ParPEST: a pipeline for EST data analysis based on parallel computing

BACKGROUND: Expressed Sequence Tags (ESTs) are short and error-prone DNA sequences generated from the 5' and 3' ends of randomly selected cDNA clones. They provide an important resource for comparative and functional genomic studies and, moreover, represent a reliable information for the annotation of genomic sequences. Because of the advances in biotechnologies, ESTs are daily determined in the form of large datasets. Therefore, suitable and efficient bioinformatic approaches are necessary to organize data related information content for further investigations. RESULTS: We implemented ParPEST (Parallel Processing of ESTs), a pipeline based on parallel computing for EST analysis. The results are organized in a suitable data warehouse to provide a starting point to mine expressed sequence datasets. The collected information is useful for investigations on data quality and on data information content, enriched also by a preliminary functional annotation. CONCLUSION: The pipeline presented here has been developed to perform an exhaustive and reliable analysis on EST data and to provide a curated set of information based on a relational database. Moreover, it is designed to reduce execution time of the specific steps required for a complete analysis using distributed processes and parallelized software. It is conceived to run on low requiring hardware components, to fulfill increasing demand, typical of the data used, and scalability at affordable costs

TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species

TomatEST is a secondary database integrating expressed sequence tag (EST)/cDNA sequence information from different libraries of multiple tomato species. Redundant EST collections from each species are organized into clusters (gene indices). A cluster consists of one or multiple contigs. Multiple contigs in a cluster represent alternatively transcribed forms of a gene. The set of stand-alone EST sequences (singletons) and contigs, representing all the computationally defined ‘Transcript Indices’, are annotated according to similarity versus protein and RNA family databases. Sequence function description is integrated with the Gene Ontologies and the Enzyme Commission identifiers for a standard classification of gene products and for the mapping of the expressed sequences onto metabolic pathways. Information on the origin of the ESTs, on their structural features, on clusters and contigs, as well as on functional annotations are accessible via a user-friendly web interface. Specific facilities in the database allow Transcript Indices from a query be automatically classified in Enzyme classes and in metabolic pathways. The ‘on the fly’ mapping onto the metabolic maps is integrated in the analytical tools. The TomatEST database website is freely available at

Effective Anomaly Detection Using Deep Learning in IoT Systems

Anomaly detection in network traffic is a hot and ongoing research theme especially when concerning IoT devices, which are quickly spreading throughout various situations of people's life and, at the same time, prone to be attacked through different weak points. In this paper, we tackle the emerging anomaly detection problem in IoT, by integrating five different datasets of abnormal IoT traffic and evaluating them with a deep learning approach capable of identifying both normal and malicious IoT traffic as well as different types of anomalies. The large integrated dataset is aimed at providing a realistic and still missing benchmark for IoT normal and abnormal traffic, with data coming from different IoT scenarios. Moreover, the deep learning approach has been enriched through a proper hyperparameter optimization phase, a feature reduction phase by using an autoencoder neural network, and a study of the robustness of the best considered deep neural networks in situations affected by Gaussian noise over some of the considered features. The obtained results demonstrate the effectiveness of the created IoT dataset for anomaly detection using deep learning techniques, also in a noisy scenario

ISOL@: an Italian SOLAnaceae genomics resource

BACKGROUND: Present-day '-omics' technologies produce overwhelming amounts of data which include genome sequences, information on gene expression (transcripts and proteins) and on cell metabolic status. These data represent multiple aspects of a biological system and need to be investigated as a whole to shed light on the mechanisms which underpin the system functionality.The gathering and convergence of data generated by high-throughput technologies, the effective integration of different data-sources and the analysis of the information content based on comparative approaches are key methods for meaningful biological interpretations.In the frame of the International Solanaceae Genome Project, we propose here ISOLA, an Italian SOLAnaceae genomics resource. RESULTS: ISOLA (available at http://biosrv.cab.unina.it/isola) represents a trial platform and it is conceived as a multi-level computational environment.ISOLA currently consists of two main levels: the genome and the expression level. The cornerstone of the genome level is represented by the Solanum lycopersicum genome draft sequences generated by the International Tomato Genome Sequencing Consortium. Instead, the basic element of the expression level is the transcriptome information from different Solanaceae species, mainly in the form of species-specific comprehensive collections of Expressed Sequence Tags (ESTs).The cross-talk between the genome and the expression levels is based on data source sharing and on tools that enhance data quality, that extract information content from the levels' under parts and produce value-added biological knowledge. CONCLUSIONS: ISOLA is the result of a bioinformatics effort that addresses the challenges of the post-genomics era. It is designed to exploit '-omics' data based on effective integration to acquire biological knowledge and to approach a systems biology view. Beyond providing experimental biologists with a preliminary annotation of the tomato genome, this effort aims to produce a trial computational environment where different aspects and details are maintained as they are relevant for the analysis of the organization, the functionality and the evolution of the Solanaceae family

Genetics of VEGF Serum Variation in Human Isolated Populations of Cilento: Importance of VEGF Polymorphisms

Vascular Endothelial Growth Factor (VEGF) is the main player in angiogenesis. Because of its crucial role in this process, the study of the genetic factors controlling VEGF variability may be of particular interest for many angiogenesis-associated diseases. Although some polymorphisms in the VEGF gene have been associated with a susceptibility to several disorders, no genome-wide search on VEGF serum levels has been reported so far. We carried out a genome-wide linkage analysis in three isolated populations and we detected a strong linkage between VEGF serum levels and the 6p21.1 VEGF region in all samples. A new locus on chromosome 3p26.3 significantly linked to VEGF serum levels was also detected in a combined population sample. A sequencing of the gene followed by an association study identified three common single nucleotide polymorphisms (SNPs) influencing VEGF serum levels in one population (Campora), two already reported in the literature (rs3025039, rs25648) and one new signal (rs3025020). A fourth SNP (rs41282644) was found to affect VEGF serum levels in another population (Cardile). All the identified SNPs contribute to the related population linkages (35% of the linkage explained in Campora and 15% in Cardile). Interestingly, none of the SNPs influencing VEGF serum levels in one population was found to be associated in the two other populations. These results allow us to exclude the hypothesis that the common variants located in the exons, intron-exon junctions, promoter and regulative regions of the VEGF gene may have a causal effect on the VEGF variation. The data support the alternative hypothesis of a multiple rare variant model, possibly consisting in distinct variants in different populations, influencing VEGF serum levels

Colorectal Cancer Stage at Diagnosis Before vs During the COVID-19 Pandemic in Italy

IMPORTANCE Delays in screening programs and the reluctance of patients to seek medical attention because of the outbreak of SARS-CoV-2 could be associated with the risk of more advanced colorectal cancers at diagnosis. OBJECTIVE To evaluate whether the SARS-CoV-2 pandemic was associated with more advanced oncologic stage and change in clinical presentation for patients with colorectal cancer. DESIGN, SETTING, AND PARTICIPANTS This retrospective, multicenter cohort study included all 17 938 adult patients who underwent surgery for colorectal cancer from March 1, 2020, to December 31, 2021 (pandemic period), and from January 1, 2018, to February 29, 2020 (prepandemic period), in 81 participating centers in Italy, including tertiary centers and community hospitals. Follow-up was 30 days from surgery. EXPOSURES Any type of surgical procedure for colorectal cancer, including explorative surgery, palliative procedures, and atypical or segmental resections. MAIN OUTCOMES AND MEASURES The primary outcome was advanced stage of colorectal cancer at diagnosis. Secondary outcomes were distant metastasis, T4 stage, aggressive biology (defined as cancer with at least 1 of the following characteristics: signet ring cells, mucinous tumor, budding, lymphovascular invasion, perineural invasion, and lymphangitis), stenotic lesion, emergency surgery, and palliative surgery. The independent association between the pandemic period and the outcomes was assessed using multivariate random-effects logistic regression, with hospital as the cluster variable. RESULTS A total of 17 938 patients (10 007 men [55.8%]; mean [SD] age, 70.6 [12.2] years) underwent surgery for colorectal cancer: 7796 (43.5%) during the pandemic period and 10 142 (56.5%) during the prepandemic period. Logistic regression indicated that the pandemic period was significantly associated with an increased rate of advanced-stage colorectal cancer (odds ratio [OR], 1.07; 95%CI, 1.01-1.13; P = .03), aggressive biology (OR, 1.32; 95%CI, 1.15-1.53; P < .001), and stenotic lesions (OR, 1.15; 95%CI, 1.01-1.31; P = .03). CONCLUSIONS AND RELEVANCE This cohort study suggests a significant association between the SARS-CoV-2 pandemic and the risk of a more advanced oncologic stage at diagnosis among patients undergoing surgery for colorectal cancer and might indicate a potential reduction of survival for these patients

Intraperitoneal drain placement and outcomes after elective colorectal surgery: international matched, prospective, cohort study

Despite current guidelines, intraperitoneal drain placement after elective colorectal surgery remains widespread. Drains were not associated with earlier detection of intraperitoneal collections, but were associated with prolonged hospital stay and increased risk of surgical-site infections.Background Many surgeons routinely place intraperitoneal drains after elective colorectal surgery. However, enhanced recovery after surgery guidelines recommend against their routine use owing to a lack of clear clinical benefit. This study aimed to describe international variation in intraperitoneal drain placement and the safety of this practice. Methods COMPASS (COMPlicAted intra-abdominal collectionS after colorectal Surgery) was a prospective, international, cohort study which enrolled consecutive adults undergoing elective colorectal surgery (February to March 2020). The primary outcome was the rate of intraperitoneal drain placement. Secondary outcomes included: rate and time to diagnosis of postoperative intraperitoneal collections; rate of surgical site infections (SSIs); time to discharge; and 30-day major postoperative complications (Clavien-Dindo grade at least III). After propensity score matching, multivariable logistic regression and Cox proportional hazards regression were used to estimate the independent association of the secondary outcomes with drain placement. Results Overall, 1805 patients from 22 countries were included (798 women, 44.2 per cent; median age 67.0 years). The drain insertion rate was 51.9 per cent (937 patients). After matching, drains were not associated with reduced rates (odds ratio (OR) 1.33, 95 per cent c.i. 0.79 to 2.23; P = 0.287) or earlier detection (hazard ratio (HR) 0.87, 0.33 to 2.31; P = 0.780) of collections. Although not associated with worse major postoperative complications (OR 1.09, 0.68 to 1.75; P = 0.709), drains were associated with delayed hospital discharge (HR 0.58, 0.52 to 0.66; P < 0.001) and an increased risk of SSIs (OR 2.47, 1.50 to 4.05; P < 0.001). Conclusion Intraperitoneal drain placement after elective colorectal surgery is not associated with earlier detection of postoperative collections, but prolongs hospital stay and increases SSI risk

La Balanced Scorecard come strumento di misurazione delle performance negli istituti bancari: due banche di credito cooperativo a confronto

A causa del notevole incremento della pressione competitiva, le banche manifestano attualmente l’esigenza di migliorare i propri risultati sotto diversi punti di vista. Oltre al classico aspetto economico-finanziario, anche altre sfere strategiche e gestionali necessitano di essere monitorate: diviene pertanto di fondamentale importanza il raggiungimento di risultati espressi anche in termini di efficienza e funzionalità organizzativa, oppure di efficacia e flessibilità organizzativa (Di Antonio, 2008). Negli ultimi anni, a causa di alcuni cambiamenti radicali che hanno interessato il settore bancario – quali la globalizzazione dei mercati finanziari, l’innovazione dei prodotti finanziari e le nuove disposizioni e cambiamenti nel comportamento dei clienti – si è avvertita l’esigenza di utilizzare strumenti di misurazione della performance capaci di misurare ulteriori fattori critici di successo, oltre che di individuare le variabili più rilevanti per il processo decisionale della banca, le risorse impiegate ed i risultati raggiunti. Il tutto con l'obiettivo di gestire la banca con maggiore consapevolezza e razionalità. Onde poter raggiungere queste finalità, gli istituti di credito stanno compiendo sforzi apprezzabili per innovare i propri sistemi di misurazione, orientandosi verso una gestione per processi e implementando nuovi strumenti di controllo in passato assolutamente ignoti al settore. Il tentativo di introdurre nuove tecniche manageriali ha comportato un cambiamento nella cultura aziendale e la necessaria apertura di tutto l’organismo personale della banca nei confronti dei nuovi strumenti. Le principali tecniche utilizzate dagli istituti di credito vanno dal Business Process Reengineering (BPR) all’Activity-Based Costing (ABC), dall’Activity-Based Managament (ABM) all’Assessment del rischio di processo, fino ai sistemi integrati di misurazione della performance, tra cui la Balanced Scorecard (BSC). Quest’ultimo strumento costituirà l’oggetto precipuo del presente lavoro di ricerca. Dal punto di vista metodologico si è proceduto attraverso un’analisi della letteratura nazionale avente ad oggetto casi studi di progettazione e/o implementazione della BSC negli istituti bancari. L’obiettivo del presente paper non è proporre nuovi case studies di applicazione della BSC da aggiungere ai precedenti contributi presenti in letteratura (Turi, 2002; Giorgino et al, 2005; Desario, 2006; Busco C. et al., 2007; Mazza, 2008; Vola et al., 2009; Castellano e Giannizzari, 2012), ma porre l’attenzione su due specifici istituti bancari proposti dalla letteratura al fine di: i) indagare come essi abbiano proceduto nella progettazione della BSC, ii) evidenziare le particolarità dell’applicazione della BSC in ciascun istituto, e iii) individuare gli elementi di comunanza e di divergenza tra i due casi. 3 Nell’ambito delle banche analizzate dalla letteratura nazionale (tra le altre Banca 121, Intesa SanPaolo, Monte Paschi di Siena, Banca di credito cooperativo di Fisciano, Banca di credito cooperativo piemontese) si è scelto di porre l’attenzione sulle banche di credito cooperativo (Bcc) a causa del rilevante ruolo di sostegno all’economia che ricoprono come risposta alla crisi (Draghi M., 2009). Le Banche di credito cooperativo sono infatti banche locali, caratterizzate da un forte legame di reciprocità con i territorio di riferimento; lo status di socio della banca può essere concesso solo a chi risiedere, ha sede, ovvero opera con carattere di continuità nel territorio di competenza e il risparmio raccolto dalla banca viene investito nel sostenimento e nei finanziamento dello sviluppo dell’economia reale locale (Castellano e Giannizzari, 2012). Nell’ambito delle banche di credito cooperativo proposte dalla letteratura, ci si è focalizzati su due banche attive su tessuti territoriali diametralmente opposti – la Banca di credito cooperativo del Piemonte (Vola et al., 2009) e la Banca di credito cooperativo della Campania (Castellano e Giannizzari, 2012) – al fine di evidenziare le differenze e le similitudini nella progettazione dello strumento analizzato. Il lavoro si articola in sei paragrafi. Il primo paragrafo pone l’attenzione sulle criticità del settore bancario ed in particolare sulle caratteristiche del sistema del credito cooperativo; il secondo paragrafo delinea lo strumento della BSC; il terzo paragrafo illustra le particolarità relative all’applicazione della BSC nelle banche; il quarto e il quinto sono dedicati all’analisi della BSC nelle due Bcc selezionate, mentre il sesto paragrafo è dedicato alle considerazioni conclusive

L’Economia Aziendale nei dottorati italiani: un’indagine esplorativa

The Accounting Education is a scientific field very flourishing outside Italy, with a rich presence of international scientific journals. Instead, the Italian researches have been focused more on scientific aspects of Accounting and Economia Aziendale, less on the educational profile. This paper, including in the studies of the Accounting education, aims to investigate the teaching of “Economia Aziendale" in Italian Phd courses, with a particular focus on the cycles XXIX. Taking a cue from a study conducted by the study group Sidrea in 2008, the information has been found both on the PhDs websites and on the Ministry of Education one. The survey has been conducted analyzing 34 Italian PhD activated by the Department of Economic, Accounting or Management and has been composed by two parts. The first part is related to the investigation of the thematic more disseminated in the 34 PhD courses analyzed. In the second part has been investigated the organization of these PhD courses. The analysis involves the use of a qualitative methodology, in which the data collected were simply observed and compared each other. In order to include this contribution in the classical taxonomy of Accounting Education studies, it could be classified as a "Curricu-lum and instruction", because the second part of the analysis has been focused on the observation of curricula, course content and teaching methods. Findings show that, in line with previous research, the thematic more widespread are the accounting, the research methodology and strategy, while scars attention have been paid to the Finance and Public sector accounting. Moreover teaching methods used in the Italian PhD courses are based on the traditional tools (compulsory lessons and seminars). However, the analysis of the programs shows a relevant role of the national and international conference and drawing up paper; which stimulate and train students to scientific research. This paper is a contribution to the existing literature by pointing out the attention on the role of the Economia Aziendale; in particular the novelty of the paper compared with the few previous studies is that the analysis was focused on all doctorates, which are involved in the scientific sector Secs P / 07