235 research outputs found
Individual variability in Diel Vertical migration of a marine copepod : why some individuals remain at depth when others migrate
The diel vertical migration (DVM) of the copepod Metridia pacifica was examined in Dabob Bay (47°45.05′N, 122°49.71′W), a fjord in Washington state. Although the population showed deep daytime residence (75-175 m), a proportion of the population was found in the surface waters at night. For individuals that migrated to the surface, the mean size of the oil sac was much smaller than those that remained at depth (mean lengths of oil sac 0.25 mm for individuals collected between 0 and 25 m at night, compared with 0.43 mm for individuals from between 125 and 175 m). Similarly, the C : N ratio was lower for animals collected from near the surface, indicative of their lower lipid reserves. These results suggest that individual variability in DVM was influenced by body condition, with those animals with larger lipid stores not needing to risk coming to the surface to feed at night
ESTIMATING GENOME-WIDE COPY NUMBER USING ALLELE SPECIFIC MIXTURE MODELS
Genomic changes such as copy number alterations are thought to be one of the major underlying causes of human phenotypic variation among normal and disease subjects [23,11,25,26,5,4,7,18]. These include chromosomal regions with so-called copy number alterations: instead of the expected two copies, a section of the chromosome for a particular individual may have zero copies (homozygous deletion), one copy (hemizygous deletions), or more than two copies (amplifications). The canonical example is Down syndrome which is caused by an extra copy of chromosome 21. Identification of such abnormalities in smaller regions has been of great interest, because it is believed to be an underlying cause of cancer.
More than one decade ago comparative genomic hybridization (CGH)technology was developed to detect copy number changes in a high-throughput fashion. However, this technology only provides a 10 MB resolution which limits the ability to detect copy number alterations spanning small regions. It is widely believed that a copy number alteration as small as one base can have significant downstream effects, thus microarray manufacturers have developed technologies that provide much higher resolution. Unfortunately, strong probe effects and variation introduced by sample preparation procedures have made single-point copy number estimates too imprecise to be useful. CGH arrays use a two-color hybridization, usually comparing a sample of interest to a reference sample, which to some degree removes the probe effect. However, the resolution is not nearly high enough to provide single-point copy number estimates. Various groups have proposed statistical procedures that pool data from neighboring locations to successfully improve precision. However, these procedure need to average across relatively large regions to work effectively thus greatly reducing the resolution. Recently, regression-type models that account for probe-effect have been proposed and appear to improve accuracy as well as precision. In this paper, we propose a mixture model solution specifically designed for single-point estimation, that provides various advantages over the existing methodology. We use a 314 sample database, constructed with public datasets, to motivate and fit models for the conditional distribution of the observed intensities given allele specific copy numbers. With the estimated models in place we can compute posterior probabilities that provide a useful prediction rule as well as a confidence measure for each call. Software to implement this procedure will be available in the Bioconductor oligo packagehttp://www.bioconductor.org)
Particle swarm optimization for the Steiner tree in graph and delay-constrained multicast routing problems
This paper presents the first investigation on applying a particle swarm optimization (PSO) algorithm to both the Steiner tree problem and the delay constrained multicast routing problem. Steiner tree problems, being the underlining models of many applications, have received significant research attention within the meta-heuristics community. The literature on the application of meta-heuristics to multicast routing problems is less extensive but includes several promising approaches. Many interesting research issues still remain to be investigated, for example, the inclusion of different constraints, such as delay bounds, when finding multicast trees with minimum cost. In this paper, we develop a novel PSO algorithm based on the jumping PSO (JPSO) algorithm recently developed by Moreno-Perez et al. (Proc. of the 7th Metaheuristics International Conference, 2007), and also propose two novel local search heuristics within our JPSO framework. A path replacement operator has been used in particle moves to improve the positions of the particle with regard to the structure of the tree. We test the performance of our JPSO algorithm, and the effect of the integrated local search heuristics by an extensive set of experiments on multicast routing benchmark problems and Steiner tree problems from the OR library. The experimental results show the superior performance of the proposed JPSO algorithm over a number of other state-of-the-art approaches
Matching action to need: an analysis of Global Burden of Disease 2017 and population health data to focus adolescent health policy and actions in Myanmar
Background: Myanmar is a country undergoing rapid transitions in health. Its national strategic policy for young people's health is being revised but there is a paucity of population data to inform local priorities and needs. Objective: In this paper we describe a comprehensive profile of adolescent health in Myanmar to focus policy and health actions. Methods: We used available primary data, and modelled estimates from the GBD 2017, to describe health outcomes (mortality and morbidity), health risks and determinants for adolescents in Myanmar between 1990-2017. A governance group of key stakeholders guided the framing of the study, interpretation of findings, and recommendations. Results: Overall health has improved for adolescents in Myanmar since 1990, however adolescent mortality remains high, particularly so for older adolescent males; all-cause mortality rate for 10-24 years was 70 per 100,000 for females and 149 per 100,000 for males (16,095 adolescent deaths in 2017). Overall, the dominant health problems were injuries for males and non-communicable disease for females in a context of ongoing burden of communicable and nutritional diseases for both sexes, and reproductive health needs for females. Health risks relating to undernutrition (thinness and anaemia) remain prevalent, with other health risks (overweight, binge alcohol use, and substance use) relatively low by global and regional standards but increasing. Gains have been made in social determinants such as adolescent fertility and modern contraception use; however, advances have been more limited in secondary education completion and engagement in employment and post education training. Conclusions: These results highlight the need to focus current efforts on addressing disease and mortality experienced by adolescents in Myanmar, with a specific focus on injury, mental health and non-communicable disease.Karly I. Cini, Phone Myint Win, Zay Yar Swe, Kyu Kyu Than, Thin Mar Win ... Peter S. Azzopardi ... et al
SU(N) gauge theories in 2+1 dimensions
We calculate the mass spectra and string tensions of SU(2), SU(3), SU(4) and
SU(5) gauge theories in 2+1 dimensions. We do so by simulating the
corresponding lattice theories and then extrapolating dimensionless mass ratios
to the continuum limit. We find that such mass ratios are, to a first
approximation, independent of the number of colours and that the remaining
dependence can be accurately reproduced by a simple O(1/N.N) correction. This
provides us with a prediction of these mass ratios for all SU(N) theories in
2+1 dimensions and demonstrates that these theories are already `close' to
N=infinity for N=2. We find that the theory retains a non-zero confining string
tension as N goes to infinity and that the dimensionful coupling g.g is
proportional to 1/N at large N, when expressed in units of the dynamical length
scale of the theory. During the course of these calculations we study in detail
the effects of including over-relaxation in the Monte Carlo, of using a
mean-field improved coupling to extrapolate to the continuum limit, and the use
of space-time asymmetric lattice actions to resolve heavy glueball correlators.Comment: 86 pages; LaTeX; typos corrected, references added and minor changes
for publicatio
The evolution of language: a comparative review
For many years the evolution of language has been seen as a disreputable topic, mired in fanciful "just so stories" about language origins. However, in the last decade a new synthesis of modern linguistics, cognitive neuroscience and neo-Darwinian evolutionary theory has begun to make important contributions to our understanding of the biology and evolution of language. I review some of this recent progress, focusing on the value of the comparative method, which uses data from animal species to draw inferences about language evolution. Discussing speech first, I show how data concerning a wide variety of species, from monkeys to birds, can increase our understanding of the anatomical and neural mechanisms underlying human spoken language, and how bird and whale song provide insights into the ultimate evolutionary function of language. I discuss the ‘‘descended larynx’ ’ of humans, a peculiar adaptation for speech that has received much attention in the past, which despite earlier claims is not uniquely human. Then I will turn to the neural mechanisms underlying spoken language, pointing out the difficulties animals apparently experience in perceiving hierarchical structure in sounds, and stressing the importance of vocal imitation in the evolution of a spoken language. Turning to ultimate function, I suggest that communication among kin (especially between parents and offspring) played a crucial but neglected role in driving language evolution. Finally, I briefly discuss phylogeny, discussing hypotheses that offer plausible routes to human language from a non-linguistic chimp-like ancestor. I conclude that comparative data from living animals will be key to developing a richer, more interdisciplinary understanding of our most distinctively human trait: language
Protein requirement of tambaqui juveniles (Colossoma macropomum) after feed deprivation
The aim of this work was evaluate protein requirement of tambaqui (Colossoma macropomum) juveniles after feed deprivation. During 60 days, fish (50,3 ± 0,26 g) were fed on four isoenergetics diets with different protein content (28, 32, 36 and 40% crude protein) at two feeding regimes (with and without feed deprivation) under completely random factorial design (4x2) in triplicate. Water quality parameters and performance index were evaluated at 1º, 15º and 60º days. Water quality parameters were kept at normal fish cultivation patterns. No mortality in the tested treatments. There were observed differences among treatments for performance indexes analyzed: growth rate, feed efficiency, daily feed consumption, crude protein consumption, efficiency protein rate and relative weight gain, except for hepatosomatic index. Hyperfagia was detected indicating the occurrence of compensatory growth. Fat content and body protein deposition increased in fishes refed on 36% of crude protein. These results explain some data observed belong the experiment like the increase of weight gain, of the hyperfagia time extension, of the growth rate and of the feed efficiency. Therefore those fish shows increase on weight gain, hyperfagia time, growth rate and feed efficiency. There is no influence of feed deprivation on protein requirement tambaqui juveniles.O objetivo deste trabalho foi avaliar a exigência protéica de juvenis de tambaqui (Colossoma macropomum) após a privação alimentar. Os peixes (50,3 ± 0,26g) foram submetidos a quatro rações isoenergéticas com diferentes concentrações protéicas (28, 32, 36 e 40% proteína bruta) e dois regimes alimentares (com privação e sem privação) durante 60 dias. O delineamento experimental foi inteiramente casualizado, em esquema fatorial 4x2, em triplicata. Avaliaram-se os parâmetros de qualidade de água e de desempenho no 1º, 15º e 60º dia de experimento. Os parâmetros da qualidade da água permaneceram dentro dos padrões de cultivo. Não houve mortalidade nos tratamentos testados. Foram observados diferenças entre os tratamentos para os índices de desempenho analisadostaxa de crescimento específico, eficiência alimentar, consumo diário de ração, consumo de proteína bruta, taxa de eficiência protéica e ganho de peso relativo, com exceção do índice hepatossomático. Houve hiperfagia, indicando a existência de crescimento compensatório. Os peixes realimentados com 36% proteína bruta tiveram incremento no teor de gordura visceral e maior deposição de proteína corporal. Estes resultados explicam uma melhora nos dados de ganho de peso, duração da hiperfagia, taxa de crescimento e eficiência alimentar. A privação alimentar não influencia a exigência protéica em juvenis de tambaqui
Associations of common breast cancer susceptibility alleles with risk of breast cancer subtypes in BRCA1 and BRCA2 mutation carriers
Introduction: More than 70 common alleles are known to be involved in breast cancer (BC) susceptibility, and several exhibit significant heterogeneity in their associations with different BC subtypes. Although there are differences in the association patterns between BRCA1 and BRCA2 mutation carriers and the general population for several loci, no study has comprehensively evaluated the associations of all known BC susceptibility alleles with risk of BC subtypes in BRCA1 and BRCA2 carriers. Methods: We used data from 15,252 BRCA1 and 8,211 BRCA2 carriers to analyze the associations between approximately 200,000 genetic variants on the iCOGS array and risk of BC subtypes defined by estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and triple-negative- (TN) status; morphologic subtypes; histological grade; and nodal involvement. Results: The estimated BC hazard ratios (HRs) for the 74 known BC alleles in BRCA1 carriers exhibited moderate correlations with the corresponding odds ratios from the general population. However, their associations with ER-positive BC in BRCA1 carriers were more consistent with the ER-positive as
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