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At least 685 records · Page 38Linked to original sources
PubMed2001

Evolution and mechanics of long jaws in butterflyfishes (family Chaetodontidae).

We analyzed the functional morphology and evolution of the long jaws found in several butterflyfishes. We used a conservative reanalysis of an existing morphological dataset to generate a phylogeny that guided our selection of seven short- and long-jawed taxa in which to investigate the functional anatomy of the head and jaws: Chaetodon xanthurus, Prognathodes falcifer (formerly Chaetodon falcifer), Chelmon rostratus, Heniochus acuminatus, Johnrandallia nigrirostris, Forcipiger flavissimus, and F. longirostris. We used manipulations of fresh, preserved, and cleared and stained specimens to develop mechanical diagrams of how the jaws might be protruded or depressed. Species differed based on the number of joints within the suspensorium. We used high-speed video analysis of five of the seven species (C. xanthurus, Chel. rostratus, H. acuminatus, F. flavissimus, and F. longirostris) to test our predictions based on the mechanical diagrams: two suspensorial joints should facilitate purely anteriorly directed protrusion of the lower jaw, one joint should allow less anterior protrusion and result in more depression of the lower jaw, and no joints in the suspensorium should constrain the lower jaw to simple ventral rotation around the jaw joint, as seen in generalized perciform fishes. We found that the longest-jawed species, F. longirostris, was able to protrude its jaws in a predominantly anterior direction and further than any other species. This was achieved with little input from cranial elevation, the principal input for other known lower jaw protruders, and is hypothesized to be facilitated by separate modifications to the sternohyoideus mechanism and to the adductor arcus palatini muscle. In F. longirostris the adductor arcus palatini muscle has fibers oriented anteroposteriorly rather than medial-laterally, as seen in most other perciforms and in the other butterflyfish studied. These fibers are oriented such that they could rotate the ventral portion of the quadrate anteriorly, thus projecting the lower jaw anteriorly. The intermediate species lack modification of the adductor arcus palatini and do not protrude their jaws as far (in the case of F. flavissimus) or in a purely anterior fashion (in the case of Chel. rostratus). The short-jawed species both exhibit only ventral rotation of the lower jaw, despite the fact that H. acuminatus is closely related to Forcipiger.

Animals↗
PubMed2002

Effects of enriched environments with different durations and starting times on learning capacity during aging in rats assessed by a refined procedure of the Hebb-Williams maze task.

Cognitive function as measured by the Hebb-Williams maze task was examined in Fischer 344 male rats that had been exposed to an enriched environment for periods of variable duration and at different starting ages. In one experiment, rats were exposed to environmental enrichment from weaning until the age of 2.5, 15, or 25 months. The results of 12 problems of the Hebb-Williams maze task showed that the enriched rearing condition improved the learning ability in all the age groups; however, factor analysis and ANOVA demonstrated that four of the 12 maze problems were not suitable for detecting the effect of age under different environmental conditions. Reanalysis of the results obtained with the other eight maze problems more clearly revealed both the effects of rearing condition and aging. The latter analysis demonstrated that the learning rate of rats reared under enriched conditions was faster than that of rats reared under standard social conditions. Short-term (3-month) exposure also had positive effects on cognitive function in both adult (11-month-old) and aged (22-month-old) animals. The effect of long-term exposure to an enriched environment starting at weaning was much greater than that of short-term exposure in aged rats, whereas the effects of both long-term and short-term exposure were almost the same in adult rats. These results show that aged animals still have appreciable plasticity in cognitive function, and suggest that environmental stimulation could benefit aging humans as well.

Aging↗
PubMed1987

Flow sorting of X and Y chromosome-bearing spermatozoa into two populations.

The only established difference on which to base the separation of X and Y chromosome-bearing spermatozoa is chromosomal constitution. This difference is quantifiable both from chromosome morphology (karyotype) and from DNA content. Flow cytometric techniques were used to measure relative DNA content of the X and Y populations and to flow-sort spermatozoa from Chinchilla laniger. Epididymal spermatozoa were recovered in PBS, fixed in 80% ethanol, treated with papain and dithioerythritol, and stained for DNA with Hoechst 33342. Sperm nuclei were analyzed and sorted on an EPICS V flow cytometer/cell sorter, modified specifically for spermatozoa. Two clearly resolved peaks (coefficient of variation less than 1.5%) with approximately 7.5% difference in DNA content between X and Y chromosome-bearing spermatozoa were evident. Sperm nuclei were sorted from a portion of the X and Y peaks at a rate of 55 nuclei/sec for each population. Purities of individual X and Y populations averaged 95% as determined by reanalysis of the sorted populations. Successful sorting of Chinchilla X and Y chromosome-bearing spermatozoa into separate populations may aid in the identification of a biochemical marker that could be used to discriminate between the two sperm populations and lead to a practical procedure for sexing spermatozoa.

Animals↗
PubMed1988

Flow sorting of X and Y chromosome-bearing mammalian sperm: activation and pronuclear development of sorted bull, boar, and ram sperm microinjected into hamster oocytes.

Flow cytometric techniques were used to measure relative DNA content of X and Y chromosome-bearing bull, boar, and ram sperm populations and to separate the two sex-determining populations. Neat semen was prepared for flow cytometric analysis by washing, light sonication, and staining with 9 microM Hoechst 33342. Computer analysis of the bimodal histograms showed mean X-Y DNA differences of 3.9, 3.7, and 4.2% for bull, boar, and ram, respectively. Flow cytometric reanalysis of sorted bull, boar, and ram sperm showed purities greater than 90%. Bull, boar, and ram sperm nuclei were microinjected into hamster oocytes. Microinjected sperm were either unsorted, sorted, unsorted plus dithiothreitol (DTT) exposure, or sorted plus DTT exposure. Following microinjection, eggs were incubated 3 hr, fixed, and stained. A total of 579 eggs was observed for sperm activation (decondensation or formation of a male pronucleus). A lower percentage of sorted than unsorted (3 vs. 23%) boar sperm was activated (P less than .05). However, sorted and unsorted DTT-exposed boar sperm or sorted and unsorted bull or ram sperm, regardless of DTT treatment, did not differ significantly. Sorted sperm nuclei of both rams and bulls exhibited higher activation rates than sorted boar sperm (P less than .05). Treatment of sperm with DTT increased the activation rate (P less than .05) for sorted boar sperm but not for bull or ram sperm.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2005

Is anoxic depolarisation associated with an ADC threshold? A Markov chain Monte Carlo analysis.

A Bayesian nonlinear hierarchical random coefficients model was used in a reanalysis of a previously published longitudinal study of the extracellular direct current (DC)-potential and apparent diffusion coefficient (ADC) responses to focal ischaemia. The main purpose was to examine the data for evidence of an ADC threshold for anoxic depolarisation. A Markov chain Monte Carlo simulation approach was adopted. The Metropolis algorithm was used to generate three parallel Markov chains and thus obtain a sampled posterior probability distribution for each of the DC-potential and ADC model parameters, together with a number of derived parameters. The latter were used in a subsequent threshold analysis. The analysis provided no evidence indicating a consistent and reproducible ADC threshold for anoxic depolarisation.

Algorithms↗
PubMed2003

Pitfalls in prenatal diagnosis: cytogenetic analysis in amniocytes fails to detect mosaic r(12).

OBJECTIVE: To review the accuracy of a prenatal diagnosis of a missed chromosomal mosaicism in amniotic fluid cell cultures and to see whether adapting the Dutch guidelines would have made any difference to the outcome in this case. METHOD: Metaphases, obtained from cultured amniocytes and peripheral blood lymphocytes, were analyzed with different results. The amniocyte cultures were then reanalyzed and the risk of missing this mosaicism in prenatal analysis was assessed. RESULTS: The prenatal tests performed according to the Dutch guidelines showed a normal female karyotype, but more extensive postnatal analysis revealed a ring chromosome in 50% of the child's lymphocytes. Reanalysis of the original amniocytes confirmed the normal diagnosis, but when more cells from the same and other colonies were analyzed, the ring chromosome was detected. CONCLUSION: The chance of missing such a supernumerary ring mosaicism is very low (about 2% in our case). Given its very rare occurrence and the low chance of it being missed if the existing Dutch guidelines are followed, adapting the number of cells or colonies to be examined for all prenatal diagnoses does not appear to be justified.

Adult↗
PubMed2005

HUPO Brain Proteome Project Pilot Studies: bioinformatics at work.

The data acquisition phase of initial pilot studies (human and mouse brain samples) of the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP) is now complete and the data generated by the participating laboratories has been submitted to the central Data Collection Center. The BPP Bioinformatics Group met on 8th April 2005 at the European Bioinformatics Institute (Hinxton, UK) to discuss strategies for the reanalysis of the pooled data from all the participating laboratories. A summary of the results of the data reprocessing will be presented at the 4th HUPO World Congress that will be held in August/September 2005.

Animals↗
PubMed1992

Sequence analysis of peptide mixtures by automated integration of Edman and mass spectrometric data.

A computer algorithm is described that utilizes both Edman and mass spectrometric data for simultaneous determination of the amino acid sequences of several peptides in a mixture. Gas phase sequencing of a peptide mixture results in a list of observed amino acids for each cycle of Edman degradation, which by itself may not be informative and typically requires reanalysis following additional chromatographic steps. Tandem mass spectrometry, on the other hand, has a proven ability to analyze sequences of peptides present in mixtures. However, mass spectrometric data may lack a complete set of sequence-defining fragment ions, so that more than one possible sequence may account for the observed fragment ions. A combination of the two types of data reduces the ambiguity inherent in each. The algorithm first utilizes the Edman data to determine all hypothetical sequences with a calculated mass equal to the observed mass of one of the peptides present in the mixture. These sequences are then assigned figures of merit according to how well each of them accounts for the fragment ions in the tandem mass spectrum of that peptide. The program was tested on tryptic and chymotryptic peptides from hen lysozyme, and the results are compared with those of another computer program that uses only mass spectral data for peptide sequencing. In order to assess the utility of this method the program is tested using simulated mixtures of varying complexity and tandem mass spectra of varying quality.

Algorithms↗
PubMed2003

Generalized monotonic regression using random change points.

We introduce a procedure for generalized monotonic curve fitting that is based on a Bayesian analysis of the isotonic regression model. Conventional isotonic regression fits monotonically increasing step functions to data. In our approach we treat the number and location of the steps as random. For each step level we adopt the conjugate prior to the sampling distribution of the data as if the curve was unconstrained. We then propose to use Markov chain Monte Carlo simulation to draw samples from the unconstrained model space and retain only those samples for which the monotonic constraint holds. The proportion of the samples collected for which the constraint holds can be used to provide a value for the weight of evidence in terms of Bayes factors for monotonicity given the data. Using the samples, probability statements can be made about other quantities of interest such as the number of change points in the data and posterior distributions on the location of the change points can be provided. The method is illustrated throughout by a reanalysis of the leukaemia data studied by Schell and Singh.

Bayes Theorem↗
PubMedDate not supplied

Fluoride and dental caries: two different statistical approaches to the same data source.

A recent analysis of data from earlier papers on the relationship between dental caries and drinking water fluoride concentration suggested that the commonly accepted inverse relationship did not exist. Our reanalysis of those data, however, confirms the well-known association between fluoride concentration and dental caries. It also shows that the contrary result arose misleadingly from three simultaneous methodological errors: use of a unifactorial instead of a multifactorial model; omission of or over-aggregation of some data, and analysis of homoscedastic probits instead of heteroscedastic counts.

Data Interpretation, Statistical↗
PubMed2006

The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast.

The last two years have seen the publication of three genome-wide gene expression studies of the fission yeast cell cycle. While these microarray papers largely agree on the main patterns of cell cycle-regulated transcription and its control, there are discrepancies with regard to the identity and numbers of periodically expressed genes. We present benchmark and reproducibility analyses showing that the main discrepancies do not reflect differences in the data themselves (microarray or synchronization methods seem to lead only to minor biases) but rather in the interpretation of the data. Our reanalysis of the three datasets reveals that combining all independent information leads to an improved identification of periodically expressed genes. These evaluations suggest that the available microarray data do not allow reliable identification of more than about 500 cell cycle-regulated genes. The temporal expression pattern of the top 500 periodically expressed genes is generally consistent across experiments and the three studies, together with our integrated analysis, provide a coherent and rich source of information on cell cycle-regulated gene expression in Schizosaccharomyces pombe. The reanalysed datasets and other supplementary information are available from an accompanying website: http://www.cbs.dtu.dk/cellcycle/. We hope that this paper will resolve the apparent discrepancies between the previous studies and be useful both for wet-lab biologists and for theoretical scientists who wish to take advantage of the data for follow-up work.

Cell Cycle↗
PubMed1999

Male choice for female colour morphs in Ischnura elegans (Odonata, Coenagrionidae): testing the hypotheses.

The occurrence of different conspecific female colour morphs, with one of the morphs resembling the male, is supposed to have consequences for mate choice. There are two hypotheses linking mate choice and female colour polymorphism. First, males may mate predominantly with female morphs that differ from the male because they do not recognize androchrome females as females (male mimic hypothesis). Second, males may be more attracted to the most common morph in the population (habituation hypothesis). We tested these hypotheses in five populations of the same species, Ischnura elegans, with a range of androchrome frequencies. In each population we performed binary choice experiments in small cages. Males did not consistently prefer gynochrome females but mated predominantly with the most common morph in the population. Moreover, a reanalysis of the available damselfly data in the literature also supported the habituation hypothesis. Copyright 1999 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed1995

Frequency of FMR1 premutations in a consecutive newborn population by PCR screening of Guthrie blood spots.

The fragile X(A) or FRAXA syndrome is the most common form of familial mental retardation and is associated with a fragile site at Xq27.3. The gene responsible for the FRAXA syndrome, the FMR1 gene, has been cloned. inactivation of the FMR1 gene is associated with amplification of a trinucle-otide CGG repeat sequence and methylation of an adjacent CpG island. Previous estimates for the prevalence of the FRAXA syndrome have been based on indirect methods of chromosome analysis in institutions and community workshops for the mentally handicapped. We have analyzed the frequency of premutations of the FMR1 gene in 3002 X chromosomes of 1000 male and 1000 female consecutive newborn nonautoclaved blood spots in an anonymous, unlinked survey. The CGG repeat sizes were calculated by measuring the length of products of the PCR reaction based on the molecular size of labeled markers in a denaturing sequencing gel assay. For consistent PCR amplification a DNA microextraction was necessary, including a phenol/chloroform series. In our population, the CGG allele ranged from 9 to 106 repeats: 97% of alleles had fewer than 40 repeats. The most frequent allele was a repeat of 28. Approximately 2.3% of alleles had CGG repeats ranging from 4 to 49 and 0.37% of alleles had repeats ranging from 50 to 59. The frequency of alleles > 60 repeats in the Manitoba male population is approximately 0.13%. The use of nonautoclaved Guthrie blood spots for population screening of FRAXA premutations is not recommended. The necessity of a phenol/chloroform DNA microextraction is tedious and time consuming. The low yield of DNA (250 ng) does not allow for reanalysis by Southern of apparently homozygous females with potentially unstable CGG alleles in the 40-60 repeat range and likely underestimates premutation carrier status.

Alleles↗
PubMed1995

The time course of syntactic activation during language processing: a model based on neuropsychological and neurophysiological data.

This paper presents a model describing the temporal and neurotopological structure of syntactic processes during comprehension. It postulates three distinct phases of language comprehension, two of which are primarily syntactic in nature. During the first phase the parser assigns the initial syntactic structure on the basis of word category information. These early structural processes are assumed to be subserved by the anterior parts of the left hemisphere, as event-related brain potentials show this area to be maximally activated when phrase structure violations are processed and as circumscribed lesions in this area lead to an impairment of the on-line structural assignment. During the second phase lexical-semantic and verb-argument structure information is processed. This phase is neurophysiologically manifest in a negative component in the event-related brain potential around 400 ms after stimulus onset which is distributed over the left and right temporo-parietal areas when lexical-semantic information is processed and over left anterior areas when verb-argument structure information is processed. During the third phase the parser tries to map the initial syntactic structure onto the available lexical-semantic and verb-argument structure information. In case of an unsuccessful match between the two types of information reanalyses may become necessary. These processes of structural reanalysis are correlated with a centroparietally distributed late positive component in the event-related brain potential.(ABSTRACT TRUNCATED AT 250 WORDS)

Aphasia, Broca↗
PubMed1998

Semantic transparency in the processing of compounds: consequences for representation, processing, and impairment.

The role of semantic transparency in morphological processing in general and in compound processing in particular is examined. It is argued that the notion of semantic transparency is crucial to an account of how compounds are represented and processed in the mind. A sketch of a model is proposed in which compound processing is described in terms of stimulus properties, lexical properties, and conceptual properties. The model represents the notion of semantic transparency in terms of a four-way classification of the semantic relationship between a compound's constituents and the corresponding independent morphemes. It also distinguishes between semantically componential and noncomponential compounds. It is proposed that the model offers a framework within which experimental psycholinguistic findings can be understood and within which aphasic deficits associated with compound processing can be characterized. As an example of this, the paper presents a reanalysis of an aphasic patient who exhibits the tendency to interpret semantically opaque compounds as though they were transparent and to interpret opaque compounds in terms of a blend of constituent and whole-word meaning. It is argued that the underlying deficit in this patient is the failure for inhibition to result from the competition among stimuli at the conceptual level of representation.

Aphasia↗
PubMed1998

First-pass versus second-pass parsing processes in a Wernicke's and a Broca's aphasic: electrophysiological evidence for a double dissociation.

The present paper is a first attempt to integrate the classical brain lesion behavioral impairment approach of functional neuroanatomy and the electrophysiological brain mapping approach in the domain of syntactic processing. In a group of normal age-matched controls we identified three electrophysiological components previously observed in correlation with language comprehension processes: an early left anterior negativity normally seen in correlation with syntactic first-pass parsing processes (ELAN), a centroparietal negativity seen in correlation with processes of lexical-semantic integration (N400), and a late centroparietal positivity observed in correlation with secondary syntactic processes of reanalysis and repair (P600). The early left anterior negativity was absent in a patient with an extended lesion in the anterior part of the left hemisphere sparing the temporal lobe, although the late centroparietal positivity and the centroparietal N400 were present. In a patient with a left temporal-parietal lesion the early left anterior negativity was found to be present, whereas the N400 component was absent. These findings suggest that first-pass parsing and secondary processes are subserved by distinct brain systems.

Adult↗
PubMed1998

Priming and aging: an electrophysiological investigation of N400 and recall.

Twenty young (20.5 years) and 20 middle-aged academics (57.2 years) performed a priming-recall task which was presented in three blocks. In each block, participants read 40 word pairs after which a recall task had to be carried out. Half of the word pairs were highly associated while the others were low associated. Targets showed the N400 of the middle-aged group to be both delayed and smaller in amplitude for low-associated items. N400 of primes, however, showed no age-related latency difference but was smaller for the middle-aged group due to a positive shift. It is argued that this shift possibly indicates age differences in semantic activation or buildup of context. A reanalysis showed individual differences in word pair processing to depend on recall performance. In general, high recallers were found to show a much larger differentiation between low- and high-associated targets. This resulted from a much larger N400 component elicited by low-associated targets and a more positive ERP in the N400-region for the high-associated targets. It is suggested that the middle-aged subjects activated the expected target word to a level at least equivalent to the younger subjects, but that the activated network itself was larger/less selective particularly in subjects showing a low recall.

Adult↗
PubMedDate not supplied

The subjects as a simple random effect fallacy: subject variability and morphological family effects in the mental lexicon.

This is a methodological study addressing the appropriateness of standard by-subject and by-item averaging procedures for the analysis of repeated-measures designs. By means of a reanalysis of published data (Schreuder & Baayen, 1997), using random regression models, we present a proof of existence of systematic variability between participants that is ignored in the standard psycholinguistic analytical procedures. By applying linear mixed effects modeling (Pinheiro & Bates, 2000), we call attention to the potential lack of power of the by-subject and by-item analyses, which in this case study fail to reveal the coexistence of a facilitatory family size effect and an inhibitory family frequency effect in visual and auditory lexical processing.

Auditory Perception↗