scholarly journals In-field whole plant maize architecture characterized by Latent Space Phenotyping

2019 ◽  
Author(s):  
Joseph L. Gage ◽  
Elliot Richards ◽  
Nicholas Lepak ◽  
Nicholas Kaczmar ◽  
Chinmay Soman ◽  
...  
Keyword(s):  
Plant Architecture ◽  
Growth Models ◽  
Principal Component ◽  
Least Squares Regression ◽  
Phenotypic Data ◽  
Efficient Manner ◽  
Biologically Relevant ◽  
Whole Plant ◽  
Latent Space ◽  
Hybrid Maize

AbstractCollecting useful, interpretable, and biologically relevant phenotypes in a resource-efficient manner is a bottleneck to plant breeding, genetic mapping, and genomic prediction. Autonomous and affordable sub-canopy rovers are an efficient and scalable way to generate sensor-based datasets of in-field crop plants. Rovers equipped with light detection and ranging (LiDar) can produce three-dimensional reconstructions of entire hybrid maize fields. In this study, we collected 2,103 LiDar scans of hybrid maize field plots and extracted phenotypic data from them by Latent Space Phenotyping (LSP). We performed LSP by two methods, principal component analysis (PCA) and a convolutional autoencoder, to extract meaningful, quantitative Latent Space Phenotypes (LSPs) describing whole-plant architecture and biomass distribution. The LSPs had heritabilities of up to 0.44, similar to some manually measured traits, indicating they can be selected on or genetically mapped. Manually measured traits can be successfully predicted by using LSPs as explanatory variables in partial least squares regression, indicating the LSPs contain biologically relevant information about plant architecture. These techniques can be used to assess crop architecture at a reduced cost and in an automated fashion for breeding, research, or extension purposes, as well as to create or inform crop growth models.

Multivariate micropollutants analysis in marine waters

1995 ◽  
Vol 32 (9-10) ◽  
pp. 341-348
Author(s):  
V. Librando ◽  
G. Magazzù ◽  
A. Puglisi
Keyword(s):  
Multivariate Data Analysis ◽  
Partial Least Squares Regression ◽  
Environmental Chemistry ◽  
Sampling Site ◽  
Principal Component ◽  
Least Squares Regression ◽  
Organic Micropollutants ◽  
Suspended Material ◽  
The Difference

The monitoring of water quality today provides a great quantity of data consisting of the values of the parameters measured as a function of time. In the marine environment, and especially in the suspended material, increasing importance is being given to the presence of organic micropollutants, particularly since some are known to be carcinogenic. As the number of measured parameters increases examining the data and their consequent interpretation becomes more difficult. To overcome such difficulties, numerous chemometric techniques have been introduced in environmental chemistry, such as Multivariate Data Analysis (MVDA), Principal Component Analysis (PCA) and Partial Least Squares Regression (PLSR). The use of the first technique in this work has been applied to the interpretation of the quality of Augusta bay, by measuring the concentration of numerous organic micropollutants, together with the classical water pollution parameters, in different sites and at different times. The MVDA has highlighted the difference between various sampling sites whose data were initially thought to be similar. Furthermore, it has allowed a choice of more significant parameters for future monitoring and more suitable sampling site locations.

Multivariate Analysis Aided Surface-Enhanced Raman Spectroscopy (MVA-SERS) Multiplex Quantitative Detection of Trace Fentanyl in Illicit Drug Mixtures Using a Handheld Raman Spectrometer

2021 ◽  
pp. 000370282110329
Author(s):  
Ling Wang ◽  
Mario O. Vendrell-Dones ◽  
Chiara Deriu ◽  
Sevde Doğruer ◽  
Peter de B. Harrington ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Principal Component ◽  
Surface Enhanced Raman Spectroscopy ◽  
Quantitative Detection ◽  
Least Squares Regression ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Sers Detection ◽  
Current Screening

Recently there has been upsurge in reports that illicit seizures of cocaine and heroin have been adulterated with fentanyl. Surface-enhanced Raman spectroscopy (SERS) provides a useful alternative to current screening procedures that permits detection of trace levels of fentanyl in mixtures. Samples are solubilized and allowed to interact with aggregated colloidal nanostars to produce a rapid and sensitive assay. In this study, we present the quantitative determination of fentanyl in heroin and cocaine using SERS, using a point-and-shoot handheld Raman system. Our protocol is optimized to detect pure fentanyl down to 0.20 ± 0.06 ng/mL and can also distinguish pure cocaine and heroin at ng/mL levels. Multiplex analysis of mixtures is enabled by combining SERS detection with principal component analysis and super partial least squares regression discriminate analysis (SPLS-DA), which allow for the determination of fentanyl as low as 0.05% in simulated seized heroin and 0.10% in simulated seized cocaine samples.

scholarly journals Investigating microcrystalline cellulose crystallinity using Raman spectroscopy

Cellulose ◽  
2021 ◽  
Author(s):  
Ana Luiza P. Queiroz ◽  
Brian M. Kerins ◽  
Jayprakash Yadav ◽  
Fatma Farag ◽  
Waleed Faisal ◽  
...  
Keyword(s):  
Raman Spectra ◽  
Microcrystalline Cellulose ◽  
Web Application ◽  
Principal Component ◽  
Raw Material ◽  
Least Squares Regression ◽  
Analysis Model ◽  
General Reference ◽  
Material Source ◽  
Univariate Model

AbstractMicrocrystalline cellulose (MCC) is a semi-crystalline material with inherent variable crystallinity due to raw material source and variable manufacturing conditions. MCC crystallinity variability can result in downstream process variability. The aim of this study was to develop models to determine MCC crystallinity index (%CI) from Raman spectra of 30 commercial batches using Raman probes with spot sizes of 100 µm (MR probe) and 6 mm (PhAT probe). A principal component analysis model separated Raman spectra of the same samples captured using the different probes. The %CI was determined using a previously reported univariate model based on the ratio of the peaks at 380 and 1096 cm−1. The univariate model was adjusted for each probe. The %CI was also predicted from spectral data from each probe using partial least squares regression models (where Raman spectra and univariate %CI were the dependent and independent variables, respectively). Both models showed adequate predictive power. For these models a general reference amorphous spectrum was proposed for each instrument. The development of the PLS model substantially reduced the analysis time as it eliminates the need for spectral deconvolution. A web application containing all the models was developed. Graphic abstract

scholarly journals Leaf life span and the leaf economic spectrum in the context of whole plant architecture

2014 ◽  
Vol 102 (2) ◽  
pp. 328-336 ◽  
Author(s):  
Erika J. Edwards ◽  
David S. Chatelet ◽  
Lawren Sack ◽  
Michael J. Donoghue
Keyword(s):  
Life Span ◽  
Plant Architecture ◽  
Leaf Life Span ◽  
Whole Plant ◽  
Leaf Economic Spectrum

Application of visible and near-infrared spectroscopy for evaluation of ewes milk with different feeds

2019 ◽  
Vol 59 (6) ◽  
pp. 1190 ◽  
Author(s):  
A. Bahri ◽  
S. Nawar ◽  
H. Selmi ◽  
M. Amraoui ◽  
H. Rouissi ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Infrared Spectroscopy ◽  
Random Forest ◽  
Near Infrared Spectroscopy ◽  
Partial Least Squares Regression ◽  
Near Infrared ◽  
Principal Component ◽  
Least Squares Regression ◽  
Random Forest Regression ◽  
Milk Samples

Rapid measurement optical techniques have the advantage over traditional methods of being faster and non-destructive. In this work visible and near-infrared spectroscopy (vis-NIRS) was used to investigate differences between measured values of key milk properties (e.g. fat, protein and lactose) in 30 samples of ewes milk according to three feed systems; faba beans, field peas and control diet. A mobile fibre-optic vis-NIR spectrophotometer (350–2500 nm) was used to collect reflectance spectra from milk samples. Principal component analysis was used to explore differences between milk samples according to the feed supplied, and a partial least-squares regression and random forest regression were adopted to develop calibration models for the prediction of milk properties. Results of the principal component analysis showed clear separation between the three groups of milk samples according to the diet of the ewes throughout the lactation period. Milk fat, protein and lactose were predicted with good accuracy by means of partial least-squares regression (R2 = 0.70–0.83 and ratio of prediction deviation, which is the ratio of standard deviation to root mean square error of prediction = 1.85–2.44). However, the best prediction results were obtained with random forest regression models (R2 = 0.86–0.90; ratio of prediction deviation = 2.73–3.26). The adoption of the vis-NIRS coupled with multivariate modelling tools can be recommended for exploring to differences between milk samples according to different feed systems, and to predict key milk properties, based particularly on the random forest regression modelling technique.

scholarly journals The Determination of Parkinson’s Drugs in Human Urine by Applying Chemometric Methods

2019 ◽  
Vol 2019 ◽  
pp. 1-8
Author(s):  
Guzide Pekcan Ertokus
Keyword(s):  
Urine Sample ◽  
Human Urine ◽  
Principal Component Regression ◽  
Principal Component ◽  
Healthy Person ◽  
Drug Analysis ◽  
Uv Spectrophotometry ◽  
Least Squares Regression ◽  
Chemometric Methods

The spectrophotometric-chemometric analysis of levodopa and carbidopa that are used for Parkinson’s disease was analyzed without any prior reservation. Parkinson’s drugs in the urine sample of a healthy person (never used drugs in his life) were analyzed at the same time spectrophotometrically. The chemometric methods used were partial least squares regression (PLS) and principal component regression (PCR). PLS and PCR were successfully applied as chemometric determination of levodopa and carbidopa in human urine samples. A concentration set including binary mixtures of levodopa and carbidopa in 15 different combinations was randomly prepared in acetate buffer (pH 3.5).). UV spectrophotometry is a relatively inexpensive, reliable, and less time-consuming method. Minitab program was used for absorbance and concentration values. The normalization values for each active substance were good (r2>0.9997). Additionally, experimental data were validated statistically. The results of the analyses of the results revealed high recoveries and low standard deviations. Hence, the results encouraged us to apply the method to drug analysis. The proposed methods are highly sensitive and precise, and therefore they were implemented for the determination of the active substances in the urine sample of a healthy person in triumph.

scholarly journals Explorative analysis on red mullet (Mullus barbatus) ageing data variability in the Mediterranean

2020 ◽  
Vol 83 (S1) ◽  
pp. 271 ◽  
Author(s):  
Pierluigi Carbonara ◽  
Walter Zupa ◽  
Aikaterini Anastasopoulou ◽  
Andrea Bellodi ◽  
Isabella Bitetto ◽  
...  
Keyword(s):  
Growth Models ◽  
Age Groups ◽  
Geographical Location ◽  
Principal Component ◽  
Age Validation ◽  
Large Variability ◽  
False Rings ◽  
Red Mullet ◽  
Mullus Barbatus ◽  
The Mediterranean

The uncertainty in age estimation by otolith reading may be at the root of the large variability in red mullet (Mullus barbatus) growth models in the Mediterranean. In the MEDITS survey, red mullet age data are produced following the same sampling protocol and otolith reading methodology. However, ageing is assigned using different interpretation schemes, including variations in theoretical birthdate and number of false rings considered, in addition to differences in the experience level of readers. The present work analysed the influence of these variations and the geographical location of sampling on red mullet ageing using a multivariate approach (principal component analysis). Reader experience was the most important parameter correlated with the variability. The number of rings considered false showed a significant effect on the variability in the first age groups but had less influence on the older ones. The effect of the theoretical birthdate was low in all age groups. Geographical location had a significant influence, with longitude showing greater effects than latitude. In light of these results, workshops, exchanges and the adoption of a common ageing protocol based on age validation studies are considered fundamental tools for improving precision in red mullet ageing.

scholarly journals Componential coding in the condition monitoring of electrical machines Part 1: Principles and illustrations using simulated typical faults

2003 ◽  
Vol 217 (8) ◽  
pp. 883-899 ◽  
Author(s):  
C J S Webber ◽  
B S Payne ◽  
F Gu ◽  
A D Ball
Keyword(s):  
Condition Monitoring ◽  
Input Data ◽  
Angular Position ◽  
Principal Component ◽  
Real Data ◽  
Companion Paper ◽  
Reference Points ◽  
Electrical Machines ◽  
Efficient Manner ◽  
Data Signal

This paper (Part 1) describes the principles of a novel unsupervised adaptive neural network anomaly detection technique, called componential coding, in the context of condition monitoring of electrical machines. Numerical examples are given to illustrate the technique's capabilities. The companion paper (Part 2), which follows, assesses componential coding in its application to real data recorded from a known machine and an entirely unseen machine (a conventional induction motor and a novel transverse flux motor respectively). Componential coding is particularly suited to applications in which no machine-specific tailored techniques have been developed or in which no previous monitoring experience is available. This is because componential coding is an unsupervised technique that derives the features of the data during training, and so requires neither labelling of known faults nor pre-processing to enhance known fault characteristics. Componential coding offers advantages over more familiar unsupervised data processing techniques such as principal component analysis. In addition, componential coding may be implemented in a computationally efficient manner by exploiting the periodic convolution theorem. Periodic convolution also gives the algorithm the advantage of time invariance; i.e. it will work equally well even if the input data signal is offset by arbitrary displacements in time. This means that there is no need to synchronize the input data signal with respect to reference points or to determine the absolute angular position of a rotating part.

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