Calcitriol Treatment Decreases Cell Migration, Viability and ß-Catenin Signaling in Oral Dysplasia.

Nearly 90% of oral cancers are characterized as oral squamous cell carcinoma (OSCC), representing the sixth most common type of cancer. OSCC usually evolves from oral potentially malignant disorders that, in some cases, are histologically consistent with a oral dysplasia. The levels of 1α,25 dihydroxyvitamin D3 (1,25-(OH)2D3; calcitriol), the active form of vitamin D3, have been shown to be decreased in patients with oral dysplasia and OSCC. Moreover, treatment with 1,25-(OH)2D3 has been proven beneficial in OSCC by inhibiting the Wnt/ß-catenin pathway, a signaling route that promotes cell migration, proliferation, and viability. However, whether this inhibition mechanism occurs in oral dysplasia is unknown. To approach this question, we used dysplastic oral keratinocyte cultures and oral explants (ex vivo model of oral dysplasia) treated with 1,25-(OH)2D3 for 48 h. Following treatment with 1,25-(OH)2D3, both in vitro and ex vivo models of oral dysplasia showed decreased levels of nuclear ß-catenin by immunofluorescence (IF) and immunohistochemistry (IHC). Consistently, reduced protein and mRNA levels of the Wnt/ß-catenin target gene survivin were observed after treatment with 1,25-(OH)2D3. Moreover, 1,25-(OH)2D3 promoted membranous localization of E-cadherin and nuclear localization of vitamin D receptor (VDR). Functionally, DOK cells treated with 1,25-(OH)2D3 displayed diminished cell migration and viability in vitro.

Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics.

MOTIVATION: Phecodes are widely used and easily adapted phenotypes based on International Classification of Diseases codes. The current version of phecodes (v1.2) was designed primarily to study common/complex diseases diagnosed in adults; however, there are numerous limitations in the codes and their structure. RESULTS: Here, we present phecodeX, an expanded version of phecodes with a revised structure and 1,761 new codes. PhecodeX adds granularity to phenotypes in key disease domains that are under-represented in the current phecode structure-including infectious disease, pregnancy, congenital anomalies, and neonatology-and is a more robust representation of the medical phenome for global use in discovery research. AVAILABILITY AND IMPLEMENTATION: phecodeX is available at https://github.com/PheWAS/phecodeX.

Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology.

Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.

The Biology and Genomics of Human Hair Follicles: A Focus on Androgenetic Alopecia.

Androgenetic alopecia is a highly prevalent condition mainly affecting men. This complex trait is related to aging and genetics; however, multiple other factors, for example, lifestyle, are also involved. Despite its prevalence, the underlying biology of androgenetic alopecia remains elusive, and thus advances in its treatment have been hindered. Herein, we review the functional anatomy of hair follicles and the cell signaling events that play a role in follicle cycling. We also discuss the pathology of androgenetic alopecia and the known molecular mechanisms underlying this condition. Additionally, we describe studies comparing the transcriptional differences in hair follicles between balding and non-balding scalp regions. Given the genetic contribution, we also discuss the most significant risk variants found to be associated with androgenetic alopecia. A more comprehensive understanding of this pathology may be generated through using multi-omics approaches.

Multiple roads lead to Rome: unique morphology and chemistry of endospores, exospores, myxospores, cysts and akinetes in bacteria.

The production of specialized resting cells is a remarkable survival strategy developed by many organisms to withstand unfavourable environmental factors such as nutrient depletion or other changes in abiotic and/or biotic conditions. Five bacterial taxa are recognized to form specialized resting cells: Firmicutes, forming endospores; Actinobacteria, forming exospores; Cyanobacteria, forming akinetes; the δ-Proteobacterial order Myxococcales, forming myxospores; and Azotobacteraceae, forming cysts. All these specialized resting cells are characterized by low-to-absent metabolic activity and higher resistance to environmental stress (desiccation, heat, starvation, etc.) when compared to vegetative cells. Given their similarity in function, we tested the potential existence of a universal morpho-chemical marker for identifying these specialized resting cells. After the production of endospores, exospores, akinetes and cysts in model organisms, we performed the first cross-species morphological and chemical comparison of bacterial sporulation. Cryo-electron microscopy of vitreous sections (CEMOVIS) was used to describe near-native morphology of the resting cells in comparison to the morphology of their respective vegetative cells. Resting cells shared a thicker cell envelope as their only common morphological feature. The chemical composition of the different specialized resting cells at the single-cell level was investigated using confocal Raman microspectroscopy. Our results show that the different specialized cells do not share a common chemical signature, but rather each group has a unique signature with a variable conservation of the signature of the vegetative cells. Additionally, we present the validation of Raman signatures associated with calcium dipicolinic acid (CaDPA) and their variation across individual cells to develop specific sorting thresholds for the isolation of endospores. This provides a proof of concept of the feasibility of isolating bacterial spores using a Raman-activated cell-sorting platform. This cross-species comparison and the current knowledge of genetic pathways inducing the formation of the resting cells highlights the complexity of this convergent evolutionary strategy promoting bacterial survival.

Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis.

At particular stages during their life cycles, fungi use multiple strategies to form specialized structures to survive unfavorable environmental conditions. These strategies encompass sporulation, as well as cell-wall melanization, multicellular tissue formation or even dimorphism. The resulting structures are not only used to disperse to other environments, but also to survive long periods of time awaiting favorable growth conditions. As a result, these specialized fungal structures are part of the microbial seed bank, which is known to influence the microbial community composition and contribute to the maintenance of diversity. Despite the importance of the microbial seed bank in the environment, methods to study the diversity of fungal structures with improved resistance only target spores dispersing in the air, omitting the high diversity of these structures in terms of morphology and environmental distribution. In this study, we applied a separation method based on cell lysis to enrich lysis-resistant fungal structures (for instance, spores, sclerotia, melanized yeast) to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in-vitro in selected species. The results obtained showed that DNA from fungal spores and from yeast was only obtained after the application of the enrichment method, while mycelium was always lysed. After validation, we compared the diversity of the total and lysis-resistant fractions in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from the salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed at lower taxonomic ranks. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.

Common and rare variants associated with cardiometabolic traits across 98,622 whole-genome sequences in the All of Us research program.

All of Us is a biorepository aiming to advance biomedical research by providing various types of data in diverse human populations. Here we present a demonstration project validating the program's genomic data in 98,622 participants. We sought to replicate known genetic associations for three diseases (atrial fibrillation [AF], coronary artery disease, type 2 diabetes [T2D]) and two quantitative traits (height and low-density lipoprotein [LDL]) by conducting common and rare variant analyses. We identified one known risk locus for AF, five loci for T2D, 143 loci for height, and nine loci for LDL. In gene-based burden tests for rare loss-of-function variants, we replicated associations between TTN and AF, GIGYF1 and T2D, ADAMTS17, ACAN, NPR2 and height, APOB, LDLR, PCSK9 and LDL. Our results are consistent with previous literature, indicating that the All of Us program is a reliable resource for advancing the understanding of complex diseases in diverse human populations.

Cytomegalovirus seropositivity correlates with both human ß-defensin 1 and IFN-γ downregulation in women with obesity.

Human ß-defensin 1 (hBD-1) is a constitutively expressed antimicrobial peptide with antiviral properties. CMV seropositivity has been associated with obesity. It is unknown if hBD-1 levels of are altered in women with obesity and/or CMV seropositivity. In a pilot project of 31 adult women with CMV seropositivity, we calculated the correlation among hBD-1 serum levels (ELISA) and IgG anti-CMV-Index with anthropometric measurements, lipid profiles and glucose levels. hBD-1 showed negative correlation with triglycerides (TG) (r = -0.617; p = 0.033,) and hip circumference (r = -0.596; p = 0.041,). IgG anti-CMV index was negatively correlated with hBD-1 levels and positively correlated with TG (r = 0.702; p = 0.011,) and HC (r = 0.583; p = 0.047,) in women with obesity. As expected, hBD-1 levels correlates with IFN-γ (an antimicrobial peptide elicitor) in the three analyzed groups.These results shows that CMV seropositivity correlates with both IFN-γ levels and hBD-1 levels which in contrast with non-CMV seropositivity scenario, is commonly found an IFN-γ upregulation in individuals with obesity. Further research is encouraged to test if CMV is causing the observed downregulation of the antiviral immune responses of both hBD-1 and IFN-γ as well as their involved mechanisms.

Is Carbon Capture and Storage (CCS) Really So Expensive? An Analysis of Cascading Costs and CO2 Emissions Reduction of Industrial CCS Implementation on the Construction of a Bridge.

Carbon capture and storage (CCS) is an essential technology to mitigate global CO2 emissions from power and industry sectors. Despite the increasing recognition of its importance to achieve the net-zero target, current CCS deployment is far behind targeted ambitions. A key reason is that CCS is often perceived as too expensive. The costs of CCS have however traditionally been looked at from the industrial plant perspective, which does not necessarily reflect the end user's one. This paper addresses the incomplete view by investigating the impact of implementing CCS in industrial facilities on the overall costs and CO2 emissions of end-user products and services. As an example, we examine the extent to which an increase in costs of raw materials (cement and steel) due to CCS impacts the costs of building a bridge. Results show that although CCS significantly increases cement and steel costs, the subsequent increment in the overall bridge construction cost remains marginal (∼1%). This 1% cost increase, however, enables a deep reduction in CO2 emissions (∼51%) associated with the bridge construction. Although more research is needed in this area, this work is the first step to a better understanding of the real cost and benefits of CCS.

Results from the Strong Families Start at Home/Familias Fuertes Comienzan en Casa: feasibility randomised control trial to improve the diet quality of low-income, predominantly Hispanic/Latinx children.

OBJECTIVE: To describe the feasibility, acceptability and results of Strong Families Start at Home, a 6-month pilot trial of a home-based food parenting/nutrition intervention. DESIGN: Pilot randomised controlled trial. SETTING: Participants received six visits with a community health worker trained in motivational interviewing (three home visits, three phone calls); an in-home cooking or reading activity; personalised feedback on a recorded family meal or reading activity; text messages and tailored printed materials. PARTICIPANTS: Parents and their 2-5-year-old child were randomised into intervention (responsive food parenting practices/nutrition) or control (reading readiness) groups. RESULTS: Parents (n 63) were mostly mothers (90 %), Hispanic/Latinx (87 %), born outside the USA (62 %), with household incomes <$25 k (54 %). Despite delivery during COVID-19, 63 % of dyads were retained at 6 months. The intervention was delivered with high fidelity. All parents in the intervention group (n 24) expressed high levels of satisfaction with the intervention, which produced positive treatment effects for whole and total fruit component Healthy Eating Index-2015 scores (point estimate (PE) = 2·14, 95 % CI (0·17, 1·48); PE = 1·71, 95 % CI (0·16, 1·47), respectively) and negative treatment effects for sodium (PE = -2·09, 95 % CI (-1·35, -0·04)). Positive treatment effects also resulted for the following food parenting practices: regular timing of meals and snacks (PE = 1·08, 95 % CI (0·61, 2·00)), reducing distractions during mealtimes (PE = -0·79, 95 % CI (-1·52, -0·19)), using food as a reward (PE = -0·54, 95 % CI (-1·35, -0·04)) and providing a supportive meal environment (PE = 0·73, 95 % CI (0·18, 1·51)). CONCLUSION: Given the continued disparities in diet quality among low-income and diverse families, continued efforts to improve child diet quality in fully powered intervention trials are needed.

Characterization of heart rate changes associated with autonomic dysreflexia during penile vibrostimulation and urodynamics.

STUDY DESIGN: Secondary data analysis. OBJECTIVES: To characterize autonomic dysreflexia (AD) associated heart rate (HR) changes during penile vibrostimulation (PVS) and urodynamic studies (UDS). SETTING: University-based laboratory. METHODS: We analyzed blood pressure (BP) and HR data, recorded continuously, from 21 individuals (4 females; median age 41 years [lower and upper quartile, 37; 47]; median time post-injury 18 years [7; 27]; all motor-complete spinal cord injury (SCI) except one; cervical SCI = 15, thoracic [T1-T6] SCI = 6), who underwent PVS (11/21) or UDS (10/21). RESULTS: Overall, 47 AD episodes were recorded (i.e. PVS = 37, UDS = 10), with at least one AD episode in each participant. At AD threshold, bradycardia was observed during PVS and UDS in 43% and 30%, respectively. At AD peak (i.e., maximum increase in systolic BP from baseline), bradycardia was observed during PVS and UDS in 65% and 50%, respectively. Tachycardia was detected at AD peak only once during UDS. Our study was limited by a small cohort of participants and the distribution of sex and injury characteristics. CONCLUSIONS: Our findings reveal that AD-associated HR changes during PVS and UDS appear to be related to the magnitude of systolic BP increases. Highly elevated systolic BP associated with bradycardia suggests the presence of severe AD. Therefore, we recommend cardiovascular monitoring (preferably with continuous beat-to-beat recordings) during PVS and UDS to detect AD early. Stopping assessments before systolic BP reaches dangerously elevated levels, could reduce the risk of life-threatening complications in this cohort.

Quantification of arbuscular mycorrhizal fungi root colonization in wheat, tomato, and leek using absolute qPCR.

Arbuscular mycorrhizal fungi (AMF) form symbioses with most terrestrial plants and are known to have a positive effect on plant growth and health. Different methodologies have been developed to assess the AMF-plant symbiosis. The most applied method, which involves staining of roots and microscopic observation of the AMF structures, is tedious and time-consuming and the results are highly dependent on the observer. Using quantitative polymerase chain reaction (qPCR) to quantify AMF root colonization represents a reliable, high-throughput technique that allows the assessment of numerous samples. Quantification with qPCR can be performed through two methods: relative quantification and absolute quantification. In relative quantification, the target gene is normalized with a reference gene. On the other hand, absolute quantification involves the use of a standard curve, for which template DNA is serially diluted. In a previous paper, we validated the primer pair AMG1F and AM1 for a relative quantification approach to assess AMF root colonization in Petunia. Here, we tested the same primers with an absolute quantification approach and compared the results with the traditional microscopy method. We evaluated the qPCR method with three different crops, namely, wheat (cv. Colmetta and Wiwa), tomato, and leek. We observed a strong correlation between microscopy and qPCR for Colmetta (r = 0.90, p < 0.001), Wiwa (r = 0.94, p < 0.001), and tomato (r = 0.93, p < 0.001), but no correlation for leek (r = 0.27, p = 0.268). This highlights the importance of testing the primer pair for each specific crop.

A Hollow Tridimensional Silicone Template for Microtia Reconstruction and Postoperative Scar Compression.

Microtia poses a great challenge in auricular reconstruction, due to a great number of anatomical details on the anterior aspect, and its tridimensional shape. Numerous techniques have been described in an attempt to optimize results. We have designed a hollow tridimensional silicon template to serve as an intrasurgical guide for ear's anatomy, size and projection, according to the normal side, which allows better results of auricular reconstruction. It also can be used as a customized post-operative compression method. We believe it could be a valuable tool for microtia reconstruction surgery. LEVEL OF EVIDENCE V: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Mutational Landscape of Bladder Cancer in Mexican Patients: KMT2D Mutations and chr11q15.5 Amplifications Are Associated with Muscle Invasion.

Bladder cancer (BC) is the most common neoplasm of the urinary tract, which originates in the epithelium that covers the inner surface of the bladder. The molecular BC profile has led to the development of different classifications of non-muscle invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC). However, the genomic BC landscape profile of the Mexican population, including NMIBC and MIBC, is unknown. In this study, we aimed to identify somatic single nucleotide variants (SNVs) and copy number variations (CNVs) in Mexican patients with BC and their associations with clinical and pathological characteristics. We retrospectively evaluated 37 patients treated between 2012 and 2021 at the National Cancer Institute-Mexico (INCan). DNA samples were obtained from paraffin-embedded tumor tissues and exome sequenced. Strelka2 and Lancet packages were used to identify SNVs and insertions or deletions. FACETS was used to determine CNVs. We found a high frequency of mutations in TP53 and KMT2D, gains in 11q15.5 and 19p13.11-q12, and losses in 7q11.23. STAG2 mutations and 1q11.23 deletions were also associated with NMIBC and low histologic grade.

Developing Motivational Interviewing Skills Among Undergraduate Nursing Students.

The current study evaluated changes in undergraduate nursing students' knowledge and self-efficacy in motivational interviewing. Fourth-year undergraduate nursing students completed a hybrid, online curriculum. Changes in knowledge and self-efficacy were assessed using a pretest/posttest design. Repeated measures analysis of variance was used to determine differences between knowledge and self-efficacy mean scores. Of the 144 students who participated in the study, 88.2% were female, 96.5% were non-Hispanic/Latino, 88.9% were White, and mean age was 21.3 years. There were significant increases in knowledge and self-efficacy mean scores between pre-survey and post-survey 1 and 2. There were no differences between post-surveys 1 and 2 scores. A hybrid, online curriculum using asynchronous modules and synchronous simulation training can facilitate nursing students' learning experiences and enhance knowledge and self-efficacy about motivational interviewing. [Journal of Psychosocial Nursing and Mental Health Services, 61(5), 17-24.].

Antibodies to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in All of Us Research Program Participants, 2 January to 18 March 2020.

BACKGROUND: With limited severe acute respiratory syndrome coronavirus (SARS-CoV-2) testing capacity in the United States at the start of the epidemic (January-March 2020), testing was focused on symptomatic patients with a travel history throughout February, obscuring the picture of SARS-CoV-2 seeding and community transmission. We sought to identify individuals with SARS-CoV-2 antibodies in the early weeks of the US epidemic. METHODS: All of Us study participants in all 50 US states provided blood specimens during study visits from 2 January to 18 March 2020. Participants were considered seropositive if they tested positive for SARS-CoV-2 immunoglobulin G (IgG) antibodies with the Abbott Architect SARS-CoV-2 IgG enzyme-linked immunosorbent assay (ELISA) and the EUROIMMUN SARS-CoV-2 ELISA in a sequential testing algorithm. The sensitivity and specificity of these ELISAs and the net sensitivity and specificity of the sequential testing algorithm were estimated, along with 95% confidence intervals (CIs). RESULTS: The estimated sensitivities of the Abbott and EUROIMMUN assays were 100% (107 of 107 [95% CI: 96.6%-100%]) and 90.7% (97 of 107 [83.5%-95.4%]), respectively, and the estimated specificities were 99.5% (995 of 1000 [98.8%-99.8%]) and 99.7% (997 of 1000 [99.1%-99.9%]), respectively. The net sensitivity and specificity of our sequential testing algorithm were 90.7% (97 of 107 [95% CI: 83.5%-95.4%]) and 100.0% (1000 of 1000 [99.6%-100%]), respectively. Of the 24 079 study participants with blood specimens from 2 January to 18 March 2020, 9 were seropositive, 7 before the first confirmed case in the states of Illinois, Massachusetts, Wisconsin, Pennsylvania, and Mississippi. CONCLUSIONS: Our findings identified SARS-CoV-2 infections weeks before the first recognized cases in 5 US states.

Nanomechanical Stability of Laterally Heterogeneous Films of Corrosion Inhibitor Molecules Obtained by Microcontact Printing on Au Model Substrates.

Self-assembled monolayers of corrosion inhibitors of the mercaptobenzimidazole family, SH-BimH, SH-BimH-5NH2, and SH-BimH-5OMe, were formed on template-stripped ultraflat Au surfaces using microcontact printing, and subsequently analyzed using X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and AFM-force spectroscopy (AFM-FS) using a quantitative imaging (QI) mode. Printing of all used inhibitor molecules resulted in clear patterns and in slightly more compact films compared to immersion. The stability of the monolayers is further probed by AFM-FS. Adhesion values of laterally heterogeneous inhibitor-modified surfaces compared to bare Au surfaces, nonpatterned areas, and fully covered surfaces are analyzed and discussed. Microcontact printing confers a superior nanomechanical stability to imidazole-modified films of the printed surface patches as compared to homogeneously covered surfaces by immersion into the inhibitor solution.

Heart rate changes associated with autonomic dysreflexia in daily life of individuals with chronic spinal cord injury.

STUDY DESIGN: Secondary data analysis. OBJECTIVE: To characterize heart rate (HR) changes during autonomic dysreflexia (AD) in daily life for individuals with chronic spinal cord injury (SCI). SETTING: University-based laboratory/community-based outpatient. METHODS: Cardiovascular data, previously collected during a 24-h ambulatory surveillance period in individuals with chronic SCI, were assessed. Any systolic blood pressure (SBP) increase ≥20 mmHg from baseline was identified and categorized into confirmed AD (i.e., diarized trigger), unknown (i.e., no diary entry), or unlikely AD (i.e., potential exertion driven SBP increase) groups. SBP-associated HR changes were categorized as unchanged, increased or decreased compared to baseline. RESULTS: Forty-five individuals [8 females, median age and time since injury of 43 years (lower and upper quartiles 36-50) and 17 years (6-23), respectively], were included for analysis. Overall, 797 episodes of SBP increase above AD threshold were identified and classified as confirmed (n = 250, 31.4%), unknown (n = 472, 59.2%) or unlikely (n = 75, 9.4%). The median number of episodes per individual within the 24-h period was 13 (8-28). HR-decrease/increase ratio was 3:1 for confirmed and unknown, and 1.5:1 for unlikely episodes. HR changes resulting in brady-/tachycardia were 34.4%/2.8% for confirmed, 39.6%/3.4% unknown, and 26.7%/9.3% for unlikely episodes, respectively. CONCLUSIONS: Our findings suggest that the majority of confirmed AD episodes are associated with a HR decrease. Using wearable-sensors-derived measures of physical activity in future studies could provide a more detailed characterization of HR changes during AD and improve AD identification.

Prp8 impacts cryptic but not alternative splicing frequency.

Pre-mRNA splicing must occur with extremely high fidelity. Spliceosomes assemble onto pre-mRNA guided by specific sequences (5' splice site, 3' splice site, and branchpoint). When splice sites are mutated, as in many hereditary diseases, the spliceosome can aberrantly select nearby pseudo- or "cryptic" splice sites, often resulting in nonfunctional protein. How the spliceosome distinguishes authentic splice sites from cryptic splice sites is poorly understood. We performed a Caenorhabditis elegans genetic screen to find cellular factors that affect the frequency with which the spliceosome uses cryptic splice sites and identified two alleles in core spliceosome component Prp8 that alter cryptic splicing frequency. Subsequent complementary genetic and structural analyses in yeast implicate these alleles in the stability of the spliceosome's catalytic core. However, despite a clear effect on cryptic splicing, high-throughput mRNA sequencing of these prp-8 mutant C. elegans reveals that overall alternative splicing patterns are relatively unchanged. Our data suggest the spliceosome evolved intrinsic mechanisms to reduce the occurrence of cryptic splicing and that these mechanisms are distinct from those that impact alternative splicing.

Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions.

INTRODUCTION: Currently, one of the commonly used methods for disseminating electronic health record (EHR)-based phenotype algorithms is providing a narrative description of the algorithm logic, often accompanied by flowcharts. A challenge with this mode of dissemination is the potential for under-specification in the algorithm definition, which leads to ambiguity and vagueness. METHODS: This study examines incidents of under-specification that occurred during the implementation of 34 narrative phenotyping algorithms in the electronic Medical Record and Genomics (eMERGE) network. We reviewed the online communication history between algorithm developers and implementers within the Phenotype Knowledge Base (PheKB) platform, where questions could be raised and answered regarding the intended implementation of a phenotype algorithm. RESULTS: We developed a taxonomy of under-specification categories via an iterative review process between two groups of annotators. Under-specifications that lead to ambiguity and vagueness were consistently found across narrative phenotype algorithms developed by all involved eMERGE sites. DISCUSSION AND CONCLUSION: Our findings highlight that under-specification is an impediment to the accuracy and efficiency of the implementation of current narrative phenotyping algorithms, and we propose approaches for mitigating these issues and improved methods for disseminating EHR phenotyping algorithms.