A multivariate approach to investigate the NMR CPMG pulse sequence for analysing low MW species in polymers.

Detection and quantification of low molecular weight components in polymeric samples via nuclear magnetic resonance (NMR) spectroscopy can be difficult due to overlapping signal caused by line broadening characteristics of polymers. A way of overcoming this problem could be the exploitation of the difference in relaxation between small molecules and macromolecular species, such as the application of a T2 filter by using the Carr-Purcell-Meiboom-Gill (CPMG) spin-echo pulse sequence. This technique, largely exploited in metabolomics studies, is applied here to material sciences. A Design of Experiments approach was used for evaluating the effect of different acquisition parameters (relaxation delay, echo time and number of cycles) and sample-related ones (concentration and polymer molecular weight) on selected responses, with a particular interest in performing a reliable quantitative analysis. Polymeric samples containing small molecules were analysed by NMR with and without the application of the filter, and analysis of variance was used to identify the most influential parameters. Results indicated that increasing the polymer concentration, hence sample viscosity, further attenuates polymer signals in CPMG experiments because the T2 of those signals tends to decrease with increasing viscosity. The signal-to-noise ratio measured for small molecules can undergo a minimum loss when specific parameters are chosen in relation to the polymer molecular weight. Furthermore, the difference in dynamics between aliphatic and aromatic nuclei, as well as between mobile and stiff polymers, translates into different results in terms of polymer signal reduction, suggesting that the relaxation filter can also be used for obtaining information on the polymer structure.

Investigation of a highly compact intracavity actively Q-switched cascade diamond Raman laser.

A laser diode (LD) pumped intracavity chemical vapor deposition (CVD) diamond cascade Raman laser is reported here. By rotating a Brewster plate (BP) in the laser resonator, the Raman laser with tunable output coupling rate is achieved. The highly compact diamond laser emitted 1240 nm and 1485 nm Stokes light simultaneously via optimization of the pumping direction. The slope efficiency of the intracavity diamond laser is improved by optimizing the output coupling rate and adjusting the repetition rate of the 1064 nm fundamental laser. Ultimately, the maximum slope efficiency of the first Stokes light (1240 nm) is 16.8%, and the corresponding output power is about 0.6 W. The maximum peak power is 2.5 kW when the power of 808 nm LD is 34.7 W.

Highly Diastereoselective Synthesis of a HCV NS5B Nucleoside Polymerase Inhibitor.

An asymmetric synthesis of HCV NS5B nucleoside polymerase inhibitor (1) is described. This novel route features several remarkably diastereoselective and high-yielding transformations, including construction of the all-carbon quaternary stereogenic center at C-2 via a thermodynamic aldol reaction. A subsequent glycosylation reaction with activated uracil via C-1 phosphate and installation of the cyclic phosphate group using an achiral phosphorus(III) reagent followed by oxidation provides 1.

Chemometrics for ion mobility spectrometry data: recent advances and future prospects.

Historically, advances in the field of ion mobility spectrometry have been hindered by the variation in measured signals between instruments developed by different research laboratories or manufacturers. This has triggered the development and application of chemometric techniques able to reveal and analyze precious information content of ion mobility spectra. Recent advances in multidimensional coupling of ion mobility spectrometry to chromatography and mass spectrometry has created new, unique challenges for data processing, yielding high-dimensional, megavariate datasets. In this paper, a complete overview of available chemometric techniques used in the analysis of ion mobility spectrometry data is given. We describe the current state-of-the-art of ion mobility spectrometry data analysis comprising datasets with different complexities and two different scopes of data analysis, i.e. targeted and non-targeted analyte analyses. Two main steps of data analysis are considered: data preprocessing and pattern recognition. A detailed description of recent advances in chemometric techniques is provided for these steps, together with a list of interesting applications. We demonstrate that chemometric techniques have a significant contribution to the recent and great expansion of ion mobility spectrometry technology into different application fields. We conclude that well-thought out, comprehensive data analysis strategies are currently emerging, including several chemometric techniques and addressing different data challenges. In our opinion, this trend will continue in the near future, stimulating developments in ion mobility spectrometry instrumentation even further.

Data size reduction strategy for the classification of breath and air samples using multicapillary column-ion mobility spectrometry.

Ion mobility spectrometry combined with multicapillary column separation (MCC-IMS) is a well-known technology for detecting volatile organic compounds (VOCs) in gaseous samples. Due to their large data size, processing of MCC-IMS spectra is still the main bottleneck of data analysis, and there is an increasing need for data analysis strategies in which the size of MCC-IMS data is reduced to enable further analysis. In our study, the first untargeted chemometric strategy is developed and employed in the analysis of MCC-IMS spectra from 264 breath and ambient air samples. This strategy does not comprise identification of compounds as a primary step but includes several preprocessing steps and a discriminant analysis. Data size is significantly reduced in three steps. Wavelet transform, mask construction, and sparse-partial least squares-discriminant analysis (s-PLS-DA) allow data size reduction with down to 50 variables relevant to the goal of analysis. The influence and compatibility of the data reduction tools are studied by applying different settings of the developed strategy. Loss of information after preprocessing is evaluated, e.g., by comparing the performance of classification models for different classes of samples. Finally, the interpretability of the classification models is evaluated, and regions of spectra that are related to the identification of potential analytical biomarkers are successfully determined. This work will greatly enable the standardization of analytical procedures across different instrumentation types promoting the adoption of MCC-IMS technology in a wide range of diverse application fields.

Use of headspace-gas chromatography-ion mobility spectrometry to detect volatile fingerprints of palm fibre oil and sludge palm oil in samples of crude palm oil.

OBJECTIVE: The addition of residual oils such as palm fibre oil (PFO) and sludge palm oil (SPO) to crude palm oil (CPO) can be problematic within supply chains. PFO is thought to aggravate the accumulation of monochloropropanediols (MCPDs) in CPO, whilst SPO is an acidic by-product of CPO milling and is not fit for human consumption. Traditional targeted techniques to detect such additives are costly, time-consuming and require highly trained operators. Therefore, we seek to assess the use of gas chromatography-ion mobility spectrometry (GC-IMS) for rapid, cost-effective screening of CPO for the presence of characteristic PFO and SPO volatile organic compound (VOC) fingerprints. RESULTS: Lab-pressed CPO and commercial dispatch tank (DT) CPO were spiked with PFO and SPO, respectively. Both additives were detectable at concentrations of 1% and 10% (w/w) in spiked lab-pressed CPO, via seven PFO-associated VOCs and 21 SPO-associated VOCs. DT controls could not be distinguished from PFO-spiked DT CPO, suggesting these samples may have already contained low levels of PFO. DT controls were free of SPO. SPO was detected in all SPO-spiked dispatch tank samples by all 21 of the previously distinguished VOCs and had a significant fingerprint consisting of four spectral regions.

Increasing conclusiveness of clinical breath analysis by improved baseline correction of multi capillary column - ion mobility spectrometry (MCC-IMS) data.

Current challenges of clinical breath analysis include large data size and non-clinically relevant variations observed in exhaled breath measurements, which should be urgently addressed with competent scientific data tools. In this study, three different baseline correction methods are evaluated within a previously developed data size reduction strategy for multi capillary column - ion mobility spectrometry (MCC-IMS) datasets. Introduced for the first time in breath data analysis, the Top-hat method is presented as the optimum baseline correction method. A refined data size reduction strategy is employed in the analysis of a large breathomic dataset on a healthy and respiratory disease population. New insights into MCC-IMS spectra differences associated with respiratory diseases are provided, demonstrating the additional value of the refined data analysis strategy in clinical breath analysis.

Boosting model performance and interpretation by entangling preprocessing selection and variable selection.

The aim of data preprocessing is to remove data artifacts-such as a baseline, scatter effects or noise-and to enhance the contextually relevant information. Many preprocessing methods exist to deliver one or more of these benefits, but which method or combination of methods should be used for the specific data being analyzed is difficult to select. Recently, we have shown that a preprocessing selection approach based on Design of Experiments (DoE) enables correct selection of highly appropriate preprocessing strategies within reasonable time frames. In that approach, the focus was solely on improving the predictive performance of the chemometric model. This is, however, only one of the two relevant criteria in modeling: interpretation of the model results can be just as important. Variable selection is often used to achieve such interpretation. Data artifacts, however, may hamper proper variable selection by masking the true relevant variables. The choice of preprocessing therefore has a huge impact on the outcome of variable selection methods and may thus hamper an objective interpretation of the final model. To enhance such objective interpretation, we here integrate variable selection into the preprocessing selection approach that is based on DoE. We show that the entanglement of preprocessing selection and variable selection not only improves the interpretation, but also the predictive performance of the model. This is achieved by analyzing several experimental data sets of which the true relevant variables are available as prior knowledge. We show that a selection of variables is provided that complies more with the true informative variables compared to individual optimization of both model aspects. Importantly, the approach presented in this work is generic. Different types of models (e.g. PCR, PLS, …) can be incorporated into it, as well as different variable selection methods and different preprocessing methods, according to the taste and experience of the user. In this work, the approach is illustrated by using PLS as model and PPRV-FCAM (Predictive Property Ranked Variable using Final Complexity Adapted Models) for variable selection.

Clear cell tumors have higher mRNA levels of ERCC1 and XPB than other histological types of epithelial ovarian cancer.

PURPOSE: The purpose of the present work was to investigate the relationship between mRNA expression of ERCC1 and XPB, two key genes in the nucleotide excision repair pathway, and clinical resistance of platinum-chemotherapy in histological subtypes of epithelial ovarian cancer. EXPERIMENTAL DESIGN: mRNA levels of ERCC1 and XPB in epithelial ovarian cancer specimens from 126 different individuals were assessed using reverse transcription-PCR and followed by Southern hybridization methodology. Data were analyzed by linear regression analyses and by exhaustive regression analyses. RESULTS: Five different histological types of tumors were examined; serous (n = 76), mucinous (n = 11), clear cell (n = 9), poorly differentiated (n = 9), and endometroid (n = 21). Numerical values for mRNA expression levels were based on internal controls for a stable comparative cell line and for beta-actin. Median values for ERCC1 and XPB mRNAs within clear cell tumors were, on average, >2-fold higher than the other histological tumor types. Linear regression analyses suggest a continuum of nucleotide excision repair gene expression among these cell types, and exhaustive regression analyses demonstrate that the higher mRNA levels seen in clear cell tumors are highly statistically significant. CONCLUSIONS: We conclude that mRNA levels of ERCC1 and XPB tend to be higher in clear cell tumors as opposed to other types of epithelial ovarian cancer. This is consistent with the long-standing observation that clear cell tumors are more likely to show de novo drug resistance against DNA damaging agents in the clinic.

Spectral variable selection for partial least squares calibration applied to authentication and quantification of extra virgin olive oils using Fourier transform Raman spectroscopy.

The limits of quantitative multivariate assays for the analysis of extra virgin olive oil samples from various Greek sites adulterated by sunflower oil have been evaluated based on their Fourier transform (FT) Raman spectra. Different strategies for wavelength selection were tested for calculating optimal partial least squares (PLS) models. Compared to the full spectrum methods previously applied, the optimum standard error of prediction (SEP) for the sunflower oil concentrations in spiked olive oil samples could be significantly reduced. One efficient approach (PMMS, pair-wise minima and maxima selection) used a special variable selection strategy based on a pair-wise consideration of significant respective minima and maxima of PLS regression vectors, calculated for broad spectral intervals and a low number of PLS factors. PMMS provided robust calibration models with a small number of variables. On the other hand, the Tabu search strategy recently published (search process guided by restrictions leading to Tabu list) achieved lower SEP values but at the cost of extensive computing time when searching for a global minimum and less robust calibration models. Robustness was tested by using packages of ten and twenty randomly selected samples within cross-validation for calculating independent prediction values. The best SEP values for a one year's harvest with a total number of 66 Cretian samples were obtained by such spectral variable optimized PLS calibration models using leave-20-out cross-validation (values between 0.5 and 0.7% by weight). For the more complex population of olive oil samples from all over Greece (total number of 92 samples), results were between 0.7 and 0.9% by weight with a cross-validation sample package size of 20. Notably, the calibration method with Tabu variable selection has been shown to be a valid chemometric approach by which a single model can be applied with a low SEP of 1.4% for olive oil samples across three different harvest years.

Breath analysis: translation into clinical practice.

Breath analysis in respiratory disease is a non-invasive technique which has the potential to complement or replace current screening and diagnostic techniques without inconvenience or harm to the patient. Recent advances in ion mobility spectrometry (IMS) have allowed exhaled breath to be analysed rapidly, reliably and robustly thereby facilitating larger studies of exhaled breath profiles in clinical environments. Preliminary studies have demonstrated that volatile organic compound (VOC) breath profiles of people with respiratory disease can be distinguished from healthy control groups but there is a need to validate, standardise and ensure comparability between laboratories before real-time breath analysis becomes a clinical reality. It is also important that breath sampling procedures and methodologies are developed in conjunction with clinicians and the practicalities of working within the clinical setting are considered to allow the full diagnostic potential of these techniques to be realised. A protocol is presented, which has been developed over three years and successfully deployed for quickly and accurately collecting breath samples from 323 respiratory patients recruited from 10 different secondary health care clinics.

Geographic classification of extra virgin olive oils from the eastern Mediterranean by chemometric analysis of visible and near-infrared spectroscopic data.

Visible and near-infrared reflectance spectra have been examined for their ability to classify extra virgin olive oils from the eastern Mediterranean on the basis of their geographic origin. Classification strategies investigated were partial least-squares regression, factorial discriminant analysis, and k-nearest neighbors analysis. Discriminant models were developed and evaluated using spectral data in the visible (400-750 nm), near-infrared (1100-2498 nm), and combined (400-2498 nm) wavelength ranges. A variety of data pretreatments was applied. Best results were obtained using factorial discriminant analysis on raw spectral data over the combined wavelength range; a correct classification rate of 93.9% was obtained on a prediction sample set. Though the overall sample set was limited in numbers, these results demonstrate the potential of near-infrared spectroscopy to classify extra virgin olive oils on the basis of their geographic origin.

Detecting and quantifying sunflower oil adulteration in extra virgin olive oils from the eastern mediterranean by visible and near-infrared spectroscopy.

One hundred and thirty-eight oil samples have been analyzed by visible and near-infrared transflectance spectroscopy. These comprised 46 pure extra virgin olive oils and the same oils adulterated with 1% (w/w) and 5% (w/w) sunflower oil. A number of multivariate mathematical approaches were investigated to detect and quantify the sunflower oil adulterant. These included hierarchical cluster analysis, soft independent modeling of class analogy (SIMCA method), and partial least squares regression (PLS). A number of wavelength ranges and data pretreatments were explored. The accuracy of these mathematical models was compared, and the most successful models were identified. Complete classification accuracy was achieved using 1st derivative spectral data in the 400-2498 nm range. Prediction of adulterant content was possible with a standard error equal to 0.8% using 1st derivative data between 1100 and 2498 nm. Spectral features and chemical literature were studied to isolate the structural basis for these models.

A novel approach to 3-methylindoles by a Heck/cyclization/isomerization process.

A novel synthesis of 3-methylindoles from chlorotriflates through a Heck reaction, carbamate/aryl chloride coupling, and isomerization sequence is presented. The three-step sequence is highly efficient and general, enabling the regiocontrolled synthesis of substituted indoles in short order.

A novel crystallization-induced diastereomeric transformation based on a reversible carbon-sulfur bond formation. Application to the synthesis of a gamma-secretase inhibitor.

This paper describes a remarkably efficient process for the preparation of gamma-secretase inhibitor 1. The target is synthesized in only five steps with an overall yield of 58%. The key operation is a highly selective and practical, crystallization-driven transformation for the conversion of a mixture of tertiary benzylic alcohols into the desired sulfide diastereomer with 94:6 dr. This unprecedented process is based upon a reversible carbon-sulfur bond formation under acidic conditions.

A practical synthesis of a gamma-secretase inhibitor.

A practical and scaleable synthesis of the gamma-secretase inhibitor 1 is reported. The inhibitor consists of a central trisubstituted cyclohexane core with appended propionic acid, 2,5-difluorophenyl, and 4-chlorophenylsulfonyl moieties. Two alternative synthetic strategies, proceeding by way of a common disubstituted cyclohexanone derivative 5, were studied. In the preferred route, conjugate reduction of acrylonitrile derivative 4 with L-Selectride configures the desired relative stereochemistry of the cyclohexane core with >99.9:0.1 dr. A second strategy, based on catalyst-controlled hydrogenation of racemic cyclohexene derivative 2, is more convergent but less diastereoselective (up to 75:25 dr). The common cyclohexanone intermediate 5 was constructed by a regioselective Diels-Alder condensation of a 1,1-disubstituted vinyl sulfone 6 with 2-trimethylsiloxybutadiene.