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

Reovirus tenosynovitis in a flock of layer breeders

The present paper describes a reovirus infection with clinical course in a flock of layer breeders. Lameness and tenosynovitis of flexor tendons were observed in approximately 15% of the cockerels and 3% of the hens from 17 weeks of age onwards. Affected birds did not die; on the contrary, most of them recovered clinically within a period of 8 weeks. Two other breeds of layer parents that were housed in close contact with the affected flock did not develop clinical signs, although serology indicated that infection with reovirus had taken place. These field observations constitute the first report of clinical reovirus tenosynovitis in layer parents and indicate different susceptibilities of layer parent breeds in developing clinical signs following reovirus infection

EFFICACY of tylosin tartrate on Mycoplasma infections and eggshell apex abnormalities in layer hens under field conditions

The aim of this report was to describe a clinical case of concurrent infection with Mycoplasma Gallisepticum (MG) and Mycoplasma Synoviae (MS) in layers, complicated with Escherichia coli and Pasteurella multocida, as well as to evaluate the efficacy of tylosin tartrate treatment (Pharmasin® 100% WSG, Huvepharma) on Mycoplasma under field conditions. A flock of 18,500 ISA Brown pullets, 21 weeks of age and MS positive, showed an increase in weekly mortality, with no influence on egg production. At 24 weeks of age, post mortem was carried out and blood samples were collected, as well as samples for microbiological cultures from the lesions. In necropsy, several findings of pericarditis, airsacculitis of posterior thoracic sacs, prolapse and egg yolk peritonitis were found. Sporadic neurological signs were also apparent and post mortem examination revealed yellow caseous exudate accumulations in cranial bones. Although egg production was not influenced, Eggshell Apex Abnormalities (EAA) were increased with a significant number of both broken and misshapen eggs together with discoloration. Elisa serological examinations for Infectious Bronchitis Virus (IBV) and Newcastle Disease Virus (NDV) were within vaccination program limits, but MS, MG and Avian Rhinotracheitis (ART) results showed a significant seroconversion. Microbiology also revealed the presence of Escherichia coli and Pasteurella multocida. On week 25, a drug treatment with tylosin tartrate was applied at a dose of 105 mg kg-1 body weight in drinking water for five consecutive days. Three days after treatment, misshapen, broken and discolored eggs were decreased. The mortality was also significantly decreased within a week since the beginning of tylosin administration and at 30 weeks of age was within acceptable levels. Post mortem evaluation confirmed the absence of previously gross lesions in primary organs. In summary, tylosin treatment in complicated Mycoplasma spp. infections under field conditions improved egg shell quality and decreased mortality, thus the economic losses linked to decreased egg production and labor costs were reduced. © 2013 Science Publication

Aragonite-calcite-dolomite relationships in UHPM polycrystalline carbonate inclusions from the Kokchetav Massif, northern Kazakhstan

The presence of aragonite in polycrystalline carbonate inclusions in garnet in diamond-grade metamorphic rocks from the Kokchetav Massif, N. Kazakhstan was identified for the first time by means of Raman analyses and mapping, cathodoluminescence images and optical and scanning electron microscopy. Aragonite appears within the inclusions as dirty, chaotically oriented materials surrounded by a clean monocrystalline calcite shell; the grain boundary between the host-garnet and the aragonite-bearing inclusions is often characterized by a wavy or amoeboid shape; no cracks occur around the aragonite-bearing inclusior s; no significant shift in the main aragonite Raman band was measured. These observations indicate that residual pressure within the inclusion is minor. These features are inconsistent with an origin of aragonite at peak metamorphic conditions (6 GPa) by decomposition of dolomite

Is quartz a potential indicator of ultrahigh-pressure metamorphism? Laser Raman spectroscopy of quartz inclusions in ultrahigh-pressure garnets

Laser Raman microspectroscopy was applied to quartz inclusions in coesite- and diamond-grade metapelites from the Kokchetav ultrahigh-pressure metamorphic (UHPM) complex, Northern Kazakhstan, and diamond-grade eclogite xenoliths from the Mir kimberlite pipe, Yakutiya, Russia to assess the quantitative correlation between the Raman frequency shift and metamorphic pressure. Quartz crystals sealed in garnets have a higher frequency shift than those in the matrix. Residual pressures retained by quartz inclusions depend on the metamorphic history of the garnet host. The Raman frequency saift of quartz inclusions in garnet from coesite-grade and diamond-grade metamorphic rocks shows no systematic change with increasing peak metamorphic pressures. The highest shifts of the main Raman bands of quartz were documented for monocrystalline quartz inclusions in garnets from a diamond-grade eclogite xenolith. Calibrations based on experimental work suggest that the measured Raman frequency shifts signify residual pressures of 0.1-0.6 GPa for quartz. inclusions from coesite-grade metapelites from Kokchetav, 0.1-0.3 GPa for quartz inclusions from diamond-grade metapelites from Kokchetav, and 1.0-1.2 GPa for quartz inclusions from the diamond-grade eclogite xenoliths from the Mir kimberlite pipe. Normal stresses and internal (residual) pressures of quartz inclusions in garnet were numerically simulated with a 3-shell elastic model. Estimated values of residual pressures are inconsistent with the residual pressures estimated from the frequency shifts. Residual pressure slightly depends on P-T conditions at peak metamorphic stage. Laser Raman microspectroscopic analysis of quartz is a potentially powerful method for recovering an ultrahigh pressure metamorphic event. Monocrystalline quartz inclusions yielding a residual pressure greater than 2.5 GPa might indicate the presence of a former coesite