Gene silencing and large-scale domain structure of the E. coli genome

The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression. Motivated by the link between chromosome organization, protein binding and gene expression, we analyzed publicly available genomic data sets of various origins, from genome-wide protein binding profiles to evolutionary information, exploring the connections between chromosomal organization, genesilencing, pseudo-gene localization and horizontal gene transfer. We report the existence of transcriptionally silent contiguous areas corresponding to large regions of H-NS protein binding along the genome, their position indicates a possible relationship with the known large-scale features of chromosome organization

MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification

Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- and character-based methods

Serum Cystatin C for the diagnosis of acute Kidney Injury in Patients Admitted in the Emergency Department

BACKGROUND: Early diagnosis of acute kidney injury (AKI) at emergency department (ED) is a challenging issue. Current diagnostic criteria for AKI poorly recognize early renal dysfunction and may cause delayed diagnosis. We evaluated the use of serum cystatin C (CysC) for the early and accurate diagnosis of AKI in patients hospitalized from the ED. METHODS: In a total of 198 patients (105 males and 93 females), serum CysC, serum creatinine (sCr), and estimated glomerular filtration rate (eGFR) were calculated at 0, 6, 12, 24, 48, and 72 hours after presentation to the ED. We compared two groups according to the presence or absence of AKI. RESULTS: Serial assessment of CysC, sCr, and eGFR was not a strong, reliable tool to distinguish AKI from non-AKI. CysC > 1.44 mg/L at admission, both alone (Odds Ratio = 5.04; 95%CI 2.20-11.52; P < 0.0002) and in combination with sCr and eGFR (Odds Ratio = 5.71; 95%CI 1.86-17.55; P < 0.002), was a strong predictor for the risk of AKI. CONCLUSIONS: Serial assessment of CysC is not superior to sCr and eGFR in distinguishing AKI from non-AKI. Admission CysC, both alone and in combination with sCr and eGFR, could be considered a powerful tool for the prediction of AKI in ED patients

Statistical Mechanics of the Chinese Restaurant Process: lack of self-averaging, anomalous finite-size effects and condensation

The Pitman-Yor, or Chinese Restaurant Process, is a stochastic process that generates distributions following a power-law with exponents lower than two, as found in a numerous physical, biological, technological and social systems. We discuss its rich behavior with the tools and viewpoint of statistical mechanics. We show that this process invariably gives rise to a condensation, i.e. a distribution dominated by a finite number of classes. We also evaluate thoroughly the finite-size effects, finding that the lack of stationary state and self-averaging of the process creates realization-dependent cutoffs and behavior of the distributions with no equivalent in other statistical mechanical models.Comment: (5pages, 1 figure

Impact of remnant vital tissue after locoregional treatment and liver transplant in hepatocellular cancer patients. A multicentre cohort study

The role of pathological findings after locoregional treatments as predictors of hepatocellular cancer recurrence after liver transplantation has been poorly addressed. The aim of the study was to identify the role of remnant vital tissue (RVT) of the target lesion in predicting hepatocellular cancer recurrence. Two hundred and seventy-six patients firstly undergoing locoregional treatment and then transplanted between January 2010 and December 2015 in four European Transplant Centres (i.e. Rome Tor Vergata, Birmingham, Brussels and Ancona) were enrolled in the study to investigate the role of pathological response at upfront locoregional treatment. At multivariable Cox regression analysis, RVT ≥2 cm was a strong independent risk factor for post-LT recurrence (HR = 5.6; P < 0.0001). Five-year disease-free survival rates were 60.8%, 80.9% and 95.0% in patients presenting a RVT ≥2 cm vs. 0.1-1.9 vs. no RVT, respectively. When only Milan Criteria-IN patients were analysed, similar results were reported, with 5-year disease-free survival rates of 58.1%, 79.0% and 94.0% in patients presenting a RVT ≥2 cm vs. 0.1-1.9 vs. no RVT, respectively. RVT is an important determinant of tumour recurrence after liver transplantation performed for hepatocellular cancer. Its discriminative power looks to be evident also in a Milan-IN setting, suggesting to more liberally use locoregional treatments also in these patients

Standardizing Navigation Data: A Status Update

This paper presents the work of the Navigation Working Group of the Consultative Committee for Space Data Systems (CCSDS) on development of standards addressing the transfer of orbit, attitude and tracking data for space objects. Much progress has been made since the initial presentation of the standards in 2004, including the progression of the orbit data standard to an accepted standard, and the near completion of the attitude and tracking data standards. The orbit, attitude and tracking standards attempt to address predominant parameterizations for their respective data, and create a message format that enables communication of the data across space agencies and other entities. The messages detailed in each standard are built upon a keyword = value paradigm, where a fixed list of keywords is provided in the standard where users specify information about their data, and also use keywords to encapsulate their data. The paper presents a primer on the CCSDS standardization process to put in context the state of the message standards, and the parameterizations supported in each standard, then shows examples of these standards for orbit, attitude and tracking data. Finalization of the standards is expected by the end of calendar year 2007

LPS-induced TNF-α factor mediates pro-inflammatory and pro-fibrogenic pattern in non-alcoholic fatty liver disease

Lipopolysaccharide (LPS) is currently considered one of the major players in non-alcoholic fatty liver disease (NAFLD) pathogenesis and progression. Here, we aim to investigate the possible role of LPS-induced TNF-α factor (LITAF) in inducing a pro-inflammatory and pro-fibrogenic phenotype of non-alcoholic steatohepatitis (NASH).We found that children with NAFLD displayed, in different liver-resident cells, an increased expression of LITAF which correlated with histological traits of hepatic inflammation and fibrosis. Total and nuclear LITAF expression increased in mouse and human hepatic stellate cells (HSCs). Moreover, LPS induced LITAF-dependent transcription of IL-1β, IL-6 and TNF-α in the clonal myofibroblastic HSC LX-2 cell line, and this effect was hampered by LITAF silencing. We showed, for the first time in HSCs, that LITAF recruitment to these cytokine promoters is LPS dependent. However, preventing LITAF nuclear translocation by p38MAPK inhibitor, the expression of IL-6 and TNF-α was significantly reduced with the aid of p65NF-ĸB, while IL-1β transcription exclusively required LITAF expression/activity. Finally, IL-1β levels in plasma mirrored those in the liver and correlated with LPS levels and LITAF-positive HSCs in children with NASH.In conclusion, a more severe histological profile in paediatric NAFLD is associated with LITAF over-expression in HSCs, which in turn correlates with hepatic and circulating IL-1β levels outlining a panel of potential biomarkers of NASH-related liver damage. The in vitro study highlights the role of LITAF as a key regulator of the LPS-induced pro-inflammatory pattern in HSCs and suggests p38MAPK inhibitors as a possible therapeutic approach against hepatic inflammation in NASH

Mining Biological Networks

This thesis addresses relevant issues related to the analysis of biological networks. Path redundancy was exploited to denoise currently available data, dominated by high levels of wrong or missing information, and applied to the local alignment of protein-protein interaction networks. On another research direction, regulatory networks were employed to explain master regulators’ ability of modulating cells’ behaviour. In this direction, an existing approach was adapted for the analysis of miRNAs’ role in Glioblastoma Multiforme cancer cells. The methodological aspects of this work represent an improvement of the foundamental elements of network analysis techniques

POLITICHE E ISTITUZIONI DEL SETTORE FORESTALE IN CINA

Il governo cinese da alcuni anni manifesta una politica a favore della protezione delle foreste naturali, dei divieti di taglio e di incentivo alla realizzazione di piantagioni arboree. La Repubblica Popolare è oggi il primo importatore di legname e il primo nella realizzazione di piantagioni con scopi produttivi e protettivi. Il presente elaborato vuole descrivere le politiche e le istituzioni del settore forestale in Cina, chiarire le modalità di gestione forestale, fornire una panoramica sul mercato dei prodotti forestali e sulla situazione delle piantagioni arboree del paese, in particolare analizzando i progetti forestali per lo sviluppo di quest’ultime. La Cina di oggi ha un urgente bisogno di legname. Nonostante sia il terzo stato al mondo per estensione del territorio, si presenta come un Paese povero di risorse forestali, con valori di stock pro capite nettamente inferiori alla media mondiale. Ciò è dovuto principalmente a quattro motivi: le caratteristiche climatiche, l’antropizzazione del territorio, le passate politiche di sfruttamento delle foreste naturali, il programma per la protezione delle foreste naturali. Per ovviare a questa carenza, oltre che per la proteggere il proprio territorio dal grave rischio di desertificazione e dalle alluvioni, il governo ha messo in atto i sei “programmi chiave” del settore forestale: il programma di protezione delle foreste naturali, il programma di conversione dei terreni agricoli in foresta, la “Grande Muraglia Verde” contro la desertificazione, il programma di protezione delle zone umide, il programma di controllo della desertificazione nei dintorni di Pechino e Tianjin, il programma di sviluppo delle piantagioni a crescita rapida e ad alta produttività. _______________________________________________________________________________________________________ From some years, the Chinese government expresses a policy for the protection and the prohibition of logging in natural forests and incentives for the creation of plantations of trees. People's Republic of China is now the largest importer of timber and the first country in the establishment of productive and protective plantations. The present study wants to describe the policies and institutions of the forestry sector in China, to clarify how forests are manages, to provide an overview of the forest products market and analyze the situation of trees plantations, notably by describing the reforestation projects. China has an urgent need for lumber. Despite being the third state in the world by extension, is presented as a poor country in forest resources, with values of stocks below comparing by the world average. This is mainly due for four reasons: the climate and land characteristics, the area of human activity, past policies of exploitation of natural forests, the program for the protection of natural forests. To remedy this deficiency, as well as for protecting its territory from the serious threat of desertification and floods, the government has implemented the “Six Key Forestry Programs": the Natural Forest Protection Program, the Program on Converting Cropland into Forest, the Shelterbelt Development Program, the Sandification Control Program near Beijing and Tianjin, the Wetlands Protection Program, the program on Fast-growing and High-yield Plantation. In addition to these, agro-forestry (mixture of trees plantations and agricultural crops, well developed in rural areas of the country), the forestry projects implemented by the Clean Development Mechanism, plantations for pulpwood financed by foreign companies and bamboo plantations contribute to a rapid increase in forest area in China. However, different issues are rising around the needing of timber in China (the largest growth in imports, the expansion of Chinese companies in the South East Asia countries) and the development of plantations (the loss of biodiversity due to the use of a few species, especially poplar, the use of genetically modified plants) shows that P.R.C. in need of further changes in forest sector, according of its economic development, its increasing population and the growing environmental problems.openTES-64

Interaction vs inhomogeneity in a periodic TASEP

We study the non-equilibrium steady states in a totally asymmetric simple exclusion process with periodic boundary conditions, also incorporating (i) an extra (nearest-neighbour) repulsive interaction and (ii) hopping rates characterized by a smooth spatial inhomogeneity. We make use of a generalized mean-field approach (at the level of nearest-neighbour pair clusters), in combination with kinetic Monte Carlo simulations. It turns out that the so-called shock phase can exhibit a lot of qualitatively different subphases, including multiple-shock phases, and a minimal-current shock phase. We argue that the resulting, considerably rich phase diagram should be relatively insensitive to minor details of either interaction or spatial inhomogeneity. As a consequence, we also expect that our results help elucidate the nature of shock subphases detected in previous studies