Peak shape clustering reveals biological insights

Background: ChIP-seq experiments are widely used to detect and study DNA-protein interactions, such as transcription factor binding and chromatin modifications. However, downstream analysis of ChIP-seq data is currently restricted to the evaluation of signal intensity and the detection of enriched regions (peaks) in the genome. Other features of peak shape are almost always neglected, despite the remarkable differences shown by ChIP-seq for different proteins, as well as by distinct regions in a single experiment. Results: We hypothesize that statistically significant differences in peak shape might have a functional role and a biological meaning. Thus, we design five indices able to summarize peak shapes and we employ multivariate clustering techniques to divide peaks into groups according to both their complexity and the intensity of their coverage function. In addition, our novel analysis pipeline employs a range of statistical and bioinformatics techniques to relate the obtained peak shapes to several independent genomic datasets, including other genome-wide protein-DNA maps and gene expression experiments. To clarify the meaning of peak shape, we apply our methodology to the study of the erythroid transcription factor GATA-1 in K562 cell line and in megakaryocytes. Conclusions: Our study demonstrates that ChIP-seq profiles include information regarding the binding of other proteins beside the one used for precipitation. In particular, peak shape provides new insights into cooperative transcriptional regulation and is correlated to gene expression

Biodiversity of grapevines (Vitis vinifera L.) grown in the Province of Verona

PCR-based DNA microsatellite analysis has been applied to define the genetic relationships among 7 most representative grapevine cultivars grown in the province of Verona, 5 ancient grapevine and two varieties grown in different regions of Italy. For each variety three different clones or accessions were investigated to assess genotypical uniformity; in 5 cases we found out intravarietal dissimilarity. SSR data were used to create a distance matrix and then a polylogenetic tree. Results show a polygenetic relationship among some cultivated (Corvina, Rondinella, Molinara, Trebbiano di Soave-Verdicchio) and ancient (Dindarella-Pelara, Oseleta, Rossetta di montagna) varieties all grown in the Valpolicella hills, suggesting the possibility that their evolution occurred in the same area and with few common anchestors. Two situations of synonyms that had already described between Trebbiano di Soave and Verdicchio, and between Dindarella and Pelara, were confirmed by a molecular method as SSR analysis. Amplification of Trebbiano di Soave/Verdicchio locus VVMD36 yielded a fragment of 500 bp, this allele provides a fast and reliable tool to differentiate among Trebbiano grapevines.

Colonisation with Extended-Spectrum Cephalosporin-Resistant Enterobacterales and Infection Risk in Surgical Patients: A Systematic Review and Meta-analysis

Introduction: Limited evidence has been reported for surgical site infections (SSIs) in patients undergoing surgery who are carriers of extended-spectrum cephalosporin-resistant Enterobacterales (ESCR-E). A systematic review and meta-analysis were conducted to evaluate the risk of postoperative infections in adult inpatients colonised with ESCR-E before surgery. Methods: The Medline, Embase and Cochrane databases were searched between January 2011 and April 2022, following PRISMA indications. Random effects meta-analysis was used to quantify the association between ESCR-E colonisation and infection. Results: Among the 467 articles reviewed, 9 observational studies encompassing 7219 adult patients undergoing surgery were included. The ESCR-E colonisation rate was 13.7% (95% CI 7.7–19.7). The most commonly reported surgeries included abdominal surgery (44%) and liver transplantation (LT; 33%). The SSI rate was 23.2% (95% CI 13.2–33.1). Pooled incidence risk was 0.36 (95% CI 0.22–0.50) vs 0.13 (95% CI 0.02–0.24) for any postoperative infection and 0.28 (95% CI 0.18–0.38) vs 0.17 (95% CI 0.07–0.26) for SSIs in ESCR-E carriers vs noncarriers, respectively. In ESCR-E carriers, the ESCR-E infection ratio was 7 times higher than noncarriers. Postoperative infection risk was higher in carriers versus noncarriers following LT. Sources of detected heterogeneity between studies included ESCR-E colonisation and the geographic region of origin. Conclusions: Patients colonised with ESCR-E before surgery had increased incidence rates of post-surgical infections and SSIs compared to noncarriers. Our results suggest considering the implementation of pre-surgical screening for detecting ESCR-E colonisation status according to the type of surgery and the local epidemiology

L'ateismo mistico di Julia Kristeva

La ricerca si occupa del tema religioso negli scritti pi\uf9 recenti di Julia Kristeva, pensatrice che intercetta le inquietudini e il disorientamento del soggetto contemporaneo e che cerca di rispondervi attraverso la proposta di un nuovo umanesimo. L\u2019umanesimo kristeviano prende forma interrogando la povert\ue0 simbolica di questo tempo a partire da alcuni luoghi d\u2019osservazione privilegiati: il sacro, il materno e l\u2019ateismo. In questo percorso, il bisogno di credere si rivela cruciale: di significato pre-religioso, esso diventa la cifra irrinunciabile per una riconfigurazione della ragione, destinata a dissolversi nel vuoto dell\u2019astrazione qualora trascurasse il livello profondo del linguaggio, dove sono sedimentate le tracce di tutte le eterogeneit\ue0 che non smettono di provocare il concetto. Solo in questa complessit\ue0 si aprono spazi di riconoscimento per il limite, il femminile e il reale.This research is concerned with the religious issue in the most recent papers by Julia Kristeva, a thinker that apprehends the unquietness and the disorientation of the contemporary Subject and that endeavors to answer to them by proposing a novel Humanism. Kristeva\u2019s Humanism takes shape by questioning the symbolic poverty of our age from some privileged observation points: the Holy, the Motherly, the Atheism. Throughout this route the need to believe is unveiled as crucial: by its pre-religious meaning it becomes the undroppable key to reconfigurate Reason, otherwise doomed to be dissolved into the emptiness of abstraction were it to neglect the deep layers of language where the remnants of all heterogenities unrelentlessly challenging the concept lie. Only within this complexity new spaces are opened to acknowledge and to recognize the Limit, the Feminine and the Real

Models of learning, training and progress evaluation of medical students.

Medical education has changed during the last century. Teachercentred medical education has been replaced by a studentcentred one. Some general educational principles have been adopted in medicine faculties, leading to more active students involved in learning, and interactive methods have been introduced, and the role of experience has been focused. Disciplinebased medical education is inadequate for developing comprehensive competence and doctoring. Integrated multidisciplinary learning, together with new clerkship approaches and organization, represent the future of medical education. Continuing, comprehensive, assessment can measure progression in knowledge, skills, attitudes and values. Progress test have recently been introduced in some medical school as a reliable tool for assessing the progressive performance of students in time and monitoring the entire learning process