Child opportunity index is associated with pediatric firearm injury in Philadelphia, Pennsylvania.

Introduction: Firearm injury is the leading cause of death in children. This study uses geospatial mapping to illustrate the burden of pediatric firearm injury in Philadelphia and assesses the relationship between Child Opportunity Index (COI) and injury, hypothesizing that lower COI zip codes would have higher injury and mortality rates. Methods: Pediatric firearm injury data for children aged 0-19 years in Philadelphia, from 2015 to February 2023, was visualized by race/ethnicity, fatal versus non-fatal status, and COI for zip code. COI was then dichotomized as "High" or "Low" based on nationally normed scores and used to compare incidence and odds of mortality. Injury incidence rates by COI were calculated using weighted Poisson regression, to adjust for the total number of children in each COI category. Odds of mortality by COI, adjusted for age, sex and race/ethnicity, were calculated using multivariable logistic regression. Results: Of 2,339 total pediatric firearm injuries, 366 (16%) were fatal. Males (89%), adolescents (95%) and Black children (88%) were predominately affected. Geospatial mapping showed highest burden in North and West Philadelphia, which corresponded with areas of low COI. The incidence rate ratio (IRR) of injury in low COI zip codes was 2.5 times greater than high COI (IRR 2.5 [1.93-3.22]; p < 0.01). After adjusting for age, sex, and race/ethnicity, odds of mortality in low COI zip codes was nearly twice that of high COI zip codes (aOR 1.95 [0.77-4.92]), though did not demonstrate statistical significance (p = 0.16). Conclusion: Child opportunity index is associated with pediatric firearm injury in Philadelphia, Pennsylvania.

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.

Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.

Pediatric Sepsis Requiring Intensive Care Admission: Potential Structured Follow-Up Protocols to Identify and Manage New or Exacerbated Medical Conditions.

Pediatric sepsis is a leading cause of morbidity and mortality in children globally. Children who require the pediatric intensive care unit (PICU) are at high risk for new or worsening co-morbidities, as well as readmission. This review describes the current state of protocolized follow-up after pediatric sepsis requiring PICU admission. We searched Medline and EMBASE databases for studies published in English from 2005 to date. Duplicates, review articles, abstracts and poster presentations were excluded; neonatal intensive care unit (NICU) patients were also excluded since neonatal sepsis is variably defined and differs from the pediatric consensus definition. The search yielded 418 studies of which 55 were duplicates; the subsequent 363 studies were screened for inclusion criteria, yielding 31 studies for which full article screening was completed. Subsequently, 23 studies were excluded due to wrong population (9), wrong publication type (10), duplicate data (3) or wrong outcome (1). In total, nine studies were included for which we described study design, setting, population, sample size, outcomes, PICU core outcome domain, and results. There were 4 retrospective cohort studies, 4 prospective cohort studies, 1 retrospective case series and no prospective trials. These studies show the varying trajectories of recovery after discharge, with the common finding that new or worsening morbidities are worse within months of discharge, but may persist. Sepsis survivors may have distinct needs and a different post-PICU trajectory compared to other critically ill children, particularly in quality of life and neurocognitive outcomes. Future research should focus on developing screening protocols and studying protocolized follow-up trials to reduce morbidity after pediatric sepsis.

DNA-Binding Activity of CAMTA3 Is Essential for Its Function: Identification of Critical Amino Acids for Its Transcriptional Activity.

Calmodulin-binding transcription activators (CAMTAs), a small family of highly conserved transcription factors, function in calcium-mediated signaling pathways. Of the six CAMTAs in Arabidopsis, CAMTA3 regulates diverse biotic and abiotic stress responses. A recent study has shown that CAMTA3 is a guardee of NLRs (Nucleotide-binding, Leucine-rich repeat Receptors) in modulating plant immunity, raising the possibility that CAMTA3 transcriptional activity is dispensable for its function. Here, we show that the DNA-binding activity of CAMTA3 is essential for its role in mediating plant immune responses. Analysis of the DNA-binding (CG-1) domain of CAMTAs in plants and animals showed strong conservation of several amino acids. We mutated six conserved amino acids in the CG-1 domain to investigate their role in CAMTA3 function. Electrophoretic mobility shift assays using these mutants with a promoter of its target gene identified critical amino acid residues necessary for DNA-binding activity. In addition, transient assays showed that these residues are essential for the CAMTA3 function in activating the Rapid Stress Response Element (RSRE)-driven reporter gene expression. In line with this, transgenic lines expressing the CG-1 mutants of CAMTA3 in the camta3 mutant failed to rescue the mutant phenotype and restore the expression of CAMTA3 downstream target genes. Collectively, our results provide biochemical and genetic evidence that the transcriptional activity of CAMTA3 is indispensable for its function.

Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention.

BACKGROUND: Alternative splicing is a widespread regulatory phenomenon that enables a single gene to produce multiple transcripts. Among the different types of alternative splicing, intron retention is one of the least explored despite its high prevalence in both plants and animals. The recent discovery that the majority of splicing is co-transcriptional has led to the finding that chromatin state affects alternative splicing. Therefore, it is plausible that transcription factors can regulate splicing outcomes. RESULTS: We provide evidence for the hypothesis that transcription factors are involved in the regulation of intron retention by studying regions of open chromatin in retained and excised introns. Using deep learning models designed to distinguish between regions of open chromatin in retained introns and non-retained introns, we identified motifs enriched in IR events with significant hits to known human transcription factors. Our model predicts that the majority of transcription factors that affect intron retention come from the zinc finger family. We demonstrate the validity of these predictions using ChIP-seq data for multiple zinc finger transcription factors and find strong over-representation for their peaks in intron retention events. CONCLUSIONS: This work opens up opportunities for further studies that elucidate the mechanisms by which transcription factors affect intron retention and other forms of splicing. AVAILABILITY: Source code available at https://github.com/fahadahaf/chromir.

Investigating Racial and Socioeconomic Characteristics in Pediatric Sepsis Using Electronic Health Data.

BACKGROUND AND OBJECTIVES: Racial/ethnic and socioeconomic disparities are reported in sepsis, with increased mortality for minority and low socioeconomic status groups; however, these studies rely on billing codes that are imprecise in identifying sepsis. Using a previously validated algorithm to detect pediatric sepsis using electronic clinical data, we hypothesized that racial/ethnic and socioeconomic status disparities would be evident in this group. METHODS: We performed a retrospective study from a large, quaternary academic center, including sepsis episodes from January 20, 2011, to May 20, 2021, identified by an algorithm indicative of bacterial infection with organ dysfunction (cardiac, respiratory, renal, or hematologic). Multivariable logistic regression was used to measure association of race/ethnicity, insurance status, and social disorganization index, with the primary outcome of mortality, adjusting for age, sex, complex chronic conditions, organ dysfunction on day 1, source of admission, and time to hospital. Secondary outcomes were ICU admission, readmission, organ dysfunction-free days, and sepsis therapies. RESULTS: Among 4532 patient episodes, the mortality rate was 9.7%. There was no difference in adjusted odds of mortality on the basis of race/ethnicity, insurance status, or social disorganization. There was no significant association between our predictors and ICU admission. Hispanic patients and publicly insured patients were more likely to be readmitted within 1 year (Hispanic odds ratio 1.28 [1.06-1.5]; public odds ratio 1.19 [1.05-1.35]). CONCLUSIONS: Previously described disparities were not observed when using electronic clinical data to identify sepsis; however, data were only single center. There were significantly higher readmissions in patients who were publicly insured or identified as Hispanic or Latino, which require further investigation.

The amino acid region from 448-517 of CAMTA3 transcription factor containing a part of the TIG domain represses the N-terminal repression module function.

CAMTA3, a Ca2+-regulated transcription factor, is a repressor of plant immune responses. A truncated version of CAMTA3; CAMTA3334 called N-terminal repression module (NRM), and its extended version (CAMTA447), which include the DNA binding domain, were previously reported to complement the camta3/2 mutant phenotype. Here, we generated a series of CAMTA3 truncated versions [the N-terminus (aa 1-517), C-terminus (aa 517-1032), R1 (aa 1-173), R2 (aa 174-345), R3 (aa 346-517), R4 (aa 517-689), R5 (aa 690-861) and R6 (aa 862-1032)], expressed in camta3 mutant and analyzed the phenotypes of the transgenic lines. Interestingly, unlike CAMTA447, extending the N-terminal region to 517 aa did not complement the camta3 phenotype, suggesting that the amino acid region from 448-517 (70 aa), which includes a part of the TIG domain suppresses the NRM activity. The C-terminus and other truncated versions (R1-R6) also failed to complement the camta3 mutant. Expressing the full length or NRM of CAMTA3 in camta3 plants suppressed the activation of immune-responsive genes and increased the expression of cold-induced genes. In contrast, the transgenic lines expressing the N- or C-terminus or R1-R6 of CAMTA3 showed expression patterns like those of the camta3 with enhanced expression of the defense genes and suppressed expression of the cold response genes. Furthermore, like camta3, the transgenic lines expressing the N- or C-terminus, or R1-R6 of CAMTA3 exhibited higher levels of H2O2 and increased resistance to a Pst DC3000 as compared to WT, NRM, or FL-CAMTA3 transgenic plants. Our studies identified a novel regulatory region in CAMTA3 that suppresses the NRM activity. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01401-w.

Assessing the health literacy of caregivers in the pediatric intensive care unit: a mixed-methods study.

Background: Limited health literacy is associated with increased hospitalizations, emergency visits, health care costs, and mortality. The health literacy levels of caregivers of critically ill children are unknown. This mixed-methods study aims to quantitatively assess the health literacy of caregivers of children admitted to the pediatric intensive care unit (PICU) and qualitatively describe facilitators and barriers to implementing health literacy screening from the provider perspective. Methods: Caregivers of patients admitted to our large, academic PICU (between August 12, 2022 and March 31, 2023) were approached to complete a survey with the Newest Vital Sign (NVS), which is a validated health literacy screener offered in English and Spanish. We additionally conducted focus groups of interdisciplinary PICU providers to identify factors which may influence implementation of health literacy screening using the Consolidated Framework for Implementation Research (CFIR) framework. Results: Among 48 surveyed caregivers, 79% demonstrated adequate health literacy using the Newest Vital Sign screener. The majority of caregivers spoke English (96%), were mothers (85%), and identified as White (75%). 83% of caregivers were able to attend rounds at least once and 98% believed attending rounds was helpful. Within the PICU provider focus groups, there were 11 participants (3 attendings, 3 fellows, 2 nurse practitioners, 1 hospitalist, 2 research assistants). Focus group participants described facilitators and barriers to implementation, which were mapped to CFIR domains. Timing of screening and person administering screening were identified as modifiable factors to improve future implementation. Conclusion: We found the health literacy levels of PICU caregivers in our setting is similar to prior assessments of parental health literacy. Participation in morning rounds was helpful for developing understanding of their child's illness, regardless of health literacy status. Qualitative feedback from providers identified barriers across all CFIR domains, with timing of screening and person administering screening as modifiable factors to improve future implementation.

SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis.

Light signals perceived by a group of photoreceptors have profound effects on the physiology, growth, and development of plants. The red/far-red light-absorbing phytochromes (phys) modulate these aspects by intricately regulating gene expression at multiple levels. Here, we report the identification and functional characterization of an RNA-binding splicing factor, SWAP1 (SUPPRESSOR-OF-WHITE-APRICOT/SURP RNA-BINDING DOMAIN-CONTAINING PROTEIN1). Loss-of-function swap1-1 mutant is hyposensitive to red light and exhibits a day length-independent early flowering phenotype. SWAP1 physically interacts with two other splicing factors, (SFPS) SPLICING FACTOR FOR PHYTOCHROME SIGNALING and (RRC1) REDUCED RED LIGHT RESPONSES IN CRY1CRY2 BACKGROUND 1 in a light-independent manner and forms a ternary complex. In addition, SWAP1 physically interacts with photoactivated phyB and colocalizes with nuclear phyB photobodies. Phenotypic analyses show that the swap1sfps, swap1rrc1, and sfpsrrc1 double mutants display hypocotyl lengths similar to that of the respective single mutants under red light, suggesting that they function in the same genetic pathway. The swap1sfps double and swap1sfpsrrc1 triple mutants display pleiotropic phenotypes, including sterility at the adult stage. Deep RNA sequencing (RNA-seq) analyses show that SWAP1 regulates the gene expression and pre-messenger RNA (mRNA) alternative splicing of a large number of genes, including those involved in plant responses to light signaling. A comparative analysis of alternative splicing among single, double, and triple mutants showed that all three splicing factors coordinately regulate the alternative splicing of a subset of genes. Our study uncovered the function of a splicing factor that modulates light-regulated alternative splicing by interacting with photoactivated phyB and other splicing factors.

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis.

BACKGROUND: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. RESULTS: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts-twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage. CONCLUSIONS: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.

The Rice Serine/Arginine Splicing Factor RS33 Regulates Pre-mRNA Splicing during Abiotic Stress Responses.

Abiotic stresses profoundly affect plant growth and development and limit crop productivity. Pre-mRNA splicing is a major form of gene regulation that helps plants cope with various stresses. Serine/arginine (SR)-rich splicing factors play a key role in pre-mRNA splicing to regulate different biological processes under stress conditions. Alternative splicing (AS) of SR transcripts and other transcripts of stress-responsive genes generates multiple splice isoforms that contribute to protein diversity, modulate gene expression, and affect plant stress tolerance. Here, we investigated the function of the plant-specific SR protein RS33 in regulating pre-mRNA splicing and abiotic stress responses in rice. The loss-of-function mutant rs33 showed increased sensitivity to salt and low-temperature stresses. Genome-wide analyses of gene expression and splicing in wild-type and rs33 seedlings subjected to these stresses identified multiple splice isoforms of stress-responsive genes whose AS are regulated by RS33. The number of RS33-regulated genes was much higher under low-temperature stress than under salt stress. Our results suggest that the plant-specific splicing factor RS33 plays a crucial role during plant responses to abiotic stresses.

Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa.

Understanding gene expression and regulation requires insights into RNA transcription, processing, modification, and translation. However, the relationship between the epitranscriptome and the proteome under drought stress remains undetermined in poplar (Populus trichocarpa). In this study, we used Nanopore direct RNA sequencing and tandem mass tag-based proteomic analysis to examine epitranscriptomic and proteomic regulation induced by drought treatment in stem-differentiating xylem (SDX). Our results revealed a decreased full-length read ratio under drought treatment and, especially, a decreased association between transcriptome and proteome changes in response to drought. Epitranscriptome analysis of cellulose- and lignin-related genes revealed an increased N6-Methyladenosine (m6A) ratio, which was accompanied by decreased RNA abundance and translation, under drought stress. Interestingly, usage of the distal poly(A) site increased during drought stress. Finally, we found that transcripts of highly expressed genes tend to have shorter poly(A) tail length (PAL), and drought stress increased the percentage of transcripts with long PAL. These findings provide insights into the interplay among m6A, polyadenylation, PAL, and translation under drought stress in P. trichocarpa SDX.

Disparities Associated with Sepsis Mortality in Critically Ill Children.

Disparities in health care related to socioeconomic status and race/ethnicity are well documented in adult and neonatal sepsis, but they are less characterized in the critically ill pediatric population. This study investigated whether socioeconomic status and/or race/ethnicity is associated with mortality among children treated for sepsis in the pediatric intensive care unit (PICU). A retrospective cohort study was conducted using information from 48 children's hospitals included in the Pediatric Health Information System database. We included visits by children ≤ 21 years with All Patients Refined Diagnosis-Related Groups (APR-DRG) diagnosis codes of septicemia and disseminated infections that resulted in PICU admission from 2010 to 2016. Multivariable logistic regression was used to measure the effect of race/ethnicity and socioeconomic status (insurance status and median household income for zip code) on mortality after adjustment for age, gender, illness severity, and presence of complex chronic condition. Among the 14,276 patients with sepsis, the mortality rate was 6.8%. In multivariable analysis, socioeconomic status, but not race/ethnicity, was associated with mortality. In comparison to privately insured children, nonprivately insured children had increased odds of mortality (public: adjusted odds ratio [aOR]: 1.2 [1.0, 1.5]; uninsured: aOR: 2.1 [1.2, 3.7]). Similarly, children living in zip codes with the lowest quartile of annual household income had higher odds of mortality than those in the highest quartile (aOR: 1.5 [1.0, 2.2]). These data suggest the presence of socioeconomic, but not racial/ethnic, disparities in mortality among children treated for sepsis. Further research is warranted to understand why such differences exist and how they may be addressed.

RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data.

BACKGROUND: Despite recent progress in basecalling of Oxford nanopore DNA sequencing data, its wide adoption is still being hampered by its relatively low accuracy compared to short read technologies. Furthermore, very little of the recent research was focused on basecalling of RNA data, which has different characteristics than its DNA counterpart. RESULTS: We fill this gap by benchmarking a fully convolutional deep learning basecalling architecture with improved performance compared to Oxford nanopore's RNA basecallers. AVAILABILITY: The source code for our basecaller is available at: https://github.com/biodlab/RODAN .

An in-frame deletion mutation in the degron tail of auxin coreceptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale.

The natural auxin indole-3-acetic acid (IAA) is a key regulator of many aspects of plant growth and development. Synthetic auxin herbicides such as 2,4-D mimic the effects of IAA by inducing strong auxinic-signaling responses in plants. To determine the mechanism of 2,4-D resistance in a Sisymbrium orientale (Indian hedge mustard) weed population, we performed a transcriptome analysis of 2,4-D-resistant (R) and -susceptible (S) genotypes that revealed an in-frame 27-nucleotide deletion removing nine amino acids in the degron tail (DT) of the auxin coreceptor Aux/IAA2 (SoIAA2). The deletion allele cosegregated with 2,4-D resistance in recombinant inbred lines. Further, this deletion was also detected in several 2,4-D-resistant field populations of this species. Arabidopsis transgenic lines expressing the SoIAA2 mutant allele were resistant to 2,4-D and dicamba. The IAA2-DT deletion reduced binding to TIR1 in vitro with both natural and synthetic auxins, causing reduced association and increased dissociation rates. This mechanism of synthetic auxin herbicide resistance assigns an in planta function to the DT region of this Aux/IAA coreceptor for its role in synthetic auxin binding kinetics and reveals a potential biotechnological approach to produce synthetic auxin-resistant crops using gene-editing.

Cyanosis in a Newborn Immediately after Birth.

Cyanosis in a Newborn Immediately after BirthA male neonate, weighing 3.9 kg, was delivered via Cesarean section at 39 weeks of gestation. He cried immediately after birth, but his whole body appeared blue and he had low muscle tone that did not improve with suctioning and stimulation. Blow-by with 100% oxygen was initiated, and pulse oximetry on his left hand measured 40%. What is the diagnosis?