Deep learning analysis provides accurate COVID-19 diagnosis on chest computed tomography

INTRODUCTION

Computed Tomography is an essential diagnostic tool in the management of COVID-19. Considering the large amount of examinations in high case-load scenarios, an automated tool could facilitate and save critical time in the diagnosis and risk stratification of the disease.

METHODS

A novel deep learning derived machine learning (ML) classifier was developed using a simplified programming approach and an open source dataset consisting of 6868 chest CT images from 418 patients which was split into training and validation subsets. The diagnostic performance was then evaluated and compared to experienced radiologists on an independent testing dataset. Diagnostic performance metrics were calculated using Receiver Operating Characteristics (ROC) analysis. Operating points with high positive (>10) and low negative (<0.01) likelihood ratios to stratify the risk of COVID-19 being present were identified and validated.

RESULTS

The model achieved an overall accuracy of 0.956 (AUC) on an independent testing dataset of 90 patients. Both rule-in and rule out thresholds were identified and tested. At the rule-in operating point, sensitivity and specificity were 84.4 % and 93.3 % and did not differ from both radiologists (p > 0.05). At the rule-out threshold, sensitivity (100 %) and specificity (60 %) differed significantly from the radiologists (p < 0.05). Likelihood ratios and a Fagan nomogram provide prevalence independent test performance estimates.

CONCLUSION

Accurate diagnosis of COVID-19 using a basic deep learning approach is feasible using open-source CT image data. In addition, the machine learning classifier provided validated rule-in and rule-out criteria could be used to stratify the risk of COVID-19 being present.

Assessing pharmaceutical contamination along the Mediterranean and Red Sea coasts of Israel: Ascidians (Chordata, Ascidiacea) as bioindicators

Global increase in the use of pharmaceutically-active compounds (PhACs), and their insufficient removal in wastewater treatment plants, have resulted in their continuous release into the marine environment. We investigated the use of the solitary ascidians Herdmania momus, Microcosmus exasperatus, and Styela plicata as bioindicators of three common PhACs in the Israeli coastal waters: Bezafibrate, carbamazepine and diclofenac. Both the Mediterranean and the Red-Sea coasts were found contaminated with PhACs, detected at all 11 sampling sites, with four sites contaminated with all three studied PhACs. Diclofenac was most frequent, present in nine of the 11 sites with concentrations reaching 51.9 ng/g of dry weight sample (dw). Bezafibrate and carbamazepine reached concentrations of 47.8 ng/g dw and 14.3 ng/g dw, respectively. The alarming detection of such high concentrations of PhACs in ascidians along Israel's coasts demonstrates both the extent of PhACs contamination in the region, and the potential of ascidians as bioindicators, and emphasizes the urgent need for additional research into PhAC contamination sources and effects.

Right ventricular strain for prediction of mortality in patients with preserved ejection fraction

Introduction

Right Ventricular (RV) dysfunction is highly prevalent and has major prognostic implication in patients with Heart Failure (HF) with Preserved Ejection Fraction (HFpEF). Different functional indices have been proposed to evaluate RV function, most common are TEI-index, TAPSE and RVFAC%. Recent works suggested that 2-dimensional speckle tracking echocardiography (2DSTE) for RV global longitudinal strain (RVGLS) and free wall strain (RVFWS) are more sensitive in evaluating RV (dys)function than other functional and hemodynamic parameters in specific populations, such as HF with reduced EF.

Purpose

We aimed to assess if endocardial RVGLS, RVFWS, and RV Septal Wall Strain (RVSWS), might have a prognostic and additive value (on top of the conventional measurements) on the outcome of patients with preserved EF.

Methods

Retrospective analysis of RV parameters including Peak and End Systolic Strain of RVGLS, RVFWS and RVSWS, RV functional indices (RVFAC% and Machine like TAPSE), Systolic Pulmonary Artery Pressure, in 375 consecutive patients with Preserved Ejection Fraction (EF ≥50%; age 69.1±19; 51% female; Co-morbidity Charlson index 1 (3)). Multivariate Cox regression hazards model was used to determine the association between RV strain parameters to all-cause mortality.

Results

RVFWS, RVSWS and RVFAC% were strong predictors of mortality in univariate analysis (HR 1.07 [1.03–1.1]; p≤0.0001, HR 1.08 [1.05–1.12]; p≤0.0001, HR 0.97 [0.95–0.99]; p≤0.0002, respectively). Moreover, after adjustment for clinical (age, gender, Charlson index) and echocardiographic parameters (LA volume, E/e' average, systolic pulmonary pressure), all three parameters remained statistically significant predictors of all-cause mortality (p=0.004, p=0.024, p=0.026, respectively).

The best strain univariate predictor of mortality was RVGLS (HR 1.09 [1.05–1.13]; p≤0.0001), being superior to other RV functional indices and systolic pulmonary pressure. Also, after multivariate analysis it remained a statistically significant predictor of mortality (p=0.007).

All measurements had good intra-observer and inter-observer reproducibility (Single Measures ICC = 0.90 and ICC = 0.88, respectively).

Conclusions

2DSTE of RVGLS, RVFWS, RVSWS provides significant prognostic value to predict overall mortality in patients with Preserved Ejection Fraction with excellent reproducibility, incremental to routine clinical, hemodynamic and diastolic parameters.

Moreover, the strain results of the septal wall showed to be significant, thereover challenging the known hypothesis that the septal wall is mainly influenced by LV function.

Figure 1

Funding Acknowledgement

Type of funding source: None

Photo-neutron cross-section calculations of 54,56Fe, 90,91,92,94Zr, 93Nb and 107Ag Isotopes with newly obtained Giant Dipole Resonance parameters

The knowledge of the interaction of photons with matter is of vital importance to investigate fundamental nuclear physics problems. Giant dipole resonance (GDR) mechanism is dominant up to 30 MeV at photo-absorption cross-section. The photo-absorption cross-section curve against the photon energy displays one or multi-peak Lorentzian functions according to the deformation of the nucleus. Theoretical photo-absorption cross-section calculations generally focus on the estimation of GDR parameters. Theoretical reaction codes use GDR parameters to reproduce photon-induced nuclear reactions. In this study, photo-neutron cross-section calculations of ^54,56Fe, ^90,91,92,94Zr, ⁹³Nb, and ¹⁰⁷Ag isotopes have been done with the TALYS 1.8 and EMPIRE 3.2.2 nuclear reaction codes in the GDR region. During these calculations, both codes were firstly operated by using the predefined and existing GDR parameters within the codes. Later on, a new set of GDR parameters have been obtained by running a Lorentzian model based code in where the available experimental data are also considered. Levenberg-Marquardt algorithm has been used with 10^-6 function tolerances and 400 iterations for optimization. These new obtained GDR parameters then replaced with the existing GDR parameters within the TALYS code and the photo-neutron cross-section calculations for the investigated isotopes have been repeated. Ultimately, in order to discuss the outcomes and the effects of using new GDR parameters, obtained results were analyzed by comparing them with the experimental data from the Experimental Nuclear Reaction Data (EXFOR) library.

Microbial and Viral Communities and Their Antibiotic Resistance Genes Throughout a Hospital Wastewater Treatment System

Antibiotic resistance poses a serious threat to global public health, and antibiotic resistance determinants can enter natural aquatic systems through discharge of wastewater effluents. Hospital wastewater in particular is expected to contain high abundances of antibiotic resistance genes (ARGs) compared to municipal wastewater because it contains human enteric bacteria that may include antibiotic-resistant organisms originating from hospital patients, and can also have high concentrations of antibiotics and antimicrobials relative to municipal wastewater. Viruses also play an important role in wastewater treatment systems since they can influence the bacterial community composition through killing bacteria, facilitating transduction of genetic material between organisms, and modifying the chromosomal content of bacteria as prophages. However, little is known about the fate and connections between ARGs, viruses, and their associated bacteria in hospital wastewater systems. To address this knowledge gap, we characterized the composition and persistence of ARGs, dsDNA viruses, and bacteria from influent to effluent in a pilot-scale hospital wastewater treatment system in Israel using shotgun metagenomics. Results showed that ARGs, including genes conferring resistance to antibiotics of high clinical relevance, were detected in all sampling locations throughout the pilot-scale system, with only 16% overall depletion of ARGs per genome equivalent between influent and effluent. The most common classes of ARGs detected throughout the system conferred resistance to aminoglycoside, cephalosporin, macrolide, penam, and tetracycline antibiotics. A greater proportion of total ARGs were associated with plasmid-associated genes in effluent compared to in influent. No strong associations between viral sequences and ARGs were identified in viral metagenomes from the system, suggesting that phage may not be a significant vector for ARG transfer in this system. The majority of viruses in the pilot-scale system belonged to the families Myoviridae, Podoviridae, and Siphoviridae. Gammaproteobacteria was the dominant class of bacteria harboring ARGs and the most common putative viral host in all samples, followed by Bacilli and Betaproteobacteria. In the total bacterial community, the dominant class was Betaproteobacteria for each sample. Overall, we found that a variety of different types of ARGs and viruses were persistent throughout this hospital wastewater treatment system, which can be released to the environment through effluent discharge.

Treatment of Diethyl Phthalate Leached from Plastic Products in Municipal Solid Waste Using an Ozone-Based Advanced Oxidation Process

Plastic products in municipal solid waste result in the extraction of phthalates in leachate that also contains large amounts of organic matter, such as humic substances, ammonia, metals, chlorinated organics, phenolic compounds, and pesticide residues. Phthalate esters are endocrine disruptors, categorized as a priority pollutant by the US Environmental Protection Agency (USEPA). Biological processes are inefficient at degrading phthalates due to their stability and toxic characteristics. In this study, the peroxone (ozone/hydrogen peroxide) process (O₃/H₂O₂), an O₃-based advanced oxidation process (AOP), was demonstrated for the removal of diethyl phthalate (DEP) in synthetic leachate simulating solid-waste leachate from an open dump. The impact of the O₃ dose during DEP degradation; the formation of ozonation intermediate by-products; and the effects of H₂O₂ dose, pH, and ultraviolet absorbance at 254 nm (UVC) were determined during ozonation. Removal of 99.9% of an initial 20 mg/L DEP was obtained via 120 min of ozonation (transferred O₃ dose = 4971 mg/L) with 40 mg/L H₂O₂ in a semi-batch O₃ system. Degradation mechanisms of DEP along with its intermediate products were also determined for the AOP treatment. Indirect OH radical exposure was determined by using a radical probe compound (pCBA) in the O₃ treatment.

Using solitary ascidians to assess microplastic and phthalate plasticizers pollution among marine biota: A case study of the Eastern Mediterranean and Red Sea

The interaction of microplastic (MP) with marine organisms is crucial for understanding the significant effect that MP and its additives may have on marine environments. However, knowledge regarding the magnitude of these pollutants in the Eastern Mediterranean Sea and the tropical Red Sea is still scarce. Here we examined the levels of phthalate acid esters (PAEs) and MP in Herdmania momus and Microcosmus exasperatus sampled along the Mediterranean and Red Sea coasts of Israel. High levels of dibutyl phthalate (DBP) and bis (2‑ethylhexyl) phthalate (DEHP) were found in ascidians at the majority of sampling sites, and MP particles were found in ascidians at all sites. As efficient filter-feeders and being widely-distributed, invasive ascidians present fundamental opportunities for the environmental monitoring of microplastic and its additives worldwide. The high levels of pollutants revealed emphasize the need for further research into the magnitude and effects of MP and PAEs in these regions.

Investigation of gamma strength functions and level density models effects on photon induced reaction cross-section calculations for the fusion structural materials 46,50Ti, 51V, 58Ni and 63Cu

Scientists have been focused on fusion reactor studies to overcome the increasing energy demand. The materials, which have the potential to be used in fusion reactors must be resistant to the harmful effects of radiation in the manner of material itself. Selection of the appropriate materials to be used in nuclear reactors has a crucial importance to achieve the maximum efficiency and security. Ti, V, Ni and Cu are known as some of the constructional fusion materials. Existence of many knowledge about those materials provides countless advantages to the researchers and one of them is the cross-section, which basically means the probability of a nuclear reaction's occurrence. In addition to the cross-section, there exist some other parameters, which could be pointed as gamma strength function and level density models that affect the theoretical calculations. In this study, photon induced reaction cross-sections of ^46,50Ti, ⁵¹V, ⁵⁸Ni and ⁶³Cu target isotopes have been calculated by using TALYS 1.8 code with different gamma strength functions in the giant dipole resonance region. For gamma strength functions Kopecky-Uhl generalised Lorentzian Model, Brink-Axel Lorentzian Model, Hartree-Fock BCS tables, Hartree-Fock-Bogolyubov tables and Goriely's Hybrid Model have been employed. To appoint the best gamma strength function model, the relative variance calculations have been performed. Also, reaction cross-sections have been recalculated by using the best gamma strength function models through the different level density options. Constant Temperature Fermi Gas Model, Back Shifted Fermi Gas Model and Generalised Super Fluid Model have been employed for level density calculations. Experimental data for the investigated reactions have been taken from EXFOR library and used for comparisons of the obtained calculation results.

The EAACI/GA²LEN/EDF/WAO guideline for the definition, classification, diagnosis and management of urticaria

This evidence- and consensus-based guideline was developed following the methods recommended by Cochrane and the Grading of Recommendations Assessment, Development and Evaluation (GRADE) working group. The conference was held on 1 December 2016. It is a joint initiative of the Dermatology Section of the European Academy of Allergology and Clinical Immunology (EAACI), the EU-founded network of excellence, the Global Allergy and Asthma European Network (GA²LEN), the European Dermatology Forum (EDF) and the World Allergy Organization (WAO) with the participation of 48 delegates of 42 national and international societies. This guideline was acknowledged and accepted by the European Union of Medical Specialists (UEMS). Urticaria is a frequent, mast cell-driven disease, presenting with wheals, angioedema, or both. The lifetime prevalence for acute urticaria is approximately 20%. Chronic spontaneous urticaria and other chronic forms of urticaria are disabling, impair quality of life and affect performance at work and school. This guideline covers the definition and classification of urticaria, taking into account the recent progress in identifying its causes, eliciting factors and pathomechanisms. In addition, it outlines evidence-based diagnostic and therapeutic approaches for the different subtypes of urticaria.

Graphene Oxide Sheets Combine into Conductive Coatings by Direct Oxidative Electropolymerization

New coatings are obtained when graphene oxide is further oxidized at moderate anodic potentials (≤~1.3 V vs. Ag/AgCl). Based on a variety of spectroscopic and electrochemical observations, the coatings are attributed to the direct electropolymerization of graphene oxide sheets via oxidation of the phenol edge groups on graphene. Depending on the applied potential, ether or carboxylic groups are formed. The coatings obtained via further oxidation are characterized by a lower O/C ratio due to decarboxylation and a higher content of C=C bonds. These bonds extend aromatic conjugation into the combined graphene oxide sheets and are responsible for the highly conductive nature of these coatings.

Surgical outcomes of a civil war in a neighbouring country

OBJECTIVES

The civil war in Syria began on 15 March 2011, and many of the injured were treated in the neighbouring country of Turkey. This study reports the surgical outcomes of this war, in a tertiary centre in Turkey.

METHODS

159 patients with civilian war injuries in Syria who were admitted to the General Surgery Department in the Research and Training Hospital of the Medical School of Mustafa Kemal University, Hatay, Turkey, between 2011 and 2012 were analysed regarding the age, sex, injury type, history of previous surgery for the injury, types of abdominal injuries (solid or luminal organ), the status of isolated abdominal injuries or multiple injuries, mortality, length of hospital stay and injury severity scoring.

RESULTS

The median age of the patients was 30.05 (18-66 years) years. Most of the injuries were gunshot wounds (99 of 116 patients, 85.3%). Primary and previously operated patients were transferred to our clinic in a median time of 6.28±4.44 h and 58.11±44.08 h, respectively. Most of the patients had intestinal injuries; although a limited number of patients with colorectal injuries were treated with primary repair, stoma was the major surgical option due to the gross peritoneal contamination secondary to prolonged transport time. Two women and 21 men died. The major cause of death was multiorgan failure secondary to sepsis (18 patients).

CONCLUSIONS

In the case of civil war in the bordering countries, it is recommended that precautions are taken, such as transformation of nearby civilian hospitals into military ones and employment of experienced trauma surgeons in these hospitals to provide effective medical care. Damage control procedures can avoid fatalities especially before the lethal triad of physiological demise occurs. Rapid transport of the wounded to the nearest medical centre is the key point in countries neighbouring a civil war.

Production cross–section calculations of medical 32P, 117Sn, 153Sm and 186,188Re radionuclides used in bone pain palliation treatment

In this study, production cross–section calculations of 32P, 117Sn, 153Sm and 186,188Re radionuclides used in bone pain palliation treatment produced by 30Si(d,γ)32P, 118Sn(γ,n)117Sn, 116Sn(n,γ)117Sn, 150Nd(α,n)153Sm, 154Sm(n,2n)153Sm, 152Sm(n,γ)153Sm, 186W(d,2n)186Re, 187Re(γ,n)186Re, 185Re(n,γ)186Re and 187Re(n,γ)188Re reactions have been investigated in the different incident energy range of 0.003–34 MeV. Two-component exciton and generalised superfluid models of the TALYS 1.6 and exciton and generalised superfluid models of the EMPIRE 3.1 computer codes have been used to pre-equilibrium (PEQ) reaction calculations. The calculated production cross–section results have been compared with available experimental results existing in the experimental nuclear reaction database (EXFOR). Except the 118Sn(γ,n)117Sn, 150Nd(α,n)153Sm and 185Re(n,γ)186Re reactions, the two-component exciton model calculations of TALYS 1.6 code exhibit generally good agreement with the experimental measurements for all reactions used in this present study.