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A total of 71 loggerhead turtles (Caretta caretta) stranded along the coasts of Sicily (Southern Italy) were examined for non-dioxine like polychlorinated biphenyl (NDL-PCB) levels in muscle and adipose tissue by a gas chromatography-mass spectrometry/mass spectrometry (GC-MS/MS) method. The results revealed 6 high-indicator congener (∑6 PCBIND ) levels in 45% of the loggerhead turtles examined, with mean values of 980.39 ± 2508.39 ng/g wet weight in adipose tissue and 102.53 ± 238.58 ng/g wet weight in muscle tissue. The hexachloro and heptachloro PCB congeners were the most abundant in both the sample types. The highest NDL-PCB levels were reached in an adipose tissue sample of a loggerhead turtle of 80 kg stranded along the coasts of Termini Imerese (14 183.85 ng/g wet wt). No significant correlation was found between modified Fulton's K values of the loggerhead turtles and PCB contents (S = 47 151, p > 0.05). Furthermore, no significant differences were found between sexes (W = 365, p > 0.05). The PCB levels found in the present study were much higher than those found in the literature. The present study is the first report on the existence of NDL-PCBs in loggerhead turtles stranded in Sicilian coasts confirming C. caretta as a valuable indicator of contaminant exposure in the marine environment because of their specific biological and ecological characteristics. Environ Toxicol Chem 2017;36:2997-3002. © 2017 SETAC.

In this study, the presence of Leishmania DNA and blood feeding sources in phlebotomine sand fly species commonly present in Sicily were investigated. A total of 1,866 female sand flies including 176 blood fed specimens were sampled over two seasons in five selected sites in Sicily (southern Italy). Sergentomyia minuta (n = 1,264) and Phlebotomus perniciousus (n = 594) were the most abundant species at all the sites, while three other species from the genus Phlebotomus (i.e., P. sergenti n = 4, P. perfiliewi n = 3 and P. neglectus n = 1) were only sporadically captured. Twenty-eight out of the 1,866 (1.5%) sand flies tested positive for Leishmania spp. Leishmania tarentolae DNA was identified in 26 specimens of S. minuta, while the DNA of Leishmania donovani complex was detected in a single specimen each of S. minuta and P. perniciosus. Interestingly, seven S. minuta specimens (0.4%) tested positive for reptilian Trypanosoma sp. Blood sources were successfully identified in 108 out of 176 blood fed females. Twenty-seven out of 82 blood sources identified in fed females of P. perniciosus were represented by blood of wild rabbit, S. minuta mainly fed on humans (16/25), while the sole P. sergenti fed specimen took a blood meal on rat. Other vertebrate hosts including horse, goat, pig, dog, chicken, cow, cat and donkey were recognized as blood sources for P. perniciosus and S. minuta, and, surprisingly, no reptilian blood was identified in blood-fed S. minuta specimens. Results of this study agree with the well-known role of P. perniciosus as vector of L. infantum in the western Mediterranean; also, vector feeding preferences herein described support the hypothesis on the involvement of lagomorphs as sylvatic reservoirs of Leishmania. The detection of L. donovani complex in S. minuta, together with the anthropophilic feeding-behaviour herein observed, warrants further research to clarify the capacity of this species in the transmission of pathogens to humans and other animals. publishersversion published

Biting midges of the genus Culicoides are known vectors of arboviruses affecting human and animal health. However, little is known about Culicoides imicola microbiota and its influence on this insect’s biology. In this study, the impact of biotic and abiotic factors on C. imicola microbiota was characterized using shotgun-metagenomic sequencing of whole-body DNA samples. Wild-caught C. imicola adult nulliparous females were sampled in two locations from Sicily, Italy. The climatic variables of temperature and soil moisture from both localities were recorded together with potential host bloodmeal sources. Shared core microbiome among C. imicola populations included Pseudomonas, Escherichia, Halomonas, Candidatus Zinderia, Propionibacterium, and Schizosaccharomyces. Specific and unique taxa were also found in C. imicola from each location, highlighting similarities and differences in microbiome composition between the two populations. DNA and protein identification showed differences in host preferences between the two populations, with Homo sapiens and Canis lupus familiaris L. being the preferred bloodmeal source in both locations. A principal component analysis showed that the combined effect of host preferences (H. sapiens) and local soil moisture factors shape the microbiome composition of wild-caught populations of C. imicola. These results contribute to characterizing the role of the microbiome in insect adaptation and its utility in predicting geographic expansion of Culicoides species with potential implications for the control of vector-borne diseases.

Purpose The Monte Carlo radiation transport method is considered the most accurate approach for absorbed dose calculations in external beam radiation therapy. In this study, an efficient and accurate source model of the Varian TrueBeam 6X STx Linac is developed and integrated with a fast Monte Carlo photon-electron transport absorbed dose engine, ARCHER-RT, which is capable of being executed on CPUs, NVIDIA GPUs, and AMD GPUs. This capability of fast yet accurate radiation dose calculation is essential for clinical utility of this new technology. This paper describes the software and algorithmic developments made to the ARCHER-RT absorbed dose engine. Methods AMD's Heterogeneous-Compute Interface for Portability (HIP) was implemented in ARCHER-RT to allow for device independent execution on NVIDIA and AMD GPUs. Architecture-specific atomic-add algorithms have been identified and both more accurate single-precision and double-precision computational absorbed dose calculation methods have been added to ARCHER-RT and validated through a test case to evaluate the accuracy and performance of the algorithms. The validity of the source model and the radiation transport physics were benchmarked against Monte Carlo simulations performed with EGSnrc. Secondary dose-check physics plans, and a clinical prostate treatment plan were calculated to demonstrate the applicability of the platform for clinical use. Absorbed dose difference maps and gamma analyses were conducted to establish the accuracy and consistency between the two Monte Carlo models. Timing studies were conducted on a CPU, an NVIDIA GPU, and an AMD GPU to evaluate the computational speed of ARCHER-RT. Results Percent depth doses were computed for different field sizes ranging from 1.5 cm2 × 1.5 cm2 to 22 cm2 × 40cm2 and the two codes agreed for all points outside high gradient regions within 3%. Axial profiles computed for a 10 cm2 × 10 cm2 field for multiple depths agreed for all points outside high gradient regions within 2%. The test case investigating the impact of native single-precision compared to double-precision showed differences in voxels as large as 71.47% and the implementation of KAS single-precision reduced the difference to less than 0.01%. The 3%/3mm gamma pass rates for an MPPG5a multileaf collimator (MLC) test case and a clinical VMAT prostate plan were 94.2% and 98.4% respectively. Timing studies demonstrated the calculation of a VMAT plan was completed in 50.3, 187.9, and 216.8 s on an NVIDIA GPU, AMD GPU, and Intel CPU, respectively. Conclusion ARCHER-RT is capable of patient-specific VMAT external beam photon absorbed dose calculations and its potential has been demonstrated by benchmarking against a well validated EGSnrc model of a Varian TrueBeam. Additionally, the implementation of AMD's HIP has shown the flexibility of the ARCHER-RT platform for device independent calculations. This work demonstrates the significant addition of functionality added to ARCHER-RT framework which has marked utility for both research and clinical applications and demonstrates further that Monte Carlo-based absorbed dose engines like ARCHER-RT have the potential for widespread clinical implementation.

A cloud-based software, VirtualDose-IR (Virtual Phantoms Inc., Albany, New York, USA), designed to report organ doses and effective doses for a diverse patient population from interventional radiology (IR) procedures has been developed and tested. This software is based on a comprehensive database of Monte Carlo-generated organ dose built with a set of 21 anatomically realistic patient phantoms. The patient types included in this database are both male and female people with different ages reflecting reference adults, obese people with different BMIs and pregnant women at different gestational stages. Selectable parameters such as patient type, tube voltage, filtration thickness, beam direction, field size, and irradiation site are also considered in VirtualDose-IR. The software has been implemented using the ‘Software as a Service (SaaS)’ delivery concept permitting simultaneous multi-user, multi-platform access without requiring local installation. The patient doses resulting from different target sites and patient populations were reported using the VirtualDose-IR system. The patient doses under different source to surface distances (SSD) and beam angles calculated by VirtualDose-IR and Monte Carlo simulations were compared. For most organs, the dose differences between VirtualDose-IR results and Monte Carlo results were less than 0.3 mGy at 15 000 mGy * cm(2) kerma-area product (KAP). The organ dose results were compared with measurement data previously reported in literatures. The doses to organs that were located within the irradiation field match closely with experimental measurement data. The differences in the effective dose values between calculated using VirtualDose-IR and those measured were less than 2.5%. The dose errors of most organs between VirtualDose-IR and literature results were less than 40%. These results validate the accuracy of organ doses reported by VirtualDose-IR. With the inclusion of pre-specified clinical IR examination parameters (such as beam direction, target location, field of view and beam quality) and the latest anatomically realistic patient phantoms in Monte Carlo simulations, VirtualDose-IR provides users with accurate dose information in order to systematically compare, evaluate, and optimize IR plans.

The loggerhead turtle Caretta caretta is a common and threatened sea turtle in the Mediterranean Sea. It is listed in the Red List of Threatened Species of the International Union for Conservation of Nature (IUCN 2012) and, although it is widely studied, little is currently known about the relationships between its phenotype and genetic variability. In the last few years some authors observed the presence of individuals, collected in different parts of the Mediterranean Sea, with a variable number of carapacial and plastron scutes. This variability, in some cases, makes difficult the sound identification of the species (Margaritoulis and Chiras, 2011; Turkozan et al. 2001; Oliver 2014). To date, no one has tried to correlate these morphological anomalies with the genetic diversity of the species, even if several studies indicate that, beyond genetic variation, natural phenotypic variations can be generated through a suite of epigenetic mechanisms. Here we present some results about the possible correlation among the variability of the number of carapacial and plastron scutes and cytosine DNA methylation. 12 specimens of Caretta caretta, collected from different parts of Sicily, were analysed. Morphological characters were used for the identification of the collected specimens according to the guidelines of Marquez (1990). Afterwards, all the individuals were subjected to genetic analysis by the sequencing of a fragment of 243 bp of the mitochondrial cytochrome b gene. Genomic DNA methylation level of cytosines was evaluated by dot blot analysis using antibodies against methylated cytosines. Four of the twelve individuals analyzed showed an unexpected number of carapacial and plastron scutes making difficult the immediate and sound identification of the specimens as C. caretta. Sequences of the mitochondrial cytochrome b gene of these four individuals did not show any difference with those obtained from the other eight loggerhead turtles and with those from Genbank, thus allowing us to assign the four individuals to the species Caretta caretta. Conversely, dot blot analysis of genomic DNA showed a reduced global level of methylated cytosines in these four “abnormal” individuals in respect to the other ones. We hypothesize that the variability of the number of scutes could be described as an epigenetic effect probably due to the environmental parameters experienced by the embryos during incubation. This finding could have implications in our understanding of the pathways of morphological evolution and diversification in the chelonians.

Tissues from thirteen specimens of marine turtles, one Dermochelys coriacea and twelve Caretta caretta, found dead along the Sicilian coasts in 2016 were analyzed for the presence of phthalates. Four phthalates (DEP, DBP, BBP, and DEHP) were found at different significant concentrations in liver and gonads, while only DBP was found in muscle tissues and at a fourfold lower concentration than other phthalates in Dermochelys coriacea. No traces of DEP were detected in C. caretta tissues where DOTP was also revealed. The presence of phthalates in fat tissue in specimens of C. caretta showed a major prevalence of the most lipophilic phthalates DEHP and DOTP. The total concentration of all analyzed phthalates, showed high values in all tissues. Results suggested that for monitoring purposes from live specimens sample collection should be addressed to fat tissue with accurate manipulations.

Currently, there are no data in the literature on the topical treatment with Thymus vulgaris essential oil (EO) in bacterial skin infections of dogs. This study evaluates the effectiveness of Thymus vulgaris EO for topical use in dogs with skin 18 half-breed dogs, affected by skin infections housed in a rescue shelter were studied. The bacteria isolated from these dogs were identified by MALDI-TOF-MS. The susceptibility of the isolated microorganisms to Thymus vulgaris L. EO was estimated in vitro by bacteriological test (CLSI 2015), in comparison to some antimicrobials drugs (amoxicillin-clavulanic acid, doxycy-cline, thiamphenicol and marbofloxacin) and to Citrus bergamia EO. The dogs, divided in two groups at random, were treated topically for 7 days with Thymus vulgaris L. EO (Group 1: n. 10 animals) and Citrus bergamia Risso e Poiteau EO (Group 2: n. 8 animals) respectively. The bacteria isolated were: Staphylococcus pseudintermedius (7 samples), Staphylococcus sciuri (4), ESBL Escherichia coli (3) and Proteus mirabilis (4). In all animals treated with Thymus vulgaris EO, the clinical signs decreased rapidly within 5 days from the administration, with complete remission 7 days after the treatment. No bacterial growth was observed from skin swabs after 7 days of treatment. None of the treated animals showed local or general side effects. The use of Thymus vulgaris EO could be a possible alternative or additional treatment to antibiotics in dermatological infections, particularly in cases refractory to conventional therapy.

External morphology has been shown to influence predation and locomotion of decapod larvae and is, therefore, directly related to their ability to survive and disperse. The first goal of this study was to characterize first-stage blue crab zoeal morphology and its variability across larval broods to test whether inter-brood differences in morphology exist. The second was to identify possible correlations between maternal characteristics and zoeal morphology. The offspring of 21 individuals were hatched in the laboratory, photographed, and measured. Zoeae exhibited substantial variability, with all metrics showing significant inter-brood differences. The greatest variability was seen in the zoeal abdomen, rostrum, and dorsal spine length. A principal component analysis showed no distinct clustering of broods, with variation generally driven by larger zoeae. Using observed morphology, models of drag induced by swimming and sinking also showed significant inter-brood differences, with a maximum twofold difference across broods. In contrast to trends in other decapod taxa, maternal characteristics (female carapace width and mass and egg sponge volume and mass) are not significant predictors of zoeal morphology. These results suggest that brood effects are present across a wide range of morphological characteristics and that future experiments involving Callinectes sapidus morphology or its functionality should explicitly account for inter-brood variation. Additionally, inter-brood morphological differences may result in differential predation mortality and locomotory abilities among broods.

The goal of this dissertation is to provide a better understanding of the intraspecific variability in morphology and swimming behavior, as well as some of the implications of such variation, in early stage Callinectes sapidus zoeae. A long-standing body of work has demonstrated that zoeal morphology is not constant, and morphological features can have an important role in survival and behavior. Additionally, given the presence in brood-dependent morphology in other species and the susceptibility of blue crab life history to generate maternal effects, the presence and magnitude of differences among larval broods should be addressed. In the second chapter, variation in C. sapidus zoeal morphology among several larval broods was identified, and used to test whether brood-dependent morphology is present. This experiment involved hatching several broods, making measurements using microscope photography, and image analysis. Simple models of swimming-induced drag and passive sinking velocity were used to create an index of vertical swimming efficiency. Results discussed in Chapter 2 demonstrate that morphology can vary significantly between broods, and these differences can translate to differing swimming efficiency. In the third chapter, larvae from the same broods described in Chapter 2 were followed further into development to investigate how brood-level morphological differences change over development. By the time of their second molt, broods of zoeae retain most differences in morphological size and shape, but shape difference decrease. These results suggest that over time, brood effects can persist, but there is a detectible morphological convergence, and differences in swimming efficiency are still present. Chapter four tested whether the brood-dependent morphology discussed in the prior chapters translated to similar differences in swimming behavior. Using mesocosm video observations, significant differences in the swimming velocity, orientation, and path straightness of larval broods was confirmed. Despite these differences, distinct modes of behavior that were conserved across broods were observed. These represent differences in swimming behavior within broods either between individuals or over time. In the fifth chapter, simulations were used to test whether the observed brood-dependent behavior and morphology can translate to differences in larval transport. A simplified model of a wind-driven estuarine plume with a sheared current was used, along with observed brood-depending swimming and sinking behaviors, to model larval transport. Model results showed brood-dependent and behaviorally-driven larval transport, where faster-swimming broods of larvae are more able to counter wind-driven vertical mixing and stay in surface waters. Likewise, the type of depth-regulation zoeae use can influence how they are transported. Overall, this dissertation finds that morphological and behavioral traits can differ substantially between larval broods. These results suggest that there may be differential success of larvae from different broods. I recommend that future work could focus on identifying maternal or environmental predictors of larval condition. Additionally, future models of C. sapidus larval dispersal should incorporate observed behavior and its variability.

We report our latest efforts to further improve long-term orbit stability at NSLS-II, on top of what is already provided by fast orbit feedback (FOFB) system. A DC local bump generation program, only utilizing RF beam position monitors (BPM) and compatible with FOFB, was first implemented and deployed in operation successfully, allowing on-demand fine adjustments of beamline source positions and angles. Then we introduced a simple feedback version that performs these bump corrections automatically as needed to maintain the sources within in 1 um/urad for select beamlines. In addition, an RF frequency feedback was also implemented to improve stability for 3-pole wigglers and bending magnet users. As a parallel effort, X-ray BPMs were included in a local feedback system to stabilize photon beam motion for several ID beamlines. However, this feedback scheme is not transparent to FOFB, and suspected to be the source of occasional saturation of fast corrector strength. As an alternative solution, the local bump program and its feedback version has been recently upgraded to include bumps with X-ray BPMs and in operation since April 2019., Proceedings of the 10th Int. Particle Accelerator Conf., IPAC2019, Melbourne, Australia

Phlebotomine sand flies are vectors for many pathogens responsible for human and animal diseases worldwide. Their identification at species level is of importance in epidemiological studies and control programmes. MALDI-TOF MS has been increasingly investigated as an alternative approach to the conventional identification of arthropods species. To establish an in-house protein spectra database for a quick and reliable species identification of phlebotomine sand flies, 166 field-caught sand fly specimens, morphologically identified as Phlebotomus perniciosus (no = 56; 26 males and 30 females), Phlebotomus neglectus (no = 4 males), Phlebotomus sergenti (no = 6; 4 males and 2 females) and Sergentomyia minuta (no = 100; 45 males and 55 females), were subjected to MALDI-TOF MS analyses. Out of 166, 149 specimens (89.8%) produced consistent species-specific protein spectra. Good quality database for P. perniciosus and S. minuta were generated; no databases have yet constructed for P. neglectus and P. sergenti due to the low number of specimens examined. The identification of 80 sand flies (no = 20 P. perniciosus; no = 60 S. minuta) were confirmed using the new generated SuperSpectra as validation test. The results reported support the use of MALDI-TOF MS for rapid, simple and reliable phlebotomine sand fly species identification suggesting its usefulness in accurate survey studies, ultimately improving biological and epidemiological knowledge on these important vectors of pathogens.

Biting midges of the genus Culicoides are known vectors of arboviruses affecting human and animal health. However, little is known about Culicoides imicola microbiota and its influence on this insect's biology. In this study, the impact of biotic and abiotic factors on C. imicola microbiota was characterized using shotgun-metagenomic sequencing of whole-body DNA samples. Wild-caught C. imicola adult nulliparous females were sampled in two locations from Sicily, Italy. The climatic variables of temperature and soil moisture from both localities were recorded together with potential host bloodmeal sources. Shared core microbiome among C. imicola populations included Pseudomonas, Escherichia, Halomonas, Candidatus Zinderia, Propionibacterium, and Schizosaccharomyces. Specific and unique taxa were also found in C. imicola from each location, highlighting similarities and differences in microbiome composition between the two populations. DNA and protein identification showed differences in host preferences between the two populations, with Homo sapiens and Canis lupus familiaris L. being the preferred bloodmeal source in both locations. A principal component analysis showed that the combined effect of host preferences (H. sapiens) and local soil moisture factors shape the microbiome composition of wild-caught populations of C. imicola. These results contribute to characterizing the role of the microbiome in insect adaptation and its utility in predicting geographic expansion of Culicoides species with potential implications for the control of vector-borne diseases.