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The recent assembly and annotation of the 26 maize nested association mapping (NAM) population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein-protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene co-expression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes, but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.

Abstract Background ​​The genus Fusarium poses significant threats to food security and safety worldwide because numerous species of the fungus cause destructive diseases and/or mycotoxin contamination in crops. The adverse effects of climate change are exacerbating some existing threats and causing new problems. These challenges highlight the need for innovative solutions, including the development of advanced tools to identify targets for control strategies. Description In response to these challenges, we developed the Fusarium Protein Toolkit (FPT), a web-based tool that allows users to interrogate the structural and variant landscape within the Fusarium pan-genome. The tool displays both AlphaFold and ESMFold-generated protein structure models from six Fusarium species. The structures are accessible through a user-friendly web portal and facilitate comparative analysis, functional annotation inference, and identification of related protein structures. Using a protein language model, FPT predicts the impact of over 270 million coding variants in two of the most agriculturally important species, Fusarium graminearum and F. verticillioides. To facilitate the assessment of naturally occurring genetic variation, FPT provides variant effect scores for proteins in a Fusarium pan-genome based on 22 diverse species. The scores indicate potential functional consequences of amino acid substitutions and are displayed as intuitive heatmaps using the PanEffect framework. Conclusion FPT fills a knowledge gap by providing previously unavailable tools to assess structural and missense variation in proteins produced by Fusarium. FPT has the potential to deepen our understanding of pathogenic mechanisms in Fusarium, and aid the identification of genetic targets for control strategies that reduce crop diseases and mycotoxin contamination. Such targets are vital to solving the agricultural problems incited by Fusarium, particularly evolving threats resulting from climate change. Thus, FPT has the potential to contribute to improving food security and safety worldwide.

Abstract Given the absence of approved treatments for pathogenic variants in Peripherin-2 (PRPH2), it is imperative to identify a universally effective therapeutic target for PRPH2 pathogenic variants. To test the hypothesis that formation of the elongated discs in presence of PRPH2 pathogenic variants is due to the presence of the full complement of rhodopsin in absence of the required amounts of functional PRPH2. Here we demonstrate the therapeutic potential of reducing rhodopsin levels in ameliorating disease phenotype in knockin models for p.Lys154del (c.458-460del) and p.Tyr141Cys (c.422 A > G) in PRPH2. Reducing rhodopsin levels improves physiological function, mitigates the severity of disc abnormalities, and decreases retinal gliosis. Additionally, intravitreal injections of a rhodopsin-specific antisense oligonucleotide successfully enhance the physiological function of photoreceptors and improves the ultrastructure of discs in mutant mice. Presented findings shows that reducing rhodopsin levels is an effective therapeutic strategy for the treatment of inherited retinal degeneration associated with PRPH2 pathogenic variants.

Abstract Background Environmental stress factors, such as biotic and abiotic stress, are becoming more common due to climate variability, significantly affecting global maize yield. Transcriptome profiling studies provide insights into the molecular mechanisms underlying stress response in maize, though the functions of many genes are still unknown. To enhance the functional annotation of maize-specific genes, MaizeGDB has outlined a data-driven approach with an emphasis on identifying genes and traits related to biotic and abiotic stress. Results We mapped high-quality RNA-Seq expression reads from 24 different publicly available datasets (17 abiotic and seven biotic studies) generated from the B73 cultivar to the recent version of the reference genome B73 (B73v5) and deduced stress-related functional annotation of maize gene models. We conducted a robust meta-analysis of the transcriptome profiles from the datasets to identify maize loci responsive to stress, identifying 3,230 differentially expressed genes (DEGs): 2,555 DEGs regulated in response to abiotic stress, 408 DEGs regulated during biotic stress, and 267 common DEGs (co-DEGs) that overlap between abiotic and biotic stress. We discovered hub genes from network analyses, and among the hub genes of the co-DEGs we identified a putative NAC domain transcription factor superfamily protein (Zm00001eb369060) IDP275, which previously responded to herbivory and drought stress. IDP275 was up-regulated in our analysis in response to eight different abiotic and four different biotic stresses. A gene set enrichment and pathway analysis of hub genes of the co-DEGs revealed hormone-mediated signaling processes and phenylpropanoid biosynthesis pathways, respectively. Using phylostratigraphic analysis, we also demonstrated how abiotic and biotic stress genes differentially evolve to adapt to changing environments. Conclusions These results will help facilitate the functional annotation of multiple stress response gene models and annotation in maize. Data can be accessed and downloaded at the Maize Genetics and Genomics Database (MaizeGDB).

Capstone courses are considered a high impact practice with the potential to positively affect student learning. This article describes the design and implementation of a capstone in speech-language pathology designed to round out the undergraduate experience by shifting the learning focus away from disorder characteristics and onto individuals living with disabilities. The course is designed to teach students compassion, self-evaluation, and strategies for personal growth.

Neurodegeneration occurs naturally as humans age, but the presence of additional pathogenic mechanisms yields harmful and consequential effects on the brain. Alzheimer’s disease (AD), the most common form of dementia, is a composite of such factors. Despite extensive research to identify the exact causes of AD, therapeutic approaches for treating the disease continue to be ineffective, indicating important gaps in our understanding of disease mechanisms. Long non-coding RNAs (lncRNAs) are an endogenous class of regulatory RNA transcripts longer than 200 nucleotides, involved in various regulatory networks, whose dysregulation is evident in several neural and extraneural diseases. LncRNAs are ubiquitously expressed across all tissues with a wide range of functions, including controlling cell differentiation and development, responding to environmental stimuli, and other physiological processes. Several lncRNAs have been identified as potential contributors in worsening neurodegeneration due to altered regulation during abnormal pathological conditions. Within neurological disease, lncRNAs are prime candidates for use as biomarkers and pharmacological targets. Gender-associated lncRNA expression is altered in a gender-dependent manner for AD, suggesting more research needs to be focused on this relationship. Overall, research on lncRNAs and their connection to neurodegenerative disease is growing exponentially, as commercial enterprises are already designing and employing RNA therapeutics. In this review we offer a comprehensive overview of the current state of knowledge on the role of lncRNAs in AD and discuss the potential implications of lncRNA as potential therapeutic targets and diagnostic biomarkers in patients with Alzheimer’s disease.

Machine learning and modeling approaches have been used to classify protein sequences for a broad set of tasks including predicting protein function, structure, expression, and localization. Some recent studies have successfully predicted whether a given gene is expressed as mRNA or even translated to proteins potentially, but given that not all genes are expressed in every condition and tissue, the challenge remains to predict condition-specific expression. To address this gap, we developed a machine learning approach to predict tissue-specific gene expression across 23 different tissues in maize, solely based on DNA promoter and protein sequences. For class labels, we defined high and low expression levels for mRNA and protein abundance and optimized classifiers by systematically exploring various methods and combinations of k-mer sequences in a two-phase approach. In the first phase, we developed Markov model classifiers for each tissue and built a feature vector based on the predictions. In the second phase, the feature vector was used as an input to a Bayesian network for final classification. Our results show that these methods can achieve high classification accuracy of up to 95% for predicting gene expression for individual tissues. By relying on sequence alone, our method works in settings where costly experimental data are unavailable and reveals useful insights into the functional, evolutionary, and regulatory characteristics of genes.

BackgroundWith the advances in the high throughput next generation sequencing technologies, genome-wide association studies (GWAS) have identified a large set of variants associated with complex phenotypic traits at a very fine scale. Despite the progress in GWAS, identification of genotype-phenotype relationship remains challenging in maize due to its nature with dozens of variants controlling the same trait. As the causal variations results in the change in expression, gene expression analyses carry a pivotal role in unraveling the transcriptional regulatory mechanisms behind the phenotypes.ResultsTo address these challenges, we incorporated the gene expression and GWAS-driven traits to extend the knowledge of genotype-phenotype relationships and transcriptional regulatory mechanisms behind the phenotypes. We constructed a large collection of gene co-expression networks and identified more than 2 million co-expressing gene pairs in the GWAS-driven pan-network which contains all the gene-pairs in individual genomes of the nested association mapping (NAM) population. We defined four sub-categories for the pan-network: (1) core-network contains the highest represented ~ 1% of the gene-pairs, (2) near-core network contains the next highest represented 1-5% of the gene-pairs, (3) private-network contains ~ 50% of the gene pairs that are unique to individual genomes, and (4) the dispensable-network contains the remaining 50-95% of the gene-pairs in the maize pan-genome. Strikingly, the private-network contained almost all the genes in the pan-network but lacked half of the interactions. We performed gene ontology (GO) enrichment analysis for the pan-, core-, and private- networks and compared the contributions of variants overlapping with genes and promoters to the GWAS-driven pan-network.ConclusionsGene co-expression networks revealed meaningful information about groups of co-regulated genes that play a central role in regulatory processes. Pan-network approach enabled us to visualize the global view of the gene regulatory network for the studied system that could not be well inferred by the core-network alone.

Many caregivers of patients with neurodegenerative disease experience physical and psychological strain, which is associated with negative health outcomes. Caregiver strain may be partly attributable to negative emotional responses (e.g.of resentment) to the behavioral, cognitive, and physical changes associated with patients' disease. The philosopher Peter Strawson observed that in dealing with people who have neurological impairments, we often choose to suspend such emotional responses, adopting what he labeled the "objective attitude," though this may come at the expense of our relationships with them. In this study, we assessed the mediating effect of caregivers' adoption of the objective attitude on caregiver strain and relationship closeness in the setting of disease progression. Caregivers of patients with neurodegenerative disorders (n = 215) completed the Clinical Dementia Rating, Relationship-Closeness scale, Caregiver Strain Index, and a novel questionnaire assessing the adoption of the objective attitude. A structural equation model assessing associations among these variables demonstrated good fit (χ2 (88)=164.621, p

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

Abstract Background The associations of multimorbidity patterns with transitions between frailty states remain unclear in older individuals. Methods We used data from the National Health and Aging Trends Study 2011–2019. Frailty was measured annually using the Fried frailty phenotype. Multimorbidity patterns at baseline were identified using latent class analysis based on 14 chronic conditions. We used the semi‐Markov multi‐state model to investigate the influences of multimorbidity characterized by condition counts and patterns on subsequent frailty transitions over follow‐ups. Results Among 9450 participants aged ≥65 years at baseline, 34.8% were non‐frail, 48.1% were pre‐frail and 17.0% were frail. Over a median follow‐up of 4.0 years, 16 880 frailty transitions were observed, with 10 527 worsening and 6353 improving. For 7675 participants with multimorbidity, four multimorbidity patterns were identified: osteoarticular pattern (62.4%), neuropsychiatric–sensory pattern (17.2%), cardiometabolic pattern (10.3%) and complex multimorbidity pattern (10.1%). Compared with no disease, multimorbidity was significantly associated with an increased risk of worsening transitions, including from non‐frail to pre‐frail (hazard ratio [HR] = 1.35; 95% confidence interval [CI] = 1.21–1.52), from non‐frail to frail (HR = 1.68; 95% CI = 1.04–2.73), from pre‐frail to frail (HR = 2.19; 95% CI = 1.66–2.90) and from pre‐frail to death (HR = 1.64; 95% CI = 1.11–2.41). Compared with the osteoarticular pattern, neuropsychiatric–sensory, cardiometabolic and complex multimorbidity patterns had a significantly higher risk of worsening frailty (all P

Abstract Protein phosphorylation is a dynamic and reversible post‐translational modification that regulates a variety of essential biological processes. The regulatory role of phosphorylation in cellular signaling pathways, protein–protein interactions, and enzymatic activities has motivated extensive research efforts to understand its functional implications. Experimental protein phosphorylation data in plants remains limited to a few species, necessitating a scalable and accurate prediction method. Here, we present PhosBoost, a machine‐learning approach that leverages protein language models and gradient‐boosting trees to predict protein phosphorylation from experimentally derived data. Trained on data obtained from a comprehensive plant phosphorylation database, qPTMplants, we compared the performance of PhosBoost to existing protein phosphorylation prediction methods, PhosphoLingo and DeepPhos. For serine and threonine prediction, PhosBoost achieved higher recall than PhosphoLingo and DeepPhos (.78, .56, and .14, respectively) while maintaining a competitive area under the precision‐recall curve (.54, .56, and .42, respectively). PhosphoLingo and DeepPhos failed to predict any tyrosine phosphorylation sites, while PhosBoost achieved a recall score of .6. Despite the precision‐recall tradeoff, PhosBoost offers improved performance when recall is prioritized while consistently providing more confident probability scores. A sequence‐based pairwise alignment step improved prediction results for all classifiers by effectively increasing the number of inferred positive phosphosites. We provide evidence to show that PhosBoost models are transferable across species and scalable for genome‐wide protein phosphorylation predictions. PhosBoost is freely and publicly available on GitHub.

Visual signal transduction takes place within a stack of flattened membranous ‘discs’ enclosed within the light-sensitive photoreceptor outer segment. The highly curved rims of these discs, formed in the process of disc enclosure, are fortified by large hetero-oligomeric complexes of two homologous tetraspanin proteins, PRPH2 (a.k.a. peripherin-2 or rds) and ROM1. While mutations in PRPH2 affect the formation of disc rims, the role of ROM1 remains poorly understood. In this study, we found that the knockout of ROM1 causes a compensatory increase in the disc content of PRPH2. Despite this increase, discs of ROM1 knockout mice displayed a delay in disc enclosure associated with a large diameter and lack of incisures in mature discs. Strikingly, further increasing the level of PRPH2 rescued these morphological defects. We next showed that disc rims are still formed in a knockin mouse in which the tetraspanin body of PRPH2 was replaced with that of ROM1. Together, these results demonstrate that, despite its contribution to the formation of disc rims, ROM1 can be replaced by an excess of PRPH2 for timely enclosure of newly forming discs and establishing normal outer segment structure.

BackgroundGene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available gene annotation software applications depend on pre-constructed full-length gene sequence assemblies which are not guaranteed to be error-free. The origins of these sequences are often uncertain, making it difficult to identify and rectify errors in them. This hinders the creation of an accurate and holistic representation of the transcriptomic landscape across multiple tissue types and experimental conditions. Therefore, to gauge the extent of diversity in gene structures, a comprehensive analysis of genome-wide expression data is imperative.ResultsWe present FINDER, a fully automated computational tool that optimizes the entire process of annotating genes and transcript structures. Unlike current state-of-the-art pipelines, FINDER automates the RNA-Seq pre-processing step by working directly with raw sequence reads and optimizes gene prediction from BRAKER2 by supplementing these reads with associated proteins. The FINDER pipeline (1) reports transcripts and recognizes genes that are expressed under specific conditions, (2) generates all possible alternatively spliced transcripts from expressed RNA-Seq data, (3) analyzes read coverage patterns to modify existing transcript models and create new ones, and (4) scores genes as high- or low-confidence based on the available evidence across multiple datasets. We demonstrate the ability of FINDER to automatically annotate a diverse pool of genomes from eight species.ConclusionsFINDER takes a completely automated approach to annotate genes directly from raw expression data. It is capable of processing eukaryotic genomes of all sizes and requires no manual supervision-ideal for bench researchers with limited experience in handling computational tools.

BACKGROUND:Maize experienced a whole-genome duplication event approximately 5 to 12 million years ago. Because this event occurred after speciation from sorghum, the pre-duplication subgenomes can be partially reconstructed by mapping syntenic regions to the sorghum chromosomes. During evolution, maize has had uneven gene loss between each ancient subgenome. Fractionation and divergence between these genomes continue today, constantly changing genetic make-up and phenotypes and influencing agronomic traits. RESULTS:Here we regenerate the subgenome reconstructions for the most recent maize reference genome assembly. Based on both expression and abundance data for homeologous gene pairs across multiple tissues, we observed functional divergence of genes across subgenomes. Although the genes in the larger maize subgenome are often expressing more highly than their homeologs in the smaller subgenome, we observed cases where homeolog expression dominance switches in different tissues. We demonstrate for the first time that protein abundances are higher in the larger subgenome, but they also show tissue-specific dominance, a pattern similar to RNA expression dominance. We also find that pollen expression is uniquely decoupled from protein abundance. CONCLUSION:Our study shows that the larger subgenome has a greater range of functional assignments and that there is a relative lack of overlap between the subgenomes in terms of gene functions than would be suggested by similar patterns of gene expression and protein abundance. Our study also revealed that some reactions are catalyzed uniquely by the larger and smaller subgenomes. The tissue-specific, nonequivalent expression-level dominance pattern observed here implies a change in regulatory control which favors differentiated selective pressure on the retained duplicates leading to eventual change in gene functions.

The first steps of vision take place within a stack of tightly packed disc-shaped membranes, or ‘discs’, located in the outer segment compartment of photoreceptor cells. In rod photoreceptors, discs are enclosed inside the outer segment and contain deep indentations in their rims called ‘incisures’. The presence of incisures has been documented in a variety of species, yet their role remains elusive. In this study, we combined traditional electron microscopy with three-dimensional electron tomography to demonstrate that incisures are formed only after discs become completely enclosed. We also observed that, at the earliest stage of their formation, discs are not round as typically depicted but rather are highly irregular in shape and resemble expanding lamellipodia. Using genetically manipulated mice and frogs and measuring outer segment protein abundances by quantitative mass spectrometry, we further found that incisure size is determined by the molar ratio between peripherin-2, a disc rim protein critical for the process of disc enclosure, and rhodopsin, the major structural component of disc membranes. While a high perpherin-2 to rhodopsin ratio causes an increase in incisure size and structural complexity, a low ratio precludes incisure formation. Based on these data, we propose a model whereby normal rods express a modest excess of peripherin-2 over the amount required for complete disc enclosure in order to ensure that this important step of disc formation is accomplished. Once the disc is enclosed, the excess peripherin-2 incorporates into the rim to form an incisure.

MotivationPlant breeding aims to improve current germplasm that can tolerate a wide range of biotic and abiotic stresses. To accomplish this goal, breeders rely on developing a deeper understanding of genetic makeup and relationships between plant varieties to make informed plant selections. Although rapid advances in genotyping technology generated a large amount of data for breeders, tools that facilitate pedigree analysis and visualization are scant, leaving breeders to use classical, but inherently limited, hierarchical pedigree diagrams for a handful of plant varieties. To answer this need, we developed a simple web-based tool that can be easily implemented at biological databases, called PedigreeNet, to create and visualize customizable pedigree relationships in a network context, displaying pre- and user-uploaded data.ResultsAs a proof-of-concept, we implemented PedigreeNet at the maize model organism database, MaizeGDB. The PedigreeNet viewer at MaizeGDB has a dynamically-generated pedigree network of 4706 maize lines and 5487 relationships that are currently available as both a stand-alone web-based tool and integrated directly on the MaizeGDB Stock Pages. The tool allows the user to apply a number of filters, select or upload their own breeding relationships, center a pedigree network on a plant variety, identify the common ancestor between two varieties, and display the shortest path(s) between two varieties on the pedigree network. The PedigreeNet code layer is written as a JavaScript wrapper around Cytoscape Web. PedigreeNet fills a great need for breeders to have access to an online tool to represent and visually customize pedigree relationships.Availability and implementationPedigreeNet is accessible at https://www.maizegdb.org/breeders_toolbox. The open source code is publically and freely available at GitHub: https://github.com/Maize-Genetics-and-Genomics-Database/PedigreeNet.Supplementary informationSupplementary data are available at Bioinformatics online.

Abstract Background With the advances in the high throughput next generation sequencing technologies, genome-wide association studies (GWAS) have identified a large set of variants associated with complex phenotypic traits at a very fine scale. Despite the progress in GWAS, identification of genotype-phenotype relationship remains challenging in maize due to its nature with dozens of variants controlling the same trait. As the causal variations results in the change in expression, gene expression analyses carry a pivotal role in unraveling the transcriptional regulatory mechanisms behind the phenotypes. Results To address these challenges, we incorporated the gene expression and GWAS-driven traits to extend the knowledge of genotype-phenotype relationships and transcriptional regulatory mechanisms behind the phenotypes. We constructed a large collection of gene co-expression networks and identified more than 2 million co-expressing gene pairs in the GWAS-driven pan-network which contains all the gene-pairs in individual genomes of the nested association mapping (NAM) population. We defined four sub-categories for the pan-network: (1) core-network contains the highest represented ~ 1% of the gene-pairs, (2) near-core network contains the next highest represented 1–5% of the gene-pairs, (3) private-network contains ~ 50% of the gene pairs that are unique to individual genomes, and (4) the dispensable-network contains the remaining 50–95% of the gene-pairs in the maize pan-genome. Strikingly, the private-network contained almost all the genes in the pan-network but lacked half of the interactions. We performed gene ontology (GO) enrichment analysis for the pan-, core-, and private- networks and compared the contributions of variants overlapping with genes and promoters to the GWAS-driven pan-network. Conclusions Gene co-expression networks revealed meaningful information about groups of co-regulated genes that play a central role in regulatory processes. Pan-network approach enabled us to visualize the global view of the gene regulatory network for the studied system that could not be well inferred by the core-network alone.

Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in addition to the B73 reference genome assembly. Curation and development efforts have targeted high quality datasets and tools to support maize trait analysis, germplasm analysis, genetic studies, and breeding. MaizeGDB hosts a wide range of data including recent support of new data types including genome metadata, RNA-seq, proteomics, synteny, and large-scale diversity. To improve access and visualization of data types several new tools have been implemented to: access large-scale maize diversity data (SNPversity), download and compare gene expression data (qTeller), visualize pedigree data (Pedigree Viewer), link genes with phenotype images (MaizeDIG), and enable flexible user-specified queries to the MaizeGDB database (MaizeMine). MaizeGDB also continues to be the community hub for maize research, coordinating activities and providing technical support to the maize research community. Here we report the changes MaizeGDB has made within the last three years to keep pace with recent software and research advances, as well as the pan-genomic landscape that cheaper and better sequencing technologies have made possible. MaizeGDB is accessible online at https://www.maizegdb.org.

ObjectivesNo gold standard for ideal body weight determination in children exists. We aimed to compare four methods of ideal body weight calculation and determine level of agreement between methods and impact of measurement variance on tidal volumes prescribed in mechanically ventilated pediatric acute respiratory distress syndrome.DesignPost hoc analysis of four multicenter pediatric acute respiratory distress syndrome studies.SettingTwenty-six academic PICUs.PatientsFive hundred eighty-nine patients.InterventionsNone.Measurements and main resultsIdeal body weight was calculated by four common methods: National Center for Health Statistics, McLaren, Moore, and body mass index, and compared in three ways: 1) determine the proportion of the cohort for which each method could successfully calculate ideal body weight; 2) compare the level of agreement between the ideal body weight methods by Bland-Altman analysis; and 3) evaluate the difference in tidal volume when 6 mL/kg ideal body weight was prescribed. We a priori defined the better method to be one that could calculate ideal body weight in most subjects, had good agreement with other methods, and led to a lower tidal volume. Only 55% could have ideal body weight measured by all four methods. National Center for Health Statistics, McLaren, and Moore methods could calculate ideal body weight in greater than or equal to 90%, whereas body mass index method was successful in only 61% because of no body mass index validation in less than 2-year-olds. In comparing each method to the others, there was great variance, particularly in greater than or equal to 10-year-olds. This variance was greatest between Moore and body mass index methods with greater than or equal to 10 kg difference in ideal body weight in some subjects. The McLaren method had the best agreement with all other methods, and yielded similar prescribed tidal volume in 2- to 10-year-olds and lower tidal volume in greater than or equal to 10 years old.ConclusionsThere is substantial variation in calculated ideal body weight among four commonly used methods, particularly in adolescents. Since varying ideal body weight may lead to discrepancies in pediatric acute respiratory distress syndrome care, a standard approach to ideal body weight measurement is needed. We recommend the McLaren method to calculate ideal body weight in children with pediatric acute respiratory distress syndrome until a gold standard method is validated.

The first steps of vision take place in the ciliary outer segment compartment of photoreceptor cells. The protein composition of outer segments is uniquely suited to perform this function. The most abundant among these proteins is the visual pigment, rhodopsin, whose outer segment trafficking involves intraflagellar transport (IFT). Here, we report three major findings from the analysis of mice in which ciliary transport was acutely impaired by conditional knockouts of IFT-B subunits. First, we demonstrate the existence of a sorting mechanism whereby mislocalized rhodopsin is recruited to and concentrated in extracellular vesicles prior to their release, presumably to protect the cell from adverse effects of protein mislocalization. Second, reducing rhodopsin expression significantly delays photoreceptor degeneration caused by IFT disruption, suggesting that controlling rhodopsin levels may be an effective therapy for some cases of retinal degenerative disease. Last, the loss of IFT-B subunits does not recapitulate a phenotype observed in mutants of the BBSome (another ciliary transport protein complex relying on IFT) in which non-ciliary proteins accumulate in the outer segment. Whereas it is widely thought that the role of the BBSome is to primarily participate in ciliary transport, our data suggest that the BBSome has another major function independent of IFT and possibly related to maintaining the diffusion barrier of the ciliary transition zone. [ABSTRACT FROM AUTHOR]

Neurodegeneration occurs naturally as humans age, but the presence of additional pathogenic mechanisms yields harmful and consequential effects on the brain. Alzheimer's disease (AD), the most common form of dementia, is a composite of such factors. Despite extensive research to identify the exact causes of AD, therapeutic approaches for treating the disease continue to be ineffective, indicating important gaps in our understanding of disease mechanisms. Long non-coding RNAs (lncRNAs) are an endogenous class of regulatory RNA transcripts longer than 200 nucleotides, involved in various regulatory networks, whose dysregulation is evident in several neural and extraneural diseases. LncRNAs are ubiquitously expressed across all tissues with a wide range of functions, including controlling cell differentiation and development, responding to environmental stimuli, and other physiological processes. Several lncRNAs have been identified as potential contributors in worsening neurodegeneration due to altered regulation during abnormal pathological conditions. Within neurological disease, lncRNAs are prime candidates for use as biomarkers and pharmacological targets. Gender-associated lncRNA expression is altered in a gender-dependent manner for AD, suggesting more research needs to be focused on this relationship. Overall, research on lncRNAs and their connection to neurodegenerative disease is growing exponentially, as commercial enterprises are already designing and employing RNA therapeutics. In this review we offer a comprehensive overview of the current state of knowledge on the role of lncRNAs in AD and discuss the potential implications of lncRNA as potential therapeutic targets and diagnostic biomarkers in patients with Alzheimer's disease. [ABSTRACT FROM AUTHOR]

https://www.maizegdb.org/snpversity.

Abstract Research in the past decade has demonstrated that a single reference genome is not representative of a species’ diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural variation, transposable elements, and diversity data across genomes so that researchers can easily track the structural and functional differences of a locus and its orthologs across maize. We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data.

SUMMARY: Responses to shifting consumer preferences and demands for alternative rearing programs have resulted in a re-evaluation of lighting programs by the commercial broiler industry. The objectives of this study were to compare light intensity levels, distribution, and uniformity in curtain-sided broiler houses using 2 lighting program treatments: (1) natural light only (NL) and (2) traditional light-emitting diode (LED). The natural light treatment was created by retrofitting an existing curtain with a translucent one. Combined area through which natural light entered the house equaled 10% of the total floor area. A high-density data acquisition system was used to measure light intensity (505 locations per replication) at a fixed point in time (static). Three house sections (pad, mid-house, and fan) were monitored over a 24 h period (temporal) in August and December 2020. Results from the static testing indicate that light intensities were significantly higher (P < 0.05) in the pad, mid-house, and fan sections of the NL house during both testing events. Mean house section light intensities ranged from 1.8 to 71.6 lx in the LED treatment and 9.2 to 545.1 lx in the NL treatment. During both temporal testing events, light intensity was also significantly higher (P < 0.05) in the pad, mid-house, and fan sections for the NL treatment. Light intensity values were as high as 6,000 lx in the NL treatment, over 600 times higher than levels generally accepted by the industry. This study showed that provision of natural light in broiler houses drastically increases light levels throughout the house and reduces overall spatial uniformity.

Abstract Background Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available gene annotation software applications depend on pre-constructed full-length gene sequence assemblies which are not guaranteed to be error-free. The origins of these sequences are often uncertain, making it difficult to identify and rectify errors in them. This hinders the creation of an accurate and holistic representation of the transcriptomic landscape across multiple tissue types and experimental conditions. Therefore, to gauge the extent of diversity in gene structures, a comprehensive analysis of genome-wide expression data is imperative. Results We present FINDER, a fully automated computational tool that optimizes the entire process of annotating genes and transcript structures. Unlike current state-of-the-art pipelines, FINDER automates the RNA-Seq pre-processing step by working directly with raw sequence reads and optimizes gene prediction from BRAKER2 by supplementing these reads with associated proteins. The FINDER pipeline (1) reports transcripts and recognizes genes that are expressed under specific conditions, (2) generates all possible alternatively spliced transcripts from expressed RNA-Seq data, (3) analyzes read coverage patterns to modify existing transcript models and create new ones, and (4) scores genes as high- or low-confidence based on the available evidence across multiple datasets. We demonstrate the ability of FINDER to automatically annotate a diverse pool of genomes from eight species. Conclusions FINDER takes a completely automated approach to annotate genes directly from raw expression data. It is capable of processing eukaryotic genomes of all sizes and requires no manual supervision—ideal for bench researchers with limited experience in handling computational tools.

The Maize Genetics and Genomics Database (MaizeGDB) team prepared a survey to identify breeders’ needs for visualizing pedigrees, diversity data and haplotypes in order to prioritize tool development and curation efforts at MaizeGDB. The survey was distributed to the maize research community on behalf of the Maize Genetics Executive Committee in Summer 2015. The survey garnered 48 responses from maize researchers, of which more than half were self-identified as breeders. The survey showed that the maize researchers considered their top priorities for visualization as: (i) displaying single nucleotide polymorphisms in a given region for a given list of lines, (ii) showing haplotypes for a given list of lines and (iii) presenting pedigree relationships visually. The survey also asked which populations would be most useful to display. The following two populations were on top of the list: (i) 3000 publicly available maize inbred lines used in Romay et al. (Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol, 2013;14:R55) and (ii) maize lines with expired Plant Variety Protection Act (ex-PVP) certificates. Driven by this strong stakeholder input, MaizeGDB staff are currently working in four areas to improve its interface and web-based tools: (i) presenting immediate progenies of currently available stocks at the MaizeGDB Stock pages, (ii) displaying the most recent ex-PVP lines described in the Germplasm Resources Information Network (GRIN) on the MaizeGDB Stock pages, (iii) developing network views of pedigree relationships and (iv) visualizing genotypes from SNP-based diversity datasets. These survey results can help other biological databases to direct their efforts according to user preferences as they serve similar types of data sets for their communities. https://www.maizegdb.org.

ObjectivesTo determine the frequency of low-tidal volume ventilation in pediatric acute respiratory distress syndrome and assess if any demographic or clinical factors improve low-tidal volume ventilation adherence.DesignDescriptive post hoc analysis of four multicenter pediatric acute respiratory distress syndrome studies.SettingTwenty-six academic PICU.PatientsThree hundred fifteen pediatric acute respiratory distress syndrome patients.Measurements and main resultsAll patients who received conventional mechanical ventilation at hours 0 and 24 of pediatric acute respiratory distress syndrome who had data to calculate ideal body weight were included. Two cutoff points for low-tidal volume ventilation were assessed: less than or equal to 6.5 mL/kg of ideal body weight and less than or equal to 8 mL/kg of ideal body weight. Of 555 patients, we excluded 240 for other respiratory support modes or missing data. The remaining 315 patients had a median PaO2-to-FIO2 ratio of 140 (interquartile range, 90-201), and there were no differences in demographics between those who did and did not receive low-tidal volume ventilation. With tidal volume cutoff of less than or equal to 6.5 mL/kg of ideal body weight, the adherence rate was 32% at hour 0 and 33% at hour 24. A low-tidal volume ventilation cutoff of tidal volume less than or equal to 8 mL/kg of ideal body weight resulted in an adherence rate of 58% at hour 0 and 60% at hour 24. Low-tidal volume ventilation use was no different by severity of pediatric acute respiratory distress syndrome nor did adherence improve over time. At hour 0, overweight children were less likely to receive low-tidal volume ventilation less than or equal to 6.5 mL/kg ideal body weight (11% overweight vs 38% nonoverweight; p = 0.02); no difference was noted by hour 24. Furthermore, in the overweight group, using admission weight instead of ideal body weight resulted in misclassification of up to 14% of patients as receiving low-tidal volume ventilation when they actually were not.ConclusionsLow-tidal volume ventilation is underused in the first 24 hours of pediatric acute respiratory distress syndrome. Age, Pediatric Risk of Mortality-III, and pediatric acute respiratory distress syndrome severity were not associated with improved low-tidal volume ventilation adherence nor did adherence improve over time. Overweight children were less likely to receive low-tidal volume ventilation strategies in the first day of illness.

Machine learning and modeling approaches have been used to classify protein sequences for a broad set of tasks including predicting protein function, structure, expression, and localization. Some recent studies have successfully predicted whether a given gene is expressed as mRNA or even translated to proteins potentially, but given that not all genes are expressed in every condition and tissue, the challenge remains to predict condition-specific expression. To address this gap, we developed a machine learning approach to predict tissue-specific gene expression across 23 different tissues in maize, solely based on DNA promoter and protein sequences. For class labels, we defined high and low expression levels for mRNA and protein abundance and optimized classifiers by systematically exploring various methods and combinations of k-mer sequences in a two-phase approach. In the first phase, we developed Markov model classifiers for each tissue and built a feature vector based on the predictions. In the second phase, the feature vector was used as an input to a Bayesian network for final classification. Our results show that these methods can achieve high classification accuracy of up to 95% for predicting gene expression for individual tissues. By relying on sequence alone, our method works in settings where costly experimental data are unavailable and reveals useful insights into the functional, evolutionary, and regulatory characteristics of genes.

The objective of the three experiments herein were to characterize the effect of pharmacological zinc and copper concentrations on nursery pig feed intake, stomach ghrelin, energy and nutrient digestibility, and mineral retention in post-weaned pigs. In Expt. 1, 300 weaned pigs were allotted across three dietary treatments (n = 10 pens/treatment) and fed in two diet phases (P1 and P2) lasting 7 and 14 days, respectively. Treatments were: (1) Control diet with no pharmacological minerals in P1 and P2, CON; (2) CON + 3,000 mg/kg Zn and 200 mg/kg Cu (P1), no pharmacological minerals in P2, ZC-CON; and (3) CON + 3,000 mg/kg Zn and 200 mg/kg Cu (P1), CON + 2,000 mg/kg Zn and 200 mg/kg Cu (P2); ZC. Over the 21-day test period, ZC pigs had 15% higher ADG and 13–24% ADFI compared to the CON and ZC-CON pigs (P < 0.05). ZC-CON and ZC pig daily feed intakes were 29 and 73% higher by day 5 and 7 post-weaning, respectively, compared to the CON pigs (P < 0.0001). However, removing pharmacological minerals in P2 abruptly decreased ZC-CON daily feed intake within 24 h to similar intakes as the CON compared to the ZC pigs (0.17, 0.14, and 0.22 kg/d, respectively, P < 0.05). Dietary pharmacological minerals increased stomach fundus ghrelin-positive cells than CON pigs at day 7 (P = 0.005) and day 21 (P < 0.001). However, fasting plasma total and acyl-ghrelin concentrations did not differ from a control in response to zinc oxide daily drenching (Expt. 2). Expt. 3 showed that zinc and copper to have moderate to low retention; however, pharmacological zinc and copper diets increased zinc (P < 0.05) and copper retention (P = 0.06) after 28 days post-weaning compared to control pigs. Pharmacological zinc and copper did not improve digestible energy, metabolizable energy or nitrogen balance. Altogether, dietary pharmacological zinc and copper concentrations improve growth rates and mineral retention in nursery pigs. This improved performance may partially be explained by increased stomach ghrelin abundance and enhanced early feed intake in newly weaned pigs fed pharmacological concentrations of zinc and copper.

Background Among combat injured, invasive fungal infections (IFIs) result in significant morbidity. Cultures and histopathology are the primary diagnostic methods for IFIs, but they have limitations. We previously evaluated a panfungal polymerase chain reaction assay, which was 83% sensitive and 99% specific for angioinvasive IFIs. Here, we evaluated 3 less resource-intensive seminested assays targeting clinically relevant fungi in the order Mucorales and genera Aspergillus and Fusarium. Methods Formalin-fixed paraffin-embedded tissue specimens from a multicenter trauma IFI cohort (2009-2014) were used. Cases were US military personnel injured in Afghanistan with histopathologic IFI evidence. Controls were patients with similar injury patterns and no laboratory IFI evidence (negative culture and histopathology). Seminested assays specific to Mucorales (V4/V5 regions of 18S rDNA), Aspergillus (mitochondrial tRNA), and Fusarium (internal transcribed spacer [ITS]/28A regions of DNA) were compared with a panfungal assay amplifying the internal transcribed spacer 2 region of rDNA and to histopathology. Results Specimens from 92 injury sites (62 subjects) were compared with control specimens from 117 injuries (101 subjects). We observed substantial agreement between the seminested and panfungal assays overall, especially for the order Mucorales. Moderate agreement was observed at the genus level for Aspergillus and Fusarium. When compared with histopathology, sensitivity and specificity of seminested assays were 67.4% and 96.6%, respectively (sensitivity increased to 91.7% when restricted to sites with angioinvasion). Conclusions Prior studies of seminested molecular diagnostics have focused on culture-negative samples from immunocompromised patients. Our findings underscore the utility of the seminested approach in diagnosing soft-tissue IFIs using formalin-fixed paraffin-embedded tissue samples, especially with angioinvasion. [ABSTRACT FROM AUTHOR]

Objectives: This study examines the association between family conflict and self-efficacy in discussing end-of-life (EOL) care with family members and whether such an association differs by acculturation levels among older Chinese Americans. Method: Data were collected from 213 Chinese Americans ages 65–102 in Phoenix, AZ, and Germantown, MD. We conducted ordinary least squares regression to examine the association between family conflict, acculturation, and self-efficacy in discussing EOL care with family. Results : Family conflict was negatively associated with older adults' self-efficacy in discussing EOL care with family. The negative association between family conflict and self-efficacy in discussing EOL care with family was more pronounced for those with higher levels of acculturation. Conclusions: As one of the first research efforts to study advance care planning among older Chinese Americans, our findings highlight differential effects of family conflict on self-efficacy of EOL care plan discussion within the context of acculturation levels. Geriatric and health social workers should assess and address acculturation to develop family-centered interventions that improve EOL care planning for older Chinese Americans. [ABSTRACT FROM AUTHOR]

Background: The toll of tuberculous meningitis (TBM) in both mortality and disability is considerable, but advancements in rehabilitation have the potential to improve the functional abilities and the quality of survivors’ lives. However, the typical phenotype of neurocognitive impairment in TBM survivors remains unstudied in HIV-predominant populations in sub-Saharan Africa. Methods: We tested 36 survivors of TBM in Uganda with a comprehensive battery of neurocognitive assessments at 8 and 24 weeks after diagnosis, and compared results to a representative cohort of HIV-uninfected Ugandans. Results: While participants had a broad range of impairments at eight weeks, there was marked improvement by 24 weeks, when a phenotype of impairment including deficits in motor functioning, verbal learning and memory, processing speed, and executive function emerged. These deficits were present despite good clinician-rated functional status. The majority (23/27, 85%) had evidence of moderate to severe depression at week 8, and at week 24 (18/24, 75%). Conclusion: These findings highlight the need for more comprehensive neurocognitive assessment in the survivors of TBM, and further investment in and study of rehabilitation, including management of depression, to improve long-term outcomes in this population.

Category: Sports; Other Introduction/Purpose: Achilles tendon repairs and reconstructions have historically been associated with high wound infection rates due to poor vascularity in this region. The risk of postoperative infection, a potentially devastating complication, has led surgeons to pursue non-operative treatment when possible for a range of Achilles tendon pathology. However, new surgical techniques have allowed for smaller incisions and modern, aggressive infection control strategies have limited the morbidity associated with these complications. The present study will review a large case series of Achilles infections, evaluating treatment strategies and outcomes for patients who developed a postoperative infection following treatment for Achilles pathology. Methods: This is a retrospective case series including all patients who experienced a postoperative Achilles tendon infection at a single hospital. Cases from 11 surgeons performed between 2011 and 2020 were reviewed for infection requiring a return to the operating room for irrigation, debridement, and any other necessary interventions. Cases that presented to our institution with an existing infection were also included. Thorough chart review was performed for all patients to determine pathology and initial treatment method, infection management, and clinical outcomes. For patients undergoing Achilles reconstruction with a graft, operative notes were reviewed to determine whether the graft was infected and thus removed during debridement. Clinical follow-up was performed and Patient-Reported Outcomes Measurement Information System (PROMIS) surveys were sent to all patients who were over 1 year out from surgery. Results: 33 patients experienced a postoperative Achilles infection, including 10 who developed infection after surgery at an outside hospital. For patients treated initially at our institution, 8 presented with an acute rupture and 15 with chronic pathology. 12 of 15 chronic cases underwent reconstruction with a graft. For 3 reconstructions and 1 acute repair (12%) the entire Achilles was infected and removed. The graft was partially removed in 2 reconstruction cases (6%) and remained fully intact in the remaining 27 cases (82%). In 2/4 cases in which the Achilles was removed, it ultimately reconstituted as confirmed on MRI. A skin graft or flap was required in 5 of 33 cases (15%) for adequate soft-tissue coverage. In 14 cases (42%), the infection was controlled after a single debridement, 17 cases (52%) required a second debridement, and 2 cases (6%) a third. Postoperative PROMIS scores were available for 17 patients (Table 1). Conclusion: To our knowledge, this case series represents the largest number of postoperative infections analyzed following Achilles tendon surgery. Relatively high postoperative PROMIS scores indicate that infected patients can ultimately reach high levels of physical function with minimal pain when managed appropriately. In many cases the Achilles or graft could be salvaged and in those where it was not, the tendon did at times reconstitute.

Category: Sports; Other Introduction/Purpose: Post-operative infections can be a devastating complication after Achilles tendon surgery. While Achilles infection rates have decreased with the development of less invasive surgical techniques, these infections remain a challenging complication for patients and clinicians due to the relative lack of vasculature in the Achilles tendon region. This study aimed to analyze rates of postoperative Achilles tendon infection based on the type of Achilles pathology and surgical approach. We hypothesized that procedures with smaller incisions that avoided the critical zone would be associated with lower infection rates than those that require larger incisions, such as reconstructions. Methods: All patients undergoing Achilles tendon surgery at a single, multi-surgeon center between 2011 and 2020 were identified. Charts were reviewed for infection, pathology, surgical approach, incision size, and risk factors such as body mass index (BMI), smoking status, and diabetes. Rates of infection were compared between groups based on pathology and operative technique. These groups included acute rupture treated immediately, chronic pathology treated with debridement and repair, and chronic pathology treated with graft reconstruction. For patients treated for an acute rupture, minimally invasive and open approach sub-groups were compared. Further, prevalence of risk factors was compared between patients with and without post- operative infections. Statistical comparisons were performed between groups using a student's t-test or Fisher's exact test. Results: A total of 1,148 cases were identified, 23 of which involved a post-operative infection requiring a return to the operating room for irrigation and debridement. The overall infection rate was 2.00%. Cases involving chronic pathology treated with graft reconstruction were associated with an infection rate of 8.96%. Acute repairs had an infection rate of 1.32% and other chronic pathologies treated without graft reconstruction had an infection rate of 0.73%. Statistical comparisons of infection rates for these sub-groups are displayed in Table 1 alongside comparisons of risk factor prevalence between the infection and non-infection groups. The comparison of risk factors between groups did not identify any significant differences. No infections were observed following the use of a distal lateral incision to treat chronic tendon pathology (179 cases) or the use of a windows incision technique for reconstructions (8 cases). Conclusion: Analysis of infection rates indicated that treatment options requiring large incisions, such as reconstruction with a graft, pose a significantly greater risk of post-operative Achilles infection. Both minimally invasive treatments and measured open incisions were associated with similarly low infection rates for primary repair of acute ruptures. Comparison of risk factors between patients with and without infection did not reveal any significant differences. Given low infection rates for chronic pathology treated with distal lateral incisions and windows-type incisions, we recommend these whenever possible.