VPMCD: variable interaction modeling approach for class discrimination in biological systems

Data classification algorithms applied for class prediction in computational biology literature are data specific and have shown varying degrees of performance. Different classes cannot be distinguished solely based on interclass distances or decision boundaries. We propose that inter-relations among the features be exploited for separating observations into specific classes. A new variable predictive model based class discrimination (VPMCD) method is described here. Three well established and proven data sets of varying statistical and biological significance are utilized as benchmark. The performance of the new method is compared with advanced classification algorithms. The new method performs better during different tests and shows higher stability and robustness. The VPMCD is observed to be a potentially strong classification approach and can be effectively extended to other data mining applications involving biological systems.     

Behaviour influences cholesterol plasma levels in a pig model

Little is known about the relationship between feed intake behaviour and cholesterol levels in humans. This can be attributed to the fact that feed intake behaviour in humans is difficult to assess. The relationships between feed intake, feed efficiency and feed intake behaviour, and cholesterol and triglyceride levels were investigated at an average age of 187 days, in a pig model consisting of 202 Duroc barrows. Feed intake and feed intake behaviour were recorded individually and daily by means of an electronic identification system. Animals with high levels of total cholesterol also had high levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides. Animals with high levels of HDL also had high levels of LDL and triglycerides, and animals with high levels of LDL also had high levels of triglycerides. Animals with higher BW, higher backfat thickness, higher BW gain, higher gain of backfat deposition, higher feed intake, higher residual feed intake (RFI) and higher feed intake rate had higher levels of total, HDL and LDL plasma cholesterol. Results indicate that the relationship between feed intake and cholesterol levels is a long-term relationship, while the relationship between RFI and cholesterol levels is more of a short-term nature. The relationship between intake rate and cholesterol plasma levels disappeared after correction for the amount of feed consumed. Results indicate that feed intake independent of metabolic BW, growth and fatness, i.e. 'RFI', was positively correlated with cholesterol plasma levels. This suggests that eating food over and above the maintenance and growth requirements constitutes a health risk independent of the level of fatness.     

Independent component analysis of Raman spectra: Application on paraffin-embedded skin biopsies

Raman spectra provide wealthy but complex information about the chemical constituents of biological samples. Digital processing techniques are usually needed to extract the spectra of chemical constituents and their associated concentration profiles. However, spectral signatures may admit transformations from those recorded on pure constituents and these techniques require a priori knowledge of spectra to be estimated. We propose in this study to analyse paraffin-embedded skin biopsies of malignant and benign tumors dedicated to oncology researches by Raman spectroscopy and advanced signal processing methods. We show that the commonly used principal component analysis (PCA) does not give physically interpretable estimators of spectra and associated concentration profiles. Based on a linear model and taking into account the statistical properties of spectra, independent component analysis (ICA) is used to better estimate the spectra of chemical constituents. The estimators of associated concentration profiles are no longer orthogonal and have only positive values, contrary to PCA. ICA allows to model the paraffin by three Raman spectra and provides good estimators of underlying spectra of the human skin, which is of great interest in oncology since the retrieval of spectral features of different types of skin tumors is sufficient for their discrimination.     

High-fat diets: modeling the metabolic disorders of human obesity in rodents

Research Methods and Procedures: High‐fat (HF) diet feeding can induce obesity and metabolic disorders in rodents that resemble the human metabolic syndrome. However, this dietary intervention is not standardized, and the HF‐induced phenotype varies distinctly among different studies. The question which HF diet type is best to model the metabolic deterioration seen in human obesity remains unclear. Therefore, in this review, metabolic data obtained with different HF diet approaches are compiled. Both whole‐body and organ‐specific diet effects are analyzed. Results: On the basis of these results, we conclude that animal fats and ω‐6/ω‐9‐containing plant oils can be used to generate an obese and insulin‐resistant phenotype in rodents, whereas fish oil‐fed animals do not develop these disorders. Discussion: Looking at the present data, it does not seem possible to define an ideal HF diet, and an exact definition of diet composition and a thorough metabolic characterization of the HF diet effects in a researcher's specific laboratory setting remains essential for metabolic studies with this model.     

A modified resonant recognition model to predict protein-protein interaction

Proteins are fundamental components of all living cells and the protein-protein interaction plays an important role in vital movement. This paper briefly introduced the original Resonant Recognition Model (RRM), and then modified it by using the wavelet transform to acquire the Modified Resonant Recognition Model (MRRM). The key characteristic of the new model is that it can predict directly the protein-protein interaction from the primary sequence, and the MRRM is more suitable than the RRM for this prediction. The results of numerical experiments show that the MRRM is effective for predicting the protein-protein interaction. Translated from Journal of Shanghai University (Natural Science), 2006, 12(1): 69–73 [译自: 上海大学学报(自然科学版)]     

关节镜制备膝关节软骨缺损的动物模型

目的:经微创手术制备膝关节软骨缺损动物模型,减少因手术创伤造成对实验结果的影响。方法:关节镜下对9只山羊(9膝)进行关节面钻孔术,造成软骨缺损模型,对其缺损位置进行准确定位。结果:9只山羊(9膝)均在关节镜下顺利进行了关节软骨缺损模型的建立,并进行了缺损部位的定位。结论:对比开放性手术,经关节镜制备关节缺损模型是一种对实验干预最少的微创方法,有助于减少手术本身造成的实验误差。     

Nonlinear modelling of renal vasoaction

The control of blood pressure is a complex mixture of neural, hormonal and intrinsic interactions at the level of the heart, kidney and blood vessels. While experimental approaches to understanding these interactions are useful, it remains difficult to conduct experiments to quantify these interactions as the number of parameters increases. Thus, modelling of such physiological systems can offer considerable assistance. Typical mathematical models which describe the ability of the blood vessels to change their diameter (vasoconstriction) assume linearity of operation. However, due to the interaction of multiple vasocontrictive and vasodilative effectors, there is a significant nonlinear response to the influence of neural factors, particularly at higher levels of nerve activity (often seen in subjects with high blood pressure) which leads to low blood flow rates. This paper proposes a number of nonlinear mathematical models for the relationship between neural influences (sympathetic nerve activity (SNA)) and renal blood flow, using a feedback path to model the predominantly nonlinear effect of local vasoactive modulators such as nitric oxide, which oppose the action of SNA. The model structures are motivated by basic physiological principles, while the model parameters are determined using numerical optimisation techniques using open-loop data collected from rabbits. The models were verified by demonstrating correlation between experimental results and model outputs.     

Influence of the physical environment and conspecific aggression on the spatial arrangement of breeding grey seals

Understanding the habitat requirements of a species for breeding is essential for its conservation, particularly if the availability of suitable habitat is a limiting factor for population growth. This is postulated to be the case for grey seals, one of the more abundant marine apex predators in northern European waters. In common with similar studies that have investigated the habitat preferences of breeding grey seals, we use abiotic (topographical, climatological) attributes but, unlike previous work, we also incorporate behavioural variables, particularly the occurrence of aggressive interactions between females and the presence of neighbouring seals. We used two Generalized Additive Models (GAM) in a sequential and iterative fashion. The first model links the occurrence of aggression at particular points in the colony to local topography derived from a Geographical Information System (GIS), presence of neighbouring seal pups and the day of the breeding season. The output of this GAM is used as one of the explanatory variables in a GAM of daily variation in the spatial distribution of births. Although proximity of a birth site to a water source and the presence of neighbouring seal pups both had significant influences on the distribution of newborn pups over time and space, at the scale of the study site it was found that simple rules could predict pup distribution more efficiently than a complex individual-based simulation model.     

Impact of Land-use Change on Dengue and Malaria in Northern Thailand

Land-use change, a major constituent of global environmental change, potentially has significant consequences for human health in relation to mosquito-borne diseases. Land-use change can influence mosquito habitat, and therefore the distribution and abundance of vectors, and land use mediates human–mosquito interactions, including biting rate. Based on a conceptual model linking the landscape, people, and mosquitoes, this interdisciplinary study focused on the impacts of changes in land use on dengue and malaria vectors and dengue transmission in northern Thailand. Extensive data on mosquito presence and abundance, land-use change, and infection risk determinants were collected over 3 years. The results of the different components of the study were then integrated through a set of equations linking land use to disease via mosquito abundance. The impacts of a number of plausible scenarios for future land-use changes in the region, and of concomitant behavioral change were assessed. Results indicated that land-use changes have a detectable impact on mosquito populations and on infection. This impact varies according to the local environment but can be counteracted by adoption of preventive measures.     

微生物谷氨酰胺转胺酶对大鼠创伤愈合作用的实验研究

本文研究了微生物谷氨酰胺转胺酶对大鼠创伤的促愈合作用。建立大鼠背部刀割伤模型,用创面照像、透明膜描记扫描记录伤后第5、10、15、20 天创面面积,计算创伤愈合率;并用注水法测量伤腔容积,同时观测肉芽组织再生及其总蛋白、氨基已糖和己糖醛酸的含量变化情况。结果实验组创面愈合时间平均为18.1天,较对照组平均缩短了2-3天(P<0.05);创伤愈合率显著提高(P<0.05或P<0.01);伤腔容积明显缩小(P<0.05);实验组肉芽干湿重较对照组显著增加(P<0.05),肉芽中蛋白质、氨基已糖和己糖醛酸含量增加显著(P<0.05)。结果显示谷氨酰胺转胺酶具有促进大鼠皮肤创伤愈合的作用,其作用机理可能是促进肉芽组织中蛋白质,氨基多糖和胶原的合成有关。