An Ewald summation based multipole method

We present a method for evaluating Coulomb interactions in periodic molecular systems. The real space term in Ewald summation is accelerated using a tree code in which interactions between clusters and distant particles are approximated by multipole expansions. The performance is reported for water systems. © 2000 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69692/2/JCPSA6-113-9-3492-1.pd

Gene Expression Based Leukemia Sub-Classification Using Committee Neural Networks

Analysis of gene expression data provides an objective and efficient technique for sub-classification of leukemia. The purpose of the present study was to design a committee neural networks based classification systems to subcategorize leukemia gene expression data. In the study, a binary classification system was considered to differentiate acute lymphoblastic leukemia from acute myeloid leukemia. A ternary classification system which classifies leukemia expression data into three subclasses including B-cell acute lymphoblastic leukemia, T-cell acute lymphoblastic leukemia and acute myeloid leukemia was also developed. In each classification system gene expression profiles of leukemia patients were first subjected to a sequence of simple preprocessing steps. This resulted in filtering out approximately 95 percent of the non-informative genes. The remaining 5 percent of the informative genes were used to train a set of artificial neural networks with different parameters and architectures. The networks that gave the best results during initial testing were recruited into a committee. The committee decision was by majority voting. The committee neural network system was later evaluated using data not used in training. The binary classification system classified microarray gene expression profiles into two categories with 100 percent accuracy and the ternary system correctly predicted the three subclasses of leukemia in over 97 percent of the cases

Aberrant Signaling Pathways in Squamous Cell Lung Carcinoma

Lung cancer is the second most commonly occurring non-cutaneous cancer in the United States with the highest mortality rate among both men and women. In this study, we utilized three lung cancer microarray datasets generated by previous researchers to identify differentially expressed genes, altered signaling pathways, and assess the involvement of Hedgehog (Hh) pathway. The three datasets contain the expression levels of tens of thousands genes in normal lung tissues and squamous cell lung carcinoma. The datasets were combined and analyzed. The dysregulated genes and altered signaling pathways were identified using statistical methods. We then performed Fisher’s exact test on the significance of the association of Hh pathway downstream genes and squamous cell lung carcinoma

Development of a Platform to Monitor User's Comfort Degree for Intelligent Environments

With the development of intelligent environments, people have increasing demands for comfortable living environments. The three major factors affecting users' comfort are thermal comfort, visual comfort and air quality. This paper presents a monitoring platform of comfort degree for intelligent environments based on ZigBee wireless sensor network that measures living environment's parameters and actively controls corresponding equipments according to the information collected and users' preferences. Wireless sensor network system is divided into three layers, the main node layer, function nodes layer and leaf nodes layer, respectively. The approach to routing is through a tree topology method. A Mini2440 development board is selected as the host computer, which communicates with the main node via serial interface. The monitoring platform presented in this paper is flexible, powerful, and scalable, which can be applied to the other monitoring fields with minor modifications

Amino Acid Function and Docking Site Prediction Through Combining Disease Variants, Structure Alignments, Sequence Alignments, and Molecular Dynamics: A Study of the HMG Domain

Background: The DNA binding domain of HMG proteins is known to be important in many diseases, with the Sox sub-family of HMG proteins of particular significance. Numerous natural variants in HMG proteins are associated with disease phenotypes. Integrating these natural variants, molecular dynamic simulations of DNA interaction and sequence and structure alignments give detailed molecular knowledge of potential amino acid function such as DNA or protein interaction. Results: A total of 33 amino acids in HMG proteins are known to have natural variants in diseases. Eight of these amino acids are normally conserved in human HMG proteins and 27 are conserved in the human Sox sub-family. Among the six non-Sox conserved amino acids, amino acids 16 and 45 are likely targets for interaction with other proteins. Docking studies between the androgen receptor and Sry/Sox9 reveals a stable amino acid specific interaction involving several Sox conserved residues. Conclusion: The HMG box has structural conservation between the first two of the three helixes in the domain as well as some DNA contact points. Individual sub-groups of the HMG family have specificity in the location of the third helix, DNA specific contact points (such as amino acids 4 and 29), and conserved amino acids interacting with other proteins such as androgen receptor. Studies such as this help to distinguish individual members of a much larger family of proteins and can be applied to any protein family of interest

Effect of shape deprivation on retinal thickness in myopic mice using an OCT method

PurposeThe purpose of this study was to study in retina thickness changes in myopic mice using optical coherence tomography (OCT).MethodsThere were 18 mice in the form-deprivation myopia (FDM) group，in which the left eye was not treated as a control;18 untreated mice served as a normal control group. The diopter of all mice was measured 21 days after birth (P21), before form deprivation. After 4 weeks of form deprivation (P49), the refraction, fundus, and retinal sublayer thickness of all mice were measured.ResultsAfter 4 weeks of form deprivation, the refractive power of the right eye in the FDM group was significantly higher than that in the left eye (p < 0.05). There was no significant change in the refractive power of the left eye in the FDM group compared with the normal control group. The retina, nerve fiber layer (NFL), inner nuclear layer (INL), and outer nuclear layer (ONL) in the right eye of the FDM group were significantly thinner than those of both the FDM and control groups (p < 0.05). There was no significant change in photoreceptor (PR).ConclusionOur study highlights that the myopic mice have decreased R thickness, which might reflect the potential pathological mechanism of myopia