New MSPQC-PLS method for the early clinic identification of commonly encountered Candida species

The early clinic identification of commonly encountered Candida species became more important with the increasing human candidiasis. In this paper, a new MSPQC-PLS (multi-channel series piezoelectric quartz crystal biosensor combined with partial least square) method was proposed for early identification of the most frequent Candida species encountered in human pathology. This method was based on these fact that (1) MSPQC method is a real-time monitoring method based on the sensitive frequency response to the change of electric parameters of the culture media caused by the growth of microorganisms; (2) various Candida species produce significantly different types of frequency curves in 1 or 2 days’ culture period; (3) this difference can be identified by the partial least square technique. Using the proposed method, three species (Candida albicans, Candida glabrata, and Candida tropicalis) from a collection of 53 clinical strains of Candida, isolated from hospitalized patients, were identified with a classification rate of 98.1%. New proposed MSPQC-PLS method is simple, rapid and convenient to perform. It can identify clinical Candida species directly without passing through pure culture process. This will save identification time greatly. It could be popularized in clinical microbiology laboratories.     

Quantum chemical calculation of vibrational spectra of large molecules--Raman and IR spectra for Buckminsterfullerene

In this work we demonstrate how different modern quantum chemical methods can be efficiently combined and applied for the calculation of the vibrational modes and spectra of large molecules. We are aiming at harmonic force fields, and infrared as well as Raman intensities within the double harmonic approximation, because consideration of higher order terms is only feasible for small molecules. In particular, density functional methods have evolved to a powerful quantum chemical tool for the determination of the electronic structure of molecules in the last decade. Underlying theoretical concepts for the calculation of intensities are reviewed, emphasizing necessary approximations and formal aspects of the introduced quantities, which are often not explicated in detail in elementary treatments of this topic. It is shown how complex quantum chemistry program packages can be interfaced to new programs in order to calculate IR and Raman spectra. The advantages of numerical differentiation of analytical gradients, dipole moments, and static, as well as dynamic polarizabilities, are pointed out. We carefully investigate the influence of the basis set size on polarizabilities and their spatial derivatives. This leads us to the construction of a hybrid basis set, which is equally well suited for the calculation of vibrational frequencies and Raman intensities. The efficiency is demonstrated for the highly symmetric C(60), for which we present the first all-electron density functional calculation of its Raman spectrum.     

The differentiation and identification of pathogenic bacteria using FT-IR and multivariate statistical analysis

Correspondence analysis was used to classify the pattern-like FT-IR spectra of intact bacteria. The analysis was performed on a data set of approximately 80 normalized spectral derivatives of a selection of pathogenic bacteria. The correspondence analysis proved that the various different bacterial species were clustering in distinct regions of the correspondence maps suggesting that there do exist correlations between spectral data and biochemical/microbiological classification.     

Application of vibrational spectroscopy techniques for material identification from fire debris

The primary goal of this research is to demonstrate the use of vibrational spectroscopy techniques as a tool for the identification of materials post fire. This paper discusses the use micro-Raman spectroscopy and ATR-FTIR to identify materials found in fire debris. The polymeric materials under study were high density and low density polyethylene (HDPE and LDPE), polyvinyl chloride (PVC), polymethyl methacrylate (PMMA) and cotton. These are commonly materials found in households around the world, their identification from the debris provides useful forensic information on the spatial distribution of fuels in a fire compartment, thus allowing for accurate analysis and modelling. Earlier work has established Raman spectroscopy to be a very good tool for material identification post fire. The addition of ATR-FTIR spectroscopy as a technique in developing this novel tool for identification of materials post fire has established vibrational spectroscopy in the area of fire investigation. This study indicated that the limitations associated with Raman spectroscopy in post fire identification, could be made insignificant by the strengths of ATR-FTIR spectroscopy and vice versa. To further establish the validity of this identification process principal component analysis was used to discriminate between the spectrum of the burnt materials and an error analysis computed. Both techniques demonstrated that identification could be done with very minimal confusion between the materials studied.     

Fourier-Filtering Methods of Interference-Patterned Spectra in Multivariate Calibration and Prediction for Sample Identification and Thickness Determination

Summary: Determining the thickness or identification of polymer materials with building a multivariate calibration model is based on the near infrared spectral information of the material. The spectrum of a thin plastic sheet is modulated by the interference of multiply reflected beams from the boundary surfaces and causes a disturbing signal component. On one hand, this yields unidentifiable samples or introduces large errors in the sample prediction set. On the other hand, interference-patterned spectra have to be excluded from the calibration set. Fourier-transformation of an interference-patterned spectrum vs. wave number leads to a Fourier-spectrum as a function of the optical path length (OPL) containing a well recognizable interference peak. After replacing these interference-components and performing an inverse Fourier-transformation, the spectra can be used for calibration or prediction. Two types of replacing were studied: the spline-interpolation on Fourier- spectrum vs. OPL and a novel method based on linear approximation between Fourier-spectra and thickness values. The effectiveness of each filtering method was tested on low-density polyethylene and polypropylene sheets.     

Application of multi-way data analysis on excitation-emission spectra for plant identification

The ability to distinguish among diets fed to Damascus goats using excitation-emission luminescence spectra was investigated. These diets consisted of Medicago sativa L. (alfalfa), Trifolium spp. (clover), Pistacia lentiscus, Phyllirea latifolia and Pinus brutia. The three-dimensional luminescence response surface from phosphate buffered saline (PBS) extracts of each material was analyzed using muti-way analysis chemometric tools (MPCA) and parallel factor analysis (PARAFAC). Using three principal components, the spectra from each diet material were distinguished. Additionally, fecal samples from goats fed diets of either alfalfa or clover hays were investigated. The application of MPCA and PARAFAC to these samples using models derived from the pre-digested diet materials was strongly suggestive of the utility of similarly derive training samples for the elucidation of botanical diet composition for animals.     

Identification of Pulsatilla chinensis (Bge.) Regel and look-alike species by UHPLC-TOF-MS using multivariate statistical analysis

Pulsatillae Radix, the root of Pulsatilla chinensis (Bge.) Regel, is recorded in the Pharmacopoeia of the People's Republic of China and has been widely used for its pharmacological activities, such as anti-inflammatory, antioxidant, antibacterial, antitumor, and cardiovascular benefits. However, there are several look-alike species that can be marketed as Pulsatillae Radix. To distinguish P. chinensis (Bge.) Regel from its look-alikes, viz. Pulsatilla cernua (Thunb.) Bercht et Opiz., Pulsatilla dahurica (Fisch.) Spreng., Anemone tomeutosa (Maxim.) Pei., and Rhaponticum uniflorum (L.) DC, we used ultra high performance liquid chromatography with time-of-flight mass spectrometry combined with principal component analysis to compare their chemical compositions. Four ions, a (RT 8.98 min, m/z 1381.6671), b (RT 10.64 min, m/z 1219.6143), c (RT 11.52 min, m/z 1217.5978), and d (RT 13.6 min, m/z 749.4463), from P. chinensis (Bge.) Regel were identified as potential chemical markers to distinguish it from look-alike species using an unsupervised statistical model combined with orthogonal partial least-squares discriminant analysis. The results of this study provide an effective method for identifying and distinguishing P. chinensis (Bge.) Regel from similar plants.     

Identification of carbonyl species of weathered LDPE films by curve fitting and derivative analysis of IR spectra

We describe the examination of the weathering degradation of LDPE (low density polyethylene - locally produced B24/2 and imported LDPE 2100T), supplied by two different manufacturers and processed into films for greenhouse coverings, over several months in a sub-Saharan region of Algeria. The three IR regions most affected by weathering degradation are 800–1100 cm⁻¹, 1680–1800 cm⁻¹ and 3300–3600 cm⁻¹. The IR spectral region most affected by the aging process is the carbonyl region. Curve fitting combined with derivative spectroscopy revealed that the composite carbonyl band encompasses more than 10 different oxidation products. The most significant among these in terms of absorbance are carboxylic acids, ketones, aldehydes and esters. The oxidation kinetics with respect to the type of LDPE film shows that B24/2 LDPE undergoes less oxidization than LDPE 2100 T. Calculating the concentrations of different carbonyl species compared to their respective absorbances indicates that the aldehydes are the predominant component of the final compound, rather than the carboxylic acids.     

Chemometrical strategies for feature selection and data compression applied to NIR and MIR spectra of extra virgin olive oils for cultivar identification

The possibility provided by Chemometrics to extract and combine (fusion) information contained in NIR and MIR spectra in order to discriminate monovarietal extra virgin olive oils according to olive cultivar (Casaliva, Leccino, Frantoio) has been investigated.Linear discriminant analysis (LDA) was applied as a classification technique on these multivariate and non-specific spectral data both separately and jointly (NIR and MIR data together).In order to ensure a more appropriate ratio between the number of objects (samples) and number of variables (absorbance at different wavenumbers), LDA was preceded either by feature selection or variable compression. For feature selection, the SELECT algorithm was used while a wavelet transform was applied for data compression.Correct classification rates obtained by cross-validation varied between 60% and 90% depending on the followed procedure. Most accurate results were obtained using the fused NIR and MIR data, with either feature selection or data compression.Chemometrical strategies applied to fused NIR and MIR spectra represent an effective method for classification of extra virgin olive oils on the basis of the olive cultivar.     

聚合酶链式反应-限制性片段长度多态性和芯片生物分析技术用于渤海地区鱼种鉴定

以渤海湾具有重要商业价值的9种海鱼(小黄鱼、花鲈、蓝点马鲛、鲐、钝吻黄盖鲽、棘头梅童鱼、许氏平鲉、高眼鲽和长蛇鲻)为研究对象,利用聚合酶链式反应(PCR)-限制性片段长度多态性(RFLP)和芯片生物分析技术对其进行鱼种鉴定。首先提取其基因组脱氧核糖核酸(DNA),对其细胞色素b的特定片段(464 bp)进行扩增,然后选择DdeI、HaeIII和NlaIII3种限制性内切酶进行酶切,并利用芯片生物分析技术得到酶切产物的特异图谱和确切的片段大小,从而有效区分了9种海鱼。研究结果表明,PCR-RFLP和芯片生物分析技术在鱼种鉴定上具有精确、鉴别和快速三大优势,可为鱼类食品检测提供科学依据。     

Comparison of multivariate calibration models for glucose,urea, and lactate from near-infrared and Raman spectra

Partial least-squares (PLS) calibration models have been generated from a series of near-infrared (near-IR) and Raman spectra acquired separately from sixty different mixed solutions of glucose, lactate, and urea in aqueous phosphate buffer. Independent PLS models were prepared and compared for glucose, lactate, and urea. Near-IR and Raman spectral features differed substantially for these solutes, with Raman spectra enabling greater distinction with less spectral overlap than features in the near-IR spectra. Despite this, PLS models derived from near-IR spectra outperformed those from Raman spectra. Standard errors of prediction were 0.24, 0.11, and 0.14 mmol L⁻¹ for glucose, lactate, and urea, respectively, from near-IR spectra and 0.40, 0.42, and 0.36 mmol L⁻¹ for glucose, lactate, and urea, respectively, from Raman spectra. Differences between instrumental signal-to-noise ratios were responsible for the better performance of the near-IR models. The chemical basis of model selectivity was examined for each model by using a pure component selectivity analysis combined with analysis of the net analyte signal for each solute. This selectivity analysis showed that models based on either near-IR or Raman spectra had excellent selectivity for the targeted analyte. The net analyte signal analysis also revealed that analytical sensitivity was higher for the models generated from near-IR spectra. This is consistent with the lower standard errors of prediction.     

A Background and noise elimination method for quantitative calibration of near infrared spectra

A new hybrid algorithm is proposed to eliminate the varying background and noise simultaneously for multivariate calibration of near infrared (NIR) spectral signals. The method is based on the use of multi-resolution, which is one of the main advantages provided by wavelet transform. The signals are firstly split into different frequency components, which keep the same data points of the original signals. In conjunction with a modified uninformative variable elimination (mUVE) criterion, the new method can be used to remove the low-frequency varying background and the high-frequency noise simultaneously. The method is successfully applied to simulated spectral data set and experimental NIR spectral data, resulting in more parsimonious multivariate models with higher precision. In addition, the proposed strategy can be applied to other spectral signals as well.     

Structural and IR Spectroscopic Analysis of Sol-Gel Processed CuFeMnO4 Spinel and CuFeMnO4/Silica Films for Solar Absorbers

Black colored CuFeMnO₄ spinel powders and films were prepared using sol-gel process from Mn-acetate and Fe- and Cu-chloride precursors. Films were deposited by dip-coating technique and heat-treated at 500°C. For CuFeMnO₄/silica films 3-aminopropyl-triethoxysilane (3-APTES) or tetraethoxysilane (TEOS) were used in molar proportion (Mn : Cu : Fe) : silica = 1 : 1. Films and powders were prepared by heating at 500°C. IR spectroscopic measurements were employed to follow the hydrolysis-condensation reactions in (Mn : Cu : Fe)/3-APTES sols hydrolysed with water, and (Mn : Cu : Fe)/TEOS sols hydrolysed with (NH₃)_aq (Stöber processing). The resulting coatings were examined with transmission electron microscopy (TEM) combined with electron dif-fraction analyses, Rutherford back scattering (RBS) and proton induced X-ray emission (PIXE) techniques. Results revealed that (Mn : Cu : Fe)/3-APTES films had a composite structure consisting of the upper Cu_1.4Mn_1.6O₄ spinel and the lower amorphous SiO₂ layer. RBS measurements confirmed the composite structure, showing also that the composition of the film was Mn : Cu : Fe = 1 : 0.96 : 0.29, i.e. close to the precursors ratio Mn : Cu : Fe = 3 : 3 : 1. (Mn : Cu : Fe)/TEOS films prepared from sols which were catalysed with (NH₃)_aq consisted of amorphous monodispersed spherical SiO₂ particles with a size of about 400–420 nm. Solar absorbance (a _s) and thermal emittance (e _T) values of CuFeMnO₄ (500°C) and (Mn : Cu : Fe)/TEOS films (500°C) showed that CuFeMnO₄ films could be used as potential selective coatings for solar absorbers in solar collector systems.     

Rapid identification of chemical compositions from three species of Siegesbeckiae Herba by ultra-performance liquid chromatography-electrospray ionization-quadrupole time of flight-mass spectrometry in combination with deoxyribonucleic acid barcoding

Siegesbeckiae Herba, a traditional Chinese medicine, originates from Siegesbeckia orientalis, S. glabrescens, and S. pubescens in the Pharmacopoeia of the People's Republic of China. However, accurate identification of decoction pieces from the three plants remains a challenge. In this study, 26 batches of Siegesbeckiae Herba were identified by deoxyribonucleic acid barcoding, and their chemical compositions were determined using ultra-performance liquid chromatography-electrospray ionization-quadrupole time of flight-mass spectrometry. The results showed that the internal transcribed spacer 2 and internal transcribed spacer 1–5.8 S- internal transcribed spacer 2 sequences could distinguish three species. In total, 48 compounds were identified including 12 marker compounds screened for three species using the partial least square discriminant analysis. Among these, two diterpenoids 16-O-malonylkirenol and 15-O-malonylkirenol, and a novel diterpenoid 15,16-di-O-malonylkirenol were isolated and identified. A convenient method for the identification of Siegesbeckiae Herba was established using kirenol and 16-O-acetlydarutoside as control standards by thin-layer chromatography. Unexpectedly, none of the batches of S. orientalis contained kirenol, which did not meet the quality standards of Siegesbeckiae Herba, suggesting that the rationality of kirenol as a quality marker for S. orientalis should be further investigated. The results of this study will contribute to the quality control of Siegesbeckiae Herba.     

Multivariate control charts based on NAS and mid‐infrared spectroscopy for quality control of B5 blends of methyl soybean biodiesel in diesel

In this work, mid‐infrared spectroscopy and multivariate control charts based on net analyte signal were applied for quality control of B5 blends of biodiesel/diesel (5% biodiesel/95% diesel). Control charts were constructed using instrumental signal decomposition, generating three charts: the net analyte signal chart for monitoring the analyte of interest (methyl soybean biodiesel); the interference chart, which corresponds to the contribution of all other compounds in the diesel sample (diesel); and the residual chart, which corresponds to non‐systematic variations. Statistical limits were established for each developed chart, using samples inside quality specifications (normal operation conditions). To validate multivariate control charts, new samples were analyzed. The new samples represented samples in‐control and samples out‐of‐control in relation to the content of biodiesel, adulterated biodiesel with severe vegetable oils and adulterated diesel with residual automotive lubricant oil, kerosene, and gasoline. The results obtained show an excellent distinction between the samples inside and out of the quality specifications, with 91% and 100% correctly classified, respectively, which demonstrates that the methodology developed is a viable alternative for quality monitoring of this type of fuel. Copyright © 2015 John Wiley & Sons, Ltd.     

Use of near-infrared reflectance spectroscopy in predicting nitrogen,phosphorus and calcium contents in heterogeneous woody plant species

Near-infrared reflectance spectroscopy was applied to determine nitrogen (N), phosphorus (P) and calcium (Ca) content in leaf samples of 18 woody species. A total of 183 samples from mountain, riparian and dry areas from the Central–Western Iberian Peninsula were collected for this purpose. The wide intervals of variation observed in nutrient concentrations (6.6–45.0 g kg^–1 for N, 0.24–2.97 g kg^–1 for P, and 1.00–20.06 g kg^–1 for Ca) were due to the great heterogeneity of the samples. To develop calibration equations, multiple linear regression, and partial least-squares regression (PLSR) were used. In both cases, three mathematical transformations of the data were applied: log1/R and first and second derivatives. The best calibration statistics were obtained using PLSR and derivative transformations (second derivative for N and first derivative for P and Ca). The following coefficients of multiple determination (R²) and standard errors of cross validation were obtained: 0.99 and 0.93 for N, 0.94 and 0.15 for P, and 0.95 and 0.88 for Ca. In the external validation the standard errors of prediction obtained were 0.76 (N), 0.11 (P) and 0.60 (Ca).     

High-throughput capillary electrophoresis for the identification and differentiation of seven species of Eimeria from chickens

A capillary electrophoretic approach has been evaluated for the identification of seven currently recognised species of Eimeria infecting chickens. The second internal transcribed spacer of ribosomal DNA is PCR-amplified from any of the seven species using a single set of oligonucleotide primers (one of which is fluorescently labelled). The amplicons are heat-denatured and subjected to capillary electrophoresis in a MegaBACE 1000 (Amersham). The chromatograms captured are stored electronically and then analysed using MegaBACE Fragment Profiler software. Using control DNA samples representing monospecific lines of Eimeria, specific peaks in the chromatograms were defined for the unequivocal identification of each of the seven species and their differentiation. Electrophoretic reading and analysis are carried out automatically, thus making it a time- and cost-effective method. This procedure should find applicability as a tool for the quality control of Eimeria vaccines, the monitoring of coccidiosis outbreaks and the high-throughput analysis of oocyst samples for epidemiological surveys.     

Comparison of calculated and experimental FTIR spectra of specifically labeled ubiquinones

Density functional theory has been used to calculate harmonic vibrational frequencies and intensities of unlabeled and labeled ubiquinone-1 in both the gas phase and in solution (CCl₄). Calculations were undertaken using the B3LYP functional and the 6-31G+(d) basis set. Calculations using larger basis sets did not significantly alter the calculated spectra. Calculations for ubiquinone-2, -3, -6 or -8 gave similar results.Calculations show that eight ubiquinone-1 conformations, which differ only in the orientation of their methoxy groups, are likely to coexist in solution at room temperature. The calculated infrared spectra for these eight conformations vary considerably. However, by averaging the Boltzmann weighted spectra for the eight conformers, composite spectra are calculated that successfully model both the frequency and intensity information inherent in the experimental FTIR spectra obtained for both unlabeled and labeled ubiquinones in solution.The calculated spectra presented here provide a robust foundation from which to consider and assess future modeling of the vibrational properties of ubiquinones embedded in protein complexes.     

Comparison and joint use of near infrared spectroscopy and Fourier transform mid infrared spectroscopy for the determination of wine parameters

A study of the statistic characteristics of the multidetermination of several enological parameters - namely, alcoholic degree, volumic mass, total acidity, glycerol, total polyphenol index, lactic acid and total sulphur dioxide - depending on the spectroscopic zone employed, was carried out. The two techniques used were near infrared spectroscopy (NIRS) and Fourier transform mid infrared spectroscopy (FT-MIRS). The combination of these two regions (sum of their spectra) was also studied. NIRS yielded better results, but the use of both zones improved the determination of glycerol and total sulphur dioxide. The training and validation sets used for developing general equations were built with samples from different apellation d’origine, different wine types, etc. Partial least squares regression was used for multivariate calibration, using systematic cross validation in the calibration stage and external validation in the testing stage. Sample preparation was not required.