Discovery of large genomic inversions using long range information.

BackgroundAlthough many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem. This is mainly due to the fact that breakpoints of such events typically lie within segmental duplications or common repeats, which reduces the mappability of short reads. The algorithms developed within the 1000 Genomes Project to identify inversions are limited to relatively short inversions, and there are currently no available algorithms to discover large inversions using high throughput sequencing technologies.ResultsHere we propose a novel algorithm, VALOR, to discover large inversions using new sequencing methods that provide long range information such as 10X Genomics linked-read sequencing, pooled clone sequencing, or other similar technologies that we commonly refer to as long range sequencing. We demonstrate the utility of VALOR using both pooled clone sequencing and 10X Genomics linked-read sequencing generated from the genome of an individual from the HapMap project (NA12878). We also provide a comprehensive comparison of VALOR against several state-of-the-art structural variation discovery algorithms that use whole genome shotgun sequencing data.ConclusionsIn this paper, we show that VALOR is able to accurately discover all previously identified and experimentally validated large inversions in the same genome with a low false discovery rate. Using VALOR, we also predicted a novel inversion, which we validated using fluorescent in situ hybridization. VALOR is available at https://github.com/BilkentCompGen/VALOR

Healthcare professional and manager perceptions on drivers, benefits, and challenges of telemedicine: results from a cross-sectional survey in the Italian NHS

Background: The Covid-19 pandemic provided new challenges and opportunities for patients and healthcare providers while accelerating the trend of digital healthcare transformation. This study explores the perspectives of healthcare professionals and managers on (i) drivers to the implementation of telemedicine services and (ii) perceived benefits and challenges related to the use of telemedicine across the Italian National Health Service. Methods: An online cross-sectional survey was distributed to professionals working within 308 healthcare organisations in different Italian regions. Quantitative and qualitative data were collected through a self-administered questionnaire (June-September 2021). Responses were analysed using summary statistics and thematic analysis. Results: Key factors driving the adoption of telemedicine have been grouped into (i) organisational drivers (reduce the virus spread-80%; enhance care quality and efficiency-61%), (ii) technological drivers (ease of use-82%; efficacy and reliability-64%; compliance with data governance regulations-64%) and (iii) regulatory drivers (regulations’ semplification-84%). Nearly all respondents perceive telemedicine as useful in improving patient care (96%). The main benefits reported by respondents are shorter waiting lists, reduced Emergency Department attendance, decreased patient and clinician travel, and more frequent patient-doctor interactions. However, only 7% of respondents believe that telemedicine services are more effective than traditional care and 66% of the healthcare professionals believe that telemedicine can’t completely substitute in-person visits due to challenges with physical examination and patient-doctor relationships. Other reported challenges include poor quality and interoperability of telemedicine platforms and scarce integration of telemedicine with traditional care services. Moreover, healthcare professionals believe that some groups of patients experience difficulties in accessing and using the technologies due to socio-cultural factors, technological and linguistic challenges and the absence of caregivers. Conclusions: Respondents believe that telemedicine can be useful to complement and augment traditional care. However, many challenges still need to be overcome to fully consider telemedicine a standard of care. Strategies that could help address these challenges include additional regulations on data governance and reimbursements, evidence-based guidelines for the use of telemedicine, greater integration of tools and processes, patient-centred training for clinicians, patient-facing material to assist patients in navigating virtual sessions, different language options, and greater involvement of caregivers in the care process

A dataset of tracer concentrations and meteorological observations from the Bolzano Tracer EXperiment (BTEX) to characterize pollutant dispersion processes in an Alpine valley

Abstract. The paper describes the dataset of concentrations and related meteorological measurements collected during the field campaign of the Bolzano Tracer Experiment (BTEX). The experiment was performed to characterize the dispersion of pollutants emitted from a waste incinerator in the basin of the city of Bolzano, in the Italian Alps. As part of the experiment, two controlled releases of a passive gas tracer (sulfur hexafluoride, SF6) were performed through the stack of the incinerator on 14 February 2017 for two different time lags, starting, respectively, at 07:00 and 12:45 LST. Samples of ambient air were collected at target sites with vacuum-filled glass bottles and polyvinyl fluoride bags, and they were later analyzed by means of a mass spectrometer (detectability limit 30 pptv). Meteorological conditions were monitored by a network of 15 surface weather stations, 1 microwave temperature profiler, 1 sodar and 1 Doppler wind lidar. The dataset represents one of the few examples available in the literature concerning dispersion processes in a typical mountain valley environment, and it provides a useful benchmark for testing atmospheric dispersion models in complex terrain. The dataset described in this paper is available at https://doi.org/10.1594/PANGAEA.898761 (Falocchi et al., 2019)

Reconstructing complex regions of genomes using long-read sequencing technology

Cataloged from PDF version of article.Obtaining high-quality sequence continuity of complex regions of recent segmental duplication remains one of the major challenges of finishing genome assemblies. In the human and mouse genomes, this was achieved by targeting large-insert clones using costly and laborious capillary-based sequencing approaches. Sanger shotgun sequencing of clone inserts, however, has now been largely abandoned, leaving most of these regions unresolved in newer genome assemblies generated primarily by next-generation sequencing hybrid approaches. Here we show that it is possible to resolve regions that are complex in a genome-wide context but simple in isolation for a fraction of the time and cost of traditional methods using long-read single molecule, real-time (SMRT) sequencing and assembly technology from Pacific Biosciences (PacBio). We sequenced and assembled BAC clones corresponding to a 1.3-Mbp complex region of chromosome 17q21.31, demonstrating 99.994% identity to Sanger assemblies of the same clones. We targeted 44 differences using Illumina sequencing and find that PacBio and Sanger assemblies share a comparable number of validated variants, albeit with different sequence context biases. Finally, we targeted a poorly assembled 766-kbp duplicated region of the chimpanzee genome and resolved the structure and organization for a fraction of the cost and time of traditional finishing approaches. Our data suggest a straightforward path for upgrading genomes to a higher quality finished state

Rehabilitation Modulates High-Order Interactions Among Large-Scale Brain Networks in Subacute Stroke

The recovery of motor functions after stroke is fostered by the functional integration of large-scale brain networks, including the motor network (MN) and high-order cognitive controls networks, such as the default mode (DMN) and executive control (ECN) networks. In this paper, electroencephalography signals are used to investigate interactions among these three resting state networks (RSNs) in subacute stroke patients after motor rehabilitation. A novel metric, the O-information rate (OIR), is used to quantify the balance between redundancy and synergy in the complex high-order interactions among RSNs, as well as its causal decomposition to identify the direction of information flow. The paper also employs conditional spectral Granger causality to assess pairwise directed functional connectivity between RSNs. After rehabilitation, a synergy increase among these RSNs is found, especially driven by MN. From the pairwise description, a reduced directed functional connectivity towards MN is enhanced after treatment. Besides, inter-network connectivity changes are associated with motor recovery, for which the mediation role of ECN seems to play a relevant role, both from pairwise and high-order interactions perspective

Novel atrazine-binding biomimetics inspired to the D1 protein from the photosystem II of Chlamydomonas reinhardtii

Biomimetic design represents an emerging field for improving knowledge of natural molecules, as well as to project novel artificial tools with specific functions for biosensing. Effective strategies have been exploited to design artificial bioreceptors, taking inspiration from complex supramolecular assemblies. Among them, size-minimization strategy sounds promising to provide bioreceptors with tuned sensitivity, stability, and selectivity, through the ad hoc manipulation of chemical species at the molecular scale. Herein, a novel biomimetic peptide enabling herbicide binding was designed bioinspired to the D1 protein of the Photosystem II of the green alga Chlamydomonas reinhardtii. The D1 protein portion corresponding to the QB plastoquinone binding niche is capable of interacting with photosynthetic herbicides. A 50-mer peptide in the region of D1 protein from the residue 211 to 280 was designed in silico, and molecular dynamic simulations were performed alone and in complex with atrazine. An equilibrated structure was obtained with a stable pocked for atrazine binding by three H-bonds with SER222, ASN247, and HIS272 residues. Computational data were confirmed by fluorescence spectroscopy and circular dichroism on the peptide obtained by automated synthesis. Atrazine binding at nanomolar concentrations was followed by fluorescence spectroscopy, highlighting peptide suitability for optical sensing of herbicides at safety limits

Measurements of radioactivity in the environment for radiation protection purposes

Measurements of radioactivity in the environment, according to Article 35 of the Euratom Treaty, are routinely carried out by regulatory bodies and operators in charge. These activities are performed both locally and nationally, in order to assess effective doses to the population. In this context, therefore, it is necessary not only to determine the component due to external irradiation, but also to evaluate the deposit and accumulation of radioactivity in the environment that can reach the public via inhalation or ingestion. The contribution presents a brief description of the aspects regarding programs of monitoring and evaluation of the radioactivity in the environment, in particular the environmental matrices to be monitored, the analyses to be carried out, the related reporting levels as well as the features concerning the influence of the climate on the variations of dose rate values. Finally, a focus on some radiometric measurements performed over the last forty years in the environmental monitoring activities carried out in the ENEA Casaccia Research Center (Rome), in which two nuclear research facilities are currently operating, is presented