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Abstract Background Left atrium (LA) is far from simply being a passive connection chamber between left ventricle and the pulmonary circulation. In patients affected by mitral regurgitation (MR) an impairment in LA compliance and reservoir function, which can be evaluated using Speckle Tracking echocardiography, lead to elevated atrial pressure, resulting in increased pulmonary capillary pressures and the onset of dyspnea. Our study aims to evaluate the correlation between left atrial dysfunction and symptoms onset in patients with severe degenerative MR. Identifying left atrial dysfunction as a predictor of symptoms could be helpful to guide management strategy of asymptomatic patients with severe degenerative MR. Methods In a retrospective analysis, we examined all patients diagnosed with severe degenerative MR who underwent evaluation for potential cardiac surgery using transthoracic and transesophageal echocardiogram between May 2019 and July 2022 at IRCCS San Raffaele Hospital. The cohort was stratified into two groups: symptomatic patients (NYHA > I) and asymptomatic (NYHA = I) patients. A comprehensive assessment of LA function and compliance was performed including: LA fractional atrial change, LA reservoir strain (LASr), LASr/E/e’, and LA reservoir work. Results The final study cohort comprised 401 patients. There were no significant differences observed in terms of left ventricle size, function, and mitral regurgitation volume between the two groups. Atrial dysfunction and dilatation were significantly associated with symptoms. Among the atrial functional indexes LASr, a marker of LA compliance, showed the strongest association with symptoms (AUC: 0.85, OR: 7.45, p

Abstract Background In November 2022, Italy participated in the third edition of the European Centre for disease prevention and control (ECDC) point prevalence survey (PPS) of healthcare-associated infections (HAIs) in acute-care hospitals. A questionnaire based on the WHO infection prevention and control assessment framework (IPCAF) was included, which aims to investigate multimodal strategies for the implementation of IPC interventions. Methods A PPS was conducted using the ECDC PPS protocol version 6.0. The Regional health authority of the region of Piedmont, in north-western Italy, chose to enlist all public acute-care hospitals. Data were collected within one day per each ward, within 3 weeks in each hospital, at hospital, ward and patient level. A score between 0–1 or 0–2 was assigned to each of the 9 items in the IPCAF questionnaire, with 14 points representing the best possible score. HAI prevalence was calculated at the hospital-level as the percentage of patients with at least one HAI over all included patients. Relations between HAI prevalence, IPCAF score, and other hospital-level variables were assessed using Spearman's Rho coefficient. Results In total, 42 acute-care hospitals of the region of Piedmont were involved, with a total of 6865 included patients. All participant hospitals reported they employed multimodal strategies to implement IPC interventions. The median IPCAF overall score was 11/14 (interquartile range, IQR: 9.25–12). The multimodal strategy with the highest level of adherence was education and training, followed by communication and reminders. Strategies with the lowest level of adherence were safety climate and culture of change, and system change. Overall HAI prevalence was 8.06%. A weak to moderate inverse relation was found between IPCAF score and HAI prevalence (Spearman’s Rho -0.340, p 0.034). No other significant correlation was found. Conclusions This study found a high self-reported overall level of implementation of multimodal strategies for IPC in the region. Results of this study suggest the relevance of the multimodal approach and the validity of the IPCAF score in measuring IPC programs, in terms of effectiveness of preventing HAI transmission.

Abstract Background Conflicting data exist regarding the effects of deep neuromuscular blockade (NMB) on abdominal dimensions during laparoscopic procedures. We performed a clinical study to establish the influence of moderate and deep neuromuscular blockade (NMB) on the abdominal working space, measured by Magnetic Resonance Imaging (MRI), during laparoscopic donor nephrectomy with standard pressure (12 mmHg) pneumoperitoneum under sevoflurane anaesthesia. Methods Ten patients were intraoperatively scanned three times in the lateral decubitus position, with pneumoperitoneum maintained by a mobile insufflator. The first scan without NMB (T1) was followed by scans with moderate (T2) and deep NMB (T3). The skin-sacral promontory (S-SP) distance was measured, and 3D pneumoperitoneum volumes were reconstructed. Results The mean difference in the S-SP distance was -0.32 cm between T2 and T3 (95% CI -1.06 - 0.42 cm; p = 0.344) and + 2.1 cm between T1 and T2 (95% CI 0.81 - 3.39 cm; p = 0.006). The mean differences in pneumoperitoneum volume were 166 mL between T2 and T3 (95% CI, 5 - 327 mL; p = 0.044) and 108 mL between T1 and T2 (95% CI, -273 - 488 mL; p = 0.525). The pneumoperitoneum volume showed high inter-individual variability and no increase in three patients with a high volume at T1. Conclusions During laparoscopic surgery in the lateral decubitus position with standard pressure under sevoflurane anaesthesia, deep NMB did not increase the S-SP distance compared to moderate NMB. Moderate NMB increased the S-SP distance by a mean of 2.1 cm (15.2%) compared with no NMB. The mean pneumoperitoneum volume increased slightly from moderate to deep NMB, with high inter-individual variability. Trial registration Clinicaltrials.gov ID: NCT03287388.

Abstract Background Minimally invasive adrenalectomy is the standard of care for small adrenal tumours. Both the transperitoneal lateral approach and posterior retroperitoneal approach are widely used and have been proven to be safe and effective. However, the prevalence of chronic postsurgical pain has not been specifically investigated in previous studies. The primary goal of this study was to identify the prevalence of chronic postsurgical pain after minimally invasive adrenalectomy. Methods A cross-sectional study was performed among all consecutive patients who had undergone minimally invasive adrenalectomy in a single university medical centre. The primary outcome was the prevalence of chronic postsurgical pain. Secondary outcomes were the prevalence of localized hypoesthesia, risk factors for the development of chronic postsurgical pain, and the Health-Related Quality of Life. Three questionnaires were used to measure the prevalence and severity of chronic postsurgical pain, hypoesthesia, and Health-Related Quality of Life. Logistic regression analysis was performed to determine risk factors for development of chronic postsurgical pain. Results Six hundred two patients underwent minimally invasive adrenalectomy between January 2007 and September 2019, of whom 328 signed informed consent. The prevalence of chronic postsurgical pain was 14.9%. In the group of patients with chronic postsurgical pain, 33% reported hypoesthesia as well. Young age was a significant predictor for developing chronic postsurgical pain. The prevalence of localized hypoesthesia was 15.2%. In patients with chronic postsurgical pain, Health-Related Quality of Life was significantly lower, compared to patients without pain. Conclusions The prevalence of chronic postsurgical pain following minimally invasive adrenalectomy is considerable. Furthermore, the presence of chronic postsurgical pain was correlated with a significant and clinically relevant lower Health-Related Quality of Life. These findings should be included in the preoperative counselling of the patient. In the absence of evidence for effective treatment in established chronic pain, prevention should be the key strategy and topic of future research.

Abstract Background Air pollution is one of the main concerns for the health of European citizens, and cities are currently striving to accomplish EU air pollution regulation. The 2020 COVID-19 lockdown measures can be seen as an unintended but effective experiment to assess the impact of traffic restriction policies on air pollution. Our objective was to estimate the impact of the lockdown measures on NO2 concentrations and health in the two largest Italian cities. Methods NO2 concentration datasets were built using data deriving from a 1-month citizen science monitoring campaign that took place in Milan and Rome just before the Italian lockdown period. Annual mean NO2 concentrations were estimated for a lockdown scenario (Scenario 1) and a scenario without lockdown (Scenario 2), by applying city-specific annual adjustment factors to the 1-month data. The latter were estimated deriving data from Air Quality Network stations and by applying a machine learning approach. NO2 spatial distribution was estimated at a neighbourhood scale by applying Land Use Random Forest models for the two scenarios. Finally, the impact of lockdown on health was estimated by subtracting attributable deaths for Scenario 1 and those for Scenario 2, both estimated by applying literature-based dose–response function on the counterfactual concentrations of 10 μg/m3. Results The Land Use Random Forest models were able to capture 41–42% of the total NO2 variability. Passing from Scenario 2 (annual NO2 without lockdown) to Scenario 1 (annual NO2 with lockdown), the population-weighted exposure to NO2 for Milan and Rome decreased by 15.1% and 15.3% on an annual basis. Considering the 10 μg/m3 counterfactual, prevented deaths were respectively 213 and 604. Conclusions Our results show that the lockdown had a beneficial impact on air quality and human health. However, compliance with the current EU legal limit is not enough to avoid a high number of NO2 attributable deaths. This contribution reaffirms the potentiality of the citizen science approach and calls for more ambitious traffic calming policies and a re-evaluation of the legal annual limit value for NO2 for the protection of human health.

Abstract Study objective To assess whether different intensities of intra-abdominal pressure and deep neuromuscular blockade influence the risk of intra-operative surgical complications during laparoscopic donor nephrectomy. Design A pooled analysis of ten previously performed prospective randomized controlled trials. Setting Laparoscopic donor nephrectomy performed in four academic hospitals in the Netherlands: Radboudumc, Leiden UMC, Erasmus MC Rotterdam, and Amsterdam UMC. Patients Five hundred fifty-six patients undergoing a transperitoneal, fully laparoscopic donor nephrectomy enrolled in ten prospective, randomized controlled trials conducted in the Netherlands from 2001 to 2017. Interventions Moderate (tetanic count of four > 1) versus deep (post-tetanic count 1–5) neuromuscular blockade and standard (≥10 mmHg) versus low (

Abstract Objective To conduct a systematic review to evaluate the association between residential or occupational short- and long–term exposure to odour pollution from industrial sources and the health status of the exposed population. Methods The searches were conducted in Medline, EMBASE and Scopus in April 2021. Exposure to an environmental odour from industrial sources in population resident near the source or in workers was considered. We considered outcomes for which there was a biological plausibility, such as wheezing and asthma, cough, headache, nausea and vomiting (primary outcomes). We also included stress-related symptoms and novel outcomes (e.g. mood states). Risk of bias was evaluated using the OHAT tool. For primary outcomes, when at least 3 studies provided effect estimates by comparing exposed subjects versus not exposed, we pooled the study-specific estimates of odour-related effect using random effects models. Heterogeneity was evaluated with Higgins I2. Results Thirty studies were eligible for this review, mainly cross-sectional (n = 23). Only one study involved school-age children and two studies involved workers. Only five studies reported odour effects on objective laboratory or clinical outcomes. Animal Feeding Operations and waste were the most common industrial sources. The overall odds ratios in exposed versus not exposed population were 1.15 (95% CI 1.01 to 1.29) for headache (7 studies), 1.09 (95% CI 0.88 to 1.30) for nausea/vomiting (7 studies), and 1.27 (95% CI 1.10 to 1.44) for cough/phlegm (5 studies). Heterogeneity was a moderate concern. Overall, the body of evidence was affected by a definitely high risk of bias in exposure and outcome assessment since most studies used self-reported information. Conclusions Findings underline the public health importance of odour pollution for population living nearby industrial odour sources. The limited evidence for most outcomes supports the need for high quality epidemiological studies on the association between odour pollution and its effects on human health.

Abstract Background Our previous study on the 2016/2017 Serie A season showed that a greater likelihood of reaching the top positions in the Italian league “Serie A” seemed to be mainly related to sprint activity, goal attempts, total throws, target shots and assists. Therefore, we aim to evaluate the following season data in the same league to compare, confirm, and improve these results. Methods The data of all the matches played during the “Serie A” 2017–2018 season were obtained from the Italian soccer league. The teams’ analysis was performed in terms of total distance covered in km, jogging, running and sprint activities, average speed, and match statistics (total shots, shots on target, goal attempts, assists, turnovers, and steals). Results Teams that reached the first four positions revealed a lower percentage of running (65.98 ± 1.51 vs. 66.84 ± 2.18; p

Abstract Background Gastric carcinoma (GC) with second primary malignancy (SPM) is the most frequent combination within the multiple primary malignancies (MPM) group. The presentation of a GC associated with a synchronized SPM in the kidney is extremely rare and unusual. This study presents a rare case of synchronous tumors, describes the main associated risk factors, and emphasizes the need to rule out SPM. Main body We present the case of a 63-year-old Hispanic woman with a history of smoking, weight loss, and gastrointestinal (GI) bleeding. GC was diagnosed by endoscopy, and during her workup for metastatic disease, a synchronous SPM was noted in the left kidney. The patient underwent resection of both tumors with a satisfactory postoperative course. A systematic review of the literature was performed using the Medline/PubMed, Science Direct, Scopus, and Google Scholar databases. A search of the literature yielded 13 relevant articles, in which the following main risk factors were reported: the treatment utilized, the grade and clinical stage, histopathological report, and in some cases survival. It is concluded that advanced age (> 60 years) and smoking are the main associated risk factors. Conclusion Gastric carcinoma is the second most frequent neoplasm of the GI tract and the main neoplasm that presents a SPM. MPM screening is recommended in patients with gastric cancer. The clinical discovery of MPM of renal origin is rare and hence the importance of the current report.

Abstract Background The METastasis Reporting and Data System for Prostate Cancer (MET-RADS-P) guidelines are designed to enable reproducible assessment in detecting and quantifying metastatic disease response using whole-body magnetic resonance imaging (WB-MRI) in patients with advanced prostate cancer (APC). The purpose of our study was to evaluate the inter-observer agreement of WB-MRI examination reports produced by readers of different expertise when using the MET-RADS-P guidelines. Methods Fifty consecutive paired WB-MRI examinations, performed from December 2016 to February 2018 on 31 patients, were retrospectively examined to compare reports by a Senior Radiologist (9 years of experience in WB-MRI) and Resident Radiologist (after a 6-months training) using MET-RADS-P guidelines, for detection and for primary/dominant and secondary response assessment categories (RAC) scores assigned to metastatic disease in 14 body regions. Inter-observer agreement regarding RAC score was evaluated for each region by using weighted-Cohen’s Kappa statistics (K). Results The number of metastatic regions reported by the Senior Radiologist (249) and Resident Radiologist (251) was comparable. For the primary/dominant RAC pattern, the agreement between readers was excellent for the metastatic findings in cervical, dorsal, and lumbosacral spine, pelvis, limbs, lungs and other sites (K:0.81–1.0), substantial for thorax, retroperitoneal nodes, other nodes and liver (K:0.61–0.80), moderate for pelvic nodes (K:0.56), fair for primary soft tissue and not assessable for skull due to the absence of findings. For the secondary RAC pattern, agreement between readers was excellent for the metastatic findings in cervical spine (K:0.93) and retroperitoneal nodes (K:0.89), substantial for those in dorsal spine, pelvis, thorax, limbs and pelvic nodes (K:0.61–0.80), and moderate for lumbosacral spine (K:0.44). Conclusions We found inter-observer agreement between two readers of different expertise levels to be excellent in bone, but mixed in other body regions. Considering the importance of bone metastases in patients with APC, our results favor the use of MET-RADS-P in response to the growing clinical need for monitoring of metastasis in these patients.

Abstract Background Intrauterine fetal death (IUFD) is a tragic event and, despite efforts to reduce rates, its incidence remains difficult to reduce. The objective of the present study was to examine the etiological factors that contribute to the main causes and conditions associated with IUFD, over an 11-year period in a region of North-East Italy (Friuli Venezia Giulia) for which reliable data in available. Methods Retrospective analysis of all 278 IUFD cases occurred between 2005 and 2015 in pregnancies with gestational age ≥ 23 weeks. Results The incidence of IUFD was 2.8‰ live births. Of these, 30% were small for gestational age (SGA), with immigrant women being significantly over-represented. The share of SGA reached 35% in cases in which a maternal of fetal pathological condition was present, and dropped to 28% in the absence of associated pathology. In 78 pregnancies (28%) no pathology was recorded that could justify IUFD. Of all IUFDs, 11% occurred during labor, and 72% occurred at a gestational age above 30 weeks. Conclusion The percentage of IUFD cases for which no possible cause can be identified is quite high. Only the adoption of evidence-based diagnostic protocols, with integrated immunologic, genetic and pathologic examinations, can help reduce this diagnostic gap, contributing to the prevention of future IUFDs.

Abstract Background Bendamustine, used for the treatment of indolent B-cell non-Hodgkin lymphoma and chronic lymphocytic leukemia, is known to cause prolonged myelosuppression and lymphocytopenia and has been associated with the risk of developing serious and fatal infections. While reports of localized CMV infections in asymptomatic patients exist, disseminated CMV disease has not been described. Case presentation We report the first case of disseminated CMV infection in a 75-year-old male diagnosed with lymphoplasmacytic lymphoma/Waldenström macroglobulinemia with massive bone marrow infiltration. Despite 6-cycle R-bendamustine chemotherapy resulted in a good partial response, the patient developed persistent fever and severe weight loss. Analysis of cerebrospinal fluid and peripheral blood revealed the presence of CMV-DNA, while the fundus oculi examination revealed bilateral CMV retinitis. Treatment with induction and maintenance drugs was complicated by neutropenia and deterioration of renal function with electrolyte imbalance. From an immunological standpoint, we observed a profound imbalances in phenotype and function of B- and T-cell subsets, with a high proportion of circulating total, activated CD69+ and CD80+ B-cells, a low γ/δ T-cell frequency with a high proportion of CD69- and CD38-expressing cells, and hyperactivated/exhausted CD4+ and CD8+ T-cell phenotypes unable to face CMV challenge. Conclusions We hereby describe a severe form of disseminated CMV disease after R-bendamustine treatment. Our observations strongly support the careful clinical monitoring of CMV reactivation/infection in oncologic patients undergoing this therapeutic regimen.

Abstract Background Data concerning the effect of chronic right ventricular pacing in patients with normal left ventricular ejection fraction (LVEF%) are contradictory. The aim of this study is to evaluate the prevalence of pacing-induced cardiomyopathy (PICM) at midterm follow-up after permanent pacemaker implantation (PPM). Methods A series of 170 patients were submitted to PPM within our facility. Inclusion criteria were the absence of structural heart disease and a preserved LVEF% (> 45%) at the time of PPM. A midterm clinical and echocardiographic follow-up was performed, and data were collected and analyzed retrospectively. PICM was defined as follow-up LVEF ≤ 45%, dyskinesia during RV pacing, and the absence of other known causes of cardiomyopathy. Results At a median echocardiographic follow-up of 24.5 months (IQR 10.0–43.0 months), the overall mean LVEF% decreased from a preimplantation value of 66.7% (± 8.6%) to 63.2% (± 10.6%) (p

Abstract Background Permanent pacemaker implantation (PPMI) after transcatheter aortic valve implantation (TAVI) remains an issue open for criticism. Aim of this study is to investigate a strategy to reduce PPMI rate after TAVI in general and more specifically after implantation of the LOTUS® prosthesis. Methods Through our learning curve, we have developed a structured protocol to reduce PPMI rate. The protocol includes: shallow implantation depth within the native annulus, strict adherence to the international guidelines for PPMI, PPMI not earlier than 5 days after TAVI, and intravenous chronotropic and steroidal treatment (orciprenaline 0.6–1.7 mg/h i.v. and dexamethasone 25 mg/day i.v. for a maximum of 5 days) in case of acute onset of intraventricular and/or atrio-ventricular conduction disturbances after TAVI. Results The first 35 patients (group A) were managed as per routine in our early stage experience with the LOTUS valve. The PPMI reduction protocol was applied in the second phase on the last 31 patients (group B). The PPMI rate was reduced from 34.3% (12/35) to 9.7% (3/31) (p = 0.02). At logistic regression analysis being treated in the second phase of our experience (group B) had a protective effect against PPMI (p = 0.05; OR = 0.1; CI = 0.01–1.0). Prosthesis implantation depth was directly related to PPMI (p = 0.005; OR = 2.0; CI = 1.2–3.2). Receiver operating characteristic curve analysis confirmed that a LOTUS implantation depth > 4.8 mm was the cut-off to predict PPMI (AUC = 0.8; p = 0.003; CI = 0.6–0.9) with maximal sensitivity (78.6%) and specificity (73.2%). Conclusions PPMI rate after LOTUS can be reduced with experience by applying specific clinical and operative strategies.

Abstract Background Nodal skip metastasis is a prognostic factor in some sites of malignancies, but its role in esophageal cancer is still unclear. The present study aimed to investigate occurrence and effect of nodal skip metastases in thoracic esophageal squamous cell carcinoma. Methods All 578 patients undergoing esophagectomy for thoracic esophageal squamous cell carcinoma at the Center for Esophageal Diseases located in Padova between January 1992 and December 2010 were retrospectively evaluated. Selection criteria were R0 resection, pathological M0 stage and pathological lymph node involvement. Patients receiving neoadjuvant therapy were excluded. Results The selection identified 88 patients with lymph node involvement confirmed by pathological evaluation. Sixteen patients (18.2%) had nodal skip metastasis. Adjusting for the number of lymph node metastases, patient with nodal skip metastasis had similar 5-year overall survival (14% vs. 13%, p = 0.93) and 5-year disease free survival (14% vs. 9%, p = 0.48) compared to patients with both peritumoral and distant lymph node metastases. The risk difference of nodal skip metastasis was: −24.1% (95% C.I. -43.1% to −5.2%) in patients with more than one lymph node metastasis compared to those with one lymph node metastasis; −2.3% (95% C.I. -29.8% to 25.2%) in middle thoracic esophagus and −23.0% (95% C.I. -47.8% to 1.8%) in lower thoracic esophagus compared to upper thoracic esophagus; 18.1% (95% C.I. 3.2% to 33.0%) in clinical N0 stage vs. clinical N+ stage. Conclusions Nodal skip metastasis is a common pattern of metastatic lymph involvement in thoracic esophageal squamous cell carcinoma. However, neither overall survival nor disease free survival are associated with nodal skip metastasis occurrence.

Abstract Background The identification of protein coding elements in sets of mammalian conserved elements is one of the major challenges in the current molecular biology research. Many features have been proposed for automatically distinguishing coding and non coding conserved sequences, making so necessary a systematic statistical assessment of their differences. A comprehensive study should be composed of an association study, i.e. a comparison of the distributions of the features in the two classes, and a prediction study in which the prediction accuracies of classifiers trained on single and groups of features are analyzed, conditionally to the compared species and to the sequence lengths. Results In this paper we compared distributions of a set of comparative and non comparative features and evaluated the prediction accuracy of classifiers trained for discriminating sequence elements conserved among human, mouse and rat species. The association study showed that the analyzed features are statistically different in the two classes. In order to study the influence of the sequence lengths on the feature performances, a predictive study was performed on different data sets composed of coding and non coding alignments in equal number and equally long with an ascending average length. We found that the most discriminant feature was a comparative measure indicating the proportion of synonymous nucleotide substitutions per synonymous sites. Moreover, linear discriminant classifiers trained by using comparative features in general outperformed classifiers based on intrinsic ones. Finally, the prediction accuracy of classifiers trained on comparative features increased significantly by adding intrinsic features to the set of input variables, independently on sequence length (Kolmogorov-Smirnov P-value ≤ 0.05). Conclusion We observed distinct and consistent patterns for individual and combined use of comparative and intrinsic classifiers, both with respect to different lengths of sequences/alignments and with respect to error rates in the classification of coding and non-coding elements. In particular, we noted that comparative features tend to be more accurate in the classification of coding sequences – this is likely related to the fact that such features capture deviations from strictly neutral evolution expected as a consequence of the characteristics of the genetic code.

Abstract Background The advent of the technology of DNA microarrays constitutes an epochal change in the classification and discovery of different types of cancer because the information provided by DNA microarrays allows an approach to the problem of cancer analysis from a quantitative rather than qualitative point of view. Cancer classification requires well founded mathematical methods which are able to predict the status of new specimens with high significance levels starting from a limited number of data. In this paper we assess the performances of Regularized Least Squares (RLS) classifiers, originally proposed in regularization theory, by comparing them with Support Vector Machines (SVM), the state-of-the-art supervised learning technique for cancer classification by DNA microarray data. The performances of both approaches have been also investigated with respect to the number of selected genes and different gene selection strategies. Results We show that RLS classifiers have performances comparable to those of SVM classifiers as the Leave-One-Out (LOO) error evaluated on three different data sets shows. The main advantage of RLS machines is that for solving a classification problem they use a linear system of order equal to either the number of features or the number of training examples. Moreover, RLS machines allow to get an exact measure of the LOO error with just one training. Conclusion RLS classifiers are a valuable alternative to SVM classifiers for the problem of cancer classification by gene expression data, due to their simplicity and low computational complexity. Moreover, RLS classifiers show generalization ability comparable to the ones of SVM classifiers also in the case the classification of new specimens involves very few gene expression levels.

Abstract Background The malignant transformation of precancerous colorectal lesions involves progressive alterations at both the molecular and morphologic levels, the latter consisting of increases in size and in the degree of cellular atypia. Analyzing preinvasive tumors of different sizes can therefore shed light on the sequence of these alterations. Methods We used a molecular pathway-based approach to analyze transcriptomic profiles of 59 colorectal tumors representing early and late preinvasive stages and the invasive stage of tumorigenesis. Random set analysis was used to identify biological pathways enriched for genes differentially regulated in tumors (compared with 59 samples of normal mucosa). Results Of the 880 canonical pathways we investigated, 112 displayed significant tumor-related upregulation or downregulation at one or more stages of tumorigenesis. This allowed us to distinguish between pathways whose dysregulation is probably necessary throughout tumorigenesis and those whose involvement specifically drives progression from one stage to the next. We were also able to pinpoint specific changes within each gene set that seem to play key roles at each transition. The early preinvasive stage was characterized by cell-cycle checkpoint activation triggered by DNA replication stress and dramatic downregulation of basic transmembrane signaling processes that maintain epithelial/stromal homeostasis in the normal mucosa. In late preinvasive lesions, there was also downregulation of signal transduction pathways (e.g., those mediated by G proteins and nuclear hormone receptors) involved in cell differentiation and upregulation of pathways governing nuclear envelope dynamics and the G2>M transition in the cell cycle. The main features of the invasive stage were activation of the G1>S transition in the cell cycle, upregulated expression of tumor-promoting microenvironmental factors, and profound dysregulation of metabolic pathways (e.g., increased aerobic glycolysis, downregulation of pathways that metabolize drugs and xenobiotics). Conclusions Our analysis revealed specific pathways whose dysregulation might play a role in each transition of the transformation process. This is the first study in which such an approach has been used to gain further insights into colorectal tumorigenesis. Therefore, these data provide a launchpad for further exploration of the molecular characterization of colorectal tumorigenesis using systems biology approaches.

Abstract Background Bone marrow-derived circulating progenitor cells (BM-CPCs) in patients with coronary heart disease are impaired with respect to number and functional activity. However, the relation between the functional activity of BM-CPCs and the number of diseased coronary arteries is yet not known. We analyzed the influence of the number of diseased coronary arteries on the functional activity of BM-CPCs in peripheral blood (PB) in patients with ischemic heart disease (IHD). Methods The functional activity of BM-CPCs was measured by migration assay and colony forming unit in 120 patients with coronary 1 vessel (IHD1, n = 40), coronary 2 vessel (IHD2, n = 40), coronary 3 vessel disease (IHD3, n = 40) and in a control group of healthy subjects (n = 40). There was no significant difference of the total number of cardiovascular risk factors between IHD groups, beside diabetes mellitus (DM), which was significantly higher in IHD3 group compared to IHD2 and IHD1. Results The colony-forming capacity (CFU-E: p Conclusions The functional activity of BM-CPCs in PB is impaired in patients with IHD. This impairment increases with the number of diseased coronary arteries. Moreover, the regenerative capacity of BM-CPCs in ischemic tissue further declines in IHD patients with DM. Furthermore, monitoring the level of BM-CPCs in PB may provide new insights in patients with IHD.

Abstract Background The typical objective of Genome-wide association (GWA) studies is to identify single-nucleotide polymorphisms (SNPs) and corresponding genes with the strongest evidence of association (the 'most-significant SNPs/genes' approach). Borrowing ideas from micro-array data analysis, we propose a new method, named RS-SNP, for detecting sets of genes enriched in SNPs moderately associated to the phenotype. RS-SNP assesses whether the number of significant SNPs, with p-value P ≤ α, belonging to a given SNP set is statistically significant. The rationale of proposed method is that two kinds of null hypotheses are taken into account simultaneously. In the first null model the genotype and the phenotype are assumed to be independent random variables and the null distribution is the probability of the number of significant SNPs in greater than observed by chance. The second null model assumes the number of significant SNPs in depends on the size of and not on the identity of the SNPs in . Statistical significance is assessed using non-parametric permutation tests. Results We applied RS-SNP to the Crohn's disease (CD) data set collected by the Wellcome Trust Case Control Consortium (WTCCC) and compared the results with GENGEN, an approach recently proposed in literature. The enrichment analysis using RS-SNP and the set of pathways contained in the MSigDB C2 CP pathway collection highlighted 86 pathways rich in SNPs weakly associated to CD. Of these, 47 were also indicated to be significant by GENGEN. Similar results were obtained using the MSigDB C5 pathway collection. Many of the pathways found to be enriched by RS-SNP have a well-known connection to CD and often with inflammatory diseases. Conclusions The proposed method is a valuable alternative to other techniques for enrichment analysis of SNP sets. It is well founded from a theoretical and statistical perspective. Moreover, the experimental comparison with GENGEN highlights that it is more robust with respect to false positive findings.

Abstract Background Transplantation is the only treatment offering long-term benefit to patients with chronic kidney failure. Live donor nephrectomy is performed on healthy individuals who do not receive direct therapeutic benefit of the procedure themselves. In order to guarantee the donor's safety, it is important to optimise the surgical approach. Recently we demonstrated the benefit of laparoscopic nephrectomy experienced by the donor. However, this method is characterised by higher in hospital costs, longer operating times and it requires a well-trained surgeon. The hand-assisted retroperitoneoscopic technique may be an alternative to a complete laparoscopic, transperitoneal approach. The peritoneum remains intact and the risk of visceral injuries is reduced. Hand-assistance results in a faster procedure and a significantly reduced operating time. The feasibility of this method has been demonstrated recently, but as to date there are no data available advocating the use of one technique above the other. Methods/design The HARP-trial is a multi-centre randomised controlled, single-blind trial. The study compares the hand-assisted retroperitoneoscopic approach with standard laparoscopic donor nephrectomy. The objective is to determine the best approach for live donor nephrectomy to optimise donor's safety and comfort while reducing donation related costs. Discussion This study will contribute to the evidence on any benefits of hand-assisted retroperitoneoscopic versus standard laparoscopic donor nephrectomy. Trial Registration Dutch Trial Register NTR1433

Abstract Background The analysis of high-throughput gene expression data with respect to sets of genes rather than individual genes has many advantages. A variety of methods have been developed for assessing the enrichment of sets of genes with respect to differential expression. In this paper we provide a comparative study of four of these methods: Fisher's exact test, Gene Set Enrichment Analysis (GSEA), Random-Sets (RS), and Gene List Analysis with Prediction Accuracy (GLAPA). The first three methods use associative statistics, while the fourth uses predictive statistics. We first compare all four methods on simulated data sets to verify that Fisher's exact test is markedly worse than the other three approaches. We then validate the other three methods on seven real data sets with known genetic perturbations and then compare the methods on two cancer data sets where our a priori knowledge is limited. Results The simulation study highlights that none of the three method outperforms all others consistently. GSEA and RS are able to detect weak signals of deregulation and they perform differently when genes in a gene set are both differentially up and down regulated. GLAPA is more conservative and large differences between the two phenotypes are required to allow the method to detect differential deregulation in gene sets. This is due to the fact that the enrichment statistic in GLAPA is prediction error which is a stronger criteria than classical two sample statistic as used in RS and GSEA. This was reflected in the analysis on real data sets as GSEA and RS were seen to be significant for particular gene sets while GLAPA was not, suggesting a small effect size. We find that the rank of gene set enrichment induced by GLAPA is more similar to RS than GSEA. More importantly, the rankings of the three methods share significant overlap. Conclusion The three methods considered in our study recover relevant gene sets known to be deregulated in the experimental conditions and pathologies analyzed. There are differences between the three methods and GSEA seems to be more consistent in finding enriched gene sets, although no method uniformly dominates over all data sets. Our analysis highlights the deep difference existing between associative and predictive methods for detecting enrichment and the use of both to better interpret results of pathway analysis. We close with suggestions for users of gene set methods.

Abstract Background Barrett's mucosa is the precursor of esophageal adenocarcinoma. The molecular mechanisms behind Barrett's carcinogenesis are largely unknown. Experimental models of longstanding esophageal reflux of duodenal-gastric contents may provide important information on the biological sequence of the Barrett's oncogenesis. Methods The expression of CDX2 hox-gene product was assessed in a rat model of Barrett's carcinogenesis. Seventy-four rats underwent esophago-jejunostomy with gastric preservation. Excluding perisurgical deaths, the animals were sacrificed at various times after the surgical treatment (Group A: 30 weeks). Results No Cdx2 expression was detected in either squamous epithelia of the proximal esophagus or squamous cell carcinomas. De novo Cdx2 expression was consistently documented in the proliferative zone of the squamous epithelium close to reflux ulcers (Group A: 68%; Group B: 64%; Group C: 80%), multilayered epithelium and intestinal metaplasia (Group A: 9%; Group B: 41%; Group C: 60%), and esophageal adenocarcinomas (Group B: 36%; Group C: 35%). A trend for increasing overall Cdx2 expression was documented during the course of the experiment (p = 0.001). Conclusion De novo expression of Cdx2 is an early event in the spectrum of the lesions induced by experimental gastro-esophageal reflux and should be considered as a key step in the morphogenesis of esophageal adenocarcinoma.

Abstract Background Aberrant DNA methylation of CpG islands of cancer-related genes is among the earliest and most frequent alterations in cancerogenesis and might be of value for either diagnosing cancer or evaluating recurrent disease. This mechanism usually leads to inactivation of tumour-suppressor genes. We have designed the current study to validate our previous microarray data and to identify novel hypermethylated gene promoters. Methods The validation assay was performed in a different set of 8 patients with colorectal cancer (CRC) by means quantitative reverse-transcriptase polymerase chain reaction analysis. The differential RNA expression profiles of three CRC cell lines before and after 5-aza-2'-deoxycytidine treatment were compared to identify the hypermethylated genes. The DNA methylation status of these genes was evaluated by means of bisulphite genomic sequencing and methylation-specific polymerase chain reaction (MSP) in the 3 cell lines and in tumour tissues from 30 patients with CRC. Results Data from our previous genome search have received confirmation in the new set of 8 patients with CRC. In this validation set six genes showed a high induction after drug treatment in at least two of three CRC cell lines. Among them, the N-myc downstream-regulated gene 2 (NDRG2) promoter was found methylated in all CRC cell lines. NDRG2 hypermethylation was also detected in 8 out of 30 (27%) primary CRC tissues and was significantly associated with advanced AJCC stage IV. Normal colon tissues were not methylated. Conclusion The findings highlight the usefulness of combining gene expression patterns and epigenetic data to identify tumour biomarkers, and suggest that NDRG2 silencing might bear influence on tumour invasiveness, being associated with a more advanced stage.

Abstract Background Socioeconomic status could affect the demand for hospital care. The aim of the present study was to assess the role of age, socioeconomic status and comorbidity on acute hospital admissions among elderly. Methods We retrospectively examined the discharge abstracts data of acute care hospital admissions of residents in Rome aged 75 or more years in the period 1997–2000. We used the Hospital Information System of Rome, the Tax Register, and the Population Register of Rome for socio-economic data. The rate of hospitalization, modified Charlson's index of comorbidity, and level of income in the census tract of residence were obtained. Rate ratios and 95% confidence limits were computed to assess the relationship between income deciles and rate of hospitalization. Cross-tabulation was used to explore the distribution of the index of comorbidity by deciles of income. Analyses were repeated for patients grouped according to selected diseases. Results Age was associated with a marginal increase in the rate of hospitalization. However, the hospitalization rate was inversely related to income in both sexes. Higher income was associated with lower comorbidity. The same associations were observed in patients admitted with a principal diagnosis of chronic condition (diabetes mellitus, heart failure, chron obstructive pulmonary disease) or stroke, but not hip fracture. Conclusion Lower social status and associated comorbidity, more than age per se, are associated with a higher rate of hospitalization in very old patients.

Abstract Background While socioeconomic inequalities in mortality have widened in many countries, evidence of social differentials is scarce in Southern Europe. We studied temporal changes in premature mortality across socioeconomic groups in Rome between 1990 and 2001. Methods We analysed all 126,511 death certificates of residents of Rome aged 0–74 years registered between 1990–2001. A 4-level census block index based on the 1991 census was used as an indicator of socioeconomic position (SEP). Using routine mortality data, standardised mortality rates (per 100,000 inhabitants) were calculated by SEP and gender for four time periods. Rate ratios were used to compare mortality by gender and age. Results Overall premature mortality decreased in both genders and in all socioeconomic groups; the change was greater in the highest socio-economic group. In both men and women, inequalities in mortality strengthened during the 1990s and appeared to stabilise at the end of the 20th century. However, for 60–74 year old women the gap continued to widen. Conclusion Socioeconomic inequalities in health in Rome are still present at the beginning of the 21st century. Strategies to monitor the impact of SEP on mortality over time in different populations should be implemented to direct health policies.

Abstract Background In this paper we present a method for the statistical assessment of cancer predictors which make use of gene expression profiles. The methodology is applied to a new data set of microarray gene expression data collected in Casa Sollievo della Sofferenza Hospital, Foggia – Italy. The data set is made up of normal (22) and tumor (25) specimens extracted from 25 patients affected by colon cancer. We propose to give answers to some questions which are relevant for the automatic diagnosis of cancer such as: Is the size of the available data set sufficient to build accurate classifiers? What is the statistical significance of the associated error rates? In what ways can accuracy be considered dependant on the adopted classification scheme? How many genes are correlated with the pathology and how many are sufficient for an accurate colon cancer classification? The method we propose answers these questions whilst avoiding the potential pitfalls hidden in the analysis and interpretation of microarray data. Results We estimate the generalization error, evaluated through the Leave-K-Out Cross Validation error, for three different classification schemes by varying the number of training examples and the number of the genes used. The statistical significance of the error rate is measured by using a permutation test. We provide a statistical analysis in terms of the frequencies of the genes involved in the classification. Using the whole set of genes, we found that the Weighted Voting Algorithm (WVA) classifier learns the distinction between normal and tumor specimens with 25 training examples, providing e = 21% (p = 0.045) as an error rate. This remains constant even when the number of examples increases. Moreover, Regularized Least Squares (RLS) and Support Vector Machines (SVM) classifiers can learn with only 15 training examples, with an error rate of e = 19% (p = 0.035) and e = 18% (p = 0.037) respectively. Moreover, the error rate decreases as the training set size increases, reaching its best performances with 35 training examples. In this case, RLS and SVM have error rates of e = 14% (p = 0.027) and e = 11% (p = 0.019). Concerning the number of genes, we found about 6000 genes (p < 0.05) correlated with the pathology, resulting from the signal-to-noise statistic. Moreover the performances of RLS and SVM classifiers do not change when 74% of genes is used. They progressively reduce up to e = 16% (p < 0.05) when only 2 genes are employed. The biological relevance of a set of genes determined by our statistical analysis and the major roles they play in colorectal tumorigenesis is discussed. Conclusions The method proposed provides statistically significant answers to precise questions relevant for the diagnosis and prognosis of cancer. We found that, with as few as 15 examples, it is possible to train statistically significant classifiers for colon cancer diagnosis. As for the definition of the number of genes sufficient for a reliable classification of colon cancer, our results suggest that it depends on the accuracy required.

Abstract Background Direct admission to Coronary Care Unit (CCU) on hospital arrival can be considered as a good proxy for adequate management in patients with acute myocardial infarction (AMI), as it has been associated with better prognosis. We analyzed a cohort of patients with AMI hospitalized in Rome (Italy) in 1997–2000 to assess the proportion directly admitted to CCU and to investigate the effect of patient characteristics such as gender, age, illness severity on admission, and socio-economic status (SES) on CCU admission practices. Methods Using discharge data, we analyzed a cohort of 9127 AMI patients. Illness severity on admission was determined using the Deyo's adaptation of the Charlson's comorbidity index, and each patient was assigned to one to four SES groups (level I referring to the highest SES) defined by a socioeconomic index, derived by the characteristics of the census tract of residence. The effect of gender, age, illness severity and SES, on risk of non-admission to CCU was investigated using a logistic regression model (OR, CI 95%). Results Only 53.9% of patients were directly admitted to CCU, and access to optimal care was more frequently offered to younger patients (OR = 0.35; 95%CI = 0.25–0.48 when comparing 85+ to >=50 years), those with less severe illness (OR = 0.48; 95%CI = 0.37–0.61 when comparing Charlson index 3+ to 0) and the socially advantaged (OR = 0.81; 95%CI = 0.66–0.99 when comparing low to high SES). Conclusion In Rome, Italy, standard optimal coronary care is underprovided. It seems to be granted preferentially to the better off, even after controversial clinical criteria, such as age and severity of illness, are taken into account.