A Multimodal Knowledge-Based Deep Learning Approach for MGMT Promoter Methylation Identification

Glioblastoma Multiforme (GBM) is considered one of the most aggressive malignant tumors, characterized by a tremendously low survival rate. Despite alkylating chemotherapy being typically adopted to fight this tumor, it is known that O(6)-methylguanine-DNA methyltransferase (MGMT) enzyme repair abilities can antagonize the cytotoxic effects of alkylating agents, strongly limiting tumor cell destruction. However, it has been observed that MGMT promoter regions may be subject to methylation, a biological process preventing MGMT enzymes from removing the alkyl agents. As a consequence, the presence of the methylation process in GBM patients can be considered a predictive biomarker of response to therapy and a prognosis factor. Unfortunately, identifying signs of methylation is a non-trivial matter, often requiring expensive, time-consuming, and invasive procedures. In this work, we propose to face MGMT promoter methylation identification analyzing Magnetic Resonance Imaging (MRI) data using a Deep Learning (DL) based approach. In particular, we propose a Convolutional Neural Network (CNN) operating on suspicious regions on the FLAIR series, pre-selected through an unsupervised Knowledge-Based filter leveraging both FLAIR and T1-weighted series. The experiments, run on two different publicly available datasets, show that the proposed approach can obtain results comparable to (and in some cases better than) the considered competitor approach while consisting of less than 0.29% of its parameters. Finally, we perform an eXplainable AI (XAI) analysis to take a little step further toward the clinical usability of a DL-based approach for MGMT promoter detection in brain MRI

Crohn's Disease Imaging: A Review

Crohn's disease is a chronic granulomatous inflammatory disease of the gastrointestinal tract, which can involve almost any segment from the mouth to the anus. Typically, Crohn's lesions attain segmental and asynchronous distribution with varying levels of seriousness, although the sites most frequently involved are the terminal ileum and the proximal colon. A single gold standard for the diagnosis of CD is not available and the diagnosis of CD is confirmed by clinical evaluation and a combination of endoscopic, histological, radiological, and/or biochemical investigations. In recent years, many studies have been performed to investigate the diagnostic potential of less invasive and more patient-friendly imaging modalities in the evaluation of Crohn's disease including conventional enteroclysis, ultrasonography, color-power Doppler, contrast-enhanced ultrasonography, multidetector CT enteroclysis, MRI enteroclysis, and 99mTc-HMPAO-labeled leukocyte scintigraphy. The potential diagnostic role of each imaging modality has to be considered in different clinical degrees of the disease, because there is no single imaging technique that allows a correct diagnosis and may be performed with similar results in every institution. The aim of this paper is to point out the advantages and limitations of the various imaging techniques in patients with suspected or proven Crohn's disease

Tolerogenic effect elicited by protein fraction derived from different hypoallergic formulas in PBMCs from children with cow milk allergy

are available for the dietary treatment of cow’s milk allergy (CMA). Safety and nutritional profile of these formulas have been well evaluated, but the potential tolerogenic activity elicited by their protein fraction is still largely undefined. We aimed to comparatively evaluate the tolerogenic effect elicited by protein fraction derived from different hypoallergenic formulas available for the dietary treatment of CMA METHODS: Four hypoallergenic formulas were compared: extensively whey formula (EHWF), extensively hydrolyzed casein formula (EHCF), hydrolyzed rice formula (RHF), amino acid based formula (AAF). Formulas were reconstituted in water according to manufacturer’s instructions, and subjected to in vitro infant gut simulated digestion using a sequential gastric and duodenal static model. Resulting protein fractions were purified using C18 reversed phase pre-packed cartridges (Sep-Pak, Waters, Milford, MA, USA),recovered in 70% acetonitrile/0.1% trifluoroacetic acid and finally vacuum-dried. Tolerogenic effects were was evaluated in peripheral blood mononuclear cells (PBMCs) from 6 patients, with challenge-proven IgE-mediated CMA (age range 1-5 yrs, all Caucasians), stimulated with different doses of digested protein fractions (from 0.25 to 250 μg/ml) or -lactoglobulin (BLG;100μg/ml) or bovine serum albumin (BSA;100μg/ml) as positive and negative control respectively. The production of Th2 (IL-4, IL-5, IL-13) and Th1 (IL-10, IFN-γ) cytokines were assessed by ELISA. Modulatory action was also evaluated on immune (IL-33) and non-immune tolerogenic factors (mucin 5AC, tight-junction proteins ZO-1 and occludin) in human enterocytes (Caco-2 cells) by ELISA and Real Time PCR, respectively. RESULTS: Th2 cytokines were unaffected by the exposure to protein fraction from all study formulas, whereas only protein fraction from EHCF was able to positively modulate IL-10, IL-33, mucin 5AC, ZO-1 and occludin expression. All protein fraction from study formulas were able to increase INF-γ expression in PBMCs. CONCLUSION: The results suggest a different regulatory action on immune and non-immune tolerogenic mechanisms elicited by protein fraction from different hypoallergenic formulas

Experimental validation of specificity of the squamous cell carcinoma antigen-immunoglobulin M (SCCA-IgM) assay in patients with cirrhosis

Background: Squamous cell carcinoma antigen-immunoglobulin M (SCCA-IgM) is a useful biomarker for the risk of development of hepatocellular carcinoma (HCC) in patients with cirrhosis due to its progressive increase associated to HCC evolution. In patients with cirrhosis, other assays have been affected by interfering reactivities of IgM. In this study, the analytical specificity of the SCCA-IgM assay was assessed by evaluating SCCA-IgM measurement dependence on different capture phases, and by measuring the recovery of SCCA-IgM reactivity following serum fractionation. Methods: Serum samples from 82 patients with cirrhosis were analyzed. SCCA-IgM was measured using the reference test (Hepa-IC, Xeptagen, Italy) that is based on rabbit oligoclonal anti-squamous cell carcinoma antigen (SCCA) and a dedicated ELISA with a mouse monoclonal anti-SCCA as the capture antibody. Results: SCCA-IgM concentrations measured with the reference assay (median value=87 AU/mL) were higher than those measured with the mouse monoclonal test (median value=78 AU/mL). However, the differences in the SCCA-IgM distribution were not statistically significant (p>0.05). When SCCA-IgM concentrations measured with both tests were compared, a linear correlation was found (r=0.77, p<0.05). Fractionation of the most reactive sera by gel-filtration chromatography showed that total recovery of SCCA-IgM reactivity was seen only in the fractions corresponding to components with a molecular weight higher than IgM and SCCA (>2000 kDa) with both tests. Conclusions: The equivalence of both SCCA-IgM assays and the absence of reactivity not related to immune complexes support the analytical specificity of SCCA-IgM measurements. The results validate the assessment of SCCA-IgM for prognostic purposes in patients with cirrhosis. Clin Chem Lab Med 2010;48:217–23.Peer Reviewe

Metformin therapy effects on the expression of sodium-glucose cotransporter 2, leptin, and sirt6 levels in pericoronary fat excised from pre-diabetic patients with acute myocardial infarction

Background and purpose: pericoronary fat over-inflammation might lead to the development and destabilization of coronary plaque in patients with pre-diabetes (PDM). Notably, pericoronary fat could over-express the sodium-glucose cotransporter 2 (SGLT2) and leptin, along with decreased sirtuin 6 (SIRT6) expression in PDM vs. normoglycemic (NG) patients undergoing coronary artery bypass grafting (CABG) for acute myocardial infarction (AMI). However, in the current study, we evaluated inflammatory markers, SGLT2, SIRT6, and leptin levels in pericoronary fat and, subsequently, 12-month prognosis comparing PDM to NG subjected to CABG for AMI. In addition, we evaluated in PDM patients the effects of metformin therapy on SIRT6 expression, leptin, and SGLT2 levels, and assessed its beneficial effect on nitrotyrosine and inflammatory cytokine levels. Methods: we studied AMI patients referred for CABG, divided into PDM and NG-patients. PDM patients were divided into never-metformin users and metformin users. Finally, we evaluated major adverse cardiac events (MACE) at a 12-month follow-up. Results: the MACE was 9.1% in all PDM and 3% in NG patients (p < 0.05). Metformin users presented a significantly lower MACE rate in PDM than never-metformin users (p < 0.05). PDM showed higher inflammatory cytokines, 3-nitrotyrosine levels, SGLT2, and leptin content, and decreased SIRT6 protein levels in pericoronary fat compared to NG-patients (p < 0.05). PDM never-metformin-users showed higher SGLT2 and leptin levels in pericoronary fat than current-metformin-users (p < 0.05). Conclusions: metformin therapy might ameliorate cardiovascular outcomes by reducing inflammatory parameters, SGLT2, and leptin levels, and finally improving SIRT6 levels in AMI-PDM patients treated with CABG

Diffusion-weighted imaging and apparent diffusion coefficient mapping of head and neck lymph node metastasis: a systematic review

Aim: Head and neck squamous cell cancer (HNSCC) is the ninth most common tumor worldwide. Neck lymph node (LN) status is the major indicator of prognosis in all head and neck cancers, and the early detection of LN involvement is crucial in terms of therapy and prognosis. Diffusion-weighted imaging (DWI) is a non- invasive imaging technique used in magnetic resonance imaging (MRI) to characterize tissues based on the displacement motion of water molecules. This review aims to provide an overview of the current literature concerning quantitative diffusion imaging for LN staging in patients with HNSCC. Methods: This systematic review performed a literature search on the PubMed database (https://pubmed.ncbi.nlm.nih.gov/) for all relevant, peer-reviewed literature on the subject following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) criteria, using the keywords: DWI, MRI, head and neck, staging, lymph node. Results: After excluding reviews, meta-analyses, case reports, and bibliometric studies, 18 relevant papers out of the 567 retrieved were selected for analysis. Conclusions: DWI improves the diagnosis, treatment planning, treatment response evaluation, and overall management of patients affected by HNSCC. More robust data to clarify the role of apparent diffusion coefficient (ADC) and DWI parameters are needed to develop models for prognosis and prediction in HNSCC cancer using MRI

Valorising faba bean residual biomass : Effect of farming system and planting time on the potential for biofuel production

Research was carried out in southern Italy with the aim to assess the quality of faba bean residual biomass and its potential for biorefinery application. Faba bean is a sustainable crop, due to its ability to fix atmospheric nitrogen, and a large amount of biomass remains after harvest which can be valorised for energy production. Greenhouse and early planting are known to affect pod yield and, in this respect, even the residual biomass quality needs to be assessed. For this purpose, the effects of five planting times (i.e. the dates of transplants ranging from 27 September to 22 November at two-week interval, earlier and later than the common planting date of 25 October in Naples province) on pods yield, residual biomass, and saccharification potential were evaluated in faba bean grown in open field and in greenhouse. The third planting time resulted in the highest fruit and residual biomass yield under greenhouse, whereas the fourth was the best in open field. Harvest index was best affected by the third and fourth planting times in open field. Greenhouse grown biomass showed higher values of lignin, hemicellulose and pectin, compared to open field, whereas the opposite trend was recorded with cellulose. Lignin content showed a gradual decrease from the first to the last planting time (17.7%–13.7% biomass fraction respectively), as well as pectin (from 14.1 to 11.5% biomass fraction); conversely, cellulose increased from the first to the last planting time (from 41.1 to 48.7% biomass fraction). Glucose was the most represented monosaccharide (46.7 mol%), followed by xylose (27.4 mol%) and galactose (9.9 mol%). Overall, the potential of faba bean residual biomass for energy production was best affected by open field growing, the latest planting time and alkali pre-treatment, the latter giving the highest value of saccharification (60.7 g kg−1 h−1 compared to 27.6 relevant to hot water pre-treatment)

Clinical patterns of hepatocellular carcinoma in nonalcoholic fatty liver disease: A multicenter prospective study

107noNonalcoholic fatty liver disease (NAFLD) represents the hepatic manifestation of metabolic syndrome and may evolve into hepatocellular carcinoma (HCC). Only scanty clinical information is available on HCC in NAFLD. The aim of this multicenter observational prospective study was to assess the clinical features of patients with NAFLD-related HCC (NAFLD-HCC) and to compare them to those of hepatitis C virus (HCV)-related HCC. A total of 756 patients with either NAFLD (145) or HCV-related chronic liver disease (611) were enrolled in secondary care Italian centers. Survival was modeled according to clinical parameters, lead-time bias, and propensity analysis. Compared to HCV, HCC in NAFLD patients had a larger volume, showed more often an infiltrative pattern, and was detected outside specific surveillance. Cirrhosis was present in only about 50% of NAFLD-HCC patients, in contrast to the near totality of HCV-HCC. Regardless of tumor stage, survival was significantly shorter (P = 0.017) in patients with NAFLD-HCC, 25.5 months (95% confidence interval 21.9-29.1), than in those with HCV-HCC, 33.7 months (95% confidence interval 31.9-35.4). To eliminate possible confounders, a propensity score analysis was performed, which showed no more significant difference between the two groups. Additionally, analysis of patients within Milan criteria submitted to curative treatments did not show any difference in survival between NAFLD-HCC and HCV-HCC (respectively, 38.6 versus 41.0 months, P = nonsignificant) Conclusions: NAFLD-HCC is more often detected at a later tumor stage and could arise also in the absence of cirrhosis, but after patient matching, it has a similar survival rate compared to HCV infection; a future challenge will be to identify patients with NAFLD who require more stringent surveillance in order to offer the most timely and effective treatment. (Hepatology 2016;63:827-838)openopenPiscaglia F.; Svegliati-Baroni G.; Barchetti A.; Pecorelli A.; Marinelli S.; Tiribelli C.; Bellentani S.; Bernardi M.; Biselli M.; Caraceni P.; Domenicali M.; Garuti F.; Gramenzi A.; Lenzi B.; Magalotti D.; Cescon M.; Ravaioli M.; Del Poggio P.; Olmi S.; Rapaccini G.L.; Balsamo C.; Di Nolfo M.A.; Vavassori E.; Alberti A.; Benvegnau L.; Gatta A.; Giacomin A.; Vanin V.; Pozzan C.; Maddalo G.; Giampalma E.; Cappelli A.; Golfieri R.; Mosconi C.; Renzulli M.; Roselli P.; Dell'isola S.; Ialungo A.M.; Risso D.; Marenco S.; Sammito G.; Bruzzone L.; Bosco G.; Grieco A.; Pompili M.; Rinninella E.; Siciliano M.; Chiaramonte M.; Guarino M.; Camma C.; Maida M.; Costantino A.; Barcellona M.R.; Schiada L.; Gemini S.; Lanzi A.; Stefanini G.F.; Dall'aglio A.C.; Cappa F.M.; Suzzi A.; Mussetto A.; Treossi O.; Missale G.; Porro E.; Mismas V.; Vivaldi C.; Bolondi L.; Zoli M.; Granito A.; Malagotti D.; Tovoli F.; Trevisani F.; Venerandi L.; Brandi G.; Cucchetti A.; Bugianesi E.; Vanni E.; Mezzabotta L.; Cabibbo G.; Petta S.; Fracanzani A.; Fargion S.; Marra F.; Fani B.; Biasini E.; Sacco R.; Morisco F.; Caporaso N.; Colombo M.; D'ambrosio R.; Croce L.S.; Patti R.; Giannini E.G.; Loria P.; Lonardo A.; Baldelli E.; Miele L.; Farinati F.; Borzio M.; Dionigi E.; Soardo G.; Caturelli E.; Ciccarese F.; Virdone R.; Affronti A.; Foschi F.G.; Borzio F.Piscaglia, F.; Svegliati-Baroni, G.; Barchetti, A.; Pecorelli, A.; Marinelli, S.; Tiribelli, C.; Bellentani, S.; Bernardi, M.; Biselli, M.; Caraceni, P.; Domenicali, M.; Garuti, F.; Gramenzi, A.; Lenzi, B.; Magalotti, D.; Cescon, M.; Ravaioli, M.; Del Poggio, P.; Olmi, S.; Rapaccini, G. L.; Balsamo, C.; Di Nolfo, M. A.; Vavassori, E.; Alberti, A.; Benvegnau, L.; Gatta, A.; Giacomin, A.; Vanin, V.; Pozzan, C.; Maddalo, G.; Giampalma, E.; Cappelli, A.; Golfieri, R.; Mosconi, C.; Renzulli, M.; Roselli, P.; Dell'Isola, S.; Ialungo, A. M.; Risso, D.; Marenco, S.; Sammito, G.; Bruzzone, L.; Bosco, G.; Grieco, A.; Pompili, M.; Rinninella, E.; Siciliano, M.; Chiaramonte, M.; Guarino, M.; Camma, C.; Maida, M.; Costantino, A.; Barcellona, M. R.; Schiada, L.; Gemini, S.; Lanzi, A.; Stefanini, G. F.; Dall'Aglio, A. C.; Cappa, F. M.; Suzzi, A.; Mussetto, A.; Treossi, O.; Missale, G.; Porro, E.; Mismas, V.; Vivaldi, C.; Bolondi, L.; Zoli, M.; Granito, A.; Malagotti, D.; Tovoli, F.; Trevisani, F.; Venerandi, L.; Brandi, G.; Cucchetti, A.; Bugianesi, E.; Vanni, E.; Mezzabotta, L.; Cabibbo, G.; Petta, S.; Fracanzani, A.; Fargion, S.; Marra, F.; Fani, B.; Biasini, E.; Sacco, R.; Morisco, F.; Caporaso, N.; Colombo, M.; D'Ambrosio, R.; Croce, L. S.; Patti, R.; Giannini, E. G.; Loria, P.; Lonardo, A.; Baldelli, E.; Miele, L.; Farinati, F.; Borzio, M.; Dionigi, E.; Soardo, G.; Caturelli, E.; Ciccarese, F.; Virdone, R.; Affronti, A.; Foschi, F. G.; Borzio, F