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PubMed2006

Nutlet morphology and anatomy of the genus Lycopus (Lamiaceae: Mentheae).

Nutlet morphology and pericarp structure of 16 species in the genus Lycopus were studied by light microscopy (LM) and scanning electron microscopy (SEM), and a detailed description of nutlet morphological features for all examined taxa is provided. The nutlets of all taxa in the genus Lycopus are well adapted to typical hydrochory (or nautochory) with an air-filled pericarp, and myxocarpy was not at all found. It is noteworthy that the nutlet morphology (in particular the shape of corky crests and corky ring and the distribution of glandular trichomes) and pericarp anatomy of Lycopus are unique and are well distinguished from the other genera in the tribe Mentheae. We also found some groups of the species within the genus Lycopus by the present nutlet morphological and anatomical data that appear to be useful as diagnostic characteristics for delineation purposes at the specific/interspecific levels. The earlier infrageneric classification for the genus Lycopus is, however, not well supported by the present results. In addition, the systematic and biological implications of the nutlet characteristics investigated are briefly discussed.

Evolution, Molecular↗

PubMed2004

Molecules consolidate the placental mammal tree.

Deciphering relationships among the orders of placental mammals remains an important problem in evolutionary biology and has implications for understanding patterns of morphological character evolution, reconstructing the ancestral placental genome, and evaluating the role of plate tectonics and dispersal in the biogeographic history of this group. Until recently, both molecular and morphological studies provided only a limited and questionable resolution of placental relationships. Studies based on larger and more diverse molecular datasets, and using an array of methodological approaches, are now converging on a stable tree topology with four major groups of placental mammals. The emerging tree has revealed numerous instances of convergent evolution and suggests a role for plate tectonics in the early evolutionary history of placental mammals. The reconstruction of mammalian phylogeny illustrates both the pitfalls and the powers of molecular systematics.

Journal Article↗

PubMed2004

Probing the origins and control of shrinkage stress in dental resin-composites: I. Shrinkage stress characterization technique.

The accurate and reliable characterization of the polymerization shrinkage stress is becoming increasingly important, as the shrinkage stress still is a major drawback of current dimethacrylate-based dental materials and restricts its range of applications. The purpose of this research is to develop a novel shrinkage stress measurement device to elucidate the shrinkage stress evolution of dental restorative composites while allowing for controlled sample deformation during the polymerization. Furthermore, the device is designed to mimic the clinically relevant cusp-to-cusp displacement by systematically adjusting the instrument compliance, the bonded surface area/unbonded area by sample geometry, and the total bonded area by sample diameter. The stress measurement device based on the cantilever beam deflection theory has been successfully developed and characterized using a commercial dental composite. It was shown that this device is a highly effective, practical and reliable shrinkage stress measurement tool, which enables its facile applications to the investigation of shrinkage stress kinetics of both commercial and experimental composites, as well as for probing various aspects that dictate shrinkage stress development.

Biocompatible Materials↗

PubMed1983

New Palaeogene primate basicrania and the definition of the order Primates.

The anatomy of the posterior basicranium has been repeatedly invoked in systematic definitions of Primates. One widely cited definition of the order claims that 'all undoubted primates' are distinguished from other mammals by two basicranial specializations: (1) absence of a major vascular foramen on the medial side of the auditory region, and (2) development of the auditory bulla from the petrosal bone. As we show here, specialization (1) does not apply to the paromomyid Ignacius, and is of uncertain incidence in other unquestioned members of suborder Plesiadapiformes (archaic primates from the early Cenozoic of Europe and North America). Specialization (2) cannot be demonstrated without ontogenetic evidence, and all relevant plesiadapiform fossils are adult. In fact, the only plesiadapiform with an arterial pattern remotely resembling that of early primates of modern aspect (or 'euprimates') is the microsyopid Cynodontomys, but it is often regarded as non-primate because it lacks a petrosal bulla. Although plesiadapiforms resemble euprimates in traits of the cheek teeth and postcranium, some other (presumably non-primate) groups possess these traits as well. Since the order Primates is not clearly definable by unique specializations, the best grounds for regarding plesiadapiforms as euprimate antecedents are stratigraphic and phenetic. This fact may be best expressed by systematic arrangements that emphasize adaptive grades rather than unsubstantiated clades.

Animals↗

PubMed2025

De novo discovery of conserved gene clusters in microbial genomes with Spacedust.

Metagenomics has revolutionized environmental and human-associated microbiome studies. However, the limited fraction of proteins with known biological processes and molecular functions presents a major bottleneck. In prokaryotes and viruses, evolution favors keeping genes participating in the same biological processes colocalized as conserved gene clusters. Conversely, conservation of gene neighborhood indicates functional association. Here we present Spacedust, a tool for systematic, de novo discovery of conserved gene clusters. To find homologous protein matches, Spacedust uses fast and sensitive structure comparison with Foldseek. Partially conserved clusters are detected using novel clustering and order conservation P values. We demonstrate Spacedust's sensitivity with an all-versus-all analysis of 1,308 bacterial genomes, identifying 72,843 conserved gene clusters containing 58% of the 4.2 million genes. It recovered 95% of antiviral defense system clusters annotated by the specialized tool PADLOC. Spacedust's high sensitivity and speed will facilitate the annotation of large numbers of sequenced bacterial, archaeal and viral genomes.

Metagenomics↗

PubMed2006

Epistasis correlates to genomic complexity.

Whether systematic genetic interactions (epistasis) occur at the genomic scale remains a challenging topic in evolutionary biology. Epistasis should make a significant contribution to variation in complex traits and influence the evolution of genetic systems as sex, diploidy, dominance, or the contamination of genomes with deleterious mutations. We have collected data from widely different organisms and quantified epistasis in a common, per-generation scale. Simpler genomes, such as those of RNA viruses, display antagonistic epistasis (mutations have smaller effects together than expected); bacterial microorganisms do not apparently deviate from independent effects, whereas in multicellular eukaryotes, a transition toward synergistic epistasis occurs (mutations have larger effects together than expected). We propose that antagonistic epistasis might be a property of compact genomes with few nonpleiotropic biological functions, whereas in complex genomes, synergism might emerge from mutational robustness.

Animals↗

PubMed2001

Generation of a database containing discordant intron positions in eukaryotic genes (MIDB).

MOTIVATION: Intron sliding is the relocation of intron-exon boundaries over short distances and is often also referred to as intron slippage or intron migration or intron drift. We have generated a database containing discordant intron positions in homologous genes (MIDB--Mismatched Intron DataBase). Discordant intron positions are those that are either closely located in homologous genes (within a window of 10 nucleotides) or an intron position that is present in one gene but not in any of its homologs. The MIDB database aims at systematically collecting information about mismatched introns in the genes from GenBank and organizing it into a form useful for understanding the genomics and dynamics of introns thereby helping understand the evolution of genes. RESULTS: Intron displacement or sliding is critically important for explaining the present distribution of introns among orthologous and paralogous genes. MIDB allows examining of intron movements and allows mapping of intron positions from homologous proteins onto a single sequence. The database is of potential use for molecular biologists in general and for researchers who are interested in gene evolution and eukaryotic gene structure. Partial analysis of this database allowed us to identify a few putative cases of intron sliding. AVAILABILITY: http://intron.bic.nus.edu.sg/midb/midb.html

Amino Acid Sequence↗

PubMed2006

Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta.

All extant green plants belong to 1 of 2 major lineages, commonly known as the Chlorophyta (most of the green algae) and the Streptophyta (land plants and their closest green algal relatives). The scaly green flagellate Mesostigma viride has an important place in the debate on the origin of green plants. However, there have been conflicting results from molecular systematics as to whether Mesostigma diverges before the Chlorophyta/Streptophyta split or is an early diverging flagellate member of the Streptophyta. Previous studies employed either a limited taxon sampling (plastid and mitochondrial genomes) or a small number of phylogenetically informative sites (single nuclear genes). Here, we use large data sets from the nuclear (125 proteins; 29,319 positions), mitochondrial (33 proteins; 6,622 positions), and plastid (50 proteins; 10,137 positions) genomes with an expanded taxon sampling (21, 13, and 28 species, respectively) to reevaluate the phylogenetic position of Mesostigma. Our study supports the placement of Mesostigma in the Streptophyta (as an early diverging lineage) and provides evidence that systematic biases have played a role in generating some of the previous conflicting results. Importantly, we demonstrate that using an increased taxon sampling as well as more realistic models of evolution allows increasing congruence among the nuclear, mitochondrial, and plastid data sets.

Base Sequence↗

PubMedDate not supplied

Estimating the age of mutant disease alleles based on linkage disequilibrium.

With more and more disease genes being mapped and/or cloned, there is a growing interest in dating the age of underlying mutations. The knowledge of the age of mutation is important to finely map disease genes by linkage disequilibrium mapping. It would also help us understand the origin, evolution, and dispersion of the mutant disease genes. Despite increasing interests in dating disease mutations, the development of appropriate statistical methods is largely fragmentary, and there is a lack of systematic treatment of the topic. We propose two classes of methods for estimating the age of mutant allele at the disease locus based on linked marker data. Our methods can not handle only single-locus marker data, but also multi-locus marker data as well. Moreover, our methods can be used even when the location of the disease locus is unknown, and/or when there are mutations at the marker or disease locus. We show that some previous results are special cases of our methods. We also derive a recursive equation previously obtained by Serre et al. [Hum Genet 1990;84:449-454] and provide an explicit solution to the equation. To illustrate our methods, we applied them to two groups of data sets, one is cystic fibrosis data collected from several European populations, and the other is data on several genetic diseases (diastrophic dysplasia, progressive myoclonus epilepsy, congenital chloride diarrhea, and Batten disease) all collected from the Finnish population. The former data set allows us to trace the origin and dispersion of the most common mutation for cystic fibrosis. The latter provides an opportunity to examine whether all mutations for these diseases have the same age.

Alleles↗

PubMedDate not supplied

Nurse practitioners - or advanced clinical nurses?

This article reviews a specific finding from a research project that examined the experiences of students, teachers and clinicians involved in a nurse practitioner degree programme. The development of advanced clinical nursing roles has presented challenges to the professional structure of nursing, particularly in the area of the unregulated and confusing array of titles adopted by nurses that infer advanced clinical practice. Over a 2-year period, practitioner ethnography was used to examine a sample of 10 student nurse practitioners who were undertaking a clinical degree programme (BSc (Hons) Nurse Practitioner). Data were also collected from 11 other individuals involved in the degree programme: teachers, medical mentors and senior academics. The data were systematically analysed and structured, leading to the inductive identification of themes and frameworks. The sample's experience of the development of advanced clinical nursing roles led to consideration of the evolution of new career structures and identities associated with advanced nursing practice. This evidence enabled a view of advanced clinical nursing roles within a framework of advanced nursing practice. The development of advanced clinical nursing is dependent on the cooperation of clinical nurses, educators, managers, doctors and politicians. Nevertheless, that development can only succeed if strategic policy is backed by the development of a professional clinical nursing career framework that enables the process.

Anthropology, Cultural↗

PubMed2002

[Intranasal rhinosporidiosis: presentation of the 1st case seen in the Congo].

Rhinosporidiosis, granulomatosis affection due to Rhinosporidium seeberi, is rare in Africa. We report the first Congolese case observed in a 37 year old adult, who presented a tumorous formation obstructing the left nasal fossa, having developed over more than 5 years, occasionally accompanied by epistaxis. Diagnosis was made through an anatomo-pathological examination of the exeresis biopsy. The treatment essentially consisted in surgical tumorous exeresis, followed by electrocoagulation of the implantation area. Evolution has been favourable with a rebound of 7 years. In order to measure the frequency of rhinosporidiosis in Africa, anatomo-pathological examination of all O.R.L. polyps must be systematic.

Adult↗

PubMed1991

[Acute osteomyelitis of the ilium. A study of 2 cases with review of the literature].

The authors have made a review of the literature about two cases of osteomyelitis of the iliac ala. They insist on rarity of the disease and how often the right diagnosis may be delayed because of misleading clinical symptoms. Any tumefaction of the buttock associated with pelvic pain and with an infectious syndrome necessarily evoke an iliac osteomyelitis. The bone scan may be negative which need not exclude the possibility. The evolution may be the formation of intra or extra or sometimes simultaneous sub-periosteal abscesses which must be drained. This is the reason why the authors advise to verify systematically the other side of the ilium by its surgical trepanning in case of a sub-periosteal abscess.

Abscess↗

PubMed1987

Implementing the Omaha classification system in a public health agency.

Systemized nursing diagnosis based on standardized, coded terminology is in the early stages of evolution. The Waukesha Health Department has been a part of that evolutionary process. Introduction of the concept of nursing diagnosis led to the conclusion that for this agency a more systematic, community tested taxonomy was needed. The OCS was the system selected. The progress of the two systems, NANDA and OCS, appears to be evolving in parallel. No doubt, in the future one system will emerge as best for all fields of nursing. Meanwhile, the use of the OCS in practice settings serves the evolutionary process well by providing a foundation of trial and experience.

Humans↗

PubMedDate not supplied

[Contribution to our knowledge of the Landau and Kleffner "acquired aphasia with epilepsy" syndrome].

The Authors describe a case of aphasia acquired in childhood together with epilepsy (syndrome of Landau and Kleffner) and treated for seven years. The patient had simple and complex partial attacks, motor dysphasia, frequent and heavy headache, and electroencephalographic paroxysmal anomalies with multifocal distribution. While the disease evolved with regression of disphasia and epilepsy, the EEG alterations persisted. In view of similar cases reported in the literature and the present treatment the Authors feel that syndrome is an inflammatory disease, its evolution being slow. The results of neuroradiological investigations support such hypothesis. The prognosis is poor (anomalies of speech persisted in 2 out of 3) and further studies are essential. A systematic use of cerebral biopsy is suggested.

Aphasia↗

PubMed1984

[Diagnosis of familial medullary cancers].

Medullary thyroid carcinoma (MTC) is hereditary in 20 to 25% of cases. It is inherited as an autosomal dominant trait. MTC can be considered as a sporadic form only after a clinical and biological survey of the two parents, siblings and children of the patient, using pentagastrin stimulation test. The authors have studied 36 patients from 26 families. Hereditary MTC with different clinical features, were discovered in two kindreds. The systematic investigation leads to the discovery of 7 cases in the first family, and of 3 in the second. The treatment of the disease at the first stage of its evolution has been possible when an early diagnosis had been made, such as in the second family.

Calcitonin↗

PubMedDate not supplied

[Social perception of arterial hypertension from a transcultural perspective].

From ethnological and psychological inquiries, during an ordinary elaboration of methodology (between France and West Africa that took place in Ivory Coast) the author emphasizes the differential value of the terms hypertension or hypotension with a systematic claim of a take of blood pressure in Europe. This uncommon fact in West Africa becomes integrated into the notion of a medical technology and raises the problem of evolution of society (non migration, new forms of alimentation, work and urbanization...). While in France the inquiry is dependent on an image of an hypertensive, his body, his personality, his problems; in Ivory Coast people refer to a body language, the psychosomatic damage including the existential malaise politics, cultural confrontations, stress pathology ... all this with periods of high or low tension internal or external pressures, getting out of the medical act consisting in a take of blood pressure or a particular psychic state testing, the nervous break down or anxiety for example. In a methodological field, the author from different levels of view points (sociological, statistical, ethnological and clinical) is in search of an adapted synthetic formula in anthropology for situations of substitution and social differences.

Attitude↗

PubMedDate not supplied

[Diagnosis and classification in psychiatric disorders].

This paper provides a general overview of the evolution of the diagnostic concepts in Psychiatry, of the research methods for future improvement, of the goals reached and of the deterrants that have to be surpassed. Classification, standardization and systematization of mental disorders has not been an easy task. For this reason, during a long period of time a wide diversity in the classification of the mental illness that ran along with the thinking trend of each and everyone of the different authors has been observed. This resulted in a division of the specialty and in the contamination of its ideologies and also, it has damaged the reputation of the diagnosis. The development of psychopharmacology and of the epidemiological systems made necessary the implementation of a strict diagnostic system that could make possible the planning of treatments, the establishment of prognosis and the design of preventive measurements. England was the cradle of this change due to the fact that the situation of the specialty availed itself of the influence of the prestigious and noteworthy German professors exiled in this country. Since 1972, some of the material that has been published illustrates the new tendency of nosology. Since then, there has been a great proliferation of works in this field. The culminating point of these investigations is represented by the Diagnosis and Statistical Manual of the American Psychiatric Association and by the International Classification of Illnesses (ICD-10). From this point of view, diagnosis is just a provisional hypothesis of a work that can be identified because of its pathological expressions and which is also of help in the communication between specialists.(ABSTRACT TRUNCATED AT 250 WORDS)

Humans↗

PubMed2005

An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing.

With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful approach for finding such elements by identifying sequences that have been highly conserved during evolution. Here, we propose an initial strategy for detecting such regions by generating low-redundancy sequence from a collection of 16 eutherian mammals, beyond the 7 for which genome sequence data are already available. We show that such sequence can be accurately aligned to the human genome and used to identify most of the highly conserved regions. Although not a long-term substitute for generating high-quality genomic sequences from many mammalian species, this strategy represents a practical initial approach for rapidly annotating the most evolutionarily conserved sequences in the human genome, providing a key resource for the systematic study of human genome function.

Animals↗