Coriolis force in Geophysics: an elementary introduction and examples

We show how Geophysics may illustrate and thus improve classical Mechanics lectures concerning the study of Coriolis force effects. We are then interested in atmospheric as well as oceanic phenomena we are familiar with, and are for that reason of pedagogical and practical interest. Our aim is to model them in a very simple way to bring out the physical phenomena that are involved.Comment: Accepted for publication in European Journal of Physic

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids being exchanged. Recent developments have shown that models which allow for amino acid pairs to have independent rates of substitution offer improved fit over single rate models. However, these approaches have been limited by the necessity for large alignments in their estimation. An alternative approach is to assume that substitution rates between amino acid pairs can be subdivided into rate classes, dependent on the information content of the alignment. However, given the combinatorially large number of such models, an efficient model search strategy is needed. Here we develop a Genetic Algorithm (GA) method for the estimation of such models. A GA is used to assign amino acid substitution pairs to a series of rate classes, where is estimated from the alignment. Other parameters of the phylogenetic Markov model, including substitution rates, character frequencies and branch lengths are estimated using standard maximum likelihood optimization procedures. We apply the GA to empirical alignments and show improved model fit over existing models of codon evolution. Our results suggest that current models are poor approximations of protein evolution and thus gene and organism specific multi-rate models that incorporate amino acid substitution biases are preferred. We further anticipate that the clustering of amino acid substitution rates into classes will be biologically informative, such that genes with similar functions exhibit similar clustering, and hence this clustering will be useful for the evolutionary fingerprinting of genes

Analytical support for SPAR experiment 76-36

The apparatus, materials, and procedures used in an analysis of thermal, convective, and rotational fluid flow for a second series of rocket experiments of dendrite growth are described. A constitutive supercooling criterion was calculated from the thermal data. A convection analysis was made of the various cases to ensure that convective velocities will not exceed about .01 cm/sec in the low-g tests. Damping times for fluid flow generated by rocket spin-up and spin-down were also determined, so that the conditions for this experiment are generally the same as those for the SPAR experiment 74-21 study of ammonium chloride low-g crystallizations

Irreducible Representations of Diperiodic Groups

The irreducible representations of all of the 80 diperiodic groups, being the symmetries of the systems translationally periodical in two directions, are calculated. To this end, each of these groups is factorized as the product of a generalized translational group and an axial point group. The results are presented in the form of the tables, containing the matrices of the irreducible representations of the generators of the groups. General properties and some physical applications (degeneracy and topology of the energy bands, selection rules, etc.) are discussed.Comment: 30 pages, 5 figures, 28 tables, 18 refs, LaTex2.0

Modeling HIV-1 Drug Resistance as Episodic Directional Selection

The evolution of substitutions conferring drug resistance to HIV-1 is both episodic, occurring when patients are on antiretroviral therapy, and strongly directional, with site-specific resistant residues increasing in frequency over time. While methods exist to detect episodic diversifying selection and continuous directional selection, no evolutionary model combining these two properties has been proposed. We present two models of episodic directional selection (MEDS and EDEPS) which allow the a priori specification of lineages expected to have undergone directional selection. The models infer the sites and target residues that were likely subject to directional selection, using either codon or protein sequences. Compared to its null model of episodic diversifying selection, MEDS provides a superior fit to most sites known to be involved in drug resistance, and neither one test for episodic diversifying selection nor another for constant directional selection are able to detect as many true positives as MEDS and EDEPS while maintaining acceptable levels of false positives. This suggests that episodic directional selection is a better description of the process driving the evolution of drug resistance

HIV-Specific Probabilistic Models of Protein Evolution

Comparative sequence analyses, including such fundamental bioinformatics techniques as similarity searching, sequence alignment and phylogenetic inference, have become a mainstay for researchers studying type 1 Human Immunodeficiency Virus (HIV-1) genome structure and evolution. Implicit in comparative analyses is an underlying model of evolution, and the chosen model can significantly affect the results. In general, evolutionary models describe the probabilities of replacing one amino acid character with another over a period of time. Most widely used evolutionary models for protein sequences have been derived from curated alignments of hundreds of proteins, usually based on mammalian genomes. It is unclear to what extent these empirical models are generalizable to a very different organism, such as HIV-1–the most extensively sequenced organism in existence. We developed a maximum likelihood model fitting procedure to a collection of HIV-1 alignments sampled from different viral genes, and inferred two empirical substitution models, suitable for describing between-and within-host evolution. Our procedure pools the information from multiple sequence alignments, and provided software implementation can be run efficiently in parallel on a computer cluster. We describe how the inferred substitution models can be used to generate scoring matrices suitable for alignment and similarity searches. Our models had a consistently superior fit relative to the best existing models and to parameter-rich data-driven models when benchmarked on independent HIV-1 alignments, demonstrating evolutionary biases in amino-acid substitution that are unique to HIV, and that are not captured by the existing models. The scoring matrices derived from the models showed a marked difference from common amino-acid scoring matrices. The use of an appropriate evolutionary model recovered a known viral transmission history, whereas a poorly chosen model introduced phylogenetic error. We argue that our model derivation procedure is immediately applicable to other organisms with extensive sequence data available, such as Hepatitis C and Influenza A viruses

Loss of the Intellectual Disability and Autism Gene Cc2d1a and Its Homolog Cc2d1b Differentially Affect Spatial Memory, Anxiety, and Hyperactivity

Hundreds of genes are mutated in non-syndromic intellectual disability (ID) and autism spectrum disorder (ASD), with each gene often involved in only a handful of cases. Such heterogeneity can be daunting, but rare recessive loss of function (LOF) mutations can be a good starting point to provide insight into the mechanisms of neurodevelopmental disease. Biallelic LOF mutations in the signaling scaffold CC2D1Acause a rare form of autosomal recessive ID, sometimes associated with ASD and seizures. In parallel, we recently reported that Cc2d1a-deficient mice present with cognitive and social deficits, hyperactivity and anxiety. In Drosophila, loss of the only ortholog of Cc2d1a, lgd, is embryonically lethal, while in vertebrates, Cc2d1a has a homolog Cc2d1b which appears to be compensating, indicating that Cc2d1a and Cc2d1b have a redundant function in humans and mice. Here, we generate an allelic series of Cc2d1a and Cc2d1b LOF to determine the relative role of these genes during behavioral development. We generated Cc2d1b knockout (KO), Cc2d1a/1b double heterozygous and double KO mice, then performed behavioral studies to analyze learning and memory, social interactions, anxiety, and hyperactivity. We found that Cc2d1a and Cc2d1b have partially overlapping roles. Overall, loss of Cc2d1b is less severe than loss of Cc2d1a, only leading to cognitive deficits, while Cc2d1a/1b double heterozygous animals are similar to Cc2d1a-deficient mice. These results will help us better understand the deficits in individuals with CC2D1A mutations, suggesting that recessive CC2D1B mutations and trans-heterozygous CC2D1A and CC2D1B mutations could also contribute to the genetics of ID

Australian long-term care personnel's knowledge and attitudes regarding palliative care for people with advanced dementia.

This study aimed to describe Australian long-term care (LTC) personnel's knowledge and attitudes concerning palliative care for residents with advanced dementia, and explore relationships with LTC facility/personnel characteristics. An analysis was undertaken of baseline data from a cluster randomised controlled trial of facilitated family case conferencing for improving palliative care of LTC residents with advanced dementia (the 'IDEAL Study'). Participants included any LTC personnel directly involved in residents' care. Knowledge and attitudes concerning palliative care for people with advanced dementia were measured using the questionnaire on Palliative Care for Advanced Dementia. Univariate and multivariate analyses explored relationships between personnel knowledge/attitudes and facility/personnel characteristics. Of 307 personnel in the IDEAL Study, 290 (94.5%) from 19/20 LTCFs provided sufficient data for inclusion. Participants included 9 (2.8%) nurse managers, 59 (20.5%) registered nurses, 25 (8.7%) enrolled nurses, 187 (64.9%) assistants in nursing/personal care assistants and 9 (3.1%) care service employees. In multivariate analyses, a facility policy not to rotate personnel through dementia units was the only variable associated with more favourable overall personnel knowledge and attitudes. Other variables associated with favourable knowledge were a designation of nursing manager or registered or enrolled nurse, and having a preferred language of English. Other variables associated with favourable attitudes were tertiary level of education and greater experience in dementia care. Like previous international research, this study found Australian LTC personnel knowledge and attitudes regarding palliative care for people with advanced dementia to be associated with both facility and personnel characteristics. Future longitudinal research is needed to better understand the relationships between knowledge and attitudes, as well as between these attributes and quality of care

Who Is Most Vulnerable to Social Rejection? The Toxic Combination of Low Self-Esteem and Lack of Negative Emotion Differentiation on Neural Responses to Rejection

People have a fundamental need to belong that, when satisfied, is associated with mental and physical well-being. The current investigation examined what happens when the need to belong is thwarted—and how individual differences in self-esteem and emotion differentiation modulate neural responses to social rejection. We hypothesized that low self-esteem would predict heightened activation in distress-related neural responses during a social rejection manipulation, but that this relationship would be moderated by negative emotion differentiation—defined as adeptness at using discrete negative emotion categories to capture one\u27s felt experience. Combining daily diary and neuroimaging methodologies, the current study showed that low self-esteem and low negative emotion differentiation represented a toxic combination that was associated with stronger activation during social rejection (versus social inclusion) in the dorsal anterior cingulate cortex and anterior insula—two regions previously shown to index social distress. In contrast, individuals with greater negative emotion differentiation did not show stronger activation in these regions, regardless of their level of self-esteem; fitting with prior evidence that negative emotion differentiation confers equanimity in emotionally upsetting situations

Phylogeography of Japanese encephalitis virus:genotype is associated with climate

The circulation of vector-borne zoonotic viruses is largely determined by the overlap in the geographical distributions of virus-competent vectors and reservoir hosts. What is less clear are the factors influencing the distribution of virus-specific lineages. Japanese encephalitis virus (JEV) is the most important etiologic agent of epidemic encephalitis worldwide, and is primarily maintained between vertebrate reservoir hosts (avian and swine) and culicine mosquitoes. There are five genotypes of JEV: GI-V. In recent years, GI has displaced GIII as the dominant JEV genotype and GV has re-emerged after almost 60 years of undetected virus circulation. JEV is found throughout most of Asia, extending from maritime Siberia in the north to Australia in the south, and as far as Pakistan to the west and Saipan to the east. Transmission of JEV in temperate zones is epidemic with the majority of cases occurring in summer months, while transmission in tropical zones is endemic and occurs year-round at lower rates. To test the hypothesis that viruses circulating in these two geographical zones are genetically distinct, we applied Bayesian phylogeographic, categorical data analysis and phylogeny-trait association test techniques to the largest JEV dataset compiled to date, representing the envelope (E) gene of 487 isolates collected from 12 countries over 75 years. We demonstrated that GIII and the recently emerged GI-b are temperate genotypes likely maintained year-round in northern latitudes, while GI-a and GII are tropical genotypes likely maintained primarily through mosquito-avian and mosquito-swine transmission cycles. This study represents a new paradigm directly linking viral molecular evolution and climate