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Biodiversity shapes tree species aggregations in tropical forests Nature Precedings
Shan-Huah Wu; Wei-Chun Chao; Chang-Fu Hsieh.
Spatial patterns of conspecific trees are considered as the consequences of biological interactions and environmental influences. They also reflect species interactions in plant communities. However, biological attributes are often neglected while deliberating the factors shaping species distributions. As rising attentions are paid to spatial patterns of tropical forest trees, we noticed that seven Center of Tropical Forest Sites and four Forest Dynamic Plots in Asia and America have presented analogously high proportions of species with aggregated conspecific individuals coincidently. This phenomenon is distinctive and repudiates fundamental ecology hypotheses which suggested dispersed distributions of conspecific tropical trees due to intensive density...
Tipo: Manuscript Palavras-chave: Ecology.
Ano: 2008 URL: http://precedings.nature.com/documents/1670/version/1
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China is on the track tackling Enteromorpha spp forming green tide Nature Precedings
Naihao Ye; Zhimeng Zhuang; Xianshi Jin; Qingyin Wang; Xiaowen Zhang; Demao Li; Hongxia Wang; Yuze Mao; Zengjie Jiang; Bin Li; Zhixin Xue.
Green tide management is supposed to be a long term fight rather than an episode during the 29th Olympic Games for China, since it has been gaining in scale and frequency during the past 3 decades in both marine and estuary environment all over the world. A number of rapid-responding studies including oceanographic comprehensive surveys along the coastline have been conducted during the bloom and post-bloom periods in 2008 by Chinese marine scientists. The preliminary results are as below: (1) phylogenetic analysis indicates that the bloom forming alga forms a clade with representatives of the green seaweed Enteromorpha linza, though, the alga has been identified as E. proliera by means of morphological; (2) the present data suggest that the bloom was...
Tipo: Manuscript Palavras-chave: Ecology; Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/2352/version/1
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Long-Lasting Context Dependence Constrains Neural Encoding Models in Rodent Auditory Cortex Nature Precedings
Hiroki Asari; Anthony M. Zador.
Acoustic processing requires integration over time. However classical linear encoding models, which typically integrate over a few hundred milliseconds, have failed to account fully for neural responses in the auditory cortex. We have used in vivo intracellular recording to measure neuronal integration times in anesthetized rats. Probing with natural sounds and other stimuli, we found that context-dependent effects in the primary auditory cortex could last for surprisingly long, up to four seconds or longer in some neurons. Thalamic neurons showed only a much faster form of adaptation, indicating that the long-lasting form originated in the cortex. Restricting knowledge of the stimulus history to only a few hundred milliseconds reduced the predictable...
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2008 URL: http://precedings.nature.com/documents/2282/version/1
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Desiderata for an ontology of diseases for the annotation of biological datasets. Nature Precedings
Olivier Bodenreider; Anita Burgun.
There is a plethora of disease ontologies available, all potentially useful for the annotation of biological datasets. We define seven desirable features for such ontologies and examine whether or not these features are supported by eleven disease ontologies. The four ontologies most closely aligned with our desiderata are Disease Ontology, SNOMED CT, NCI thesaurus and UMLS.
Tipo: Manuscript Palavras-chave: Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3531/version/1
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Trans-Disciplinary Protein Binding Of Drug: Docking Approach Nature Precedings
Ajeet Ajeet.
The purpose of present work is to introduce the binding of existing drugs to the trans-disciplinary protein with the help of docking procedures. Docking procedures allows virtually screening a database of compounds and predict the strongest binder based on various scoring functions. This work has been performed with the help of Molegro Virtual docker, in which two drugs are docked with their corresponding and non-corresponding (trans-disciplinary) protein. Results reveals that the protein-ligand interaction energy, hydrogen bond energy and MolDock scores provided by molegro virtual docker, between legands (Levodopa and Acyclovir) and trans-disciplinary proteins have been equivalent or even better than that of between legands and corresponding proteins.
Tipo: Manuscript Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6702/version/1
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Towards Context Driven Modularization of Large Biomedical Ontologies Nature Precedings
Pinar Wennerberg; Sonja Zillner.
Formal knowledge about human anatomy, radiology or diseases is necessary to support clinical applications such as medical image search. This machine processable knowledge can be acquired from biomedical domain ontologies, which however, are typically very large and complex models. Thus, their straightforward incorporation into the software applications becomes difficult. In this paper we discuss first ideas on a statistical approach for modularizing large medical ontologies and we prioritize the practical applicability aspect. The underlying assumption is that the application relevant ontology fragments, i.e. modules, can be identified by the statistical analysis of the ontology concepts in the domain corpus. Accordingly, we argue that most frequently...
Tipo: Manuscript Palavras-chave: Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3522/version/1
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Chemical Profiles of Essential Oils and Non-Polar Extractables from Sumac (Rhus spp.) Nature Precedings
Sierra Rayne.
Sumac is the common name for a genus (Rhus) with >250 individual species of flowering plants in the family Anacardiaceae. These plants are globally distributed in temperate and tropical regions and can grow on marginal lands, making them strong candidates for renewable bioproduct sources. Despite the extensive historical use of some members of Rhus spp. for tannins and other commercial phenolics, little is known about the non-phenolic components of extracts and essentials oils. The current review highlights opportunities available to extend these limited prior studies to other sumac species, and for obtaining value-added compounds to complement already established phenolic extractions in these commercial plant species. To date, a number of...
Tipo: Manuscript Palavras-chave: Chemistry; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5926/version/1
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Secondary water pore formation for proton transport in a ClC exchanger revealed by an atomistic molecular dynamics simulation Nature Precedings
Youn Jo Ko; Won Ho Jo.
Several prokaryotic ClC proteins have been demonstrated to function as exchangers that transport both chloride ions and protons simultaneously in opposite directions. However, the path of the proton through the ClC exchanger and how the protein brings about the coupled movement of both ions are still unknown. In the present work, we demonstrate that a previously unknown secondary water pore is formed inside a ClC exchanger by using an atomistic molecular dynamics (MD) simulation. From the systematic simulations, it was determined that the glutamate residue exposed to the intracellular solution, E203, plays an important role as a trigger for the formation of the secondary water pore. Based on our simulation results, we conclude that protons in the ClC...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry.
Ano: 2008 URL: http://precedings.nature.com/documents/2168/version/1
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Logarithmic laws of echoic memory and auditory change detection in humans Nature Precedings
Koji Inui; Tomokazu Urakawa; Koya Yamashiro; Naofumi Otsuru; Yasuyuki Takeshima; Ryusuke Kakigi.
The cortical mechanisms underlying echoic memory and change detection were investigated using an auditory change-related component (N100c) of event-related brain potentials. N100c was elicited by paired sound stimuli, a standard followed by a deviant, while subjects watched a silent movie. The amplitude of N100c elicited by a fixed sound pressure deviance (70 dB vs. 75 dB) was negatively correlated with the logarithm of the interval between the standard sound and deviant sound (1 ~ 1000 ms), while positively correlated with the logarithm of the duration of the standard sound (25 ~ 1000 ms), indicating that the temporal representation of echoic memory is logarithmic. The amplitude of N100c elicited by a deviance in sound pressure, sound frequency and sound...
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/3652/version/1
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Designing nature reserves in the face of uncertainty Nature Precedings
Michael McCarthy; Colin Thompson; Hugh Possingham.
Conservation reserves are one of the most important tools for managing biodiversity. Ever since Diamond, based on theory of island biogeography, proposed that a single large reserve was preferable to several small reserves of the same total area, there has been an enduring debate about the veracity of his assertion. The so-called SLOSS debate - should we have a Single Large reserve Or Several Small reserves - features in every conservation text book and is central to conservation theory. Population dynamic models suggest that the design that minimizes the risk of extinction of species is case-specific, with the optimal number of reserves ranging between one and very many. Uncertainty is pervasive in ecology, but, the previous analyses of the SLOSS debate...
Tipo: Manuscript Palavras-chave: Ecology.
Ano: 2009 URL: http://precedings.nature.com/documents/3387/version/1
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Magnetic Resonance imaging (MRI) in detection of _Bifidobacterium longum_ and _Clostridium novyi-NT_ labeled with superparamagnetic iron oxide (SPIO) nanoparticle Nature Precedings
Jianhua Wang; Xuebin Zhang; Dayong Zhou; Qingguo Wang; Dan Li.
*Purpose:* To investigate the MR imaging of _Bifidobacterium longum_ and _Clostridium novyi-NT_ labeling with superparamagnetic iron oxide (SPIO) nanoparticles.

*Materials and methods:* Tubes containing _B. longum_-SPIO, Free-SPIO, _B. longum_ and PYG Medium were incubated under anaerobic condition in _in vitro_ experiment. Transmission electron microscope and Prussian blue staining were used to demonstrate intra-bacteria nanoparticles. R~2~^*^ mapping and R~2~ mapping were reconstructed after MR scanning. _B. longum_-SPIO and _C. novyi_-NT-SPIO were injected respectively _in vivo_ to show whether it might be traced by MR imaging.

*Results:* Magnetosomes in bacteria were observed by...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Microbiology.
Ano: 2009 URL: http://precedings.nature.com/documents/3435/version/1
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Neurodegeneration: Potential Causes, Prevention, and Future Treatment Options Nature Precedings
Zhongtao Zhang.
Here I advance a hypothesis that neurodegeneration is a natural process associated with aging due to the loss of genetic redundancy following a mathematical model R(t) = R0(1-αe(βC+γI+δEt)t), where the calorie intake (C) and immune response (I) play critical roles. The early onset of neurodegenerative diseases such as Alzheimer’s disease is due to metabolic imbalance or chronic immune reactions to various infections. Therefore, the potential treatment options for neurodegenerative diseases are to modulate metabolism and immune response.
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2011 URL: http://precedings.nature.com/documents/6324/version/1
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Palaeobathymetry of the Abderaz Formation using foraminifera, Iran Nature Precedings
Meysam Shafiee Ardestani; Ebrahim Ghasemi-Nejad.
Abderaz Formation at its type section with an age of Turonian-early Campanian and a thickness of 300 m contains light grey shale and marl. The study of the planktonic foraminifera in isolated form led to differentiate three morphotype groups. The first group is characterized by trochospiral tests usually indicate shallow waters, the second group contains forms with strong ornamentations and the primary keels representing mid waters and finally compact trochospiral tests with keels known as deep water indices are included in the third group. Studies on the morphotypes showed a regressive cycle for Abderaz Formation. Also the planktonic to benthic ratio was calculated using Depth = e^(3.58718 + (0.03534 × %*p)^ equilibrium which explains that at the...
Tipo: Manuscript Palavras-chave: Ecology; Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/2787/version/1
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Ecological control on micro-ornamentation of conodont elements Nature Precedings
Andrey V. Zhuravlev.
Conodonts are considered now as specific group of early Chordata or even Vertebrata. Fifteen tooth-like conodont elements of seven morphological types compose the oral apparatus of conodonts. The elements demonstrate complex morphology. All the elements bear polygonal micro-ornamentation. The ornamentation is considered as representing imprints of the epithelium cells. Ecological dependencies of the cell sizes are known for some recent organisms.
The maximum cell sizes are characteristic of optimal environmental conditions. Thus, one can supposes that decreasing in cell imprint size in the conodonts marks disturbance in water temperature or/and oxygen content.

Tipo: Manuscript Palavras-chave: Earth & Environment.
Ano: 2007 URL: http://precedings.nature.com/documents/659/version/1
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Sex-Related Moral Behavior Nature Precedings
Alberto Priori; Manuela Fumagalli; Sara Marceglia; Roberta Ferrucci; Francesca Mameli; Stefano Zago; Sergio Barbieri; Giuseppe Sartori; Stefano Cappa.
The moral sense is one of the most complex aspects of the human mind. While neurobiological, cognitive and behavioural gender-related differences are increasingly studied and verified, the common belief that morality differs between men and women has not been experimentally investigated. We assessed the impact of gender on moral choices by testing thirty men and thirty women with the Moral Sense Task (MST) (Greene _et al_. 2001, 2004; Koenigs _et al_. 2007). Whereas the two genders did not differ in utilitarian responses to non-moral dilemmas (NM) and to impersonal moral dilemmas (MI), men gave significantly more utilitarian answers to personal moral dilemmas (MP; i.e. that action whose endorsement involves highly emotional decision). These results...
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2007 URL: http://precedings.nature.com/documents/1467/version/1
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Third-codon transversion rate-based _Nymphaea_ basal angiosperm phylogeny -- concordance with developmental evidence Nature Precedings
Xiaohan Yang; Gerald A. Tuskan; Timothy J. Tschaplinski; (Max) Zong-Ming Cheng.
Flowering plants (angiosperms) appeared on Earth rather suddenly approximately 130 million years ago and underwent a massive expansion in the subsequent 10-12 million years. Current molecular phylogenies have predominantly identified _Amborella_, followed by _Nymphaea_ (water lilies) or _Amborella_ plus _Nymphaea_, in the ANITA clade (_Amborella_, Nymphaeales, Illiciaceae, Trimeniaceae and Austrobaileyaceae) as the earliest angiosperm. However, developmental studies suggest that the earliest angiosperm had a 4-cell/4-nucleus female gametophyte and a diploid endosperm represented by _Nymphaea_, suggesting that _Amborella_, having an 8-cell/9-nucleus female gametophyte and a triploid endosperm, cannot be representative of the basal angiosperm. This...
Tipo: Manuscript Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/320/version/1
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Genes of the serotonergic and dopaminergic pathways and their interaction affect the expression of Behavioural and Psychological Symptoms in Dementia (BPSD). Nature Precedings
Petroula Proitsi; Michelle Lupton; Suzanne Reeves; Gillian Hamilton; Nicola Archer; Belinda Martin; Paul hollingworth; Brian Lawlord; Michael Gill; Michael J. Owen; Julie Williams; Simon Lovestone; John Powell.
Although there is evidence for the involvement of genes of serotonergic and dopaminergic systems in the manifestation of the Behavioural and Psychological Symptoms in Dementia (BPSD), genetic association studies are contradictory. We used 1008 probable AD patients from the UK and applied a Multiple Indicators Multiple Causes (MIMIC) approach to investigate the effect of 11 polymorphisms in the serotonergic and dopaminergic systems, on four behavioural sub-phenotypes, namely "psychosis"," moods", "agitation" and "behavioural dyscontrol", as well as on 12 NPI items. Significant findings included the association of DRD1 A48G with "psychosis" (p=0.037), the association of...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/3896/version/1
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A Mathematical Model of a Neuron with Synapses based on Physiology Nature Precedings
Xiaolin Zhang.
The neuron, when considered as a signal processing device, itsinputs are the frequency of pulses received at the synapses, and its output is the frequency of action potentials generated- in essence, a neuron is a pulse frequency signal processing device. In comparison, electrical devices use either digital or analog signals for communication or processing, and the mathematics behind these subjects is well understood. However, in regards to pulse frequency processing devices, there has not yet been a clear and persuasive mathematical model to describe the functions of neurons. It goes without saying that such a model is very important, not only for understanding neuron and neural system behavior, but also for undeveloped potential applications in industry....
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2008 URL: http://precedings.nature.com/documents/1703/version/1
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Solubilization of M2 Transmembrane Peptide of Influenza A in Pure Water: Implications for Emergence of Proteins and Protein-embedded Primeval Membranes in Unsalted Oceans Nature Precedings
Jianxing Song; Linlin Miao.
We demonstrated that M2 transmembrane peptide, one of the most hydrophobic sequences in nature, can be solublized to at least ~100 µM in unsalted water without any lipid molecules. Strikingly, the M2 peptide also forms a highly-helical conformation in water which remains almost unchanged even at 95 ºC, as characterized by CD spectroscopy. Our result has critical implications in understanding emergence of proteins and protein-embedded primeval membranes in unsalted oceans.
Tipo: Manuscript Palavras-chave: Chemistry; Molecular Cell Biology; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/6773/version/1
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Synthesis and characterization of chemically modified sago starch with potential biomedical application (Presented at ChemFerence-2010 at IIT Kanpur, 13 July 2010) Nature Precedings
Akhilesh V. Singh.
This study was undertaken to assess the potential of highly substitute acetylated sago starch (SS) to be used as a platform for controlled drug delivery. The acetylated sago starch was synthesized and the two parameters i.e. duration of reaction and temperature were optimized. FT-IR spectra showed the corresponding group attachment in the modified form. XRD pattern exhibits change in the physical nature i.e. from crystalline to amorphous. Swelling, hydration and viscosity value exhibits decrease in the respective values in comparison to its native form which is due a to decrease in its hydrophilic value.
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2011 URL: http://precedings.nature.com/documents/5768/version/1
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