Gene co-expression analyses: an overview from microarray collections in Arabidopsis thaliana

4noBioinformatics web-based resources and databases are precious references for most biological laboratories worldwide. However, the quality and reliability of the information they provide depends on them being used in an appropriate way that takes into account their specific features. Huge collections of gene expression data are currently publicly available, ready to support the understanding of gene and genome functionalities. In this context, tools and resources for gene co-expression analyses have flourished to exploit the ‘guilty by association' principle, which assumes that genes with correlated expression profiles are functionally related. In the case of Arabidopsis thaliana, the reference species in plant biology, the resources available mainly consist of microarray results. After a general overview of such resources, we tested and compared the results they offer for gene co-expression analysis. We also discuss the effect on the results when using different data sets, as well as different data normalization approaches and parameter settings, which often consider different metrics for establishing co-expression. A dedicated example analysis of different gene pools, implemented by including/excluding mutant samples in a reference data set, showed significant variation of gene co-expression occurrence, magnitude and direction. We conclude that, as the heterogeneity of the resources and methods may produce different results for the same query genes, the exploration of more than one of the available resources is strongly recommended. The aim of this article is to show how best to integrate data sources and/or merge outputs to achieve robust analyses and reliable interpretations, thereby making use of diverse data resources an opportunity for added value.openembargoed_20170219Di Salle, Pasquale; Incerti, Guido; Colantuono, Chiara; Chiusano, Maria LuisaDi Salle, Pasquale; Incerti, Guido; Colantuono, Chiara; Chiusano, Maria Luis

Identifying reliable predictors of protein-energy malnutrition in hospitalized frail older adults. A prospective longitudinal study

BACKGROUND: Decreased food intake is a risk factor for relevant complications (e.g. infections, pressure ulcers), longer hospital stays, higher readmission rates, greater health care costs and increased patient mortality, particularly in frail hospitalized older adults who are malnourished or at risk of malnutrition. Nurses are called to improve this criticality, starting from accurately identify patients for malnutrition at hospital admission and effectively monitoring their food intake. OBJECTIVES: The primary aim was to identify reliable predictive indicators of reduced food intake at hospital admission. The secondary aims were to assess the adequacy of daily energy and protein intake and the impact of nutrient intake on patient outcomes. DESIGN: Prospective observational longitudinal study. SETTING: Internal Medicine Ward of an Academic Teaching University Hospital. PARTICIPANTS: Acute older adults who were malnourished or at risk of malnutrition (Nutritional Risk Score-2002\u202f 65\u202f3, middle-upper arm circumference\u2009<23.5\u202fcm or impaired self-feeding ability) at admission. METHODS: The effective energy and protein intake was monitored during the first 5\u202fdays of hospital stay by a photographic method and compared to the daily energy and protein requirement calculated by specific equations. Data on anthropometry, inflammation/malnutrition laboratory data and body composition (phase\u202fangle calculated using bioelectrical impedance analysis) were collected. RESULTS: Eighty-one subjects (age 81.5\u202f\ub1\u202f11.5\u202fyears) were enrolled. Mean energy intake was 669.0\u202f\ub1\u202f573.9\u202fkcal/day, and mean protein intake was 30.7\u202f\ub1\u202f25.8\u202fg/day. Over 60% of patients ingested\u2009 6450% of their calculated energy and protein requirements: these patients were older (p\u202f=\u202f0.026), had a lower middle-upper arm circumference (p\u202f=\u202f0.022) and total arm area (p\u202f=\u202f0.038), a higher C-reactive protein/albumin ratio and Instant Nutritional Assessment score (p\u202f<\u202f0.01), and experienced longer hospital stays (p\u202f 64\u202f0.04) and higher in-hospital and 30-day post-discharge mortality (p\u202f<\u202f0.001). In the multivariate analysis, lower middle-upper arm circumference, higher C-reactive protein/albumin ratio, and impaired self-feeding at admission were independently associated with critically reduced energy and protein intake. CONCLUSIONS: Middle-upper arm circumference, C-reactive protein/albumin ratio, and impaired self-feeding are easily obtainable indicators of impaired energy and protein intake and poor clinical outcomes. Such parameters should be adopted as screening criteria to assess the risk for critically reduced energy/protein intake in hospitalized older adults. These findings are relevant to improve clinical practice through the implementation of multidisciplinary strategies, given the adverse clinical outcomes related to hospital malnutrition

Relationship Between Human Leucocyte Antigen Class I and Class II and Chronic Idiopathic Urticaria Associated With Aspirin and/or NSAIDs Hypersensitivity

Background. HLA genes play a role in the predisposition of several diseases. The aim was to analyze the prevalence of HLA class I phenotypes and HLA-DRB1* genotype in patients with CIU associated with ASA and NSAIDs hypersensitivity (AICU). Methods. 69 patients with AICU, and 200 healthy subjects. Results. Subjects with HLA-B44 and HLA-Cw5 antigens were more represented in patients with AICU than in control group. Subjects with HLA-A11, HLA-B13, HLACw4, and HLA-Cw7 antigen were more represented in control group than in patients with AICU. Multiple logistic regression demonstrated an association of HLA-Cw4 and HLA-Cw7 with a lower risk of AICU, whereas carriers of HLA-B44 phenotype had a higher risk of AICU. No differences were found between patients and controls as regards to HLA-DRB1* genotype. Conclusions. We observed an association between some HLA class-I antigens and AICU. To the best of our knowledge this is the first description of such association

Detection of Alkaline Sphingomyelinase Activity in Human Stool: Proposed Role as a New Diagnostic and Prognostic Marker of Colorectal Cancer

Abstract Objectives: Intestinal alkaline sphingomyelinase, by exerting a major role in dietary sphingomyelin digestion, is responsible for the generation of messengers able to trigger the rapid turnover and apoptosis in intestinal epithelial cells. Markedly reduced mucosal alkaline sphingomyelinase activity has been associated with human colorectal neoplasms. The aim of this study was to analyze the alkaline sphingomyelinase activity in feces from healthy subjects and colorectal adenocarcinoma patients and to correlate it with the enzyme activity in intestinal tissues. Materials and Methods: The enzyme activity was measured both in the intestinal samples from 12 healthy controls and 51 patients with colorectal adenocarcinoma (tumoral and paratumoral tissue) and in the fecal samples of 34 healthy subjects and 29 patients with adenocarcinoma. The relation between sphingomyelinase activity and Dukes' stage, cell differentiation degree, age, and gender was also analyzed. Results: Alkaline sphingomyelinase was significantly decreased (P &lt; 0.001; mean reduction &gt;90%) in tumoral intestinal mucosa of patients compared with controls independently of Dukes' stage and tumor differentiation grade. Interestingly, the enzyme activity in histologically normal paratumoral tissues was statistically lower than control samples (P &lt; 0.001). As occurs in neoplastic tissues, a relevant mean reduction (P &lt; 0.0001; almost 90%) of alkaline sphingomyelinase was revealed in stool samples from tumor patients when compared with controls. Conclusion: These findings may have implications for cancer biology and perhaps also for the design of clinical test, thus suggesting that the fecal sphingomyelinase activity could really reflect the human intestinal mucosa enzyme level and could represent a new marker for human colorectal adenocarcinoma, mainly taking into account its early appearance in intestinal neoplasms

Green synthesis of privileged benzimidazole scaffolds using active deep eutectic solvent

The exploitation and use of alternative synthetic methods, in the face of classical procedures that do not conform to the ethics of green chemistry, represent an ever-present problem in the pharmaceutical industry. The procedures for the synthesis of benzimidazoles have become a focus in synthetic organic chemistry, as they are building blocks of strong interest for the development of compounds with pharmacological activity. Various benzimidazole derivatives exhibit important activities such as antimicrobial, antiviral, anti-inflammatory, and analgesic activities, and some of the already synthesized compounds have found very strong applications in medicine praxis. Here we report a selective and sustainable method for the synthesis of 1,2-disubstituted or 2-substituted benzimidazoles, starting from o-phenylenediamine in the presence of different aldehydes. The use of deep eutectic solvent (DES), both as reaction medium and reagent without any external solvent, provides advantages in terms of yields as well as in the work up procedure of the reaction.Fil: Gioia, Maria Luisa Di. Università della Calabria; ItaliaFil: Cassano, Roberta. Università della Calabria; ItaliaFil: Costanzo, Paola. Magna Græcia University. Department of Health Sciences; ItaliaFil: Herrera Cano, Natividad Carolina. Universidad Nacional de Córdoba; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Ciencia y Tecnología de Alimentos Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Ciencia y Tecnología de Alimentos Córdoba; ArgentinaFil: Maiuolo, Loredana. Università della Calabria; ItaliaFil: Nardi, Monica. Magna Græcia University. Department of Health Sciences; ItaliaFil: Nicoletta, Fiore Pasquale. Università della Calabria; ItaliaFil: Oliverio, Manuela. Magna Græcia University. Department of Health Sciences; ItaliaFil: Procopio, Antonio. Magna Græcia University. Department of Health Sciences; Itali

Serum levels of soluble CD30 in adult patients affected by atopic dermatitis and its relation to age, duration of disease and Scoring Atopic Dermatitis index.

The value of CD30 and the soluble circulating fragment of CD30 (sCD30) for atopic dermatitis (AD) remains unclear. In particular, little is known about the effects of age, duration of disease and Scoring Atopic Dermatitis index (SCORAD) on the levels of serum sCD30 in patients affected by AD. In the present study, we have analysed serum sCD30 levels of adult patients affected by AD. The study's population includes 18 non-smoking outpatients, with a diagnosis of AD. As a control group we studied 18 non-atopic subjects from laboratory staff, matched for sex and age. These subjects had no history of AD, urticaria or seasonal or perennial rhinitis or asthma, and had negative skin prick test to a panel of allergens. The sCD30 serum levels were clearly higher in patients affected by AD (14.2+/-9.0 IU/ml) than in healthy subjects (1.2+/-0.8 IU/ml) (p<0.001). No differences were observed between males and females affected by atopic dermatitis, regarding age, duration of disease and SCORAD. Significant correlations were found between serum levels of sCD30 levels and age (r=-0.55; 95% confidence interval (CI) for r (Fisher's z transformed)=-0.81 to -0.12; p=0.01), duration of the disease (months) (r=-0.64; 95% CI for r (Fisher's z transformed)=-0.85 to -0.24; p=0.004) and SCORAD (r=-0.74; 95% CI for r (Fisher's z transformed)=-0.89 to -0.42; p=0.004). As demonstrated by the close correlation with age, duration of disease and SCORAD, serum levels of sCD30 appear to be an additional marker for the follow-up of AD

Relations Between Mood States and Eating Behavior During COVID-19 Pandemic in a Sample of Italian College Students

The fear of contagion during the COVID-19 pandemic has been indicated as a relevant cause of psychological pathologies occurring in this period. Food represents a compensating experience, distracting from the experiences of uncertainty, fear and despair, causing alterations in eating habits and behaviors. The study aims at evaluating the relations between fear of a pandemic, mood states and eating disorders in Italian college students, taking into account gender differences. During the lockdown for the pandemic, a sample of 469 college students equally distributed by gender, was recruited online using a questionnaire including the FCV-19S for the assessment of fear of COVID-19, the profile of mood states (POMS) for the evaluation of different emotional states, the eating disorder inventory-2 (EDI-2) and the binge eating scale (BES) to evaluate the presence of the levels of eating disorders. As expected, all emotive states measured by POMS (tension, depression, anger, tiredness, confusion) resulted significantly correlated with the fear of COVID-19. Women were more exposed to fear of COVID-19 showing greater tension, fatigue, depression and confusion, and a significantly higher total mood disturbance score than males. Regarding the EDI-2 and BES variables, tension and anxiety resulted significantly correlated also with bulimic behavior, while depression with interoceptive awareness, impulsivity, and binge eating behaviors, without gender differences. In conclusion, the negative impact of the fear of COVID-19 on the emotional profile and eating behavior suggests the need to implement strategies against psychological distress during the pandemic emergency, and to design psycho-educational interventions aimed at modifying the lifestyle for preventing risks of mental disorders fostering health-oriented behaviors

Comparison of the CBA-H and SF-36 for the screening of the psychological and behavioural variables in chronic dialysis patients

The aim of the study was to perform an analysis of the emotional reactions, perception of stressful life and behavioural changes related to Haemodialysis (HD) in order to identify those variables that can improve lifestyle and the adherence to treatment. Some psycho- metric assessment, such as the Cognitive Behavioural Assessment, Hospital Form, (CBA- H) and the Health Survey (SF-36), which provides two indexes: the Physical Component Score (PCS) and the Mental Component Score (MCS), are suitable to assess a patient’s psychological and behavioural style and their health-related quality of life. The study involved 37 Italian out-patients with end-stage renal disease under HD therapy. We calcu- lated the Spearman correlation between variables of CBA-H, SF-36, age and time on HD. We also performed a multivariate linear regression using the CBA-H variables as predictors and PCS and MCS as dependent variables. From the CBA-H, 95% of participants self- reported psychological characteristics comparable to Type A personality, which identifies an anxious, hyperactive and hostile subject. Physical limitations were found to be directly pro- portional to the time on dialysis (rs = -0.42). The condition of perceived stress worsens the state of mental health (rs = -0.68) and general health perception (rs = -0.44). The condition of vital exhaustion correlates both the PCS and the MCS (p<0.01) with possible outcomes of physical and mental illness. The psychological wellbeing of a dialyzed patient could be due to the combination of several factors, including life parameters, the positive perception of psychosocial outcomes, and the perceived quality of life. A multidisciplinary team (neurolo- gists, psychiatrists, psychologists, and nurses) is essential to plan effective psychological and psychotherapeutic interventions to improve a mind-body integration

Shaping Mediterranean landscapes:The cultural impact of anthropogenic fires in Tyrrhenian southern Tuscany during the Iron and Middle Ages (800–450 BC / AD 650–1300)

Charcoal analysis, applied in sediment facies analysis of the Pecora river palaeochannel (Tyrrhenian southern Tuscany, Italy), detected the occurrence of past fire events in two different fluvial landforms at 800–450 BC and again at AD 650–1300. Taking place in a central Mediterranean district adequately studied through palaeoenvironmental and archaeological research, the investigation determined land changes, time phases and socio-economic driving forces involved in dynamic processes of fire. The fire sequences had purely anthropogenic origins and were linked to forest opening and reduction by local communities. Introduced by the Etruscans, fires dated to 800–450 BC involved mainly the forest cover on the hilly slopes, ensuring agricultural exploitation. From AD 650, fires contributed to Medieval upstream reclamation and vegetation clearing of flat swamplands. From AD 850 to 1050, the use of fire spread over a wider area in the river valley, increasing arable lands. Between AD 1150 and 1300, fires belonged to a regional forest clearance phase. Medieval fire episodes had a paramount importance in shaping and determining the character of the Tuscan Mediterranean landscape. From AD 850, Medieval fire clearing influenced regional vegetation history contributing to the decline of the dominant deciduous Quercus woodland. Open habitats became the new form of a clearly detectable agricultural landscape from AD 950. The use of fire clearing and the resulting landscape changes in the Pecora river valley depended on the political strategies adopted by Medieval authorities and marked, in fact, the progression of a cultural landscape still characterizing central Tyrrhenian Italy

The burden of breast cancer in Italy: mastectomies and quadrantectomies performed between 2001 and 2008 based on nationwide hospital discharge records.

BACKGROUND: Where population coverage is limited, the exclusive use of Cancer Registries might limit ascertainment of incident cancer cases. We explored the potentials of Nationwide hospital discharge records (NHDRs) to capture incident breast cancer cases in Italy. METHODS: We analyzed NHDRs for mastectomies and quadrantectomies performed between 2001 and 2008. The average annual percentage change (AAPC) and related 95% Confidence Interval (CI) in the actual number of mastectomies and quadrantectomies performed during the study period were computed for the full sample and for subgroups defined by age, surgical procedure, macro-area and singular Region. Re-admissions of the same patients were separately presented. RESULTS: The overall number of mastectomies decreased, with an AAPC of -2.1% (-2.3 -1.8). This result was largely driven by the values observed for women in the 45 to 64 and 65 to 74 age subgroups (-3.0%, -3.4 -3.6 and -3.3%, -3.8 -2.8, respectively). We observed no significant reduction in mastectomies for women in the remaining age groups. Quadrantectomies showed an overall +4.7 AAPC (95%CI:4.5-4.9), with no substantial differences by age. Analyses by geographical area showed a remarkable decrease in mastectomies, with inter-regional discrepancies possibly depending upon variability in mammography screening coverage and adherence. Quadrantectomies significantly increased, with Southern Regions presenting the highest average rates. Data on repeat admissions within a year revealed a total number of 46,610 major breast surgeries between 2001 and 2008, with an overall +3.2% AAPC (95%CI:2.8-3.6). CONCLUSIONS: In Italy, NHDRs might represent a valuable supplemental data source to integrate Cancer Registries in cancer surveillance