Accessible viral metagenomics for public health and clinical domains with Jovian.

The integration of next-generation sequencing into clinical diagnostics and surveillance initiatives is impeded by the lack of data analysis pipelines that align with privacy legislation and laboratory certification protocols. To address these challenges, we developed Jovian, an open-source, virus-focused, metagenomic analysis workflow for Illumina data. Jovian generates scaffolds enriched with pertinent annotations, including taxonomic classification, combined with metrics needed for quality assessment (coverage depth, average GC content, localization of open reading frames, minority single nucleotide polymorphisms), and incorporates host and disease metadata.

Elucidating the reaction mechanism of SO with Cu-CHA catalysts for NH-SCR by X-ray absorption spectroscopy.

The application of Cu-CHA catalysts for the selective catalytic reduction of NO by ammonia (NH-SCR) in exhaust systems of diesel vehicles requires the use of fuel with low sulfur content, because the Cu-CHA catalysts are poisoned by higher concentrations of SO. Understanding the mechanism of the interaction between the Cu-CHA catalyst and SO is crucial for elucidating the SO poisoning and development of efficient catalysts for SCR reactions. Earlier we have shown that SO reacts with the [Cu(NH)O] complex that is formed in the pores of Cu-CHA upon activation of O in the NH-SCR cycle.

Reliability Testing of a Low-Cost, Multi-Purpose Arduino-Based Data Logger Deployed in Several Applications Such as Outdoor Air Quality, Human Activity, Motion, and Exhaust Gas Monitoring.

This contribution shows the possibilities of applying a low-cost, multi-purpose data logger built around an Arduino Mega 2560 single-board computer. Most projects use this kind of hardware to develop single-purpose data loggers. In this work, a data logger with a more general hardware and software architecture was built to perform measurement campaigns in very different domains.

Biotechnological and Medical Aspects of Lactic Acid Bacteria Used for Plant Protection: A Comprehensive Review.

The use of chemical pesticides in agriculture goes hand in hand with some crucial problems. These problems include environmental deterioration and human health complications. To eliminate the problems accompanying chemical pesticides, biological alternatives should be considered.

Assessing the Influence of Zeolite Composition on Oxygen-Bridged Diamino Dicopper(II) Complexes in Cu-CHA DeNO Catalysts by Machine Learning-Assisted X-ray Absorption Spectroscopy.

Cu-exchanged chabazite is the catalyst of choice for NO abatement in diesel vehicles aftertreatment systems via ammonia-assisted selective catalytic reduction (NH-SCR). Herein, we exploit X-ray absorption spectroscopy powered by wavelet transform analysis and machine learning-assisted fitting to assess the impact of the zeolite composition on NH-mobilized Cu-complexes formed during the reduction and oxidation half-cycles in NH-SCR at 200 °C. Comparatively analyzing well-characterized Cu-CHA catalysts, we show that the Si/Al ratio of the zeolite host affects the structure of mobile dicopper(II) complexes formed during the oxidation of the [Cu(NH)] complexes by O.

ERS International Congress 2021: highlights from the Allied Respiratory Professionals assembly.

This paper provides an overview of some of the most memorable sessions that were (co)organised by the Allied Respiratory Professionals Assembly during the 2021 European Respiratory Society International Congress, which was held online for the second consecutive year due to the COVID-19 pandemic. Early Career Members from Assembly 9 summarised the content of the sessions (three oral communication sessions, two symposia and one Expert View) with the support of the chairs from the four Assembly groups: Respiratory Function Technologists and Scientists (Group 9.01); Physiotherapists (Group 9.

SO Poisoning of Cu-CHA deNO Catalyst: The Most Vulnerable Cu Species Identified by X-ray Absorption Spectroscopy.

Cu-exchanged chabazite zeolites (Cu-CHA) are effective catalysts for the NH-assisted selective catalytic reduction of NO (NH-SCR) for the abatement of NO emission from diesel vehicles. However, the presence of a small amount of SO in diesel exhaust gases leads to a severe reduction in the low-temperature activity of these catalysts. To shed light on the nature of such deactivation, we characterized a Cu-CHA catalyst under well-defined exposures to SO using X-ray absorption spectroscopy.

PhAc-ALGP-Dox, a Novel Anticancer Prodrug with Targeted Activation and Improved Therapeutic Index.

Clinical use of doxorubicin (Dox) is limited by cumulative myelo- and cardiotoxicity. This research focuses on the detailed characterization of PhAc-ALGP-Dox, a targeted tetrapeptide prodrug with a unique dual-step activation mechanism, designed to circumvent Dox-related toxicities and is ready for upcoming clinical investigation. Coupling Dox to a phosphonoacetyl (PhAc)-capped tetrapeptide forms the cell-impermeable, inactive compound, PhAc-ALGP-Dox.

The "can do, do do" concept in individuals with chronic obstructive pulmonary disease: an exploration of psychological mechanisms.

Background: The "can do, do do" concept aims at identifying subgroups among persons with chronic obstructive pulmonary disease (COPD). Following a two-dimensional categorization, individuals are binarily classified with respect to their levels of physical capacity ("can't do" or "can do") and physical activity ("don't do" or "do do"), resulting in four disjunct quadrants. The approach has been debated recently and the latest articles have concluded that the quadrants should be specifically examined in terms of psychological aspects of physical activity.

Investigating the role of Cu-oxo species in Cu-nitrate formation over Cu-CHA catalysts.

The speciation of framework-interacting Cu sites in Cu-chabazite zeolite catalysts active in the selective catalytic reduction of NO with NH is studied, to investigate the influence of the Al content on the copper structure and their reactivity towards a NO/O mixture. To this aim, three samples with similar Cu densities and different Si/Al ratios (5, 15 and 29) were studied using in situ X-ray absorption spectroscopy (XAS), FTIR and diffuse reflectance UV-Vis during pretreatment in O followed by the reaction. XAS and UV-Vis data clearly show the main presence of ZCu sites (with Z representing a framework negative charge) at a low Si/Al ratio, as predicted.

Structure and Reactivity of Oxygen-Bridged Diamino Dicopper(II) Complexes in Cu-Ion-Exchanged Chabazite Catalyst for NH-Mediated Selective Catalytic Reduction.

The NH-mediated selective catalytic reduction (NH-SCR) of NOx over Cu-ion-exchanged chabazite (Cu-CHA) catalysts is the basis of the technology for abatement of NOx from diesel vehicles. A crucial step in this reaction is the activation of oxygen. Under conditions for low-temperature NH-SCR, oxygen only reacts with Cu ions, which are present as mobile Cu diamine complexes [Cu(NH)].

Acquisition and generalization of cough trigger beliefs in allergic rhinitis.

In allergic conditions, trigger identification is often inaccurate, and may be influenced by pre-existing beliefs. In this study, we investigated the acquisition and generalization of symptom trigger beliefs in individuals with allergic rhinitis (n = 24) and control participants (n = 24). In a lab-based trigger acquisition task, unique exemplars of two trigger categories were either paired with saline inhalation (CS- category) or citric acid inhalation (CS+ category).

In the spotlight: first ERS Early Career Member Award winner, the ERS Lung Science Conference 2020 and new ECMC members.

http://bit.ly/2OTgQlo.

Respiratory syncytial, parainfluenza and influenza virus infection in young children with acute lower respiratory infection in rural Gambia.

Respiratory viral infections contribute significantly to morbidity and mortality worldwide, but representative data from sub-Saharan Africa are needed to inform vaccination strategies. We conducted population-based surveillance in rural Gambia using standardized criteria to identify and investigate children with acute lower respiratory infection (ALRI). Naso- and oropharyngeal swabs were collected.

Placebo and nocebo effects and operant pain-related avoidance learning.

Introduction: Research on learning in placebo and nocebo has relied predominantly on Pavlovian conditioning procedures. Operant learning procedures may more accurately model learning in real-life situations in which placebo and nocebo effects occur.

Objectives: To investigate the development and persistence of placebo and nocebo effects using an operant avoidance learning task.

Impact of Disease-Specific Fears on Pulmonary Rehabilitation Trajectories in Patients with COPD.

Disease-specific fears predict health status in chronic obstructive pulmonary disease (COPD), but their role in pulmonary rehabilitation (PR) remains poorly understood and especially longer-term evaluations are lacking. We therefore investigated changes in disease-specific fears over the course of PR and six months after PR, and investigated associations with PR outcomes (COPD assessment test (CAT) and St. Georges respiratory questionnaire (SGRQ)) in a subset of patients with COPD ( = 146) undergoing a 3-week inpatient PR program as part of the STAR study (Clinicaltrials.

Subcortical gray matter volumes in asthma: associations with asthma duration, control, and anxiety.

Asthma as a chronic inflammatory disease can be expected to affect central nervous system structures but little is known about subcortical structures in asthma and their potential association with illness-specific outcomes and anxiety. A total of 40 young adults (20 with asthma and 20 gender- and age-matched controls) underwent high-resolution T1-weighted MRI scan, viewed short distressing film clips, and filled in questionnaires about anxious and depressed mood, as well as asthma history, control, and catastrophizing thoughts about asthma, for those with asthma. The structural scans were processed in FSL's FIRST program to delineate subcortical structures of interest: amygdala, hippocampus, putamen, pallidum, caudate nucleus, nucleus accumbens, and thalamus.

Assessment of Anterior Cruciate Ligament Graft Maturity With Conventional Magnetic Resonance Imaging: A Systematic Literature Review.

Background: Magnetic resonance imaging (MRI) signal intensity (SI) measurements are being used increasingly in both clinical and research studies to assess the maturity of anterior cruciate ligament (ACL) grafts in humans. However, SI in conventional MRI with weighted images is a nonquantitative measure dependent on hardware and software.

Purpose: To conduct a systematic review of studies that have used MRI SI as a proxy for ACL graft maturity and to identify potential confounding factors in assessing the ACL graft in conventional MRI studies.

A comparative test of different density functionals for calculations of NH-SCR over Cu-Chabazite.

A general challenge in density functional theory calculations is to simultaneously account for different types of bonds. One such example is reactions in zeolites where both van der Waals and chemical bonds should be described accurately. Here, we use different exchange-correlation functionals to explore O dissociation over pairs of Cu(NH) complexes in Cu-Chabazite.

Biological activities associated with the volatile compound 2,5-bis(1-methylethyl)-pyrazine.

Pyrazines are 1,4-diazabenzene-based volatile organic compounds and known for their broad-spectrum antimicrobial activity. In the present study, we assessed the antimicrobial activity of 2,5-bis(1-methylethyl)-pyrazine, produced by Paenibacillus sp. AD87 during co-culture with Burkholderia sp.

Influence of incubation conditions on the formation of model biofilms by Listeria monocytogenes and Salmonella Typhimurium on abiotic surfaces.

Aims: This research aims to develop strongly adherent and mature model biofilms (on a 20 cm² polystyrene surface) for two pathogenic species, i.e. Listeria monocytogenes and Salmonella Typhimurium.

Investigating the Low Temperature Formation of Cu -(N,O) Species on Cu-CHA Zeolites for the Selective Catalytic Reduction of NO.

In this work, we show the potentiality of operando FTIR spectroscopy to follow the formation of Cu -(N,O) species on Cu exchanged chabazite zeolites (Cu-CHA), active for the selective catalytic reduction of NO with NH (NH -SCR). In particular, we investigated the reaction of NO and O at low temperature (200 and 50 °C) on a series of Cu-CHA zeolites with different composition (Si/Al and Cu/Al ratios), to investigate the nature of the formed copper nitrates, which have been proposed to be key intermediates in the oxidation part of the SCR cycle. Our results show that chelating bidentate nitrates are the main structures formed at 200 °C.

Towards an assessment of perceived COPD exacerbation triggers: Initial development and validation of a questionnaire.

Background And Objective: Prevention of exacerbations in chronic obstructive pulmonary disease (COPD) is important to decrease overall declines in functioning and improve quality of life. The present study sought to develop a psychometrically valid measure of perceived triggers of exacerbations in COPD patients, the COPD Exacerbation Trigger Inventory (CETI).

Methods: Participants (n = 192) were recruited through local clinics and online to complete surveys of the CETI, demographic information, disease-specific information and the COPD Assessment Test (CAT).