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Background Lung rest has been recommended during extracorporeal membrane oxygenation (ECMO) for severe acute respiratory distress syndrome (ARDS). Whether positive end-expiratory pressure (PEEP) confers lung protection during ECMO for severe ARDS is unclear. We compared the effects of three different PEEP levels whilst applying near-apnoeic ventilation in a model of severe ARDS treated with ECMO. Methods Acute respiratory distress syndrome was induced in anaesthetised adult male pigs by repeated saline lavage and injurious ventilation for 1.5 h. After ECMO was commenced, the pigs received standardised near-apnoeic ventilation for 24 h to maintain similar driving pressures and were randomly assigned to PEEP of 0, 10, or 20 cm H2O (n=7 per group). Respiratory and haemodynamic data were collected throughout the study. Histological injury was assessed by a pathologist masked to PEEP allocation. Lung oedema was estimated by wet-to-dry-weight ratio. Results All pigs developed severe ARDS. Oxygenation on ECMO improved with PEEP of 10 or 20 cm H2O, but did not in pigs allocated to PEEP of 0 cm H2O. Haemodynamic collapse refractory to norepinephrine (n=4) and early death (n=3) occurred after PEEP 20 cm H2O. The severity of lung injury was lowest after PEEP of 10 cm H2O in both dependent and non-dependent lung regions, compared with PEEP of 0 or 20 cm H2O. A higher wet-to-dry-weight ratio, indicating worse lung injury, was observed with PEEP of 0 cm H2O. Histological assessment suggested that lung injury was minimised with PEEP of 10 cm H2O. Conclusions During near-apnoeic ventilation and ECMO in experimental severe ARDS, 10 cm H2O PEEP minimised lung injury and improved gas exchange without compromising haemodynamic stability.

Purpose: To evaluate cardiac function in mechanically ventilated patients with COVID-19. Materials and methods: Prospective, cross-sectional multicenter study in four university-affiliated hospitals in Chile. All consecutive patients with COVID-19 ARDS requiring mechanical ventilation admitted between April and July 2020 were included. We performed systematic transthoracic echocardiography assessing right and left ventricular function within 24 h of intubation. Results: 140 patients aged 57 ± 11, 29% female were included. Cardiac output was 5.1 L/min [IQR 4.5–6.2] and 86% of the patients required norepinephrine. ICU mortality was 29% (40 patients). Fifty-four patients (39%) exhibited right ventricle dilation out of whom 20 patients (14%) exhibited acute cor pulmonale (ACP). Eight out of the twenty patients with ACP exhibited pulmonary embolism (40%). Thirteen patients (9%) exhibited left ventricular systolic dysfunction (ejection fraction 2/FiO2 ratio were independent predictors of ICU mortality. Conclusions: Right ventricular dilation is highly prevalent in mechanically ventilated patients with COVID-19 ARDS. Acute cor pulmonale was associated with reduced pulmonary function and, in only 40% of patients, with co-existing pulmonary embolism. Acute cor pulmonale is an independent risk factor for ICU mortality.

Superconducting traveling-wave parametric amplifiers are a promising amplification technology suitable for applications in submillimeter astronomy. Their implementation relies on the use of Floquet transmission lines in order to create strong stopbands to suppress undesired harmonics. In the design process, amplitude equations are used to predict their gain, operation frequency, and bandwidth. However, usual amplitude equations do not take into account the real and imaginary parts of the dispersion and characteristic impedance that results from the use of Floquet lines, hindering reliable design. In order to overcome this limitation, we have used the multiple-scales method to include those effects. We demonstrate that complex dispersion and characteristic impedance have a stark effect on the transmission line's gain, even suppressing it completely in certain cases. The equations presented here can, thus, guide to a better design and understanding of the properties of this kind of amplifiers., 7 pages, 7 figures, submitted to IEEE Transactions on Applied Superconductivity

Summary Members of the genus Pseudomonas inhabit diverse environments, such as soil, water, plants and humans. The variability of habitats is reflected in the diversity of the structure and composition of their genomes. This cosmopolitan bacterial genus includes species of biotechnological, medical and environmental importance. In this study, we report on the most relevant genomic characteristics of Pseudomonas sp. strain ABC1, a siderophore‐producing fluorescent strain recently isolated from soil. Phylogenomic analyses revealed that this strain corresponds to a novel species forming a sister clade of the recently proposed Pseudomonas kirkiae. The genomic information reveals an overrepresented repertoire of mechanisms to hoard iron when compared to related strains, including a high representation of fecI‐fecR family genes related to iron regulation and acquisition. The genome of the Pseudomonas sp. ABC1 contains the genes for non‐ribosomal peptide synthetases (NRPSs) of a novel putative Azotobacter‐related pyoverdine‐type siderophore, a yersiniabactin‐type siderophore and an antimicrobial betalactone; the last two are found only in a limited number of Pseudomonas genomes. Strain ABC1 can produce siderophores in a low‐cost medium, and the supernatants from cultures of this strain promote plant growth, highlighting their biotechnological potential as a sustainable industrial microorganism., ‘Pseudomonas chilensis’ strain ABC1 was fully sequenced. About 5% of the ABC1 genome is devoted to iron acquisition, including 37 ECF sigma factors. Strain ABC1 produces pyoverdine and has the genes for the production of yersiniabactin.

Background A lung rest strategy is recommended during extracorporeal membrane oxygenation in severe acute respiratory distress syndrome (ARDS). However, spontaneous breathing modes are frequently used in this context. The impact of this approach may depend on the intensity of breathing efforts. The authors aimed to determine whether a low spontaneous breathing effort strategy increases lung injury, compared to a controlled near-apneic ventilation, in a porcine severe ARDS model assisted by extracorporeal membrane oxygenation. Methods Twelve female pigs were subjected to lung injury by repeated lavages, followed by 2-h injurious ventilation. Thereafter, animals were connected to venovenous extracorporeal membrane oxygenation and during the first 3 h, ventilated with near-apneic ventilation (positive end-expiratory pressure, 10 cm H2O; driving pressure, 10 cm H2O; respiratory rate, 5/min). Then, animals were allocated into (1) near-apneic ventilation, which continued with the previous ventilatory settings; and (2) spontaneous breathing: neuromuscular blockers were stopped, sweep gas flow was decreased until regaining spontaneous efforts, and ventilation was switched to pressure support mode (pressure support, 10 cm H2O; positive end-expiratory pressure, 10 cm H2O). In both groups, sweep gas flow was adjusted to keep Paco2 between 30 and 50 mmHg. Respiratory and hemodynamic as well as electric impedance tomography data were collected. After 24 h, animals were euthanized and lungs extracted for histologic tissue analysis. Results Compared to near-apneic group, the spontaneous breathing group exhibited a higher respiratory rate (52 ± 17 vs. 5 ± 0 breaths/min; mean difference, 47; 95% CI, 34 to 59; P < 0.001), but similar tidal volume (2.3 ± 0.8 vs. 2.8 ± 0.4 ml/kg; mean difference, 0.6; 95% CI, –0.4 to 1.4; P = 0.983). Extracorporeal membrane oxygenation settings and gas exchange were similar between groups. Dorsal ventilation was higher in the spontaneous breathing group. No differences were observed regarding histologic lung injury. Conclusions In an animal model of severe ARDS supported with extracorporeal membrane oxygenation, spontaneous breathing characterized by low-intensity efforts, high respiratory rates, and very low tidal volumes did not result in increased lung injury compared to controlled near-apneic ventilation. Editor’s Perspective What We Already Know about This Topic What This Article Tells Us That Is New

Background Capillary refill time (CRT) may improve more rapidly than lactate in response to increments in systemic flow. Therefore, it can be assessed more frequently during septic shock (SS) resuscitation. Hyperlactatemia, in contrast, exhibits a slower recovery in SS survivors, probably explained by the delayed resolution of non-hypoperfusion-related sources. Thus, targeting lactate normalization may be associated with impaired outcomes. The ANDROMEDA-SHOCK trial compared CRT- versus lactate-targeted resuscitation in early SS. CRT-targeted resuscitation associated with lower mortality and organ dysfunction; mechanisms were not investigated. CRT was assessed every 30 min and lactate every 2 h during the 8-h intervention period, allowing a first comparison between groups at 2 h (T2). Our primary aim was to determine if SS patients evolving with normal CRT at T2 after randomization (T0) exhibited a higher mortality and organ dysfunction when allocated to the LT arm than when randomized to the CRT arm. Our secondary aim was to determine if those patients with normal CRT at T2 had received more therapeutic interventions when randomized to the LT arm. To address these issues, we performed a post hoc analysis of the ANDROMEDA-SHOCK dataset. Results Patients randomized to the lactate arm at T0, evolving with normal CRT at T2 exhibited significantly higher mortality than patients with normal CRT at T2 initially allocated to CRT (40 vs 23%, p = 0.009). These results replicated at T8 and T24. LT arm received significantly more resuscitative interventions (fluid boluses: 1000[500–2000] vs. 500[0–1500], p = 0.004; norepinephrine test in previously hypertensive patients: 43 (35) vs. 19 (19), p = 0.001; and inodilators: 16 (13) vs. 3 (3), p = 0.003). A multivariate logistic regression of patients with normal CRT at T2, including APACHE-II, baseline lactate, cumulative fluids administered since emergency admission, source of infection, and randomization group) confirmed that allocation to LT group was a statistically significant determinant of 28-day mortality (OR 3.3; 95%CI[1.5–7.1]); p = 0.003). Conclusions Septic shock patients with normal CRT at baseline received more therapeutic interventions and presented more organ dysfunction when allocated to the lactate group. This could associate with worse outcomes.

Motivation Variant calling workflows that utilize a single reference sequence are the de facto standard elementary genomic analysis routine for resequencing projects. Various ways to enhance the reference with pangenomic information have been proposed, but scalability combined with seamless integration to existing workflows remains a challenge. Results We present PanVC with founder sequences, a scalable and accurate variant calling workflow based on a multiple alignment of reference sequences. Scalability is achieved by removing duplicate parts up to a limit into a founder multiple alignment, that is then indexed using a hybrid scheme that exploits general purpose read aligners. Our implemented workflow uses GATK or BCFtools for variant calling, but the various steps of our workflow (e.g. vcf2multialign tool, founder reconstruction) can be of independent interest as a basis for creating novel pangenome analysis workflows beyond variant calling. Availability and implementation Our open access tools and instructions how to reproduce our experiments are available at the following address: https://github.com/algbio/panvc-founders. Supplementary information Supplementary data are available at Bioinformatics online.

Critical care echocardiography is a fundamental tool in the hemodynamic evaluation of critically ill patients and prone position ventilation might limit its application. We aim to evaluate the feasibility of transthoracic echocardiography to assess different measurements performed in prone vs supine position in patients during COVID-19 pandemic to answer our research question: What is the feasibility of classic echocardiographic measurements in COVID-19 patients in prone position ventilation?Patients with covid-19 admitted to ICUs in four academic hospitals with respiratory failure and on mechanical ventilation were evaluated with critical care echocardiography. The first ultrasound assessment was compared between prone and supine patients recording feasibility of several echocardiographic measurements, using Fisher's exact test complementing with Crombach's Alpha.139 patients were included. Sixty-eight (49%) were evaluated in prone position and seventy one (51%) in supine position. Most variables were highly feasible, left ventricular volumes and ejection fraction were more possible to obtain in prone position, while cardiac output was in supine position. Tricuspid regurgitation was the least feasible overall measurement.Prone position ultrasound achieved a high feasibility of measurements compared with supine ultrasound in critically ill patients with COVID-19 respiratory failure and on mechanical ventilation.Post hoc analysis of Echo-COVID study (NTC04628195, registered November 13, 2020, retrospectively registered).

Publisher Copyright: Copyright © 2021 Maarala et al. Computational pan-genomics utilizes information from multiple individual genomes in largescale comparative analysis. Genetic variation between case-controls, ethnic groups, or species can be discovered thoroughly using pan-genomes of such subpopulations. Wholegenome sequencing (WGS) data volumes are growing rapidly, making genomic data compression and indexing methods very important. Despite current space-efficient repetitive sequence compression and indexing methods, the deployed compression methods are often sequential, computationally time-consuming, and do not provide efficient sequence alignment performance on vast collections of genomes such as pan-genomes. For performing rapid analytics with the ever-growing genomics data, data compression and indexing methods have to exploit distributed and parallel computing more efficiently. Instead of strict genome data compression methods, we will focus on the efficient construction of a compressed index for pan-genomes. Compressed hybrid-index enables fast sequence alignments to several genomes at once while shrinking the index size significantly compared to traditional indexes. We propose a scalable distributed compressed hybrid-indexing method for large genomic data sets enabling pan-genome-based sequence search and read alignment capabilities. We show the scalability of our tool, DHPGIndex, by executing experiments in a distributed Apache Spark-based computing cluster comprising 448 cores distributed over 26 nodes. The experiments have been performed both with human and bacterial genomes. DHPGIndex built a BLAST index for n = 250 human pan-genome with an 870:1 compression ratio (CR) in 342 minutes and a Bowtie2 index with 157:1 CR in 397 minutes. For n = 1,000 human pan-genome, the BLAST index was built in 1520 minutes with 532:1 CR and the Bowtie2 index in 1938 minutes with 76:1 CR. Bowtie2 aligned 14.6 GB of paired-end reads to the compressed (n = 1,000) index in 31.7 minutes on a single node. Compressing n = 13,375,031 (488 GB) GenBank database to BLAST index resulted in CR of 62:1 in 575 minutes. BLASTing 189,864 Crispr-Cas9 gRNA target sequences (23 MB in total) to the compressed index of human pan-genome (n = 1,000) finished in 45 minutes on a single node. 30 MB mixed bacterial sequences were (n = 599) were blasted to the compressed index of 488 GB GenBank database (n = 13,375,031) in 26 minutes on 25 nodes. 78 MB mixed sequences (n = 4,167) were blasted to the compressed index of 18 GB E. coli sequence database (n = 745,409) in 5.4 minutes on a single node

Purpose To characterize the microvascular effects of a brief period of hyperoxia, in patients with septic shock and in healthy volunteers. Materials and methods In 20 patients with septic shock, we assessed systemic hemodynamics, sublingual microcirculation by SDF-videomicroscopy, and skin perfusion by capillary refill time (CRT), central-peripheral temperature (ΔT°), and perfusion index. Measurements were performed at baseline and after 5 min of inspired oxygen fraction of 1.00. Additionally, we studied 8 healthy volunteers, in whom hyperoxia was prolonged to 30 min. Results In septic patients, hyperoxia increased mean arterial pressure and systemic vascular resistance, but cardiac output remained unchanged. The only significant change in sublingual microcirculation was a decreased heterogeneity flow index (1.03 [1.01–1.07] vs 1.01 [0.34–1.05], P = .002). Perfused vascular density (13.1 [12.0–15.0] vs 14.0 [12.2–14.8] mm/mm2, P = .21) and the other sublingual microvascular variables were unmodified. CRT and ΔT° did not change but perfusion index slightly decreased. In healthy volunteers, sublingual microcirculation and skin perfusion were stable. Conclusions Short-term hyperoxia induced systemic cardiovascular changes but was not associated with noticeable derangement in sublingual microcirculation and skin perfusion. Nevertheless, longer exposures to hyperoxia might have produced different results.

A novel continuous flow system with “flat geometry” composed by two completely mixed aerobic tanks in series and a settler was used to promote the formation of aerobic granular sludge. Making similarities of this system with a typical sequencing batch reactor (SBR), for aerobic granules cultivation, the value of the tank 1/tank 2 vol ratio and the biomass recirculation rate would correspond with the feast/famine length ratio and the length of the operational cycle, respectively, while the settler upflow liquid velocity imposed would be related to the settling time. From the three experiments performed the best results were obtained when the tank 1/tank 2 vol ratio was of 0.28, the sludge recycling ratio of 0.25 and the settler upflow velocity of 2.5 m/h. At these conditions the aggregates had settling velocities between 29 and 113 m/h, sludge volume index at 10 min (SVI10) of 70 mL/g TSS and diameters between 1.0 and 5.0 mm.

The draft genome sequence of Streptomyces fildesensis strain INACH3013, a psychrotrophic bacterium isolated from Northwest Antarctic soil, was reported. The genome sequence totaling 9,306,785 bp resulted from 122 contigs characterized by a GC content of 70.55%.

Despite being a critical environmental problem, soil pollution is not usually considered as a relevant issue by the general public. This disinterest derives from traditional procedures to assess soil pollution that are quite complex and costly, not considering any form of citizen involvement. Seeking to challenge this situation, the project “Nuestros Suelos” (Our Soil) aimed at designing and testing a low-cost participative soil pollution assessment toolkit. The final prototype included several participative modules, going from an assessment of the history of local soils to measuring heavy metals such as Arsenic and Copper. Tested with low-income communities in northern Chile, the toolkit was able not only to produce multiple kinds of data but also a public that started to understand and care about the issue.

A two-stage system (partial nitritation (PN) and anammox processes) was used to remove nitrogen from the dewatering liquor originating from the thermal hydrolysis/anaerobic digestion (THP/AD) of municipal WWTP sludge. Two strategies were tested to start up the PN reactor: 1) maintaining a fixed hydraulic retention time (HRT) and increasing the ammonium loading rate (ALR) by decreasing the feeding dilution ratio and 2) feeding undiluted dewatering liquor and gradually decreasing the HRT. With diluted feeding, the reactor performance had destabilization episodes that were statistically correlated with the application of high specific ammonium (> 0.6 g NH4+-N/(g TSS·d)) and organic (> 0.7 g COD/(g TSS·d)) loading rates. The second strategy allowed stable PN reactor operation while treating ALR up to 4.8 g NH4+-N/(L·d) and demonstrating that dilution of THP/AD effluents is not required. The operating conditions promoted the presence of free nitrous acid levels (> 0.14 mg HNO2-N/L) inside the PN reactor that inhibited the proliferation of nitrite oxidizing bacteria. Batch activity tests showed that the inhibitory effects of organic compounds present in the THP/AD dewatering liquor on the ammonia oxidizing bacteria activity can be removed in the PN reactor. Thus, aerobic pretreatment would not be necessary when two-stage systems are used. The PN reactor effluent was successfully treated by an anammox reactor. An economic analysis showed that using two-stage systems is advantageous for treating THP/AD dewatering liquor. The implementation of an aerobic pre-treatment unit is recommended for WWTPs capacities higher than 5·105 inhabitants equivalent when one-stage systems are used This research was funded by the Chilean Government through the Projects ANID/FONDECYT/1200850 and CRHIAM Centre grant number ANID/FONDAP/15130015, by the Spanish Government through TREASURE [CTQ2017-83225-C2-1-R] and by the European Commission LIFE ZERO WASTE WATER [LIFE19ENV/ES/000631] projects. The authors from Universidade de Santiago de Compostela belong to CRETUS Strategic Partnership [ED431E 2018/01] and the Galician Competitive Research Group [GRC ED431C 2017/29]. All the Spanish programs are co-funded by FEDER (EU) 2023-07-15 SI

Here, we report the complete genome sequence of

Here, we report the complete genome sequence of Pseudomonas chilensis strain ABC1, which was isolated from a soil interstitial water sample collected at the University Adolfo Ibañez, Valparaiso, Chile. We assembled PacBio reads into a single closed contig with 209× mean coverage, yielding a 4,035,896-bp sequence with 62% GC content and 3,555 predicted genes.

High-throughput sequencing (HTS) technologies have enabled rapid sequencing of genomes and large-scale genome analytics with massive data sets. Traditionally, genetic variation analyses have been based on the human reference genome assembled from a relatively small human population. However, genetic variation could be discovered more comprehensively by using a collection of genomes i.e., pan-genome as a reference. The pan-genomic references can be assembled from larger populations or a specific population under study. Moreover, exploiting the pan-genomic references with current bioinformatics tools requires efficient compression and indexing methods. To be able to leverage the accumulating genomic data, the power of distributed and parallel computing has to be harnessed for the new genome analysis pipelines. We propose a scalable distributed pipeline, PanGenSpark, for compressing and indexing pan-genomes and assembling a reference genome from the pan-genomic index. We experimentally show the scalability of the PanGenSpark with human pan-genomes in a distributed Spark cluster comprising 448 cores distributed to 26 computing nodes. Assembling a consensus genome of a pan-genome including 50 human individuals was performed in 215 min and with 500 human individuals in 1468 min. The index of 1.41 TB pan-genome was compressed into a size of 164.5 GB in our experiments.