Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks

Background: Genome browsers are widely used for locating interesting genomic regions, but their interactive use is obviously limited to inspecting short genomic portions. An ideal interaction is to provide patterns of regions on the browser, and then extract other genomic regions over the whole genome where such patterns occur, ranked by similarity. Results: We developed SimSearch, an optimized pattern-search method and an open source plugin for the Integrated Genome Browser (IGB), to find genomic region sets that are similar to a given region pattern. It provides efficient visual genome-wide analytics computation in large datasets; the plugin supports intuitive user interactions for selecting an interesting pattern on IGB tracks and visualizing the computed occurrences of similar patterns along the entire genome. SimSearch also includes functions for the annotation and enrichment of results, and is enhanced with a Quickload repository including numerous epigenomic feature datasets from ENCODE and Roadmap Epigenomics. The paper also includes some use cases to show multiple genome-wide analyses of biological interest, which can be easily performed by taking advantage of the presented approach. Conclusions: The novel SimSearch method provides innovative support for effective genome-wide pattern search and visualization; its relevance and practical usefulness is demonstrated through a number of significant use cases of biological interest. The SimSearch IGB plugin, documentation, and code are freely available at https://deibgeco.github.io/simsearch-app/ and https://github.com/DEIB-GECO/simsearch-app/

Fluid conduits and shallow-reservoir structure defined by geoelectrical tomography at the Nirano Salse (Italy)

Mud volcanoes are fluid escape structures allowing for surface venting of hydrocarbons (mostly gas but also liquid condensates and oils) and water–sediment slurries. For a better understanding of mud volcano dynamics, the characterization of the fluid dynamics within mud volcano conduits; the presence, extent, and depth of the fluid reservoirs; and the connection among aquifers, conduits, and mud reservoirs play a key role. To this aim, we performed a geoelectricalsurvey in the Nirano Salse Regional Nature Reserve, located at the edge of the northern Apennines (Fiorano Modenese, Italy), an area characterized by several active mud fluid vents. This study, for the first time, images the resistivity structure of the subsoil along two perpendicular cross sections down to a depth of 250 m. The electrical models show a clear difference between the northern and southern sectors of the area, where the latter hosts the main discontinuities. Shallow reservoirs, where fluid muds accumulate, are spatially associated with the main fault/fracture controlling the migration routes associated with surface venting and converge at depth towards a common clayey horizon. There is no evidence of a shallow mud caldera below the Nirano area. These findings represent a step forward in the comprehension of the Nirano Salse plumbing system and in pinpointing local site hazards, which promotes safer tourist access to the area along restricted routes

WARP: accurate retrieval of shapes using phase of fourier descriptors and time warping distance

Abstract-Effective and efficient retrieval of similar shapes from large image databases is still a challenging problem in spite of the high relevance that shape information can have in describing image contents. In this paper, we propose a novel Fourier-based approach, called WARP, for matching and retrieving similar shapes. The unique characteristics of WARP are the exploitation of the phase of Fourier coefficients and the use of the Dynamic Time Warping (DTW) distance to compare shape descriptors. While phase information provides a more accurate description of object boundaries than using only the amplitude of Fourier coefficients, the DTW distance permits us to accurately match images even in the presence of (limited) phase shiftings. In terms of classical precision/recall measures, we experimentally demonstrate that WARP can gain, say, up to 35 percent in precision at a 20 percent recall level with respect to Fourier-based techniques that use neither phase nor DTW distance

Type A Acute Aortic Dissection in Nonagenarian: Rare but Possible

Acute type A aortic dissection (TA-AAD) is a highly lethal clinical entity that can occur within a wide age range, associated with multiple aetiologies and various clinical presentations. In the very elderly type A aortic dissection frequently presents with non-specific symptoms and signs and is associated with high mortality and morbidity. Thus the clinician must have a high index of clinical suspicion in order to prompt the most appropriate diagnostic-therapeutic strategy.We report a nonagenarian women with TA-AAD, treated successfully with medical therapy

Electrochemical sensor for evaluating oxidative stress in airway epithelial cells

Cigarette smoke exposure induces oxidative stress within the airways. Increased oxidative burden contributes to the pathogenesis of chronic lung disorders and is associated with aging and chronic inflammation. Airway epithelial cells highly contribute to Reactive Oxygen Species (ROS) generation within injured and inflamed lung tissues. Among ROS, hydrogen peroxide (H2O2) can be monitored in the extracellular space. Herein, we present an amperometric/voltammetric sensor based on gold nanoparticles and graphene oxide able to detect H2O2 with good sensitivity and selectivity. Using this sensor, H2O2 release was measured in conditioned medium from primary bronchial epithelial cells (PBEC), bronchial epithelial cell line, 16HBE, and adenocarcinoma alveolar basal epithelial cell line, A549, exposed to cigarette smoke extracts (CSE). 16HBE were also treated with resveratrol, an anti-oxidant compound. The results were compared with those obtained by flow cytometry using the same cells stained with Carboxy-H2DCFDA and MitoSOX Red, which detect intracellular ROS and mitochondrial superoxide, respectively. The exposure to CSE resulted in a significant increase of the cathodic current due to the reduction of H2O2 indicating an increased release. Addition of resveratrol decreased CSE-induced release of H2O2 in 16HBE. All the results paralleled those obtained by flow cytometry. The proposed sensor is highly sensitive and selective, fast and cost effective and can potentially be applied for real time and easy monitoring of oxidative stress

On Transport Monitoring and Forecasting during COVID-19 Pandemic in Rome

This paper presents the results of a study on the Rome mobility system aiming at estimating the impacts of the progressive lockdown, imposed by the government, due to the Covid-19 pandemic as well as to support decision makers in planning the transport system for the restart towards a post-Covid "new normal". The analysis of data obtained by the transport monitoring system has been fundamental for both investigating effects of the lockdown and feeding transport models to predict the impacts on future actions. At first, the paper focuses on the so-called transport analytics, by describing mobility trends for the multimodal transportation system of Rome. Then, the results of the simulated scenarios to design public transport services, able to ensure passengers social distancing required in the first post-Covid months, are presented and discussed

Disease awareness in patients with COPD: measurement and extent

Background: Patient awareness of COPD refers to knowledge and acceptance of the disease and its treatment. Although it is relevant to management and outcomes, the disease awareness of patients is poorly investigated, and no validated questionnaires are currently available. We aimed to develop the novel Disease Awareness in COPD Questionnaire (DACQ), which was validated in relation to demographic and clinical features, in patients participating in the SATisfaction and Adherence to COPD Treatment (SAT) study. Methods: DACQ was developed according to a list of items regarding the patient's knowledge, acceptance, and perception of COPD as well as of treatment needs. The questionnaire was validated by assessing internal structure and consistency, correlations with other patient-reported outcomes, and stability over time. Furthermore, the extent of disease awareness of patients enrolled in the SAT study was assessed by using DACQ, and correlations with demographic and clinical features were evaluated. Results: DACQ was composed of four domains. Overall reliability and stability over time were adequate; correlations between DACQ and other tools measuring different constructs (ie, treatment satisfaction, illness perception, impact of COPD symptoms on daily life, and dyspnea severity) were, as expected, more limited. In the enrolled patient sample, a suboptimal level of disease awareness (<70%) was detected, especially in terms of disease acceptance and perception. Disease knowledge was positively associated with COPD severity, while the impact of symptoms on daily life was negatively associated with disease acceptance, awareness of treatment needs, and overall awareness. Conclusion: DACQ proved to be a reliable tool to assess awareness in COPD patients. Awareness of COPD patients need to be improved. Clinical trial registration: ClinicalTrials.gov ID# NCT02689492

Dissemination of patient blood management practices in Swiss intensive care units: a cross-sectional survey

BACKGROUND Patient blood management (PBM) promotes the routine detection and treatment of anaemia before surgery, optimising the management of bleeding disorders, thus minimising iatrogenic blood loss and pre-empting allogeneic blood utilisation. PBM programmes have expanded from the elective surgical setting to nonsurgical patients, including those in intensive care units (ICUs), but their dissemination in a whole country is unknown. METHODS We performed a cross-sectional, anonymous survey (10 October 2018 to 13 March 2019) of all ordinary medical members of the Swiss Society of Intensive Care Medicine and the registered ICU nurses from the 77 certified adult Swiss ICUs. We analysed PBM-related interventions adopted in Swiss ICUs and related them to the spread of PBM in Swiss hospitals. We explored blood test ordering policies, blood-sparing strategies and red blood cell-related transfusion practices in ICUs. RESULTS A total of 115 medical doctors and 624 nurses (response rates 27% and 30%, respectively) completed the surveys. Hospitals had implemented a PBM programme according to 42% of physicians, more commonly in Switzerland's German-speaking regions (Odds Ratio [OR] 3.39, 95% confidence interval [CI] 1.23-9.35; p = 0.018) and in hospitals with more than 500 beds (OR 3.91, 95% CI 1.48-10.4; p = 0.006). The PBM programmes targeted the detection and correction of anaemia before surgery (79%), minimising perioperative blood loss (94%) and optimising anaemia tolerance (98%). Laboratory tests were ordered in 70.4% by the intensivist during morning rounds; the nurses performed arterial blood gas analyses autonomously in 48.4%. Blood-sparing techniques were used by only 42.1% of nurses (263 of 624, missing: 6) and 47.0% of physicians (54 of 115). Approximately 60% of respondents used an ICU-specific transfusion guideline. The reported haemoglobin threshold for the nonbleeding ICU population was 70 g/l and, therefore, was at the lower limit of current guidelines. CONCLUSIONS Based on this survey, the estimated proportion of the intensivists working in hospitals with a PBM initiative is 42%, with significant variability between regions and hospitals of various sizes. The risk of iatrogenic anaemia is relevant due to liberal blood sample collection practices and the underuse of blood-sparing techniques. The reported transfusion threshold suggests excellent adherence to current international ICU-specific transfusion guidelines

The incidence of hip, forearm, humeral, ankle, and vertebral fragility fractures in Italy: results from a 3-year multicenter study

INTRODUCTION: We aimed to assess the incidence and hospitalization rate of hip and "minor" fragility fractures in the Italian population. METHODS: We carried out a 3-year survey at 10 major Italian emergency departments to evaluate the hospitalization rate of hip, forearm, humeral, ankle, and vertebral fragility fractures in people 45 years or older between 2004 and 2006, both men and women. These data were compared with those recorded in the national hospitalizations database (SDO) to assess the overall incidence of fragility fractures occurring at hip and other sites, including also those events not resulting in hospital admissions. RESULTS: We observed 29,017 fractures across 3 years, with hospitalization rates of 93.0% for hip fractures, 36.3% for humeral fractures, 31.3% for ankle fractures, 22.6% for forearm/wrist fractures, and 27.6% for clinical vertebral fractures. According to the analyses performed with the Italian hospitalization database in year 2006, we estimated an annual incidence of 87,000 hip, 48,000 humeral, 36,000 ankle, 85,000 wrist, and 155,000 vertebral fragility fractures in people aged 45 years or older (thus resulting in almost 410,000 new fractures per year). Clinical vertebral fractures were recorded in 47,000 events per year. CONCLUSIONS: The burden of fragility fractures in the Italian population is very high and calls for effective preventive strategies