Discrimination of Transgenic Rice Based on Near Infrared Reflectance Spectroscopy and Partial Least Squares Regression Discriminant Analysis

Near infrared reflectance spectroscopy （NIRS）, a non-destructive measurement technique, was combined with partial least squares regression discrimiant analysis （PLS-DA） to discriminate the transgenic （TCTP and mi166） and wild type （Zhonghua 11） rice. Furthermore, rice lines transformed with protein gene （OsTCTP） and regulation gene （Osmi166） were also discriminated by the NIRS method. The performances of PLS-DA in spectral ranges of 4 000-8 000 cm-1 and 4 000-10 000 cm-1 were compared to obtain the optimal spectral range. As a result, the transgenic and wild type rice were distinguished from each other in the range of 4 000-10 000 cm-1, and the correct classification rate was 100.0% in the validation test. The transgenic rice TCTP and mi166 were also distinguished from each other in the range of 4 000-10 000 cm-1, and the correct classification rate was also 100.0%. In conclusion, NIRS combined with PLS-DA can be used for the discrimination of transgenic rice.

Estimating Wheat Grain Protein Content Using Multi-Temporal Remote Sensing Data Based on Partial Least Squares Regression

Estimating wheat grain protein content by remote sensing is important for assessing wheat quality at maturity and making grains harvest and purchase policies. However, spatial variability of soil condition, temperature, and precipitation will affect grain protein contents and these factors usually cannot be monitored accurately by remote sensing data from single image. In this research, the relationships between wheat protein content at maturity and wheat agronomic parameters at different growing stages were analyzed and multi-temporal images of Landsat TM were used to estimate grain protein content by partial least squares regression. Experiment data were acquired in the suburb of Beijing during a 2-yr experiment in the period from 2003 to 2004. Determination coefficient, average deviation of self-modeling, and deviation of cross- validation were employed to assess the estimation accuracy of wheat grain protein content. Their values were 0.88, 1.30%, 3.81% and 0.72, 5.22%, 12.36% for 2003 and 2004, respectively. The research laid an agronomic foundation for GPC （grain protein content） estimation by multi-temporal remote sensing. The results showed that it is feasible to estimate GPC of wheat from multi-temporal remote sensing data in large area.

Partial Least Squares Regression Model to Predict Water Quality in Urban Water Distribution Systems

The water distribution system of one residential district in Tianjin is taken as an example to analyze the changes of water quality.Partial least squares(PLS) regression model,in which the turbidity and Fe are regarded as control objectives,is used to establish the statistical model.The experimental results indicate that the PLS regression model has good predicted results of water quality compared with the monitored data.The percentages of absolute relative error(below 15%,20%,30%) are 44.4%,66.7%,100%(turbidity) and 33.3%,44.4%,77.8%(Fe) on the 4th sampling point;77.8%,88.9%,88.9%(turbidity) and 44.4%,55.6%,66.7%(Fe) on the 5th sampling point.

Simultaneous Spectrophotometric Determination of Three Components Including Deoxyschizandrin by Partial Least Squares Regression

The computer auxiliary partial least squares is introduced to simultaneously determine the contents of Deoxyschizandin, Schisandrin, r-Schisandrin in the extracted solution of wuweizi. Regression analysis of the experimental results shows that the average recovery of each component is all in the range from 98.9% to 110.3% , which means the partial least squares regression spectrophotometry can circumvent the overlappirtg of absorption spectrums of mlulti-components, so that sctisfactory results can be obtained without any scrapple pre-separation.

Quantum partial least squares regression algorithm for multiple correlation problem

Partial least squares(PLS) regression is an important linear regression method that efficiently addresses the multiple correlation problem by combining principal component analysis and multiple regression. In this paper, we present a quantum partial least squares(QPLS) regression algorithm. To solve the high time complexity of the PLS regression, we design a quantum eigenvector search method to speed up principal components and regression parameters construction. Meanwhile, we give a density matrix product method to avoid multiple access to quantum random access memory(QRAM)during building residual matrices. The time and space complexities of the QPLS regression are logarithmic in the independent variable dimension n, the dependent variable dimension w, and the number of variables m. This algorithm achieves exponential speed-ups over the PLS regression on n, m, and w. In addition, the QPLS regression inspires us to explore more potential quantum machine learning applications in future works.

Quick assessment of chicken spoilage based on hyperspectral NIR spectra combined with partial least squares regression

Pseudomonas spp.and Enterobacteriaceae are dominant spoilage bacteria in chicken during cold storage(0°C-4°C).In this study,high resolution spectra in the range of 900-1700 nm were acquired and preprocessed using Savitzky-Golay convolution smoothing(SGCS),standard normal variate(SNV)and multiplicative scatter correction(MSC),respectively,and then mined using partial least squares(PLS)algorithm to relate to the total counts of Pseudomonas spp.and Enterobacteriaceae(PEC)of fresh chicken breasts to predict PEC rapidly.The results showed that with full 900-1700 nm range wavelength,MSC-PLS model built with MSC spectra performed better than PLS models with other spectra(RAW-PLS,SGCS-PLS,SNV-PLS),with correlation coefficient(RP)of 0.954,root mean square error of prediction(RMSEP)of 0.396 log10 CFU/g and residual predictive deviation(RPD)of 3.33 in prediction set.Based on the 12 optimal wavelengths(902.2 nm,905.5 nm,923.6 nm,938.4 nm,946.7 nm,1025.7 nm,1124.4 nm,1211.6 nm,1269.2 nm,1653.7 nm,1691.8 nm and 1693.4 nm)selected from MSC spectra by successive projections algorithm(SPA),SPA-MSC-PLS model had RP of 0.954,RMSEP of 0.397 log10 CFU/g and RPD of 3.32,similar to MSC-PLS model.The overall study indicated that NIR spectra combined with PLS algorithm could be used to detect the PEC of chicken flesh in a rapid and non-destructive way.

Modeling of daily pan evaporation using partial least squares regression

This study presented the application of partial least squares regression （PLSR） in estimating daily pan evaporation by utilizing the unique feature of PLSR in eliminating collinearity issues in predictor variables. The climate variables and daily pan evaporation data measured at two weather stations located near Elephant Butte Reservoir, New Mexico, USA and a weather station located in Shanshan County, Xinjiang, China were used in the study. The nonlinear relationship between climate variables and daily pan evaporation was successfully modeled using PLSR approach by solving collinearity that exists in the climate variables. The modeling results were compared to artificial neural networks （ANN） models with the same input variables. The resuits showed that the nonlinear equations developed using PLSR has similar performance with complex ANN approach for the study sites. The modeling process was straightforward and the equations were simpler and more explicit than the ANN black-box models.

Based on Partial Least-squares Regression to Build up and Analyze the Model of Rice Evapotranspiration

During the course of calculating the rice evapotranspiration using weather factors,we often find that some independent variables have multiple correlation.The phenomena can lead to the traditional multivariate regression model which based on least square method distortion.And the stability of the model will be lost.The model will be built based on partial least square regression in the paper,through applying the idea of main component analyze and typical correlation analyze,the writer picks up some component from original material.Thus,the writer builds up the model of rice evapotranspiration to solve the multiple correlation among the independent variables (some weather factors).At last,the writer analyses the model in some parts,and gains the satisfied result.

Incorporating empirical knowledge into data-driven variable selection for quantitative analysis of coal ash content by laser-induced breakdown spectroscopy

Laser-induced breakdown spectroscopy(LIBS)has become a widely used atomic spectroscopic technique for rapid coal analysis.However,the vast amount of spectral information in LIBS contains signal uncertainty,which can affect its quantification performance.In this work,we propose a hybrid variable selection method to improve the performance of LIBS quantification.Important variables are first identified using Pearson's correlation coefficient,mutual information,least absolute shrinkage and selection operator(LASSO)and random forest,and then filtered and combined with empirical variables related to fingerprint elements of coal ash content.Subsequently,these variables are fed into a partial least squares regression(PLSR).Additionally,in some models,certain variables unrelated to ash content are removed manually to study the impact of variable deselection on model performance.The proposed hybrid strategy was tested on three LIBS datasets for quantitative analysis of coal ash content and compared with the corresponding data-driven baseline method.It is significantly better than the variable selection only method based on empirical knowledge and in most cases outperforms the baseline method.The results showed that on all three datasets the hybrid strategy for variable selection combining empirical knowledge and data-driven algorithms achieved the lowest root mean square error of prediction(RMSEP)values of 1.605,3.478 and 1.647,respectively,which were significantly lower than those obtained from multiple linear regression using only 12 empirical variables,which are 1.959,3.718 and 2.181,respectively.The LASSO-PLSR model with empirical support and 20 selected variables exhibited a significantly improved performance after variable deselection,with RMSEP values dropping from 1.635,3.962 and 1.647 to 1.483,3.086 and 1.567,respectively.Such results demonstrate that using empirical knowledge as a support for datadriven variable selection can be a viable approach to improve the accuracy and reliability of LIBS quantification.

Quantitative structure-property relationship study of cathode volume changes in lithium ion batteries using ab-initio and partial least squares analysis

In this paper,we report a method through the combination of ab-initio calculations and partial least squares(PLS)analysis to develop the Quantitative Structure eActivity Relationship(QSAR)formulations of cathode volume changes in lithium ion batteries.The PLS analysis is based on ab-initio calculation data of 14 oxide cathodes with spinel structure LiX2O4 and 14 oxide cathodes with layered-structure LiXO_(2)(X=Ti,V,Cr,Mn,Fe,Co,Ni,Nb,Mo,Ru,Rh,Pd,Ta,Ir).Five types of descriptors,describing the characteristics of each compound from crystal structure,element,composition,local distortion and electronic level,with 34 factors in total,are adopted to obtain the QSAR formulation.According to the variable importance in projection analysis,the radius of X4t ion,and the X octahedron descriptors make major contributions to the volume change of cathode during delithiation.The analysis is hopefully applied to the virtual screening and combinatorial design of low-strain cathode materials for lithium ion batteries.

A novel procedure for identifying a hybrid QTL-allele system for hybrid-vigor improvement, with a case study in soybean(Glycine max)yield

“Breeding by design” for pure lines may be achieved by construction of an additive QTL-allele matrix in a germplasm panel or breeding population, but this option is not available for hybrids, where both additive and dominance QTL-allele matrices must be constructed. In this study, a hybrid-QTL identification approach, designated PLSRGA, using partial least squares regression(PLSR) for model fitting integrated with a genetic algorithm(GA) for variable selection based on a multi-locus, multi-allele model is described for additive and dominance QTL-allele detection in a diallel hybrid population(DHP). The PLSRGA was shown by simulation experiments to be superior to single-marker analysis and was then used for QTL-allele identification in a soybean DPH yield experiment with eight parents. Twenty-eight main-effect QTL with 138 alleles and nine QTL × environment QTL with 46 alleles were identified, with respective contributions of 61.8% and 23.5% of phenotypic variation. Main-effect additive and dominance QTL-allele matrices were established as a compact form of the DHP genetic structure. The mechanism of heterosis superior-to-parents(or superior-to-parents heterosis, SPH) was explored and might be explained by a complementary locus-set composed of OD+(showing positive over-dominance, most often), PD+(showing positive partial-to-complete dominance, less often) and HA+(showing positive homozygous additivity, occasionally) loci, depending on the parental materials. Any locus-type, whether OD+, PD + and HA+, could be the best genotype of a locus. All hybrids showed various numbers of better or best genotypes at many but not necessarily all loci, indicating further SPH improvement. Based on the additive/dominance QTL-allele matrices, the best hybrid genotype was predicted, and a hybrid improvement approach is suggested. PLSRGA is powerful for hybrid QTL-allele detection and cross-SPH improvement.

Feasibility study of assessing cotton fiber maturity from near infrared hyperspectral imaging technique

Background Fiber maturity is a key cotton quality property,and its variability in a sample impacts fiber processing and dyeing performance.Currently,the maturity is determined by using established protocols in laboratories under a controlled environment.There is an increasing need to measure fiber maturity using low-cost(in general less than $20000)and small portable systems.In this study,a laboratory feasibility was performed to assess the ability of the shortwave infrared hyperspectral imaging(SWIR HSI)technique for determining the conditioned fiber maturity,and as a comparison,a bench-top commercial and expensive(in general greater than $60000)near infrared(NIR)instrument was used.Results Although SWIR HSI and NIR represent different measurement technologies,consistent spectral characteristics were observed between the two instruments when they were used to measure the maturity of the locule fiber samples in seed cotton and of the well-defined fiber samples,respectively.Partial least squares(PLS)models were established using different spectral preprocessing parameters to predict fiber maturity.The high prediction precision was observed by a lower root mean square error of prediction(RMSEP)(<0.046),higher R_(p)^(2)(>0.518),and greater percentage(97.0%)of samples within the 95% agreement range in the entire NIR region(1000-2500 nm)without the moisture band at 1940 nm.Conclusion SWIR HSI has a good potential for assessing cotton fiber maturity in a laboratory environment.

Retrieval of Winter Wheat Canopy Carotenoid Content with Ground-and Airborne-Based Hyperspectral Data

Accurate assessment of canopy carotenoid content(CC_(x+c)C)in crops is central to monitor physiological conditions in plants and vegetation stress,and consequently supporting agronomic decisions.However,due to the overlap of absorption peaks of carotenoid(C_(x+c))and chlorophyll(C_(a+b)),accurate estimation of carotenoid using reflectance where carotenoid absorb is challenging.The objective of present study was to assess CC_(x+c)C in winter wheat(Triticum aestivum L.)with ground-and aircraft-based hyperspectral measurements in the visible and near-infrared spectrum.In-situ hyperspectral reflectance were measured and airborne hyperspectral data were acquired during major growth stages of winter wheat in five consecutive field experiments.At the canopy level,a remarkable linear relationship(R^(2)=0.95,p<0.001)existed between C_(x+c) and Ca+b,and correlation between CC_(x+c)C and wavelengths within 400 to 1000 nm range indicated that CC_(x+c)C could be estimated using reflectance ranging from visible to near-infrared wavebands.Results of Cx+c assessment based on chlorophyll and carotenoid indices showed that red edge chlorophyll index(CI red edge)performed with the highest accuracy(R^(2)=0.77,RMSE=22.27μg/cm^(2),MAE=4.97μg/cm^(2)).Applying partial least square regression(PLSR)in CC_(x+c)C retrieval emphasized the significance of reflectance within 700 to 750 nm range in CC_(x+c)C assessment.Based on CI red edge index,use of airborne hyperspectral imagery achieved satisfactory results in mapping the spatial distribution of CC_(x+c)C.This study demonstrates that it is feasible to accurately assess CC_(x+c)C in winter wheat with red edge chlorophyll index provided that C_(x+c) correlated well with C_(a+b) at the canopy scale.it is therefore a promising method for CC_(x+c)C retrieval at regional scale from aerial hyperspectral imagery.

Estimating the Texture of Purple Soils Using Vis-NIR Spectroscopy and Optimized Conversion Models

Soil texture is an indicator of soil physical structure which delivers many ecological functions of soils such as thermal regime, plant growth, and soil quality. However, traditional methods for soil texture measurement are time-consuming and labor-intensive. This study attempts to explore an indirect method for rapid estimating the texture of three subgroups of purple soils (i.e. calcareous, neutral, and acidic). 190 topsoil (0 - 10 cm) samples were collected from sloping croplands in Tongnan and Beibei Districts of Chongqing Municipality in China. Vis-NIR spectrum was measured and processed, and stepwise multiple linear regression (SMLR), partial least squares regression (PLSR), and back propagation neural network (BPNN) models were constructed to inform the soil texture. The clay fractions ranged from 4.40% to 27.12% while sand fractions ranged from 0.34% to 36.57%, hereby soil samples encompass three textural classes (i.e. silt, silt loam, and silty clay loam). For the original spectrum, the texture of calcareous and neutral purple soils was not significantly correlated with spectral reflectance and linear models (SMLR and PLSR) exhibited low prediction accuracy. The correlation coefficients and the goodness-of-fits between soil texture and the transformed spectra of all soil groups increased by continuum-removal (CR), first-order differential (R'), and second-order differential (R") transformations. Among them, the R" had the best performance in terms of improving the correlation coefficients and the goodness-of-fits. For the calcareous purple soil, the SMLR exceeds PLSR and BPNN with a higher coefficient of determination (R2) and the ratio of performance to inter-quartile distance (RPIQ) values and lower root mean square error of validation (RMSEV), but for the neutral and acidic purple soils, the PLSR model has a better prediction accuracy. In summary, the linear methods (SMLR and PLSR) are more reliable in estimating the texture of the three purple soil groups when using Vis-NIR spectroscopy inversion.

Correlation Analysis between Quality Characteristics and Fruit Mineral Element Contents in 'Fuji' Apples

[Objective] The aims were to explore the relationship between the contents of fruit mineral elements and quality features of the ＇Fuji＇ apple, screen major mineral elements of the fruit affecting fruit quality features, and set up optimum proposals of fruit mineral elements for good fruit qualities, so as to provide a theoretical basis for the reasonable orchard soil and foliar fertilizer applications to increase fruit quality and reduce the physiological diseases related to the ＇Fuji＇ apple. [Methods] The fruit mineral elements and quality indicators of ＇Fuji＂ apples were in- vestigated and analyzed, which were collected from the 153 commercial apple or- chards of ＂Fuji＇ apple located in 51 counties. The variable importance for projection （VlP） of partial least squares regression （PLS） method was used to analyze the model effect and weight analysis impact of the fruit mineral element contents to fruit quality, screen out major factors of fruit mineral elements influencing the different fruit qualities, and set up the regression equation of the fruit qualities and major fruit mineral elements. Linear programming was used to obtain optimum proposals of the fruit mineral elements to achieve good ＇Fuji＇ apple qualities. [Results] The mineral elements content and quality characteristics in ＂Fuji＇ apple fruit had great differences in the different produce regions in which the maximum content of nitro- gen, iron, zinc and boron in the ＇Fuji＇ fruit were12.06, 6.17, 7.7, and 10.08 times greater than the minimum respectively, and the differences for titratable acid and the SSC/TA ratio were 2.33 and 2.16 times respectively. The correlation analysis between the fruit mineral element contents and qualities showed that the nitrogen content of fruit had a significantly negative correlation with the soluble solid content, SSC/TA ratio and red color area, while the calcium and iron contents in the fruit were in significantly positive correlation with the soluble solid content and SSC/TA ratio. The model effect and weight analysis showed that the content of nitrogen and iron in the fruit had a greater influence on the integral fruit quality, followed by phosphorus, potassium and calcium. The variable importance for projection （VlP） technology of PLS found that the mean fruit weight was primarily affected by nitro- gen, phosphorus and potassium, and the soluble solid was primarily affected by ni- trogen, calcium and iron, while the red color area was primarily affected by nitro- gen, potassium, calcium, iron and zinc. The regression equation between fruit quality and mineral element contents showed that the mean fruit weight had a greater pos- itive effect coefficient with the content of phosphorus and potassium, and a greater negative effect coefficient with the content of nitrogen in the fruit. Moreover, the sol- uble solid had the largest negative effect coefficient with nitrogen and largest posi- tive effect coefficient with calcium and iron in the fruit. [Conclusion] The maximum content of soluble solid and titratable acid were 1.5 times more than the minimum, and nitrogen, iron, zinc and boron were 6 times more than in the ＇Fuji＇ apple fruit in the different produce regions. Therefore, it is a key technological measure to improve the overall qualities of the ＂Fuji＇ apple by decreasing the content of nitrogen, and increasing the contents of iron, phosphorus, potassium and calcium in the fruit.

Estimating purple-soil moisture content using Vis-NIR spectroscopy

Soil moisture is essential for plant growth in terrestrial ecosystems.This study investigated the visible-near infrared(Vis-NIR)spectra of three subgroups of purple soils(calcareous,neutral,and acidic)from western Chongqing,China,containing different water contents.The relationship between soil moisture and spectral reflectivity(R)was analyzed using four spectral transformations,and estimation models were established for estimating the soil moisture content(SMC)of purple soil based on stepwise multiple linear regression(SMLR)and partial least squares regression(PLSR).We found that soil spectra were similar for different moisture contents,with reflectivity decreasing with increasing moisture content and following the order neutral>calcareous>acidic purple soil(at constant moisture content).Three of the four spectral transformations can highlight spectral sensitivity to SMC and significantly improve the correlation between the reflectance spectra and SMC.SMLR and PLSRmethods provide similar prediction accuracy.The PLSR-based model using a first-order reflectivity differential(R?)is more effective for estimating the SMC,and gave coefficient of determination(v2),root mean square errors of validation(RMSEV),and ratio of performance to inter-quartile distance(RPIQ)values of 0.946,1.347,and 6.328,respectively,for the calcareous purple soil,and 0.944,1.818,and 6.569,respectively,for the acidic purple soil.For neutral purple soil,the best prediction was obtained using the SMLR method with R?transformation,yieldingv2,RMSEV and RPIQ values of 0.973,0.888 and 8.791,respectively.In general,PLSR is more suitable than SMLR for estimating the SMC of purple soil.

Measuring Spatio-temporal Characteristics of City Expansion and Its Driving Forces in Shanghai from 1990 to 2015

Urbanization has both direct and indirect impacts on land use change, and analyzing spatio-temporal characteristics of land use change is essential for understanding these impacts. By comparing Landsat TM images, this paper examines the changes of land use structure and landscape patterns in Shanghai from 1990 to 2015. It finds that the city doubled in size, with the growth of isolated construction land being most significant among eight land use types. A land use change matrix was established and landscape indices were selected to evaluate the change of spatial structure in Shanghai. In order to identify the main driving forces of city expansion in Shanghai, this research ran partial least square regression models to assess the impact of 10 social-economic factors on land use change of Shanghai from 1990 to 2015. It then conducted bivariate correlation analysis to explore the drivers of change of various land use types: urban settlement, rural settlement and isolated construction land. Besides quantitative analysis, this paper analyzes the influence of policy-dimensional factors in land use change. It concludes with future potential research topics on land use change in a rapidly urbanizing context.

Monthly Changes in the Influence of the Arctic Oscillation on Surface Air Temperature over China

Partial Least Squares Regression （PLSR） is used to study monthly changes in the influence of the Arctic Oscillation （AO） on spring, summer and autumn air temperature over China with the January 500 hPa geopotential height data from 1951 to 2004 and monthly temperature data from January to November at 160 stations in China. Several AO indices have been defined with the 500-hPa geopotential data and the index defined as the first principal component of the normalized geopotential data is best to be used to study the influence of the AO on SAT （surface air temperature） in China. There are three modes through which the AO in winter influences SAT in China. The influence of the AO on SAT in China changes monthly and is stronger in spring and summer than in autumn. The main influenced regions are Northeast China and the Changjiang River drainage area.

Estimation of Some Chemical Properties of an Agricultural Soil by Spectroradiometric Measurements

The contents of nitrogen and organic carbon in an agricultural soil were analyzed using reflectance measurements （n = 52） performed with an ASD FieldSpee-Ⅱ spectroradiometer. For parameter prediction, empirical models based on partial least squares （PLS） regression were defined from the measured reflectance spectra （0.4 to 2.4 μm）. Here, reliable estimates were obtained for nitrogen content, but prediction accuracy was only moderate for organic carbon. For nitrogen, the real spatial pattern of within-field variability was reproduced with high accuracy. The results indicate the potential of this method as a quick screening tool for the spatial assessment of nitrogen and organic carbon, and therefore an appropriate alternative to time- and cost-intensive chemical analysis in the laboratory.

Rapid estimation of soil heavy metal nickel content based on optimized screening of near-infrared spectral bands

In near-infrared spectroscopy,the traditional feature band extraction method has certain limitations.Therefore,a band extraction method named the three-step extraction method was proposed.This method combines characteristic absorption bands and correlation coefficients to select characteristic bands corresponding to various spectral forms and then uses stepwise regression to eliminate meaningless variables.Partial least squares regression(PLSR)and extreme learning machine(ELM)models were used to verify the effect of the band extraction method.Results show that the differential transformation of the spectrum can effectively improve the correlation between the spectrum and nickel(Ni)content.Most correlation coefficients were above 0.7 and approximately 20%higher than those of other transformation methods.The model effect established by the feature variable selection method based on comprehensive spectral transformation is only slightly affected by the spectral transformation form.Infive types of spectral transformation,the RPD values of the proposed method were all within the same level.The RPD values of the PLSR model were concentrated between 1.6 and 1.8,and those of the ELM model were between 2.5 and2.9,indicating that this method is beneficial for extracting more complete spectral features.The combination of the three-step extraction method and ELM algorithm can effectively retain important bands associated with the Ni content of the soil.The model based on the spectral band selected by the three-step extraction method has better prediction ability than the other models.The ELM model of the first-order differential transformation has the best prediction accuracy(RP^2=0.923,RPD=3.634).The research results provide some technical support for monitoring heavy metal content spectrum in local soils.