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Biochemical Processes (60):
  • Up-Regulation
  • Signal Transduction
  • Phosphorylation
  • Nitrosation
  • Hydroxylation
  • Citric Acid Cycle
  • Biotinylation
  • Aerobiosis
  • Osmosis
  • Lipogenesis
  • Dimerization
  • Dealkylation
  • Biosynthetic Pathways
  • Ubiquitination
  • Protein Folding
  • Energy Transfer
  • Down-Regulation
  • DNA Cleavage
  • RNA Processing, Post-Transcriptional
  • Protein Renaturation
  • Molecular Mimicry
  • Lipid Peroxidation
  • Evolution, Chemical
  • Alkylation
  • Transcription, Genetic
  • Prenylation
  • Enzyme Activation
  • Electron Transport
  • Anaerobiosis
  • Protein Multimerization
  • Protein Modification, Translational
  • Protein Denaturation
  • Protein Binding
  • Phototrophic Processes
  • Hydrolysis
  • Hydrogenation
  • DNA Replication
  • Peptide Biosynthesis
  • Lipoylation
  • Heterotrophic Processes
  • Halogenation
  • DNA Methylation
  • Biocatalysis
  • Autotrophic Processes
  • Allosteric Regulation
  • Nucleic Acid Renaturation
  • Nucleic Acid Hybridization
  • Decarboxylation
  • Cyclization
  • Binding, Competitive
  • Substrate Cycling
  • Nucleic Acid Denaturation
  • Lipolysis
  • Esterification
  • DNA Repair
  • Carbohydrate Metabolism
  • Amination
  • Protein Carbonylation
  • Deamination
  • Acylation
Home > Chemical Phenomena > Biochemical Phenomena > Biochemical Processes

Recent article

Biochemical Processes

Kardiologiia (51)8 2011
[Heart failure and imbalance of chemical elements in myocardium of patients with ishemic heart disease].
A M AM Cherniavskiĭ, E N EN Levicheva, I Iu IIu Loginova, O V OV Kamenskaia, G N GN Okuneva, A M AM Volkov and E É EÉ Kliver
Abstract
We have analyzed content of chemical elements in left and right ventricular myocardium of patients with ischemic heart disease with progressing heart failure and have shown that during development and progression of heart failure metabolic processes have unidirectional character in myocardium of bot... | PMID: 21942953

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Human Genetics (128)2 2010
Identification of HAVCR1 gene haplotypes associated with mRNA expression levels and susceptibility to autoimmune diseases.
José Raúl García-Lozano, Cristina Abad, Ana Escalera, Belén Torres, Olga Fernández, Alicia García, Julio Sánchez-Román, José-Mario Sabio, Norberto Ortego-Centeno, Enrique Raya-Alvarez, Antonio Núñez-Roldán, Javier Martín and María Francisca González-Escribano
Abstract
We defined four major haplotypes in our population: the two major haplotypes (named haplotypes A and B) bear both the 5383_5397del variant and the two most common SNP sets found in the CEU population. Quantification analysis revealed that genotype B/B had the highest median of mRNA expression levels... | PMID: 20549518

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FEBS Letters (584)14 2010
HECT ubiquitin ligase Smurf1 targets the tumor suppressor ING2 for ubiquitination and degradation.
Jing Nie, Lin Liu, Min Wu, Guichun Xing, Shan He, Yuxin Yin, Chunyan Tian, Fuchu He and Lingqiang Zhang
Abstract
We show that the homologous to E6AP carboxyl terminus (HECT)-type ubiquitin ligase Smad ubiquitination regulatory factor 1 (Smurf1) interacts with and targets ING2 for poly-ubiquitination and proteasomal degradation. Intriguingly, the ING2 binding domain in Smurf1 was mapped to the catalytic HECT do... | PMID: 20621832

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Nanotechnology (21)25 2010
Monitoring ligand-receptor interactions by photonic force microscopy.
Sylvia Jeney, Flavio Mor, Roland Koszali, László Forró and Vincent T Moy
Abstract
We introduce a method for the acquisition of single molecule force measurements of ligand-receptor interactions using the photonic force microscope (PFM). Biotin-functionalized beads, manipulated with an optical trap, and a streptavidin-functionalized coverslip were used to measure the effect of dif... | PMID: 20516583

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FEBS Letters (584)11 2010
Curcumin inhibits hepatitis B virus via down-regulation of the metabolic coactivator PGC-1alpha.
Maya Mouler Rechtman, Ofir Har-Noy, Iddo Bar-Yishay, Sigal Fishman, Yaarit Adamovich, Yosef Shaul, Zamir Halpern and Amir Shlomai
Abstract
We show that treating HBV expressing cells with the natural phenolic compound curcumin inhibits HBV gene expression and replication. This inhibition is mediated via down-regulation of PGC-1alpha, a starvation-induced protein that initiates the gluconeogenesis cascade and that has been shown to robus... | PMID: 20434445

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Metabolic Engineering (12)3 2010
Analysis of polyhydroxybutyrate flux limitations by systematic genetic and metabolic perturbations.
Keith E J Tyo, Curt R Fischer, Fritz Simeon and Gregory Stephanopoulos
Abstract
These results imply that PHB flux is primarily controlled by the expression levels of the product forming pathway and not by the availability of precursors. These results confirm prior in vitro measurements and metabolic models and show expression level is a major affecter of PHB flux. 2009 Elsevier... | PMID: 19879956

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Metabolic Engineering (12)3 2010
Metabolic engineering of omega-3 long-chain polyunsaturated fatty acids in plants using an acyl-CoA Delta6-desaturase with omega3-preference from the marine microalga Micromonas pusilla.
James R Petrie, Pushkar Shrestha, Maged P Mansour, Peter D Nichols, Qing Liu and Surinder P Singh
Abstract
We here describe the metabolic engineering of an artificial pathway that produces 26% EPA in leaf triacylglycerol using a newly-identified Delta6-desaturase from the marine microalga Micromonas pusilla. We also demonstrate that this enzyme appears to function as an acyl-CoA desaturase that has prefe... | PMID: 20004733

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Annals of the New York Academy of Sciences (1194) 2010
Overexpression of the natural tetrapeptide acetyl-N-ser-asp-lys-pro derived from thymosin beta4 in neoplastic diseases.
Jian-Miao Liu, Maria-Concepcion Garcia-Alvarez, Jerome Bignon, Michal Kusinski, Krzysztof Kuzdak, Andrew Riches and Joanna Wdzieczak-Bakala
Abstract
Our studies revealed that AcSDKP levels were markedly elevated in neoplastic diseases including hematologic malignancies and solid neoplasms. Consistent with this finding, the enhanced activity of POP was also detected in all analyzed specimens of cancer tissues. Both these novel findings are in con... | PMID: 20536450

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Genes to Cells (15)4 2010
Tumor growth suppression in vivo by overexpression of the circadian component, PER2.
Koyomi Miyazaki, Miyuki Wakabayashi, Yasuhiro Hara and Norio Ishida
Abstract
These results suggest that sarcoma cells overexpressing PER2 suppress tumors in vivo by changing the nature of tumor cell adhesion.... | PMID: 20236181

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Genes to Cells (15)4 2010
Tumor growth suppression in vivo by overexpression of the circadian component, PER2.
Koyomi Miyazaki, Miyuki Wakabayashi, Yasuhiro Hara and Norio Ishida
Abstract
These results suggest that sarcoma cells overexpressing PER2 suppress tumors in vivo by changing the nature of tumor cell adhesion.... | PMID: 20236181

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Genes to Cells (15)4 2010
Tumor growth suppression in vivo by overexpression of the circadian component, PER2.
Koyomi Miyazaki, Miyuki Wakabayashi, Yasuhiro Hara and Norio Ishida
Abstract
These results suggest that sarcoma cells overexpressing PER2 suppress tumors in vivo by changing the nature of tumor cell adhesion.... | PMID: 20236181

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Genes to Cells (15)4 2010
Tumor growth suppression in vivo by overexpression of the circadian component, PER2.
Koyomi Miyazaki, Miyuki Wakabayashi, Yasuhiro Hara and Norio Ishida
Abstract
These results suggest that sarcoma cells overexpressing PER2 suppress tumors in vivo by changing the nature of tumor cell adhesion.... | PMID: 20236181

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Genes to Cells (15)4 2010
Tumor growth suppression in vivo by overexpression of the circadian component, PER2.
Koyomi Miyazaki, Miyuki Wakabayashi, Yasuhiro Hara and Norio Ishida
Abstract
These results suggest that sarcoma cells overexpressing PER2 suppress tumors in vivo by changing the nature of tumor cell adhesion.... | PMID: 20236181

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Genes to Cells (15)4 2010
Tumor growth suppression in vivo by overexpression of the circadian component, PER2.
Koyomi Miyazaki, Miyuki Wakabayashi, Yasuhiro Hara and Norio Ishida
Abstract
These results suggest that sarcoma cells overexpressing PER2 suppress tumors in vivo by changing the nature of tumor cell adhesion.... | PMID: 20236181

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Genes to Cells (15)4 2010
Tumor growth suppression in vivo by overexpression of the circadian component, PER2.
Koyomi Miyazaki, Miyuki Wakabayashi, Yasuhiro Hara and Norio Ishida
Abstract
These results suggest that sarcoma cells overexpressing PER2 suppress tumors in vivo by changing the nature of tumor cell adhesion.... | PMID: 20236181

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Lab On a Chip (10)4 2010
Integration and detection of biochemical assays in digital microfluidic LOC devices.
Lidija Malic, Daniel Brassard, Teodor Veres and Maryam Tabrizian
Abstract
The ambition of lab-on-a-chip (LOC) systems to achieve chip-level integration of a complete analytical process capable of performing a complex set of biomedical protocols is hindered by the absence of standard fluidic components able to be assembled. As a result, most microfluidic platforms built to... | PMID: 20126681

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Annali dell’Istituto Superiore di Sanità (46)1 2010
Molecular aspects of tumor cell migration and invasion.
Giuseppina Bozzuto, Paola Ruggieri and Agnese Molinari
Abstract
Cell migration and invasion are crucial steps in many physiological events. However, they are also implicated in the physiopathology of many diseases, such as cancer. To spread through the tissues, tumor cells use mechanisms that involve several molecular actors: adhesion receptor families, receptor... | PMID: 20348621

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Artificial Intelligence in Medicine (48)2-3 2010
Hierarchically organized layout for visualization of biochemical pathways.
Jyh-Jong Tsay, Bo-Liang Wu and Yu-Sen Jeng
Abstract
Experiment shows that our algorithm is able to give comprehensible visualization for pathways with hierarchies, cycles as well as complex structures. It clearly renders the global component structures as well as the local structure in each component. In addition, it runs very fast, and gives better... | PMID: 20036522

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Audio, Transactions of the IRE Professional Group on (4) 2010
Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks.
Philipp P Rumschinski, Steffen S Borchers, Sandro S Bosio, Robert R Weismantel and Rolf R Findeisen
Abstract
The practicability of our approach is illustrated with two case studies. The first study shows that our approach allows to conclusively rule out wrong model hypotheses. The second study focuses on parameter estimation, and shows that the proposed method allows to evaluate the global influence of mea... | PMID: 20500862

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Nature Materials (8)8 2009
Sequential click reactions for synthesizing and patterning three-dimensional cell microenvironments.
Cole A CA DeForest, Brian D BD Polizzotti and Kristi S KS Anseth
Abstract
Click chemistry provides extremely selective and orthogonal reactions that proceed with high efficiency and under a variety of mild conditions, the most common example being the copper(I)-catalysed reaction of azides with alkynes. While the versatility of click reactions has been broadly exploited, a... | PMID: 19543279

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Cancer Biology & Therapy (8)10 2009
GPRC5A: A potential tumor suppressor and oncogene
Thais Acquafreda, Kenneth J Soprano and Dianne R Soprano
Abstract
PMID: 19593893

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Biotechnology and Bioengineering (103)1 2009
Application of macroscopic principles to microbial metabolism.
J A Roels
Abstract
PMID: 19309739

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Hereditas (Beijing) (31)2 2009
[Research progress on genetic diversity of sheep PRNP and resistance breeding].
Feng F Guan, Lei L Pan, Guo-Qing GQ Shi, Shou-Ren SR Liu and Li-Guo LG Yang
Abstract
Prion protein (PrP) is a pathogeny identified in recent years, which infects both mankind and other mammals. It has been proved that PrP is a sole protein able to duplicate and propagate with itself. PrP can express in many tissues and has important physiological functions in many species of animals... | PMID: 19273420

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Renal Failure (31)5 2009
Geometric analysis of melamine crystal: a problematic molecule inducing renal failure in melamine intoxication.
Viroj Wiwanitkit
Abstract
In 2007, there was emerging toxic nephropathy due to melamine. Renal failure due to melamine crystal is noted in cases of melamine intoxication. In this article, the author studies the melamine crystal by the molecular docking technique and found that the size of crystal is a possible explanation fo... | PMID: 19839845

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Biological & Pharmaceutical Bulletin (32)1 2009
Functional analysis of aldehyde oxidase using expressed chimeric enzyme between monkey and rat.
Kunio K Itoh, Tasuku T Asakawa, Kouichi K Hoshino, Mayuko M Adachi, Kensuke K Fukiya, Nobuaki N Watanabe and Yorihisa Y Tanaka
Abstract
Aldehyde oxidase (AO) is a homodimer with a subunit molecular mass of approximately 150 kDa. Each subunit consists of about 20 kDa 2Fe-2S cluster domain storing reducing equivalents, about 40 kDa flavine adenine dinucleotide (FAD) domain and about 85 kDa molybdenum cofactor (MoCo) domain containing... | PMID: 19122276

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Applied Microbiology and Biotechnology (81)5 2009
Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism.
Cong T Trinh, Aaron Wlaschin and Friedrich Srienc
Abstract
Elementary mode analysis is a useful metabolic pathway analysis tool to identify the structure of a metabolic network that links the cellular phenotype to the corresponding genotype. The analysis can decompose the intricate metabolic network comprised of highly interconnected reactions into uniquely... | PMID: 19015845

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Artificial Life (15)1 2009
Modeling biochemical pathways using an artificial chemistry.
Kazuto K Tominaga, Yoshikazu Y Suzuki, Keiji K Kobayashi, Tooru T Watanabe, Kazumasa K Koizumi and Koji K Kishi
Abstract
We illustrate four models of biochemical pathways described in our artificial chemistry based on string pattern matching and recombination. The modeled pathways are the replication of DNA, transcription from DNA to mRNA, translation from mRNA to protein, and the oxidation of fatty acids. The descrip... | PMID: 18855562

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Artificial Life (15)1 2009
An effective hierarchical model for the biomolecular covalent bond: an approach integrating artificial chemistry and an actual terrestrial life system.
Tsutomu T Oohashi, Osamu O Ueno, Tadao T Maekawa, Norie N Kawai, Emi E Nishina and Manabu M Honda
Abstract
We propose a hierarchical model for the biomolecular covalent bond (HBCB model). This model assumes that terrestrial organisms arrange their biomolecules in a hierarchical structure according to the energy strength of their covalent bonds. It also assumes that they have evolutionarily selected the P... | PMID: 18855570

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Artificial Life (15)1 2009
A topological approach to chemical organizations.
Gil G Benkö, Florian F Centler, Peter P Dittrich, Christoph C Flamm, Bärbel M R BM Stadler and Peter F PF Stadler
Abstract
We review mathematical approaches that exploit the stoichiometric structure, which can be seen as a particular directed hypergraph, to derive an algebraic picture of chemical organizations. We then give an alternative interpretation in terms of set-valued set functions that encapsulate the productio... | PMID: 18855563

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Artificial Life (15)1 2009
Computing algebraic functions with biochemical reaction networks.
H J HJ Buisman, H M M HM ten Eikelder, P A J PA Hilbers and A M L AM Liekens
Abstract
We construct functional motifs from the bottom up. We formulate conceptual networks of biochemical reactions that implement elementary algebraic operations over the domain and range of positive real numbers. We discuss how the steady state behavior relates to algebraic functions, and study the stabi... | PMID: 18855568

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Audio, Transactions of the IRE Professional Group on (4)1 2009
Overexpression of myocilin in the Drosophila eye activates the unfolded protein response: implications for glaucoma.
Mary Anna MA Carbone, Julien F JF Ayroles, Akihiko A Yamamoto, Tatiana V TV Morozova, Steven A SA West, Michael M MM Magwire, Trudy F C TF Mackay and Robert R H RR Anholt
Abstract
We used a transgenic Drosophila model to analyze whole-genome transcriptional profiles in flies that express human wild-type or mutant MYOC in their eyes. The transgenic flies display ocular fluid discharge, reflecting ocular hypertension, and a progressive decline in their behavioral responses to l... | PMID: 19148291

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Audio, Transactions of the IRE Professional Group on (28)1 2009
A proposal for a convenient notation for P-chiral nucleotide analogues. Part 4. A relationship between the Dp/Lp notation and stereochemistry of reactions.
Michal M Sobkowski, Jacek J Stawinski and Adam A Kraszewski
Abstract
We have proposed a new D(P)/L(P) stereochemical notation for P-chiral dinucleoside monophosphate analogues based on a structural relationship between compounds. As an extension of this work, we present here applications of the D(P)/L(P) notation for tracking stereochemistry of reaction pathways invo... | PMID: 19116868

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BMC Bioinformatics (10)1 2009
Estimating parameters for generalized mass action models with connectivity information.
Ko
Abstract
In this study we introduce a constrained optimization method for estimating parameter values of biochemical pathway models using steady-state information and transient measurements. The constraints are derived from the flux connectivity relationships of the system at the steady state. Two case studi... | PMID: 19432964

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Audio, Transactions of the IRE Professional Group on (4)12 2008
Spontaneous reaction silencing in metabolic optimization.
Takashi T Nishikawa, Natali N Gulbahce and Adilson E AE Motter
Abstract
We predict computationally and analytically that any organism evolving to maximize growth rate, ATP production, or any other linear function of metabolic fluxes tends to significantly reduce the number of active metabolic reactions compared to typical nonoptimal states. The reduced number appears to... | PMID: 19057639

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Oncogene (27)55 2008
Biomechanical regulation of cell orientation and fate.
J I Lopez, J K Mouw and V M Weaver
Abstract
We examine the dynamic interaction between the developing epithelia and the extracellular matrix, and discuss how similar interactions are exploited by the genetically modified epithelium during tumor progression. We emphasize the process of mechanoreciprocity, which is a phenomenon observed during... | PMID: 19029939

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Analytical Chemistry (Washington) (80)22 2008
Modeling and quantifying biochemical changes in C6 tumor gliomas by Fourier transform infrared imaging.
Abdelilah Beljebbar, Nadia Amharref, Antoine Lévèques, Sylvain Dukic, Lydie Venteo, Laurence Schneider, Michel Pluot and Michel Manfait
Abstract
We have developed a spectroscopic model of glioma to quantify these chemical changes. The model constructed includes individual FT-IR spectra of normal and glioma brain constituents such as lipids, DNA, and proteins (measured on delipidized tissue). Modeling of FT-IR spectra yielded fit coefficients... | PMID: 18937421

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Methods in Molecular Biology (478) 2009
Transformation of oats and its application to improving osmotic stress tolerance.
Shahina B SB Maqbool, Heng H Zhong, Hesham F HF Oraby and Mariam B MB Sticklen
Abstract
Oat (Avena sativa L.), a worldwide temperate cereal crop, is deficient in tolerance to osmotic stress due to drought and/or salinity. To genetically transform the available commercial oat cultivars, a genotype-independent and efficient regeneration system from shoot apical meristems was developed us... | PMID: 19009445

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Chemical Reviews (108)11 2008
Controlling Mineral Morphologies and Structures in Biological and Synthetic Systems [Review]
Fiona C Meldrum and Helmut Cölfen
Abstract
PMID: 19006397

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Chemical Reviews (108)11 2008
Relationships between polyphosphate chemistry, biochemistry and apatite biomineralization.
Sidney J Omelon and Marc D Grynpas
Abstract
PMID: 18975924

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Biophysical Journal (95)9 2008
Different types of cell-to-cell connections mediated by nanotubular structures.
Peter Veranic, Marusa Lokar, Gerhard J Schütz, Julian Weghuber, Stefan Wieser, Henry Hägerstrand, Veronika Kralj-Iglic and Ales Iglic
Abstract
I are shorter and more dynamic than those of type II, and they contain actin filaments. They are formed when cells explore their surroundings to make contact with another cell. The nanotubes of type II are longer and more stable than type I, and they have cytokeratin filaments. They are formed when... | PMID: 18658210

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Medicine & Science in Sports & Exercise (40)11 Suppl 2008
Female marine recruit training: mood, body composition, and biochemical changes.
Harris R Lieberman, Mark D Kellogg and Gaston P Bathalon
Abstract
Over the course of USMC RT, mood and body composition improved substantially and dramatically, an indication of the effectiveness of USMC RT for altering the physical and the cognitive status of trainees.... | PMID: 18849867

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Arquivos Brasileiros de Endocrinologia & Metabologia (52)7 2008
[Oxidative stress: a review on metabolic signaling in type 1 diabetes]
Janice Sepúlveda Reis, Clara Araújo Veloso, Rafael Teixeira Mattos, Saulo Purish and José Augusto Nogueira-Machado
Abstract
We report as oxidative stress may exert deleterious effects in diabetes, as well as address current strategies in study to down-regulating vascular injury.... | PMID: 19082297

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Biosystems (94)1-2 2008
Automatic analysis of computation in biochemical reactions.
Attila Egri-Nagy, Chrystopher L Nehaniv, John L Rhodes and Maria J Schilstra
Abstract
We propose a modeling and analysis method for biochemical reactions based on finite state automata. This is a completely different approach compared to traditional modeling of reactions by differential equations. Our method aims to explore the algebraic structure behind chemical reactions using auto... | PMID: 18606208

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