Multi-scale theoretical approach to X-ray absorption spectra in disordered systems: an application to the study of Zn(II) in water

We develop a multi-scale theoretical approach aimed at calculating from first principles X-ray absorption spectra of liquid solutions and disordered systems. We test the method by considering the paradigmatic case of Zn(II) in water which, besides being relevant in itself, is also of interest for biology. With the help of classical molecular dynamics simulations we start by producing bunches of configurations differing for the Zn(II)-water coordination mode. Different coordination modes are obtained by making use of the so-called dummy atoms method. From the collected molecular dynamics trajectories, snapshots of a more manageable subsystem encompassing the metal site and two solvation layers are cut out. Density functional theory is used to optimize and relax these reduced system configurations employing a uniform dielectric to mimic the surrounding bulk liquid water. On the resulting structures, fully quantum mechanical X-ray absorption spectra calculations are performed by including core-hole effects and core-level shifts. The proposed approach does not rely on any guessing or fitting of the force field or of the atomic positions of the system. The comparison of the theoretically computed spectrum with the experimental Zn K-edge XANES data unambiguously demonstrates that among the different a priori possible geometries, Zn(II) in water lives in an octahedral coordination mode.Comment: 8 pages, 3 figure

SARS-CoV-2 virion stabilization by Zn binding

Zinc plays a crucial role in the process of virion maturation inside the host cell. The accessory Cys-rich proteins expressed in SARS-CoV-2 by genes ORF7a and ORF8 are likely involved in zinc binding and in interactions with cellular antigens activated by extensive disulfide bonds. In this report we provide a proof of concept for the feasibility of a structural study of orf7a and orf8 proteins. A conceivable hypothesis is that lack of cellular zinc, or substitution thereof, might lead to a significant slowing down of viral maturation

Abdominal Computed Tomography Imaging Findings in Hospitalized COVID-19 Patients: A Year-Long Experience and Associations Revealed by Explainable Artificial Intelligence.

The aim of this retrospective study is to assess any association between abdominal CT findings and the radiological stage of COVID-19 pneumonia, pulmonary embolism and patient outcomes. We included 158 adult hospitalized COVID-19 patients between 1 March 2020 and 1 March 2021 who underwent 206 abdominal CTs. Two radiologists reviewed all CT images. Pathological findings were classified as acute or not. A subset of patients with inflammatory pathology in ACE2 organs (bowel, biliary tract, pancreas, urinary system) was identified. The radiological stage of COVID pneumonia, pulmonary embolism, overall days of hospitalization, ICU admission and outcome were registered. Univariate statistical analysis coupled with explainable artificial intelligence (AI) techniques were used to discover associations between variables. The most frequent acute findings were bowel abnormalities

Effects of Oestrogen on MicroRNA Expression in Hormone-Responsive Breast Cancer Cells

Oestrogen receptor alpha (ERα) is a ligand-dependent transcription factor that mediates oestrogen effects in hormone-responsive cells. Following oestrogenic activation, ERα directly regulates the transcription of target genes via DNA binding. MicroRNAs (miRNAs) represent a class of small noncoding RNAs that function as negative regulators of protein-coding gene expression. They are found aberrantly expressed or mutated in cancer, suggesting their crucial role as either oncogenes or tumour suppressor genes. Here, we analysed changes in miRNA expression in response to oestrogen in hormone-responsive breast cancer MCF-7 and ZR-75.1 cells by microarray-mediated expression profiling. This led to the identification of 172 miRNAs up- or down-regulated by ERα in response to 17β-oestradiol, of which 52 are similarly regulated by the hormone in the two cell models investigated. To identify mechanisms by which ERα exerts its effects on oestrogen-responsive miRNA genes, the oestrogen-dependent miRNA expression profiles were integrated with global in vivo ERα binding site mapping in the genome by ChIP-Seq. In addition, data from miRNA and messenger RNA (mRNA) expression profiles obtained under identical experimental conditions were compared to identify relevant miRNA target transcripts. Results show that miRNAs modulated by ERα represent a novel genomic pathway to impact oestrogen-dependent processes that affect hormone-responsive breast cancer cell behaviour. MiRNome analysis in tumour tissues from breast cancer patients confirmed a strong association between expression of these small RNAs and clinical outcome of the disease, although this appears to involve only marginally the oestrogen-regulated miRNAs identified in this study

AIforCOVID: predicting the clinical outcomes in patients with COVID-19 applying AI to chest-X-rays. An Italian multicentre study

Recent epidemiological data report that worldwide more than 53 million people have been infected by SARS-CoV-2, resulting in 1.3 million deaths. The disease has been spreading very rapidly and few months after the identification of the first infected, shortage of hospital resources quickly became a problem. In this work we investigate whether chest X-ray (CXR) can be used as a possible tool for the early identification of patients at risk of severe outcome, like intensive care or death. CXR is a radiological technique that compared to computed tomography (CT) it is simpler, faster, more widespread and it induces lower radiation dose. We present a dataset including data collected from 820 patients by six Italian hospitals in spring 2020 during the first COVID-19 emergency. The dataset includes CXR images, several clinical attributes and clinical outcomes. We investigate the potential of artificial intelligence to predict the prognosis of such patients, distinguishing between severe and mild cases, thus offering a baseline reference for other researchers and practitioners. To this goal, we present three approaches that use features extracted from CXR images, either handcrafted or automatically by convolutional neuronal networks, which are then integrated with the clinical data. Exhaustive evaluation shows promising performance both in 10-fold and leave-one-centre-out cross-validation, implying that clinical data and images have the potential to provide useful information for the management of patients and hospital resources

The potential of eupraxia@sparc_lab for radiation based techniques

A proposal for building a Free Electron Laser, EuPRAXIA@SPARC_LAB, at the Laboratori Nazionali di Frascati, is at present under consideration. This FEL facility will provide a unique combination of a high brightness GeV-range electron beam generated in a X-band RF linac, a 0.5 PW-class laser system and the first FEL source driven by a plasma accelerator. The FEL will produce ultra-bright pulses, with up to 1012 photons/pulse, femtosecond timescale and wavelength down to 3 nm, which lies in the so called “water window”. The experimental activity will be focused on the realization of a plasma driven short wavelength FEL able to provide high-quality photons for a user beamline. In this paper, we describe the main classes of experiments that will be performed at the facility, including coherent diffraction imaging, soft X-ray absorption spectroscopy, Raman spectroscopy, Resonant Inelastic X-ray Scattering and photofragmentation measurements. These techniques will allow studying a variety of samples, both biological and inorganic, providing information about their structure and dynamical behavior. In this context, the possibility of inducing changes in samples via pump pulses leading to the stimulation of chemical reactions or the generation of coherent excitations would tremendously benefit from pulses in the soft X-ray region. High power synchronized optical lasers and a TeraHertz radiation source will indeed be made available for THz and pump–probe experiments and a split-and-delay station will allow performing XUV-XUV pump–probe experiments.Fil: Balerna, Antonella. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Bartocci, Samanta. Università degli studi di Sassari; ItaliaFil: Batignani, Giovanni. Università degli studi di Roma "La Sapienza"; ItaliaFil: Cianchi, Alessandro. Universita Tor Vergata; Italia. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Chiadroni, Enrica. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Coreno, Marcello. Istituto Nazionale Di Fisica Nucleare.; Italia. Istituto di Struttura della Materia; ItaliaFil: Cricenti, Antonio. Istituto di Struttura della Materia; ItaliaFil: Dabagov, Sultan. Istituto Nazionale Di Fisica Nucleare.; Italia. National Research Nuclear University; Rusia. Lebedev Physical Institute; RusiaFil: Di Cicco, Andrea. Universita Degli Di Camerino; ItaliaFil: Faiferri, Massimo. Università degli studi di Sassari; ItaliaFil: Ferrante, Carino. Università degli studi di Roma “La Sapienza”; Italia. Center for Life Nano Science @Sapienza; ItaliaFil: Ferrario, Massimo. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Fumero, Giuseppe. Università degli studi di Roma “La Sapienza”; ItaliaFil: Giannessi, Luca. Elettra-Sincrotrone Trieste; Italia. ENEA C.R. Frascati; ItaliaFil: Gunnella, Roberto. Universita Degli Di Camerino; ItaliaFil: Leani, Juan Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; ArgentinaFil: Lupi, Stefano. Università degli studi di Roma “La Sapienza”; Italia. Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Roma La Sapienza; ItaliaFil: Macis, Salvatore. Università degli Studi di Roma Tor Vergata; Italia. Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Roma Tor Vergata; ItaliaFil: Manca, Rosa. Università degli studi di Sassari; ItaliaFil: Marcelli, Augusto. Istituto Nazionale Di Fisica Nucleare.; Italia. Consiglio Nazionale delle Ricerche; ItaliaFil: Masciovecchio, Claudio. Elettra-Sincrotrone Trieste; ItaliaFil: Minicucci, Marco. Universita Degli Di Camerino; ItaliaFil: Morante, Silvia. Universita Tor Vergata; Italia. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Perfetto, Enrico. Universita Tor Vergata; Italia. Consiglio Nazionale delle Ricerche; ItaliaFil: Petrarca, Massimo. Università degli studi di Roma "La Sapienza"; Italia. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Pusceddu, Fabrizio. Università degli studi di Sassari; ItaliaFil: Rezvani, Javad. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Robledo, José Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; ArgentinaFil: Rossi, Giancarlo. Centro Fermi—Museo Storico della Fisica e Centro Studi e Ricerche “Enrico Fermi”; Italia. Istituto Nazionale Di Fisica Nucleare.; Italia. Universita Tor Vergata; ItaliaFil: Sanchez, Hector Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; ArgentinaFil: Scopigno, Tullio. Center for Life Nano Science @Sapienza; Italia. Università degli studi di Roma "La Sapienza"; ItaliaFil: Stefanucci, Gianluca. Universita Tor Vergata; Italia. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Stellato, Francesco. Universita Tor Vergata; Italia. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Trapananti, Angela. Universita Degli Di Camerino; ItaliaFil: Villa, Fabio. Istituto Nazionale Di Fisica Nucleare.; Itali

Differentiation of COVID-19 signs and symptoms from allergic rhinitis and common cold : An ARIA-EAACI-GA(2)LEN consensus

Background Although there are many asymptomatic patients, one of the problems of COVID-19 is early recognition of the disease. COVID-19 symptoms are polymorphic and may include upper respiratory symptoms. However, COVID-19 symptoms may be mistaken with the common cold or allergic rhinitis. An ARIA-EAACI study group attempted to differentiate upper respiratory symptoms between the three diseases. Methods A modified Delphi process was used. The ARIA members who were seeing COVID-19 patients were asked to fill in a questionnaire on the upper airway symptoms of COVID-19, common cold and allergic rhinitis. Results Among the 192 ARIA members who were invited to respond to the questionnaire, 89 responded and 87 questionnaires were analysed. The consensus was then reported. A two-way ANOVA revealed significant differences in the symptom intensity between the three diseases (p < .001). Conclusions This modified Delphi approach enabled the differentiation of upper respiratory symptoms between COVID-19, the common cold and allergic rhinitis. An electronic algorithm will be devised using the questionnaire.Peer reviewe

ARIA 2016 : Care pathways implementing emerging technologies for predictive medicine in rhinitis and asthma across the life cycle

The Allergic Rhinitis and its Impact on Asthma (ARIA) initiative commenced during a World Health Organization workshop in 1999. The initial goals were (1) to propose a new allergic rhinitis classification, (2) to promote the concept of multi-morbidity in asthma and rhinitis and (3) to develop guidelines with all stakeholders that could be used globally for all countries and populations. ARIA-disseminated and implemented in over 70 countries globally-is now focusing on the implementation of emerging technologies for individualized and predictive medicine. MASK [MACVIA (Contre les Maladies Chroniques pour un Vieillissement Actif)-ARIA Sentinel NetworK] uses mobile technology to develop care pathways for the management of rhinitis and asthma by a multi-disciplinary group and by patients themselves. An app (Android and iOS) is available in 20 countries and 15 languages. It uses a visual analogue scale to assess symptom control and work productivity as well as a clinical decision support system. It is associated with an inter-operable tablet for physicians and other health care professionals. The scaling up strategy uses the recommendations of the European Innovation Partnership on Active and Healthy Ageing. The aim of the novel ARIA approach is to provide an active and healthy life to rhinitis sufferers, whatever their age, sex or socio-economic status, in order to reduce health and social inequalities incurred by the disease.Peer reviewe