Global Population Genomic Structure and Life History Trait Analysis of Yellowfin Tuna (Thunnus Albacares)

Yellowfin tuna (Thunnus albacares; YFT) represents one of the most important seafood commodities in the world. The rationale of this Ph.D. project was identified by prioritizing key issues as objectives for contributing to the conservation of YFT and helping to develop a more realistic stock assessment and sustainable management of this species. Specifically, in this work the current mismatch between the biology and/or ecology and the realized management strategies was highlighted, putting particular emphasis on YFT population structure, which is currently characterized by a high degree of uncertainty at both local and global scale. This general pattern was confirmed by the results obtained using a panel of microsatellite loci, which cannot reject the null hypothesis of the existence of only one panmictic population at the global scale. On the contrary, the access to more powerful and cost effective genetic tools would represent the first step for resolving YFT population structure at both global and local scale. After having evaluated the efficiency and usefulness of 2b-RAD genotyping technique for investigating population genetic structure in highly migratory fish species, a panel of 972 SNPs (Single Nucleotide Polymorphisms) was generated. Using this panel, three distinct populations were identified in the Atlantic, Indian and Pacific Oceans. Additionally, it was possible to define a subset of 33 outlier loci putatively under selection to delineate and separate sub-populations within both the Atlantic and the Pacific Oceans (following an east-west division). Finally, it was emphasized for the first time that in the Atlantic Ocean larger YFT females allocate a greater fraction of surplus energy to egg production than smaller ones, improving noticeably the spawning quality. This result sheds light on the important contribution that larger and most experienced spawners have for the YFT productivity

Prostate cancer screening research can benefit from network medicine: an emerging awareness

Up to date, screening for prostate cancer (PCa) remains one of the most appealing but also a very controversial topics in the urological community. PCa is the second most common cancer in men worldwide and it is universally acknowledged as a complex disease, with a multi-factorial etiology. The pathway of PCa diagnosis has changed dramatically in the last few years, with the multiparametric magnetic resonance (mpMRI) playing a starring role with the introduction of the “MRI Pathway”. In this scenario the basic tenet of network medicine (NM) that sees the disease as perturbation of a network of interconnected molecules and pathways, seems to fit perfectly with the challenges that PCa early detection must face to advance towards a more reliable technique. Integration of tests on body fluids, tissue samples, grading/staging classification, physiological parameters, MR multiparametric imaging and molecular profiling technologies must be integrated in a broader vision of “disease” and its complexity with a focus on early signs. PCa screening research can greatly benefit from NM vision since it provides a sound interpretation of data and a common language, facilitating exchange of ideas between clinicians and data analysts for exploring new research pathways in a rational, highly reliable, and reproducible way

Gastric cancer is the leading cause of death in Italian adult patients with common variable immunodeficiency

An increased prevalence of malignant lymphoma and of gastric cancer has been observed in large cohorts of patients with common variable immunodeficiency (CVID), the most frequently symptomatic primary immunodeficiency. Surveillance strategies for cancers in CVID should be defined based on epidemiological data. Risks and mortality for cancers among 455 Italian patients with CVID were compared to cancer incidence data from the Italian Cancer Registry database. CVID patients showed an increased cancer incidence for all sites combined (Obs = 133, SIR = 2.4; 95%CI = 1.7\u20133.5), due to an excess of non-Hodgkin lymphoma (Obs = 33, SIR = 14.3; 95%CI = 8.4\u201322.6) and of gastric cancer (Obs = 25; SIR = 6.4; 95%CI = 3.2\u201312.5). CVID patients with gastric cancer and lymphoma had a worse survival in comparison to cancer-free CVID (HR: 4.8, 95%CI: 4.2\u201344.4 and HR: 4.2, 95%CI: 2.8\u201344.4). Similar to what observed in other series, CVID-associated lymphomas were more likely to be of B cell origin and often occurred at extra-nodal sites. We collected the largest case-series of gastric cancers in CVID subjects. In contrast to other reports, gastric cancer was the leading cause of death in CVID. Standardized mortality ratio indicated a 10.1-fold excess mortality among CVID patients with gastric cancer. CVID developed gastric cancer 15 years earlier than the normative population, but they had a similar overall survival. Only CVID diagnosed at early stage gastric cancer survived >24 months. Stomach histology from upper endoscopy performed before cancer onset showed areas of atrophic gastritis, intestinal metaplasia or dysplasia. CVID patients might progress rapidly to an advanced cancer stage as shown by patients developing a III-IV stage gastric cancer within 1 year from an endoscopy without signs of dysplasia. Based on high rate of mortality due to gastric cancer in Italian CVID patients, we hereby suggest a strategy aimed at early diagnosis, based on regular upper endoscopy and on Helicobacter pylori infection treatment, recommending an implementation of national guidelines

Health-Related Quality of Life in Patients with CVID Under Different Schedules of Immunoglobulin Administration: Prospective Multicenter Study

We assessed the health-related quality of life (HRQoL) in CVID adults receiving different schedules of immunoglobulin replacement therapy (IgRT) by intravenous (IVIG), subcutaneous (SCIG), and facilitated (fSCIG) preparations. For these patients, IgRT schedule was chosen after a period focused on identifying the most suitable individual option

In Situ Aerobic Biostimulation of Groundwater at a National Priority Site in Italy

Sarroch plant (CA, Italy) is an industrial area listed in the Italian Priority List of polluted sites. Pollution in groundwater has been addressed thanks to the design of a remediation action based on the aerobic biodegradation of petroleum hydrocarbons (predominantly mono-aromatic and short-chain aliphatic hydrocarbons) promoted by the injection of oxygen-releasing compounds. The feasibility of biostimulation at the site was preliminary assessed by means of laboratory tests. The direct push injection of the product has been foreseen at 2800 points, distributed along multiple lines perpendicular to the groundwater flow direction, over a total length of approximately 8 km and a total area of 90 hectares. According to the pollutant concentration measured in the different zones of the site, a different number of injection campaigns and injection frequency has been scheduled (3 to 10 campaigns, every 5 to 12 months). The estimated cost for the bioremediation action is 23 million Euros. Compared to the previous project approved in 2010, including a seafront physical barrier and groundwater circulation wells – in situ well stripping, the in situ injection of the oxygen-releasing compounds is an improvement toward a quicker, more effective and sustainable remediation of groundwater at the site. In view of all this, in 2017 the public authorities approved the variant of the project

Canning Processes Reduce the DNA-Based Traceability of Commercial Tropical Tunas

Canned tuna is one of the most widely traded seafood products internationally and is of growing demand. There is an increasing concern over the vulnerability of canned tuna supply chains to species mislabelling and fraud. Extensive processing conditions in canning operations can lead to the degradation and fragmentation of DNA, complicating product traceability. We here employed a forensically validated DNA barcoding tool (cytochrome b partial sequences) to assess the effects of canning processes on DNA degradation and the identification of four tropical tuna species (yellowfin, bigeye, skipjack and longtail tuna) collected on a global scale, along their commercial chains. Each species was studied under five different canning processes i.e., freezing, defrosting, cooking, and canning in oil and brine, in order to investigate how these affect DNA-based species identification and traceability. The highest percentage of nucleotide substitutions were observed after brine-canning operations and were greatest for yellowfin and skipjack tuna. Overall, we found that DNA degradation significantly increased along the tuna canning process for most specimens. Consequently, most of the specimens canned in oil or brine were misidentified due to the high rate of nucleotide substitution in diagnostic sequences

Biparametric prostate MRI: impact of a deep learning-based software and of quantitative ADC values on the inter-reader agreement of experienced and inexperienced readers

Objective To investigate the impact of an artificial intelligence (AI) software and quantitative ADC (qADC) on the inter-reader agreement, diagnostic performance, and reporting times of prostate biparametric MRI (bpMRI) for experienced and inexperienced readers. Materials and methods A total of 170 multiparametric MRI (mpMRI) of patients with suspicion of prostate cancer (PCa) were retrospectively reviewed by one experienced and one inexperienced reader three times, following a wash-out period. First, only the bpMRI sequences, including T2-weighted imaging (T2WI), diffusion-weighted imaging (DWI) sequences, and apparent diffusion coefficient (ADC) maps, were used. Then, bpMRI and quantitative ADC values were used. Lastly, bpMRI and the AI software were used. Inter-reader agreement between the two readers and between each reader and the mpMRI original reports was calculated. Detection rates and reporting times were calculated for each group. Results Inter-reader agreement with respect to mpMRI was moderate for bpMRI, Quantib, and qADC for both the inexperienced (weighted k of 0.42, 0.45, and 0.41, respectively) and the experienced radiologists (weighted k of 0.44, 0.46, and 0.42, respectively). Detection rate of PCa was similar between the inexperienced (0.24, 0.26, and 0.23) and the experienced reader (0.26, 0.27 and 0.27), for bpMRI, Quantib, and qADC, respectively. Reporting times were lower for Quantib (8.23, 7.11, and 9.87 min for the inexperienced reader and 5.62, 5.07, and 6.21 min for the experienced reader, for bpMRI, Quantib, and qADC, respectively). Conclusions AI and qADC did not have a significant impact on the diagnostic performance of both readers. The use of Quantib was associated with lower reporting times

Quality of Life: Effects of Physical Activity in an Anthropometric, Cognitive and Psychosocial Background, and Variation of Odontoiatric Parameters

The "Quality of Life" project arises from the need to observe and define the existing interconnection between a "healthy" lifestyle and the quality of life perceived by people. Starting from the W.H.O. (World Health Organization) definitions of quality of life and health, and analyzing the studies that describe the benefits of both movement physical and mental, a protocol three months has been set for the pursuit of a diet and personalized training. For this purpose, 20 healthy subjects from the 1st year of the Physiotherapy degree, who had never practiced sports at an agonistic level, have been recruited. All individuals were subject to initial evaluations to define psycho-physical wellbeing, then they have been divided into two groups: the first group, defined as experimental, followed the protocol for the duration of the study, while the second, was only subject to evaluation. At the end of the three months period, the subjects of both groups were evaluated twice, the first immediately after the last training session, the second was evaluated one month from the latter. The final evaluation aimed at verifying a possible conservative effect on modification of experimental group parameters, even when physical activity and nutrition were not supervised by us. The ultimate goal of the project was to specifically analyze, after three months, the changes in cognitive memory capacity and concentration, the stress experienced in work or study, and psycho-physical wellbeing perceived by the concerned subjects. Data collected during the three evaluations showed that, in the experimental group, as our scientific protocol has altered all these parameters in terms of quality of life in positive terms, modifications are susceptible to changes in the event that physical activity and proper nutrition are not followed

Low cancer yield in pi-rads 3 upgraded to 4 by dynamic contrast-enhanced mri. is it time to reconsider scoring categorization

Objectives: To evaluate MRI diagnostic performance in detecting clinically significant prostate cancer (csPCa) in peripheral-zone PI-RADS 4 lesions, comparing those with clearly restricted diffusion (DWI-score 4), and those with equivocal diffusion pattern (DWI-score 3) and positive dynamic contrast-enhanced (DCE) MRI. Methods: This observational prospective study enrolled 389 men referred to MRI and, if positive (PI-RADS 3 with PSA-density [PSAD] ≥ 0.15 ng/mL/mL, 4 and 5), to MRI-directed biopsy. Lesions with DWI-score 3 and positive DCE were classified as "PI-RADS 3up," instead of PI-RADS 4. Univariable and multivariable analyses were implemented to determine features correlated to csPCa detection. Results: Prevalence of csPCa was 14.5% and 53.3% in PI-RADS categories 3up and 4, respectively (p < 0.001). MRI showed a sensitivity of 100.0%, specificity 40.9%, PPV 46.5%, NPV 100.0%, and accuracy 60.9% for csPCa detection. Modifying the threshold to consider MRI positive and to indicate biopsy (same as previously described, but PI-RADS 3up only when associated with elevated PSAD), the sensitivity changed to 93.9%, specificity 57.2%, PPV 53.0%, NPV 94.8%, and accuracy 69.7%. Age (p < 0.001), PSAD (p < 0.001), positive DWI (p < 0.001), and PI-RADS score (p = 0.04) resulted in independent predictors of csPCa. Conclusions: Most cases of PI-RADS 3up were false-positives, suggesting that upgrading peripheral lesions with DWI-score 3 to PI-RADS 4 because of positive DCE has a detrimental effect on MRI accuracy, decreasing the true prevalence of csPCa in the PI-RADS 4 category. PI-RADS 3up should not be upgraded and directed to biopsy only if associated with increased PSAD. Key points: • As per PI-RADS v2.1 recommendations, in case of a peripheral zone lesion with equivocal diffusion-weighted imaging (DWI score 3), but positive dynamic contrast-enhanced (DCE) MRI, the overall PI-RADS score should be upgraded to 4. • The current PI-RADS recommendation of upgrading PI-RADS 3 lesions of the peripheral zone to PI-RADS 4 because of positive DCE decreased clinically significant prostate cancer detection rate in our series. • According to our results, the most accurate threshold for setting indication to prostate biopsy is PI-RADS 3 or PI-RADS 3 with positive DCE both associated with increased PSA density

Standardization of body composition status in patients with advanced urothelial tumors: the role of a CT-based aI-powered software for the assessment of sarcopenia and patient outcome correlation

Background: Sarcopenia is a well know prognostic factor in oncology, influencing patients' quality of life and survival. We aimed to investigate the role of sarcopenia, assessed by a Computed Tomography (CT)-based artificial intelligence (AI)-powered-software, as a predictor of objective clinical benefit in advanced urothelial tumors and its correlations with oncological outcomes. Methods: We retrospectively searched patients with advanced urothelial tumors, treated with systemic platinum-based chemotherapy and an available total body CT, performed before and after therapy. An AI-powered software was applied to CT to obtain the Skeletal Muscle Index (SMI-L3), derived from the area of the psoas, long spine, and abdominal muscles, at the level of L3 on CT axial images. Logistic and Cox-regression modeling was implemented to explore the association of sarcopenic status and anthropometric features to the clinical benefit rate and survival endpoints. Results: 97 patients were included, 66 with bladder cancer and 31 with upper-tract urothelial carcinoma. Clinical benefit outcomes showed a linear positive association with all the observed body composition variables variations. The chances of not experiencing disease progression were positively associated with ∆_SMI-L3, ∆_psoas, and ∆_long spine muscle when they ranged from ~10-20% up to ~45-55%. Greater survival chances were matched by patients achieving a wider ∆_SMI-L3, ∆_abdominal and ∆_long spine muscle. Conclusions: A CT-based AI-powered software body composition and sarcopenia analysis provide prognostic assessments for objective clinical benefits and oncological outcomes