39 research outputs found

    Effective evaluation of clustering algorithms on single-cell CNA data

    Get PDF
    Clustering methods are increasingly applied to single-cell DNA sequencing (scDNAseq) data to infer the subclonal structure of cancer. However, the complexity of these data exacerbates some data-science issues and affects clustering results. Additionally, determining whether such inferences are accurate and clusters recapitulate the real cell phylogeny is not trivial, mainly because ground truth information is not available for most experimental settings. Here, by exploiting simulated sequencing data representing known phylogenies of cancer cells, we propose a formal and systematic assessment of well-known clustering methods to study their performance and identify the approach providing the most accurate reconstruction of phylogenetic relationships

    Single-cell DNA Sequencing Data: a Pipeline for Multi-Sample Analysis

    Get PDF
    In order to help cancer researchers in understanding tumor heterogeneity and its evolutionary dynamics, we propose a software pipeline to explore intra-tumor heterogeneity by means of scDNA sequencing data

    Oxidative Stress: Harms and Benefits for Human Health

    Get PDF
    Oxidative stress is a phenomenon caused by an imbalance between production and accumulation of oxygen reactive species (ROS) in cells and tissues and the ability of a biological system to detoxify these reactive products. ROS can play, and in fact they do it, several physiological roles (i.e., cell signaling), and they are normally generated as by-products of oxygen metabolism; despite this, environmental stressors (i.e., UV, ionizing radiations, pollutants, and heavy metals) and xenobiotics (i.e., antiblastic drugs) contribute to greatly increase ROS production, therefore causing the imbalance that leads to cell and tissue damage (oxidative stress). Several antioxidants have been exploited in recent years for their actual or supposed beneficial effect against oxidative stress, such as vitamin E, flavonoids, and polyphenols. While we tend to describe oxidative stress just as harmful for human body, it is true as well that it is exploited as a therapeutic approach to treat clinical conditions such as cancer, with a certain degree of clinical success. In this review, we will describe the most recent findings in the oxidative stress field, highlighting both its bad and good sides for human health

    Levels of Heavy Metals in Adolescents Living in the Industrialised Area of Milazzo-Valle del Mela (Northern Sicily)

    Get PDF
    In the Milazzo-Valle del Mela area, the presence of industrial plants and the oil refinery make local residents concerned for their health. For this reason, we evaluated the levels of heavy metals in 226 children aged 12–14 years, living in the 7 municipalities of the area. A control age-matched population (n=29) living 45 km far from the industrial site was also enrolled. Arsenic, cadmium, chromium, mercury, nickel, and vanadium were analysed in 24 h urine samples, while lead concentration was evaluated in blood samples. A questionnaire regarding life style and risk perception was also administered. Adolescents from Milazzo-Valle del Mela had cadmium levels significantly higher compared to either controls  (P<0.0001) or the reference values of the European Germany Environmental Survey (GerES-IV) and the American National Health and Nutrition Examination Survey (NHANES). Furthermore, children had higher perception of living in a high-risk environment. The present data, for the first time, clearly indicate that adolescents living in Milazzo-Valle del Mela have increased body concentration of cadmium, which may be harmful to human health. These results deserve particular attention by the local and regional government to initiate prevention programmes in this susceptible population

    CO 2

    Get PDF
    Laparoscopy (LS) has been shown to decrease the inflammatory sequelae of endotoxemia. β-arrestin 2 plays an important function in signal transduction pathway of TLR4. High mobility group box-1 (HMGB-1) is involved in the delayed systemic inflammatory response. We investigated the effects of CO2 insufflation on liver, lung, and kidney expression of both β-arrestin 2 and HMGB-1 during sepsis. Cecal ligation and puncture (CLP) was performed in male rats and 6 h later the animals were randomly assigned to receive a CO2 pneumoperitoneum or laparotomy. Animals were euthanized; liver, lung, and kidney were removed for the evaluation of β-arrestin 2 and HMGB-1 expression. Immunohistochemical detection of myeloperoxidase (MPO) was investigated in lung and liver and bacterial load was determined in the peritoneal fluid. CO2 pneumoperitoneum reduced peritoneal bacterial load, increased the expression of β-arrestin 2, and blunted the expression of the potent proinflammatory HMGB-1 in liver, lung, and kidney compared with laparotomy. Liver and lung MPO was markedly reduced in rats subjected to LS compared with laparotomy. We believe that CO2 exerts an early protective effect by reducing bacterial load and likely toll-like receptor activation which in turn leads to a preserved β-arrestin 2 expression and a reduced HMGB-1 expression

    Role of NLRP3 in an experimental model of testicular ischemia and reperfusion in mice

    Get PDF
    Inflammasomes are multi-protein complexes composed of one of several leucinerich repeat receptors (NLRs) including NLRP1, NLRP3, NLRC4 and AIM2: NLRP3 is currently the most fully characterized inflammasome. Testicular torsion leads to tissue degeneration and, after reperfusion, results in production of reactive oxygen species and triggers the apoptosis machinery. To better understand the role of NLRP3 during testicular ischemia/reperfusion (TI/R), we investigated the morphological aspects of spermatogenesis underlying the effects of inflammasome in KO mice during TI/R. KO (Nlrp3tm1bhk) and wild-type (WT: C57Bl6) animals underwent 1h testicular-ischemia followed by reperfusion. The mice were killed after 1 day and 7 days of reperfusion and the determination of caspase-3 activity was executed. Furthermore, both the tubular (mean seminiferous tubule diameter and Johnsen’s scoring system [1]) and extratubular (edema, hemorrhagic extravasation, vessels dilation, and Leydig cells changes [2]) compartments were evaluated. The TUNEL assay for apoptosis was also performed. After 1 and 7 days of reperfusion in WT mice an increase of caspase-3 was observed. Structurally, marked histological damages characterized by altered spermatogenesis, evident extratubular changes and increased TUNEL activity were observed. In KO mice caspase-3 was inhibited. Histological damages were significantly decreased, TUNEL activity was reduced and extratubular changes were significantly milder. We suggest that NLRP3 inhibition might have a protective role on spermatogenesis and it can be proposed in patients with unilateral testicular torsion

    Blockade of the JNK Signalling as a Rational Therapeutic Approach to Modulate the Early and Late Steps of the Inflammatory Cascade in Polymicrobial Sepsis

    Full text link
    Cecal ligation and puncture (CLP) is an experimental polymicrobial sepsis induced systemic inflammation that leads to acute organ failure. Aim of our study was to evaluate the effects of SP600125, a specific c-Jun NH2-terminal kinase (JNK) inhibitor, to modulate the early and late steps of the inflammatory cascade in a murine model of CLP-induced sepsis. CB57BL/6J mice were subjected to CLP or sham operation. Animals were randomized to receive either SP600125 (15 mg/kg) or its vehicle intraperitoneally 1 hour after surgery and repeat treatment every 24 hours. To evaluate survival, a group of animals was monitored every 24 hours for 120 hours. Two other animals were sacrificed 4 or 18 hours after surgical procedures; lung and liver samples were collected for biomolecular and histopathologic analysis. The expression of p-JNK, p-ERK, TNF-α, HMGB-1, NF-κB, Ras, Rho, Caspase 3, Bcl-2, and Bax was evaluated in lung and liver samples; SP600125 improved survival, reduced CLP induced activation of JNK, NF-κB, TNF-α, and HMGB-1, inhibited proapoptotic pathway, preserved Bcl-2 expression, and reduced histologic damage in both lung and liver of septic mice. SP600125 protects against CLP induced sepsis by blocking JNK signalling; therefore, it can be considered a therapeutic approach in human sepsis

    The PREdictor of MAlnutrition in Systemic Sclerosis (PREMASS) Score:A Combined Index to Predict 12 Months Onset of Malnutrition in Systemic Sclerosis

    Get PDF
    Objective: Malnutrition is a severe complication in Systemic Sclerosis (SSc) and it is associated with significant mortality. Notwithstanding, there is no defined screening or clinical pathway for patients, which is hampering effective management and limiting the opportunity for early intervention. Here we aim to identify a combined index predictive of malnutrition at 12 months using clinical data and specific serum adipokines. Methods: This was an international, multicentre observational study involving 159 SSc patients in two independent discovery (n = 98) and validation (n = 61) cohorts. Besides routine clinical and serum data at baseline and 12 months, Malnutrition Universal Screening Tool (MUST) score and serum concentration of leptin and adiponectin were measured for each participant at baseline. The endpoint of malnutrition was defined according to European Society of Clinical Nutrition and Metabolism (ESPEN) recommendation. Significant parameters from univariate analysis were tested in logistic regression analysis to identify the predictive index of malnutrition in the derivation cohort. Results: The onset of malnutrition at 12 months correlated with adiponectin, leptin and their ratio (A/L), MUST, clinical subset, disease duration, Scl70 and Forced Vital Capaciy (FVC). Logistic regression analysis defined the formula: −2.13 + (A/L*0.45) + (Scl70*0.28) as the best PREdictor of MAlnutrition in SSc (PREMASS) (AUC = 0.96; 95% CI 0.93, 0.99). PREMASS 62% and negative predictive value (NPV) > 97% for malnutrition at 12 months. Conclusion: PREMASS is a feasible index which has shown very good performance in two independent cohorts for predicting malnutrition at 12 months in SSc. The implementation of PREMASS could aid both in clinical management and clinical trial stratification/enrichment to target malnutrition in SSc
    corecore