Validation Sample Set Research Articles

Quantification and Classification of Corn and Sunflower Oils as Adulterants in Olive Oil Using Chemometrics and FTIR Spectra

Commercially, extra virgin olive oil (EVOO) is subjected to be adulterated with low-price oils having similar color to EVOO. Fourier transform infrared (FTIR) spectroscopy combined with chemometrics has been successfully used for classification and quantification of corn (CO) and sunflower oils (SFOs) in EVOO sets. The combined frequency regions of 3027–3000, 1076–860, and 790–698 cm−1 were used for classification and quantification of CO in EVOO; meanwhile, SFO was analyzed using frequency regions of 3025–3000 and 1400–985 cm−1. Discriminant analysis can make classification of pure EVOO and EVOO adulterated with CO and SFO with no misclassification reported. The presence of CO in EVOO was determined with the aid of partial least square calibration using FTIR normal spectra. The calibration and validation errors obtained in CO's quantification are 0.404 and 1.13%, respectively. Meanwhile, the first derivative FTIR spectra and PLS calibration model were preferred for quantification of SFO in EVOO with high coefficient of determination (R 2) and low errors, either in calibration or in validation sample sets.

Prediction of high-grade vesicoureteral reflux after pediatric urinary tract infection: external validation study of procalcitonin-based decision rule.

BackgroundPredicting vesico-ureteral reflux (VUR) ≥3 at the time of the first urinary tract infection (UTI) would make it possible to restrict cystography to high-risk children. We previously derived the following clinical decision rule for that purpose: cystography should be performed in cases with ureteral dilation and a serum procalcitonin level ≥0.17 ng/mL, or without ureteral dilatation when the serum procalcitonin level ≥0.63 ng/mL. The rule yielded a 86% sensitivity with a 46% specificity. We aimed to test its reproducibility.Study DesignA secondary analysis of prospective series of children with a first UTI. The rule was applied, and predictive ability was calculated.ResultsThe study included 413 patients (157 boys, VUR ≥3 in 11%) from eight centers in five countries. The rule offered a 46% specificity (95% CI, 41–52), not different from the one in the derivation study. However, the sensitivity significantly decreased to 64% (95%CI, 50–76), leading to a difference of 20% (95%CI, 17–36). In all, 16 (34%) patients among the 47 with VUR ≥3 were misdiagnosed by the rule. This lack of reproducibility might result primarily from a difference between derivation and validation populations regarding inflammatory parameters (CRP, PCT); the validation set samples may have been collected earlier than for the derivation one.ConclusionsThe rule built to predict VUR ≥3 had a stable specificity (ie. 46%), but a decreased sensitivity (ie. 64%) because of the time variability of PCT measurement. Some refinement may be warranted.

MicroRNA Signature in Thyroid Fine Needle Aspiration Cytology Applied to “Atypia of Undetermined Significance” Cases

MicroRNA (miR) expression signatures are proposed to be able to differentiate thyroid cancer from benign thyroid lesions. We selected eight miRs (miR-146b, -221, -187, -197, -346, -30d, -138, and -302c) to examine the potential use of miRs to supplement diagnostic cytology in cases designated as "atypia of undetermined significance." miR expression was measured in thyroid fine needle aspiration (FNA) specimens by quantitative polymerase chain reaction. Gene expression analyses and linear discriminant analysis (LDA) were performed in a training sample set (n=60) to obtain a classification rule to predict FNA cases as benign or malignant. The predictions were cross-validated by comparing with the corresponding histological diagnoses. A validation sample set (n=68) was further tested with the established four-miR LDA classification rule. A set of four miRs (miR-146b, -221, -187, and -30d) was identified that could differentiate malignant from benign lesions. A four-miR LDA classification rule was obtained and used to predict FNA cases as benign or malignant. For the training sample set, we obtained a diagnostic accuracy of 93.3%, sensitivity of 93.2%, specificity of 93.8%, positive predictive value (PPV) of 0.98, and negative predictive value (NPV) of 0.83. For the validation sample set, we obtained a diagnostic accuracy of 85.3%, sensitivity of 88.9%, specificity of 78.3%, PPV of 0.89, and NPV of 0.78. For the 30 atypia cases in the validation sample set, we obtained a diagnostic accuracy of 73.3%, sensitivity of 63.6%, specificity of 78.9%, PPV of 0.64, and NPV of 0.79. Based on the miR predictions, we classified the atypia cases predicted as "malignant" into "high risk" and those predicted as "benign" into "low risk" categories. While thyroid carcinomas, particularly papillary thyroid carcinomas (PTCs), were relatively enriched in the high-risk category, this particular miR panel is subject to inaccurate results in follicular neoplasias in atypia cases. We demonstrate that miR amplification from FNA samples is feasible and that the particular four miR profile in this study can identify PTCs. However, further refinement is required for application to FNA cytology of "atypia of undetermined significance" cases due to low accuracy in classifying follicular neoplasias.

Lipid MALDI profile classifies non-small cell lung cancers according to the histologic type

We investigated whether direct tissue matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) analysis on lipid may assist with the histopathologic diagnosis of non-small cell lung cancers (NSCLCs). Twenty-one pairs of frozen, resected NSCLCs and adjacent normal tissue samples were initially analyzed using histology-directed, MALDI MS. 2,5-dihydroxybenzoic acid/α-cyano-4-hydroxycinnamic acid were manually deposited on areas of each tissue section enriched in epithelial cells to identify lipid profiles, and mass spectra were acquired using a MALDI-time of flight instrument. A lipid profile that could differentiate cancer and adjacent normal samples with a median accuracy of 92.9% was discovered. Several phospholipids including phosphatidylcholines (PC) {34:1} were overexpressed in lung cancer.Squamous cell carcinomas and adenocarcinomas were found to have different lipid profiles. Discriminatory lipids correctly classified the histology of 80.4% of independent NSCLC surgical tissue samples (41 out of 51) in validation set. MALDI MS image of 11 discriminatory lipids validated their differential expression according to the histologic type in cancer cells of bronchoscopic biopsy samples. PC {32:0} [M+Na]+ (m/z 756.68) and ST-OH {42:1} [M−H]− (m/z 906.89) were overexpressed in adenocarcinomas. Thus, lipid profiles accurately distinguish tumor from adjacent normal tissue and classify non-small cell lung cancers according to the histologic type.

Near-Infrared Spectroscopic Determination of Degradation in Vegetable Oils Used To Fry Various Foods

Near-infrared (NIR) spectroscopic methods for measuring degradation products, including total polar materials (TPMs) and free fatty acids (FFAs), in soy-based frying oil used for frying various foods have been successfully developed. Calibration models were developed using forward stepwise multiple linear regression (FSMLR) and partial least-squares (PLS) regression techniques and then tested with an independent set of validation samples. The results show that the quality of oil used for frying different foods can be measured with a single model. First-derivative treatments improved results for TPM measurement. In addition, PLS models gave better prediction results than FSMLR models. For PLS models, the best correlations (r) between the NIR-predicted data and the chemical method data for TPMs and FFAs in oils were 0.995 and 0.981, respectively. For FSMLR models, the best r values for TPMs and FFAs in oils were 0.993 and 0.963, respectively.

Feasibility study of FT-MIR spectroscopy and PLS-R for the fast determination of anthocyanins in wine

The feasibility of using Fourier Transform Mid-Infrared Spectroscopy (FT-MIR) combined with Partial Least Squares Regression (PLS-R) for the determination of 12 anthocyanins (3-O-glucosides of delphinidin, cyanidin, petunidin, peonidin and malvidin, as well as acetic acid esters and p-coumaric acid esters of petunidin, peonidin and malvidin and caffeic acid ester of malvidin) and three sums (sum of non-acylated anthocyanins, sum of acetylated anthocyanins and sum of coumaroylated anthocyanins), in red wines has been tested. Reference values of anthocyanin concentrations by reverse-phase High Performance Liquid Chromatography with Diode Array Detection (HPLC–DAD) were used to calibrate the models. A Principal Component Analysis (PCA) was applied to these reference values and a differentiation of wine samples by wine type (young wines of 2005, young wines of 2004 and crianza and reserva wines) has been possible.A calibration model using PLS-R was built with 153 samples of Rioja wines and the prediction of the anthocyanin concentrations using this model was evaluated by internal and external validation sample sets. Most of the anthocyanins and their sums have been predicted with a Standard Error of Prediction (SEP) of 15–30% for young wines recently bottled. However, for young wines after one year of being bottled, and for crianza and reserva wines, these errors were unacceptable. The obtained results suggest that the model built for FT-IR instrument calibration is a useful tool for a quick determination of the anthocyanin content of young wines of the current vintage, but a careful robust external validated calibration of the technique is necessary in order to maintain the prediction errors within controlled limits.

Early Second-Trimester Serum MiRNA Profiling Predicts Gestational Diabetes Mellitus

BackgroundGestational diabetes mellitus (GDM) is one type of diabetes that presents during pregnancy and significantly increases the risk of a number of adverse consequences for the fetus and mother. The microRNAs (miRNA) have recently been demonstrated to abundantly and stably exist in serum and to be potentially disease-specific. However, no reported study investigates the associations between serum miRNA and GDM.Methodology/Principal FindingsWe systematically used the TaqMan Low Density Array followed by individual quantitative reverse transcription polymerase chain reaction assays to screen miRNAs in serum collected at 16–19 gestational weeks. The expression levels of three miRNAs (miR-132, miR-29a and miR-222) were significantly decreased in GDM women with respect to the controls in similar gestational weeks in our discovery evaluation and internal validation, and two miRNAs (miR-29a and miR-222) were also consistently validated in two-centric external validation sample sets. In addition, the knockdown of miR-29a could increase Insulin-induced gene 1 (Insig1) expression level and subsequently the level of Phosphoenolpyruvate Carboxy Kinase2 (PCK2) in HepG2 cell lines.Conclusions/SignificanceSerum miRNAs are differentially expressed between GDM women and controls and could be candidate biomarkers for predicting GDM. The utility of miR-29a, miR-222 and miR-132 as serum-based non-invasive biomarkers warrants further evaluation and optimization.

Circulating MicroRNA Is a Biomarker of Pediatric Crohn Disease

The gold standard for the diagnosis and evaluation of Crohn disease (CD) is endoscopy/colonoscopy, although this is invasive, costly, and associated with risks to the patient. Recently, circulating microRNAs (miRNAs) have emerged as promising noninvasive biomarkers. Here, we examined the utility of serum miRNAs as biomarkers of CD in children. Studies were conducted using sera samples from patients with pediatric CD, healthy controls, and a comparison group of patients with pediatric celiac disease. Serum miRNA levels were explored initially using a microfluidic quantitative reverse transcription-polymerase chain reaction array platform. Findings were subsequently validated using quantitative reverse transcription-polymerase chain reaction in larger validation sample sets. The diagnostic utility of CD-associated serum miRNA was examined using receiver operating characteristic analysis. A survey of miRNA levels in the sera of control and patients with CD detected significant elevation of 24 miRNAs, 11 of which were chosen for further validation. All of the candidate biomarker miRNAs were confirmed in an independent CD sample set (n = 46). To explore the specificity of the CD-associated miRNAs, they were measured in the sera of patients with celiac disease (n = 12); none were changed compared with healthy controls. Receiver operating characteristic analyses revealed that serum miRNAs have promising diagnostic utility, with sensitivities for CD above 80%. Significant decreases in serum miRNAs were observed in 24 incident patients with pediatric CD after 6 months of treatment. The present study identifies 11 CD-associated serum miRNA with encouraging diagnostic potential. Our findings suggest serum miRNAs may prove useful as noninvasive biomarkers in CD.

The Roche Elecsys and Siemens-Centaur Thyroglobulin Autoantibody Assays Show Comparable Clinical Performance to the Recently Unavailable Beckman-Coulter Access Thyroglobulin Autoantibody Assay in Identifying Samples with Potentially False-Low Thyroglobulin Measurements Due to Thyroglobulin Autoantibody Interference

Dear Editor: Approximately 25% of thyroid cancer patients have circulating antithyroglobulin autoantibodies (anti-TgAB), which can cause false-low interference in Tg assays (1). It is therefore recommended that all Tg measurements are accompanied by TgAB testing (1). The Beckman-Coulter Access Tg- and TgAB assays have become perhaps the most widely used assay combination for thyroid cancer follow-up in the United States, because they run on the same automated instrument and they are more sensitive than most alternative Tg/TgAB assays. Unfortunately, Beckman-Coulter has recently indicated that their TgAB assay will be unavailable for the foreseeable future, necessitating a switch to other TgAB assays to accompany Tg testing. Such a change has a high risk of interfering with patient management. Different TgAB assays show at best a moderate numerical agreement with each other, have different detection sensitivities, and have different cutoffs for TgAB positivity (2–4). We have therefore performed a comparison study of the Beckman-Coulter TgAB assay with three other automated TgAB assays: Roche Elecsys TgAB, Siemens-Centaur TgAB, and Siemens-Immulite TgAB. As these assays are primarily marketed for the diagnosis of autoimmune thyroid disease, the manufacturer-provided diagnostic cutoffs are not optimized for the detection of interference in Tg assays. Therefore, we first determined optimal cutoffs for these assays by comparing them with the Beckman-Coulter assay in 100 archival patient samples. Next, we performed a clinical validation of these cutoffs in 130 samples from 113 Mayo Clinic patients. These samples were selected to include patients with (43 patients with 51 samples) and without (70 patients with 79 samples) definitive persistent/recurrent disease (clinical or imaging proven) (see Supplementary Methods; Supplementary Data are available online at www.liebertonline.com/thy). We found poor numerical agreement between the Beckman-Coulter assay and the other TgAB assays, but receiver-operating characteristics (ROC) curve analysis, using the Beckman-Coulter TgAB results as the “gold standard” (negative: <4 IU/mL, N = 32; positive: ≥4 IU/mL, N = 68), showed comparable areas under the curves (see Supplementary Fig. S1): Siemens-Centaur 0.88 (95% confidence interval [CI]: 0.79–0.97), Siemens-Immulite 0.86 (95% CI: 0.81–0.92), and Roche 0.87 (95% CI: 0.77–0.95). At their respective ROC curve–derived cutoffs, the Siemens-Centaur (44 IU/mL) and Roche (22 IU/mL) missed only 1 and 3 samples, respectively, which had been positive with the Beckman-Coulter assay, whereas the Siemens-Immulite (20 IU/mL) missed 18. The Roche assay showed the best agreement with the Beckman-Coulter assay in the clinical validation sample set with verified disease status (see Supplementary Table S1), with a negative and positive agreement of 96% and 95%, respectively. The Siemens-Immulite assay showed the worst agreement (negative and positive agreement of 79% and 78%). The Siemens-Centaur assay's performance fell in between these two with 92% negative agreement and 94% positive agreement. All 16 samples from 15 patients with clinical recurrent/persistent disease, who had undetectable serum Tg levels (<0.1 ng/mL), were positive for TgAB in all four assays, using the respective cutoffs. However, of 31 samples from 26 patients with clinical recurrence and a Tg of <2 ng/mL, a total of 3 samples from 3 patients (1 per patient) had a negative TgAB result in the Beckman-Coulter, Roche, and Siemens-Centaur TgAB assays, whereas 6 samples from 5 patients (1 patient with 2 samples) had a negative TgAB result by the Siemens-Immulite assay. We conclude that the automated Roche Elecsys (cutoff: 22 IU/mL) and Siemens-Centaur (cutoff: 44 IU/mL) TgAB assays show comparable clinical performance to the Beckman-Coulter Access TgAB assay (cutoff: 4 IU/mL). The Siemens-Immulite assay (cutoff: 20 IU/mL) had lesser TgAB detection sensitivity than the other assays. Incidentally, all these cutoffs are much lower than those listed in the respective package inserts, which are targeted at diagnosis of autoimmune thyroid disease. These manufacturer-stated cutoffs would miss many cases of clinically relevant TgAB levels that could cause interferences in Tg measurements. The satisfactory performance of the Roche and Siemens-Centaur TgAB assays in identifying samples with TgAB levels that might interfere with Tg measurements does not solve all problems related to the sudden unavailability of the Beckman-Coulter TgAB assay. In particular, it remains important for laboratorians and clinicians to be mindful of the poor numerical agreement between the Beckman-Coulter assay and the other TgAB assays, when analyzing patient samples. Practitioners, who have used serial TgAB measurements with the Beckman-Coulter assay as a semiquantitative follow-up marker in TgAB-positive patients, need to re-baseline these patients with one of the alternative assays and should ensure that subsequent samples are measured using the same assay.

Quantitative analysis of essential oils in perfume using multivariate curve resolution combined with comprehensive two-dimensional gas chromatography

The use of multivariate curve resolution (MCR) to build multivariate quantitative models using data obtained from comprehensive two-dimensional gas chromatography with flame ionization detection (GC × GC-FID) is presented and evaluated. The MCR algorithm presents some important features, such as second order advantage and the recovery of the instrumental response for each pure component after optimization by an alternating least squares (ALS) procedure. A model to quantify the essential oil of rosemary was built using a calibration set containing only known concentrations of the essential oil and cereal alcohol as solvent. A calibration curve correlating the concentration of the essential oil of rosemary and the instrumental response obtained from the MCR-ALS algorithm was obtained, and this calibration model was applied to predict the concentration of the oil in complex samples (mixtures of the essential oil, pineapple essence and commercial perfume). The values of the root mean square error of prediction (RMSEP) and of the root mean square error of the percentage deviation (RMSPD) obtained were 0.4% (v/v) and 7.2%, respectively. Additionally, a second model was built and used to evaluate the accuracy of the method. A model to quantify the essential oil of lemon grass was built and its concentration was predicted in the validation set and real perfume samples. The RMSEP and RMSPD obtained were 0.5% (v/v) and 6.9%, respectively, and the concentration of the essential oil of lemon grass in perfume agreed to the value informed by the manufacturer. The result indicates that the MCR algorithm is adequate to resolve the target chromatogram from the complex sample and to build multivariate models of GC × GC-FID data.

Genetic variants of 6q25 and breast cancer susceptibility: a two-stage fine mapping study in a Chinese population

A recent genome-wide association study identified a novel single nucleotide polymorphism (SNP), rs2046210, in the 6q25 region as a breast cancer susceptibility locus in Chinese and subsequently replicated in a multicenter study. Further fine-mapping of this region may help identify the potential causative SNPs of breast cancer. We employed a block-based fine mapping analysis to investigate the tagging SNPs in a 41 kb block with the marker-SNP rs2046210 in the 6q25 region, and also extended our study by including two potentially functional SNPs (rs2234693 and rs1801132) within the ESR1 gene by a two-stage case-control study with 1,792 breast cancer cases and 1,867 controls (878 cases and 900 controls in the testing set and 914 cases and 967 controls in the validation set). Significant associations with breast cancer risk were observed for rs1038304, rs6929137, rs2046210, and rs10484919 in the 41 kb block of the 6q25 region in the testing set after controlling multiple testing. Together with the validation set samples, these four SNPs were all significantly associated with increased risk of breast cancer (additive OR from 1.25 to 1.34, additive P from 4.84 × 10(-6) to 7.17 × 10(-9)). After conditional regression and linkage disequilibrium analyses, rs6929137 and rs10484919 tend to be susceptible markers of breast cancer in this region and both of them were located at sites of histone modification according to the UCSC (http://genome.ucsc.edu/) genome database. Our results support that the 6q25 region is an important susceptibility region for breast cancer in Chinese women, and rs6929137 and rs10484919 are causative or marker SNPs for this region.

Abstract 4350: Translating diagnostic gene expression profiles for pediatric solid tumors

Abstract BACKGROUND: Features of cancer genomics including gene expression levels can be employed to create biomarker profiles that can predict prior to therapy the diagnosis and prognosis of an individual patient. We aim to translate robust and reproducible diagnostic and prognostic profiles for pediatric solid tumors into clinical tools applicable to all tumor specimens, fresh frozen (FF) or formalin fixed (FFPE). RESULTS: We used Affymetrix GeneChip Human Exon 1.0 ST (HuEx) arrays on 24 cell lines or tumors (4 fusion-positive rhabdomyosarcoma [RMSpos], 5 fusion-negative RMS [RMSneg], 6 Ewing sarcoma family of tumors [ESFT], 5 neuroblastoma [NB], and 4 osteosarcoma [OS]) to identify a 41-feature diagnostic metagene that clearly distinguished both the original test samples and a set of validation samples. We then incorporated the 41-feature metagene into a 48-gene panel. To translate this diagnostic signature, we compared the performance of HuEx arrays with several mid-plex assay platforms including Fluidigm's quantitative reverse-transcriptase PCR (q-RT-PCR) and NanoString's nCounter™ Digital Analyzer by measuring gene expression on an 18-cell line panel (4 RMSpos, 4 RMSneg, 5 ESFT, 1 NB, and 4 OS). With q-RT-PCR, we observed r2 values of 0.703 ± 0.085 (RMSpos), 0.558 ± 0.138 (RMSneg), 0.689 ± 0.070 (ESFT), and 0.607 ± 0.121 (OS). nCounter reported r2 values of 0.672 ± 0.171 (RMSpos), 0.620 ± 0.143 (RMSneg), 0.675 ± 0.094 (ESFT), and 0.583 ± 0.129 (OS). Hierarchical clustering with all platforms was able to distinguish the RMSpos, ESFT, and NB cell lines; however, the RMSneg and OS cell lines were less clearly distinguished because some of the OS cell lines lacked high expression of genes characteristic of OS tumors. Cross-platform comparisons yielded good correlation between nCounter and Q-RT-PCR (average r2 = 0.710 ± 0.183). An 18-sample dilution series revealed that EWS-FLI1 type I or PAX3-FKHR transcripts were consistently detected by q-RT-PCR or nCounter even at 1:1000 RNA dilution. Among biological duplicates, q-RT-PCR reported an average r2 = 0.916 ± 0.039 while nCounter obtained average r2 = 0.983 ± 0.011 including raw cell lysates. In addition, we also compared Fluidigm's q-RT-PCR with Applied Biosystems’ Taqman Low-Density Arrays (TLDA) on five NB patient bone marrow samples to detect residual tumor cells. We observed an average r2 = 0.929 ± 0.119 across five NB genes and one housekeeping gene. Finally, we have also successfully profiled FF vs. FFPE tumors on HuEx and are currently applying these mid-plex technologies to paired FF and FFPE samples in order to create diagnostic profiles applicable to routine FFPE material. CONCLUSIONS: Mid-plex platform can reliably distinguish bone and soft tissue sarcoma cell lines and can be used to translate the application of diagnostic signatures. These data warrant further studies to analyze FFPE samples, to compare additional mid-plex platforms, and to test potential prognostic signatures. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4350. doi:10.1158/1538-7445.AM2011-4350

Sensor array-based optical portable instrument for determination of pH

A portable optical instrument is presented that makes it possible to determine pH with a colorimetric sensor array. The use of four membranes containing acid–base indicators makes it possible to cover the full range of pH using the H (hue) coordinate measurements of the HSV colour space. pH sensitive membranes were directly cast onto a plastic support to form a two-dimensional array, located between an OLED display as the programmable light source and a set of digital colour detectors. The resulting microcontroller-based system is immune to optical and electrical interferences. A complete optical and electrical characterization and optimization of the hand-held instrument was carried out. The instrument was used to determine pH using a simple algorithm to select the sensor output that was programmed in the microcontroller. The initial eleven candidate pH membranes were reduced to only four, which permit to obtain reliable pH values. The pH response of the selected four sensing elements was modelled, and calibration curves were applied to a validation set and real samples obtaining positive correlations between the real and predicted data.

Validation of Preexisting Reference Intervals: Can the Procedure be Applied to Canine Hemostasis?

The de novo establishment of reference intervals (RIs) for all variables is beyond the capabilities of many small laboratories. Thus, recent international recommendations propose procedures to adopt RIs established by "donor" laboratories after validation in "receiving" laboratories. The objective of the current study was to use recently published RIs of canine hemostasis tests as possible donor values and evaluate the validation procedure with randomized sets of values obtained in another study of canine RI determination of prothrombin time (PT), activated partial thromboplastin time (APTT), fibrinogen, and antithrombin (AT). The preanalytical, analytical, and demographic conditions of the donor and receiving laboratories were first compared. To represent new reference individuals, 25 validation sample sets of 20 results of the receiving laboratory were randomly selected for each variable and compared with the RI of the donor laboratory. Validation was rejected in all cases for APTT and AT. Donor RI could be validated in 14 of 25 cases for fibrinogen and in 4 of 25 cases for PT. When preanalytical and analytical differences existed between donor and receiving laboratories, validation procedures consistently rejected preexisting RI. When the differences are smaller, the variability of the results obtained in the validation sample sets tested may be responsible for validations or rejections, which can lead to further misinterpretations of results from patients. Validation of a preexisting reference interval is certainly an interesting option for small laboratories, but progressive determination of the laboratory's own reference interval is probably a better long-term solution.

Soil Carbon Determination in a Mediterranean Vertisol by Visible and near Infrared Reflectance Spectroscopy

The monitoring of the C content of agricultural lands requires long-term experiments, the analysis of a large number of samples, various sampling depths and adequate analytical tools to perform the experiments. Near infrared (NIR) reflectance spectroscopy is a fast, reliable and low-cost analytical tool for the determination of soil C content. The objective of this study was to present NIR spectroscopy technology as a reliable method to monitor C concentration (total C, inorganic C and organic C) of soil samples from a long-term experiment established in 1986 in Cordoba (Spain). The soil is a rain-fed vertisol, characteristic of Mediterranean agricultural systems. The soil samples studied from four different years (1997, 2000, 2003 and 2006) included all of the variabilities existing in the long-term experiment: tillage system (conventional tillage vs no tillage), crop rotations [wheat ( Triticum aestivum L)-chickpea ( Cicer arietinum L), wheat-faba bean ( Vicia faba L), wheat-sunflower ( Helianthus annus L), wheat-fallow and wheat-wheat], N fertiliser rate (0 kg N ha−1, 50 kg N ha−1, 100 kg N ha−1 and 150 kg N ha−1), as well as different soil depths (0–15 cm, 15–30 cm, 30–60 cm and 60–90 cm). Calibration models were obtained with 492 samples from the aforementioned vertisol using visible and NIR spectroscopy (vis-NIR) and, when tested using a validation sample set, returned the values: total C ( r2 = 0.92, SEP = 1 g kg−1, RER = 26, RPD = 4.8); inorganic C ( r2 = 0.95, SEP = 1.5 g kg−1, RER = 26.6, RPD = 4.6) and organic C ( r2 = 0.76, SEP = 0.8 g kg−1 RER = 12.3, RPD = 2). The vis-NIR models developed reliably predicted the total, inorganic and organic C content at plot scale (homogeneous sample set). The advantage deriving from very specific vis-NIR calibrations for prediction of soil C is that one can rapidly and economically predict C in the study area, enabling monitoring to compare soil C evolution depending on time and variables such as tillage, crop rotation and fertilisation. To develop vis-NIR models at local and regional scales would require a more heterogeneous sample set and adequate calibration/validation strategies.

17p12 deletion in breast cancer predicts resistance to neoadjuvant chemotherapy

Numerous studies have attempted to identify gene expression profiles which can be utilized to predict responses to neoadjuvant chemotherapy (NAC), but their findings are not clinically applicable at present. In the present study, we sought to determine DNA copy number alterations (CNAs) in breast cancer tissues which are associated with the response to NAC. Frozen tumor tissues from 63 breast cancer patients were obtained using core needle biopsy prior to NAC (3 cycles of docetaxel plus adriamycin) and were microdissected. Array comparative genomic hybridization (array CGH) with 4,045 bacterial artificial chromosome (BAC) probes was performed to identify the CNAs. Changes in tumor size in response to NAC were measured via magnetic resonance imaging. Fluorescence in situ hybridization (FISH) was conducted to verify array CGH results and for independent validation studies. CNAs at eight chromosomal loci encompassing 24 clones were correlated with changes in tumor size after NAC (p<0.05; t-test). Two CNAs were selected, 17p12 deletion and 17q21.32-33 gain, which were significantly associated with a smaller reduction in tumor size following NAC, via prioritization of the regions containing the candidate genes. In an independent validation set of samples from 39 patients, FISH assay further showed that the 17p12 deletion was markedly associated with smaller changes in tumor size (p=0.006), while the 17q21.32-33 gain was not significant (p=0.309). In conclusion, we successfully identified a 17p12 deletion in breast cancer tissue which can be applied in predicting tumor resistance to NAC.

Developing Robust Faecal near Infrared Spectroscopy Calibrations to Predict Diet Dry Matter Digestibility in Cattle Consuming Tropical Forages

Various studies, mainly from temperate areas, have reported calibrations developed from the near infrared (NIR) spectra of faeces (F.NIRS) for predicting diet digestibility in ruminants and there has been substantial variation in predictive accuracy as indicated by calibration and validation statistics. The present study was conducted to develop and examine the reliability and robustness of F.NIRS calibration equations to estimate dry matter digestibility (DMD) of forage diets ingested by cattle grazing in the rangelands of northern Australia. A large and diverse calibration data set of matched diet–faecal pairs was obtained over 10 years using three sampling methods: (1) grazed pasture with diet samples collected from oesophageal fistulated steers and faeces collected from resident cattle; (2) in vivo digestibility experiments with penned cattle fed forage hays; and (3) penned cattle fed pasture freshly harvested from the field. Estimated in vivo DMD reference values were determined using pepsin–cellulase in vitro analysis of diet samples. The final calibration set of 1052 samples represented 264 diets with DMD ranging from 38% to 75%. Calibration statistics for DMD% were: standard error of calibration = 1.87, standard error of cross validation = 1.91, and the coefficient of determination, r2 = 0.90. Factors of particular importance, with regard to the accuracy of DMD reference values, are identified and discussed and recommendations made for minimising reference errors. A comprehensive series of independent validation tests was conducted by selecting validation sample sets from the entire sample set according to a range of criteria. Each validation sub-set was tested using the calibration calculated from the remainder of the sample set. These tests showed that sampling method and experimental site often had important effects on calibration statistics and performance and also that the standard error of performance of the overall calibration would likely be &lt;2.5 DMD percentage units when applied to samples sourced from regions and pasture types represented in the calibration. Despite the large size and diversity of the calibration data set it was concluded that robustness would likely be improved by expansion of the calibration data set.

Application of class-modelling techniques to near infrared data for food authentication purposes

Following the introduction of legal identifiers of geographic origin within Europe, methods for confirming any such claims are required. Spectroscopic techniques provide a method for rapid and non-destructive data collection and a variety of chemometric approaches have been deployed for their interrogation. In this present study, class-modelling techniques (SIMCA, UNEQ and POTFUN) have been deployed after data compression by principal component analysis for the development of class-models for a set of olive oils and honeys. The number of principal components, the confidence level and spectral pre-treatments (1st and 2nd derivative, standard normal variate) were varied, and a strategy for variable selection was tried. Models were evaluated on a separate validation sample set. The outcomes are reported and criteria for selection of the most appropriate models for any given application are discussed.

Mid-infrared spectroscopy as a tool for rapid determination of internal quality parameters in tomato

The objective of this study was to investigate the possibility of predicting the quality parameters of tomato by mid-infrared spectroscopy. For 2 years, tomato samples, representing a large variability in the chemical composition, were scanned using the attenuated total reflectance accessory of a Fourier transform spectrometer in the wavenumber region between 4000 and 400 cm −1 . Calibration models were developed using partial least squares (PLS) regression method and were tested with internal validation sample set in the first year. Different spectral preprocessing techniques were investigated and different spectral regions were selected to optimise the calibration models. In addition, the models obtained in 2007 were used to predict the soluble solids, dry matter and total acidity in tomato harvested in 2008. The regression models of the spectra showed reasonable ability to estimate the dry matter, soluble solids, total acidity, citric acid and individual sugars contents in tomatoes grown in 2007, with high coefficients of determination (from 0.98 for soluble solids to 0.92 for fructose) and low percentage errors of prediction (from 3% to 7% for soluble solids and citric acid, respectively). By contrast, the predictive capability of model for malic acid was unsatisfactory with error of prediction of 26%. When the best calibration models from 2007 were used to predict the selected parameters in tomato picked in 2008, very high correlations were obtained, confirmed by low errors of prediction, from 4% to 7% for dry matter and total acidity, respectively. Mid-infrared spectroscopy is an attractive alternative for standard methods for determination of internal quality parameters in tomato.

Rapid FTIR determination of water, phenolics and antioxidant activity of olive oil

AbstractA rapid Fourier transformed infrared (FTIR) attenuated total reflectance (ATR) spectroscopic method was applied to the determination of water content (WC), total phenol amount (TP) and antioxidant activity (ABTS.+) of virgin olive oils (VOO) and olive oils. Calibration models were constructed using partial least squares regression. Oil samples with WC ranging from 289 to 1402 mg water/kg oil, with TP from 46 to 877 mg gallic acid/kg oil and with ABTS.+ from 0 to 5.7 mmol Trolox/kg oil were considered for chemometric analysis. Better results were obtained when selecting suitable spectral ranges; in particular, from 2260 to 1008 cm−1 for WC, from 3610 to 816 cm−1 for TP and from 3707 to 1105 cm−1 for ABTS.+. Satisfactory LOD values by the FTIR‐chemometric methods were achieved: 9.4 (mg/kg oil) for WC; 12.5 (mg gallic acid/kg oil) for TP, and 0.76 (mmol Trolox/kg oil) for ABTS.+. The evaluation of the applicability of these analytical approaches was tested by use of validation sample sets (n = 16 for WC, n = 11 for TP and n = 14 for ABTS) with nearly quantitative recovery rates (99–114%). The FTIR–ATR method provided results that were comparable to conventional procedures.Practical applications: The presented method is based on ATR–FTIR in combination with multivariate calibration methodologies and permits a simultaneous evaluation of important quality parameters of VOO (WC, TP and ABTS.+). This approach represents an easy and convenient means for monitoring olive oil quality with the advantage of ease of operation, speed, no sample pretreatment and no consumption of solvents. The data obtained with this method are comparable to those obtained using the official reference method. Therefore, the technique is highly plausible as an alternative to the standard procedure for routine analysis or control at‐line of production processes.