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PubMed1995

[Respiratory sounds].

After having invented the stethoscope, Laennec published his treatise on auscultation in 1819, describing the acoustic events generated by ventilation and linking them with anatomopathological findings. The weak points of his semiology lay in its subjective and interpretative character, expressed by an imprecise and picturesque nomenclature. Technical studies of breath sounds began in the middle of the twentieth century, and this enabled the American Thoracic Society to elaborate a new classification of adventitious noises based on a few physical characteristics. This terminology replaced that of Laennec or his translators (except in France). The waveforms of the different normal and adventitious noises have been well described. However, only the study of the time evolution of their tone (frequency-amplitude-time relationship) will enable a complete analysis of these phenomena. This approach has been undertaken by a few teams but much remains to be done, in particular in relation to discontinuous noises (crackles). Technology development raises hope for the design, in near future, of automatic processes for respiratory noise detection and classification. Systematic research into the production mechanisms and sites of these noises has progressed equally. It should, in time, reinforce their semiological value and give to auscultation, either instrumental or using the stethoscope or instrumentally, an increased diagnostic power and the status of respiratory function test.

Auscultation↗

PubMed1998

Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.

Experimental investigations of eukaryotic enhancers suggest that multiple binding sites and trans-acting regulatory factors are often required for wild-type enhancer function. Genetic analysis of the stripe 2 enhancer of even-skipped (eve), an important developmental gene in Drosophila, provides support for this view. Given the importance of even-skipped expression in early Drosophila development, it might be predicted that many structural features of the stripe 2 enhancer will be evolutionarily conserved, including the DNA sequences of protein binding sites and the spacing between them. To test this hypothesis, we compared sequences of the stripe 2 enhancer between four species of Drosophila: D. melanogaster, D. yakuba, D. erecta and D. pseudoobscura. Our analysis revealed a large number of nucleotide substitutions in regulatory protein binding sites for bicoid, hunchback, Kruppel and giant, as well as a systematic change in the size of the enhancer. Some of the binding sites in D. melanogaster are either absent or modified in other species. One functionally important bicoid-binding site in D. melanogaster appears to be recently evolved. We, therefore, investigated possible functional consequences of sequence differences among these stripe 2 enhancers by P-element-mediated transformation. This analysis revealed that the eve stripe 2 enhancer from each of the four species drove reporter gene expression at the identical time and location in D. melanogaster embryos. Double staining of native eve protein and transgene mRNA in early embryos showed that the reporter gene mimicked native eve expression and, in every case, produced sharply defined stripes at the blastoderm stage that were coincident with eve stripe 2 protein. We argue that stripe 2 eve expression in Drosophila evolution can be viewed as being under constant stabilizing selection with respect to the location of the anterior and posterior borders of the stripe. We further hypothesize that the stripe 2 enhancer is functionally robust, so that its evolution may be governed by the fixation of both slightly deleterious and adaptive mutations in regulatory protein binding sites as well as in the spacing between binding sites. This view allows for a slow but continual turnover of functionally important changes in the stripe 2 enhancer.

Animals↗

PubMed1997

Mental time travel and the evolution of the human mind.

This article contains the argument that the human ability to travel mentally in time constitutes a discontinuity between ourselves and other animals. Mental time travel comprises the mental reconstruction of personal events from the past (episodic memory) and the mental construction of possible events in the future. It is not an isolated module, but depends on the sophistication of other cognitive capacities, including self-awareness, meta-representation, mental attribution, understanding the perception-knowledge relationship, and the ability to dissociate imagined mental states from one's present mental state. These capacities are also important aspects of so-called theory of mind, and they appear to mature in children at around age 4. Furthermore, mental time travel is generative, involving the combination and recombination of familiar elements, and in this respect may have been a precursor to language. Current evidence, although indirect or based on anecdote rather than on systematic study, suggests that nonhuman animals, including the great apes, are confined to a "present" that is limited by their current drive states. In contrast, mental time travel by humans is relatively unconstrained and allows a more rapid and flexible adaptation to complex, changing environments than is afforded by instincts or conventional learning. Past and future events loom large in much of human thinking, giving rise to cultural, religious, and scientific concepts about origins, destiny, and time itself.

Animals↗

PubMed2001

Variation in the nrDNA ITS of Pinus subsection Cembroides: implications for molecular systematic studies of pine species complexes.

The pinyon pines (Pinus subsection Cembroides), distributed in semiarid regions of the western United States and Mexico, include a mixture of relictual and more recently evolved taxa. To investigate relationships among the pinyons, we screened and partially sequenced 3000-bp clones of the nuclear ribosomal DNA internal transcribed spacer (ITS) region for 16 taxa from subsect. Cembroides and nine representatives from four other subsections of subgenus Strobus. Restriction digests of clones reveal within-individual heterogeneity, suggesting that concerted evolution is operating slowly on the ITS in pine species. Two ITS clones were identified as pseudogenes. Tandem subrepeats in the ITS1 form stem loops comparable to those in other genera of Pinaceae and may be promoting recombination between rDNA repeats, resulting in ITS1 chimeras. Within the pinyon clade, phylogenetic structure is present, but different clones from the same (or different) individuals of a species are polyphyletic, indicating that coalescence of ITS copies within individual genomes predates evolutionary divergence in the group. At the level of subsection and above, the ITS region corresponds well with morphological and cpDNA evidence. Except for P. nelsonii, the pinyons are monophyletic, with both subsect. Cembroides and P. nelsonii forming a clade with the foxtail and bristlecone pines (subsect. Balfourianae) of western North America.

Base Sequence↗

PubMed2003

Molecular systematics and adaptive radiation of Hawaii's endemic Damselfly genus Megalagrion (Odonata: Coenagrionidae).

Damselflies of the endemic Hawaiian genus Megalagrion have radiated into a wide variety of habitats and are an excellent model group for the study of adaptive radiation. Past phylogenetic analysis based on morphological characters has been problematic. Here, we examine relationships among 56 individuals from 20 of the 23 described species using maximum likelihood (ML) and Bayesian phylogenetic analysis of mitochondrial (1287 bp) and nuclear (1039 bp) DNA sequence data. Models of evolution were chosen using the Akaike information criterion. Problems with distant outgroups were accommodated by constraining the best ML ingroup topology but allowing the outgroups to attach to any ingroup branch in a bootstrap analysis. No strong contradictions were obtained between either data partition and the combined data set. Areas of disagreement are mainly confined to clades that are strongly supported by the mitochondrial DNA and weakly supported by the elongation factor 1alpha data because of lack of changes. However, the combined analysis resulted in a unique tree. Correlation between Bayesian posterior probabilities and bootstrap percentages decreased in concert with decreasing information in the data partitions. In cases where nodes were supported by single characters bootstrap proportions were dramatically reduced compared with posterior probabilities. Two speciation patterns were evident from the phylogenetic analysis. First, most speciation is interisland and occurred as members of established ecological guilds colonized new volcanoes after they emerged from the sea. Second, there are several instances of rapid radiation into a variety of specialized habitats, in one case entirely within the island of Kauai. Application of a local clock procedure to the mitochondrial DNA topology suggests that two of these radiations correspond to the development of habitat on the islands of Kauai and Oahu. About 4.0 million years ago, species simultaneously moved into fast streams and plant leaf axils on Kauai, and about 1.5 million years later another group moved simultaneously to seeps and terrestrial habitats on Oahu. Results from the local clock analysis also strongly suggest that Megalagrion arrived in Hawaii about 10 million years ago, well before the emergence of Kauai. Date estimates were more sensitive to the particular node that was fixed in time than to the model of local branch evolution used. We propose a general model for the development of endemic damselfly species on Hawaiian Islands and document five potential cases of hybridization (M. xanthomelas x M. pacificum, M. eudytum x M. vagabundum, M. orobates x M. oresitrophum, M. nesiotes x M. oahuense, and M. mauka x M. paludicola).

Adaptation, Biological↗

PubMed2001

[Sickle cell anemia and pregnancy: considerations on systematic prophylactic transfusion].

Sickle cell anemia, a congenital hemolytic type of anemia due to a genetic defect in the beta chain of the globin molecule can cause severe disease. During pregnancy, the risk for preeclampsia and deep venous thrombosis is increased in patients with sickle cell anemia. Occlusion of placenta blood vessels with rigid deformed erythrocytes can cause repeated miscarriages and intra-uterine fetal death. Repeated blood transfusions can prevent these complications by reducing the concentration of abnormal hemoglobin S. We report on the evolution of five pregnancies in three patients with sickle cell anemia who received multiple blood transfusions during gestation, and discuss advantages and risks involved in the care of such cases.

Abortion, Spontaneous↗

PubMedDate not supplied

Field homology as a way to reconcile genetic and developmental variability with adult homology.

The theoretical and developmental fundament of field homology is here examined, particularly as applied by the authors to comparative neurobiology. Preliminary considerations explore conceptual differences between sameness (homology) and similarity. The source of sameness (the biological evolutionary relationship properly sought in homology analysis) is thought to lie in morphostatic evolutionary and morphogenetic processes, which constrain organismal variation at the level of its fundamental structural organization (Bauplan). This occurs via regulation of the branching mode of the morphogenetic sequence or epigenetic landscape. Of fundamental importance in this context is the role of developmental (morphogenetic) fields. The latter concept is analyzed in its general properties and is postulated to underpin the stability of the developing Bauplan down to the ultimate conserved details. Developmental fields subdivide during ontogenesis into ever smaller fields in a complex hierarchy, defining at each stage the developmental entities which are subjected to regulatory, morphostatic effects via the genome and indirect phenotypic selection. These fields thus represent the natural characters for considerations of embryonic homology, and underlie adult homology, rather than arbitrarily selected embryonic parts. Field subdivision proceeds into the constitution of individually specified cell populations. Field regulatory properties, however, do not extend to all differentiation phenomena observed in embryos. This means there is a limit to the applicability of field homology analysis, leaving space for biological variation and convergence outside of proper homology relationships. Genetic and developmental variability are compensated by the regulatory functions of the developmental fields insofar as they relate to correct Bauplan construction. These ideas suggest the convenience of a more systematic use of field homology methods, which start with appropriately identified developmental fields to expand knowledge on adult homology (sameness) and eventually also on accessory structural and functional similarities or differences.

Aging↗

PubMed1999

Observing the living genome.

Dynamic pictures of living genomes are now beginning to emerge from systematic studies of gene expression patterns using DNA microarrays. The rich information represented in the variation in each gene's expression provides the basis for a new kind of genomic map.

Animals↗

PubMed2004

Phylogenetic relationships of nearctic Reticulitermes species (Isoptera: Rhinotermitidae) with particular reference to Reticulitermes arenincola Goellner.

DNA sequence comparisons of the mitochondrial COII, 16S, and 12S rRNA genes were used to infer phylogenetic relationships among the six known US Reticulitermes species (Reticulitermes flavipes, Reticulitermes arenincola, Reticulitermes tibialis, Reticulitermes hageni, Reticulitermes virginicus, and Reticulitermes hesperus) and the closely related European species Reticulitermes santonensis. The interspecific pairwise sequence divergence, based on uncorrected "p" distance, varied up to 10% across the COII, 4.9% across the 16S, and 3% across the 12S fragments. Phylogenetic trees were constructed using maximum parsimony, likelihood, and distance methods. The combined results suggest several phylogenetic relationships including: (i) R. flavipes, R. arenincola, and European R. santonensis are possibly conspecific; (ii) R. virginicus and R. hageni are closely related species; and (iii) R. tibialis and R. hesperus are closely related species. Interestingly, while there is apparent synonymity between R. flavipes and R. arenincola by DNA sequence, there are clear morphological differences in the soldier caste. This finding suggests a combination of molecular and morphological approaches are necessary for accurate species identification. These data lend resolution to the complex problem of Reticulitermes systematics, and will assist future efforts directed toward characterizing species distribution and ecology.

Animals↗

PubMed1982

Uterine height and umbilical perimeter curves in twin pregnancies.

From previous research, which gave standard curves for the evolution of uterine height and umbilical perimeter according to gestational age in the case of single pregnancies, the authors propose curves which show the variations of these two parameters in twin pregnancies. The observed differences are sufficient to allow a diagnosis of twin pregnancy as soon as the 18th week of amenorrhea. This observation is interesting because, until now, a systematic early B-scan examination has not been performed as a rule.

Female↗

PubMed2002

N-terminus of the photosystem II manganese stabilizing protein: effects of sequence elongation and truncation.

The importance of the N-terminal domain of manganese stabilizing protein in binding to photosystem II has been previously demonstrated [Eaton-Rye and Murata (1989) Biochim. Biophys. Acta 977, 219-226; Odom and Bricker (1992) Biochemistry 31, 5616-5620]. In this paper, we report results from a systematic study of functional and structural consequences of N-terminal elongation and truncation of manganese stabilizing protein. Precursor manganese stabilizing protein is the unprocessed wild-type protein, which carries an N-terminal extension of 84 amino acids in the form of its chloroplastic signal peptide. Despite its increased size, this protein is able to reconstitute O(2) evolution activity to levels observed with the mature, processed protein, but it also binds nonspecifically to PSII. Truncation of wild-type manganese stabilizing protein by site-directed mutagenesis to remove three N-terminal amino acids, resulting in a mutant called DeltaG3M, causes no loss of activity reconstitution, but this protein also exhibits nonspecific binding. Further truncation of the wild-type protein by ten N-terminal amino acids, producing DeltaE10M, limits binding of manganese stabilizing protein to 1 mol/mol of photosystem II and decreases activity reconstitution to about 65% of that obtained with the wild-type protein. Because two copies of wild type normally bind to photosystem II, amino acids in the domain (4)K-(10)E must be involved in the binding of one copy of manganese stabilizing protein to photosystem II. Spectroscopic analysis (CD and UV spectra) reveals that N-terminal elongation and deletion of manganese stabilizing protein influence its overall conformation, even though secondary structure content is not perturbed. Our data suggest that the solution structure of manganese stabilizing protein attains a more compact solution structure upon removal of N-terminal amino acids.

Amino Acid Sequence↗

PubMed2002

Recent philosophy of biology: a review.

Academia is subdivided into separate disciplines, most of which are quite discrete. In this review I trace the interactions between two of these disciplines: biology and philosophy of biology. I concentrate on those topics that have the most extensive biological content: function, species, systematics, selection, reduction and development. In the final section of this paper I touch briefly on those issues that biologists and philosophers have addressed that do not have much in the way of biological content.

Animals↗

PubMed1977

Rates, sample sizes, and the neutrality hypothesis for electrophoresis in evolutionary studies.

It is shown that electrophoretic genetic distance estimates are highly correlated with albumin immunological distances between the same pairs of species. The bimodality of rates of electrophoretic differentiation at various loci is then documented and the electrophoretic clocks involved are calibrated. The differences between the systematics and population genetics uses of electrophoretic data are then discussed. Finally, a direct electrophoretic test of the neutral alleles hypothesis is presented and exemplified on a set of Thomomys bottae-umbrinus data.

Alleles↗

PubMed2005

Integration of morphological data sets for phylogenetic analysis of Amniota: the importance of integumentary characters and increased taxonomic sampling.

Several mutually exclusive hypotheses have been advanced to explain the phylogenetic position of turtles among amniotes. Traditional morphology-based analyses place turtles among extinct anapsids (reptiles with a solid skull roof), whereas more recent studies of both morphological and molecular data support an origin of turtles from within Diapsida (reptiles with a doubly fenestrated skull roof). Evaluation of these conflicting hypotheses has been hampered by nonoverlapping taxonomic samples and the exclusion of significant taxa from published analyses. Furthermore, although data from soft tissues and anatomical systems such as the integument may be particularly relevant to this problem, they are often excluded from large-scale analyses of morphological systematics. Here, conflicting hypotheses of turtle relationships are tested by (1) combining published data into a supermatrix of morphological characters to address issues of character conflict and missing data; (2) increasing taxonomic sampling by more than doubling the number of operational taxonomic units to test internal relationships within suprageneric ingroup taxa; and (3) increasing character sampling by approximately 25% by adding new data on the osteology and histology of the integument, an anatomical system that has been historically underrepresented in morphological systematics. The morphological data set assembled here represents the largest yet compiled for Amniota. Reevaluation of character data from prior studies of amniote phylogeny favors the hypothesis that turtles indeed have diapsid affinities. Addition of new ingroup taxa alone leads to a decrease in overall phylogenetic resolution, indicating that existing characters used for amniote phylogeny are insufficient to explain the evolution of more highly nested taxa. Incorporation of new data from the soft and osseous components of the integument, however, helps resolve relationships among both basal and highly nested amniote taxa. Analysis of a data set compiled from published sources and data original to this study supports monophyly of Amniota, Synapsida, Reptilia, Parareptilia, Eureptilia, Eosuchia, Diapsida, Neodiapsida, Sauria, Lepidosauria, and Archosauriformes, as well as several more highly nested divisions within the latter two clades. Turtles are here resolved as the sister taxon to a monophyletic Lepidosauria (squamates + Sphenodon), a novel phylogenetic position that nevertheless is consistent with recent molecular and morphological studies that have hypothesized diapsid affinities for this clade.

Animals↗

PubMed2001

Rate matrices for analyzing large families of protein sequences.

We propose and study a new approach for the analysis of families of protein sequences. This method is related to the LogDet distances used in phylogenetic reconstructions; it can be viewed as an attempt to embed these distances into a multidimensional framework. The proposed method starts by associating a Markov matrix to each pairwise alignment deduced from a given multiple alignment. The central objects under consideration here are matrix-valued logarithms L of these Markov matrices, which exist under conditions that are compatible with fairly large divergence between the sequences. These logarithms allow us to compare data from a family of aligned proteins with simple models (in particular, continuous reversible Markov models) and to test the adequacy of such models. If one neglects fluctuations arising from the finite length of sequences, any continuous reversible Markov model with a single rate matrix Q over an arbitrary tree predicts that all the observed matrices L are multiples of Q. Our method exploits this fact, without relying on any tree estimation. We test this prediction on a family of proteins encoded by the mitochondrial genome of 26 multicellular animals, which include vertebrates, arthropods, echinoderms, molluscs, and nematodes. A principal component analysis of the observed matrices L shows that a single rate model can be used as a rough approximation to the data, but that systematic deviations from any such model are unmistakable and related to the evolutionary history of the species under consideration.

Computational Biology↗

PubMed1995

Management of subglottic haemangioma.

Between 1980 and 1993, 10 infants underwent endoscopic treatment and/or open surgical excision of a subglottic haemangioma. Of the eight children treated with the laser, four showed simple evolution following a single laser treatment, one required repeated laser treatments and two needed tracheotomy despite repeated laser treatments. The last three children developed moderate subglottic stenosis. Laser treatment was followed by open surgical excision in one child. Two children underwent primary surgical excision, allowing extubation between 8 and 10 days post-operatively. After a period in which we systematically treated subglottic haemangiomas with the laser, these findings have led us to employ open surgery in children with large subglottic haemangiomas or when airway obstruction requires a tracheostomy.

Airway Obstruction↗

PubMed2003

Are audits wasting resources by measuring the wrong things? A survey of methods used to select audit review criteria.

OBJECTIVES: This study measured the extent to which a systematic approach was used to select criteria for audit, and identified problems in using such an approach with potential solutions. DESIGN: A questionnaire survey using the Audit Criteria Questionnaire (ACQ), created, piloted, and validated for the purpose. Possible ACQ scores ranged from 0 to 1, indicating how systematically the criteria had been selected and how usable they were. SETTING: A stratified random sample of 10 audit leads in each of 83 randomly selected NHS trusts and all practices in each of 11 randomly selected primary care audit group areas in England and Wales. PARTICIPANTS: Audit leads of ongoing audits in each organisation in which a first data collection had started less than 12 months earlier and a second data collection was not completed. MAIN OUTCOME MEASURES: ACQ scores, problems identified in the audit criteria selection process, and solutions found. RESULTS: The mean ACQ score from all 83 NHS trusts and the 11 primary care audit groups was 0.52 (range 0.0-0.98). There was no difference between mean ACQ scores for criteria used in audits on clinical (0.51) and non-clinical (0.52) topics. The mean ACQ scores from nationally organised audits (0.59, n=33) was higher than for regional (0.51, n=21), local (0.53, n=77), or individual organisation (0.52, n=335) audits. The mean ACQ score for published audit protocols (0.56) was higher than for locally developed audits (0.49). There was no difference in ACQ scores for audits reported by general practices (0.49, n=83) or NHS trusts (0.53, n=383). Problems in criteria selection included difficulties in coordination of staff to undertake the task, lack of evidence, poor access to literature, poor access to high quality data, lack of time, and lack of motivation. Potential solutions include investment in training, protected time, improved access to literature, support staff and availability of published protocols. CONCLUSIONS: Methods of selecting review criteria were often less systematic than is desirable. Published usable audit protocols providing evidence based review criteria with information on their provenance enable appropriate review criteria to be selected, so that changes in practice based on these criteria lead to real improvement in quality rather than merely change. The availability and use of high quality audit protocols would be a valuable contribution to the evolution of clinical governance. The ACQ should be developed into a tool to help in selecting appropriate criteria to increase the effectiveness of audit.

England↗

PubMed2004

[The place of interventional endoscopy in the treatment of lung cancer].

Interventional endoscopy, by eliminating an obstacle compromising the survival of a patient, has its place in the treatment of bronchial cancer whatever its stage of evolution. Forty percent of patients have not been treated yet, 30 still have therapeutic possibilities at the time of their relapse and for 30% all the possible treatments have been administered and interventional endoscopy remains their only chance of survival. A strict operational protocol ensures safety: operating theatre, general anaesthesia, rigid bronchoscopy, jet-ventilation, post-surgery ICU, and systematic post-surgery fibroscopy. Eighty percent of the patients retrieve normal ventilation. 12% are not sufficiently improved and 3% die either from uncontrollable haemorrhage or from the impossibility of repermeation. The nature of the tumour (primary bronchial cancer, metastasis at distance, invasion from a surrounding cancer) does not enter into the decision to intervene. The benefits of the latter are assessed by the pneumologist or oncologist who is in charge of the patient, but the final decision to intervene naturally remains with the endoscopist.

Bronchoscopy↗