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One promising goal for utilizing the molecular information circulating in biofluids is the discovery of clinically useful biomarkers. Extracellular RNAs (exRNAs) are one of the most diverse classes of molecular cargo, easily assayed by sequencing and with expressions that rapidly change in response to subject status. Despite diverse exRNA cargo, most evaluations from biofluids have focused on small RNA sequencing and analysis, specifically on microRNAs (miRNAs). Another goal of characterizing circulating molecular information, is to correlate expression to injuries associated with specific tissues of origin. Biomarker candidates are often described as being specific, enriched in a particular tissue or associated with a disease process. Likewise, miRNA data is often reported to be specific, enriched for a tissue, without rigorous testing to support the claim. Here we provide a tissue atlas of small RNAs from 30 different tissues and three different blood cell types. We analyzed the tissues for enrichment of small RNA sequences and assessed their expression in biofluids: plasma, cerebrospinal fluid, urine, and saliva. We employed published data sets representing physiological (resting vs. acute exercise) and pathologic states (early- vs. late-stage liver fibrosis, and differential subtypes of stroke) to determine differential tissue-enriched small RNAs. We also developed an online tool that provides information about exRNA sequences found in different biofluids and tissues. The data can be used to better understand the various types of small RNA sequences in different tissues as well as their potential release into biofluids, which should help in the validation or design of biomarker studies.

Objectives: We sought to document the mucin gene profile in normal human laryngeal epithelium and compare it with that in patients with reflux-attributed laryngeal injury or disease. We also investigated the effect of low pH with or without pepsin on mucin messenger RNA levels in vitro. Methods: Laryngeal biopsy specimens were obtained from 3 patients with clinically diagnosed laryngopharyngeal reflux and from 2 control subjects who had no signs or symptoms of reflux. Signs and symptoms were assessed by the Reflux Finding Score and the Reflux Symptom Index, respectively. Reverse transcription–polymerase chain reaction (RT-PCR) was performed to establish the mucin gene profile. Human hypopharyngeal epithelial cells were exposed to pH 7, 5, 4, and 2 with and without pepsin (0.1 mg/mL) for 20 minutes at 37°C, and expression of selected mucins was analyzed via real-time RT-PCR. Results: Mucin 1–5, 7, 9, 13, 15, 16, and 18–20 transcripts were detected in normal laryngeal epithelium, whereas mucin 6, 8, and 17 transcripts were not. Mucins 2, 3, and 5 were expressed at reduced levels in patients with reflux-attributed laryngeal injury or disease. These mucin genes were up-regulated after exposure to low pH in vitro (p < 0.005). Pepsin inhibited this up-regulation (p < 0.001). Conclusions: Reflux laryngitis is associated with down-regulation of mucin gene expression.

Non-coding regions of the genome are just as important as coding regions for understanding the mapping from genotype to phenotype. Interpreting deep learning models trained on RNA-seq is an emerging method to highlight functional sites within non-coding regions. Most of the work on RNA abundance models has been done within humans and mice, with little attention paid to plants. Here, we benchmark four genomic deep learning model architectures with genomes and RNA-seq data from 18 species closely related to maize and sorghum within the Andropogoneae. The Andropogoneae are a tribe of C4 grasses that have adapted to a wide range of environments worldwide since diverging 18 million years ago. Hundreds of millions of years of evolution across these species has produced a large, diverse pool of training alleles across species sharing a common physiology. As model input, we extracted 1,026 base pairs upstream of each gene’s translation start site. We held out maize as our test set and two closely related species as our validation set, training each architecture on the remaining Andropogoneae genomes. Within a panel of 26 maize lines, all architectures predict expression across genes moderately well but poorly across alleles. DanQ consistently ranked highest or second highest among all architectures yet performance was generally very similar across architectures despite orders of magnitude differences in size. This suggests that state-of-the-art supervised genomic deep learning models are able to generalize moderately well across related species but not sensitively separate alleles within species, the latter of which agrees with recent work within humans. We are releasing the preprocessed data and code for this work as a community benchmark to evaluate new architectures on our across-species and across-allele tasks.

Abstract 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 data indicate that the number of pan-genes exceeds 103,000 and 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 further reveal the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that overlap QTL and contribute to changes in gene expression. One sentence summary A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation. Competing Interest Statement RJS is a co-founder of REquest Genomics, LLC, a company that provides epigenomic services. All other authors declare no competing interests. Footnotes * https://github.com/HuffordLab/NAM-genomes

This dissertation explores, ethnographically, what the terms \"family,\" \"home,\" and \"place\" mean for individuals in a specific place, the Texas Hill Country. Contemporary mobility makes the meanings of these terms complex and crucial. While most academic research dismisses nostalgia, I argue that it continues to have powerful familial, regional, national, and even transnational attraction. Such nostalgia suggests a longing for connectedness to the stories and memories embedded in places. It relies especially on rural, or marginalized areas to convey some feeling of richness and fullness, what theorists identify as an \"aura of authenticity,\" for modern urban culture. Through storytelling I evoke local practices that create a sense of place. I also show how rural places like the Texas Hill Country become identified as places of tradition and rootedness to the earth where mobile, urban Americans eagerly seek connection by purchasing antiques and sacred objects. This dissertation lays intellectual and emotional groundwork by orienting the reader to the place and people of the Texas Hill Country, then continues with several narratives focused on a single site to explore how \"place\" can become a container for memory and story. Subsequent sections include a more essayistic grappling with family, home, and place; a life history of an 80-year old native of Blanco County, Texas; and an examination of the problematics of the social construction of Fredericksburg, Texas, as a \"home\" and place of history. While I partially focus on narratives of history and how they are constructed, I also tell stories about people of my own times--about how we live in cities created either as placeless, ahistorical malls, or in towns self-consciously constructed as tourist sites; what we do with a commodified history; what life is like in a problematic world of questions regarding our places.

Tyrolean Grey cattle represent a local breed with a population size of ∼5000 registered cows. In 2003, a previously unknown neurological disorder was recognized in Tyrolean Grey cattle. The clinical signs of the disorder are similar to those of bovine progressive degenerative myeloencephalopathy (weaver syndrome) in Brown Swiss cattle but occur much earlier in life. The neuropathological investigation of an affected calf showed axonal degeneration in the central nervous system (CNS) and femoral nerve. The pedigrees of the affected calves suggested a monogenic autosomal recessive inheritance. We localized the responsible mutation to a 1.9 Mb interval on chromosome 16 by genome-wide association and haplotype mapping. The MFN2 gene located in this interval encodes mitofusin 2, a mitochondrial membrane protein. A heritable human axonal neuropathy, Charcot-Marie-Tooth disease-2A2 (CMT2A2), is caused by MFN2 mutations. Therefore, we considered MFN2 a positional and functional candidate gene and performed mutation analysis in affected and control Tyrolean Grey cattle. We did not find any non-synonymous variants. However, we identified a perfectly associated silent SNP in the coding region of exon 20 of the MFN2 gene. This SNP is located within a putative exonic splice enhancer (ESE) and the variant allele leads to partial retention of the entire intron 19 and a premature stop codon in the aberrant MFN2 transcript. Thus we have identified a highly unusual splicing defect, where an exonic single base exchange leads to the retention of the preceding intron. This splicing defect represents a potential explanation for the observed degenerative axonopathy. Marker assisted selection can now be used to eliminate degenerative axonopathy from Tyrolean Grey cattle.

Background A significant and growing portion of the global burden of diseases is caused by neurological disorders. Tele-neurology has the potential to improve access to health care services and the quality of care, particularly in rural and underserved areas. The economic evaluation of the stepped wedge randomised controlled trial NeTKoH aims to ascertain the cost-effectiveness and cost-utility regarding the effects of a tele-neurologic intervention in primary care in a rural area in Germany. Methods This protocol outlines the methods used when conducting the trial-based economic evaluation of NeTKoH. The outcomes used in our economic analysis are all prespecified endpoints of the NeTKoH trial. Outcomes considered for the cost-utility and cost-effectiveness analyses will be quality-adjusted life years (QALYs) derived from the EQ-5D-5L, proportion of neurologic problems being solved at the GP’s office (primary outcome), hospital length-of-stay and number of hospital stays. Costs will be prospectively collected during the trial by the participating statutory health insurances, and will be analysed from a statutory health insurance perspective within the German health care system. This economic evaluation will be reported complying with the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) checklist. Discussion This within-trial economic evaluation relaying the costs and outcomes of an interdisciplinary tele-consulting intervention will provide high-quality evidence for cost-effectiveness and policy implications of a tele-neurological programme, including the potential for application in other rural areas in Germany or other jurisdictions with a comparable health system. Trial registration German Clinical Trials Register (DRKS00024492), date registered: September 28, 2021.

Background As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Results Here, using North American pines, we empirically evaluate the behavior of 24 strategies for species tree inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup species from subsection Strobus and three outgroup species from subsection Gerardianae , spanning ∼47 kilobases of sequence at 121 loci. Each “strategy” for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify tree characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce trees with similar features. We find that strategies that construct species trees using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a species to infer gene trees tend to produce estimates of species trees that contain clades present in trees estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct species trees tend to produce species tree estimates that contain clades that are not present in trees estimated by the Concatenation, RTC, SMRT, STAR, and STEAC methods, and that in general are more balanced than those inferred by these other strategies. Conclusions When constructing a species tree from a multilocus set of sequences, our observations provide a basis for interpreting differences in species tree estimates obtained via different approaches that have a two-stage structure in common, one step for gene tree estimation and a second step for species tree estimation. The methods explored here employ a number of distinct features of the data, and our analysis suggests that recovery of the same results from multiple methods that tend to differ in their patterns of inference can be a valuable tool for obtaining reliable estimates.

Globally, thousands of institutions house nearly three billion scientific collections offering unparallelled resources that contribute to both science and society. For herbaria alone - facilities housing dried plant collections - there are over 3,000 herbaria worldwide with an estimated 350 million specimens that have been collected over the past four centuries. Digitisation has greatly enhanced the use of herbarium data in scientific research, impacting diverse research areas, including biodiversity informatics, global climate change, analyses using next-generation sequencing technologies and many others. Despite the entrance of herbaria into a new era with enhanced scientific, educational and societal relevance, museum specimens remain underused. Natural history museums can enhance learning and engagement in science, particularly for school-age and undergraduate students. Here, we outline a novel approach of a natural history museum using touchscreen technology that formed part of an interactive kiosk in a temporary museum exhibit on biological specimens. We provide some preliminary analysis investigating the efficacy of the tool, based on the Zooniverse platform, in an exhibit environment to engage patrons in the collection of biological data. We conclude there is great potential in using crowd‐sourced science, coupled with online technology to unlock data and information from digital images of natural history specimens themselves. Sixty percent of the records generated by community scientists (citizen scientists) were of high enough quality to be utilised by researchers. All age groups produced valid, high quality data that could be used by researchers, including children (10 and under), teens and adults. Significantly, the paper outlines the implementation of experiential learning through an undergraduate mathematics course that focuses on projects with actual data to gain a deep, practical knowledge of the subject, including observations, the collection of data, analysis and problem solving. We here promote an intergenerational model including children, high school students, undergraduate students, early career scientists and senior scientists, combining experiential learning, museum patrons, researchers and data derived from natural history collections. Natural history museums with their dual remit of education and collections-based research can play a significant role in the field of community engagement and people-powered research. There also remains much to investigate on the use of interactive displays to help learners interpret and appreciate authentic research. We conclude with a brief insight into the next phase of our ongoing people-powered research activities developed and designed by high school students using the Zooniverse platform.

Purpose Results of a retrospective single-institution study recently suggested improved prognostic outcomes in patients undergoing photodynamic diagnosis (PDD)-assisted transurethral resection of bladder tumor (TURBT) prior to radical cystectomy (RC). We sought to validate the prognostic influence of PDD-assisted TURBT on survival after RC by relying on a multi-institutional dataset. Methods To provide a homogeneous study population, patients with organ metastasis at the time of RC and/or after neoadjuvant chemotherapy were excluded from analysis, which resulted in overall 549 bladder cancer (BC) patients from 18 centers of the Prospective Multicenter Radical Cystectomy Series 2011 (PROMETRICS 2011). To evaluate the influence of PDD conducted during primary or final TURBT on cancer-specific mortality (CSM) and overall mortality (OM) after RC, bootstrap-corrected multivariate Cox proportional-hazards regression models were applied (median follow-up: 25 months; IQR: 19–30). Sensitivity analyses were performed for both patients with pure urothelial carcinoma and patients undergoing one single TURBT only. Results In 88 (16.0 %) and 100 (18.2 %) patients, PDD was used in primary and final TURBTs, respectively. In 335 (61.0 %) patients, a single TURBT was performed prior to RC; in 194 patients (35.3 %), TURBT had been performed in a different center. CSM and OM rates at 3 years were 32 and 40 %, respectively. Use of PDD during primary or final TURBT was no independent predictor of CSM or OM. These results were internally valid and were confirmed in sensitivity analyses. Conclusions PDD utilization during TURBT prior to RC does not independently impact the prognosis of BC patients after RC.