invasive breast cancer. In an earlier study, 45% of the invasive cancers were classified as Phenotype B. In this study, 82% of DCIS were Phenotype B. This may indicate that invasive breast cancer of Phenotype B is derived from DCIS of Phenotype B. The distribution of DCIS phenotypes with a small proportion of Phenotype A DCIS may be due to that Phenotype A DCIS is less likely to be detected by mammography, or that some invasive breast cancers of Phenotype A progress to invasiveness without passing the in situ phase.

Adult↗

PubMed1978

Decision-sharing in elementary school children: effects on body-concept and anxiety.

To determine the effects of teacher-directed and decision-sharing models of instruction on the development of body-concept and reduction of anxiety 99 Greensboro public school children in Grades 3 and 4 participated in either a movement program in which the teacher made all the decisions or in a program where they shared in the decision-making. The Cheffers adaptation of Flanders' Interaction Analysis System was used to verify the two treatments. The dependent variables were measured by Osgood's semantic differential for body-concept measures, and Sarason's General Anxiety Scale for Children. There was no significant difference between the groups for improvement in body-concept. Also, girls have more positive concepts about their bodies than do boys. Anxiety scores indicated that levels in fourth-grade children appear to be reduced when exposed to a teacher-directed model. However, a decision-sharing approach had a significant effect on reducing anxiety levels in third-grade children.

Anxiety↗

PubMed1990

Structure and variability of recently inserted Alu family members.

The HS subfamily of Alu sequences is comprised of a group of nearly identical members. Individual subfamily members share 97.7% nucleotide identity with each other and 98.9% nucleotide identity with the HS consensus sequence. Individual subfamily members are on the average 2.8 million years old, and were probably derived from a single source 'master' gene sometime after the human/great ape divergence. The recent Alu family member insertions provide a better image of the structure of Alu retroposons before they have had the opportunity to change significantly. All of the HS subfamily members are flanked by perfect direct repeats as a result of insertion at staggered nicks. The 'master' gene from which the HS subfamily members were derived had an oligo-dA rich tail at least 40 bases long. The 'master' gene is very rich in CpG dinucleotides, but nucleotide substitutions within subfamily members accumulated in a random manner typical for Alu sequence with CpG substitutions occurring 9.2 fold faster than non-CpG substitutions.

Base Sequence↗

PubMed1998

Coding spatial variations in faces and simple shapes: a test of two models.

Faces all have the same basic elements in the same overall arrangement, and must be discriminated using variations in this shared configuration. An efficient way to represent these variations would be to code how each configuration differs from an average face (norm-based coding model). Alternatively, configurations could be represented simply by coding their absolute values in some coordinate system (absolute coding model). The two models differ in the variables they predict will influence an image's recognizability. Absolute coding predicts that recognizability will depend on an image's distinctiveness and degree of distortion from its veridical target. Norm-based coding predicts that recognizability will also depend on the way the image differs from a norm or average face, namely its distance from the norm and/or its degree of displacement from the norm-deviation vector for the target. We determined the effects of these four critical variables on recognition of undistorted (veridical) images, caricatures, anticaricatures and 'lateral' distortions of famous faces (Experiment 1), newly learned faces (Experiment 2), and simple shapes that also share a configuration (Experiment 2). The results favored absolute coding of both faces and shapes, and indicate that caricatures derive their power from their distinctiveness.

Adult↗

PubMed2005

Patterns of variability at the major histocompatibility class II alpha locus in Atlantic salmon contrast with those at the class I locus.

In order to investigate the mechanisms creating and maintaining variability at the major histocompatibility (MH) class II alpha (DAA) locus we examined patterns of polymorphism in two isolated Atlantic salmon populations which share a common post-glacial origin. As expected from their common origin, but contrary to the observation at the MH class I locus, these populations shared the majority of DAA alleles: out of 17 sequences observed, 11 were common to both populations. Recombination seems to play a more important role in the origin of new alleles at the class II alpha locus than at the class I locus. A greater than expected proportion of sites inferred to be positively selected (potentially peptide binding residues, PBRs) were found to be involved in recombination events, suggesting a mechanism for increasing MH variability through an interaction between recombination and natural selection. Thus it appears that although selection and recombination are important mechanisms for the evolution of both class II alpha and class I loci in the Atlantic salmon, the pattern of variability differs markedly between these classes of MH loci.

Amino Acid Sequence↗

PubMed1981

[Summer camping for juvenile diabetics: effects on psychological variables (author's transl)].

The course of diabetes mellitus does not only depend on mere medical treatment. Psychological factors also play an important part. Since 1955 summer camping for diabetic children has been organized in Austria enabling juvenile diabetics to live together with a group of children sharing the same fate. This community offers the opportunity for experience to be interchanged and for knowledge about diabetes to be increased. The children's self confidence and independence is improved. In this study the changes of psychological variables during a 4 week camping period are documented. 49 children between the ages of 8-14 years were tested by a special questionnaire which registered 4 dimensions: social behavior, independency, the attitude of the children to their disease and the knowledge about it. At the end of the camping period a significant improvement in the 4 variables was found when compared to the beginning of the course. These results indicate that the institution of a diabetic camp is very important for the psychological and personal development of juvenile diabetics.

Adolescent↗

PubMed1996

Human population variability in relative dental development.

Using dental X-rays, the calcification of various teeth was compared between samples of black southern Africans, white French-Canadians, and prehistoric Native Americans sharing the same stage of calcification of a specified "reference tooth." The French-Canadians have markedly delayed relative development of the M3 compared to the Africans. They also appear delayed in their M2 development compared to both the Africans and Amerindians. While no difference in relative mandibular canine development is found between the African and French-Canadian males, French-Canadian females are advanced over the African females. Prehistoric Native Americans may be delayed in mandibular central incisor development compared to French-Canadians. These results are in general accord with other studies of variability in dental development between Africans/African Americans, Europeans/European Americans, and Native Americans, and demonstrate that population differences in ages of eruption are attributable in part to differences in relative dental development. Two potentially falsifiable hypotheses concerning the significance of population variability in relative dental development are discussed: 1) the variability (at least for molars) is associated with the amount of space in the jaws for developing teeth, 2) the variability is due to population differences in the timing of dental and skeletal development.

Animals↗

PubMed2006

Clinical findings in a multigeneration family with autosomal dominant central areolar choroidal dystrophy associated with an Arg195Leu mutation in the peripherin/RDS gene.

OBJECTIVE: To characterize clinical findings associated with a mutation in codon 195 (Arg195Leu) of the peripherin/RDS gene in a large multigeneration family of European decent. METHODS: Sixteen members from 2 generations underwent ophthalmologic examination, including best-corrected visual acuity, examination of the anterior segments, and inspection of the ocular fundus after pharmacologic mydriasis. All affected family members underwent Farnsworth Panel-D15 color testing. Five selected family members with early stages of the disease underwent multifocal electroretinography. Full-field electroretinography was performed in 2 family members with more advanced fundus changes. Finally, former patients' records and fundus images were analyzed to determine the course of the disease in affected individuals. RESULTS: Nine family members in 2 generations were diagnosed as having autosomal dominant central areolar choroidal dystrophy. The family demonstrated an age-dependent increase of central granular fundus abnormalities with progressive development of geographic atrophy. Interindividual phenotypic variability was apparent and ranged from predominantly drusenlike depositions to single perifoveal pigment clumps. Age of onset of visual disturbances varied between 27 and 48 years. All individuals who manifested signs of disease were found to carry an Arg195Leu mutation in the peripherin/RDS gene. CONCLUSIONS: Age of onset, progression of the disease, and characteristic fundus abnormalities share similarities to previous reports on families with central areolar choroidal dystrophy associated with peripherin/RDS gene mutations in codons 172, 142, and 195, respectively. However, striking variability in individual phenotypic findings and age of onset in our family suggests that additional factors that modify the defined peripherin/RDS gene mutation Arg195Leu likely influence the severity of the disease. CLINICAL RELEVANCE: Caution should be advised in predicting the clinical course and severity of the disease based solely on a specific mutation in the peripherin/RDS gene.

Adolescent↗