Estimating the number of components and detecting outliers using Angle Distribution of Loading Subspaces (ADLS) in PCA analysis.

Principal Component Analysis (PCA) is widely used in analytical chemistry, to reduce the dimensionality of a multivariate data set in a few Principal Components (PCs) that summarize the predominant patterns in the data. An accurate estimate of the number of PCs is indispensable to provide meaningful interpretations and extract useful information. We show how existing estimates for the number of PCs may fall short for datasets with considerable coherence, noise or outlier presence. We present here how Angle Distribution of the Loading Subspaces (ADLS) can be used to estimate the number of PCs based on the variability of loading subspace across bootstrap resamples. Based on comprehensive comparisons with other well-known methods applied on simulated dataset, we show that ADLS (1) may quantify the stability of a PCA model with several numbers of PCs simultaneously; (2) better estimate the appropriate number of PCs when compared with the cross-validation and scree plot methods, specifically for coherent data, and (3) facilitate integrated outlier detection, which we introduce in this manuscript. We, in addition, demonstrate how the analysis of different types of real-life spectroscopic datasets may benefit from these advantages of ADLS.

International consensus (ICON) on assessment of oropharyngeal dysphagia.

OBJECTIVE: To present international recommendations regarding the proper evaluation of oropharyngeal dysphagia (OD), both objectively and subjectively (self-evaluation). METHODS: Following a thorough review of the literature, 5 experts in the field from 4 different continents answered separately a questionnaire regarding the work-up of OD. Individual answers were presented and discussed during the world ENT conference that was held in Paris in June 2017. This article will present the recommendations issued from that meeting. RESULTS: For the initial objective assessment of OD, it is recommended to perform either a functional endoscopic evaluation of swallowing (FEES) or a videofluoroscopic swallowing study (VFSS). FEES is the more popular investigation given its increased ease of use and accessibility. When evaluating for the presence of aspiration during the objective evaluation of OD, it is recommended to perform either a FEES or a VFSS. In this case, FEES is the favored investigation given its likely increased sensitivity. In order to highlight the presence of oropharyngeal food residue following the deglutition process, it is recommended to perform either a FEES or a VFSS; FEES likely being the more sensitive investigation while VFSS allows a better quantification of the amount of pharyngeal residue. Is it also recommended to objectify the quality of the deglutition process by means of a score during the objective evaluation of OD. Finally, it is recommended to utilize a self-evaluation questionnaire during research studies exploring the deglutition process.

Plasma biomarker discovery for early chronic kidney disease diagnosis based on chemometric approaches using LC-QTOF targeted metabolomics data.

Chronic kidney disease (CKD) is a progressive pathological condition in which renal function deteriorates in time. The first diagnosis of CKD is often carried out in general care attention by general practitioners by means of serum creatinine (CNN) levels. However, it lacks sensitivity and thus, there is a need for new robust biomarkers to allow the detection of kidney damage particularly in early stages. Multivariate data analysis of plasma concentrations obtained from LC-QTOF targeted metabolomics method may reveal metabolites suspicious of being either up-regulated or down-regulated from urea cycle, arginine methylation and arginine-creatine metabolic pathways in CKD pediatrics and controls. The results show that citrulline (CIT), symmetric dimethylarginine (SDMA) and S-adenosylmethionine (SAM) are interesting biomarkers to support diagnosis by CNN: early CKD samples and controls were classified with an increase in classification accuracy of 18% when using these 4 metabolites compared to CNN alone. These metabolites together allow classification of the samples into a definite stage of the disease with an accuracy of 74%, being the 90% of the misclassifications one level above or below the CKD stage set by the nephrologists. Finally, sex-related, age-related and treatment-related effects were studied, to evaluate whether changes in metabolite concentration could be attributable to these factors, and to correct them in case a new equation is developed with these potential biomarkers for the diagnosis and monitoring of pediatric CKD.

Comparison of swallowing outcomes of laryngotracheal separation versus total laryngectomy in a validated ovine model of profound oropharyngeal dysphagia.

OBJECTIVES: To validate the ovine model of profound oropharyngeal dysphagia and compare swallowing outcomes of laryngotracheal separation with those of total laryngectomy. METHODS: Under real-time fluoroscopy, swallowing trials were conducted using the head and neck of two Dorper cross ewes and one human cadaver, secured in lateral fluoroscopic orientation. Barium trials were administered at baseline, pre- and post-laryngohyoid suspension, following laryngotracheal separation, and following laryngectomy in the ovine model. RESULTS: Mean pre-intervention Penetration Aspiration Scale and National Institutes of Health Swallow Safety Scale scores were 8 ± 0 and 6 ± 0 respectively in sheep and human cadavers, with 100 per cent intra- and inter-species reproducibility. These scores improved to 1 ± 0 and 2 ± 0 post-laryngohyoid suspension (p < 0.01). Aerodigestive tract residue was 18.6 ± 2.4 ml at baseline, 15.4 ± 3.8 ml after laryngotracheal separation and 3.0 ± 0.7 ml after total laryngectomy (p < 0.001). CONCLUSION: The ovine model displayed perfect intra- and inter- species reliability for the Penetration Aspiration Scale and Swallow Safety Scale. Less aerodigestive tract residue after narrow-field laryngectomy suggests that swallowing outcomes after total laryngectomy are superior to those after laryngotracheal separation.

On the relevance of glycolysis process on brain gliomas.

The proposed analysis considers aspects of both statistical and biological validation of the glycolysis effect on brain gliomas, at both genomic and metabolic level. In particular, two independent datasets are analyzed in parallel, one engaging genomic (Microarray Expression) data and the other metabolomic (Magnetic Resonance Spectroscopy Imaging) data. The aim of this study is twofold. First to show that, apart from the already studied genes (markers), other genes such as those involved in the human cell glycolysis significantly contribute in gliomas discrimination. Second, to demonstrate how the glycolysis process can open new ways towards the design of patient-specific therapeutic protocols. The results of our analysis demonstrate that the combination of genes participating in the glycolytic process (ALDOA, ALDOC, ENO2, GAPDH, HK2, LDHA, LDHB, MDH1, PDHB, PFKM, PGI, PGK1, PGM1 and PKLR) with the already known tumor suppressors (PTEN, Rb, TP53), oncogenes (CDK4, EGFR, PDGF) and HIF-1, enhance the discrimination of low versus high-grade gliomas providing high prediction ability in a cross-validated framework. Following these results and supported by the biological effect of glycolytic genes on cancer cells, we address the study of glycolysis for the development of new treatment protocols.

Statistical methods for improving verification of claims of origin for Italian wines based on stable isotope ratios.

Wine derives its economic value to a large extent from geographical origin, which has a significant impact on the quality of the wine. According to the food legislation, wines can be without geographical origin (table wine) and wines with origin. Wines with origin must have characteristics which are essential due to its region of production and must be produced, processed and prepared, exclusively within that region. The development of fast and reliable analytical methods for the assessment of claims of origin is very important. The current official method is based on the measurement of stable isotope ratios of water and alcohol in wine, which are influenced by climatic factors. The results in this paper are based on 5220 Italian wine samples collected in the period 2000-2010. We evaluate the univariate approach underlying the official method to assess claims of origin and propose several new methods to get better geographical discrimination between samples. It is shown that multivariate methods are superior to univariate approaches in that they show increased sensitivity and specificity. In cases where data are non-normally distributed, an approach based on mixture modelling provides additional improvements.

Opening the kernel of kernel partial least squares and support vector machines.

Kernel partial least squares (KPLS) and support vector regression (SVR) have become popular techniques for regression of complex non-linear data sets. The modeling is performed by mapping the data in a higher dimensional feature space through the kernel transformation. The disadvantage of such a transformation is, however, that information about the contribution of the original variables in the regression is lost. In this paper we introduce a method which can retrieve and visualize the contribution of the variables to the regression model and the way the variables contribute to the regression of complex data sets. The method is based on the visualization of trajectories using so-called pseudo samples representing the original variables in the data. We test and illustrate the proposed method to several synthetic and real benchmark data sets. The results show that for linear and non-linear regression models the important variables were identified with corresponding linear or non-linear trajectories. The results were verified by comparing with ordinary PLS regression and by selecting those variables which were indicated as important and rebuilding a model with only those variables.

Discrimination between metastasis and glioblastoma multiforme based on morphometric analysis of MR images.

BACKGROUND AND PURPOSE: Solitary MET and GBM are difficult to distinguish by using MR imaging. Differentiation is useful before any metastatic work-up or biopsy. Our hypothesis was that MET and GBM tumors differ in morphology. Shape analysis was proposed as an indicator for discriminating these 2 types of brain pathologies. The purpose of this study was to evaluate the accuracy of this approach in the discrimination of GBMs and brain METs. MATERIALS AND METHODS: The dataset consisted of 33 brain MR imaging sets of untreated patients, of which 18 patients were diagnosed as having a GBM and 15 patients, as having solitary metastatic brain tumor. The MR imaging was segmented by using the K-means algorithm. The resulting set of classes (also called "clusters") represented the variety of tissues observed. A morphology-based approach allowed discrimination of the 2 types of tumors. This approach was validated by a leave-1-patient-out procedure. RESULTS: A method was developed for the discrimination of GBMs and solitary METs. Two masses out of 33 were wrongly classified; the overall results were accurate in 93.9% of the observed cases. CONCLUSIONS: A semiautomated method based on a morphologic analysis was developed. Its application was found to be useful in the discrimination of GBM from solitary MET.

Revealing the metabolic profile of brain tumors for diagnosis purposes.

The metabolic behavior of complex brain tumors, like Gliomas and Meningiomas, with respect to their type and grade was investigated in this paper. Towards this direction the smallest set of the most representative metabolic markers for each brain tumor type was identified, using ratios of peak areas of well established metabolites, from (1)H-MRSI (Proton Magnetic Resonance Spectroscopy Imaging) data of 24 patients and 4 healthy volunteers. A feature selection method that embeds Fisher's filter criterion into a wrapper selection scheme was applied; Support Vector Machine (SVM) and Least Squares-SVM (LS-SVM) classifiers were used to evaluate the ratio markers classification significance. The area under the Receiver Operating Characteristic curve (AUROC) was adopted to evaluate the classification significance. It is found that the NAA/CHO, CHO/S, MI/S ratios can be used to discriminate Gliomas and Meningiomas from Healthy tissue with AUROC greater than 0.98. Ratios CHO/S, CRE/S, MI/S, LAC/CRE, ALA/CRE, ALA/S and LIPS/CRE can identify type and grade differences in Gliomas giving AUROC greater than 0.98 apart from the scheme of Gliomas grade II vs grade III where 0.84 was recorded due to high heterogeneity. Finally NAA/CRE, NAA/S, CHO/S, MI/S and ALA/S manage to discriminate Gliomas from Meningiomas providing AUROC exceeding 0.90.

Review article: diagnosis and management of night-time reflux.

Symptoms of gastro-oesophageal reflux disease (GERD) range from mild to severe and, when they occur during night-time hours, can interfere with sleep patterns and reduce overall quality of life. The clinical presentation of GERD is characterized by oesophageal as well as supra-oesophageal symptoms, including otolaryngologic and pulmonary complications. However, GERD may be overlooked as the cause of a patient's supra-oesophageal symptoms because these complaints can occur in the absence of oesophageal symptoms or endoscopic changes. The role of available tools used for GERD diagnosis, including endoscopy, oesophageal pH monitoring and an empirical course of proton pump inhibitor therapy, is discussed. Interventions available to achieve the therapeutic goals of symptom relief and prevention include specific lifestyle modifications and over-the-counter as well as prescription pharmacological agents. Patient-initiated, as-needed treatment may not be the best choice for managing persistent night-time reflux because it requires patient arousal from sleep. Proton pump inhibitor therapy remains the treatment of choice for patients with more severe symptoms and those with erosive oesophagitis. Few studies have specifically evaluated the role of pharmacological agents in the management of night-time reflux and comparisons are difficult due to the variability in study design and endpoints assessed.

Effect on the partial least-squares prediction of yarn properties combining raman and infrared measurements and applying wavelength selection.

The combination of Raman and infrared spectroscopy on the one hand and wavelength selection on the other hand is used to improve the partial least-squares (PLS) prediction of seven selected yarn properties. These properties are important for on-line quality control during production. From 71 yarn samples, the Raman and infrared spectra are measured and reference methods are used to determine the selected properties. Making separate PLS models for all yarn properties using the Raman and infrared spectra, prior to wavelength selection, reveals that Raman spectroscopy outperforms infrared spectroscopy. If wavelength selection is applied, the PLS prediction error decreases and the correlation coefficient increases for all properties. However, a substantial wavelength selection effect is present for the infrared spectra compared to the Raman spectra. For the infrared spectra, wavelength selection results in PLS prediction errors comparable with the prediction performance of the Raman spectra prior to wavelength selection. Concatenating the Raman and infrared spectra does not enhance the PLS prediction performance, not even after wavelength selection. It is concluded that an infrared spectrometer, combined with a wavelength selection procedure, can be used if no (suitable) Raman instrument is available.

Transnasal esophagoscopy.

BACKGROUND: Transnasal esophagoscopy (TNE), a new diagnostic technology, allows comprehensive, in-office examination of the esophagus without sedation. OBJECTIVE: To report the authors' experience using TNE. METHODOLOGY: Retrospective review of 100 consecutive patients undergoing TNE. RESULTS: The most frequent indications for TNE were screening examination of the esophagus in reflux, globus, and/or dysphagia patients (n = 79), biopsy of a lesion in the laryngopharynx, trachea, or esophagus (n = 8), screening examination of the esophagus in head and neck cancer patients (n = 5), tracheoscopy and bronchoscopy (n = 4), and evaluation for an esophageal foreign body (n = 2). Four procedures were aborted secondary to a tight nasal vault. Significant findings were found in 44% (42/96). The most frequent findings were esophagitis (n = 19), Barrett's (n = 6), hiatal hernia (n = 4), and carcinoma (n = 5). CONCLUSIONS: TNE is safe and well tolerated by patients with topical anesthesia alone. TNE may replace radiographic imaging of the esophagus in otolaryngology patients with reflux, globus, and dysphagia.

Proton pump inhibitor resistance in the treatment of laryngopharyngeal reflux.

OBJECTIVE: To describe the occurrence of relative proton pump inhibitor (PPI) drug resistance in the treatment of laryngopharyngeal reflux (LPR). STUDY DESIGN AND SETTING: A retrospective review was performed for 1053 consecutive adults undergoing double-probe (simultaneous esophageal and pharyngeal) pH testing in our laboratory. Two hundred five patients who had pH studies performed while taking at least a daily dose of PPI therapy were identified; 167 qualified for further analysis. The pH data was reviewed for the presence of abnormalities in either esophageal or pharyngeal acid exposure to evaluate drug efficacy. RESULTS: Forty-four percent (74/167) of the study patients demonstrated abnormal levels of acid exposure. Results were further analyzed to compare failure rates based on different dosage regimens. Patients on once daily doses of PPI failed at a rate of 56%, with lower failure rates for higher-dose regimens. CONCLUSIONS: A significant number of LPR patients on PPI therapy demonstrate relative drug resistance.

The validity and reliability of the reflux finding score (RFS).

BACKGROUND: The evaluation of medical and surgical outcomes relies on methods of accurately quantifying treatment results. Currently, there is no validated instrument whose purpose is to document the physical findings and severity of laryngopharyngeal reflux (LPR). OBJECTIVE: To evaluate the validity and reliability of the reflux finding score (RFS). METHODS: Forty patients with LPR confirmed by double-probe pH monitoring were evaluated pretreatment and 2, 4, and 6 months after treatment. The RFS was documented for each patient at each visit. For test-retest intraobserver reliability assessment, a blinded laryngologist determined the RFS on two separate occasions. To evaluate interobserver reliability, the RFS was determined by two different blinded laryngologists. RESULTS: The mean age of the cohort was 50 years (+/- 12 standard deviation [SD]). Seventy-three percent were women. The RFS at entry was 11.5 (+/- 5.2 SD). This score improved to 9.3 (+/- 4.7 SD) at 2 months, 7.3 (+/- 5.5 SD) at 4 months, and 6.1 (+/- 5.2 SD) at 6 months of treatment (P <.001 with trend). The mean RFS for laryngologist no. 1 was 10.8 (+/- 4.1 SD) at the initial screening and 10.8 (+/- 4.0 SD) at the repeat evaluation (r = 0.95, P <.001). The mean RFS for laryngologist no. 2 was 11.1 (+/- 3.8 SD) at the initial screening and 10.9 (+/- 3.7 SD) at the repeat evaluation (r = 0.95, P <.001). The correlation coefficient for interobserver variability was 0.90 (P <.001). CONCLUSIONS: The RFS accurately documents treatment efficacy in patients with LPR. It demonstrates excellent inter- and intraobserver reproducibility.

Laryngospasm and diaphragmatic arrest in immature dogs after laryngeal acid exposure: a possible model for sudden infant death syndrome.

Laryngopharyngeal reflux has been proposed as a possible cause of sudden infant death syndrome (SIDS). We investigated the efferent laryngeal and diaphragmatic responses to acid exposure on the laryngeal mucosa using a neonatal canine model. Electromyographic (EMG) recordings from the thyroarytenoid muscle and the diaphragm were measured with hooked-wire electrodes. Reproducible laryngospasm responses occurred in all animals after laryngeal exposure to hydrochloric acid at pH 2.0 or less. Laryngospasm occurred in combination with tachypnea and increased diaphragmatic activity in most of the animals. Laryngospasm was associated with prolonged apnea and total cessation of diaphragmatic EMG activity in 1 animal, and in another, initial tachypnea was followed by erratic diaphragmatic activity and brief apnea. Laryngeal acid exposure (below pH 2.0) causes laryngospasm and may result in paradoxical apneic events in neonatal dogs. Acid-induced, laryngospasm-associated apnea may represent a potential cause of SIDS, and the immature dog appears to be an excellent model for further investigations.

Diagnostic laryngeal electromyography: The Wake Forest experience 1995-1999.

BACKGROUND: Laryngeal electromyography (LEMG) is a valuable diagnostic/prognostic test for patients with suspected laryngeal neuromuscular disorders. OBJECTIVE: To report our experience with diagnostic LEMG at the Center for Voice Disorders of Wake Forest University and to evaluate the impact of LEMG on clinical management. METHODS: Retrospective chart review of 415 patients who underwent diagnostic LEMG over a 5-year period (1995-1999). RESULTS: Of 415 studies, 83% (346 of 415) were abnormal, indicating a neuropathic process. LEMG results altered the diagnostic evaluation (eg, the type of radiographic imaging) in 11% (46 of 415) of the patients. Unexpected LEMG findings (eg, contralateral neuropathy) were found in 26% (107 of 415) of the patients, and LEMG results differentiated vocal fold paralysis from fixation in 12% (49 of 415). Finally, LEMG results altered the clinical management (eg, changed the timing and/or type of surgical procedure) in 40% (166 of 415) of the patients. CONCLUSIONS: LEMG is a valuable diagnostic test that aids the clinician in the diagnosis and management of laryngeal neuromuscular disorders.