Digital restoration of colour cinematic films using imaging spectroscopy and machine learning.

Digital restoration is a rapidly growing methodology within the field of heritage conservation, especially for early cinematic films which have intrinsically unstable dye colourants that suffer from irreversible colour fading. Although numerous techniques to restore film digitally have emerged recently, complex degradation remains a challenging problem. This paper proposes a novel vector quantization (VQ) algorithm for restoring movie frames based on the acquisition of spectroscopic data with a custom-made push-broom VNIR hyperspectral camera (380-780 nm). The VQ algorithm utilizes what we call a multi-codebook that correlates degraded areas with corresponding non-degraded ones selected from reference frames. The spectral-codebook was compared with a professional commercially available film restoration software (DaVinci Resolve 17) tested both on RGB and on hyperspectral providing better results in terms of colour reconstruction.

Near-infrared hyperspectral imaging (NIR-HSI) and normalized difference image (NDI) data processing: An advanced method to map collagen in archaeological bones.

In the present study, an innovative and highly efficient near-infrared hyperspectral imaging (NIR-HSI) method is proposed to provide spectral maps able to reveal collagen distribution in large-size bones, also offering semi-quantitative estimations. A recently introduced method for the construction of chemical maps, based on Normalized Difference Images (NDI), is declined in an innovative approach, through the exploitation of the NDI values computed for each pixel of the hyperspectral image to localize collagen and to extract information on its content by a direct comparison with known reference samples. The developed approach addresses an urgent issue of the analytical chemistry applied to bioarcheology researches, which rely on well-preserved collagen in bones to obtain key information on chronology, paleoecology and taxonomy. Indeed, the high demand for large-sample datasets and the consequent application of a wide variety of destructive analytical methods led to the considerable destruction of precious bone samples. NIR-HSI pre-screening allows researchers to properly select the sampling points for subsequent specific analyses, to minimize costs and time and to preserve integrity of archaeological bones (which are available in a very limited amount), providing further opportunities to understand our past.

Evaluation of 793/B-like and Mass-like vaccine strain kinetics in experimental and field conditions by real-time RT-PCR quantification.

Infectious bronchitis virus (IBV) is a great economic burden both for productive losses and costs of the control strategies. Many different vaccination protocols are applied in the same region and even in consecutive cycles on the same farm in order to find the perfect balance between costs and benefits. In Northern Italy, the usual second vaccination is more and more often moved up to the chick's first d of life. The second strain administration together with the common Mass priming by spray at the hatchery allows saving money and time and reducing animal stress. The present work compared the different vaccine strains (Mass-like or B48, and 1/96) kinetics both in field conditions and in a 21-day-long experimental trial in broilers, monitoring the viral replication by upper respiratory tract swabbing and vaccine specific real time reverse transcription PCR (RT-PCR) quantification. In both field and experimental conditions, titers for all the vaccines showed an increasing trend in the first 2 wk and then a decrease, though still remaining detectable during the whole monitored period. IBV field strain and avian Metapneumovirus (aMPV) presence also was also investigated by RT-PCR and sequencing, and by multiplex real-time RT-PCR, respectively, revealing a consistency in the pathogen introduction timing at around 30 d, in correspondence with the vaccine titer's main decrease. These findings suggest the need for an accurate knowledge of live vaccine kinetics, whose replication can compete with the other pathogen one, providing additional protection to be added to what is conferred by the adaptive immune response.

Genome sequence analysis of a distinctive Italian infectious bursal disease virus.

In a recent study, an emerging infectious bursal disease virus (IBDV) genotype (ITA) was detected in IBDV-live vaccinated broilers without clinical signs of infectious bursal disease (IBD). VP2 sequence analysis showed that strains of the ITA genotype clustered separately from vaccine strains and from other IBDV reference strains, either classic or very virulent. In order to obtain a more exhaustive molecular characterization of the IBDV ITA genotype and speculate on its origin, genome sequencing of the field isolate IBDV/Italy/1829/2011, previously assigned to the ITA genotype, was performed, and the sequences obtained were compared to the currently available corresponding sequences. In addition, phylogenetic and recombination analyses were performed. Interestingly, multiple amino acid (AA) sequence alignments revealed that the IBDV/Italy/1829/2011 strain shared several AA residues with very virulent IBDV strains as well as some virulence markers, especially in the VP1 protein. Nevertheless, sequence analysis demonstrated the presence of several residues typical of IBDV strains at a low degree of virulence in the IBDV/Italy/1829/2011 strain. Although homologous recombination and reassortant phenomena may occur naturally among different IBDV strains, no evidence of those events was found in the genome of the IBDV/Italy/1829/2011 strain, which was confirmed to be a genetically distinctive IBDV genotype.

Gamma and Deltacoronaviruses in quail and pheasants from Northern Italy1.

In view of the restricted knowledge on the diversity of coronaviruses in poultry other than chicken, this study aimed to investigate the genetic diversity of coronaviruses in quail, pheasant, and partridge from two regions of Northern Italy. To this end, pools of tracheal and cloacal swabs from European quail (Coturnix Coturnix) and intestinal tract from pheasants (Phasianus Colchicus) and partridge (Perdix Perdix) flocks, with or without enteric signs, were collected during 2015. Avian coronavirus (Gammacoronavirus) was detected in quail not vaccinated against Infectious Bronchitis Virus (IBV) and in pheasants vaccinated with an IBV Massachusetts serotype. Based on DNA sequences for the gene encoding the S protein, the avian coronaviruses detected in the quail and pheasant are related to the IBV 793B and Massachusetts types, respectively. However, RNA-dependent RNA polymerase (RdRp) analyses showed the susceptibility of quail also to Deltacoronaviruses, suggesting that quail and pheasant avian coronaviruses share spike genes identical to chicken IBV spike genes and quail might host Deltacoronavirus.

Subpopulations in aMPV vaccines are unlikely to be the only cause of reversion to virulence.

Avian metapneumovirus (aMPV) infects respiratory and reproductive tracts of domestic poultry, often involving secondary infections, and leads to serious economic losses in most parts of the world. While in general disease is effectively controlled by live vaccines, reversion to virulence of those vaccines has been demonstrated on several occasions. Consensus sequence mutations involved in the process have been identified in more than one instance. In one previous subtype A aMPV candidate vaccine study, small subpopulations were implicated. In the current study, the presence of subpopulations in a subtype B vaccine was investigated by deep sequencing. Of the 19 positions where vaccine (strain VCO3/50) and progenitor (strain VCO3/60616) consensus sequences differed, subpopulations were found to have sequence matching progenitor sequence in 4 positions. However none of these mutations occurred in a virulent revertant of that vaccine, thereby demonstrating that the majority progenitor virus population had not survived the attenuation process, hence was not obviously involved in any return to virulence. However within the vaccine, a single nucleotide variation was found which agreed with consensus sequence of a derived virulent revertant virus, hence this and other undetected, potentially virulent subpopulations, can be involved in reversion. Much deeper sequencing of progenitor, vaccine and revertant may clarify whether problematic virulent subpopulations are present and therefore whether these need to be routinely removed during aMPV vaccine preparation prior to registration and release.

A sensitive, reproducible, and economic real-time reverse transcription PCR detecting avian metapneumovirus subtypes A and B.

Use of real-time PCR is increasing in the diagnosis of infectious disease due to its sensitivity, specificity, and speed of detection. These characteristics make it particularly suited for the diagnosis of viral infections, like avian metapneumovirus (AMPV), for which effective control benefits from continuously updated knowledge of the epidemiological situation. Other real-time reverse transcription (RT)-PCRs have been published based on highly specific fluorescent dye-labeled probes, but they have high initial cost, complex validation, and a marked susceptibility to the genetic variability of their target sequence. With this in mind, we developed and validated a SYBR Green I-based quantitative RT-PCR for the detection of the two most prevalent AMPV subtypes (i.e., subtypes A and B). The assay demonstrated an analytical sensitivity comparable with that of a previously published real-time RT-PCR and the ability to detect RNA equivalent to approximately 0.5 infectious doses for both A and B subtypes. The high efficiency and linearity between viral titer and crossing point displayed for both subtypes make it suited for viral quantification. Optimization of reaction conditions and the implementation of melting curve analysis guaranteed the high specificity of the assay. The stable melting temperature difference between the two subtypes indicated the possibility of subtyping through melting temperature analysis. These characteristics make our assay a sensitive, specific, and rapid tool, enabling contemporaneous detection, quantification, and discrimination of AMPV subtype A and B.

An outbreak of blindness due to retinopathy in nine flocks of guinea fowl.

Blindness was observed in 10- to 14-day-old guinea fowl. The incidence ranged from 25% to 80% in nine flocks within a total population of 110,000 guinea fowls. Clinical signs of blindness in birds included aimless wandering, failure to find feed and water, lateral recumbency, loss of weight, and increased mortality. The birds lacked papillary reflexes to light, and there were no gross lesions in the eyes. Histologically there was degeneration and disorganization of photoreceptors in the retina. The guinea fowl came from three different breeder sources but all of the birds were given the same feed. The condition was not observed in the subsequent flocks that came from the same breeder sources but that were given different feed. Based on these observations, toxicity of an unknown ingredient in the feed is suspected as the cause of blindness in the guinea fowl.

Reversion to virulence of a subtype B avian metapneumovirus vaccine: is it time for regulators to require availability of vaccine progenitors?

Empirically derived live avian metapneumovirus (AMPV) vaccines developed during the late 80s and early 90s have generally performed well in controlling turkey rhinotracheitis. Nonetheless, unstable attenuation was previously demonstrated in an AMPV subtype A vaccine. Until now this had not been investigated in subtype B vaccines due to lack of any similar availability of a vaccine progenitor or its sequence. The publication of the full genome sequence for the VCO3 vaccine progenitor facilitated a conclusive investigation of two AMPVs isolated from poults on a farm which had been vaccinated with VCO3 derived vaccine. Full genome sequencing of the isolates and their comparison to sequences of the vaccine and its progenitor, confirmed their vaccine origin. After determining the absence of extraneous infectious agents, one of these virus isolates was inoculated into 1-day-old turkeys in disease secure isolators and shown to cause disease with a severity similar to that caused by virulent field virus. This suggests that instability in live AMPV vaccines may be generalized and highlights the need for availability of vaccine progenitor sequences for the field assessment of all live viral vaccines.

Development of innovative embedding procedures for the analyses of paint cross sections in ATR FITR microscopy.

We report the development of innovative embedding procedures for the analysis of paint cross sections by attenuated total reflection (ATR) Fourier transform IR microscopy. This technique was chosen because it is widely employed for the characterization and spatial location of organic and inorganic components in artistic samples. Moreover, the performance of the technique may be critically affected by sample preparation in terms of surface morphology and the presence of contamination. First, we evaluated the use of KBr as a barrier to contamination by the embedding synthetic medium. In this way, the sample cross section can be polished by means of a sample holder, which allows a controlled pressure to be applied to the sample, thus improving the reproducibility and quality of the surface cross section. In addition, argon ion milling was used for the polishing of samples embedded in KBr, and provided very promising results in terms of surface planarity and reduction of superficial contamination by KBr. Finally, the use of NaCl as an alternative to KBr was proposed thanks to its advantages in terms of hygroscopicity, cost, and toxicity. In addition, cross sections embedded in NaCl were characterized by greater hardness, a feature that allowed us to obtain improved contact with the ATR crystal.

A round robin exercise in archaeometry: analysis of a blind sample reproducing a seventeenth century pharmaceutical ointment.

Chemical analysis of ancient residues of pharmaceutical or cosmetic preparations such as balms or ointments is made problematic by the high complexity of these mixtures, composed of organic and inorganic materials. Consequently, a multi-analytical approach and special caution in the interpretation of the results are necessary. In order to contribute to the improvement of analytical strategies for the characterization of complex residues and to reconstruct ancient medical practices, a replica of a pharmaceutical formulation of the seventeenth century was prepared in the laboratory according to a historically documented recipe. In a round robin exercise, a portion of the preparation was analysed as a blind sample by 11 laboratories using various analytical techniques. These included spectroscopic, chromatographic and mass spectrometric methods. None of the laboratories was able to completely reconstruct the complex formulation, but each of them gave partial positive results. The round robin exercise has demonstrated that the application of a multi-analytical approach can permit a complete and reliable reconstruction of the composition. Finally, on the basis of the results, an analytical protocol for the study of residues of ancient medical and pharmaceutical preparations has been outlined.

Pediocin A improves growth performance of broilers challenged with Clostridium perfringens.

The aim of this study was to investigate the efficacy of the anticlostridial pediocin A from Pediococcus pentosaceus FBB61 to contain negative effects associated to Clostridium proliferation in broilers, through 2 subsequent investigations. In the first study, 36 Ross 508 broilers were divided into 3 groups and fed for 21 d as follows: the control diet (CTR), the control diet supplemented with supernatant filtrate of a culture of P. pentosaceus FBB61-2 (Bac-, isogenic mutant nonproducing pediocin A), and the control diet supplemented with supernatant filtrate of a culture of P. pentosaceus FBB61 (Bac+) containing pediocin A. Birds were challenged with 10(6) cells of Clostridium perfringens. In the second study, 216 Ross 508 broilers were allocated in 18 pens and divided into 3 groups fed the same diet for 42 d: a control group (CTR), a group challenged with 10(8) cells of C. perfringens (CP), and a group challenged with 10(8) cells of C. perfringens and receiving the control diet supplemented with P. pentosaceus FBB61 and pediocin A (PA). Broiler BW, ADG, ADFI, and feed conversion rate were measured throughout the studies. At the end of both experiments, an appropriate number of birds was killed and analyzed for necrotic enteritis lesions and microbiological examinations. In the first study, on d 9, ADG and BW were 20% higher for Bac+ compared with CTR and Bac-; on d 14, ADG was higher for Bac+ (+23%, P<0.05), whereas BW was higher for Bac+ and Bac- compared with CTR (+23 and +14%, respectively; P<0.05). In the second study, on d 14, ADG and BW were higher for PA compared with CTR and CP (+15% on average; P<0.05), whereas between 15 and 42 d, there was only a tendency toward a higher ADG for PA when compared with the CP group (+4%, P=0.08). Diet supplementation with pediocin A improved broiler growth performance during the challenge with C. perfringens and tended to restore the ADG depletion during the 42-d period.

In vitro antiviral activity of chestnut and quebracho woods extracts against avian reovirus and metapneumovirus.

Field evidences have suggested that a natural extract, containing tannins, could be effective against poultry enteric viral infections. Moreover previous studies have shown that vegetable tannins can have antiviral activity against human viruses. Based on this knowledge three different Chestnut (Castanea spp.) wood extracts and one Quebracho (Schinopsis spp.) wood extract, all containing tannins and currently used in the animal feed industry, were tested for in vitro antiviral activity against avian reovirus (ARV) and avian metapneumovirus (AMPV). The MTT assay was used to evaluate the 50% cytotoxic compounds concentration (CC(50)) on Vero cells. The antiviral properties were tested before and after the adsorption of the viruses to Vero cells. Antiviral activities were expressed as IC(50) (concentration required to inhibit 50% of viral cytopathic effect). CC(50)s of tested compounds were > 200 microg/ml. All compounds had an extracellular antiviral effect against both ARV and AMPV with IC(50) values ranging from 25 to 66 microg/ml. Quebracho extract had also evident intracellular anti-ARV activity (IC(50) 24 microg/ml). These preliminary results suggest that the examined vegetable extracts might be good candidates in the control of some avian virus infections. Nevertheless further in vivo experiments are required to confirm these findings.

The use of virus isolation, histopathology and immunoperoxidase techniques to study the dissemination of a chicken isolate of avian pneumovirus in chickens.

A subgroup B isolate of turkey rhinotracheitis virus (TRTV) or avian pneumovirus (APV), obtained from a flock of commercial breeding chickens experiencing poor egg production, mortality and swollen head syndrome, was shown to cause substantial respiratory signs in both young SPF chickens and chicks with high levels of maternally derived TRT antibodies. This isolate replicated to high titre in the respiratory tract of experimentally inoculated SPF chickens for approximately 5 days after inoculation, but was recovered only occasionally after that time. It was never recovered from non-respiratory tract tissues. A detailed, sequential histological and immunoperoxidase study was performed. This revealed that, whilst TRT virus could be demonstrated consistently in the epithelium of upper respiratory tract tissue, although only for a short time after inoculation, the damage which it caused was minimal and recovery was rapid. This study, using a pathogenic TRT isolate obtained from diseased chickens, provides clear evidence that TRT virus can cause damage to the respiratory tract of chickens and that this damage is both localized and short lived.