Calibration of spectra in presence of non-stationary background using unsupervised physics-informed deep learning

: Calibration is a key part of the development of a diagnostic. Standard approaches require the setting up of dedicated experiments under controlled conditions in order to find the calibration function that allows one to evaluate the desired information from the raw measurements. Sometimes, such controlled experiments are not possible to perform, and alternative approaches are required. Most of them aim at extracting information by looking at the theoretical expectations, requiring a lot of dedicated work and usually involving that the outputs are extremely dependent on some external factors, such as the scientist experience. This work presents a possible methodology to calibrate data or, more generally, to extract the information from the raw measurements by using a new unsupervised physics-informed deep learning methodology. The algorithm allows to automatically process the data and evaluate the searched information without the need for a supervised training by looking at the theoretical expectations. The method is examined in synthetic cases with increasing difficulties to test its potentialities, and it has been found that such an approach can also be used in very complex behaviours, where human-drive results may have huge uncertainties. Moreover, also an experimental test has been performed to validate its capabilities, but also highlight the limits of this method, which, of course, requires particular attention and a good knowledge of the analysed phenomena. The results are extremely interesting, and this methodology is believed to be applied to several cases where classic calibration and supervised approaches are not accessible

New insights on Avian orthoreovirus and Chicken astrovirus co-infection in an Italian broiler flock: preliminary biomolecular and pathological results

Summary Common pathogens of intensive poultry farms, either parasitic or bacterial, such as Coccidia or Salmonella, are well known and strictly controlled by veterinary management. This case study reports an unusual case of runting stunting syndrome (RSS) observed on a Sicilian poultry farm of broiler chickens during 2019. The investigation was carried out on five chickens which present delayed in body weight and growth performance. Animals showed also difficulty in deambulation and diarrhea. At necropsy, intestinal lesions were detected in three of the five clinical cases. Gut samples were collected and analyzed to identify potential pathogens responsible for the RSS. Presence of viruses was detected by using quantitative reverse transcription PCR (RT‑qPCR), while selected tissues were fixed and embedded in paraffin wax according to routine procedures. All histological sections were stained with hematoxylin‑eosin. RT‑qPCR successfully detected both Chicken astrovirus (CAstV) and Avian orthoreovirus (ARV). Histology evidenced severe specific lesions on the intestinal mucosa in liver and kidneys. Chicken astrovirus and Avian orthoreovirus RNA was also detected in cecal tonsils, kidney and liver, thus implying their possible primary role in inducing the disease. Further studies are needed to evaluate the role of other possible factors (low biosecurity measures, e.g.) and, most of all, the consequences in terms of economic losses and animal health impairment

Effects of Microencapsulated Blends of Organics Acids (OA) and Essential Oils (EO) as a Feed Additive for Broiler Chicken. A Focus on Growth Performance, Gut Morphology and Microbiology

Simple Summary Replacing antibiotics with natural alternative compounds in poultry feeding is being increased in the last few years to challenge the antibiotic resistance problem. Among natural compounds, organic acids and essential oils could be a favorable option. The goal of the trial was testing the dietary supplementation of a blend of organic acids and essential oils in broiler diets in order to evaluate growth performance and gut healthiness. The blend of organic acids and essential oils improved growth performances at the end of the growing period and favorably affected, to a certain extent, gut morphology at different gut districts. Moreover, a selective microbial control against Clostridium perfringens, Enterobacteriaceae, Enterococci and Mesophilic bacteria was found. Additionally, in litter, organic acids and essential oils dietary treatment drove to an overall decrease of Mesophilic bacteria and Enterococci counts. Overall, dietary strategy oriented to a supplementation of a mixture of organic acids and essential oils in broiler diets could offer some favorable perspectives in order to maintain adequate growth performance and gut healthiness either in term of morphology or of microbiology. Nevertheless, improving knowledge on the mechanisms of action of these natural additives together with a potential synergistic action is pivotal to clarify their potential as antibiotic replacers. Abstract The goal of the trial was testing the effects of a blend of organic acids and essential oils dietary supplementation on growth performance and gut healthiness in broiler chickens. In total, 420 male Ross 308 chicks (1-day old) were randomly assigned to two dietary treatments: basal (BD) and organic acids and essential oils (OA&EO) diets (three replicates/treatment; 70 broilers/replicate). BD group received commercial diets whereas OA&EO group basal diets + 5 g/kg of microencapsulated organic acids and essential oils. OA&EO treatment improved the average daily gain (p < 0.01) and feed conversion ratio at 37–47 days compared to BD treatment. OA&EO treatment improved gut morphology mostly at ileum and duodenum levels in terms of villi height, crypt depth, number of villi, mucosa thickness and villi area at 24 and 34 sampling days. A certain selective action against Clostridium perfringens in ileum of OA&EO group was shown at 33 (p = 0.053) and 46 days (p = 0.09) together with lower median values for Enterobacteriaceae, Enterococci, Mesophilic bacteria and Clostridium perfringens at ceca level. Overall, organic acids and essential oils supplementation improved growth performance in the final growth stage and some morphological gut traits and reduced to a certain extent Clostridium perfringens count in ileum

Morphological and Immunohistochemical Examination of Lymphoproliferative Lesions Caused by Marek's Disease Virus in Breeder Chickens

Simple Summary The poultry industry is the most intensive and fastest growing among all livestock production systems, and, in the last decades, it has expanded exponentially due to an increasing demand for meat and eggs. Marek’s disease is a highly contagious and rapidly progressive lymphoproliferative disease. It is one of the most dangerous diseases of those affecting the sector because it causes important economic losses. Although widely controlled by vaccination programs, sometimes chickens are not totally protected, and the presence of virulent field strains can allow outbreaks. This case describes the occurrence of Marek’s disease observed in a breeder chicken flock that reported an increase in mortality rate (+0.4–0.6%) after the 32nd week. Histological analysis has highlighted severe lesions on visceral organs of chickens caused by Marek’s disease, especially in the intestinal tract of a hen that had a tumor mass in the distal part of the cloaca. Immunohistochemical staining confirmed the disease-associated tumor. The aim of this study was to underline the importance of vaccine administration related to the maintenance of proper biosecurity practice, especially in the first week of the raising cycle. In addition, monitoring for disease even after vaccination is crucial to minimize economic loss. Abstract Marek’s disease is widely controlled by vaccination programs; however, chickens are not totally protected, especially immediately after the vaccination when a strong challenge could interfere with the effectiveness of vaccination in the absence of proper biosecurity practice. This case report describes the occurrence of Marek’s disease (MD) observed in a breeder chicken flock reared southeast of Sicily. MD outbreak occurred from 32 to 47 weeks with an increase in weekly mortality rate (+0.4–0.6%). Overall, mortality rate related to Marek’s disease was about 6% at the end of the cycle. Carcasses of chickens found during the occurrence of disease underwent necropsy, and tissues were collected to confirm the infection. Gizzard, cecal tonsil, intestine, spleen and tumor mass were collected and analyzed from a carcass of one hen, 32 weeks old and apparently asymptomatic. Multiplex real-time PCR performed on spleen tissues detected the presence of MD virus pathogenic strain. Macroscopic and microscopic evaluation of the rest of the samples confirmed the neoplastic disease. Moreover, the immunophenotype of the tumor cells was identified as CD3 positive by immunohistochemical (IHC) staining. The vaccinated flock had become rapidly infected with the MD virus, which proves that the challenge of the MD virus was too strong in the rearing house at the beginning of the cycle, causing the outbreak

Investigation of an Autochthonous Outbreak of Bovine Besnoitiosis in Northwestern Sicily

Abstract Bovine besnoitiosis is a parasitic disease caused by the protozoan Besnoitia besnoiti, leading to infertility in bulls and abortions in cows. In Italy, it is considered an emerging disease, recently introduced by the importation of animals from Spain and France. In the last decade, many outbreaks have been reported and confirmed in native cattle, mostly in northern and central Italy. This study reports on an autochthonous outbreak of bovine besnoitiosis in two nearby farms located in northwestern Sicily. A 15-month-old Limousine bull born on the farm showed typical clinical signs of the chronic disease phase, such as edema of the scrotum with subsequent hyperkeratosis associated with eschars and thickening of the skin. A histopathological examination revealed the presence of Besnoitia tissue cysts containing bradyzoites in the eyes, tendons, testicles, dermis, and nictitating membrane. A serological investigation using a commercial ELISA kit revealed a high seroprevalence of the antibody anti-B. besnoiti (79.2% for the farms in this study). Clinical disease showed low prevalence (1.5%) despite the high seroprevalence of specific antibodies in the herd, confirming that bovine besnoitiosis is an emergent endemic pathogen in Sicily, but its clinical behavior still remains sporadic

BOVINE BESNOITIOSIS: A CASE REPORT IN SICILY

IINTRODUCTION Bovine besnoitiosis is a parasitic disease caused by the tissue cyst forming protozoan Besnoitia besnoiti The European Food Safety Authority ( has reported that bovine besnoitiosis is re emerging in Europe 1 It represents a chronic and debilitating disease that is responsible for severe economic losses such as poor body condition, decreased milk production, infertility in bulls and occasional abortion 2 Autochthonous outbreaks of the disease were reported in Central Italy for the first time in 2009 3 In Sicily, although the disease was observed in a heifer in 2014 4 no epidemiological data is known AIM OF THE WORK This study describes an autochthonous outbreak of Bovine besnoitiosis in North Western Sicily a bull that shows typical clinical symptoms related to bovine besnoitiosis and moreover, the serological investigation of the herd, suspected of being infected by B besnoiti MATERIALS AND METHODS In a 16 month old affected bull, clinical status was evaluated both in acute and chronic stage After slaughtering, samples of skin, conjunctiva, tongue, and tendons were collected for histopathological examination Furthermore, i n the bull and in the Limousine herd of 72 animals, serological investigation using ID Screen® Besnoitia Indirect 2 0 ID vet was performed. RESULT The bull showed typical clinical signs of besnoitiosis such as: high fever, diffuse oedema at the joints of limbs and scrotum, hyperemia of muzzle and eyes, orchitis , thickening of the nasal planum and wheezing. About 1 0 12 days later, skin lesions ( hyperkeratosis, alopecia, dandruff and scab) appeared (Figure 1). At the 58th day after the beginning of the first signs, the animal showed diffuse skin thickening, was emaciated and reluctant to move. Histological examination showed multifocal coalescing thick wall cysts surrounding parasitophorous vacuole containing thousands of banana shaped bradyzoites all the collected samples (Figure 2 3). ELISA confirmed the seropositivity of the bull, moreover, 79,17% of the herd resulted positive (Tab 1) CONCLUSION. Finally, since all the animals were born in the farm or were bought from nearby farms this case confirms the presence of autochthonous B. besnoiti also in Sicily and may contribute to a further epidemiological study in this area. REFERENCES [1] EFSA Journal, 2010, EFSA Journal 8: 1499-514 [2]Gutiérrez Expósito et al., 2017 Int J Parasitol . 47: 737 51 [3]A. Gentile et al., 2012 Vet Parasitol . 184: 108 15 [4]Di Marco et al., 2016 LXX SISVET. 430

Determination of composition of mixed biological samples using laser-induced fluorescence and combined classification/regression models

Abstract Laser-induced fluorescence (LIF) provides the ability to distinguish organic materials by a fast and distant in situ analysis. When detecting the substances directly in the environment, e.g. in an aerosol cloud or on surfaces, additional fluorescence signals of other fluorophores occurring in the surrounding are expected to mix with the desired signal. We approached this problem with a simplified experimental design for an evaluation of classification algorithms. An upcoming question for enhanced identification capabilities is the case of mixed samples providing different signals from different fluorophores. For this work, mixtures of up to four common fluorophores (NADH, FAD, tryptophan, and tyrosine) were measured by a dual wavelength setup and spectrally analyzed. Classification and regression are conducted with neural networks and show an excellent performance in predicting the ratios of the selected ingredients

A Weighted-LSM Method to Improve Classification and Concentration Evaluation from Laser-Induced Fluorescence Spectra

The detection of biological agents using optical systems is an open field of research. Currently, different spectroscopic techniques allow to detect and classify chemical agents while a fast and accurate technique able to identify biological agents is still under investigation. Some optical techniques, such as Laser-Induced Breakdown Spectroscopy (LIBS) or Laser-Induced Fluorescence (LIF), are already used as classification methods. However, the presence of background, spectrum similarities and other confounders make these techniques not very specific. This work shows a new method to achieve better performances in terms of classification and concentration evaluations. The method is based on the Weighted Least Square Minimization method. In fact, by using ad hoc weights, the LSM looks at specific features of the spectra, resulting in higher accuracy. In order to make a systematic analysis, numerical tests have been conducted. With these tests, the authors were able to highlight the various advantages and drawbacks of the new methodology proposed. Then, the method was applied to some LIF measurements to investigate the applicability of the method to preliminary experimental cases. The results show that, by using this new weighted LSM, it is possible to achieve better classification and concentration evaluation performances. Finally, the possible application of the new method is discussed

HER-2 expression in canine morphologically normal, hyperplastic and neoplastic mammary tissues and its correlation with the clinical outcome

The proto-oncogene HER-2/neu (c-erbB-2) encodes a transmembrane receptor protein with tyrosine-kinase activity. Previous studies have shown that HER-2 protein over-expression is present in canine mammary tumours, however, possible prognostic and predictive analogies between protein over-expression patterns in canine and human species are still controversial. Thirty-five canine mammary carcinomas, 11 mammary adenomas, and normal, hyperplastic or dysplastic tissues taken at the marginal area of the tumours were evaluated by immunohistochemistry (IHC) for HER-2 expression, using the Hercept Test ® system scoring guidelines. HER-2 over-expression was detected in 3/11 adenomas and 10/35 carcinomas. Normal, hyperplastic and dysplastic mammary tissues were also found to be positive. The correlations between HER-2 expression and tumour histological grading, mitotic index, the presence of lymphatic invasion, and overall survival (OS) were evaluated. In carcinomas, HER-2 positive status only correlated with the mitotic index. A positive correlation was also found between HER-2 positive status and the presence of HER-2 over-expression in normal, hyperplastic or/and dysplastic mammary tissues surrounding the tumours. The percentage of HER-2 over-expressing tumours was similar to the percentage previously observed in canine benign and malignant mammary tumours. However an investigation regarding morphologically normal and hyperplastic or dysplastic tissues surrounding neoplastic lesions also showed HER-2 over-expression. In contrast with human mammary tumours, this study confirmed that in canine species, HER-2 over-expression does not identify a subgroup of tumours with a poor prognosis. In fact, we found HER-2 over-expression in morphologically non-neoplastic mammary tissues, surrounding hyperplastic and neoplastic lesions