The power of genetic diversity in genome-wide association studies of lipids.

Increased blood lipid levels are heritable risk factors of cardiovascular disease with varied prevalence worldwide owing to different dietary patterns and medication use1. Despite advances in prevention and treatment, in particular through reducing low-density lipoprotein cholesterol levels2, heart disease remains the leading cause of death worldwide3. Genome-wideassociation studies (GWAS) of blood lipid levels have led to important biological and clinical insights, as well as new drug targets, for cardiovascular disease. However, most previous GWAS4-23 have been conducted in European ancestry populations and may have missed genetic variants that contribute to lipid-level variation in other ancestry groups. These include differences in allele frequencies, effect sizes and linkage-disequilibrium patterns24. Here we conduct a multi-ancestry, genome-wide genetic discovery meta-analysis of lipid levels in approximately 1.65 million individuals, including 350,000 of non-European ancestries. We quantify the gain in studying non-European ancestries and provide evidence to support the expansion of recruitment of additional ancestries, even with relatively small sample sizes. We find that increasing diversity rather than studying additional individuals of European ancestry results in substantial improvements in fine-mapping functional variants and portability of polygenic prediction (evaluated in approximately 295,000 individuals from 7 ancestry groupings). Modest gains in the number of discovered loci and ancestry-specific variants were also achieved. As GWAS expand emphasis beyond the identification of genes and fundamental biology towards the use of genetic variants for preventive and precision medicine25, we anticipate that increased diversity of participants will lead to more accurate and equitable26 application of polygenic scores in clinical practice.

Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq.

BACKGROUND: Parent-of-origin allele-specific gene expression (ASE) can be detected in interspecies hybrids by virtue of RNA sequence variants between the parental haplotypes. ASE is detectable by differential expression analysis (DEA) applied to the counts of RNA-seq read pairs aligned to parental references, but aligners do not always choose the correct parental reference. RESULTS: We used public data for species that are known to hybridize. We measured our ability to assign RNA-seq read pairs to their proper transcriptome or genome references. We tested software packages that assign each read pair to a reference position and found that they often favored the incorrect species reference. To address this problem, we introduce a post process that extracts alignment features and trains a random forest classifier to choose the better alignment. On each simulated hybrid dataset tested, our machine-learning post-processor achieved higher accuracy than the aligner by itself at choosing the correct parent-of-origin per RNA-seq read pair. CONCLUSIONS: For the parent-of-origin classification of RNA-seq, machine learning can improve the accuracy of alignment-based methods. This approach could be useful for enhancing ASE detection in interspecies hybrids, though RNA-seq from real hybrids may present challenges not captured by our simulations. We believe this is the first application of machine learning to this problem domain.

Structural evidence for MADS-box type I family expansion seen in new assemblies of Arabidopsis arenosa and A. lyrata.

Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The three species differ by genome-wide polymorphisms and morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based on the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS-box type I family of transcription factors is specifically expressed in the endosperm and has been proposed to play a role in endosperm-based hybridization barriers. The gene family is well known for its high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS-box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de-novo assembled and annotated chromosome-level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS-box type I gene family in Arabidopsis to predict orthologs, copy number, and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS-box type I loci in endosperm-based hybridization barriers. We observed substantial differences in type-I expression in the endosperm of A. arenosa and A. lyrata ssp. petraea, suggesting a genetic cause for the endosperm-based hybridization barrier between A. arenosa and A. lyrata ssp. petraea.

Spatial and temporal regulation of parent-of-origin allelic expression in the endosperm.

Genomic imprinting promotes differential expression of parental alleles in the endosperm of flowering plants and is regulated by epigenetic modification such as DNA methylation and histone tail modifications in chromatin. After fertilization, the endosperm develops through a syncytial stage before it cellularizes and becomes a nutrient source for the growing embryo. Regional compartmentalization has been shown both in early and late endosperm development, and different transcriptional domains suggest divergent spatial and temporal regional functions. The analysis of the role of parent-of-origin allelic expression in the endosperm as a whole and the investigation of domain-specific functions have been hampered by the inaccessibility of the tissue for high-throughput transcriptome analyses and contamination from surrounding tissue. Here, we used fluorescence-activated nuclear sorting (FANS) of nuclear targeted GFP fluorescent genetic markers to capture parental-specific allelic expression from different developmental stages and specific endosperm domains. This approach allowed us to successfully identify differential genomic imprinting with temporal and spatial resolution. We used a systematic approach to report temporal regulation of imprinted genes in the endosperm, as well as region-specific imprinting in endosperm domains. Analysis of our data identified loci that are spatially differentially imprinted in one domain of the endosperm, while biparentally expressed in other domains. These findings suggest that the regulation of genomic imprinting is dynamic and challenge the canonical mechanisms for genomic imprinting.

Reassessing retinal pigment epithelial ketogenesis: Enzymatic assays for ketone body levels provide inaccurate results.

The retinal pigment epithelium (RPE) is omnivorous and can utilize a wide range of substrates for oxidative phosphorylation. Certain tissues with high mitochondrial metabolic load are capable of ketogenesis, a biochemical pathway that consolidates acetyl-CoA into ketone bodies. Earlier work demonstrated that the RPE expresses the rate-limiting enzyme for ketogenesis, 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), and that the RPE indeed produces ketone bodies, including beta-hydroxybutyrate (ß-HB). Prior work, based on detecting ß-HB via enzymatic assays, suggested that differentiated cultures of primary RPE preferentially export ß-HB across the apical membrane. Here, we compare the accuracy of measuring ß-HB by enzymatic assay kits to mass spectrometry analysis. We found that commercial kits lack the sensitivity to accurately measure the levels of ß-HB in RPE cultures and are prone to artifact. Using mass spectrometry, we found that while RPE cultures secrete ß-HB, they do so equally to both apical and basal sides. We also find RPE is capable of consuming ß-HB as levels rise. Using isotopically labeled glucose, amino acid, and fatty acid tracers, we found that carbons from both fatty acids and ketogenic amino acids, but not from glucose, produce ß-HB. Altogether, we substantiate ß-HB secretion in RPE but find that the secretion is equal apically and basally, RPE ß-HB can derive from ketogenic amino acids or fatty acids, and accurate ß-HB assessment requires mass spectrometric analysis.

Retinal artery occlusion in young patients without typical cardiovascular risk factors: etiologies, prognosis, and suggested work-up.

PURPOSE: To understand the etiology, work-up, and secondary systemic and ocular events of retinal artery occlusion (RAO) in young patients (≤ 45 years old) without typical cardiovascular risk factors. METHODS: Retrospective longitudinal case series of 18 young patients with RAO and without typical cardiovascular risk factors evaluated at the University of Michigan Medicine Health System between the year 2000 and 2022. Laboratory and imaging studies performed at the time of RAO diagnosis, along with systemic and ocular events during follow-up, were recorded. These data were combined with data from a literature review of 74 similar patients experiencing a RAO. RESULTS: Fifteen (83%) of patients were female and 10 (56%) suffered a branch retinal artery occlusion (BRAO). 56% of patients had one risk factor associated with cryptogenic stroke, most commonly a migraine history (33%). The most frequent etiology of RAO was vasculitis (28%), followed by idiopathic (22%) and patent foramen ovale (PFO, 17%). Three out of four patients with idiopathic RAOs developed new migraines around the time of RAO diagnosis, whereas none of the patients with a clear etiology had new onset migraines (n = 14). No patients suffered a stroke or myocardial infarction (MI) in the follow-up period (average 3.6 years ± 3.2 years). Two patients (11%) suffered a repeat RAO, both of whom were diagnosed with a vasculitis. Patients with isolated retinal vasculitis required repeat fluorescein angiograms for up to 2 years after the initial event to definitively identify the vasculitic etiology of the RAO. When our data are pooled with similarly healthy patients from previously published RAO series, structural/functional cardiac abnormalities and vasculitides are the most common identifiable etiologies for RAOs in this group. CONCLUSION: The most common identifiable etiologies of RAO in young patients with low cardiovascular risk are structural/functional cardiac abnormalities and vasculitides, with a small range of additional causes/associations accounting for remaining cases. We suggest a focused work-up algorithm to rapidly identify etiologies in this group while minimizing unnecessary testing. The long-term risk of systemic or ocular secondary events in these patients is low regardless of the etiology of their RAO.

Human-Disease Phenotype Map Derived from PheWAS across 38,682 Individuals.

Phenome-wide association studies (PheWASs) have been a useful tool for testing associations between genetic variations and multiple complex traits or diagnoses. Linking PheWAS-based associations between phenotypes and a variant or a genomic region into a network provides a new way to investigate cross-phenotype associations, and it might broaden the understanding of genetic architecture that exists between diagnoses, genes, and pleiotropy. We created a network of associations from one of the largest PheWASs on electronic health record (EHR)-derived phenotypes across 38,682 unrelated samples from the Geisinger's biobank; the samples were genotyped through the DiscovEHR project. We computed associations between 632,574 common variants and 541 diagnosis codes. Using these associations, we constructed a "disease-disease" network (DDN) wherein pairs of diseases were connected on the basis of shared associations with a given genetic variant. The DDN provides a landscape of intra-connections within the same disease classes, as well as inter-connections across disease classes. We identified clusters of diseases with known biological connections, such as autoimmune disorders (type 1 diabetes, rheumatoid arthritis, and multiple sclerosis) and cardiovascular disorders. Previously unreported relationships between multiple diseases were identified on the basis of genetic associations as well. The network approach applied in this study can be used to uncover interactions between diseases as a result of their shared, potentially pleiotropic SNPs. Additionally, this approach might advance clinical research and even clinical practice by accelerating our understanding of disease mechanisms on the basis of similar underlying genetic associations.

The Atlantic salmon genome provides insights into rediploidization.

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.

Comparison of Two Thermal Pulsation Systems in the Treatment of Meibomian Gland Dysfunction: A Randomized, Multicenter Study.

SIGNIFICANCE: Given the significance of meibomian gland dysfunction subjects in evaporative dry eye, its chronic and progressive nature, limited promising treatment options, and novel treatment techniques are important. This randomized clinical study evaluated the noninferiority of SYSTANE iLux with LipiFlow in meibomian gland dysfunction treatment at 12 months. PURPOSE: This study aimed to demonstrate noninferiority of SYSTANE iLux compared with LipiFlow at 12 months after single treatment in meibomian gland dysfunction subjects with evaporative dry eye. METHODS: In this prospective, randomized, multicenter, assessor-masked, parallel-group trial, subjects (N = 236; aged ≥18 years) with meibomian gland score (MGS) of ≤12 in lower eyelids, noninvasive tear breakup time (NITBUT; first breakup) of <10 seconds, and Impact of Dry Eye on Everyday Life-Symptom Bother (IDEEL-SB) module score of >16 were randomized (1:1) to receive SYSTANE iLux (n = 119) or LipiFlow (n = 117). Subjects attended a total of eight visits, including screening, treatment, and follow-up visits at 2 weeks and at 1, 3, 6, 9, and 12 months/exit, to evaluate change from baseline in MGS, NITBUT, IDEEL-SB module score, and safety outcomes. RESULTS: A total of 227 subjects completed the study (mean ± standard deviation age, 57.3 ± 13.8 years). At 12 months, least squares mean change from baseline in MGS was similar between iLux and LipiFlow (17.4 ± 1.97 vs. 17.8 ± 1.98). Noninferiority of SYSTANE iLux compared with LipiFlow in change from baseline in MGS (95% lower confidence limit of least squares mean difference, >-5), NITBUT (>-2.5 seconds), and IDEEL-SB score (95% upper confidence limit, <12) was achieved at all post-treatment visits. No other serious ocular or device-related adverse events were reported. CONCLUSIONS: The treatment outcomes with SYSTANE iLux were noninferior to LipiFlow during the 12-month follow-up in subjects with dry eye-associated meibomian gland dysfunction.

Exploring structure/property relationships to health and environmental hazards of polymeric polyisocyanate prepolymer substances-2. Dermal sensitization potential in the mouse local lymph node assay.

The sensitization potencies of twenty custom-designed monomer-depleted polymeric polyisocyanate prepolymer substances and their associated toluene diisocyanate (TDI), methylene diphenyl diisocyanate (MDI), hexamethylene diisocyanate (HDI), and isophorone diisocyanate (IPDI) monomer precursors were investigated by means of the mouse Local Lymph Node Assay (LLNA). These polymeric prepolymers were designed to represent the structural features and physical-chemical properties exhibited by a broad range of commercial polymeric polyisocyanate prepolymers that are produced from the reaction of aromatic and aliphatic diisocyanate monomers with aliphatic polyether and polyester polyols. The normalization of LLNA responses to the applied (15-45-135 mM) concentrations showed that the skin sensitization potency of polymeric polyisocyanate prepolymers is at least 300 times less than that of the diisocyanate monomers from which they are derived. The sensitization potency of the prepolymers was shown to be mainly governed by their hydrophobicity (as expressed by the calculated octanol-water partition coefficient, log Kow) and surfactant properties. Neither hydrophilic (log Kow <0) nor very hydrophobic (log Kow >25) prepolymers stimulated lymphocyte proliferation beyond that of the dosing vehicle control. The findings of this investigation challenge the generally held assumption that all isocyanate (-N=C=O) bearing substances are potential skin (and respiratory) sensitizers. Further, these findings can guide the future development of isocyanate chemistries and associated polyurethane applications toward reduced exposure and health hazard potentials.

The Impact of a New On-site Inpatient Psychiatric Unit in an Urban Pediatric Emergency Department.

OBJECTIVE: The objective of this study was to describe the impact of opening an inpatient child psychiatric unit in an urban tertiary care pediatric emergency department (PED). DESIGN/METHODS: A retrospective chart review was performed of pediatric patients seen in the PED at a large tertiary care center who presented for a primary psychiatric concern before opening of the inpatient psychiatric unit within the same hospital and 6 months following, allowing for a 6-month adjustment period. Patients were identified via query of the ED Cube model, an institutional database by a "behavioral health" flag that is documented in triage. Patients were excluded if subsequent chart review did not reveal a psychiatric concern and the patient did not undergo psychiatric evaluation during the PED visit. Charts were reviewed for baseline patient demographics, psychiatric interventions performed, and disposition. Additional flow metrics obtained were PED volume, percentage of psychiatric visits, and length of stay for both psychiatric-related visits compared with the general population. RESULTS: Visits to the PED for psychiatric evaluation increased 135% from 91 to 226 after initiation of an inpatient psychiatric unit. There was no difference in baseline patient demographics or rate of medical/mechanical restraints used. Percentage of behavioral health patients admitted to medical units decreased, although overall admission rate remained stable. Length of stay for behavioral health patients was longer after opening of the unit and remained significantly higher than the general population before opening of the inpatient unit, 363 minutes versus 177 minutes, respectively, and further lengthened after to 418 minutes versus 188 minutes. DISCUSSION: Patients presenting for psychiatric evaluation are a significant burden to PED flow both in volume and time for evaluation and boarding. This is to the detriment of patients seeking appropriate mental health services and to the rest of patients in the PED. Both inpatient and outpatient psychiatric services are overwhelmed creating a downstream affect; limited resources delays disposition and increases boarding in the PED. Further resources are needed to appropriately address psychiatric concerns, such as dedicated psychiatric holding units and brief PED interventions targeted to safety planning and interventions.

A novel OCT signature in leukemic papillopathy masquerading as autoimmune or infectious uveitis.

PURPOSE: With therapeutic advances, central nervous system (CNS) involvement in leukemia has become more common. Leukemic optic disc infiltration, often a clinical diagnosis, can present as an isolated finding in primary or relapsed CNS disease and therefore requires early recognition. Not previously well appreciated, we report here signs of intraocular inflammation accompanying leukemic optic disc infiltration, suggesting infectious or non-infectious uveitis as an alternative diagnosis. We describe a novel optical coherence tomography (OCT) sign favoring leukemic infiltration. METHODS: Retrospective consecutive case series of all leukemic patients with disc edema (5 patients, 6 eyes) presenting to the University of Michigan's Ocular Oncology Clinic between October 2019 and March 2020. RESULTS: We report five leukemic patients (6 eyes) who were evaluated for disc edema and vitritis and eventually diagnosed with leukemic papillopathy. All five patients initially had a bland lumbar puncture (LP), and all four patients who underwent magnetic resonance imaging (MRI) had no retrobulbar nerve involvement. Clinical findings included preserved visual acuity (n = 5 eyes, 83%), anterior chamber (AC) cell (n = 3 eyes, 50%), vitreous cell (n = 6 eyes, 100%), and retinal whitening (n = 4 eyes, 66%). In five eyes (83%), a diagnosis of infectious or non-infectious uveitis was initially considered. The OCT finding of inner retinal thickening and loss of inner retinal lamination with largely preserved outer retinal architecture helped point towards a leukemic infiltrative process emanating from the disc and spreading retrograde through the nerve fiber layer. CONCLUSIONS: These cases highlight the difficulty of distinguishing intraocular inflammation associated with leukemic papillopathy from infectious or non-infectious uveitis, especially considering bland LP and negative retrobulbar MRI signal in all our patients. We propose juxtapapillary inner retinal infiltration with the loss of inner retinal lamination and relative preservation of outer retinal architecture on OCT imaging as a finding that supports the diagnosis of leukemic papillopathy.

Rates and clinical impact of discordant X-ray and CT imaging in transfers to a pediatric emergency department.

OBJECTIVES: Children are often transferred to a Pediatric Emergency Department (PED) for definitive care after completion of diagnostic imaging. There is a paucity of data on the concordance rates of interpretation of imaging studies between referral and PED. Our objective is to describe the rates and clinical impact of discordant interpretation of X-rays and CT in children transferred to a PED. METHODS: This was a retrospective cohort study of patients over a 12-month period from 12/1/2017-11/30/2018 with X-ray (XR) and CT performed prior to transfer to our PED. We compared referral radiology interpretations to those of pediatric radiologists to determine concordance. Encounters with discordant imaging interpretations were further evaluated for clinical impact (none, minor or major) based on need for additional laboratory workup, consultation, and changes in management and disposition. RESULTS: We analyzed 899 patient encounters. There were high rates of concordance in both XR and CT interpretation (668/743; 89.9%, 95% CI 0.87-0.91 and 205/235; 87.2%, 95% CI 0.82-0.91, respectively). XR discordance resulted in minor clinical impact in 34 patients (45%, 95% CI 0.35-0.57) and a major clinical impact in 28 patients (37%, 95% CI 0.27-0.49). CT discordance resulted in minor clinical impact in 10 patients (33%, 95% CI 0.19-0.51) of patients and major clinical impact in 15 patients (50%, 95% CI 0.33-0.67). The most common discordances with major clinical impact were related to pneumonia on XR chest and appendicitis or inflammatory bowel disease on CT abdomen. CONCLUSIONS: In patients transferred to the PED, concordance of XR and CT interpretations was high. A majority of discordant interpretations led to clinical impact meaningful to the patient and emergency medicine (EM) physician. Referring EM physicians might consider the benefit of pediatric radiology consultation upon transfer, especially for imaging diagnoses related to pneumonia, appendicitis, or inflammatory bowel disease.

Multisystem inflammatory syndrome in children associated with novel coronavirus SARS-CoV-2: Presentations to a pediatric emergency department in Michigan.

The SARS-CoV-2 is a respiratory virus of the coronavirus family responsible for a global pandemic since December 2019. More than 35 million people have been affected with the novel coronavirus disease (COVID-19), with more than one million deaths worldwide. Michigan was one of the top three states in the United States that was severely affected by the SAR-CoV-2 pandemic with more than 7000 deaths in adults and greater than 145,000 confirmed infections. However, compared to adults, the majority of children until recently were either asymptomatic or had a mild illness with SARS-CoV-2. Recently, a rare but potentially serious presentation associated with SARS-CoV-2 called multisystem inflammatory syndrome in children (MIS-C) has been recently reported and the Centers for Disease Control (CDC) released a case definition for the same. We report the clinical and laboratory presentations and outcomes of 34 children with MIS-C who were evaluated within a 12 week period at a pediatric emergency department (PED) of single institution in Michigan. These cases presented approximately three weeks after the peak of adult SAR-CoV-2 related deaths occurred in the state. While many children presented with clinical characteristics similar to incomplete Kawasaki disease (KD), they also exhibited certain unique features which differentiated MIS-C from KD. The information presented below will aid clinicians with early recognition, evaluation and management of MIS-C in the emergency department.

Lethal and sublethal toxicity of perfluorooctanoic acid (PFOA) in chronic tests with Hyalella azteca (amphipod) and early-life stage tests with Pimephales promelas (fathead minnow).

Perfluoroalkyl substances (PFAS), including perfluorooctanoic acid (PFOA), are industrial chemicals that are of concern due to their environmental presence, persistence, bioaccumulative potential, toxicity, and capacity for long-range transport. Despite a large body of research on environmental exposure, insufficient chronic aquatic toxicity data exist to develop water quality targets for clean-up of federal contaminated sites in Canada. Thus, our objective was to assess the aqueous toxicity of PFOA in chronic tests with Hyalella azteca (amphipod) and early-life stage tests with Pimephales promelas (fathead minnow). Toxicity data were analyzed based on measured PFOA concentrations. Amphipod exposures were 42 d (0.84-97 mg/L) and examined survival, growth, and reproduction. Fathead minnow exposures were 21 d (0.010-76 mg/L), which encompassed hatching (5 d) and larval stages until 16 d post-hatch; endpoints included hatching success, deformities at hatch, and larval survival and growth. Amphipod survival was significantly reduced at 97 mg/L (42-d LC50 = 51 mg/L), but growth and reproduction were more sensitive endpoints (42-d EC50 for both endpoints = 2.3 mg/L). Fathead minnows were less sensitive than amphipods, exhibiting no significant effects in all endpoints with the exception of uninflated swim bladder, which was significantly higher at 76 mg/L (15%) than controls (0%). Maximum concentrations of PFOA are generally in the ng/L range in global surface waters, but can reach the µg/L range in close proximity to major source inputs; therefore, environmental concentrations are well below those that caused toxicity in the current study. Our data will provide valuable information with which to assess the risk of PFOA at contaminated sites, and to set a target for site remediation.

Simultaneous Superiorly Based Pharyngeal Flap and Tonsillectomy: Evaluation of Speech and Pain Outcomes.

ABSTRACT: Controversy remains whether to perform a pharyngeal flap simultaneously with a tonsillectomy in patients with velopharyngeal insufficiency. The aim of this study is to revisit the speech outcomes and complications associated with the combined superiorly based pharyngeal flap and tonsillectomy procedure, while comparing pain outcomes. We hypothesize that the combined procedure will improve speech outcomes with minimal complications, but patients will experience more pain in the combined procedure.A 5-year retrospective review of registry data from Boys Town National Research Hospital was conducted from 2014 to 2019. Data collection included age, surgeries performed, length of stay, pain medication administration occurrences, immediate postoperative complications, postoperative speech outcomes specifically related to articulation (audible nasal airway emissions) and resonance (hypernasality).Eighty-eight patients had a superiorly based pharyngeal flap over this 5-year period. Eighteen patients (20%) had a simultaneous procedure performed. There were no patients who had immediate postoperative complications such as upper airway obstruction or bleeding complications that necessitated a reoperation. One of the patients had a pharyngeal flap dehiscence that required a revision pharyngeal flap in the combined group. Nasal airway emissions and hypernasality were eliminated in 58.3% and 75%of the combined patients, respectively. The total number of narcotic administration occurrences were significantly higher in the combined group than the pharyngeal flap only group (9.0 versus 7.0; P = 0.03).A number of velopharyngeal patients will present with hypertrophied tonsils. We believe that it is safe and beneficial to perform the combined procedure in the same setting.

Effectiveness of the TightRope® Fixation in Treating Ankle Syndesmosis Injuries: A Critically Appraised Topic.

Clinical Scenario: Ankle fractures are a frequent occurrence, and they carry the potential for syndesmosis injury. The syndesmosis is important to the structural integrity of the ankle joint by maintaining the proximity of the tibia, fibula, and talus. Presently, the gold standard for treating an ankle syndesmosis injury is to insert a metallic screw through the fibula and into the tibia. This technique requires a second intervention to remove the hardware, but also carries an inherent risk of breaking the screw during rehabilitation. Another fixation technique, the Tightrope™, has gained popularity in treating ankle syndesmosis injuries. The TightRope™ involves inserting Fiberwire® through the tibia and fibula, which allows for stabilization of the ankle mortise and normal range of motion. Clinical Question: In patients suffering from ankle syndesmosis injuries, is the Tightrope™ ankle syndesmosis fixation system more effective than conventional screw fixation at improving return to work, pain, and patient-reported outcome measures? Summary of Key Findings: Five studies were selected to be critically appraised. The PEDro checklist was used to score 2 randomized control trials, and the Downs & Black checklist was used to score the cohort study on methodology and consistency. Two systematic reviews were also appraised. All 5 articles demonstrated support for using the TightRope™ fixation. Clinical Bottom Line: There is moderate evidence to support the use of the TightRope™ syndesmosis fixation system, as it provides both clinician- and patient-reported outcomes that are similar to those using the conventional metallic screw, with a shortened time to recover and return to activity. Strength of Recommendation: Grade A evidence exists in support of using the TightRope™ fixation system in place of the metallic screw following ankle syndesmosis injury.

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. However, given the relatively high error rates of such technologies, efficient and accurate assembly of large repeats and closely related haplotypes remains challenging. We address these issues with Canu, a successor of Celera Assembler that is specifically designed for noisy single-molecule sequences. Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while simultaneously reducing runtime by an order of magnitude on large genomes versus Celera Assembler 8.2. These advances result from new overlapping and assembly algorithms, including an adaptive overlapping strategy based on tf-idf weighted MinHash and a sparse assembly graph construction that avoids collapsing diverged repeats and haplotypes. We demonstrate that Canu can reliably assemble complete microbial genomes and near-complete eukaryotic chromosomes using either Pacific Biosciences (PacBio) or Oxford Nanopore technologies and achieves a contig NG50 of >21 Mbp on both human and Drosophila melanogaster PacBio data sets. For assembly structures that cannot be linearly represented, Canu provides graph-based assembly outputs in graphical fragment assembly (GFA) format for analysis or integration with complementary phasing and scaffolding techniques. The combination of such highly resolved assembly graphs with long-range scaffolding information promises the complete and automated assembly of complex genomes.

Regulation of Parent-of-Origin Allelic Expression in the Endosperm.

Genomic imprinting is an epigenetic phenomenon established in the gametes prior to fertilization that causes differential expression of parental alleles, mainly in the endosperm of flowering plants. The overlap between previously identified panels of imprinted genes is limited. To investigate imprinting, we used high-resolution sequencing data acquired with sequence-capture technology. We present a bioinformatics pipeline to assay parent-of-origin allele-specific expression and report more than 300 loci with parental expression bias in Arabidopsis (Arabidopsis thaliana). In most cases, the level of expression from maternal and paternal alleles was not binary, instead supporting a differential dosage hypothesis for the evolution of imprinting in plants. To address imprinting regulation, we systematically employed mutations in regulative epigenetic pathways suggested to be major players in the process. We established the mechanistic mode of imprinting for more than 50 loci regulated by DNA methylation and Polycomb-dependent histone methylation. However, the imprinting patterns of most genes were not affected by these mechanisms. To this end, we also demonstrated that the RNA-directed DNA methylation pathway alone does not substantially influence imprinting patterns, suggesting that more complex epigenetic pathways regulate most of the identified imprinted genes.