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.

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.

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.

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.

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.

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.

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.

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.

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.

A pragmatic methodology to extract anesthetic and physiological data from the electronic health record.

BACKGROUND/AIMS: Traditional manual methods of extracting anesthetic and physiological data from the electronic health record rely upon visual transcription by a human analyst that can be labor-intensive and prone to error. Technical complexity, relative inexperience in computer coding, and decreased access to data warehouses can deter investigators from obtaining valuable electronic health record data for research studies, especially in under-resourced settings. We therefore aimed to develop, pilot, and demonstrate the effectiveness and utility of a pragmatic data extraction methodology. METHODS: Expired sevoflurane concentration data from the electronic health record transcribed by eye was compared to an intermediate preprocessing method in which the entire anesthetic flowsheet narrative report was selected, copy-pasted, and processed using only Microsoft Word and Excel software to generate a comma-delimited (.csv) file. A step-by-step presentation of this method is presented. Concordance rates, Pearson correlation coefficients, and scatterplots with lines of best fit were used to compare the two methods of data extraction. RESULTS: A total of 1132 datapoints across eight subjects were analyzed, accounting for 18.9 h of anesthesia time. There was a high concordance rate of data extracted using the two methods (median concordance rate 100% range [96%, 100%]). The median time required to complete manual data extraction was significantly longer compared to the time required using the intermediate method (240 IQR [199, 482.5] seconds vs 92.5 IQR [69, 99] seconds, p = .01) and was linearly associated with the number of datapoints (rmanual = .97, p < .0001), whereas time required to complete data extraction using the intermediate approach was independent of the number of datapoints (rintermediate = -.02, p = .99). CONCLUSIONS: We describe a pragmatic data extraction methodology that does not require additional software or coding skills intended to enhance the ease, speed, and accuracy of data collection that could assist in clinician investigator-initiated research and quality/process improvement projects.

Effect of Repeated Exposure to Sevoflurane on Electroencephalographic Alpha Oscillation in Pediatric Patients Undergoing Radiation Therapy: A Prospective Observational Study.

BACKGROUND: Pharmacological tolerance is defined as a decrease in the effect of a drug over time, or the need to increase the dose to achieve the same effect. It has not been established whether repeated exposure to sevoflurane induces tolerance in children. METHODS: We conducted an observational study in children younger than 6 years of age scheduled for multiple radiotherapy sessions with sevoflurane anesthesia. To evaluate the development of sevoflurane tolerance, we analyzed changes in electroencephalographic spectral power at induction, across sessions. We fitted individual and group-level linear regression models to evaluate the correlation between the outcomes and sessions. In addition, a linear mixed-effect model was used to evaluate the association between radiotherapy sessions and outcomes. RESULTS: Eighteen children were included and the median number of radiotherapy sessions per child was 28 (interquartile range: 10 to 33). There was no correlation between induction time and radiotherapy sessions. At the group level, the linear mixed-effect model showed, in a subgroup of patients, that alpha relative power and spectral edge frequency 95 were inversely correlated with the number of anesthesia sessions. Nonetheless, this subgroup did not differ from the other subjects in terms of age, sex, or the total number of radiotherapy sessions. CONCLUSIONS: Our results suggest that children undergoing repeated anesthesia exposure for radiotherapy do not develop tolerance to sevoflurane. However, we found that a group of patients exhibited a reduction in the alpha relative power as a function of anesthetic exposure. These results may have implications that justify further studies.

Ecological and metabolic implications of the nurse effect of Maihueniopsis camachoi in the Atacama Desert.

Plant-plant positive interactions are key drivers of community structure. Yet, the underlying molecular mechanisms of facilitation processes remain unexplored. We investigated the 'nursing' effect of Maihueniopsis camachoi, a cactus that thrives in the Atacama Desert between c. 2800 and 3800 m above sea level. We hypothesised that an important protective factor is thermal amelioration of less cold-tolerant species with a corresponding impact on molecular phenotypes. To test this hypothesis, we compared plant cover and temperatures within the cactus foliage with open areas and modelled the effect of temperatures on plant distribution. We combined eco-metabolomics and machine learning to test the molecular consequences of this association. Multiple species benefited from the interaction with M. camachoi. A conspicuous example was the extended distribution of Atriplex imbricata to colder elevations in association with M. camachoi (400 m higher as compared to plants in open areas). Metabolomics identified 93 biochemical markers predicting the interaction status of A. imbricata with 79% accuracy, independently of year. These findings place M. camachoi as a key species in Atacama plant communities, driving local biodiversity with an impact on molecular phenotypes of nursed species. Our results support the stress-gradient hypothesis and provide pioneer insights into the metabolic consequences of facilitation.

Developmental trajectories of EEG aperiodic and periodic components: Implications for understanding thalamocortical development during infancy.

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. Consistent with the transient developmental progression of thalamocortical circuitry, we observe the presence and then absence of periodic alpha and high beta peaks across the three-year period, as well as the emergence of a low beta peak (12-20Hz) after six months of age. We present preliminary evidence that the emergence of the low beta peak is associated with higher thalamocortical-dependent, anesthesia-induced alpha coherence. Together, these findings suggest that early age-dependent changes in alpha and beta periodic peaks may reflect the state of thalamocortical network development.

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.

Effect of Inlet Air Temperature and Quinoa Starch/Gum Arabic Ratio on Nanoencapsulation of Bioactive Compounds from Andean Potato Cultivars by Spray-Drying.

Nanoencapsulation of native potato bioactive compounds by spray-drying improves their stability and bioavailability. The joint effect of the inlet temperature and the ratio of the encapsulant (quinoa starch/gum arabic) on the properties of the nanocapsules is unknown. The purpose of this study was to determine the best conditions for the nanoencapsulation of these compounds. The effects of two inlet temperatures (96 and 116 °C) and two ratios of the encapsulant (15 and 25% w/v) were evaluated using a factorial design during the spray-drying of native potato phenolic extracts. During the study, measurements of phenolic compounds, flavonoids, anthocyanins, antioxidant capacity, and various physical and structural properties were carried out. Higher inlet temperatures increased bioactive compounds and antioxidant capacity. However, a higher concentration of the encapsulant caused the dilution of polyphenols and anthocyanins. Instrumental analyses confirmed the effective encapsulation of the nuclei in the wall materials. Both factors, inlet temperature, and the encapsulant ratio, reduced the nanocapsules' humidity and water activity. Finally, the ideal conditions for the nanoencapsulation of native potato bioactive compounds were determined to be an inlet temperature of 116 °C and an encapsulant ratio of 15% w/v. The nanocapsules obtained show potential for application in the food industry.

Development and prospective validation of postoperative pain prediction from preoperative EHR data using attention-based set embeddings.

Preoperative knowledge of expected postoperative pain can help guide perioperative pain management and focus interventions on patients with the greatest risk of acute pain. However, current methods for predicting postoperative pain require patient and clinician input or laborious manual chart review and often do not achieve sufficient performance. We use routinely collected electronic health record data from a multicenter dataset of 234,274 adult non-cardiac surgical patients to develop a machine learning method which predicts maximum pain scores on the day of surgery and four subsequent days and validate this method in a prospective cohort. Our method, POPS, is fully automated and relies only on data available prior to surgery, allowing application in all patients scheduled for or considering surgery. Here we report that POPS achieves state-of-the-art performance and outperforms clinician predictions on all postoperative days when predicting maximum pain on the 0-10 NRS in prospective validation, though with degraded calibration. POPS is interpretable, identifying comorbidities that significantly contribute to postoperative pain based on patient-specific context, which can assist clinicians in mitigating cases of acute pain.

Developmental trajectories of EEG aperiodic and periodic power: Implications for understanding the timing of thalamocortical development during infancy.

The development of neural circuits over the first years of life has long-lasting effects on brain function, yet our understanding of early circuit development in humans remains limited. Here, aperiodic and periodic EEG power features 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. Consistent with the transient developmental progression of thalamocortical circuitry, we observe the presence and then absence of periodic alpha and high beta peaks across the three-year period, as well as the emergence of a low beta peak (12-20Hz) after six months of age. We present preliminary evidence that the emergence of the low beta peak is associated with thalamocortical connectivity sufficient for anesthesia-induced alpha coherence. Together, these findings suggest that early age-dependent changes in alpha and beta periodic peaks may reflect the state of thalamocortical network development.