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Photometric properties of microfossil shells Nature Precedings
Stergios Zarkogiannis; Ruediger Henrich.
The chromatic characteristics of fossil planktonic foraminifera were measured with the use of an opticoelectric microscope and a new aspect of their nature has been revealed.
Tipo: Manuscript Palavras-chave: Chemistry; Earth & Environment; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/4037/version/1
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Earth History and the Evolution of Caribbean Bats Nature Precedings
Liliana Dávalos.
Although the natural history of the Caribbean is better understood now than ever before, a general biogeographic explanation for the peculiar faunal composition of the islands remains elusive. New molecular phylogenetic and divergence analyses presented here show that dispersal and diversification in Caribbean bats are synchronous with sea level drops during inter-stage transitions in the Miocene. The phylogenies indicate that several continental bat species descended from West Indian ancestors, as the exceptionally low sea level of the Miocene transitions allowed for two-way biotic exchange between the islands and the continent. These results suggest a common mechanism underlies colonization and subsequent speciation in the Caribbean, and underscore the...
Tipo: Manuscript Palavras-chave: Earth & Environment; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3901/version/1
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Modeling, Simulation and Application of Bacterial Transduction in Genetic Algorithms Nature Precedings
Carlos Perales-Gravan; Javier de Vicente Buendia; Rafael Lahoz-Beltra.
At present, all methods in Evolutionary Computation are bioinspired in the fundamental principles of neo-Darwinism as well as on a vertical gene transfer. Thus, on a mechanism in which an organism receives genetic material from its ancestor. Horizontal, lateral or cross-population gene transfer is any process in which an organism transfers a genetic segment to another one that is not its offspring. Virus transduction is one of the key mechanisms of horizontal gene propagation in microorganism (e.g. bacteria). In the present paper, we model and simulate a transduction operator, exploring a possible role and usefulness of transduction in a genetic algorithm. The genetic algorithm including transduction has been named PETRI (abbreviation of Promoting...
Tipo: Manuscript Palavras-chave: Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3732/version/1
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Molecular evolution of RRM-containing proteins and glycine-rich RNA-binding proteins in plants Nature Precedings
Judith L. Gomez-Porras; Martin Lewinski; Diego Mauricio Riaño-Pachón; Dorothee Staiger.
*Abstract*

*Background:*
In angiosperms, RNA-binding proteins with an RNA recognition motif (RRM)-type RNA interaction domain play an important role in developmental and environmental responses. Despite their pivotal role, a comprehensive analysis of their number and diversity has only been performed in _Arabidopsis_ so far.

*Results:*
Here we present a detailed phylogenetic analysis of RRM-containing proteins in plants, the red algae _Cyanidioschyzon merolae_ and cyanobacteria. We identified two major events during the diversification of the RRM in plants, one at the emergence of green plants, and the other at the water-to-land transition. We focused on...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5970/version/1
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11[beta]-hydroxysteroid dehydrogenase-type 2 evolved from an ancestral 17[beta]-hydroxysteroid dehydrogenase-type 2 Nature Precedings
Michael E. Baker.
11[beta]-hydroxysteroid dehydrogenase type-2 (11[beta]-HSD2) regulates the local concentration of cortisol that can activate the glucocorticoid receptor and mineralocorticoid receptor, as well as the concentration of 11-keto-testosterone, the active androgen in fish. Similarly, 17[beta]-HSD2 regulates the levels of testosterone and estradiol that activate the androgen receptor and estrogen receptor, respectively. Interestingly, although human 11[beta]-HSD2 and 17[beta]-HSD2 act at different positions on different steroids, these enzymes are paralogs. Despite the physiological importance of 11[beta]-HSD2 and 17[beta]-HSD2, details of their origins and divergence from a common ancestor are not known. An opportunity to understand their evolution is...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4649/version/1
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Cortical Bone Ontogeny: Activity, Nutritional Stress and Archaeology Nature Precedings
Gwen Robbins.
This poster introduces the idea that femoral compact bone growth and development demonstrates a very different pattern among infants and children in a contemporary sample of well-nourished active children versus archaeological samples of stressed, malnourished children.
Tipo: Poster Palavras-chave: Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2470/version/1
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Evidence of Massive Horizontal Gene Transfer Between Humans and Plasmodium vivax Nature Precedings
Daniel Z. Bar.
The horizontal transfer of DNA between different organisms is a major force shaping the genomes of prokaryotes, but is considered to have a minor role in eukaryotes, with only a handful of known examples, mostly of limited size. The nucleotide databases of Plasmodium genomes were divided into small fragments and compared to human, as well as to other Plasmodium genomes. This computational approach revealed that the Plasmodium vivax genome is interlaced with multiple DNA fragments that were likely acquired via horizontal transfer from humans. Contamination is a major concern in such studies; moreover, it must be determined if the identified homologies might be due to chance. These reservations are supported by the fact that the identified homologous...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5690/version/1
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Crosstalk and the spectrum of biological global broadcasts: Toward generalization of the Baars consciousness model across physiological subsystems Nature Precedings
Rodrick Wallace.
Once cognitive biological phenomena are recognized as necessarily having 'dual' information sources, it is easy to show that the information theory chain rule implies isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to dynamic global broadcasts of interacting cognitive biological processes analogous to, but slower than, consciousness, itself included within the paradigm. The argument is closely analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems.
Tipo: Manuscript Palavras-chave: Biotechnology; Developmental Biology; Immunology; Molecular Cell Biology; Neuroscience; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/6898/version/1
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NamesforLife Semantic Resolution Services for the Life Sciences Nature Precedings
Charles T. Parker; Dorothea K. Taylor; Kara Mannor; Sarah Wigley; Nicole Osier; Catherine Lyons; George M. Garrity.
A major challenge in bioinformatics, life sciences, and medicine is using correct and informative names. While this sounds simple enough, many different naming conventions exist in the life sciences and medicine that may be either complementary or competitive with other naming conventions. For a variety of reasons, proper names are not always used, leading to an accumulated semantic ambiguity that readers of the literature and end users of databases are left to resolve on their own. This ambiguity is a growing problem and the biocuration community is aware of its consequences. 

To assist those confronted with ambiguous names (which not only includes researchers but clinicians, manufacturers, patent attorneys, and others...
Tipo: Poster Palavras-chave: Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5137/version/1
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Thermal characterization of Plasmodium falciparum species specific proteins in Indian geographical area. Nature Precedings
Mohit Bhardwaj; Leena Bharadwaj; Kritika Trigunayat; Madan Mohan Trigunayat.
The paper reveals thermal characteristics of _P.falciparum_ species specific proteins. These proteins determine why _P. vivex_ species are dominant over _P.falciparum_ in Indian geographical area. Outside human host plasmodium parasite survives in poikilothermal mosquitoes. Climatic temperature conditions greatly affect native state of _P.falciparum_ species specific proteins in mosquitoes. Study of climatic temperature conditions in Indian geographical area reveals that Pfsd protein for _Plasmodium falciparum_ can remain in native state between ≥7 degree centigrade and ≤42.6 degree centigrade temperature conditions. While their best optimum functions (activity) was noted between 25.3 degree centigrade to 33degree centigrade. Pfsd...
Tipo: Manuscript Palavras-chave: Ecology; Molecular Cell Biology; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4565/version/1
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Investigating prostate cancer tumour-stroma interactions - clinical and biological insights from an evolutionary game Nature Precedings
David Basanta; Jacob G. Scott; Mayer N. Fishman; Gustavo E. Ayala; Simon W. Hayward; Alexander R. A. Anderson.
BACKGROUND: Tumours are made up of a mixed population of different types of cells that include normal structures as well as ones associated with the malignancy, and there are multiple interactions between the malignant cells and the local microenvironment. These intercellular interactions, modulated by the microenvironment, effect tumour progression and represent a largely under appreciated therapeutic target. We use observations of primary tumor biology from prostate cancer to extrapolate a mathematical model: specifically; it has been observed that in prostate cancer three disparate cellular outcomes predominate: (i) the tumour remains well differentiated and clinically indolent - in this case the local stromal cells may act to restrain the growth of the...
Tipo: Manuscript Palavras-chave: Cancer; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6385/version/1
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A logistic regression model for microalbuminuria prediction in overweight male population Nature Precedings
BaoDe Chen; WeiYi Xu; Chen Yu; ZhenYun Ni; XueFen Li; DaWei Cui.
Background: Obesity promotes progression to microalbuminuria and increases the risk of chronic kidney disease. Current protocols of screening microalbuminuria are not recommended for the overweight or obese.

Design and Methods: A cross-sectional study was conducted. The relationship between metabolic risk factors and microalbuminuria was investigated. A regression model based on metabolic risk factors was developed and evaluated for predicting microalbuminuria in the overweight or obese.

Results: The prevalence of MA reached up to 17.6% in Chinese overweight men. Obesity, hypertension, hyperglycemia and hyperuricemia were the important risk factors for microalbuminuria in the overweight....
Tipo: Manuscript Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5372/version/1
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Assessment Of Response To Heart Failure Therapy: Ventricular Volume Changes Versus Shape Changes Nature Precedings
Srilakshmi Adhyapak; V.Rao Parachuri.
The prolate ellipsoid left ventricular geometry is crucial for its unique contraction and relaxation patterns. Perturbations in optimal cardiac function preceding overt heart failure ensue when this ellipsoid shape assumes a more spherical configuration. This stage of spherical configuration, prior to overt dilatation, is when therapy should be intensified. The dynamic shape changes during the cardiac cycle of systole and diastole in valvular regurgitations when ventricular volumes are within normal range have proved that shape changes are clearly dissociated from volume changes in the early stages. In the scenario of advanced heart failure, several therapeutic interventions have been tried with variable success. These therapies aim at decreasing the...
Tipo: Manuscript Palavras-chave: Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6707/version/1
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Altruism among relatives and non-relatives Nature Precedings
Howard Rachlin; Bryan A. Jones.
The amount of their own monetary reward that undergraduate participants claimed they were willing to forgo, in order to give $75 to another person, decreased hyperbolically as social distance increased between the participant and the other person. Relatives tended to be ranked at closer social distances than were non-relatives. However, even at the same social distance, participants were willing to forgo significantly more money for the benefit of relatives than for the benefit of non-relatives. These results imply that altruism is determined by factors in addition to social distance.
Tipo: Manuscript Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1565/version/1
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Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA) Nature Precedings
Xiaolong Wang; Yu Fu; Yue Zhao; Qi Wang; Chandra Sekhar Pedamallu; Shuang-yong Xu; Yingbo Niu; Jingjie Hu.
Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used for inferring evolutionary history of organisms and individual genes. Traditionally, alignments and phylogeny trees of proteins and their coding DNA sequences are constructed separately, thus often different conclusions were drawn. Here we present a new strategy for sequence alignment and phylogenetic tree reconstruction, codon and amino acid unified sequence alignment (CAUSA), which aligns DNA and protein sequences and draw phylogenetic trees in a unified manner. We demonstrated that CAUSA improves both the accuracy of multiple sequence alignments and phylogenetic trees by solving a variety of molecular evolutionary problems in...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6730/version/1
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Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds Nature Precedings
Shi Huang.
Molecular analysis of collagen sequences from an 80 million year old hadrosaur _B. canadensis_ and a 68 million year old dinosaur _T. rex_ suggest strongly that _B. canadensis_ is an outgroup to a clade containing _T. rex_ and birds, fully consistent with the well-established phylogeny based on morphological analyses of fossils.
Tipo: Manuscript Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3255/version/1
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When Spandrels Become Arches: Neural crosstalk and the evolution of consciousness Nature Precedings
Rodrick Wallace.
Once cognition is recognized as having a 'dual' information source, the information theory chain rule implies that isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to the rapid, shifting global neural broadcasts of consciousness. The argument is quite analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in neurons and neuronal subsystems. Astrobiological implications are obvious.
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/6115/version/2
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Extending Astrobiology: Consciousness and Culture Nature Precedings
Rodrick Wallace.
The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, evolutionary trajectory found on Earth. Are many alien organisms likely to be conscious in ways that we would recognize? Almost certainly. Will some develop high order technology? Less likely, but still fairly probable. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is fairly direct.
Tipo: Manuscript Palavras-chave: Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5286/version/2
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Evolution as a language that speaks itself Nature Precedings
Rodrick Wallace.
The 'self-referential' character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated through a 'language' model in which genes, gene expression, and environment are represented as interacting information sources. The larger, composite, source that characterizes the high probability evolutionary paths then becomes, in a real sense, a language that speaks itself. The approach represents a significant extension of nonequilibrium condensed matter formalism in which the asymptotic limit theorems of information theory beat back the mathematical thicket a full step, providing necessary, but not sufficient, conditions for punctuated evolutionary transitions that can themselves be expressed as highly...
Tipo: Manuscript Palavras-chave: Chemistry; Ecology; Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5339/version/1
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An insight into the kinships of the fungi Nature Precedings
Riddhi Datta; Joy Sarkar; Krishnendu Acharya.
The evolutionary origin of fungi is important in determining the phylogenetic relationships between fungi, animals and plants. However, determining the true relationship of fungi has been somewhat difficult owing to their simple morphology and presence of convergent characters. With the advent of newer molecular techniques, analysis of conserved protein sequences, cytochrome systems, mitochondrial and nuclear genetic material and rRNAs are being employed in elucidating phylogenetic kinships among the eukaryotes. These emerging evidences suggest that the derivation of the fungi from plants or algae would require more evolutionary changes than its derivation from protozoa, the unicellular ancestor of the animals. To gain an overview of the current state of...
Tipo: Manuscript Palavras-chave: Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7095/version/1
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