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Optimal control circuitry design for the digital p53 dynamics in cancer cell and apoptosis Nature Precedings
Rosario M. Ardito Marretta.
Experimental work and theoretical models deduce a "digital" response of the p53 transcription factor when genomic integrity is damaged. The mutual influence of p53 and its antagonist, the Mdm2 oncogene, is closed in feedback. This paper proposes an aerospace architecture for translating the p53/Mdm2/DNA damage network into a digital circuitry in which the optimal control theory is applied for obtaining the requested dynamic evolutions of some considered cell species for repairing a DNA damage. The purpose of this paper is not to improve the analysis of the actual mathematical models but to demonstrate the usefulness of such digital circuitry design capable to predict and detect the cell species dynamics for finding more information...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Developmental Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2870/version/1
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Organic consequences of ileal transposition in rats with diet-induced obesity Nature Precedings
Lucas P. F. F. Leal; Joao Luiz M. C. Azevedo; Gilmara S. Aguiar-Yamaguchi; Wellington Cardia; Bianca Marigliani; Karina F. Neves; Paolo H. B. Lourenço; Marcelo C. Carlini; Joao L. C. Azevedo; Otávio C. Azevedo; Gui M. Ko; Gustavo P. S. Miguel; Valderez B. V. Lapchick.
INTRODUCTION: The clinical management of metabolic syndrome - especially diabetes mellitus type 2 - is notoriously complex due to the progressive nature of this disease. At present, there is a need for a surgical procedure that is effective for the treatment of diabetes mellitus type 2, even in non-obese individuals. The isolated ileal transposition theory could lead to an effective alternative therapy. This intervention has not yet been performed in humans, and there are no reports of its use in an experimental model of diet-induced metabolic syndrome.
 OBJECTIVES: The objective of this study is to evaluate the physiological effects of ileal transposition in rats with diet-induced metabolic syndrome. The effects of this procedure on...
Tipo: Manuscript Palavras-chave: Developmental Biology; Genetics & Genomics; Molecular Cell Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6122/version/1
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Origin and diversification of steroids: Co-evolution of enzymes and nuclear receptors Nature Precedings
Michael E. Baker.
Recent sequencing of amphioxus and sea urchin genomes has provided important data for understanding the origins of enzymes that synthesize adrenal and sex steroids and the receptors that mediate physiological response to these vertebrate steroids. Phylogenetic analyses reveal that CYP11A and CYP19, which are involved in the synthesis of adrenal and sex steroids, first appear in the common ancestor of amphioxus and vertebrates. This correlates with recent evidence for the first appearance in amphioxus of receptors with close similarity to vertebrate steroid receptors. Other CYP450 enzymes involved in steroid synthesis can be traced back to invertebrates, in which they have at least two functions: detoxifying xenobiotics and catalyzing the synthesis of...
Tipo: Manuscript Palavras-chave: Developmental Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4674/version/1
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Pachydermoperiostosis-Like Disease In Captive Red Ruffled Lemurs (Varecia Variegatus Rubra) Nature Precedings
Bruce Rothschild; Donald Neiffer; Steve Marks.
Pachydermatoperiostosis, a rare form of hypertrophic osteoarthropathy, is of unknown etiology and previously thought limited to humans. The only periosteal reaction previously reported in prosimians is related to renal disease. Notation of hypertrophic osteoarthritis in three prosimians led to recognition that this was the first non-human documentation of the disease. Three related red ruffed lemurs (Varecia variegatus rubra) had diaphyseal periosteal reaction classic for hypertrophic osteoarthropathy. Workup was negative for known underlying causes and for the secondary hyperparathyroidism which produces bone alterations in black Eulemur macao, black and white Varecia variegatatus varigatus and ringtail Lemur catta lemurs. Recognition of facial coarsening...
Tipo: Manuscript Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6374/version/1
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Porous Chitsan-Gelatin Scaffolds Embedded with PLGA Nanoparticles for Bone Repair Nature Precedings
Vijay Kumar Nandagiri; Piergiergio Gentile; Valeria Chiono; Clara Muttu; Gianluca Ciardelli; Franco Maria Montevecchi; Ziebun Ramtoola.
Bone regeneration can be accelerated by localized delivery of appropriate growth factors/bio active molecules. Localized delivery can be achieved by incorporating bioactive molecules within biodegradable particulate carrier system followed by embed them in a suitable porous scaffolds. These carrier system facilitates the impregnated growth factor(s) to release at a desirable rate and concentration, and to linger at injury sites for a sufficient time to recruit progenitors and stimulate tissue healing processes. In this study, an attempt has been made to engraft the porous chitosan-gelatin scaffolds with PLGA nanoparticles for localized delivery of bioactive components. Scaffolds loaded with PLGA nanoparticles were subjected to physical and mechanical...
Tipo: Poster Palavras-chave: Developmental Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4728/version/1
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Precise Atomic Structures of two Important Molecules in Biochemistry: Nature Precedings
Raji Heyrovska; Saraswathi Narayan; Lakshmi Atchison.
This work celebrates the “International Year of Chemistry – 2011”, by providing “for the first time”, the structures at the atomic level of two important molecules, namely, ascorbic acid and aspirin. Ascorbic acid, also known as vitamin C, was discovered as a cure for scurvy which claimed many human lives and hence got its name. It is also supposed to be an antioxidant and to prevent flu. Aspirin is synthesized from salicylic acid and is widely used as a remedy for flu and has other medical uses such as saving the lives of cardiac patients as an anticoagulant of blood. The biochemistry and chemistry of both these compounds have been evolving for nearly a century ever since their discoveries. Here, the...
Tipo: Poster Palavras-chave: Chemistry; Developmental Biology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/5966/version/1
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Pregnancy Obstructs Involution Stage II of the Mammary Gland in Cows: General Biological Implications Nature Precedings
Gabriel Leitner; Ana-Maria Anug; Uzi Merin; Nissim Silanikove.
*Background*
Repeated research findings over the last 4 decades show that involution of mammary glands in dairy cows did not regress to same extend as that noticed in other mammalian species.

*Methodology/Principal Findings*
We took an advantage of a rare event in the normal modern dairy farming: A cow that was false-positively identified as being pregnant was "dried up" (i.e., induced into involution) conventionally about 60 before her expected parturition. This cow was culled, and samples of her mammary gland tissue were examined for gross histology. In this study we demonstrate for the first time that modern dairy cow may undergo extensive obliteration of the...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Immunology.
Ano: 2007 URL: http://precedings.nature.com/documents/846/version/2
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Pregnancy Obstructs Involution Stage II of the Mammary Gland in Cows: General Biological Implications Nature Precedings
Nissim Silanikove; Gabriel Leitner; Ana-Maria Anug; Uzi Merin.
*Background*
Repeated research findings over the last 4 decades show that involution of mammary glands in dairy cows did not regress to same extend as that noticed in other mammalian species.

*Methodology/Principal Findings*
We took an advantage of a rare event in the normal modern dairy farming: A cow that was false-positively identified as being pregnant was "dried up" (i.e., induced into involution) conventionally about 60 before her expected parturition. This cow was culled, and samples of her mammary gland tissue were examined for gross histology. In this study we demonstrate for the first time that modern dairy cow may undergo extensive obliteration of the...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Immunology.
Ano: 2007 URL: http://precedings.nature.com/documents/846/version/1
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Prevalence of sarcopenia and sarcopenic obesity in Korean adults: The Korean Sarcopenic Obesity Study (KSOS) Nature Precedings
Tae Nyun Kim; Sae Jeong Yang; Hye Jin Yoo; Kang Il Lim; Hyun Joo Kang; Wook Song; Ji A Seo; Sin Gon Kim; Nan Hee Kim; Sei Hyun Baik; Dong Seop Choi; Kyung Mook Choi.
*Context:* Sarcopenic obesity (SO), a combination of excess weight and reduced muscle mass and/or strength, is suggested to be associated with an increased risk of adverse health outcomes. 
*Objectives:* To examine the prevalence and characteristics of Sarcopenic and SO defined by using different indices such as Appendicular Skeletal muscle Mass (ASM)/height^2^ and Skeletal Muscle Index (SMI (%): skeletal muscle mass (kg)/weight (kg) × 100) for Korean adults. 
*Methods:* 591 participants were recruited from the Korean Sarcopenic Obesity Study (KSOS) which is an ongoing prospective observational cohort study. Analysis was conducted in 526 participants (328 women, 198 men) who had complete data on body composition...
Tipo: Manuscript Palavras-chave: Developmental Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2915/version/1
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Production of Transgenic Cloned Miniature Pigs with Membrane-bound Human Fas Ligand (FasL) by Somatic Cell Nuclear Transfer Nature Precedings
Jae Goo Seol; Soo Hyun Kim; Dong-Il Jin; Seung Pyo Hong; Ji Yeon Yoo; Ki Myung Choi; Young Chul Park; Yun Jin Yun; Kwang Wook Park; Jae Young Heo.
Cell-mediated xenograft rejection, including NK cells and CD8+ CTL, is a major obstacle in successful pig-to-human xenotransplantation. Human CD8+ CTL and NK cells display high cytotoxicity for pig cells, mediated at least in part by the Fas/FasL pathway. To prevent cell-mediated xenocytotoxicity, a membrane-bound form of human FasL (mFasL) was generated as an inhibitor for CTL and NK cell cytotoxicity that could not be cleaved by metalloproteinase to produce putative soluble FasL. We produced two healthy transgenic pigs harboring the mFasL gene via somatic cell nuclear transfer (SCNT). In a cytotoxicity assay using transgenic clonal cell lines and transgenic pig ear cells, the rate of CD8+ CTL-mediated cytotoxicity was significantly reduced in transgenic...
Tipo: Manuscript Palavras-chave: Biotechnology; Developmental Biology; Immunology.
Ano: 2010 URL: http://precedings.nature.com/documents/4539/version/1
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Proliferating Cell Nuclear Antigen (PCNA) allows the automatic identification of follicles in microscopic images of human ovarian tissue Nature Precedings
Tom Kelsey; Benedicta Caserta; Luis Castillo; Hamish Wallace; Francisco Cóppola Gonzálvez.
Background: Human ovarian reserve is defined by the population of non-growing follicles (NGFs) in the ovary. Direct estimation of ovarian reserve involves the identification of NGFs in prepared ovarian tissue. Previous studies involving human tissue have used hematoxylin and eosin (HE) stain, with NGF populations estimated by human examination either of tissue under a microscopic, or of images taken of this tissue.
 
Methods: In this study we replace HE with Proliferating Cell Nuclear Antigen (PCNA), and automate the identification and enumeration of NGFs that appear in the resulting microscopic images. We compared the automated estimates to those obtained by human experts, with the gold standard taken to be the average of...
Tipo: Manuscript Palavras-chave: Developmental Biology; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4418/version/1
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Pro-social motive promotes early understanding of false belief Nature Precedings
Tomoko Matsui; Yui Miura.
Ever since Premack & Woodruff's classic article^1^, which introduced the term "theory of mind", researchers have claimed that strategic deception is the most natural behavioural consequence of understanding false belief. Here we challenge that claim, and provide evidence for the first time that the earliest manifestation of false belief understanding in human development is found in young children's emerging pro-social behaviours. In a modified false belief task, children were asked either to choose one protagonist they should help to find the object (the pro-social context), or to choose one they need to deceive so that none of the protagonists can find the object (the competitive context). The results show...
Tipo: Manuscript Palavras-chave: Developmental Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1695/version/1
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Protein folding disorders: Toward a basic biological paradigm Nature Precedings
Rodrick Wallace.
Mechanistic 'physics' models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a more appropriately biological paradigm will be needed for understanding the etiology, prevention, and treatment of these diseases.
Tipo: Manuscript Palavras-chave: Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4344/version/1
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Quantitative Models for Efficient Cloning of Different Vectors with Various Clone sites Nature Precedings
Gang Zhang; Anurag Tandon.
We developed an efficient "Combinatorial Strategy” for cloning different vectors with various clone sites. 1) Using originally existed clone sites from circular vectors to prepare the inserts, and if no appropriate sites are available, performing SDM to create compatible sites, to achieve maximal correct digestion of the inserts. 2) Different vectors were digested with various restriction endonucleases, and then dephosphorylated with CIP. 3) Top10 competent cells were used for transformation to increase the transformant colonies. Our results showed that, when blunt sites, or a Xba I site was adopted for ligation, the percentages of positive clones were about 50%. Whereas, when different sites, including one blunt and another Pst I...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics & Genomics; Immunology; Microbiology; Molecular Cell Biology; Neuroscience.
Ano: 2012 URL: http://precedings.nature.com/documents/6965/version/1
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Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species Nature Precedings
I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012 URL: http://precedings.nature.com/documents/7083/version/2
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Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species Nature Precedings
I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012 URL: http://precedings.nature.com/documents/7083/version/1
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Querying Drosophila In-Situ Expression Data using SPARQL and D2RQ Nature Precedings
Chris Mungall.
I describe a SPARQL endpoint for a database containing annotated images of gene expression in fruitfly embryogenesis. The images depict the actual expression of genes at a microscopic level using a technique called insitu hybridisation. The results were recorded in a relational database, and the images were annotated using the fly anatomy ontology.
Tipo: Marker Paper / Data Plan Palavras-chave: Developmental Biology; Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/5522/version/1
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Regrowing the adult brain: NF-κB controls functional circuit formation and tissue homeostasis in the dentate gyrus Nature Precedings
Yvonne Imielski; Jens C. Schwamborn; Patrick Lüningschrör; Peter Heimann; Magdalena Holzberg; Hendrikje Werner; Oliver Leske; Andreas W. Püschel; Sylvie Memet; Rolf Heumann; Alain Israel; Christian Kaltschmidt; Barbara Kaltschmidt.
Cognitive decline during aging is correlated with a continuous loss of cells within the brain and especially within the hippocampus, which could be regenerated by adult neurogenesis. Here we show that genetic ablation of NF-κB resulted in severe defects in the neurogenic region (dentate gyrus) of the hippocampus. Despite increased stem cell proliferation, axogenesis, synaptogenesis and neuroprotection were hampered, leading to disruption of the mossy fiber pathway and to atrophy of the dentate gyrus during aging. Here, NF-κB controls the transcription of FOXO1 and PKA, regulating axogenesis. Structural defects culminated in behavioral impairments in pattern separation. Re-activation of NF-κB resulted in integration of newborn...
Tipo: Manuscript Palavras-chave: Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Neuroscience.
Ano: 2011 URL: http://precedings.nature.com/documents/6096/version/1
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Regulated peristalsis into the acidic region of the _Drosophila_ larval midgut is controlled by a novel component of the Autonomic Nervous System Nature Precedings
Dennis Richard LaJeunesse; Brooke Ann Johnson; Jason Presnell; Kathleen K. Catignas; Grzegorz Zapotoczny.
The underlying cellular and molecular mechanisms that regulate and coordinate critical physiological processes such as peristalsis are complex, often cryptic, and involve the integration of multiple tissues and organ systems within the organism. We have identified a completely novel component of the larval autonomic nervous system in the _Drosophila_ larval midgut that is essential for the peristaltic movement of food from the anterior midgut into the acidic region of the midgut. We have named this region the Superior Cupric Autonomic Nervous System or SCANS. Located at the junction of the anterior and the acidic portions of the midgut, the SCANS is characterized by a cluster of a novel neuro-enteroendocrine cells that we call Lettuce Head Cells, a valve,...
Tipo: Manuscript Palavras-chave: Developmental Biology; Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/3873/version/1
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Regulation of Phosphatase Homologue of Tensin Protein Expression by Bone Morphogenetic Proteins in Prostate Epithelial Cells Nature Precedings
Travis Jerde; Zhong Wu; Dan Theodorescu; Wade Bushman.
Phosphatase homologue of tensin (PTEN) is the key endogenous inhibitor of phosphoinositide signaling and is the most commonly mutated gene in human prostate cancer. The bone morphogenetic proteins (BMPs) are secreted developmental signaling molecules known to promote differentiation in the prostate. BMP ligands have been shown to inhibit prostate cancer cell line proliferation and tumor growth and expression of BMPs, BMP ligands, receptors and signaling effectors are diminished in prostate cancer. A previous report in the colon led us to investigate the potential mechanistic relationship between PTEN and BMP signaling in prostate epithelial cells. We show here that BPM signaling positively regulates PTEN in normal and malignant prostate cells by increasing...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4311/version/1
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