RhizoBindingSites v2.0 Is a Bioinformatic Database of DNA Motifs Potentially Involved in Transcriptional Regulation Deduced From Their Genomic Sites.

RhizoBindingSites is a de novo depurified database of conserved DNA motifs potentially involved in the transcriptional regulation of the Rhizobium, Sinorhizobium, Bradyrhizobium, Azorhizobium, and Mesorhizobium genera covering 9 representative symbiotic species, deduced from the upstream regulatory sequences of orthologous genes (O-matrices) from the Rhizobiales taxon. The sites collected with O-matrices per gene per genome from RhizoBindingSites were used to deduce matrices using the dyad-Regulatory Sequence Analysis Tool (RSAT) method, giving rise to novel S-matrices for the construction of the RizoBindingSites v2.0 database. A comparison of the S-matrix logos showed a greater frequency and/or re-definition of specific-position nucleotides found in the O-matrices. Moreover, S-matrices were better at detecting genes in the genome, and there was a more significant number of transcription factors (TFs) in the vicinity than O-matrices, corresponding to a more significant genomic coverage for S-matrices. O-matrices of 3187 TFs and S-matrices of 2754 TFs from 9 species were deposited in RhizoBindingSites and RhizoBindingSites v2.0, respectively. The homology between the matrices of TFs from a genome showed inter-regulation between the clustered TFs. In addition, matrices of AraC, ArsR, GntR, and LysR ortholog TFs showed different motifs, suggesting distinct regulation. Benchmarking showed 72%, 68%, and 81% of common genes per regulon for O-matrices and approximately 14% less common genes with S-matrices of Rhizobium etli CFN42, Rhizobium leguminosarum bv. viciae 3841, and Sinorhizobium meliloti 1021. These data were deposited in RhizoBindingSites and the RhizoBindingSites v2.0 database (http://rhizobindingsites.ccg.unam.mx/).

Host population structure and species resolution reveal prophage transmission dynamics.

Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages (4,152 prophages + 122 virulent phages, distributed in 46 countries in the world), we show that 91% (875 out of 963) of the prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are not only cosmopolitan but also the most abundant species. We also noted that polylysogens had very divergent prophages, belonging to different prophage species, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. Our study highlights how integrating the host population structure and a solid operational definition of phage species allows us to better appreciate phage diversity and its transmission dynamics. IMPORTANCE: Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages, we show that most prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are cosmopolitan and the most abundant species. Prophages in the same bacterial genome are very divergent, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. This study shows how integrating the host population structure and clustering at the species level allows us to better appreciate phage diversity and its transmission dynamics.

Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis.

Rhizobium etli CFN42 proteome-transcriptome mixed data of exponential growth and nitrogen-fixing bacteroids, as well as Sinorhizobium meliloti 1021 transcriptome data of growth and nitrogen-fixing bacteroids, were integrated into transcriptional regulatory networks (TRNs). The one-step construction network consisted of a matrix-clustering analysis of matrices of the gene profile and all matrices of the transcription factors (TFs) of their genome. The networks were constructed with the prediction of regulatory network application of the RhizoBindingSites database (http://rhizobindingsites.ccg.unam.mx/). The deduced free-living Rhizobium etli network contained 1,146 genes, including 380 TFs and 12 sigma factors. In addition, the bacteroid R. etli CFN42 network contained 884 genes, where 364 were TFs, and 12 were sigma factors, whereas the deduced free-living Sinorhizobium meliloti 1021 network contained 643 genes, where 259 were TFs and seven were sigma factors, and the bacteroid Sinorhizobium meliloti 1021 network contained 357 genes, where 210 were TFs and six were sigma factors. The similarity of these deduced condition-dependent networks and the biological E. coli and B. subtilis independent condition networks segregates from the random Erdös-Rényi networks. Deduced networks showed a low average clustering coefficient. They were not scale-free, showing a gradually diminishing hierarchy of TFs in contrast to the hierarchy role of the sigma factor rpoD in the E. coli K12 network. For rhizobia networks, partitioning the genome in the chromosome, chromids, and plasmids, where essential genes are distributed, and the symbiotic ability that is mostly coded in plasmids, may alter the structure of these deduced condition-dependent networks. It provides potential TF gen-target relationship data for constructing regulons, which are the basic units of a TRN.

Assessing heavy metal contamination in a Brazilian metropolis: a case study with a focus on (bio)indicators.

The continuous expansion of the global vehicle fleet poses a growing threat to environmental quality through heavy metal contamination. In this scenario, monitoring to safeguard public health in urban areas is necessary. Our study involved the collection of 36 street dust and 29 moss samples from roads of a Brazilian metropolis (Recife) with varying traffic intensities as follows: natural reserve (0 vehicles per day), low (< 15,000 vehicles per day), medium (15,000-30,000 vehicles per day), and high (> 30,000 vehicles per day). ICP-AES analysis was performed to determine the concentrations of nine potentially toxic metals (Ba, Cd, Cr, Cu, Mn, Ni, Pb, V, and Zn) to assess the influence of vehicular flow on urban contamination. In the street dust samples, the mean metal concentrations (mg kg-1) exhibited the following order: Ba (503.7) > Mn (303.0) > Zn (144.4) > Cu (95.3) > Cr (56.1) > Pb (34.2) > V (28.7) > Ni (11.3) > Cd (1.5). Conversely, in the moss samples, the metal concentration order was as follows (mg kg-1): Mn (63.8) > Zn (62.5) > Ba (61.0) > Cu (17.7) > Cr (8.0) > V (7.3) > Pb (7.0) > Ni (2.9) > Cd (0.3). Roads with higher traffic volumes exhibited the highest metal enrichments in moss samples for all metals and in dust samples for Cd, Cr, Mn, Ni, and V. However, dust from low-flow roads had higher enrichments for Ba, Cu, and Zn, indicating the influential role of other traffic-related factors in metal deposition. Our findings highlight traffic flow as the predominant source of pollution in urban centers, with both street dust and moss serving as sensitive indicators of metal input attributable to vehicular traffic. These indicators offer valuable insights for urban quality monitoring and pollution control efforts.

Mobility networks in Greater Mexico City.

Based on more than 11 billion geolocated cell phone records from 33 million different devices, daily mobility networks were constructed over a 15-month period for Greater Mexico City, one of the largest and most diverse metropolitan areas globally. The time frame considered spans the entire year of 2020 and the first three months of 2021, enabling the analysis of population movement dynamics before, during, and after the COVID-19 health contingency. The nodes within the 456 networks represent the basic statistical geographic areas (AGEBs) established by the National Institute of Statistics, Geography, and Informatics (INEGI) in Mexico. This framework facilitates the integration of mobility data with numerous indicators provided by INEGI. Edges connecting these nodes represent movement between AGEBs, with edge weights indicating the volume of trips from one AGEB to another. This extensive dataset allows researchers to uncover travel patterns, cross-reference data with socio-economic indicators, and conduct segregation studies, among other potential analyses.

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrieval and accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0 can be accessed at https://regulondb.ccg.unam.mx.

Impact of Treatment with Antioxidants as an Adjuvant to Standard Therapy in Patients with Septic Shock: Analysis of the Correlation between Cytokine Storm and Oxidative Stress and Therapeutic Effects.

Cellular homeostasis is lost or becomes dysfunctional during septic shock due to the activation of the inflammatory response and the deregulation of oxidative stress. Antioxidant therapy administered alongside standard treatment could restore this lost homeostasis. We included 131 patients with septic shock who were treated with standard treatment and vitamin C (Vit C), vitamin E (Vit E), N-acetylcysteine (NAC), or melatonin (MT), in a randomized trial. Organ damage quantified by Sequential Organ Failure Assessment (SOFA) score, and we determined levels of Interleukins (IL) IL1ß, Tumor necrosis factor alpha (TNFα), IL-6, monocyte chemoattractant protein-1 (MCP-1), Transforming growth factor B (TGFß), IL-4, IL-10, IL-12, and Interferon-γ (IFNγ). The SOFA score decreased in patients treated with Vit C, NAC, and MT. Patients treated with MT had statistically significantly reduced of IL-6, IL-8, MCP-1, and IL-10 levels. Lipid peroxidation, Nitrates and nitrites (NO3- and NO2-), glutathione reductase, and superoxide dismutase decreased after treatment with Vit C, Vit E, NAC, and MT. The levels of thiols recovered with the use of Vit E, and all patients treated with antioxidants maintained their selenium levels, in contrast with controls (p = 0.04). The findings regarding oxidative stress markers and cytokines after treatment with antioxidants allow us to consider to future the combined use of antioxidants in a randomized clinical trial with a larger sample to demonstrate the reproducibility of these beneficial effects.

Intermunicipal travel networks of Mexico during the COVID-19 pandemic.

Human mobility networks are widely used for diverse studies in geography, sociology, and economics. In these networks, nodes usually represent places or regions and links refer to movement between them. They become essential when studying the spread of a virus, the planning of transit, or society's local and global structures. Therefore, the construction and analysis of human mobility networks are crucial for a vast number of real-life applications. This work presents a collection of networks that describe the human travel patterns between municipalities in Mexico in the 2020-2021 period. Using anonymized mobile location data, we constructed directed, weighted networks representing the volume of travels between municipalities. We analysed changes in global, local, and mesoscale network features. We observe that changes in these features are associated with factors such as COVID-19 restrictions and population size. In general, the implementation of restrictions at the start of the COVID-19 pandemic in early 2020, induced more intense changes in network features than later events, which had a less notable impact in network features. These networks will result very useful for researchers and decision-makers in the areas of transportation, infrastructure planning, epidemic control and network science at large.

Randomized Clinical Trial of Antioxidant Therapy Patients with Septic Shock and Organ Dysfunction in the ICU: SOFA Score Reduction by Improvement of the Enzymatic and Non-Enzymatic Antioxidant System.

BACKGROUND AND AIM: Here, we assess the effect of adjuvant antioxidant therapies in septic shock patients with organ dysfunction and their effect on the enzymatic and non-enzymatic antioxidant systems. METHODS: Randomized clinical trial run between 2018 and 2022. One hundred and thirty-one patients with septic shock were included in five groups with 25, 27, 24, 26 and 29 patients each. Group 1 received vitamin C (Vit C), Group 2 vitamin E (Vit E), Group 3 n-acetylcysteine (NAC), Group 4 melatonin (MT) and group 5 no treatment. All antioxidants were administered orally or through a nasogastric tube for 5 days as an adjuvant to standard therapy. RESULTS: All patients had multiple organ failure (MOF) and low Vit C levels. Vit C therapy decreased CRP, PCT and NO3-/NO2- but increased Vit C levels. The SOFA score decreased with MT in 75%, Vit C 63% and NAC 50% vs. controls 33% (p = 0.0001, p = 0.03 and p = 0.001 respectively). MT diminished lipid peroxidation (LPO) (p = 0.01) and improved total antioxidant capacity (TAC) (p = 0.04). Vit E increased thiol levels (p = 0.02) and tended to decrease LPO (p = 0.06). Selenium levels were decreased in the control group (p = 0.04). CONCLUSIONS: Antioxidants used as an adjuvant therapy in the standard treatment of septic shock decrease MOF and oxidative stress markers. They increase the TAC and thiols, and maintain selenium levels.

Rabies, the cause of fatal encephalitis.

To describe the clinical progression and medical protocols applied in a 41 year old man who was bited by a bat three months before. The patient did not ask for medical care until acute tremor and pain in the right thoracic limb and hydro-phobia started. For a history of a wild animal bite associated with a unique clinical condition, we suspected of rabies encephalitis, confirming the diagnostic by pathology after his death. This case ocurred in Guadalajara, Jalisco, México, in April, 2022. The last case of human rabies reported in Jalisco secondary to bat bite was almost 30 years ago. As an uncomon disease, medical personnel and facilities should be prepared to attend this sort of cases after clinical suspicion. For the present case, the medical history was the key for diagnosis. Rabies is a disease caused by the neurotropic virus belonging to the Rhabdoviridae family whose prognosis is bleak, with mortality close to 100% and therapeutic options limited. This case emphasizes the high mortality of rabies virus infection and the importance of increasing awareness and education to the public in general, with regard to applying the vaccine as post-exposure prophylaxis.

Estudio de cohorte para evaluar la asociación entre el tiempo de inicio de nutrición con días de ventilación mecánica invasiva en pacientes con choque séptico / Cohort study to evaluate the association between the start time of nutrition with days of invasive mechanical ventilation in patients with septic shock / Estudo de coorte para avaliar a associação entre o tempo de início da nutrição com os dias de ventilação mecânica invasiva em pacientes com choque séptico

Resumen: Introducción: estudio de cohorte para evaluar la asociación entre el tiempo de inicio de nutrición con los días de ventilación mecánica invasiva (VMI) en pacientes con choque séptico. La ventilación mecánica (VM) es un soporte que mantiene al paciente mientras la lesión estructural o funcional por la que se indicó se corrige. La sepsis es una causa de disfunción diafragmática que contribuye a insuficiencia respiratoria; sin embargo, se dispone de pocos datos sobre la interacción entre sepsis y VM prolongada. Actualmente, aunque la nutrición se ha establecido como un pilar de apoyo y tratamiento en pacientes críticamente enfermos, el impacto de esta intervención es poco clara. Objetivo: verificar la existencia de la asociación entre el tiempo de inicio de la nutrición y la duración de la VMI en pacientes con choque séptico. Material y métodos: se realizó un estudio de cohorte prolectivo en pacientes con choque séptico y VMI, se documentó el tiempo de inicio de la nutrición, esta decisión fue independiente del estudio. Se dio seguimiento diario con respecto a los días que requirieron VMI y el inicio de nutrición enteral o parenteral. La nutrición temprana es cuando se inicia en las primeras 48 horas del ingreso a terapia intensiva. Se empleó Stata para el análisis estadístico, en el cual se utilizaron pruebas χ2 y regresión logística. Resultados: se incluyeron 131 pacientes con choque séptico y VMI, a 110 pacientes se les inició nutrición temprana y a 21 nutrición tardía. La edad promedio fue de 69 años, 23% (31) del total de los pacientes tenía diabetes mellitus (DM), que se presentó con mayor frecuencia en el grupo de nutrición tardía. En cuanto a la gravedad, no se encontró diferencia entre ambos grupos. La duración promedio con ventilación fue de dos días, con mayor tiempo en el grupo de inicio tardío de la nutrición (dos días vs cinco días, p = 0.012). No obstante, al ajustar por regresión logística, no se encontró diferencia estadísticamente significativa (OR 0.13, IC 95% 0.14-1.17, p = 0.69). Conclusiones: aunque la nutrición se considera un pilar de apoyo necesario en todo paciente crítico, de acuerdo con nuestros resultados, el momento de inicio no afecta directamente los días de VMI.

Abstract: Introduction: cohort study to evaluate the association between the start time of nutrition with the days of invasive mechanical ventilation (IMV) in patients with septic shock. Mechanical ventilation (MV) is a support that maintains the patient while the structural or functional injury for which it was indicated is corrected. Sepsis is a cause of diaphragmatic dysfunction, contributing to respiratory failure; however, few data are available on the interaction between sepsis and prolonged MV. Currently, although nutrition has been established as a mainstay of support and treatment in critically ill patients, the impact of this intervention is unclear. Objective: to verify the existence of the association between the start time of nutrition and the duration of IMV in patients with septic shock. Material and methods: a prolective cohort study was carried out in patients with septic shock and IMV was documented at the start of nutrition, this decision being independent of the study. Daily follow-up was given regarding the days that required IMV and the start of enteral or parenteral nutrition. Early nutrition is when it is started within the first 48 hours of admission to intensive care. Stata was used for statistical analysis in which χ2 tests and logistic regression were used. Results: 131 patients with septic shock and IMV were included, 110 patients started early nutrition and 21 delayed nutrition. The average age was 69 years, 23% (31) of the total patients had diabetes mellitus (DM), presenting more frequently in the late nutrition group. Regarding severity, no difference was found between the two groups. The average duration with ventilation was two days, with a longer time in the late start of nutrition group (2 days vs 5 days, p = 0.012). However, when adjusting for logistic regression, no statistically significant difference was found (OR 0.13, CI 95% 0.14-1.17, p = 0.69). Conclusions: although nutrition is considered a necessary support pillar in all critical patients, according to our results, the start time does not directly affect the days of invasive mechanical ventilation.

Resumo: Introdução: estudo de coorte para avaliar a associação entre o tempo de início da nutrição com os dias de ventilação mecânica invasiva (VMI) em pacientes com choque séptico. A ventilação mecânica (VM) é um suporte que mantém o paciente enquanto se corrige a lesão estrutural ou funcional para a qual foi indicada. A sepse é a causa da disfunção diafragmática, contribuindo para a insuficiência respiratória; no entanto, poucos dados estão disponíveis sobre a interação entre sepse e VM prolongada. Atualmente, embora a nutrição tenha se estabelecido como pilar de suporte e tratamento em pacientes críticos, o impacto dessa intervenção não está claro. Objetivo: verificar a existência de associação entre o tempo de início da nutrição e a duração da VMI em pacientes com choque séptico. Material e métodos: foi realizado um estudo de coorte proletivo em pacientes com choque séptico e VMI, o tempo para iniciar a nutrição foi documentado, sendo esta decisão independente do estudo. Foi feito acompanhamento diário dos dias que necessitaram de VMI e início de nutrição enteral ou parenteral. A nutrição precoce é quando é iniciada nas primeiras 48 horas de internação na terapia intensiva. Utilizou-se o Stata para a análise estatística em que foram utilizados os testes χ2 e regressão logística. Resultados: foram incluídos 131 pacientes com choque séptico e VMI, 110 pacientes iniciaram nutrição precoce e 21 nutrição tardia. A média de idade foi de 69 anos, 23% (31) do total de pacientes apresentavam diabetes mellitus (DM), apresentando-se com maior frequência no grupo de nutrição retardada. Em relação à gravidade, não foi encontrada diferença entre os dois grupos. A duração média da ventilação foi de 2 dias, com maior tempo no grupo de nutrição de início tardio (2 dias vs 5 dias, p = 0.012). No entanto, ao ajustar por regressão logística, não foi encontrada diferença estatisticamente significativa OR 0.13, IC (0.14-1.17) p = 0.69. Conclusões: embora a nutrição seja considerada um pilar de suporte necessário em todos os pacientes críticos, de acordo com nossos resultados, o horário de início não afeta diretamente os dias de ventilação mecânica invasiva.

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.

Distribution Patterns of Invasive Buffelgrass (Cenchrus ciliaris) in Mexico Estimated with Climate Niche Models under the Current and Future Climate.

In Mexico, buffelgrass (Cenchrus ciliaris) was introduced in the middle of the 20th century. Currently, buffelgrass has become an invasive species and has colonized various ecosystems in the country. In addition to its invasive capacity, climate change is a factor that has to be taken into account when considering how to effectively manage and control this species. The climatic niche models (CNM) and their projections for climate change scenarios allow for estimating the extent of biological invasions. Our study aimed to calibrate a CNM for buffelgrass in Mexico under the current climatic conditions and to project the extent of its biological invasion under climate change scenarios. For that, we used MaxEnt to generate the current CNM and to detect if climate change could cause future changes, we then evaluated the distribution patterns over the periods of 2041-2060, 2061-2080, and 2081-2100 for all the shared socioeconomic pathways (SSPs). Linear regressions were used to compare the outputs between current and future scenarios. Under the current climate, the CNM estimated that 42.2% of the continental surface of Mexico is highly suitable for buffelgrass. The regression analyses indicated no effects from climate change on the distribution of buffelgrass. Moreover, when the projected period is further in the future, and when the SSPs intensify, the surface of suitable areas for the species increases. These analyses clearly suggest Mexico is facing a biological invasion from buffelgrass, which may represent a threat to native biodiversity.

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.

Hyperglycemia and Loss of Redox Homeostasis in COVID-19 Patients.

The infection with SARS-CoV-2 impairs the glucose−insulin axis and this contributes to oxidative (OS) and nitrosative (NSS) stress. Here, we evaluated changes in glucose metabolism that could promote the loss of redox homeostasis in COVID-19 patients. This was comparative cohort and analytical study that compared COVID-19 patients and healthy subjects. The study population consisted of 61 COVID-19 patients with and without comorbidities and 25 healthy subjects (HS). In all subjects the plasma glucose, insulin, 8-isoprostane, Vitamin D, H2S and 3-nitrotyrosine were determined by ELISA. The nitrites (NO2−), lipid-peroxidation (LPO), total-antioxidant-capacity (TAC), thiols, glutathione (GSH) and selenium (Se) were determined by spectrophotometry. The glucose, insulin and HOMA-IR (p < 0.001), 8-isoprostanes, 3-nitrotyrosine (p < 0.001) and LPO were increased (p = 0.02) while Vitamin D (p = 0.01), H2S, thiols, TAC, GSH and Se (p < 0.001) decreased in COVID-19 patients in comparison to HS. The SARS-CoV-2 infection resulted in alterations in the glucose−insulin axis that led to hyperglycemia, hyperinsulinemia and IR in patients with and without comorbidities. These alterations increase OS and NSS reflected in increases or decreases in some oxidative markers in plasma with major impact or fatal consequences in patients that course with metabolic syndrome. Moreover, subjects without comorbidities could have long-term alterations in the redox homeostasis after infection.

Environmental Niche Dynamics of Blue Grama (Bouteloua gracilis) Ecotypes in Northern Mexico: Genetic Structure and Implications for Restoration Management.

Understanding the genetic structure adopted by natural populations and its relation to environmental adaptation is critical for the success of restoration programs. We evaluated the genetic structure and temporal environmental niche dynamics of blue grama (Bouteloua gracilis) in 48 populations. The genetic evaluation was performed through amplified fragment length polymorphism (AFLP) molecular markers. The maximum entropy method was used to model the past, present, and future environmental niches of the three clusters derived from the genetic analysis. The environmental niches of the three genetic clusters showed dynamic overlaps and isolations during the last interglacial and glacial maximum. The paleoclimatic events, which occurred during those periods, may have reinforced genetic exchange among populations and affected their genetic structure. Genetic clusters also presented different environmental niches in the present. Thus, they can be considered as three distinct ecotypes and restoration programs must be carried out using local germplasm from each environmental niche to increase their chance of success. Based on the environmental niches of the genetic clusters, changes are expected in the near and mid-century future. Therefore, climate change must be considered for species conservation management and future restoration programs.