Nitrogen sensing and regulatory networks: it's about time and space.

A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its "hit-and-run" mode of target gene regulation, and temporal transcriptional cascade identified by "network walking." Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.

Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes.

BACKGROUND: To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order. RESULTS: We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group. CONCLUSIONS: The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.

Nakazawaea atacamensis f.a., sp. nov. a novel nonconventional fermentative ascomycetous yeast species from the Atacama Desert.

In this study, we describe Nakazawaea atacamensis f. a., sp. nov., a novel species obtained from Neltuma chilensis plant samples in Chile's hyperarid Atacama Desert. In total, three strains of N. atacamensis were obtained from independent N. chilensis samples (synonym Prosopis chilensis, Algarrobo). Two strains were obtained from bark samples, while the third strain was obtained from bark-exuded gum from another tree. The novel species was defined using molecular characteristics and subsequently characterized with respect to morphological, physiological, and biochemical properties. A neighbor-joining analysis using the sequences of the D1/D2 domains of the large subunit ribosomal RNA gene revealed that N. atacamensis clustered with Nakazawaea pomicola. The sequence of N. atacamensis differed from closely related species by 1.3%-5.2% in the D1/D2 domains. A phylogenomic analysis based on single-nucleotide polymorphism's data confirms that the novel species belongs to the genus Nakazawaea, where N. atacamensis clustered with N. peltata. Phenotypic comparisons demonstrated that N. atacamensis exhibited distinct carbon assimilation patterns compared to its related species. Genome sequencing of the strain ATA-11A-BT revealed a genome size of approximately 12.4 Mbp, similar to other Nakazawaea species, with 5116 protein-coding genes annotated using InterProScan. In addition, N. atacamensis exhibited the capacity to ferment synthetic wine must, representing a potential new yeast for mono or co-culture wine fermentations. This comprehensive study expands our understanding of the genus Nakazawaea and highlights the ecological and industrial potential of N. atacamensis in fermentation processes. The holotype of N. atacamensis sp. nov. is CBS 18375T . The Mycobank number is MB 849680.

Dynamic changes in mRNA nucleocytoplasmic localization in the nitrate response of Arabidopsis roots.

Nitrate is a nutrient and signal that regulates gene expression. The nitrate response has been extensively characterized at the organism, organ, and cell-type-specific levels, but intracellular mRNA dynamics remain unexplored. To characterize nuclear and cytoplasmic transcriptome dynamics in response to nitrate, we performed a time-course expression analysis after nitrate treatment in isolated nuclei, cytoplasm, and whole roots. We identified 402 differentially localized transcripts (DLTs) in response to nitrate treatment. Induced DLT genes showed rapid and transient recruitment of the RNA polymerase II, together with an increase in the mRNA turnover rates. DLTs code for genes involved in metabolic processes, localization, and response to stimulus indicating DLTs include genes with relevant functions for the nitrate response that have not been previously identified. Using single-molecule RNA FISH, we observed early nuclear accumulation of the NITRATE REDUCTASE 1 (NIA1) transcripts in their transcription sites. We found that transcription of NIA1, a gene showing delayed cytoplasmic accumulation, is rapidly and transiently activated; however, its transcripts become unstable when they reach the cytoplasm. Our study reveals the dynamic localization of mRNAs between the nucleus and cytoplasm as an emerging feature in the temporal control of gene expression in response to nitrate treatment in Arabidopsis roots.

Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert.

The best ideotypes are under mounting pressure due to increased aridity. Understanding the conserved molecular mechanisms that evolve in wild plants adapted to harsh environments is crucial in developing new strategies for agriculture. Yet our knowledge of such mechanisms in wild species is scant. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama and phylogenetically related species that do not live in Atacama (sister species). We analyzed reaction enrichment to understand the commonalities and differences of Atacama plants. To gain insights into the mechanisms that ensure survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and sister species. We found biochemical convergences characterized by reactions enriched in at least 50% of the Atacama species, pointing to potential advantages against drought and nitrogen starvation, for instance. These findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses. Convergent adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.

The Characterization of a Novel PrMADS11 Transcription Factor from Pinus radiata Induced Early in Bent Pine Stem.

A novel MADS-box transcription factor from Pinus radiata D. Don was characterized. PrMADS11 encodes a protein of 165 amino acids for a MADS-box transcription factor belonging to group II, related to the MIKC protein structure. PrMADS11 was differentially expressed in the stems of pine trees in response to 45° inclination at early times (1 h). Arabidopsis thaliana was stably transformed with a 35S::PrMADS11 construct in an effort to identify the putative targets of PrMADS11. A massive transcriptome analysis revealed 947 differentially expressed genes: 498 genes were up-regulated, and 449 genes were down-regulated due to the over-expression of PrMADS11. The gene ontology analysis highlighted a cell wall remodeling function among the differentially expressed genes, suggesting the active participation of cell wall modification required during the response to vertical stem loss. In addition, the phenylpropanoid pathway was also indicated as a PrMADS11 target, displaying a marked increment in the expression of the genes driven to the biosynthesis of monolignols. The EMSA assays confirmed that PrMADS11 interacts with CArG-box sequences. This TF modulates the gene expression of several molecular pathways, including other TFs, as well as the genes involved in cell wall remodeling. The increment in the lignin content and the genes involved in cell wall dynamics could be an indication of the key role of PrMADS11 in the response to trunk inclination.

Drug rash with eosinophilia and systemic symptoms to anti-tuberculosis therapy: A retrospective review of inpatients at an academic medical centre in the United States.

This retrospective cohort study analyzes the presentation, diagnosis, and treatment outcomes of patients who developed drug rash with eosinophilia and systemic symptoms (DRESS) to tuberculosis (TB) therapy in a TB non-endemic region. Anti-TB agents represented 7.5% of all antimicrobial-induced DRESS cases, and rifampin was the most commonly implicated agent among drugs used to treat TB.

Recent advances in local and systemic nitrate signaling in Arabidopsisthaliana.

Nitrate is the most abundant form of inorganic nitrogen in aerobic soils, serving both as a nutrient and a signaling molecule. Central to nitrate signaling in higher plants is the intricate balance between local and systemic signaling and response pathways. The interplay between local and systemic responses allows plants to regulate their global gene expression, metabolism, physiology, growth, and development under fluctuating nitrate availability. This review offers an overview of recent discoveries regarding new players on nitrate sensing and signaling, in local and systemic contexts in Arabidopsis thaliana. Additionally, it addresses unanswered questions that warrant further investigation for a better understanding of nitrate signaling and responses in plants.

Exploring the effects of competition and predation on the success of biological invasion through mathematical modeling.

Biological invasions are a major cause of species extinction and biodiversity loss. Exotic predators are the type of introduced species that have the greatest negative impact, causing the extinction of hundreds of native species. Despite this, they continue to be intentionally introduced by humans. Understanding the causes that determine the success of these invasions is a challenge within the field of invasion biology. Mathematical models play a crucial role in understanding and predicting the behavior of exotic species in different ecosystems. This study examines the effect of predation and competition on the invasion success of an exotic generalist predator in a native predator-prey system. Considering that the exotic predator both consumes the native prey and competes with the native predator, it is necessary to study the interplay between predation and competition, as one of these interspecific interactions may either counteract or contribute to the impact of the other on the success of a biological invasion. Through a mathematical model, represented by a system of ordinary differential equations, it is possible to describe four different scenarios upon the arrival of the exotic predator in a native predator-prey system. The conditions for each of these scenarios are described analytically and numerically. The numerical simulations are performed considering the American mink (Mustela vison), an invasive generalist predator. The results highlight the importance of considering the interplay between interspecific interactions for understanding biological invasion success.

Developmental trajectories of EEG aperiodic and periodic components in children 2-44 months of age.

The development of neural circuits has long-lasting effects on brain function, yet our understanding of early circuit development in humans remains limited. Here, periodic EEG power features and aperiodic components were examined from longitudinal EEGs collected from 592 healthy 2-44 month-old infants, revealing age-dependent nonlinear changes suggestive of distinct milestones in early brain maturation. Developmental changes in periodic peaks include (1) the presence and then absence of a 9-10 Hz alpha peak between 2-6 months, (2) nonlinear changes in high beta peaks (20-30 Hz) between 4-18 months, and (3) the emergence of a low beta peak (12-20 Hz) in some infants after six months of age. We hypothesized that the emergence of the low beta peak may reflect maturation of thalamocortical network development. Infant anesthesia studies observe that GABA-modulating anesthetics do not induce thalamocortical mediated frontal alpha coherence until 10-12 months of age. Using a small cohort of infants (n = 23) with EEG before and during GABA-modulating anesthesia, we provide preliminary evidence that infants with a low beta peak have higher anesthesia-induced alpha coherence compared to those without a low beta peak.

Impact of Fee For Service on the Efficiency and Survival of Seguro Popular's Patients With Acute Lymphoblastic Leukemia in Mexico.

PURPOSE: Cost containment and efficiency in the provision of health care are primary concerns for health systems that aim to provide affordable, high-quality care. Between 2005 and 2015, Seguro Poplar's Fund against Catastrophic Expenditures (FPGC) funded ALL treatment in Mexico. Before January 1, 2011, FPGC reimbursed a fixed amount per patient according to risk. In 2011, the per capita reimbursement method changed to fee for service. We used this natural experiment to estimate the impact of the reimbursement policy change on average expenditure and quality of care for ALL treatment in Mexico. METHODS: We used nationwide reimbursement data from the Seguro Poplar's FPGC from 2005 to 2015. We created a patient cohort to assess 3-year survival and estimate the average reimbursement before and after the fee-for-service policy. We examined survival and expenditure impacts, controlling for patients' and providers' characteristics, including sex, risk (standard and high), the volume of patients served, type of institution (federally funded v other), and level of care. To quantify the impact, we used a regression discontinuity approach. RESULTS: The average reimbursement for standard-risk patients in the 3-year survival cohort was $16,512 US dollars (USD; 95% CI, 16,042 to 17,032) before 2011 and $10,205 USD (95% CI, 4,659 to 12,541) under the fee-for-service reimbursement scheme after 2011. The average annual reimbursement per patient decreased by 136% among high-risk patients. The reduction was also significant for the standard-risk cohort, although the magnitude was substantially smaller (34%). CONCLUSION: As Mexico's government is currently restructuring the health system, our study provides evidence of the efficiency and effectiveness of the funding mechanism in the Mexican context. It also serves as a proof of concept for using administrative data to evaluate economic performance and quality of care of publicly funded health programs.

An Open One-Step RT-qPCR for SARS-CoV-2 detection.

The COVID-19 pandemic has resulted in millions of deaths globally, and while several diagnostic systems were proposed, real-time reverse transcription polymerase chain reaction (RT-PCR) remains the gold standard. However, diagnostic reagents, including enzymes used in RT-PCR, are subject to centralized production models and intellectual property restrictions, which present a challenge for less developed countries. With the aim of generating a standardized One-Step open RT-qPCR protocol to detect SARS-CoV-2 RNA in clinical samples, we purified and tested recombinant enzymes and a non-proprietary buffer. The protocol utilized M-MLV RT and Taq DNA pol enzymes to perform a Taqman probe-based assay. Synthetic RNA samples were used to validate the One-Step RT-qPCR components, demonstrating sensitivity comparable to a commercial kit routinely employed in clinical settings for patient diagnosis. Further evaluation on 40 clinical samples (20 positive and 20 negative) confirmed its comparable diagnostic accuracy. This study represents a proof of concept for an open approach to developing diagnostic kits for viral infections and diseases, which could provide a cost-effective and accessible solution for less developed countries.

Childhood cancer mutagenesis caused by transposase-derived PGBD5.

Genomic rearrangements are a hallmark of most childhood tumors, including medulloblastoma, one of the most common brain tumors in children, but their causes remain largely unknown. Here, we show that PiggyBac transposable element derived 5 (Pgbd5) promotes tumor development in multiple developmentally accurate mouse models of Sonic Hedgehog (SHH) medulloblastoma. Most Pgbd5-deficient mice do not develop tumors, while maintaining normal cerebellar development. Ectopic activation of SHH signaling is sufficient to enforce cerebellar granule cell progenitor-like cell states, which exhibit Pgbd5-dependent expression of distinct DNA repair and neurodevelopmental factors. Mouse medulloblastomas expressing Pgbd5 have increased numbers of somatic structural DNA rearrangements, some of which carry PGBD5-specific sequences at their breakpoints. Similar sequence breakpoints recurrently affect somatic DNA rearrangements of known tumor suppressors and oncogenes in medulloblastomas in 329 children. This identifies PGBD5 as a medulloblastoma mutator and provides a genetic mechanism for the generation of oncogenic DNA rearrangements in childhood cancer.

DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species

BACKGROUND: Despite representing the largest fraction of animal life, the number of insect species whose genome has been sequenced is barely in the hundreds. The order Dermaptera (the earwigs) suffers from a lack of genomic information despite its unique position as one of the basally derived insect groups and its importance in agroecosystems. As part of a national educational and outreach program in genomics, a plan was formulated to engage the participation of high school students in a genome sequencing project. Students from twelve schools across Chile were instructed to capture earwig specimens in their geographical area, to identify them and to provide material for genome sequencing to be carried out by themselves in their schools. RESULTS: The school students collected specimens from two cosmopolitan earwig species: Euborellia annulipes (Fam. Anisolabididae) and Forficula auricularia (Fam. Forficulidae). Genomic DNA was extracted and, with the help of scientific teams that traveled to the schools, was sequenced using nanopore sequencers. The sequence data obtained for both species was assembled and annotated. We obtained genome sizes of 1.18 Gb (F. auricularia) and 0.94 Gb (E. annulipes) with the number of predicted protein coding genes being 31,800 and 40,000, respectively. Our analysis showed that we were able to capture a high percentage (≥ 93%) of conserved proteins indicating genomes that are useful for comparative and functional analysis. We were also able to characterize structural elements such as repetitive sequences and non-coding RNA genes. Finally, functional categories of genes that are overrepresented in each species suggest important differences in the process underlying the formation of germ cells, and modes of reproduction between them, features that are one of the distinguishing biological properties that characterize these two distant families of Dermaptera. CONCLUSIONS: This work represents an unprecedented instance where the scientific and lay community have come together to collaborate in a genome sequencing project. The versatility and accessibility of nanopore sequencers was key to the success of the initiative. We were able to obtain full genome sequences of two important and widely distributed species of insects which had not been analyzed at this level previously. The data made available by the project should illuminate future studies on the Dermaptera.

Efecto del óxido nítrico inhalado en la mecánica ventilatoria y oxigenación de pacientes con hipoxemia grave refractaria a prono prolongado y bloqueo neuromuscular secundario a infección por SARS-CoV-2 / Effect of inhaled nitric oxide on ventilatory mechanics and oxygenation of patients with severe hypoxemia refractory to prolonged prone and neuromuscular blockade secondary to SARS-CoV-2 / Efeito do óxido nítrico inalado na mecânica ventilatória e oxigenação de pacientes com hipoxemia grave refratária a pronação prolongada e bloqueio neuromuscular secundário à infecção por SARS-CoV-2

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Abstract: Introduction: Among the patients infected with SARS-CoV-2, 14.6% were admitted to intensive care unit. this 29 to 75% required invasive mechanical ventilation with an associated mortality of 12 to 81%. Acute respiratory distress syndrome (ARDS) is the most serious form of presentation. The pathophysiology of ARDS secondary to SARS-CoV-2 differs from conventional causes. It presents dysregulation in hypoxic pulmonary vasoconstriction, secondary acute pulmonary hypertension and microthrombotic phenomena. The development of refractory severe hypoxemia (PaO2 < 60 mmHg or PaO2/FiO2 < 100 mmHg, with FiO2 80 to 100%, with PEEP > 10 to 20 cmH2O for at least 10 to 12 hours) constitutes the scenario of maximum severity with an associated mortality of 71 to 94%. The use of rescue strategies that impact on the specific pathophysiology of this entity such as the use of inhaled nitric oxide, neuromuscular blockade and prone ventilation have emerged as therapeutic targets of interest. Protective mechanical ventilation (plateau pressure [Pplat] < 27 cmH2O and driving pressure [DP] < 15 cmH2O) continues to be the cornerstone of the management. Objectives: To determine whether there is an association between the use of inhaled nitric oxide and prone ventilation with ventilatory mechanics in patients with severe refractory hypoxemia secondary to SARS-CoV-2 infection. Material and methods: A historical, retrospective, descriptive, comparative and retrolective cohort study was carried out. Data from the records of patients admitted to the Respiratory ICU of the ABC Medical Center with a diagnosis of ARDS secondary to SARS-CoV-2 infection who required iNO and mechanical ventilation in prone from April 1 to December 31, 2020 were analyzed. A univariate analysis was performed, the statistical analysis was performed in SPSS v 21, measures of trend, dispersion were analyzed as well as the analysis of risk factors with Student's t test and χ2. Results: A total of 108 patients were analyzed, of which 54 received iNO, neuromuscular blockade and prone and 54 only neuromuscular blockade and prone ventilation. 81.5% (n = 88) were men. The most common comorbidity was diabetes mellitus in 51.9% (n = 56). The increase in oxygenation (delta PaO2/FiO2) was with a median of 31.9 ± 15.2 mmHg in the iNO group and 52.9 ± 16.74 mmHg in the control group (p = 0.001). The postintervention Pplat in the iNO group was 26.3 ± 3 and 34.5 ± 1.9 cmH2O in the control group (p = 0.792). The preintervention DP in the iNO group was 17.2 ± 3.9 and 13.4 ± 2.8 cmH2O in control group vs 13.1 ± 1.29 and 12 ± 1.92 cmH2O after the intervention (p = 0.001). Conclusions: The use of iNO in patients with severe hypoxemia refractory to prone ventilation and neuromuscular blockade did not produce a statistically significant improvement in oxygenation, however it allowed to reprogram the ventilatory support to keep the patient in goals of alveolar protection.

Resumo: Introdução: 14.6% dos pacientes infectados com SARS-CoV-2 são internados em terapia intensiva. Destes, 29 a 75% necessitam de ventilação mecânica invasiva com mortalidade associada de 12 a 81%. A síndrome do desconforto respiratório agudo (SDRA) é a forma mais grave de apresentação. A fisiopatologia da SDRA secundária ao SARS-CoV-2 difere das causas convencionais. Apresenta desregulação na vasoconstrição pulmonar hipóxica, hipertensão pulmonar aguda secundária e fenômenos microtrombóticos. O desenvolvimento de hipoxemia grave refratária (PaO2 < 60 mmHg ou PaO2/FiO2 < 100 mmHg, com FiO2 de 80 a 100%, PEEP > 10 a 20 cmH2O por pelo menos 10 a 12 horas) constitui o cenário mais grave com mortalidade associada de 71 a 94%. O uso de estratégias de resgate que impactam na fisiopatologia específica dessa entidade, como o uso de óxido nítrico inalatório (NOi), bloqueio neuromuscular e ventilação prona, surgiram como alvos terapêuticos de interesse. A ventilação mecânica protetora (Pressão de Platô [PPLAT] < 27 cmH2O e Pressão de Condução [CP] < 15 cmH2O) continua sendo a base de seu manejo. Objetivo: Determinar se existe associação entre o uso de óxido nítrico inalatório e ventilação prona prolongada com mecânica ventilatória em pacientes com hipoxemia refratária grave secundária à infecção por SARS-CoV-2. Material e métodos: Realizou-se um estudo de coorte histórico, retrospectivo, descritivo, comparativo e retroletivo. Analisaram-se dados dos prontuários de pacientes internados na UTI Respiratória do Centro Médico ABC com diagnóstico de SDRA secundária à infecção por SARS-CoV-2 que necessitaram de óxido nítrico inalatório e ventilação mecânica prona no período de 1o de abril a 31 de dezembro de 2020. Realizou-se uma análise univariada , a análise estatística foi realizada no SPSS v 21, foram analisadas as medidas de tendência e dispersão, assim como a análise dos fatores de risco com teste t de Student e χ2. Resultados: Analisaram-se 108 pacientes, dos quais 54 receberam NOi, bloqueio neuromuscular e prono e 54 apenas bloqueio neuromuscular e ventilação prona. 81.5% (n = 88) eram homens. A comorbidade mais comum foi diabetes mellitus em 51.9% (n = 56). O aumento da oxigenação (Delta PaO2/FiO2) foi com mediana de 31.9 ± 15.2 mmHg no grupo NOi e 52.9 ± 16.74 mmHg no grupo controle (p = 0.001). A PPLAT após a intervenção no grupo NOi foi de 26.3 ± 3 e 34.5 ± 1.9 cmH2O no grupo controle (p = 0.792). A PC antes da intervenção no grupo NOi foi de 17.2 ± 3.9 e 13.4 ± 2.8 cmH2O no grupo controle vs 13.1 ± 1.29 e 12 ± 1.92 cmH2O após a intervenção (p = 0.001). Conclusões: O uso de NOi em pacientes com hipoxemia grave refratária à ventilação em pronação e bloqueio neuromuscular não produziu melhora estatisticamente significativa na oxigenação, porém permitiu que o suporte ventilatório fosse reprogramado para manter as metas de proteção alveolar do paciente.

Factores de riesgo para lesión renal aguda y terapia de reemplazo renal en pacientes con ventilación mecánica invasiva y COVID-19 / Risk factors for acute kidney injury and renal replacement therapy in severe critically ill patients with COVID-19 under invasive mechanical ventilation / Fatores de risco para lesão renal aguda e terapia de substituição renal em pacientes com ventilação mecânica invasiva e COVID-19

Resumen: Introducción: Desde diciembre de 2019, cuando el coronavirus respiratorio tipo 2 y el síndrome de insuficiencia respiratoria agudo (SDRA) por coronavirus tipo 2 (enfermedad por coronavirus 2019 [COVID-19]), se desarrolló en Wuhan, China, se ha convertido en una pandemia mundial, con 105'333.798 casos reportados el 04 de febrero de 2021. El 27 de febrero de 2020, la Ciudad de México reportó el primer caso de COVID-19, seguido de un crecimiento masivo de infecciones en todo el país. El número total de casos hasta hoy es de 1,886.245 con 81,223 casos activos estimados. El 18.77% de los pacientes han requerido hospitalización. El número total de muertes es de 164.290, con una estimación de 184.125. La lesión renal aguda (LRA) se encontró en 28% de los pacientes hospitalizados y en 46% de los pacientes en estado crítico, contribuyendo a una mortalidad significativamente mayor. La identificación de los factores de riesgo es importante para orientar la toma de decisiones tempranas en la clasificación de los pacientes para una monitorización más intensiva y prevenir el aumento de la mortalidad. Objetivo: Analizar el nivel de presión positiva al final de la espiración (PEEP) y factores inflamatorios que intervienen en el desarrollo de LRA e inicio de terapia de reemplazo renal (TRR) en pacientes con COVID-19. Material y métodos: Se realizó un estudio observacional, transversal y retrolectivo en pacientes con ventilación mecánica con SARS-CoV-2 que presentaron LRA y necesidad de TRR ingresados en la Unidad de Cuidados Intensivos Respiratorios del Centro Médico ABC. Se realizó análisis estadístico de medidas de tendencia central, descriptivo; para la identificación de la variable con mayor impacto para el desarrollo de LRA y terapia dialítica se realizó factor predictivo positivo, prueba Pearson para correlacionar con terapia de reemplazo renal. El estudio se aprobó por el Comité de Ética del Centro Médico ABC, Ciudad de México (Folio: ABC TAEABC-22-117). Resultados: Se analizaron en total 210 pacientes con ventilación mecánica con SARS-CoV-2 en la Unidad de Cuidados Intensivos Respiratorios del Centro Médico ABC, de los cuales, 51 (24.17%) desarrollaron LRA y 21 requirieron TRR. Se realizó una curva ROC para predecir el factor con mayor riesgo para presentar LRA, encontrando diferencias significativas en IL-6 con un área bajo la curva ROC de 0.909 (CI: 0.86-0.95). También se encontró significancia estadística en LRA a partir de PEEP por arriba de 13 cmH2O y terapia de reemplazo renal con PEEP > 15 cmH2O. Conclusión: Se encontró una correlación de niveles altos de PEEP y lesión renal aguda. Los marcadores inflamatorios al ingreso del paciente (específicamente IL-6) son parámetros adecuados para guiar el tratamiento; sin embargo, también son de utilidad para orientar a un pronóstico.

Abstract: Introduction: Since December 2019, when respiratory coronavirus type 2 and acute respiratory failure syndrome (ARDS) due to coronavirus type 2 (coronavirus disease 2019 [COVID-19]), developed in Wuhan, China, it has become a global pandemic, with 105,333,798 cases reported on February 4, 2021. On February 27, 2020, Mexico City reported the first case of COVID-19, followed by a massive growth of infections across the country. The total number of cases today is 1,886,245 with 81,223 estimated active cases. 18.77% of patients have required hospitalization. The total number of deaths is 164,290 with an estimated 184,125. AKI was found in 28% of hospitalized patients and 46% of critically ill patients, contributing to significantly higher mortality. Identification of risk factors is important to guide early decision making in triaging patients for more intensive monitoring and prevent increased mortality. Objective: To analyze the level of PEEP and inflammatory factors involved in the development of AKI and onset of RRT in patients with COVID-19. Material and methods: An observational, cross-sectional and retrolective study was performed in mechanically ventilated patients with SARS-CoV-2 who presented AKI and need for RRT admitted to the respiratory intensive care unit of the ABC Medical Center. Statistical analysis of measures of central tendency, descriptive; for the identification of the variable with the greatest impact for the development of AKI and dialytic therapy, a positive predictive factor was performed, Pearson test to correlate with renal replacement therapy. The study was approved by the ethics committee of the ABC Medical Center, Mexico City (Number: ABC TAEABC-22-117). Results: A total of 210 mechanically ventilated patients with SARS-CoV-2 in the Respiratory Intensive Care Unit of the ABC Medical Center were analyzed, of whom 51 patients (24.17%) developed AKI and 21 patients required RRT. An ROC curve was performed to predict the factor with the highest risk of developing AKI, finding significant differences in IL-6 with an area under the ROC curve of 0.909 (CI: 0.86-0.95). Statistical significance was found in AKI with PEEP above 13cmH2O and renal replacement therapy with PEEP > 15cmH2O. Conclusion: A correlation was found between high PEEP levels and acute kidney injury. Inflammatory markers at patient admission (specifically IL-6) are adequate parameters to guide treatment; however, they are also useful to guide prognosis.

Resumo: Introdução: Desde dezembro de 2019, quando o coronavírus respiratório tipo 2 e a síndrome do desconforto respiratório agudo do coronavírus (SDRA) (doença de coronavírus 2019 [COVID-19]), desenvolvida em Wuhan, China, tornou-se uma pandemia em todo o mundo, com 105'333.798 casos relatados em fevereiro 4, 2021. Em 27 de fevereiro de 2020, a Cidade do México relatou o primeiro caso de COVID-19, seguido por um crescimento maciço de infecções em todo o país. O número total de casos até o momento é de 1,886.245, com uma estimativa de 81,223 casos ativos. 18.77% dos pacientes necessitaram de internação. O número total de óbitos é de 164.290, com estimativa de 184.125. A LRA foi encontrada em 28% dos pacientes hospitalizados e 46% dos pacientes críticos, contribuindo para uma mortalidade significativamente maior. A identificação dos fatores de risco é importante para orientar a tomada de decisão precoce na classificação dos pacientes para monitoramento mais intensivo e para evitar o aumento da mortalidade. Objetivo: Analisar o nível de PEEP e fatores inflamatórios envolvidos no desenvolvimento de LRA e início de TRS em pacientes com COVID-19. Material e métodos: Realizou-se um estudo observacional, transversal e retroletivo em pacientes ventilados mecanicamente com SARS-CoV-2 que apresentavam LRA e necessidade de TRS internados na unidade de terapia intensiva respiratória do Centro Médico ABC. Foi realizado análise estatística de medidas de tendência central, descritiva; para identificar a variável de maior impacto no desenvolvimento de LRA e terapia dialítica, realizou-se fator preditivo positivo, o teste de Pearson para correlacionar com a terapia renal substitutiva. O estudo foi aprovado pelo comitê de ética do Centro Médico ABC, Cidade do México (Folio: ABC TAEABC-22-117). Resultados: Foram analisados um total de 210 pacientes com ventilação mecânica com SARS-CoV-2 na unidade de terapia intensiva respiratória do Centro Médico ABC, dos quais 51 pacientes (24.17%) desenvolveram LRA e 21 pacientes requereram TRS. Realizou-se uma curvatura ROC para prever o fator com maior risco para apresentar LRA encontrando diferenças significativas em IL-6 com uma área sob a curvatura ROC de 0.909(CI: 0.86-0.95). Da mesma forma, foi encontrada significância estatística na LRA por PEEP acima de 13 cmH2O e terapia renal substitutiva com PEEP > 15 cmH2O. Conclusão: Encontrou-se uma correlação entre níveis elevados de PEEP e lesão renal aguda. Marcadores inflamatórios na admissão do paciente (especificamente IL-6) são parâmetros adequados para orientar o tratamento; no entanto, eles também são úteis para orientar uma previsão.

Respuesta inmune e inmunosupresión en pacientes con ventilación mecánica por infección por SARS-CoV-2 / Immune response and immune suppression in patients with mechanical ventilation secondary to SARS-CoV-2 infection / Resposta imune e imunossupressão em pacientes com ventilação mecânica devido à infecção por SARS-CoV-2

Resumen Introducción: La pandemia por SARS-CoV-2 ha inspirado intriga sobre la respuesta inmune a dicho virus, especialmente en pacientes graves con síndrome de dificultad respiratoria aguda (SDRA). Este estudio describe el comportamiento de la respuesta inmune, la inmunosupresión y sus desenlaces en los pacientes con ventilación mecánica (VM). Material y métodos: Cohorte prospectiva. Del 23 de marzo al 31 de diciembre de 2020 se recolectó información basal, parámetros ventilatorios, gasométricos y estudios de laboratorio de todos los pacientes mayores de 18 años que recibieron VM por COVID-19 con registros hasta el día 15 de VM. Se dividieron los grupos en pacientes vivos a los 90 días y defunciones. Resultados: Registramos 218 pacientes, con mortalidad de 23%. En el día 1 de VM, los pacientes no presentaron diferencias en conteos celulares o reactantes de fase aguda, excepto dímero D de 1,020 (705-1,711) vs 1,328 (940-2,340) ng/dL p = 0.035. En el análisis de regresión lineal de efectos mixtos se observaron diferencias cronológicas estadísticamente significativas en leucocitos y proteína C reactiva (PCR) concordante con la elevación de la presión de distensión alveolar (PDalv). No se encontró asociación con mortalidad en el uso de tocilizumab 2.20 (0.279-17.358) y corticosteroides 0.54 (0.229-1.273) en riesgos proporcionales de Cox al día 1 de VM. Durante los 15 días de VM los pacientes que fallecieron recibieron dosis más altas de corticosteroides, dosis mayores de 150 mg/día equivalente a prednisona se asocian a mortalidad. Conclusiones: Existe evolución cronológica similar en elevación de PCR, leucocitos y elevación de la PDalv, las cuales se explican por la disminución de la distensibilidad pulmonar estática (Cstat) y la presión positiva al final de la espiración total (PEEP total). El uso de tocilizumab no tuvo asociación con la mortalidad y dosis equivalentes a prednisona entre 100-150 mg/día se asocian a mejores resultados.

Abstract Introduction: The SARS-CoV-2 pandemic has inspired interest in the immune response to the virus, especially in severe patients with acute respiratory distress syndrome (ARDS). The study describes the behaviour of the immune response, immune suppression, and their results in patients under mechanical ventilation (MV). Material and methods: Prospective cohort. From March 23rd to December 31st, 2020, we recollected basal information, MV parameters, blood gas analysis and laboratory studies of all the patients over 18 years who received MV secondary to COVID-19. We registered 15 continuous days of MV. We divided the groups in patients alive at day 60 and deaths. Results: We included 218 patients with a mortality of 23%. In day 1 of MV, the patients didn't have any differences in cell counts or acute phase reactants, except for D Dimer (705-1,711) vs 1,328 (940-2,340) ng/dL p = 0.035. In mixed effects linear regressions, we found statistically significant chronological differences in C reactive protein (CPR) and leucocyte count, concordant with the elevation of the driving pressure (DP). In the Cox regression we found no association with tocilizumab and corticosteroids with mortality on day 1 of MV. Patients who died received higher doses of corticosteroids throughout the 15 days of MV, with doses equivalent to prednisone over 150 mg/day are associated with mortality. Conclusions: There is a similar chronological behaviour in the elevation of acute phase reactants and the elevation con DP with no elevation of Vt, which can be explained by the drop of total PEEP and Cstat. There was no association with the use of tocilizumab and mortality, and a dose of 100-150 mg/día of equivalent of prednisone was associated with better results.

Resumo Introdução: A pandemia de SARS-CoV-2 inspirou intrigas sobre a resposta imune ao referido vírus, especialmente em pacientes gravemente doentes com síndrome do desconforto respiratório do adulto (SDRA). Este estudo descreve o comportamento da resposta imune, imunossupressão e seus desfechos em pacientes em ventilação mecânica (VM). Material e métodos: Coorte prospectiva. De 23 de março a 31 de dezembro de 2020, foram coletadas informações basais, parâmetros ventilatórios e gasométricos e estudos laboratoriais de todos os pacientes maiores de 18 anos que receberam VM para COVID-19 com registros até o dia 15 de VM. Os grupos foram divididos em pacientes vivos em 90 dias e óbitos. Resultados: Registramos 218 pacientes, com mortalidade de 23%. No dia 1 de VM, os pacientes não apresentaram diferenças na contagem de células ou reagentes de fase aguda, exceto dimero D 1020 (705-1711) vs 1328 (940-2340) ng/dL p = 0.035. Na análise de regressão linear dos efeitos mistos, observam-se diferenças cronológicas estatisticamente significativas nos leucócitos e na proteína C reativa (PCR), consistentes com o aumento da pressão de distensão alveolar (PDalv). Não foi encontrada associação com mortalidade no uso de tocilizumab 2.20 (0.279-17.358) e corticoide 0.54 (0.229-1.273) nos riscos proporcionais de COX no 1o dia de VM. Durante os 15 dias de VM, os pacientes que foram a óbito receberam doses maiores de corticosteróides, doses a partir de 150 mg/dia equivalentes a prednisona estão associadas à mortalidade. Conclusões: Há evolução cronológica semelhante em PCR e leucócitos elevados e PDalv elevados, explicados pela diminuição da complacência pulmonar estática (Cstat) e da pressão positiva ao final da expiração total (PEEPtotal). O uso de tocilizumab não foi associado à mortalidade e doses equivalentes à prednisona entre 100-150 mg/dia estão associadas a melhores resultados.

Eventos trombóticos y marcadores inflamatorios en pacientes con neumonía grave por síndrome respiratorio agudo severo coronavirus-2 (SARS-CoV-2) / Thrombotic events and inflammatory markers in patients with severe pneumonia due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) / Eventos trombóticos e marcadores inflamatórios em pacientes com pneumonia grave devido à síndrome respiratória aguda grave coronavirus-2 (SARS-CoV-2)

Resumen: Introducción: La neumonía por SARS-CoV-2 se asocia a secreción importante de citoquinas y aglomeramiento de células inmunológicas, que activan las células endoteliales condicionando coagulopatía, afectando al pulmón en una fase temprana, con un fenotipo clínico del síndrome de dificultad respiratoria aguda (SDRA), que posteriormente progresa a respuesta inflamatoria sistémica desregulada por marcadores inflamatorios que causan mayor lesión endotelial generando trombosis. Muchos pacientes presentan niveles elevados de dímero D (DD), así como de proteína-C-reactiva (PCR), interleucina-6 (IL-6) y ferritina, supeditando la formación de coágulos, con la interrupción de la circulación (arterial o venosa) a cualquier nivel del sistema circulatorio. Objetivos: Determinar si existe relación entre los niveles elevados de marcadores inflamatorios y eventos trombóticos en pacientes con neumonía por SARS-CoV-2 con ventilación mecánica invasiva (VMI). Material y métodos: Realizamos estudio de una cohorte, observacional, retrospectivo y longitudinal, en pacientes que ingresaron a la Unidad de Terapia Respiratoria del Centro Médico ABC, de abril a julio de 2020, con diagnóstico de neumonía por SARS-CoV-2 con VMI. Utilizamos el programa STATA para el análisis estadístico. Efectuamos un análisis lineal de medidas repetitivas por regresión logística para evaluar el comportamiento cronológico de las variables inflamatorias. Posteriormente, ajustamos los marcadores inflamatorios con variables demográficas, para la obtención de certeza diagnóstica y predicción de riesgo de eventos trombóticos. Resultados: Analizamos un total de 100 pacientes, predominando el sexo masculino en 78%. El 18% presentó trombosis. Inicialmente, los marcadores inflamatorios estadísticamente significativos fueron DD (p = 0.010) con niveles de 1375.5 ng/mL (967-2651) y ferritina (p = 0.030) con niveles 1391.5 ng/mL (622-1779). Con el ajuste de variables inflamatorias por edad, género, índice de masa corporal (IMC) y escalas de gravedad, las variables estadísticamente significativas fueron DD (p = 0.001) y ferritina (p = 0.004), obteniendo certeza diagnóstica de 80.57% para predecir el riesgo de eventos trombóticos. Conclusión: El control estricto de los parámetros de laboratorio y un alto índice de sospecha son vitales para formular un enfoque de tratamiento personalizado para los pacientes, y también pueden ayudar a clasificar a los pacientes con alto riesgo de presentar eventos trombóticos. Nuestro modelo enfatiza que hay que tener precaución con niveles elevados de DD y ferritina.

Abstract: Introduction: SARS-CoV-2 pneumonia is associated with an important secretion of cytokines and agglomeration of immune cells, which activate endothelial cells conditioning coagulopathy, affecting the lung at an early stage, with a clinical phenotype of Acute Respiratory Distress Syndrome (ARDS), which later progresses to a systemic inflammatory response deregulated by inflammatory markers that cause greater endothelial injury generating thrombosis. Many patients present high levels of D-dimer (DD), as well as C-reactive protein (CRP), interleukin-6 (IL-6) and ferritin, subordinating the formation of clots, with the interruption of circulation (arterial or venous) at any level of the circulatory system. Objectives: To determine if there is a relationship between elevated levels of inflammatory markers and thrombotic events in patients with SARS-CoV-2 pneumonia with invasive mechanical ventilation (IMV). Material and methods: We conducted an observational, retrospective and longitudinal cohort study in patients admitted to the Respiratory Therapy Unit of the ABC Medical Center, from April to July 2020, with a diagnosis of SARS-CoV-2 pneumonia with IMV. We use the STATA program for statistical analysis. We performed a linear analysis of repetitive measures by logistic regression to evaluate the chronological behavior of the inflammatory variables. Subsequently, we adjusted the inflammatory markers with demographic variables, to obtain diagnostic certainty and prediction of risk of thrombotic events. Results: We analyzed a total of 100 patients, the male sex prevailing in 78%. 18% had thrombosis. Initially the statistically significant inflammatory markers were DD (p = 0.010) with levels of 1375.5 ng/mL (967-2651) and ferritin (p = 0.030) with levels 1391.5 ng/mL (622-1779). With the adjustment of inflammatory variables by age, gender, Body Mass Index (BMI) and severity scales, the statistically significant variables were DD (p = 0.001) and ferritin (p = 0.004), obtaining a diagnostic certainty of 80.57% to predict risk of thrombotic events. Conclusion: Tight control of laboratory parameters and a high index of suspicion are vital to formulating a personalized treatment approach for patients, and can also help classify patients at high risk for thrombotic events. Our model emphasizes that caution must be exercised with elevated levels of DD and ferritin.

Resumo: Introdução: A pneumonia por SARS-CoV-2 está associada à secreção significativa de citocinas e aglomeração de células imunes, que ativam as células endoteliais, causando coagulopatia, afetando o pulmão em estágio inicial, com um fenótipo clínico de Síndrome do Desconforto Respiratório Agudo (SDRA), que posteriormente progride para uma resposta inflamatória sistêmica desregulada por marcadores inflamatórios que causam maior lesão endotelial gerando trombose. Muitos pacientes apresentam níveis elevados de D-dímero (DD), bem como de proteína C-reativa (PCR), Interleucina-6 (IL-6) e ferritina, causando formação de coágulos, com interrupção da circulação (arterial ou venosa) em qualquer nível do sistema circulatório. Objetivos: Determinar se existe uma relação entre níveis elevados de marcadores inflamatórios e eventos trombóticos em pacientes com pneumonia por SARS-CoV-2 com ventilação mecânica invasiva (VMI). Material e métodos: Foi realizado um estudo de coorte observacional, retrospectivo e longitudinal em pacientes internados na Unidade de Terapia Respiratória do Centro Médico ABC, de abril a julho de 2020, com diagnóstico de pneumonia por SARS-CoV-2 com VMI. Usamos o programa STATA para análise estatística. Realizamos uma análise linear de medidas repetitivas por regressão logística para avaliar o comportamento cronológico das variáveis inflamatórias. Posteriormente, ajustamos os marcadores inflamatórios com variáveis demográficas, para obter certeza diagnóstica e predizer o risco de eventos trombóticos. Resultados: Analisamos um total de 100 pacientes, com predominância do sexo masculino em 78%. 18% apresentaram trombose. Inicialmente, os marcadores inflamatórios estatisticamente significativos foram DD (p = 0.010) com níveis de 1375.5 ng/mL (967-2651) e ferritina (p = 0.030) com níveis de 1391.5 ng/mL (622-1779). Com o ajuste das variáveis inflamatórias por idade, sexo, índice de massa corporal (IMC) e escalas de gravidade, as variáveis estatisticamente significativas foram DD (p = 0.001) e ferritina (p = 0.004), obtendo-se certeza diagnóstica de 80.57% para predizer o risco de eventos trombóticos. Conclusão: O controle estrito dos parâmetros laboratoriais e um alto índice de suspeita são vitais na formulação de uma abordagem de tratamento personalizado para os pacientes, e também podem ajudar a classificar os pacientes com alto risco de apresentar eventos trombóticos. Nosso modelo enfatiza que deve-se ter cautela com níveis elevados de DD e ferritina.