VARVI: A Software Tool for Analyzing the Variability of the Heart Rate in Response to Visual Stimuli

Abstract This paper describes a free software tool (VARVI) developed in our research group to facilitate the analysis of heart rate variability (HRV) in response to different visual stimuli. This tool was developed after the realization that this type of studies are becoming to be used in fields such as psychiatry, psychology and marketing and that there are no specific tools for this purpose. It has been developed in python language and tested on Linux but extensible to other operating systems. It requires the connection of a Bluetooth chest strap Polar WearLink to the subject. The researcher selects a set of videos of any duration and the application shows them to the subject in a predefined or random order, while the heart rate is recorded. The result is a pair of text files that can be read by other HRV tools developed in our group (RHRV or gHRV). VARVI has been used for analyzing the response to watching the videos of the last Galician election campaign in a group of 90 people. It will be used in a project whose goal is to analyze the impact of traffic accidents prevention campaign in Spain and also in a research with depressed patients, in collaboration with the Hospital of Ourense

Antagonistic pleiotropy in the bifunctional surface protein FadL (OmpP1) during adaptation of Haemophilus influenzae to chronic lung infection associated with Chronic Obstructive Pulmonary Disease

Tracking bacterial evolution during chronic infection provides insights into how host selection pressures shape bacterial genomes. The human-restricted opportunistic pathogen nontypeable Haemophilus influenzae (NTHi) infects the lower airways of patients suffering chronic obstructive pulmonary disease (COPD) and contributes to disease progression. To identify bacterial genetic variation associated with bacterial adaptation to the COPD lung, we sequenced the genomes of 92 isolates collected from the sputum of 13 COPD patients over 1 to 9years. Individuals were colonized by distinct clonal types (CTs) over time, but the same CT was often reisolated at a later time or found in different patients. Although genomes from the same CT were nearly identical, intra-CT variation due to mutation and recombination occurred. Recurrent mutations in several genes were likely involved in COPD lung adaptation. Notably, nearly a third of CTs were polymorphic for null alleles of ompP1 (also called fadL), which encodes a bifunctional membrane protein that both binds the human carcinoembryonic antigen-related cell adhesion molecule 1 (hCEACAM1) receptor and imports long-chain fatty acids (LCFAs). Our computational studies provide plausible three-dimensional models for FadL's interaction with hCEACAM1 and LCFA binding. We show that recurrent fadL mutations are likely a case of antagonistic pleiotropy, since loss of FadL reduces NTHi's ability to infect epithelia but also increases its resistance to bactericidal LCFAs enriched within the COPD lung. Supporting this interpretation, truncated fadL alleles are common in publicly available NTHi genomes isolated from the lower airway tract but rare in others. These results shed light on molecular mechanisms of bacterial pathoadaptation and guide future research toward developing novel COPD therapeutics.IMPORTANCE Nontypeable Haemophilus influenzae is an important pathogen in patients with chronic obstructive pulmonary disease (COPD). To elucidate the bacterial pathways undergoing in vivo evolutionary adaptation, we compared bacterial genomes collected over time from 13 COPD patients and identified recurrent genetic changes arising in independent bacterial lineages colonizing different patients. Besides finding changes in phase-variable genes, we found recurrent loss-of-function mutations in the ompP1 (fadL) gene. We show that loss of OmpP1/FadL function reduces this bacterium's ability to infect cells via the hCEACAM1 epithelial receptor but also increases its resistance to bactericidal fatty acids enriched within the COPD lung, suggesting a case of antagonistic pleiotropy that restricts DeltafadL strains' niche. These results show how H. influenzae adapts to host-generated inflammatory mediators in the COPD airways

Higher COVID-19 pneumonia risk associated with anti-IFN-α than with anti-IFN-ω auto-Abs in children

We found that 19 (10.4%) of 183 unvaccinated children hospitalized for COVID-19 pneumonia had autoantibodies (auto-Abs) neutralizing type I IFNs (IFN-alpha 2 in 10 patients: IFN-alpha 2 only in three, IFN-alpha 2 plus IFN-omega in five, and IFN-alpha 2, IFN-omega plus IFN-beta in two; IFN-omega only in nine patients). Seven children (3.8%) had Abs neutralizing at least 10 ng/ml of one IFN, whereas the other 12 (6.6%) had Abs neutralizing only 100 pg/ml. The auto-Abs neutralized both unglycosylated and glycosylated IFNs. We also detected auto-Abs neutralizing 100 pg/ml IFN-alpha 2 in 4 of 2,267 uninfected children (0.2%) and auto-Abs neutralizing IFN-omega in 45 children (2%). The odds ratios (ORs) for life-threatening COVID-19 pneumonia were, therefore, higher for auto-Abs neutralizing IFN-alpha 2 only (OR [95% CI] = 67.6 [5.7-9,196.6]) than for auto-Abs neutralizing IFN-. only (OR [95% CI] = 2.6 [1.2-5.3]). ORs were also higher for auto-Abs neutralizing high concentrations (OR [95% CI] = 12.9 [4.6-35.9]) than for those neutralizing low concentrations (OR [95% CI] = 5.5 [3.1-9.6]) of IFN-omega and/or IFN-alpha 2

Spectral estimation of HRV in signals with gaps

Heart rate variability is commonly quantified following spectral estimation. However, it is often difficult to obtain continuous recordings of beat-to-beat intervals without interruptions due to artefacts, noise or sporadic arrhythmias. Such data loss may be seen as gaps in the recordings, and often results in such signals being discarded. While a number of methods has been proposed for spectral estimation in heart rate records with gaps, there are no comprehensive comparisons between them. This paper tries to fill this void, comparing methods and identifying the most versatile and reliable one. The mean (bias error)and standard deviation (random error)of estimates of power in the low frequency band (LF), from 0.04 to 0.15 Hz; in the high frequency band (HF), from 0.15 to 0.4 Hz; and their ratio (LF/HF), were calculated in RR-interval time-series with up to 50% of samples missing through large or small gaps introduced into recordings. ‘Correlogram (bridging)’ and ‘Burg for segments’ methods proved to be the most robust methods for dealing with gaps, but Burg for segments was found to be more robust, especially in the HF band. Our results clearly show that even large gaps (covering a total of 50% of the recording time)can still yield robust spectral estimates of HRV, provided appropriate methods are used.</p

Effects of Psychological Stress and Alprazolam on Development of Oral Candidiasis in Rats

Psychological stress has been found to suppress cell-mediated immune responses that are important in limiting the proliferation of Candida albicans. Since anxiolytic drugs can restore cellular immunity in rodents exposed to stress conditions, we designed experiments conducted to evaluate the effects of alprazolam (1 mg/kg of body weight/day), a central benzodiazepine anxiolytic agonist, on the development of oral candidiasis in Sprague-Dawley rats exposed to a chronic auditory stressor. Animals were submitted to surgical hyposalivation in order to facilitate the establishment and persistence of C. albicans infection. Application of stress and treatment with drugs (placebo or alprazolam) were initiated 7 days before C. albicans inoculation and lasted until the end of the experiments (day 15 postinoculation). Establishment of C. albicans infection was evaluated by swabbing the inoculated oral cavity with a sterile cotton applicator on days 2 and 15 after inoculation, followed by plating on YEPD (yeast extract-peptone-dextrose) agar. Tissue injury was determined by the quantification of the number and type (normal or abnormal) of papillae on the dorsal tongue per microscopic field. A semiquantitative scale was devised to assess the degree of colonization of the epithelium by fungal hyphae. Our results show that stress exacerbates C. albicans infection of the tongues of rats. Significant increases in Candida counts, the percentage of the tongue's surface covered with clinical lesions, the percentage of abnormal papillae, and the colonization of the epithelium by fungal hyphae were found in stressed rats compared to those found in the unstressed rats. Treatment with alprazolam significantly reversed these adverse effects of stress, showing that, besides the psychopharmacological properties of this anxiolytic drug against stress, it has consequences for Candida infection

Nontypable haemophilus influenzae genomic patho-adaptation in the airways of chronic obstructive pulmonary disease patients with long-term microbial persistence

Trabajo presentado en el 7th Congress of European Microbiologists (FEMS2017), celebrado en Valencia (España), del 9 al 13 de julio de 2017Backgrounds The respiratory pathogen nontypeable Haemophilus influenzae (NTHi) is encountered in a significant proportion in the lower airways of Chronic Obstructive Pulmonary Disease (COPD) patients. The COPD lung is likely to be a unique niche favouring its adaptation to persistent infection. Objectives To unravel NTHi evolutionary dynamics in the lung of the COPD patient over time, and to identify microbial patho-adaptive features. Methods Ninety-two NTHi isolates from sputum samples of 13 COPD patients at exacerbation, recovered in a prospective longitudinal study (2000-2014), were genome sequenced: (a) Pacific Biosciences longread sequencing was used to generate complete assemblies for one representative of each clonal type; (b) Illumina short-read sequencing was applied to all isolates. Genome assembly used a customized pipeline and raw reads were also aligned to the PacBio reference genomes to generate variant tables for each set of clonal type isolates. Functional characterization of parallel evolutionrelated allelic variation was analyzed for selected genes. Conclusions Ninety-two NTHi COPD isolates have been (i) phylogenomically analyzed in the context of all publicly available NTHi genome sequences, (ii) organized in 33 clonal types, (iii) used to establish variation in NTHi genome architecture, (iv) used to identify traits of parallel evolution by fixing at least one single nucleotide variant in more than one clonal type. Detailed analysis of the fadL-ompP1 gene parallel evolution and allelic variation will be discussed, in terms of its role as an exogenous long-chain fatty acids transporter, as a ligand of the human receptor CEACAM-1 and as a source of antigenic variation.Peer reviewe

Nontypeable Haemophilus influenzae patho-adaptation within the aireways of chronic obstructive pulmoray disease patients with long-term microbial persistence

Trabajo presentado en el 7th European Conference on Prokaryotic and Fungal Genomics (ProkaGENOMICS), celebrado en Gottingen (Alemania), del 19 al 22 de septiembre de 2017)Introduction. The respiratory pathogen nontypeable Haemophilus influenzae (NTHi) persistently infects a significant proportion of Chronic Obstructive Pulmonary Disease (COPD) patients’ lower airways, and is usually associated with acute exacerbations of this chronic disease. Objectives. Based on the hypothesis that the COPD may be a unique niche favouring NTHi adaptation, this work aimed to unravel NTHi evolutionary dynamics in the COPD lungs over time, with the goal of identifying genomic patho-adaptive features.Peer reviewe

Iridea, fario e salmerino: così si allevano

Tracking bacterial evolution during chronic infection provides insights into how host selection pressures shape bacterial genomes. The human-restricted opportunistic pathogen nontypeable Haemophilus influenzae (NTHi) infects the lower airways of patients suffering chronic obstructive pulmonary disease (COPD) and contributes to disease progression. To identify bacterial genetic variation associated with bacterial adaptation to the COPD lung, we sequenced the genomes of 92 isolates collected from the sputum of 13 COPD patients over 1 to 9 years. Individuals were colonized by distinct clonal types (CTs) over time, but the same CT was often reisolated at a later time or found in different patients. Although genomes from the same CT were nearly identical, intra-CT variation due to mutation and recombination occurred. Recurrent mutations in several genes were likely involved in COPD lung adaptation. Notably, nearly a third of CTs were polymorphic for null alleles of ompP1 (also called fadL), which encodes a bifunctional membrane protein that both binds the human carcinoembryonic antigen-related cell adhesion molecule 1 (hCEACAM1) receptor and imports long-chain fatty acids (LCFAs). Our computational studies provide plausible three-dimensional models for FadL’s interaction with hCEACAM1 and LCFA binding. We show that recurrent fadL mutations are likely a case of antagonistic pleiotropy, since loss of FadL reduces NTHi’s ability to infect epithelia but also increases its resistance to bactericidal LCFAs enriched within the COPD lung. Supporting this interpretation, truncated fadL alleles are common in publicly available NTHi genomes isolated from the lower airway tract but rare in others. These results shed light on molecular mechanisms of bacterial pathoadaptation and guide future research toward developing novel COPD therapeutics. IMPORTANCE Nontypeable Haemophilus influenzae is an important pathogen in patients with chronic obstructive pulmonary disease (COPD). To elucidate the bacterial pathways undergoing in vivo evolutionary adaptation, we compared bacterial genomes collected over time from 13 COPD patients and identified recurrent genetic changes arising in independent bacterial lineages colonizing different patients. Besides finding changes in phase-variable genes, we found recurrent loss-of-function mutations in the ompP1 (fadL) gene. We show that loss of OmpP1/FadL function reduces this bacterium’s ability to infect cells via the hCEACAM1 epithelial receptor but also increases its resistance to bactericidal fatty acids enriched within the COPD lung, suggesting a case of antagonistic pleiotropy that restricts ΔfadL strains’ niche. These results show how H. influenzae adapts to host-generated inflammatory mediators in the COPD airways.This work has been funded by MINECO grants SAF2012-31166 and SAF2015-66520-R to J.G. and grants CTQ2014-57141-R and CTQ2017-88353-R to S.M.-S.; grant 03/2016 from the Health Department, Regional Government of Navarra, Spain, and SEPAR grant 31/2015 to J.G.; and NIDCD grant 5R01 DC 02148 and NIDDK grant 1U01 DK082316 from the U.S. National Institutes of Health to G.D.E. CIBERES is an initiative from the Instituto de Salud Carlos III (ISCIII), Madrid, Spain. J.M. and L.P.-R. were funded by Ph.D. studentships BES-2013-062644 and BES-2012-053653 from MINECO, Spain. A.F.-C. was funded by a contract from MINECO, reference number 20132RC947. I.R.-A. was funded by a Ph.D. studentship from the Universidad Pública de Navarra, Spain. S.M. is funded by a postdoctoral contract from CIBERES