Natural variation in HIV infection: Monte Carlo estimates that include CD8 effector cells

Viral load and CD4 T-cell counts in patients infected with the human immunodeficiency virus (HIV) are commonly used to guide clinical decisions regarding drug therapy or to assess therapeutic outcomes in clinical trials. However, random fluctuations in these markers of infection can obscure clinically significant change. We employ a Monte Carlo simulation to investigate contributing factors in the expected variability in CD4 T-cell count and viral load due solely to the stochastic nature of HIV infection. The simulation includes processes that contribute to the variability in HIV infection including CD4 and CD8 T-cell population dynamics as well as T-cell activation and proliferation. The simulation results may reconcile the wide range of variabilities in viral load observed in clinical studies, by quantifying correlations between viral load measurements taken days or weeks apart. The sensitivity of variability in T-cell count and viral load to changes in the lifetimes of CD4 and CD8 T-cells is investigated, as well as the effects of drug therapy.     

Influence of segmentation on morphological parameters and computed hemodynamics in cerebral aneurysms

This article focuses on the effects of segmentation on cerebral aneurysm's morphological parameters and on blood flow patterns computed using computational fluid dynamics. Segmentation is a non-negligible source of uncertainty that may have a consequent impact on the morphological assessment and the resulting hemodynamical simulations, the latter potentially being a key element in the decision-making therapeutic armamentarium for neuroradiologists and neurosurgeons. From the three patient-specific cases investigated, medical imaging data sets were collected, and four different three-dimensional segmentations were generated by the same senior technician. Morphological parameters were measured, and the aspect ratio was derived. Numerical simulations were performed; flow pattern changes, their impact on wall shear stress (WSS) and their sensitivity within the four reconstructed geometries were analyzed. Aneurysm velocity, vorticity and shear magnitudes were computed and compared. The morphological parameters having the highest variability were the aneurysm lobe dimensions (20 %). The neck length was the second parameter presenting the highest variability (21 %). The neck width variability reached 13.8 %, and the aspect ratio variability reached 14.2 %. The artery height and the artery width presented a variability of 13.7 and 10.8 %, respectively. Finally, the aneurysm depth, aneurysm height and aneurysm width presented variabilities of 12.8, 9.4 and 7.3 %, respectively. Differences in the flow path lines, velocity magnitude, wall shear stress and vorticity are also reported and discussed. The average variability reached 15.6 % for velocity, 25.2 % for vorticity and 25.2 % for shear, these parameters being computed inside the aneurysm. The maximum variability reached 31.0 % for velocity, 54.8 % for vorticity and 58.1 % for shear. A segmentation process reconstructing anatomies that is less sensitive to human intervention would be a future goal worth pursuing.     

Morphological Adaptations to Migration in Birds

Migratory flight performance has direct or carry-over effects on fitness. Therefore, selection is expected to act on minimizing the costs of migratory flight, which increases with the distance covered. Aerodynamic theory predicts how morphological adaptations improve flight performance. These predictions have rarely been tested in comparative analyses that account for scaling and phylogenetic effects. We amassed a unique dataset of 149 European bird species and 10 morphological traits. Mass-adjusted aspect ratio increased, while mass-adjusted heart weight and wing loading decreased with increasing migration distance. These results were robust to whether the analyses were based on the entire species pool or limited to passerines or migrants. Our findings indicate that selection due to migration acts on wing traits that reduce the energetic cost of transportation to increase the flight range. Consequently, the demands for high ‘exercise organ’ performance might be low, and hence such energetically expensive tissues are not associated (pectoral muscle) or are inversely associated (heart) with migration distance.     

Evaluation and comparison of multi-omics data integration methods for cancer subtyping

Computational integrative analysis has become a significant approach in the data-driven exploration of biological problems. Many integration methods for cancer subtyping have been proposed, but evaluating these methods has become a complicated problem due to the lack of gold standards. Moreover, questions of practical importance remain to be addressed regarding the impact of selecting appropriate data types and combinations on the performance of integrative studies. Here, we constructed three classes of benchmarking datasets of nine cancers in TCGA by considering all the eleven combinations of four multi-omics data types. Using these datasets, we conducted a comprehensive evaluation of ten representative integration methods for cancer subtyping in terms of accuracy measured by combining both clustering accuracy and clinical significance, robustness, and computational efficiency. We subsequently investigated the influence of different omics data on cancer subtyping and the effectiveness of their combinations. Refuting the widely held intuition that incorporating more types of omics data always produces better results, our analyses showed that there are situations where integrating more omics data negatively impacts the performance of integration methods. Our analyses also suggested several effective combinations for most cancers under our studies, which may be of particular interest to researchers in omics data analysis.     

Development of a statistical shape-function model of the implanted knee for real-time prediction of joint mechanics

Outcomes of total knee arthroplasty (TKA) are dependent on surgical technique, patient variability, and implant design. Non-optimal design or alignment choices may result in undesirable contact mechanics and joint kinematics, including poor joint alignment, instability, and reduced range of motion. Implant design and surgical alignment are modifiable factors with potential to improve patient outcomes, and there is a need for robust implant designs that can accommodate patient variability. Our objective was to develop a statistical shape-function model (SFM) of a posterior stabilized implanted knee to instantaneously predict joint mechanics in an efficient manner. Finite element methods were combined with Latin hypercube sampling and regression analyses to produce modeling equations relating nine implant design and six surgical alignment parameters to tibiofemoral (TF) joint mechanics outcomes during a deep knee bend. A SFM was developed and TF contact mechanics, kinematics, and soft tissue loads were instantaneously predicted from the model. Average normalized root-mean-square error predictions were between 2.79% and 9.42%, depending on the number of parameters included in the model. The statistical shape-function model generated instantaneous joint mechanics predictions using a maximum of 130 training simulations, making it ideally suited for integration into a patient-specific design and alignment optimization pipeline. Such a tool may be used to optimize kinematic function to achieve more natural motion or minimize implant wear, and may aid the engineering and clinical communities in improving patient satisfaction and surgical outcomes.     

Testing the covarion hypothesis of molecular evolution

The covarion hypothesis of molecular evolution states that the fixation of mutations may alter the probability that any given position will fix the next change. Tests of this hypothesis using the divergence of real sequences are compromised because models of rate variation among sites (e.g., the gamma version of the one-parameter equation) predict sequence divergence values similar to those for the covarion process. This study therefore focuses on the extent to which the varied and unvaried codons of two well-diverged taxa are the same, because fewer are expected by the covarion hypothesis than by the gamma model. The data for these tests are the protein sequences of Cu, Zn superoxide dismutase (SOD) for mammals and plants. Simulation analyses show that the covarion hypothesis makes better predictions about the frequencies of varied and unhit positions in common between these two taxa than does the gamma version of the one-parameter model. Furthermore, the analysis of SOD tertiary structure demonstrates that mammal and plant variabilities are distributed differently on the protein. These results support the conclusions that the variable and invariable codons of mammal and plant SODs are different and that the covarion model explains the evolution of this protein better than the gamma version of the one-parameter process. Unlike other models, the covarion hypothesis accounts for rate fluctuations among positions over time, which is an important parameter of molecular evolution.      

Ten polymorphic microsatellite loci in the giant scallop (Mizuhopecten yessoensis)

Ten novel microsatellite loci were isolated from giant scallop Mizuhopecten yessoensis, and the polymorphisms were examined to estimate genetic variability. The genetic variabilities varied depending on the locus. The number of alleles ranged from two to 17, and the observed and expected heterozygosities ranged from 0.17 to 0.99 and 0.33 to 0.90, respectively. Six loci showed significant Hardy–Weinberg disequilibrium. The high variabilities revealed in this study suggest that microsatellites should prove useful for various genetic investigations.     

Relationship between enzyme heterozygosity and quaternary structure

The need for proteins to maintain particular quaternary structures constrains variability in amino acid sequence. Monomeric enzymes are then expected to be more variable than dimeric forms, which in turn are expected to be more variable than tetrameric forms. These predictions are confirmed by analysis of available data on enzyme variation. Theories relating enzyme heterozygosity to metabolic function are discussed in the light of these findings.Financial support for part of the work described in this article was derived from NERC Grant GR3/1558 to J. A. Beardmore.     

Neuromotor noise, error tolerance and velocity-dependent costs in skilled performance

In motor tasks with redundancy neuromotor noise can lead to variations in execution while achieving relative invariance in the result. The present study examined whether humans find solutions that are tolerant to intrinsic noise. Using a throwing task in a virtual set-up where an infinite set of angle and velocity combinations at ball release yield throwing accuracy, our computational approach permitted quantitative predictions about solution strategies that are tolerant to noise. Based on a mathematical model of the task expected results were computed and provided predictions about error-tolerant strategies (Hypothesis 1). As strategies can take on a large range of velocities, a second hypothesis was that subjects select strategies that minimize velocity at release to avoid costs associated with signal- or velocity-dependent noise or higher energy demands (Hypothesis 2). Two experiments with different target constellations tested these two hypotheses. Results of Experiment 1 showed that subjects chose solutions with high error-tolerance, although these solutions also had relatively low velocity. These two benefits seemed to outweigh that for many subjects these solutions were close to a high-penalty area, i.e. they were risky. Experiment 2 dissociated the two hypotheses. Results showed that individuals were consistent with Hypothesis 1 although their solutions were distributed over a range of velocities. Additional analyses revealed that a velocity-dependent increase in variability was absent, probably due to the presence of a solution manifold that channeled variability in a task-specific manner. Hence, the general acceptance of signal-dependent noise may need some qualification. These findings have significance for the fundamental understanding of how the central nervous system deals with its inherent neuromotor noise.     

PATTERNS IN THE GEOGRAPHICAL RANGES OF SPECIES

1. A growing number of studies have documented patterns in species geographic ranges relevant to the study of community structure. These include patterns in the frequency of geographic ranges of different sizes, and in the interaction of range sizes with population abundances and variabilities, body sizes, trophic characteristics and extinction probabilities.
2. Agreement between hypothesized and observed relationships is reasonably good, but we do not know how general the patterns are. Analysis of patterns has focused upon a few taxonomic groups, a bias largely resulting from a lack of information on the geographic distributions of most taxa.
3. Many of the patterns are interrelated, and although theoretical bases to all the patterns can be suggested, it is possible that some are artifacts.
4. Taylor power plots give us a means of making predictions about population behaviour as it pertains to geographic ranges. Some of these predictions suggest that previous conceptions of such interactions have been too narrow, but empirical analyses of these patterns will be hampered by the difficulty of measuring population variability.
5. In general, our knowledge of the structure, and spatial and temporal behaviour, of species geographic ranges remains poor.     

Prediction of the intramembranous tissue formation during perisprosthetic healing with uncertainties. Part 2. Global clinical healing due to combination of random sources

This work proposes to examine the variability of the bone tissue healing process in the early period after the implantation surgery. The first part took into account the effect of variability of individual biochemical factors on the solid phase fraction, which is an indicator of the quality of the primary fixation and condition of its long-term behaviour. The next issue, addressed in this second part, is the effect of cumulative sources of uncertainties on the same problem of a canine implant. This paper is concerned with the ability to increase the number of random parameters to assess the coupled influence of those variabilities on the tissue healing. To avoid an excessive increase in the complexity of the numerical modelling and further, to maintain efficiency in computational cost, a collocation-based polynomial chaos expansion approach is implemented. A progressive set of simulations with an increasing number of sources of uncertainty is performed. This information is helpful for future implant design and decision process for the implantation surgical act.     

The role of fire in structuring trait variability in Neotropical savannas

Intraspecific trait variability plays a fundamental role in community structure and dynamics; however, few studies have evaluated its relative importance to the overall response of communities to environmental pressures. Since fire is considered a key factor in Neotropical savannas, we investigated to what extent the functional effects of fire in a Brazilian savanna occurs via intra- or interspecific trait variability. We sampled 12 traits in communities subjected to three fire regimes in the last 12 years: annual, biennial, and protected. To evaluate fire’s relative effects, we fitted a general linear mixed models with species as random and fire as fixed factors, using: (1) all species in the communities (i.e., considering intra- and interspecific variabilities); (2) 18 species common to all fire regimes (i.e., intraspecific variability only); and (3) all species with their overall average trait values (i.e., interspecific variability only). We assessed the relative role of intra- or interspecific variability by comparing the significance of each trait in the three analyses. We also compared the within and between fire variabilities with a variance component analysis. Five traits presented larger intraspecific than interspecific variability, and the main effect of fire occurred at the intraspecific level. These results confirm that it is important to consider intraspecific variability to fully understand fire-prone communities. Moreover, trait variability was larger within than among fire regimes. Thus, fire may act more as an external filter, preventing some of the species from the regional pool from colonizing the cerrado, than as an internal factor structuring the already filtered cerrado communities.     

The relative influence of competition and prey defences on the trophic structure of animalivorous bat ensembles

Deterministic filters such as competition and prey defences should have a strong influence on the community structure of animals like animalivorous bats which have life histories characterized by low fecundity, low predation risk, long life expectancy and stable populations. We investigated the relative influence of these two deterministic filters on the trophic structure of animalivorous bat assemblages in South Africa. We used null models to test if patterns of dietary overlap were significantly different from patterns expected by chance and multivariate analyses to test the correlations between diet and phenotype (body size, wing morphology and echolocation). We found little evidence that competition structured the trophic niche of coexisting bats. Contrary to predictions from competition, dietary overlap between bats of ensembles and functional groups (open-air, clutter-edge, and clutter foragers) were significantly higher than expected by chance. Instead, we found support for the predictions of the allotonic frequency hypothesis: there were significant relationships between peak echolocation frequency and the proportion of moths in the diets of bats at local and regional scales, and peak echolocation frequency was the best predictor of diet even after we controlled for the influence of body size and phylogeny. These results suggest that echolocation frequency and prey hearing exert more influence on the trophic structure of sympatric animalivorous bats than competition. Nonetheless, differential habitat use and sensory bias may also be major determinants of trophic structure because these are also correlated with frequencies of bat calls.     

Effects of developmental and functional interactions on mouse cranial variability through late ontogeny

The mammalian skull performs a variety of functions and its growth and development mirrors this complexity. Cranial growth and development have been actively studied for many years. Despite this interest, the variation in the patterns and processes of skull growth has attracted little attention. An important and unanswered question is the extent to which patterns of cranial covariation and variation are dynamically reworked throughout postnatal growth. To address this question, we examine patterns of variability in random-bred mouse skulls aged 35, 90, and 150 days. Using a battery of both Procrustes coordinate and Euclidean distance-based methods, we measure mean shape, canalization, developmental stability, and morphological integration in these skulls. We predict that the patterns of variability are dynamic, particularly between the youngest and the two oldest age groups due to the influence of functional effects such as postweaning mastication. We also hypothesize that patterns of variability are structured by the same functional and developmental factors that have been shown to influence cranial growth in primates. Our results indicate that contrary to our predictions, patterns of canalization, developmental stability, and morphological integration are stabilized before 35 days. The mean shape, however, changed significantly with growth. We found that only the facial region showed significant integration as predicted by the functional matrix model used in other studies of integration. These results indicate that phenotypic integration in these mice does not closely match those found for primate species, suggesting that comparisons between species should be made with care.     

Strain Analysis as a Tool for Functional Morphology

Strain gauge analysis can provide tremendous benefits to functionalmorphologists by accurately assessing the performance of a particularhard tissue structure in the mechanicalloading environmentsin which it functions. This method replaces estimated calculationsof skeletal stresses or strains with empirical measurements,and thus allows explicit testing of predictions derived fromtheoretical mechanical analyses or models. This direct measurementis particularly useful and important when the assumptions ofmechanical models are violated in the biological world, suchas when the geometry of the element of interest is complex and/orwhen the loads applied to a structure are either poorly knownof dynamically changing. In many, perhaps most, systems of interestto functional morphologists, the assumptions of simple shapeand well-defined loading necessary for most theoretical analysesare untenable; in these situations, strain gauge analysis canprovide considerable crucial information not obtainable anyother way. Although there are important limitations to the useof this approach, it can be applied to a variety of kinds offunctional analyses and may supply information about skeletalperformance that can contribute to meaningful functional interpretationsof morphological design.     

Carpenter Bee (Xylocopa micans) Risk Indifference and a Review of Nectarivore Risk-sensitivity Studies

This paper presents new results of risk-sensitive foraging studiesof the carpenter bee, Xylocopa micans, and reviews the workto date on risk sensitivity in nectarivores. In the field, nectarivoreschoose among alternative food sources (flowers) that differin the variabilities of their nectar rewards. In the lab, theforaging situation for carpenter bees was experimentally simplifiedby offering the bees a choice between either "low variance"or "high variance" artificial flowers. The two flower typesdiffered in their variabilities but offered the same expectedshortterm rates of net energy gain to test the predictions ofthe short-term rate maximization mechanism. Foragers were testedunder two energy budget conditions, hungry and well-fed, totest the predictions of the z-score model. Individual carpenterbees were indifferent to variability in both nectar volume andnectar sugar concentrations, and their risk-indifference wasunaffected by energy budget. These findings of risk indifferencesupport neither the variance discounting nor the z-score modelof risk sensitivity. Since the low and high variance flowertypes are equivalent for carpenter bees in short-term rate ofenergy gain, there can be no selection on carpenter bees tobe sensitive to variability based on differences in rate ofgain. Studies of risk sensitivity in honey bees and bumble beesusing variance in nectar concentration support this contention.These findings are compared with other nectarivore risk sensitivitystudies in order to highlight the most likely mechanisms underlyingaversion to variation in nectar rewards (short-term rate maximizing,the Weber-Fechner law of perception and learning non-empty flowers)and to suggest future research in the interplay of these threemechanisms.     

Ten new highly polymorphic microsatellite loci in the blood clam Scapharca broughtonii

Ten novel microsatellite loci were isolated from blood clam Scapharca broughtonii, and the polymorphisms were examined to estimate genetic variability. The genetic variabilities varied depending on the locus. The number of alleles ranged from 11 to 23, and the observed and expected heterozygosities ranged from 0.63 to 0.93 and 0.66 to 0.95, respectively. Four loci showed significant Hardy–Weinberg disequilibrium at P < 0.05 level. The high variabilities revealed in this study suggest that microsatellites should prove useful for various genetic investigations.     

New microsatellite markers for the snow crab Chionoecetes opilio (Brachyura: Majidae)

Nine novel microsatellite loci were isolated from Chionoecetes opilio by screening an enriched genomic library using nonradioactive polymerase chain reaction techniques, and the polymorphisms were examined to estimate genetic variability. The genetic variabilities varied depending on the locus. All loci were found to be polymorphic with an average of 9.7 alleles per locus (range 3–25). The observed and expected heterozygosities ranged from 0.80 to 0.98 and from 0.56 to 0.95, respectively. Five loci showed significant Hardy–Weinberg disequilibrium at the P < 0.05 level. The high variabilities revealed in this study suggest that these microsatellite loci should provide useful markers for genetic variation monitoring of C. opilio.     

Cluster and information entropy patterns in immunoglobulin complementarity determining regions

Previous studies of antibody binding domains have established many crucial features that include important structural positions, canonical formations, and the geometric correlations with the binding site nature and topography. In this work, position-specific frequency and hierarchical clustering analysis are used to explore the statistical pattern of the residues in the complementarity determining regions of human antibodies. In addition, Shannon's information entropy is computed for the entire heavy and light chains and compared with germline patterns to seek variability due to antibody clonal selection. Results are compared with reported analyses based on structural data and ligand-protein contact point computations based on Protein Data Bank records. Observations derived from the present sequence analysis are consistent with previous structural based methods. In the absence of structural data, methods used in this work can be effective and efficient computational tools used for identifying residues that are important for antigen targeting and predicting the probable amino acid distribution expected at these positions. The results in turn can be applied to help design or plan mutagenesis experiments to improve the binding properties of antibodies.