On the Consistency of a Physical Mapping Method to Reconstruct a Chromosome in Vitro

During recent years considerable effort has been invested in creating physical maps for a variety of organisms as part of the Human Genome Project and in creating various methods for physical mapping. The statistical consistency of a physical mapping method to reconstruct a chromosome, however, has not been investigated. In this paper, we first establish that a model of physical mapping by binary fingerprinting of DNA fragments is identifiable using the key assumption--for a large randomly generated recombinant DNA library, there exists a staircase of DNA fragments across the chromosomal region of interest. Then we briefly introduce epi-convergence theory of variational analysis and transform the physical mapping problem into a constrained stochastic optimization problem. By doing so, we prove epi-convergence of the physical mapping model and epi-convergence of the physical mapping method. Combining the identifiability of our physical mapping model and the epi-convergence of a physical mapping method, finally we establish strong consistency of a physical mapping method.     

Physical attractiveness as a phenotypic marker of health: an assessment using a nationally representative sample of American adults

Evolutionary explanations regarding the differential preference for particular traits hold that preferences arose due to traits' association with increased potential for reproductive fitness. Assessments of physical attractiveness have been shown to be related to perceived and measured levels of health, an important fitness-related trait. Despite the robust association between physical attractiveness and health observed in the extant literature, a number of theoretical and methodological concerns remain. Specifically, the research in this area possesses a lack of specificity in terms of measures of health, a reliance on artificial social interactions in assessing physical attractiveness, and a relatively infrequent use of non-student samples and leaves unaddressed the confounding effects of raters of attractiveness. Using these concerns as a springboard, the current study employed data from the National Longitudinal Study for Adolescent Health (N ≈ 15,000; aged 25 to 34 years) to assess the relationship between physical attractiveness and various specific and overall measures of health. Logistic and OLS regression models illustrated a robust association between physical attractiveness and various measures of health, controlling for a variety of confounding factors. In sum, the more attractive a respondent was rated, the less likely he or she was to report being diagnosed with a wide range of chronic diseases and neuropsychological disorders. Importantly, this finding was observed for both sexes. These analyses provide further support for physical attractiveness as a phenotypic marker of health. The findings are discussed in reference to evolutionary theory, and the limitations of the study and future research suggestions are also addressed.     

Growth of a species,an association,a science: 80 years of growth and development research

Physical anthropological research was codified in the United States with the creation of the American Association of Physical Anthropology (AAPA) in 1929. That same year, a study began in yellow springs, Ohio, with a goal of identifying “what makes people different.” The approach used to answer that question was to study the growth and development of Homo sapiens. The resulting study, the Fels Longitudinal Study, is currently the longest continuous study of human growth and development in the world. Although the AAPA and the Fels Longitudinal Study have existed as separate entities for more than 80 years now, it is not surprising, given the relationship between anatomical and developmental research, there has been considerable overlap between the two. As the field of physical anthropology has blossomed to include subdisciplines such as forensics, genetics, primatology, as well as sophisticated statistical methodologies, the importance of growth and development research has escalated. Although current Fels Longitudinal Study research is largely directed at biomedical questions, virtually all findings are relevant to physical anthropology, providing insights into basic biological processes and life history parameters. Some key milestones from the early years of the AAPA and the Fels Longitudinal Study are highlighted here that address growth and development research in physical anthropology. These are still held as fundamental concepts that underscore the importance of this line of inquiry, not only across the subdisciplines of physical anthropology, but also among anthropological, biological, and biomedical inquiries. Am J Phys Anthropol, 2013. © 2012 Wiley Periodicals, Inc.     

Low prairie plant communities of wetlands as a function of disturbance: Physical parameters

Understanding how physical parameters within and adjacent to Prairie Pothole Region wetlands affect the surrounding biological communities is important for sound management decisions for agricultural and rangeland settings. We evaluated the wetland, adjacent non-wetland, and landscape physical parameters role in determining low prairie (sub-irrigated) species composition. We first developed hypothetical models using the physical variables collected from 193 wetlands in relation to the existing plant communities. The models were then evaluated using structural equation modeling and a final (alternative) model was developed from these results. The models developed indicated the importance of the low prairie community in proper ecological functioning of associated wetlands. A number of physical parameters measured can be used as indicators of declining plant community condition, one example being the potential of the low prairie plant community to be invaded by exotic species such as Bromus inermis Leyss.     

Comorbidity between major depressive disorder and physical diseases: a comprehensive review of epidemiology,mechanisms and management

Populations with common physical diseases – such as cardiovascular diseases, cancer and neurodegenerative disorders – experience substantially higher rates of major depressive disorder (MDD) than the general population. On the other hand, people living with MDD have a greater risk for many physical diseases. This high level of comorbidity is associated with worse outcomes, reduced adherence to treatment, increased mortality, and greater health care utilization and costs. Comorbidity can also result in a range of clinical challenges, such as a more complicated therapeutic alliance, issues pertaining to adaptive health behaviors, drug-drug interactions and adverse events induced by medications used for physical and mental disorders. Potential explanations for the high prevalence of the above comorbidity involve shared genetic and biological pathways. These latter include inflammation, the gut microbiome, mitochondrial function and energy metabolism, hypothalamic-pituitary-adrenal axis dysregulation, and brain structure and function. Furthermore, MDD and physical diseases have in common several antecedents related to social factors (e.g., socioeconomic status), lifestyle variables (e.g., physical activity, diet, sleep), and stressful live events (e.g., childhood trauma). Pharmacotherapies and psychotherapies are effective treatments for comorbid MDD, and the introduction of lifestyle interventions as well as collaborative care models and digital technologies provide promising strategies for improving management. This paper aims to provide a detailed overview of the epidemiology of the comorbidity of MDD and specific physical diseases, including prevalence and bidirectional risk; of shared biological pathways potentially implicated in the pathogenesis of MDD and common physical diseases; of socio-environmental factors that serve as both shared risk and protective factors; and of management of MDD and physical diseases, including prevention and treatment. We conclude with future directions and emerging research related to optimal care of people with comorbid MDD and physical diseases.     

Effect of a staphylococcaL infection on the development of an immune response after physical loading

The infection of rats with staphylococci enhances the suppressing effect of physical loading on the development of immune response induced by the injection of sheep red blood cells. Intensive physical loading is accompanied by the release of the substance activating the function of splenic suppressor cells into the blood. Staphylococcal infection increases the action of the serum substance of rats performing physical work on splenic suppressor cells, as well as on the action of the suppressor factor released by these cells on immunocompetent cells.     

Parallel computation of a maximum-likelihood estimator of a physical map

Reconstructing a physical map of a chromosome from a genomic library presents a central computational problem in genetics. Physical map reconstruction in the presence of errors is a problem of high computational complexity that provides the motivation for parallel computing. Parallelization strategies for a maximum-likelihood estimation-based approach to physical map reconstruction are presented. The estimation procedure entails a gradient descent search for determining the optimal spacings between probes for a given probe ordering. The optimal probe ordering is determined using a stochastic optimization algorithm such as simulated annealing or microcanonical annealing. A two-level parallelization strategy is proposed wherein the gradient descent search is parallelized at the lower level and the stochastic optimization algorithm is simultaneously parallelized at the higher level. Implementation and experimental results on a distributed-memory multiprocessor cluster running the parallel virtual machine (PVM) environment are presented using simulated and real hybridization data.     

Somatotype and physical performance in a sample of university students from Madrid

A sample of 303 Madrid Complutense University students (100 males and 203 females), aged 21–29 years has been studied in order to establish the relationship between somatotype components and physical work performance. Since particular interest is focused on a possible sexual difference in that relationship, males and females were analyzed separately. Results prove the high correlation of test scores implying muscularity (hand grips, pulling strength) with the mesomorphic component of the somatotype, mainly in males. Variability in tests relative to physical totype, mainly in males. Variability in tests relative to physical fitness is mainly explained by differences in endomorphy, although regarding the step test, ectomorphy is also a factor to be taken into account in females, as well as the pulling strength in males.     

Endometriosis and physical exercises: a systematic review

Regular physical exercise seems to have protective effects against diseases that involve inflammatory processes since it induces an increase in the systemic levels of cytokines with anti-inflammatory and antioxidant properties and also acts by reducing estrogen levels. Evidence has suggested that the symptoms associated with endometriosis result from a local inflammatory peritoneal reaction caused by ectopic endometrial implants. Thus, the objective of the present review was to assess the relationship between physical exercise and the prevalence and/or improvement of the symptoms associated with endometriosis. To this end, data available in PubMed (1985–2012) were surveyed using the terms “endometriosis and physical exercises”, “endometriosis and life style and physical exercises” in the English language literature. Only 6 of the 935 articles detected were included in the study. These studies tried establish a possible relationship between the practice of physical exercise and the prevalence of endometriosis. The data available are inconclusive regarding the benefits of physical exercise as a risk factor for the disease and no data exist about the potential impact of exercise on the course of the endometriosis. In addition, randomized studies are necessary.     

Physical Activity as a Predictor of Body Composition in American Indian Children

Objective: To examine physical activity in second grade American Indian children as a predictor of percentage body fat 3 years later. Research Methods and Procedures: Physical activity was assessed as average vector magnitude (AVM) counts from an accelerometer in 454 second grade children as part of the Pathways study. BMI was assessed, and skinfolds and bioelectrical impedance were used to estimate fat mass, fat‐free body mass, and percentage body fat in validated prediction equations. Associations were examined using mixed models regression controlling for baseline body composition. Results: In normal‐weight children, higher AVM counts were significantly associated with decreases in percentage body fat. Among overweight children, higher AVM counts were significantly associated with increases in BMI, fat mass, and fat‐free mass but not percentage body fat. Discussion: Higher physical activity levels in second grade were associated with lower levels of percentage body fat in fifth grade in normal‐weight but not in overweight children. BMI showed no association with physical activity among normal‐weight children, and increases in BMI were associated with increasing amounts of physical activity among overweight children. These findings emphasize the importance of valid body composition measures and may indicate important differences in associations between physical activity and adiposity in normal‐weight as compared with overweight children.     

The use of a detector of the extremely weak radiation as a variometer of gravitation field

It was shown that the detector of extremely weak radiation with selectively increased sensitivity to the nonelectromagnetic, including the gravitational component of the spectrum of active physical fields can be used as the basis for constructing a variometer of gravitational field of a new type.     

An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research

The pooid subfamily of grasses includes some of the most important crop, forage and turf species, such as wheat, barley and Lolium. Developing genomic resources, such as whole-genome physical maps, for analysing the large and complex genomes of these crops and for facilitating biological research in grasses is an important goal in plant biology. We describe a bacterial artificial chromosome (BAC)-based physical map of the wild pooid grass Brachypodium distachyon and integrate this with whole genome shotgun sequence (WGS) assemblies using BAC end sequences (BES). The resulting physical map contains 26 contigs spanning the 272 Mb genome. BES from the physical map were also used to integrate a genetic map. This provides an independent validation and confirmation of the published WGS assembly. Mapped BACs were used in Fluorescence In Situ Hybridisation (FISH) experiments to align the integrated physical map and sequence assemblies to chromosomes with high resolution. The physical, genetic and cytogenetic maps, integrated with whole genome shotgun sequence assemblies, enhance the accuracy and durability of this important genome sequence and will directly facilitate gene isolation.     

A physical context for gelatinous zooplankton aggregations: a review

The magnitude and extent of jellyfish blooms are influenced not only by the biology and behavior of the animal, but also by the geographic setting and physical environment. Hydrography alone is often thought to cause or favor gelatinous zooplankton aggregations, however, it is clear that interactions between biology of the animal and physics of the water are very important sources of population variations, especially at local scales. We summarize the role of physical processes and phenomena that promote aggregations of gelatinous zooplankton. We have identified and discussed a suite of physical gradients that can be perceived by gelatinous zooplankton. These include light, gravity, temperature, salinity, pressure and turbulence. A recurring theme is accumulation of jellyfish around physical discontinuities such as fronts (shelf-break, upwelling, tidal and estuarine) and pycnoclines (thermoclines and haloclines). Interestingly, there are few data to suggest that large-scale, quasi-stationary features, such as the largest oceanic fronts, serve to physically aggregate gelatinous animals at a similar scale. Rather, examples of local aggregations appear to dominate the literature. We also discuss various jellyfish behaviors that are theorized to promote aggregation, feeding and reproduction in relation to physical discontinuities.     

Characterization of a lipophilic plasmid DNA condensate formed with a cationic peptide fatty acid conjugate

In the presence of cationic ligands, DNA molecules can become aggregated into larger particles in a process known as condensation. DNA condensates are of interest as models for the dense packing found in naturally occurring structures such as phage heads and chromatin. They have found extensive application in DNA transfection and also provide convenient models with which to study DNA damage by the direct effect of ionizing radiation. Further, conjugates of cationic peptides with fatty acids may represent a class of attractive ligands for these areas because of their simple synthesis. When plasmid pUC18 is used as the DNA target and N-caproyl-penta-arginine amide (Cap-R(5)-NH(2)) is used as the ligand, the physical properties of the resulting mixtures were characterized using static and dynamic light scattering, sedimentation, dye exclusion, circular dichroism, nanoparticle tracking, and atomic force microscopy. Their chemical properties were assayed using solvent extraction and protection against hydroxyl radical attack and nuclease digestion. Titration of the plasmid with the Cap-R(5)-NH(2) ligand produced sharply defined changes in both chemical and physical properties, which was associated with the formation of condensed DNA particles in the 100-2000 nm size range. The caproyl group at the ligand's N-terminus produced a large increase in the partitioning of the resulting condensate from water into chloroform and in its binding to the neutral detergent Pluronic F-127. Both the physical and chemical data were all consistent with condensation of the plasmid by the ligand where the presence in the ligand of the caproyl group conferred an extensive lipophilic character upon the condensate.     

MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly

MapLinker is an analysis tool, as well as a browsing interface, that facilitates integration of whole genome sequence assembly with a clone-based physical map. Using the locations of sequence markers on the physical map, MapLinker generates a tentative sequence map of the genome that serves to verify the map and to guide genome-wide finishing.     

Application of an efficient strategy with a phage lambda vector for constructing a physical map of the amyloplast genome of sycamore (Acer pseudoplatanus)

Amyloplasts were isolated from a heterotrophic culture cell line of a woody plant, sycamore (Acer pseudoplatanus), and their DNA was purified. Conventional procedures for making a physical map were not easily applicable to the amyloplast DNA, since the yield of DNA was too low and the presence of repeated sequences interfered with the analysis. Therefore, the pieces of amyloplast DNA starting with a few micrograms of DNA were cloned in the lambda Fix vector, which is a derivative of lambda EMBL vectors improved for efficient cloning and gene walking. Cloned DNA fragments were randomly picked, mapped for restriction endonuclease sites by a refined procedure, and combined by overlapping their physical maps. The DNA library was also subjected to screening by gene walking using promoters recognized by T3 and T7 RNA polymerases in the vector to fill the gaps between sequences determined by overlapping the physical maps. In this way, we constructed the entire DNA library and the complete physical map of the amyloplast DNA. The sycamore amyloplast genome was composed of 141.7-kbp nucleotides with the same gene arrangement as that of tobacco chloroplasts.     

Physical properties of VNTR data, and their impact on a test of allelic independence.

In this article we describe the physical properties of VNTR data, as well as their effects on the two-dimensional distribution of fragment pairs. Tests of independence of alleles at a locus may confound those physical properties with allele independence. A recently proposed test by Geisser and Johnson is an example. We show that alleles can be strictly independent, yet the proposed test suggests large violations of allele independence because it is sensitive to well-known electrophoretic phenomena.     

Self-reported physical activity correlates in Swedish adults with multiple sclerosis: a cross-sectional study

Background

The benefits of physical activity in persons with Multiple Sclerosis (MS) are considerable. Knowledge about factors that correlate to physical activity is helpful in order to develop successful strategies to increase physical activity in persons with MS. Previous studies have focused on correlates to physical activity in MS, however falls self-efficacy, social support and enjoyment of physical activity are not much studied, as well as if the correlates differ with regard to disease severity. The aim of the study was to examine associations between physical activity and age, gender, employment, having children living at home, education, disease type, disease severity, fatigue, self-efficacy for physical activity, falls self-efficacy, social support and enjoyment of physical activity in a sample of persons with MS and in subgroups with regard to disease severity.

Methods

This is a cross-sectional survey study including Swedish community living adults with MS, 287 persons, response rate 58.2%. The survey included standardized self-reported scales measuring physical activity, disease severity, fatigue, self-efficacy for physical activity, falls self-efficacy, and social support. Physical activity was measured by the Physical Activity Disability Survey – Revised.

Results

Multiple regression analyzes showed that 59% (F(6,3)?=?64.9, p?=?0.000) of the variation in physical activity was explained by having less severe disease (β?=??0.30), being employed (β?=?0.26), having high falls self-efficacy (β?=?0.20), having high self-efficacy for physical activity (β?=?0.17), and enjoying physical activity (β?=?0.11). In persons with moderate/severe MS, self-efficacy for physical activity explained physical activity.

Conclusions

Consistent with previous research in persons with MS in other countries this study shows that disease severity, employment and self-efficacy for physical activity are important for physical activity. Additional important factors were falls self-efficacy and enjoyment. More research is needed to confirm this and the subgroup differences.