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Genome Replikin Count Predicts Increased Lethality of Resistant Tuberculosis Nature Precedings
Samuel Bogoch; Elenore S. Bogoch.
The genomic Replikin Count of all the sequences on Pubmed of different strains of tuberculosis were analyzed. The lowest Counts occurred with species within the lowest drug resistance, the highest Counts with sequences of the highest drug resistance and lethality.
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7141/version/1
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Study on the effect of toxicity under highly arsenic prone zone in Nadia district of West Bengal in India Nature Precedings
Tanmoy Rana; Samar Sarkar; Tapan K. Mandal; Subhasis Batabyal; Bakul K. Datta; Sumanta De; Sourav Sikdar.
The present study was carried out on the basis of status of arsenic in soil, drinking water and plants, blood, urine and faeces of animals at arsenic prone zone. Within the ambit with the environment, the examination of animals was taken into consideration. They were screened and categorised on the degree of As toxicity. For field works animals were randomly selected from arsenic prone zone. The external manifestation indicated a complex syndrome and characteristic signs such as increased heart rate and respiratory rate, red urine, congested mucous membrane, anorexia, absence of ruminal motility, diarrhoea with blood, polyuria and unusual weight loss. The haematobiochemical changes such as low Hb level, decreased level of TEC, TLC and increased level ALT,...
Tipo: Manuscript Palavras-chave: Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/2992/version/1
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Sandy bottom communities at the end of a cold (1971-1975) and warm (1997-1998) regime in the California Current: impacts of high and low plankton production Nature Precedings
John S. Oliver; Stacy L. Kim; Peter N. Slattery; James A. Oakden; Kamille K. Hammerstrom; Ethan M. Barnes.
There were highly significant changes in the structure of benthic infaunal communities at the end of the last cold regime (1976) compared to the end of the last warm regime (1999) in the California Current. The warm regime is characterized by much lower plankton production, which we argue is the primary cause of the degraded infaunal community at the end of the warm regime. In 1997-98, we resampled a depth gradient along a subtidal, high-energy sandy beach (6-24m) in Monterey Bay that was sampled for five years at the end of the last cold regime (1971-75). There was a dramatic decline in the total number species, number of individuals, and biomass by the end of the warm period. There was no overlap in benthic assemblages at all water depths between the...
Tipo: Manuscript Palavras-chave: Ecology.
Ano: 2008 URL: http://precedings.nature.com/documents/2103/version/1
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P300- like event related potential amplitude in rats is a correlate of conditioned reinforcement Nature Precedings
William D. Klipec; Steven Faux.
We have developed a methodology for recording a robust P300 event related potential (ERP) in rats. In these experiments a contingency shaped model of the human “oddball’ paradigm was employed in which rats were shaped to press a lever for food reinforcement signaled by the click of the pellet dispenser. A target tone cued the insertion of the lever that retracted after 1­sec or immediately following a single reinforced response, while a non­target tone was randomly presented. Brain activity was recorded through stainless steel electrodes implanted 1mm below the skull. Here, we compared the amplitude of the P300 response to the click of the pellet dispenser to the amplitude of the P300 response to the target and...
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2012 URL: http://precedings.nature.com/documents/7100/version/1
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Factors influencing impala distribution patterns in Nairobi National Park, Kenya Nature Precedings
Vincent Obade; Eva Clercq.
Monitoring the distribution of wild animals using appropriate methods and survey techniques is essential not only for sustainable management but also to avoid wastage of resources. This study applied remote sensing to investigate the factors influencing the distribution of herbivores in Nairobi National Park, Kenya. Impala was selected as indicator specie for the herbivores within the park, because the population of impala had drastically reduced over time. The influence of food availability, water and disturbance on herbivore presence was investigated. A positive significant statistical relationship between impala population density and feed availability was observed. However, the correlation between impala population density and water distance was...
Tipo: Manuscript Palavras-chave: Ecology; Plant Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3799/version/1
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Kinetic model based on molecular mechanism for action potential Nature Precedings
Lizhong Xu.
The Hodgkin-Huxley model for action potentials has been widely used but was not built on a microscopic description of the neuronal membrane. Through molecular dynamics simulations, the molecular mechanism of the channel currents is becoming clear. However, the quantitative link between molecular mechanism and action potential remains to be elucidated. Here, a kinetic model for action potential based on the molecular mechanism of the channel currents is proposed. Using it, the experimental observations about action potential are reproduced quantitatively and explained based on molecular mechanism. We find that the accumulation of Na+ ions near exit of the electivity filter is the dominant event to cause the refractory period of the Na+ channel and the types...
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2011 URL: http://precedings.nature.com/documents/5697/version/1
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Discovery of the Principal Cystic Fibrosis Mutation (F508del) in Ancient DNA from Iron Age Europeans Nature Precedings
Philip Farrell; Cedric Le Marechal; Claude Ferec; Malika Siker; Maria Teschler-Nicola.
The most common, life-threatening autosomal recessive disease of Europeans and Euro-Americans, cystic fibrosis (CF), occurs predominately in patients with the F508del mutation.1 Although F508del is currently detectable as a single allele in 1/30-1/40 Europeans2-4 and Euro-Americans,5 it has not been determined what heterozygote selective advantage(s) might account for its relatively high prevalence. Indirect evidence6 suggests that this mutation was present in Brittany at least 3000 years ago, but no direct analyses of ancient DNA have been reported to identify F508del and clarify its frequency in prehistoric inhabitants of Europe. Here we show that F508del was present in 3 of 32 Iron Age inhabitants of Austria from whom DNA could be recovered from molar...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1276/version/1
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Sociability is decreased following deletion of the _trpc4_ gene Nature Precedings
Kristin C. Rasmus; Jun-Gang Wang; Andrew L. Varnell; Eric M. Ostertag; Donald C. Cooper.
Shyness and social anxiety are predominant features of some psychiatric disorders including autism, schizophrenia, anxiety and depression. Understanding the cellular and molecular determinants of sociability may reveal therapeutic approaches to treat individuals with these disorders and improve their quality of life. Previous experiments from our laboratory have identified selective mRNA and protein expression of a nonselective cation channel known as the canonical transient receptor potential channel 4 (TRPC4s) in brain regions implicated in emotional regulation and anxiety. TRPC4 is highly expressed in the corticolimbic regions of the mammalian brain. We hypothesized that robust corticolimbic expression of TRPC4 may regulate the brain’s...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2011 URL: http://precedings.nature.com/documents/6367/version/1
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Design and Implementation of the UniProt Website Nature Precedings
Eric Jain; Isabelle Phan; Severine Duvaud; Elisabeth Gasteiger; Nicole Redaschi; Maria J. Martin; Peter McGarvey; Amos Bairoch.
The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The "www.uniprot.org":http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access.
Tipo: Manuscript Palavras-chave: Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/2611/version/1
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Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications Nature Precedings
Shang-Hong Zhang; Ya-Zhi Huang.
One of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist;...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2146/version/1
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More damn lies about data access Nature Precedings
Myles Axton.
More data than we can handle is no excuse to give up our efforts to promote data access, but it may make us think about new ways to make it sustainable.
[This draft was written in the hope that participants of the Sage Congress will write an Nature Genetics Editorial in the manner of Tom Sawyer’s white fence (Twain M. 1876). All contributions received by April 10th 2011 will be attributed.]

Tipo: Manuscript Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/5873/version/1
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Consciousness and subjective time: a plausible auditory approach Nature Precedings
Sepehr Ehsani.
The perception of time is an indispensable facet of human consciousness, and may in fact be dynamically present in primates and other species, albeit with different manifestations. Moreover, contrary to the physical measures of time, cognitive temporal perception may be subjectively affected by both internal and environmental cues. Here we review the evidence for the potential role of the auditory system in shaping the cortical measures of time, and propose possible auditory methods for studying this aspect of consciousness.
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2011 URL: http://precedings.nature.com/documents/5941/version/1
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Intrarectal administration of hCG (Human Choriogonadotropin) and fat loss as assessed by Dual energy X-ray absorptiometry (DXA) in experimental animals. Nature Precedings
Daniel Belluscio; Ezequiel Klimovsky; Alejandro Kaniuk; Sergio Vaney.
Our studies suggest that in experimental animals, submitted to a hypocaloric diet, the intrarectal administration of hCG (Human Chorionic Gonadotropin) decreases body fat and increases lean mass content in relative values to a greater extent that control animals who did not receive hCG.

Tipo: Manuscript Palavras-chave: Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/7074/version/2
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Aging-associated Alteration in the Cardiac MIF-AMPK Cascade in Response to Ischemic Stress Nature Precedings
Heng Ma; Jingying Wang; Erin Lane; Lin Leng; Wenkui Wang; Jun Ren; Richard Bucala; Ji Li.
An important role for a macrophage migration inhibitory factor (MIF)-AMP-activated protein kinase (AMPK) signaling pathway in ameliorating myocardial damage following ischemia/reperfusion has been described. An aging-associated reduction in AMPK activity may be associated with a decline in the ability of cardiac cells to activate the MIF-AMPK cascade, thereby resulting in reduced tolerance to ischemic insults. To test this hypothesis, _in vivo_ regional ischemia was induced by occlusion of the left anterior descending (LAD) coronary artery in young (4-6 months) and aged (24-26 months) mice. The ischemic AMPK activation response was impaired in aged hearts compared to young ones (p<0.01). Notably, cardiac MIF expression in aged hearts was lower...
Tipo: Manuscript Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2008 URL: http://precedings.nature.com/documents/2466/version/1
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Circadian Preference and Sexual Selection: A Novel Evolutionary Approach Nature Precedings
Davide Piffer.
Human sleep patterns differ across age groups and between males and females, and their association with age and gender suggest that they might have been the target of sexual selection during human evolutionary history. In this study, I will test the hypothesis that a phase-delayed circadian phase is a sexually selected trait in humans. A short version of the Horne and Ostberg questionnaire and a questionnaire on sexual behaviour were administered to 134 males and 140 females. A significant negative relationship was found between the MEQ score and the number of sexual partners among males, with evening types reporting more sexual partners than morning types. No significant relationship between females MEQ and number of sexual partners was found. Findings...
Tipo: Manuscript Palavras-chave: Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/2964/version/2
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Lego DNA assembling, a simple in vitro method for constructing DNA molecule Nature Precedings
Mo Xian; Xinglin Jiang; Jianming Yang; Haibo Zhang; Huaiwei Liu; Yanning Zheng; Cong Wang; Sizheng Su.
Digestion-ligation based and recombination based methods for constructing recombinant DNA are the basic techniques in molecular biology and thus built one of the foundations for the modern life sciences. Here we describe a new strategy that can radically simplify some of the same task. The lego DNA assembling, based on strand annealing, allows in vitro assembly of multi DNA fragments in one step with precise junctions and excludes the need for any enzyme. As a proof of concept, we rapidly constructed plasmids from 4, 6 and 8 fragments with very high efficiencies (100%). And we found this method a powerful tool for synthetic biology, constructing a partial isoprene biosynthesis pathway (consisting of four genes) in 2 days. We also assembled a customized...
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics.
Ano: 2010 URL: http://precedings.nature.com/documents/5147/version/1
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A Unified Approach for Representing Structurally-Complex Models in SBML Level 3 Nature Precedings
Robert Muetzelfeldt.
The aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification. The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure. Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.

The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page...
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/4372/version/1
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Expression of Green Fluorescence Protein (GFP) in Zebrafish Muscle through Injection: A Gene Therapy Model Nature Precedings
C. S. Lin; Jhen Ru Shih; C. H. Hsu; Z.H. Wen; Chiranjib Chakraborty.
Expression of the target gene is important for gene therapy. Presently, localized transgenesis is used for gene therapy which can be achieved by a target gene expression. Here, we have reported the plasmid mediated gene therapy to zebrafish model. For this purpose, we have chosen green fluorescent protein (GFP) as a target gene because the expression can be detected easily. GFP was inserted in a plasmid vector, pQE30 to develop the vector pQE30GFP. The plasmid pQE30GFP was constructed form plasmid, pQE30 and pEGFPC2. pQE30GFP injected directly in one group of fish into the muscle where luciferase expression was noted. In another group, after injection electroporation was performed where we have also noted luciferase expression; but, electroporation cause...
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Pharmacology.
Ano: 2008 URL: http://precedings.nature.com/documents/2718/version/1
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Persistence of Edge-State in Stacked Graphene and Nano-Graphene Materials Nature Precedings
Kikuo Harigaya.
Nano-carbon materials are investigated intensively. In this paper, the edge-state in nanographene materials with zigzag edges is studied theoretically. In particular, while the inter-layer interactions are considered, we prove that edge states exist at the energy of the Dirac point in the doubly stacked nanographene, and in the case of the infinitely-wide lower layer case. This property applies both for the A-B and A-C stackings.
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2009 URL: http://precedings.nature.com/documents/3878/version/1
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Performance of the M062X density functional against the ISOL set of benchmark isomerization energies for large organic molecules Nature Precedings
Sierra Rayne; Kaya Forest.
Gas phase standard state (298.15 K, 1 atm) isomerization energies were calculated using the M062X functional with the QZVP, 6-311++G(d,p), 6-311++G(2d,2p), and cc-pVTZ basis sets against the 24 reactions in the ISOL set of benchmark isomerization energies for large organic molecules. The M062X functional appears to offer comparable isomerization energy prediction performance to the best performing currently available dispersion corrected functionals against this benchmark dataset.
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2010 URL: http://precedings.nature.com/documents/5183/version/1
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