基于逐步提取偏最小二乘主成分的特征选择方法

特征选择技术被广泛应用于生物信息学中。通过重复利用偏最小二乘（partial least square,PLS）方法提取主成分,通过逐次选择在主成分中权重较大的基因,将PLS应用于特征选择中。将这种方法用于对肿瘤基因表达谱数据的特征基因选择中,并用提取的特征基因分类,用8个特征基因进行分类时,能达到92.5%的正确率。     

Introgressive hybridization between two species of waterstriders (Hemiptera: Gerridae: Limnoporus): geographical structure and temporal change of a hybrid zone

Where the distribution ranges of the waterstriders Limnoporus notabilis and L. dissortis meet in western Canada, extensive hybridization and introgression occurs. Multivariate ordination analyses of genetic and morphometric data by principal component analysis revealed that a single axis separating the two parent species could account for nearly all the variation in both data sets. Maps of principal component scores for both data sets revealed geographical patterns of variation reflecting specific topographic features in the region. Comparisons of morphometric data from some of the samples collected in the 1980s and from the same sites revisited in the 1990s revealed substantial changes. An ‘island’ of dissortis‐like populations inside the range of L. notabilis in interior British Columbia expanded, and a marked local protrusion of notabilis‐like phenotypes into the range of L. dissortis on the east slope of the Rocky Mountains diminished during the decade between collections. We conclude that introgressive hybridization between these two species of waterstriders is a spatially complex and highly dynamic process.     

Rapid and quantitative detection of the microbial spoilage in chicken meat by diffuse reflectance spectroscopy (600-1100 nm)

AIMS: To evaluate the feasibility of visible and short-wavelength near-infrared (SW-NIR) diffuse reflectance spectroscopy (600-1100 nm) to quantify the microbial loads in chicken meat and to develop a rapid methodology for monitoring the onset of spoilage. METHODS AND RESULTS: Twenty-four prepackaged fresh chicken breast muscle samples were prepared and stored at 21 degrees C for 24 h. Visible and SW-NIR was used to detect and quantify the microbial loads in chicken breast muscle at time intervals of 0, 2, 4, 6, 8, 10, 12 and 24 h. Spectra were collected in the diffuse reflectance mode (600-1100 nm). Total aerobic plate count (APC) of each sample was determined by the spread plate method at 32 degrees C for 48 h. Principal component analysis (PCA) and partial least squares (PLS) based prediction models were developed. PCA analysis showed clear segregation of samples held 8 h or longer compared with 0-h control. An optimum PLS model required eight latent variables for chicken muscle (R = 0.91, SEP = 0.48 log CFU g(-1)). CONCLUSIONS: Visible and SW-NIR combined with PCA is capable of perceiving the change of the microbial loads in chicken muscle once the APC increases slightly above 1 log cycle. Accurate quantification of the bacterial loads in chicken muscle can be calculated from the PLS-based prediction method. SIGNIFICANCE AND THE IMPACT OF THE STUDY: Visible and SW-NIR spectroscopy is a technique with a considerable potential for monitoring food safety and food spoilage. Visible and SW-NIR can acquire a metabolic snapshot and quantify the microbial loads of food samples rapidly, accurately, and noninvasively. This method would allow for more expeditious applications of quality control in food industries.     

Fingerprint detection and process prediction by multivariate analysis of fed‐batch monoclonal antibody cell culture data

This work presents a sequential data analysis path, which was successfully applied to identify important patterns (fingerprints) in mammalian cell culture process data regarding process variables, time evolution and process response. The data set incorporates 116 fed‐batch cultivation experiments for the production of a Fc‐Fusion protein. Having precharacterized the evolutions of the investigated variables and manipulated parameters with univariate analysis, principal component analysis (PCA) and partial least squares regression (PLSR) are used for further investigation. The first major objective is to capture and understand the interaction structure and dynamic behavior of the process variables and the titer (process response) using different models. The second major objective is to evaluate those models regarding their capability to characterize and predict the titer production. Moreover, the effects of data unfolding, imputation of missing data, phase separation, and variable transformation on the performance of the models are evaluated. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1633–1644, 2015     

Near‐infrared spectroscopic evaluation of lyophilized viral vaccine formulations

This article examines the applicability of near‐infrared spectroscopy (NIRS) to evaluate the virus state in a freeze‐dried live, attenuated vaccine formulation. Therefore, this formulation was freeze‐dried using different virus volumes and after applying different pre‐freeze‐drying virus treatments (resulting in different virus states): (i) as used in the commercial formulation; (ii) without antigen (placebo); (iii) concentrated via a centrifugal filter device; and (iv) stressed by 96 h exposure to room temperature. Each freeze‐dried product was measured directly after freeze‐drying with NIR spectroscopy and the spectra were analyzed using principal component analysis (PCA). Herewith, two NIR spectral regions were evaluated: (i) the 7300–4000 cm^?1 region containing the amide A/II band which might reflect information on the coated proteins of freeze‐dried live, attenuated viruses; and (ii) the C–H vibration overtone regions (10,000–7500 and 6340–5500 cm^?1) which might supply information on the lipid layer surrounding the freeze‐dried live, attenuated viruses. The different pre‐freeze‐drying treated live, attenuated virus formulations (different virus states and virus volumes) resulted in different clusters in the scores plots resulting from the PCA of the collected NIR spectra. Secondly, partial least squares discriminant analysis models (PLS‐DA) were developed and evaluated, allowing classification of the freeze‐dried formulations according to virus pretreatment. The results of this study suggest the applicability of NIR spectroscopy for evaluating live, attenuated vaccine formulations with respect to their virus pretreatment and virus volume. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1573–1586, 2013     

四川南充市夜鹭的巢址选择

2006年3~6月,在四川省南充市太和保护区对夜鹭的巢址选择进行了研究。野外调查了夜鹭巢47个,对照样方26个,通过主成分分析和对比分析,表明影响夜鹭巢址选择的主要因子依次为:营巢树高度、植被平均高度、巢高、竹平均直径、隐蔽度、巢上方盖度、距水(西河)距离、距白鹭巢距离、植被盖度、巢下盖度。     

核桃品种绿岭杂交后代主要性状的遗传分析与优株选择研究

为了培育出矮化、早实、丰产、优质等综合性状优于绿岭的核桃新品种,以绿岭核桃为亲本与辽宁1号、绿早进行杂交,测定了正反交组合374个杂交单株的13个性状,并对其进行了遗传分析,结果表明:杂交后代的表型性状具有较高的遗传多样性,各性状的变异系数均在17%以上,最高达72.40%;而果实相关性状的变异系数除可溶性蛋白质之外,均在20%以下。青皮率和脂肪含量的遗传传递力在4个杂交组合中均大于97%,其遗传受加性效应影响较大。果实相关性状的广义遗传力均在90%以上,说明其在遗传上是比较稳定的,可以在早代进行选择。从杂交后代中初选21个优株,采用主成分分析的方法,对其进行评价和优株选择。结果表明,以性状的累积方差贡献率达到74.3%,确定了4个反映核桃主要性状的主成分;通过计算各单株的综合评价值,在供试的21个优株中,选出了3个综合性状优良的单株,其结果与单株的实际表型相近;并发现短结果枝率、矮化指数和节间长度3个指标能够反映出核桃的矮化优良性状。     

Raman spectroscopy and chemometrics for on‐line control of glucose fermentation by Saccharomyces cerevisiae

This work presents the use of Raman spectroscopy and chemometrics for on‐line control of the fermentation process of glucose by Saccharomyces cerevisiae. In a first approach, an on‐line determination of glucose, ethanol, glycerol, and cells was accomplished using multivariate calibration based on partial least squares (PLS). The PLS models presented values of root mean square error of prediction (RMSEP) of 0.53, 0.25, and 0.02% for glucose, ethanol and glycerol, respectively, and RMSEP of 1.02 g L^?1 for cells. In a second approach, multivariate control charts based on multiway principal component analysis (MPCA) were developed for detection of fermentation fault‐batch. Two multivariate control charts were developed, based on the squared prediction error (Q) and Hotelling's T². The use of the Q control chart in on‐line monitoring was efficient for detection of the faults caused by temperature, type of substrate and contamination, but the T² control chart was not able to monitor these faults. On‐line monitoring by Raman spectroscopy in conjunction with chemometric procedures allows control of the fermentative process with advantages in relation to reference methods, which require pretreatment, manipulation of samples and are time consuming. Also, the use of multivariate control charts made possible the detection of faults in a simple way, based only on the spectra of the system. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

小波分析在人血清中葡萄糖短波近红外定量中的应用

利用小波分析对13名志愿者18个血清样品的短波近红外光谱进行去噪预处理,以血糖仪测定的血糖为参考,采用间隔偏最小二乘法（iPLS）在700nm～1060nm短波近红外波段建立血糖浓度预测模型。由相关系数（R）和预测标准差（RMSEP）对预测模型的精确度进行了评价。预测模型的相关系数为0．9654,均方根预测误差为0．2435,并和采用傅立叶变换去噪方法及iPLS建模的结果进行了比较。结果表明：小波分析预处理数据的方法能更有效地扣除噪声干扰,使模型具有更强的抗干扰能力和更高的预测精度。