A Computational Approach to Gene Expression Data Extraction and Analysis

The rapid advancement of DNA microarray technology has revolutionalized genetic research in bioscience. Due to the enormous amount of gene expression data generated by such technology, computer processing and analysis of such data has become indispensable. In this paper, we present a computational framework for the extraction, analysis and visualization of gene expression data from microarray experiments. A novel, fully automated, spot segmentation algorithm for DNA microarray images, which makes use of adaptive thresholding, morphological processing and statistical intensity modeling, is proposed to: (i) segment the blocks of spots, (ii) generate the grid structure, and (iii) to segment the spot within each subregion. For data analysis, we propose a binary hierarchical clustering (BHC) framework for the clustering of gene expression data. The BHC algorithm involves two major steps. Firstly, the fuzzy C-means algorithm and the average linkage hierarchical clustering algorithm are used to split the data into two classes. Secondly, the Fisher linear discriminant analysis is applied to the two classes to assess whether the split is acceptable. The BHC algorithm is applied to the sub-classes recursively and ends when all clusters cannot be split any further. BHC does not require the number of clusters to be known in advance. It does not place any assumption about the number of samples in each cluster or the class distribution. The hierarchical framework naturally leads to a tree structure representation for effective visualization of gene expressions.     

Electrocutaneous Stimulation for Sensory Communication in Rehabilitation Engineering

Physiological and psychophysical functions underlying electrocutaneous stimulation are discussed, including a comparative review of stimulus parameters and coding formats. Procedures are recommended for implementing electrotactile displays and for generating reliable, painfree sensations with a useful communications bandwidth.     

When is a device passive?

Passivity is perhaps the most basic concept in circuit theory. Unfortunately, the existing definitions of passivity are too restrictive and often contradict one another. In this paper, a new passivity definition is proposed which is applicable to all n-port and (n + 1)-terminal devices—including time-varying, non-linear, and distributed circuit elements. This definition generalizes and reconciles several recent conflicting definitions.     

6‐Gingerol inhibits fungal alpha amylase: Enzyme kinetic and molecular modeling studies

Alpha amylases are hydrolytic enzymes that are widespread in nature, being found in animals, microorganisms, and plants. These enzymes hydrolyze starch molecules into reducing sugars. Alpha amylases from microbial sources have several applications in industrial sectors. This enzyme is an effective target for the development of anti‐fungal agents. The binding affinity and enzyme inhibitory properties of 6‐gingerol toward alpha amylase have been determined. Molecular modeling and docking has been carried out, in order to get the molecular level interactions. Enzyme inhibition studies proved that 6‐gingerol is a competitive inhibitor of fungal alpha amylase. It was inferred that 6‐gingerol is a potent natural inhibitor of alpha amylase.     

Studies of IAA and IBA as fungal α‐amylase inhibitors using enzyme kinetics,molecular modeling and thermodynamics

Simple sugars like glucose and maltose are found to induce the production of aflatoxin. Since the formation of simple sugars is directly linked to α‐amylase function in fungus, it is considered that the inhibition of this enzyme is an effective approach to control the production of aflatoxins. The action of two indole derivatives such as indoleacetic acid (IAA) and indolebutyric acid (IBA) has been investigated by means of enzyme kinetics, isothermal titration calorimetric and molecular docking analysis. The results suggested that both IAA and IBA can inhibit α‐amylase in a competitive manner.     

母乳成分在-80 ℃保存过程中的稳定性研究

通过对母乳脂肪酸、维生素、活性成分以及p H值和酸度在超低温冷冻条件下的稳定性研究,最终制定伊利母乳研究实物库的母乳质量标准,以确保伊利母乳研究实物库中的母乳样本在-80℃保存过程中营养成分的损失率最小。试验结果表明,母乳在-80℃冷冻保存12个月的过程中,随着保存时间的延长,维生素含量显著降低,脂肪酸、核苷酸含量以及p H值和酸度没有发生显著性变化。母乳-80℃保存3个月时,V_B_2和V_A的含量分别减少为新鲜母乳的35%和29%,V_C含量无法检出;-80℃保存12个月时,烟酸含量减少为新鲜母乳的69%。因此,从现有检测指标来看,母乳库的质量标准应根据分析研究的母乳成分而定,若分析稳定性较差的营养成分如维生素尽量使用新鲜母乳。     

TCR Recognition of Peptide–MHC-I: Rule Makers and Breakers

T cells are a critical part of the adaptive immune system that are able to distinguish between healthy and unhealthy cells. Upon recognition of protein fragments (peptides), activated T cells will contribute to the immune response and help clear infection. The major histocompatibility complex (MHC) molecules, or human leukocyte antigens (HLA) in humans, bind these peptides to present them to T cells that recognise them with their surface T cell receptors (TCR). This recognition event is the first step that leads to T cell activation, and in turn can dictate disease outcomes. The visualisation of TCR interaction with pMHC using structural biology has been crucial in understanding this key event, unravelling the parameters that drive this interaction and their impact on the immune response. The last five years has been the most productive within the field, wherein half of current unique TCR–pMHC-I structures to date were determined within this time. Here, we review the new insights learned from these recent TCR–pMHC-I structures and their impact on T cell activation.     

Perception of safety of cyclists in Dublin City

In recent years, cycling has been recognized and is being promoted as a sustainable mode of travel. The perception of cycling as an unsafe mode of travel is a significant obstacle in increasing the mode share of bicycles in a city. Hence, it is important to identify and analyze the factors which influence the safety experiences of the cyclists in an urban signalized multi-modal transportation network. Previous researches in the area of perceived safety of cyclists primarily considered the influence of network infrastructure and operation specific variables and are often limited to specific locations within the network. This study explores the factors that are expected to be important in influencing the perception of safety among cyclists but were never studied in the past. These factors include the safety behavior of existing cyclists, the users of other travel modes and their attitude toward cyclists, facilities and network infrastructures applicable to cycling as well as to other modes in all parts of an urban transportation network. A survey of existing cyclists in Dublin City was conducted to gain an insight into the different aspects related to the safety experience of cyclists. Ordered Logistic Regression (OLR) and Principal Component Analysis (PCA) were used in the analysis of survey responses. This study has revealed that respondents perceive cycling as less safe than driving in Dublin City. The new findings have shown that the compliance of cyclists with the rules of the road increase their safety experience, while the reckless and careless attitudes of drivers are exceptionally detrimental to their perceived safety. The policy implications of the results of analysis are discussed with the intention of building on the reputation of cycling as a viable mode of transportation among all network users.     

Artificial neural networks and naturally ventilated buildings

The author found that the results obtained were reliable and indicates that neural networks can be used as a predictor for investigating window opening configurations to study the effects on interior air motion. Further study is needed in the development of the database to cover wider architectural parameters and the implementation of new types of network is also needed, as well as the need to consider variation spatial coefficients more fully.     

Artificial neural networks and naturally ventilated buildings

The author found that the results obtained were reliable and indicates that neural networks can be used as a predictor for investigating window opening configurations to study the effects on interior air motion. Further study is needed in the development of the database to cover wider architectural parameters and the implementation of new types of network is also needed, as well as the need to consider variation spatial coefficients more fully.