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Results for “variational inference”

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PubMed2003

Ribosomal ITS sequences and plant phylogenetic inference.

One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of the 18S-5.8S-26S nuclear ribosomal cistron. The prominence of this source of nuclear DNA sequence data is underscored by a survey of phylogenetic publications involving comparisons at the genus level or below, which reveals that of 244 papers published over the last five years, 66% included ITS sequence data. Perhaps even more striking is the fact that 34% of all published phylogenetic hypothesis have been based exclusively on ITS sequences. Notwithstanding the many important contributions of ITS sequence data to phylogenetic understanding and knowledge of genome relationships, a number of molecular genetic processes impact ITS sequences in ways that may mislead phylogenetic inference. These molecular genetic processes are reviewed here, drawing attention to both underlying mechanism and phylogenetic implications. Among the most prevalent complications for phylogenetic inference is the existence in many plant genomes of extensive sequence variation, arising from ancient or recent array duplication events, genomic harboring of pseudogenes in various states of decay, and/or incomplete intra- or inter-array homogenization. These phenomena separately and collectively create a network of paralogous sequence relationships potentially confounding accurate phylogenetic reconstruction. Homoplasy is shown to be higher in ITS than in other DNA sequence data sets, most likely because of orthology/paralogy conflation, compensatory base changes, problems in alignment due to indel accumulation, sequencing errors, or some combination of these phenomena. Despite the near-universal usage of ITS sequence data in plant phylogenetic studies, its complex and unpredictable evolutionary behavior reduce its utility for phylogenetic analysis. It is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes.

DNA, Ribosomal Spacer↗

PubMed2003

Molecular study of Dermatocarpon miniatum (Verrucariales) and allied taxa.

The phylogeny of the Dermatocarpon miniatum-complex (Verrucariales, lichenized Ascomycota) was studied using nuclear ITS sequence data by both parsimony and Bayesian inference of phylogeny. The ITS region contains a substantial amount of variation which resolves the relationships of terminal groups, while the more basal clades have low support in the analyses. D. miniatum var. miniatum and var. complicatum are polyphyletic, while var. cirsodes is monophyletic but located within the complex, as are both D. leptophyllum and D. linkolae. The variation within the D. miniatum-complex is significantly greater than that between some transatlantic species such as D. luridum and D. meiophyllizum. The new names D. taminium sp. nov. from the Greater Sonoran area, and D. tenue comb. nov. (syn. D. muehlenbergii var. tenue) are introduced.

Ascomycota↗

PubMed2002

The dusk flank of Jupiter's magnetosphere.

Limited single-spacecraft observations of Jupiter's magnetopause have been used to infer that the boundary moves inward or outward in response to variations in the dynamic pressure of the solar wind. At Earth, multiple-spacecraft observations have been implemented to understand the physics of how this motion occurs, because they can provide a snapshot of a transient event in progress. Here we present a set of nearly simultaneous two-point measurements of the jovian magnetopause at a time when the jovian magnetopause was in a state of transition from a relatively larger to a relatively smaller size in response to an increase in solar-wind pressure. The response of Jupiter's magnetopause is very similar to that of the Earth, confirming that the understanding built on studies of the Earth's magnetosphere is valid. The data also reveal evidence for a well-developed boundary layer just inside the magnetopause.

Journal Article↗

PubMed2006

Uplift, thermal unrest and magma intrusion at Yellowstone caldera.

The Yellowstone caldera, in the western United States, formed approximately 640,000 years ago when an explosive eruption ejected approximately 1,000 km3 of material. It is the youngest of a series of large calderas that formed during sequential cataclysmic eruptions that began approximately 16 million years ago in eastern Oregon and northern Nevada. The Yellowstone caldera was largely buried by rhyolite lava flows during eruptions that occurred from approximately 150,000 to approximately 70,000 years ago. Since the last eruption, Yellowstone has remained restless, with high seismicity, continuing uplift/subsidence episodes with movements of approximately 70 cm historically to several metres since the Pleistocene epoch, and intense hydrothermal activity. Here we present observations of a new mode of surface deformation in Yellowstone, based on radar interferometry observations from the European Space Agency ERS-2 satellite. We infer that the observed pattern of uplift and subsidence results from variations in the movement of molten basalt into and out of the Yellowstone volcanic system.

Journal Article↗

PubMed1977

[Statistical aspects in planning psychotropic drug trials (author's transl)].

It has become virtually unthinkable to objectively judge trials of comparisons without statistical inference. For studies involving psychopharmaceuticals the requirements have especially grown, since variations of efficacy are difficult to differentiate and objectivate. The basic principles of statistical planning must be applied to studies with psychopharmaceuticals. On the basis of these general principles the relevant points of the clinical and statistical models and their relationship to one another are discussed. Special aspects of the study objectives, the clinical model, the medical trial plan, the statistical model and design, the execution of the trials, statistical evaluation and its interpretation are presented. The setting up of hypotheses, balancing and maintenance of factors of disturbances, sample sizes, randomizing techniques and the confrontation of clinical relevance with statistical significance are some of the important points discussed.

Clinical Trials as Topic↗

PubMed2003

Low-temperature specific heat of the heavy-fermion superconductor PrOs4Sb12.

We report the magnetic field dependence of the specific-heat C of single crystals of the first Pr-based heavy-fermion superconductor Pr(Os4Sb12. The variation of C at low temperature and the magnetic phase diagram inferred from C, the resistivity and magnetization provide compelling evidence of a doublet ground state. Two distinct superconducting anomalies in C indicate an unconventional superconducting state, where the splitting may arise from a weak lifting of the ground state degeneracy. In combination this identifies Pr(Os4Sb12 as a strong contender for quadrupolar pairing, i.e., superconductivity that is neither electron-phonon nor magnetically mediated.

Journal Article↗

PubMed2003

Stochasticity overrules the "three-times rule": genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA.

Palumbi et al. (2001) proposed a "three-times rule" that uses mitochondrial DNA (mtDNA) sequences to predict probabilities of monophyly for nuclear loci (i.e., whether the alleles within a taxon coalesce with one another before they coalesce with alleles from a sister taxon). They use neutral coalescent theory to infer these probabilities from the ratio of interspecific divergence to intraspecific variation of mtDNA. We show that the estimated probabilities have very wide confidence intervals because of the inherent stochasticity of the mtDNA coalescent process. Under neutrality, the true probability of monophyly can be much higher, or much lower, than predicted by the three-times rule. We also review recent empirical and theoretical studies that refute neutrality-based predictions concerning mtDNA variation and divergence. We conclude that the three-times rule is neither a useful test for neutral molecular evolution nor a reliable guide to genealogical species.

Cell Nucleus↗

PubMed1977

Axial forces in the bronchial tree.

Dog airways in situ are longer and extend more with inflation than when dissected out. The associated deformation of the parenchyma, from considerations of elasticity, appears to be small. The associated axial forces, to the extent they are transmitted along the tree, are governed by branching angles. Overall, average angles are such as would maintain constant axial stress along the tree and thus favor symmetrical lengthening. But locally, angles indicate considerable variation of transmitted stresses. Since radiography shows relatively homogeneous lengthening, we infer powerful local axial stabilization. In confirmation, dog airways were much less extended by locally applied forces in situ than excised. Do forced expirations apply substantial axial forces? In one subjects, during forced expiration, airway pressure fell abruptly near the carina but calculations showed relatively small axial forces applied to the airway. However, we speculate that large forces may be applied by airway plugs. We conclude that parenchyma stabilizes airway length against variably transmitted axial forces, and, perhaps, forces on airway plugs.

Airway Obstruction↗

PubMedDate not supplied

On the correlation between the amplitude of the electrochromic absorption changes and the number of bulk pigments.

A correlation between the amplitude of the electrochromic absorption changes measured at 480 nm and 520 nm and the size of the photosynthetic unit is found. Three tobacco mutants which differ with respect to their photosynthetic unit size exhibit decreased amplitudes of the electrochromic absorption changes which parallel the size of the photosynthetic units. Under these conditions the ATP-yield per flash is unaffected by the photosynthetic unit size. From this it is deduced that the correlation between the amplitude of the electrochromic absorption change and the photosynthetic unit size is due to the fact that the number of pigments undergoing an electrochromic bandshift is proportional to the total pigment content. As the influence on the electrochromic effect at 520 nm is too pronounced as to be simply explainable by the variation of the carotenoid content in the different mutants it is inferred that either structural effects leading to a modification of the carotenoid orientation in the mutants or an indirect influence of chlorophyll on the electrochromic bandshift which depend on the number of chlorophyll molecules are responsible.

Adenosine Triphosphate↗

PubMed1994

Does vitamin C alleviate the symptoms of the common cold?--a review of current evidence.

Since 1971, 21 placebo-controlled studies have been made to establish whether vitamin C at a dosage of > or = 1 g/day affects the common cold. These studies have not found any consistent evidence that vitamin C supplementation reduces the incidence of the common cold in the general population. Nevertheless, in each of the 21 studies, vitamin C reduced the duration of episodes and the severity of the symptoms of the common cold by an average of 23%. However, there have been large variations in the benefits observed, and clinical significance cannot be clearly inferred from the results. Still, the consistency of the results indicates that the role of vitamin C in the treatment of the common cold should be reconsidered.

Ascorbic Acid↗

PubMed1999

Interocular symmetry in nerve fiber layer thickness of normal eyes as determined by polarimetry.

PURPOSE: The existence of asymmetries between the two eyes in number and distribution of nerve fibers may provide an early anatomic indication of glaucomatous disruption if a symmetrical pattern of nerve fibers can be shown in normal eyes. Normal eyes were tested to determine whether a high degree of correspondence of regional nerve fiber layer thickness exists between fellow eyes. METHODS: Nerve fiber layer thickness was inferred from retardation shift measured by a scanning laser polarimeter (Laser Diagnostic Technologies, Inc.) in 40 volunteers without glaucoma or ocular disease (80 eyes). Total thickness and the pattern of nerve fiber thickness over 208 regions was compared between the paired eyes. RESULTS: Inferred nerve fiber layer thickness in companion eyes was highly correlated. Variation of the total nerve fiber thickness was much less between companion eyes than between eyes of different individuals. In terms of regional (i.e., local) interocular correspondence, the measurements in the inferior retina were observed to be highly similar in the two eyes, but a pronounced shift of the location of the superior peak (maximum thickness) in the left eye relative to the right was observed, as were differences between the two eyes in the thickness measurements at the nasal and temporal minima. CONCLUSION: Significant interocular asymmetries were detected in regions other than the interior hemiretina. These interocular asymmetries may reflect previously unrecognized anatomic nerve fiber differences or systematic angular bias in the instrument for one eye relative to the other. In contrast to the regional measures, the measures of total thickness were very similar between companion eyes, suggesting that the assessment of interocular asymmetries of total thickness determined by polarimetry may offer potential for detecting glaucoma.

Adult↗

PubMed1999

Historical biogeography of tamarins, genus Saguinus: the molecular phylogenetic evidence.

Hypotheses of the historical biogeography of tamarins (genus Saguinus) based on variation in coat colors and body size are tested using phylogenetic relationships inferred from mitochondrial DNA (mtDNA) sequence data. Samples from all 12 species of Saguinus and several subspecies are included in the analysis. Approximately 1,200 bases of mtDNA sequence from the cytochrome b and D-loop regions are reported for the tamarins and several outgroup taxa. Parsimony analysis of the mtDNA sequence data reveals Saguinus to be a monophyletic taxon composed of two major clades: one, the Small-bodied clade, contains S. nigricollis, S. tripartitus, and S. fuscicollis, and the other, the Large-bodied clade, contains the other nine species. The phylogenetic relationships among tamarins inferred from the mtDNA sequence data reject previous hypotheses for the historical biogeography of tamarins and suggest different dispersal routes for this group of New World monkeys. The molecular data suggest that tamarins dispersed across South America in two major waves from an origin somewhere south of the Amazon. One wave moved in a westerly direction, whereas the other moved in a northeastern direction toward the Amazon delta and then west along the northern portion of the continent into northern Colombia and Panama.

Animals↗

PubMed1999

Phylogenetic relationships of seven palearctic members of the maculipennis complex inferred from ITS2 sequence analysis.

The sequences of the second internal transcribed spacer (ITS2) of ribosomal DNA (rDNA) were determined from seven palearctic mosquitoes species belonging to the Anopheles maculipennis species complex, namely An. atroparvus, An. labranchiae, An. maculipennis, An. messeae, An. melanoon, An. sacharovi and An. martinius. The length of the ITS2 ranged from 280 to 300 bp, with a GC content of 49.4-54.1%. With the exception of An. messeae, negligible levels of intraspecific polymorphism and no intrapopulation variation were observed. The phylogenetic relationships among the members of the maculipennis complex were inferred by maximum-parsimony analysis of the PAUP program and the neighbour-joining and maximum-likelihood analysis of the PHYLIP program. All of the trees obtained were almost identical in topology, although the relationships among three species, i.e. An. maculipennis, An. messeae and An. melanoon, remained unresolved. The phylogenies were in good agreement with the previous gene-enzyme and polytene chromosome banding pattern studies.

Animals↗

PubMed1989

Variation in salmonid mitochondrial DNA: evolutionary constraints and mechanisms of substitution.

Sequence comparisons were made from 2214 bp of mitochondrial DNA cloned from six Pacific salmonid species. These sequences include the genes for ATPase subunit 6, cytochrome oxidase subunit 3, NADH dehydrogenase subunit 3, NADH dehydrogenase subunit 4L, tRNA(GLY), and tRNA(ARG). Variation is found at 338 silent and 12 nonsilent positions of protein coding genes and 10 positions in the two tRNA sequences. A single 3-bp length difference was also detected. In all pairwise comparisons the sequence divergence observed in the fragment was higher than that previously predicted by restriction enzyme analysis of the entire molecule. The inferred evolutionary relationship of these species is consistent between methods. The distribution of silent variation shows a complex pattern with greatly reduced variation at the junctions of genes. The variation in the tRNA sequences is concentrated in the DHU loop. The close relationship of these species and extensive sequence analyzed allows for an analysis of the spectrum of substitutions that includes the frequencies of all 12 possible substitutions. The observed spectrum of substitutions is related to potential pathways of spontaneous substitution. The salmonid sequences show an extremely high ratio of silent to replacement substitutions. In addition the amino acid sequences of the four proteins coded in this fragment show a consistently high level of identity with the Xenopus sequences. Taken together these data are consistent with a slower rate of amino acid substitution among the cold-blooded vertebrates when compared to mammals.

Adenosine Triphosphatases↗

PubMed2003

Sources of variation in consumer-diet delta 15N enrichment: a meta-analysis.

Measurements of delta15N of consumers are usually higher than those of their diet. This general pattern is widely used to make inferences about trophic relationships in ecological studies, although the underlying mechanisms causing the pattern are poorly understood. However, there can be substantial variation in consumer-diet delta15N enrichment within this general pattern. We conducted an extensive literature review, which yielded 134 estimates from controlled studies of consumer-diet delta15N enrichment, to test the significance of several potential sources of variation by means of meta-analyses. We found patterns related to processes of nitrogen assimilation and excretion. There was a significant effect of the main biochemical form of nitrogenous waste: ammonotelic organisms show lower delta15N enrichment than ureotelic or uricotelic organisms. There were no significant differences between animals feeding on plant food, animal food, or manufactured mixtures, but detritivores yielded significantly lower estimates of enrichment. delta15N enrichment was found to increase significantly with the C:N ratio of the diet, suggesting that a nitrogen-poor diet can have an effect similar to that already documented for fasting organisms. There were also differences among taxonomic classes: molluscs and crustaceans generally yielded lower delta15N enrichment. The lower delta 15N enrichment might be related to the fact that molluscs and crustaceans excrete mainly ammonia, or to the fact that many were detritivores. Organisms inhabiting marine environments yielded significantly lower estimates of delta15N enrichment than organisms inhabiting terrestrial or freshwater environments, a pattern that was influenced by the number of marine, ammonotelic, crustaceans and molluscs. Overall, our analyses point to several important sources of variation in delta15N enrichment and suggest that the most important of them are the main biochemical form of nitrogen excretion and nutritional status. The variance of estimates of delta15N enrichment, as well as the fact that enrichment may be different in certain groups of organisms should be taken into account in statistical approaches for studying diet and trophic relationships.

Animals↗

PubMed2005

Inter-gene correlation on oligonucleotide arrays: how much does normalization matter?

BACKGROUND AND OBJECTIVE: Normalization is a standard low-level preprocessing procedure in microarray data analysis to minimize the systematic technological variations and produce more reliable results. A variety of normalization approaches have been introduced and are widely applied. Normalization, however, remains controversial. The sensitivity of array results to normalization is an open question. No clear standard for comparing or judging normalization methods has yet emerged, and the effects of normalization on gene-to-gene co-expression are unclear. METHODS: In this investigation, we applied 1-, 2-, and N-quantile normalization to several publicly available microarray datasets quantified with either MAS 5.0 or dCHIP and evaluated the effect on gene-to-gene co-expression. We introduced a graphical method to explore trends in gene correlation. RESULTS: We found clear differences in the distributions of gene dependencies by normalization method. Increasing the number of standardized quantiles in the normalization reduced trends in correlation by signal intensity in MAS 5.0 quantifications but not dCHIP. Increasing the number of standardized quantiles did not markedly reduce the correlation of known overlapping targets with MAS 5.0. CONCLUSIONS: Normalization plays a very important role in the estimation of inter-gene dependency. Caution should be used when making inferences concerning gene-wise dependencies with microarrays until this source of variation is better understood.

Algorithms↗

PubMedDate not supplied

Bilateral variation in limb articular surface dimensions.

Joint form is frequently used to interpret locomotor and manipulative adaptations and infer physical behavioral patterns in past humans, yet the precise genetic and environmental determinants of joint size are incompletely understood. The aim of this research is to assess the plasticity of limb articular dimension through the use of directional asymmetry as an indicator of mechanical stress during skeletal development. Directional asymmetry is largely attributable to differential mechanical loading during bone growth related to handedness. Because the large majority of individuals are right-handed, it is hypothesized that joint dimensions will be significantly larger in the upper right limb and lower left limb in the crossed symmetry pattern that is typically exhibited in bone lengths. Patterns of bilateral variation were explored by sex and skeletal location. Significant levels of directional asymmetry (P < 0.05) suggest that limb articular surfaces are adapted to the mechanical environment. Biomechanical factors are important in the development and maintenance of articular morphology. Further research, however, is needed to establish the exact relationship between joint size and the mechanical environment.

Adaptation, Physiological↗

PubMed2026

PyEvoMotion: a Python tool for population-based time-course analysis of genome evolution.

SUMMARY: We present PyEvoMotion, an open-source Python tool for inferring molecular clock models with time-dependent Gaussian noise from high-throughput genomic datasets. PyEvoMotion features a command-line interface and a modular architecture, allowing seamless integration into larger bioinformatic pipelines. The tool supports customizable filtering, temporal discretization definition, and mutation classification, making it adaptable to diverse research needs. While traditional phylogenetic methods may encounter computational challenges with large datasets, PyEvoMotion can process thousands to millions of sequences to compute statistical parameters associated with a stochastic differential equation model, thereby weighting the genetic variation within the population. Using viral genomic data, we demonstrate its capability to infer evolutionary rates and detect non-Brownian evolutionary motions with subdiffusive behavior. PyEvoMotion shows potential to provide overlooked insights into genome evolution in different contexts. AVAILABILITY AND IMPLEMENTATION: The open source software is available on GitHub at https://github.com/luksgrin/PyEvoMotion and on SourceForge at https://sourceforge.net/projects/pyevomotion.

Software↗