Tutorial: Multivariate Classification for Vibrational Spectroscopy in Biological Samples

Vibrational spectroscopy techniques, such as Fourier-transform infrared (FTIR) and Raman spectroscopy, have been successful methods for studying the interaction of light with biological materials and facilitating novel cell biology analysis. Spectrochemical analysis is very attractive in disease screening and diagnosis, microbiological studies and forensic and environmental investigations because of its low cost, minimal sample preparation, non-destructive nature and substantially accurate results. However, there is now an urgent need for multivariate classification protocols allowing one to analyze biologically derived spectrochemical data to obtain accurate and reliable results. Multivariate classification comprises discriminant analysis and class-modeling techniques where multiple spectral variables are analyzed in conjunction to distinguish and assign unknown samples to pre-defined groups. The requirement for such protocols is demonstrated by the fact that applications of deep-learning algorithms of complex datasets are being increasingly recognized as critical for extracting important information and visualizing it in a readily interpretable form. Hereby, we have provided a tutorial for multivariate classification analysis of vibrational spectroscopy data (FTIR, Raman and near-IR) highlighting a series of critical steps, such as preprocessing, data selection, feature extraction, classification and model validation. This is an essential aspect toward the construction of a practical spectrochemical analysis model for biological analysis in real-world applications, where fast, accurate and reliable classification models are fundamental

Dermacentor reticulatus: a vector on the rise

Dermacentor reticulatus is a hard tick species with extraordinary biological features. It has a high reproduction rate, a rapid developmental cycle, and is also able to overcome years of unfavourable conditions. Dermacentor reticulatus can survive under water for several months and is cold-hardy even compared to other tick species. It has a wide host range: over 60 different wild and domesticated hosts are known for the three active developmental stages. Its high adaptiveness gives an edge to this tick species as shown by new data on the emergence and establishment of D. reticulatus populations throughout Europe. The tick has been the research focus of a growing number of scientists, physicians and veterinarians. Within the Web of Science database, more than a fifth of the over 700 items published on this species between 1897 and 2015 appeared in the last three years (2013–2015). Here we attempt to synthesize current knowledge on the systematics, ecology, geographical distribution and recent spread of the species and to highlight the great spectrum of possible veterinary and public health threats it poses. Canine babesiosis caused by Babesia canis is a severe leading canine vector-borne disease in many endemic areas. Although less frequently than Ixodes ricinus, D. reticulatus adults bite humans and transmit several Rickettsia spp., Omsk haemorrhagic fever virus or Tick-borne encephalitis virus. We have not solely collected and reviewed the latest and fundamental scientific papers available in primary databases but also widened our scope to books, theses, conference papers and specialists colleagues’ experience where needed. Besides the dominant literature available in English, we also tried to access scientific literature in German, Russian and eastern European languages as well. We hope to inspire future research projects that are necessary to understand the basic life-cycle and ecology of this vector in order to understand and prevent disease threats. We conclude that although great strides have been made in our knowledge of the eco-epidemiology of this species, several gaps still need to be filled with basic research, targeting possible reservoir and vector roles and the key factors resulting in the observed geographical spread of D. reticulatus. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13071-016-1599-x) contains supplementary material, which is available to authorized users

NMR-Based Screening for Inborn Errors of Metabolism: Initial Results from a Study on Turkish Neonates

WOS: 000376979100015PubMed ID: 25012580Approximately 1 in 400 neonates in Turkey is affected by inherited metabolic diseases. This high prevalence is at least in part due to consanguineous marriages. Standard screening in Turkey now covers only three metabolic diseases (phenylketonuria, congenital hypothyroidism, and biotinidase deficiency). Once symptoms have developed, tandem-MS can be used, although this currently covers only up to 40 metabolites. NMR potentially offers a rapid and versatile alternative. We conducted a multi-center clinical study in 14 clinical centers in Turkey. Urine samples from 989 neonates were collected and investigated by using NMR spectroscopy in two different laboratories. The primary objective of the present study was to explore the range of variation of concentration and chemical shifts of specific metabolites without clinically relevant findings that can be detected in the urine of Turkish neonates. The secondary objective was the integration of the results from a healthy reference population of neonates into an NMR database, for routine and completely automatic screening of congenital metabolic diseases. Both targeted and untargeted analyses were performed on the data. Targeted analysis was aimed at 65 metabolites. Limits of detection and quantitation were determined by generating urine spectra, in which known concentrations of the analytes were added electronically as well as by real spiking. Untargeted analysis involved analysis of the whole spectrum for abnormal features, using statistical procedures, including principal component analysis. Outliers were eliminated by model building. Untargeted analysis was used to detect known and unknown compounds and jaundice, proteinuria, and acidemia. The results will be used to establish a database to detect pathological concentration ranges and for routine screening

Effect of residual interatrial shunt on migraine burden after transcatheter closure of patent foramen ovale

OBJECTIVES: This study sought to evaluate the long-term effect of transcatheter patent foramen ovale (PFO) closure on migraineurs with and without aura and examine the effect of residual right-to-left shunt. BACKGROUND: Many studies reported improvement in migraine symptoms after PFO closure, yet randomized trials failed to reach its clinical endpoints. METHODS: The study retrospectively analyzed data from 474 patients who underwent transcatheter PFO closure at Massachusetts General Hospital. Patients completed a migraine burden questionnaire at baseline and at follow-up. Migraine severity is reported as migraine frequency (days/month), average duration (min), and migraine burden (days × min/month). Improvement following closure was defined as complete abolishment of symptoms or >50% reduction in migraine burden. RESULTS: A total of 110 migraineurs who underwent PFO closure were included; 77.0% had aura and 23.0% were without aura, and 91.0% had a cryptogenic stroke. During long-term median follow-up of 3.2 (interquartile range: 2.1 to 4.9) years, there was a significant improvement in migraine symptoms in migraineurs with or without aura. Migraine burden was reduced by >50% in 87.0% of patients, and symptoms were completely abolished in 48%. Presence of aura was associated with abolishment of migraine (odds ratio: 4.30; 95% confidence interval: 1.50 to 12.30; p = 0.006). At 6 months after PFO closure, residual right-to-left shunt was present in 26% of patients. Absence of right-to-left shunt was associated with improvement in migraine burden by >50% (odds ratio: 4.60; 95% confidence interval: 1.30 to 16.10; p = 0.017). CONCLUSIONS: Long-term follow-up after transcatheter PFO closure was associated with significant improvement in migraine burden. Aura was a predictor of abolishing symptoms. Absence of residual right-to-left shunt was a predictor of significant reduction in migraine burden.Accepted manuscrip