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This paper describes an immunoassay-based biosensor which is composed of a disposable sensor device and a prototype electric reader with 14 × 10 × 4 cm3 in size. The sensor devices are fabricated using a 250 MHz shear horizontal surface acoustic wave (SH-SAW) delay-line on quartz substrates, which is composed of a transmitting interdigital transducer (IDT), receiving IDT, and a biochemical reaction...
Maps of protein-protein interactions (PPIs) are essential to uncover cellular processes and metabolic processes in a cell. However, various high-throughput biological experiments are time-consuming and labor-intensive, resulting in interactions of high false positive and false negative rates. The fact that most interaction networks remain sparse and incomplete motivates scientists to develop computational...
MicroRNAs are small regulatory RNAs that play an important role in diverse biological processes, by post-transcriptionally regulating the expression of messenger RNAs. Recent advances in genome synthesis technology allow for manipulation of existing genes and the creation of novel genomic sequences to specification, with a tremendous number of applications. Incorporation of miRNA sites in synthetic...
Summary form only given. Arsenic is shown to participate in many of transduction pathways in cancer cells. However, up to now, the mechanism of protein-arsenic interactions is still remaining unknown. This study aims at investigating whether the sequence composition of arsenic-binding proteins is distinct to that of background distribution. We first collected two sets of potential arsenic-binding...
Traditionally, most researches in development of new drug target focus on relationship between a target protein and a related compound by experimental or computational approaches. In addition to the translational level, it is useful tool control disease at the transcriptional level, if we identify transcription factors that regulate expression of target proteins. We introduce new methodology that...
It is well established that oxidative stress (OS) plays a major role in male infertility. OS occurs when the production of potentially destructive reactive oxygen species (ROS) exceeds the body's own natural antioxidant defenses, resulting in cellular damage. Antioxidant and trace element supplementation to infertile men has shown considerable improvement in sperm parameters; however, the issue of...
Identifying possible viral-host protein-protein interactions is an important and useful approach in developing new drugs targeting those interactions. In this article, a recently published dataset containing records of interactions between a set of HIV-1 proteins and a set of human proteins has been analyzed using association rule mining. The main objective is to identify a set of association rules...
The attachment of a glycosylphosphatidylinositol (GPI) is one of the most important posttranslational protein modifications and plays an important role in many vital reactions. It is well known that most GPI-anchored proteins (GPI-APs), such as receptors, nucleotidases, proteinases, immune antigens, and prion protein, are associated with serious human diseases. Consequently, the annotation of novel...
In this investigation, we present a novel label-free immunosensor platform based on inorganic barium strontium titanate (BST) thin film and interdigitated microelectrodes for clinical point-of-care application. The immunosensor is based on non-faradaic process, using DI water as electrolyte. As proof of concept, anti-human IgG, a common biomarker found and associated with many diseases was immobilized...
Protein-protein interactions (PPI) play an important role in cellular processes and metabolic processes within a cell. An important task is to determine the existence of interactions among proteins. Unfortunately, existing biological experimental techniques are expensive, time-consuming and labor-intensive. The network structures of many such networks are sparse, incomplete and noisy, containing many...
The aim of this study is to make a functional selection of the highly migratory orbital fat-derived stem cells (OFSCs) using a 3D collagen gel as a selection barrier. Firstly we isolated OFSCs by regular digestion. Passage 2-3 OFSCs were used to verify their multiple differentiation potentials. Then we encapsulated passage 2-6 OFSCs into collagen type I microspheres, followed by a well-established...
It is possible that protein carbonylation in the stratum corneum might be used as an index of skin photo-stress. In order to evaluate the relationship between the protein carbonyl/total protein ratio (carbonylation ratio) and skin photo-stress, the authors established a methodology by which protein carbonyl can be quantitatively analyzed using an optical technique based on surface plasmon resonance...
Mining published articles in biology and medicine is a favored means of identifying potential biomarkers in comparison to conventional reviewing process. This is made possible by the development of public literature databases and data mining algorithms. In this article, we present a method to extract novel protein interactions from online full-text articles for biomarker discovery. By evaluating support...
In extraction of information from the biomedical literature, name disambiguation of domain-specific entities, such as proteins, is one of the most important issues. The entity ambiguity with the highest dimension is the species to which an entity is associated with. Furthermore, one of the bottlenecks in inter-species gene name normalization is species disambiguation. To enhance the performance of...
In this work, we define generalized (sequence) patterns, which is based on several real Biological problems, including transcription factors (TFs) binding to transcription factor binding sites (TFBSs), cis-regulatory modules, protein domain analysis, and alternative splicing etc. Simply speaking, a generalized pattern is composed of several substrings with gaps in-between two substrings. We propose...
In this paper we propose a new algorithm to predict the phosphorylation site specificities of 478 human protein kinases based on the primary structures of the catalytic domains of these enzymes. Existing methods deduce the specificity of a protein kinase through the alignment of the amino acid sequences of phospho-sites targeted by the kinase to generate a consensus sequence or they use machine learning...
Despite intense investment growth and technology development, there is an observed bottleneck in drug discovery and development over the past decade. NIH started the Molecular Libraries Initiative (MLI) in 2004 to enlarge the pool for potential drug targets, especially from the “undruggable” part of human genome, and potential drug candidates from much broader types of drug-like small molecules. In...
Identification of genes and pathways involving in diseases and physiological conditions is a major task in systems biology. In this study, we develop a new non-parameter Ising model to integrate protein-protein interaction network and microarray data for identifying differentially expressed (DE) genes. We also propose a simulated annealing algorithm to find the optimal configuration of the Ising model...
Metallothioneins (MTs) are small cysteine-rich proteins that are involved in many diverse biological processes, which are interesting especially due to their influence on therapy of cancer. The primary structures of MTs from different organisms are various despite they have the same purpose - a transport of metal ions in organisms. Every single mutation in amino acid sequences can have a drastic effect...
The identification of unknown amino acid sequences of peptides as well as protein identification is of great significance in proteomics. Measured molecular masses from protein digestion techniques or from MS/MS analysis open the gates of proteome computational analysis. The uniqueness of a measured molecular mass or a peptide sequence plays a very important role in the fields of protein identification...
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