Correcting signal biases and detecting regulatory elements in STARR-seq data.

High-throughput reporter assays such as self-transcribing active regulatory region sequencing (STARR-seq) have made it possible to measure regulatory element activity across the entire human genome at once. The resulting data, however, present substantial analytical challenges. Here, we identify technical biases that explain most of the variance in STARR-seq data. We then develop a statistical model to correct those biases and to improve detection of regulatory elements. This approach substantially improves precision and recall over current methods, improves detection of both activating and repressive regulatory elements, and controls for false discoveries despite strong local correlations in signal.

Estimating FST and kinship for arbitrary population structures.

FST and kinship are key parameters often estimated in modern population genetics studies in order to quantitatively characterize structure and relatedness. Kinship matrices have also become a fundamental quantity used in genome-wide association studies and heritability estimation. The most frequently-used estimators of FST and kinship are method-of-moments estimators whose accuracies depend strongly on the existence of simple underlying forms of structure, such as the independent subpopulations model of non-overlapping, independently evolving subpopulations. However, modern data sets have revealed that these simple models of structure likely do not hold in many populations, including humans. In this work, we analyze the behavior of these estimators in the presence of arbitrarily-complex population structures, which results in an improved estimation framework specifically designed for arbitrary population structures. After generalizing the definition of FST to arbitrary population structures and establishing a framework for assessing bias and consistency of genome-wide estimators, we calculate the accuracy of existing FST and kinship estimators under arbitrary population structures, characterizing biases and estimation challenges unobserved under their originally-assumed models of structure. We then present our new approach, which consistently estimates kinship and FST when the minimum kinship value in the dataset is estimated consistently. We illustrate our results using simulated genotypes from an admixture model, constructing a one-dimensional geographic scenario that departs nontrivially from the independent subpopulations model. Our simulations reveal the potential for severe biases in estimates of existing approaches that are overcome by our new framework. This work may significantly improve future analyses that rely on accurate kinship and FST estimates.

Domain prediction with probabilistic directional context.

MOTIVATION: Protein domain prediction is one of the most powerful approaches for sequence-based function prediction. Although domain instances are typically predicted independently of each other, newer approaches have demonstrated improved performance by rewarding domain pairs that frequently co-occur within sequences. However, most of these approaches have ignored the order in which domains preferentially co-occur and have also not modeled domain co-occurrence probabilistically. RESULTS: We introduce a probabilistic approach for domain prediction that models 'directional' domain context. Our method is the first to score all domain pairs within a sequence while taking their order into account, even for non-sequential domains. We show that our approach extends a previous Markov model-based approach to additionally score all pairwise terms, and that it can be interpreted within the context of Markov random fields. We formulate our underlying combinatorial optimization problem as an integer linear program, and demonstrate that it can be solved quickly in practice. Finally, we perform extensive evaluation of domain context methods and demonstrate that incorporating context increases the number of domain predictions by ∼15%, with our approach dPUC2 (Domain Prediction Using Context) outperforming all competing approaches. AVAILABILITY AND IMPLEMENTATION: dPUC2 is available at http://github.com/alexviiia/dpuc2. CONTACT: mona@cs.princeton.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.

E-values have been the dominant statistic for protein sequence analysis for the past two decades: from identifying statistically significant local sequence alignments to evaluating matches to hidden Markov models describing protein domain families. Here we formally show that for "stratified" multiple hypothesis testing problems-that is, those in which statistical tests can be partitioned naturally-controlling the local False Discovery Rate (lFDR) per stratum, or partition, yields the most predictions across the data at any given threshold on the FDR or E-value over all strata combined. For the important problem of protein domain prediction, a key step in characterizing protein structure, function and evolution, we show that stratifying statistical tests by domain family yields excellent results. We develop the first FDR-estimating algorithms for domain prediction, and evaluate how well thresholds based on q-values, E-values and lFDRs perform in domain prediction using five complementary approaches for estimating empirical FDRs in this context. We show that stratified q-value thresholds substantially outperform E-values. Contradicting our theoretical results, q-values also outperform lFDRs; however, our tests reveal a small but coherent subset of domain families, biased towards models for specific repetitive patterns, for which weaknesses in random sequence models yield notably inaccurate statistical significance measures. Usage of lFDR thresholds outperform q-values for the remaining families, which have as-expected noise, suggesting that further improvements in domain predictions can be achieved with improved modeling of random sequences. Overall, our theoretical and empirical findings suggest that the use of stratified q-values and lFDRs could result in improvements in a host of structured multiple hypothesis testing problems arising in bioinformatics, including genome-wide association studies, orthology prediction, and motif scanning.

Evolution and diversity in human herpes simplex virus genomes.

Herpes simplex virus 1 (HSV-1) causes a chronic, lifelong infection in >60% of adults. Multiple recent vaccine trials have failed, with viral diversity likely contributing to these failures. To understand HSV-1 diversity better, we comprehensively compared 20 newly sequenced viral genomes from China, Japan, Kenya, and South Korea with six previously sequenced genomes from the United States, Europe, and Japan. In this diverse collection of passaged strains, we found that one-fifth of the newly sequenced members share a gene deletion and one-third exhibit homopolymeric frameshift mutations (HFMs). Individual strains exhibit genotypic and potential phenotypic variation via HFMs, deletions, short sequence repeats, and single-nucleotide polymorphisms, although the protein sequence identity between strains exceeds 90% on average. In the first genome-scale analysis of positive selection in HSV-1, we found signs of selection in specific proteins and residues, including the fusion protein glycoprotein H. We also confirmed previous results suggesting that recombination has occurred with high frequency throughout the HSV-1 genome. Despite this, the HSV-1 strains analyzed clustered by geographic origin during whole-genome distance analysis. These data shed light on likely routes of HSV-1 adaptation to changing environments and will aid in the selection of vaccine antigens that are invariant worldwide.

Dermatologic health literacy in underserved communities: a case report of south Los Angeles middle schools.

BACKGROUND: The incidence of melanoma and other skin cancers has risen drastically in the United States.  As with most types of cancer, the prognosis and survival rates are significantly improved with early diagnosis, but dismal for patients who present with advanced disease.  It remains a fact that although melanoma is most common in Caucasian populations, ethnic minorities have a worse prognosis. Our hypothesis in this dermatologic health literacy study was that before necessary education, the required fund of knowledge with respect to skin cancer risk is lacking in several ethnic communities, but that intended compliance occurs when educational intervention occurs. METHODS: Three middle schools in South Los Angeles with predominantly Latino and African American youth were surveyed. Permission was obtained from the principals of the middle schools for the multi-day educational initiative. A total of 150 students were ultimately recruited and a pre-intervention survey administered. After preliminary review of the pre-intervention dermatologic health literacy results, a set of "core" learning concepts about sun safety were summarized and solidified for incorporation into the adolescent-appropriate sun safety protection pamphlet that was designed by designers at UCLA/Johnson & Johnson Health Care Institute. A full day of education on skin disease and the importance of sun protection from an early age was executed, followed three months later by a post-intervention visit that assessed compliance with the sun protection products and intended future use. RESULTS:   Results from the pre- and post-intervention surveys/questionnaires were analyzed and interpreted. Of 150 pre-intervention surveys that were distributed, 54 identified as African American and 96 of whom identified as Latino. Of these, 75% of Latino students reported having a sunburn in the last year, whereas only 38.9% of African American students reported a sunburn.  A total of 80% of the students reported as least some use of sunscreen in the 3 months prior to the post-intervention survey.  Only 8% of African American students reported "everyday" use, whereas 24% of Latino students reported "everyday" use (P < 0.05).  A total of 94% of the students intend to wear sunscreen in the future (89% of African American students and 97% of Latino students, with a P < 0.05 calculated using a two-sample t test).  However, it should be noted that more than half (54%) of the total students reported that although they planned to apply the sunscreen daily, they deemed it too expensive, which might prevent consistent future use. CONCLUSIONS: Our hypothesis in this dermatologic health literacy study was that before necessary education, the required fund of knowledge with respect to skin cancer risk is lacking in several ethnic communities, but that intended compliance occurs when educational intervention occurs.  The data, both quantitative and qualitative, demonstrate that our hypothesis is substantiated.

Socioeconomic Disparities and Emergency Department Visits for Diabetic Retinopathy in California.

Purpose: To investigate the association between neighborhood-level socioeconomic factors, quantified by the Distressed Communities Index, and emergency department visits for diabetic retinopathy (DR). Methods: All patients who presented to the emergency department for DR in California were analyzed using the State Emergency Department Database (2018-2020). Patients were stratified by Distressed Communities Index score and DR severity. Logistic regression was applied to explore the independent correlation between Distressed Communities Index scores and proliferative DR (PDR). Results: Of 2 725 195 emergency department visits for diabetic patients, Distressed Communities Index data were available for 2 459 577 (90.3%); 39 693 were for DR, including 13 617 (34.3%) for PDR. Hispanics (44.2%) were the largest racial/ethnic group to present for PDR, followed by non-Hispanic Whites (19.6%) and non-Hispanic Blacks (19.3%). A significant association was observed between the Distressed Communities Index and emergency department visits for PDR, with distressed neighborhoods having the highest incidence (adjusted odds ratio [aOR], 1.63; 95% CI, 1.20-2.23; P = .001). Other predictors included Hispanic ethnicity (aOR, 2.21; 95% CI, 1.97-2.48; P < .001) and Black race (aOR, 1.46; 95% CI, 1.28-1.67; P < .001) compared with White race and having Medicaid (aOR, 1.37; 95% CI, 1.13-1.65; P = .001) compared with private insurance. Conclusions: The Distressed Communities Index identified patients residing in the most distressed neighborhoods as being at the highest risk for presenting to the emergency department for PDR based on 7 socioeconomic factors. Policymakers may consider the Distressed Communities Index as a tool for targeting DR prevention strategies and improving healthcare accessibility.

Correction to: VEIN STEP: A Prospective, Observational, International Study to Assess Effectiveness of Conservative Treatments in Chronic Venous Disease.

Video Abstract.

Genetic association models are robust to common population kinship estimation biases.

Common genetic association models for structured populations, including principal component analysis (PCA) and linear mixed-effects models (LMMs), model the correlation structure between individuals using population kinship matrices, also known as genetic relatedness matrices. However, the most common kinship estimators can have severe biases that were only recently determined. Here we characterize the effect of these kinship biases on genetic association. We employ a large simulated admixed family and genotypes from the 1000 Genomes Project, both with simulated traits, to evaluate key kinship estimators. Remarkably, we find practically invariant association statistics for kinship matrices of different bias types (matching all other features). We then prove using statistical theory and linear algebra that LMM association tests are invariant to these kinship biases, and PCA approximately so. Our proof shows that the intercept and relatedness effect coefficients compensate for the kinship bias, an argument that extends to generalized linear models. As a corollary, association testing is also invariant to changing the reference ancestral population of the kinship matrix. Lastly, we observed that all kinship estimators, except for popkin ratio-of-means, can give improper non-positive semidefinite matrices, which can be problematic although some LMMs handle them surprisingly well, and condition numbers can be used to choose kinship estimators. Overall, we find that existing association studies are robust to kinship estimation bias, and our calculations may help improve association methods by taking advantage of this unexpected robustness, as well as help determine the effects of kinship bias in related problems.

Limitations of principal components in quantitative genetic association models for human studies.

Principal Component Analysis (PCA) and the Linear Mixed-effects Model (LMM), sometimes in combination, are the most common genetic association models. Previous PCA-LMM comparisons give mixed results, unclear guidance, and have several limitations, including not varying the number of principal components (PCs), simulating simple population structures, and inconsistent use of real data and power evaluations. We evaluate PCA and LMM both varying number of PCs in realistic genotype and complex trait simulations including admixed families, subpopulation trees, and real multiethnic human datasets with simulated traits. We find that LMM without PCs usually performs best, with the largest effects in family simulations and real human datasets and traits without environment effects. Poor PCA performance on human datasets is driven by large numbers of distant relatives more than the smaller number of closer relatives. While PCA was known to fail on family data, we report strong effects of family relatedness in genetically diverse human datasets, not avoided by pruning close relatives. Environment effects driven by geography and ethnicity are better modeled with LMM including those labels instead of PCs. This work better characterizes the severe limitations of PCA compared to LMM in modeling the complex relatedness structures of multiethnic human data for association studies.

Genetic risk variants for childhood nephrotic syndrome and corticosteroid response.

Introduction: The etiology of most cases of nephrotic syndrome (NS) remains unknown, therefore patients are phenotypically categorized based on response to corticosteroid therapy as steroid sensitive NS (SSNS), or steroid resistant NS (SRNS). Genetic risk factors have been identified for SSNS from unbiased genome-wide association studies (GWAS), however it is unclear if these loci are disease risk loci in other forms of NS such as SRNS. Additionally, it remains unknown if these risk loci are associated with response to therapy. Thus, we investigated the association between SSNS risk loci and therapy response in a large, multi-race cohort of children along the entire spectrum of childhood-onset NS. Methods: We enrolled 1,000 patients with childhood-onset NS comprised of SSNS and SRNS. Genotyping was done using TaqMan and Direct Sanger Sequencing for 9 previously reported childhood SSNS risk loci. We compared the allele frequencies (AF) and variant burden between NS vs. controls and SRNS vs. SSNS. Results: All 9 risk loci were associated with NS compared with healthy controls (p = 3.5 × 10-3-<2.2 × 10-16). Variant burden greater than 7 was associated with risk of SRNS (OR 7.4, 95% CI 4.6-12.0, p = 8.2 × 10-16). Conclusion: Our study showed that genetic risk loci for childhood SSNS are associated with pattern of therapy response, may help predict disease outcome, and set the stage for individualized treatment of NS.

VEIN STEP: A Prospective, Observational, International Study to Assess Effectiveness of Conservative Treatments in Chronic Venous Disease.

INTRODUCTION: VEIN STEP was conducted to collect international data on the management of chronic venous disease (CVD) and to assess the effectiveness of conservative treatments for the relief of CVD signs and symptoms. METHODS: This international, observational, prospective, longitudinal, cohort study recruited adult outpatients consulting for symptomatic CVD. The primary objective was the effectiveness of conservative treatments on symptoms, signs and quality of life in a real-life setting assessed using a range of patient-reported outcome measures: 10-cm Visual Analog and Patient Global Impression of Change scales for symptoms; Venous Clinical Severity Score for physician assessment of signs; and 14-item ChronIc Venous Insufficiency Questionnaire (CIVIQ-14) for quality of life. At inclusion, patients were prescribed conservative treatment according to the physicians' usual practice. Follow-up visits took place at weeks 2 and 4, with an optional week 8 visit. RESULTS: The analysis set comprised 6084 subjects (78% female) from nine countries with a mean age of 50.6 ± 13.8 years and BMI of 28.0 ± 4.9 kg/m2. The most common CEAP classifications were C1 (23.0%), C2 (31.6%), and C3 (30.7%). Conservative therapy consisted of oral venoactive drugs (VADs; 95.8% of subjects) including micronized purified flavonoid fraction (MPFF 75.5%) and diosmin (18.8%), compression (52.0%), and topicals (31.5%). Conservative therapy led to global symptom improvement in 89% of patients after 2 weeks and 96% at 4 weeks. Pain, leg heaviness, cramps, and sensation of swelling were improved in 82%, 71%, 45.5%, and 46% of patients, respectively. Conservative therapy was associated with a decrease over time in patient-assessed global symptom intensity: - 2.37 ± 1.73 (P < 0.001) and physician-assessed disease severity - 1.83 ± 2.82 (P < 0.001). Among the VADs, MPFF-based conservative therapy was associated with the greatest reduction in symptom and sign intensity. Improvements in CIVIQ-14 were observed with all treatments but were greatest for MPFF. CONCLUSION: In this prospective study conducted in the real-world setting, treatment with conservative therapy, in particular MPFF, was associated with meaningful improvements in the clinical signs and symptoms of disease as well as in quality of life in patients with CVD. TRIAL REGISTRATION: ClinicalTrials.gov identifier NCT04574375.

STUDY AIM: The VEIN STEP study aimed to gather global data on managing chronic venous disease (CVD) and evaluate the usefulness of conservative (non-surgical) treatments for improving CVD signs and symptoms. METHODS: Persons included in the study group had symptomatic CVD and were visiting outpatient clinics. The main aim was to measure how well treatments improved symptoms, physical signs of the illness, and quality of life. Different methods were used to measure these aspects, such as rating symptoms on a 10-point scale and using questionnaires completed by patients and doctors. STUDY FINDINGS: 6084 participants from nine countries joined the study. They were mostly women (78%) with an average age of around 50. Common symptoms included leg pain and leg heaviness. Treatments consisted mainly of drugs active on vein function, like MPFF and diosmin, along with compression stockings and creams. Conservative treatment led to symptom improvement in 89% of patients after 2 weeks and 96% at 4 weeks. Pain and leg heaviness improved in most patients (82% and 71% over the same period) while cramps, and swelling showed improvement in 45.5% and 46% of patients, respectively. Patients reported a significant decrease in symptom intensity, and doctors observed a reduction in disease severity. MPFF was associated with the highest reduction in symptom intensity. Improvements in quality of life were observed with all treatments but were greatest for MPFF. CONCLUSION: The study highlights that conservative treatments, especially MPFF, are associated with significant improvements in the clinical signs and symptoms of patients with CVD as well as in their quality of life.

Steroid-sensitive nephrotic syndrome candidate gene CLVS1 regulates podocyte oxidative stress and endocytosis.

We performed next-generation sequencing in patients with familial steroid-sensitive nephrotic syndrome (SSNS) and identified a homozygous segregating variant (p.H310Y) in the gene encoding clavesin-1 (CLVS1) in a consanguineous family with 3 affected individuals. Knockdown of the clavesin gene in zebrafish (clvs2) produced edema phenotypes due to disruption of podocyte structure and loss of glomerular filtration barrier integrity that could be rescued by WT CLVS1 but not the p.H310Y variant. Analysis of cultured human podocytes with CRISPR/Cas9-mediated CLVS1 knockout or homozygous H310Y knockin revealed deficits in clathrin-mediated endocytosis and increased susceptibility to apoptosis that could be rescued with corticosteroid treatment, mimicking the steroid responsiveness observed in patients with SSNS. The p.H310Y variant also disrupted binding of clavesin-1 to α-tocopherol transfer protein, resulting in increased reactive oxygen species (ROS) accumulation in CLVS1-deficient podocytes. Treatment of CLVS1-knockout or homozygous H310Y-knockin podocytes with pharmacological ROS inhibitors restored viability to control levels. Taken together, these data identify CLVS1 as a candidate gene for SSNS, provide insight into therapeutic effects of corticosteroids on podocyte cellular dynamics, and add to the growing evidence of the importance of endocytosis and oxidative stress regulation to podocyte function.

Using context to improve protein domain identification.

BACKGROUND: Identifying domains in protein sequences is an important step in protein structural and functional annotation. Existing domain recognition methods typically evaluate each domain prediction independently of the rest. However, the majority of proteins are multidomain, and pairwise domain co-occurrences are highly specific and non-transitive. RESULTS: Here, we demonstrate how to exploit domain co-occurrence to boost weak domain predictions that appear in previously observed combinations, while penalizing higher confidence domains if such combinations have never been observed. Our framework, Domain Prediction Using Context (dPUC), incorporates pairwise "context" scores between domains, along with traditional domain scores and thresholds, and improves domain prediction across a variety of organisms from bacteria to protozoa and metazoa. Among the genomes we tested, dPUC is most successful at improving predictions for the poorly-annotated malaria parasite Plasmodium falciparum, for which over 38% of the genome is currently unannotated. Our approach enables high-confidence annotations in this organism and the identification of orthologs to many core machinery proteins conserved in all eukaryotes, including those involved in ribosomal assembly and other RNA processing events, which surprisingly had not been previously known. CONCLUSIONS: Overall, our results demonstrate that this new context-based approach will provide significant improvements in domain and function prediction, especially for poorly understood genomes for which the need for additional annotations is greatest. Source code for the algorithm is available under a GPL open source license at http://compbio.cs.princeton.edu/dpuc/. Pre-computed results for our test organisms and a web server are also available at that location.

Reducing hyperpigmentation after sclerotherapy: A randomized clinical trial.

OBJECTIVE: Sclerotherapy for the treatment of varicose veins is one of the most common medical procedures performed in the Western world, and hyperpigmentation is one of the most frequent, dreaded, minor adverse events. There has recently been some interest in investigating the inflammatory response of the local endothelium after sclerotherapy and the possible benefits of venoactive drugs because of their pleiotropic properties. The aim of this study was to evaluate whether adding a venoactive drug (sulodexide) to the standard sclerotherapy treatment protocol for patients with varicose veins can reduce the occurrence of postsclerotherapy hyperpigmentation. METHODS: We carried out a prospective, multicenter, randomized controlled trial with a parallel group design. It included 720 patients with telangiectasia, reticular veins, or varicose veins who were candidates for sclerotherapy. Patients with reflux in deep system or saphenous veins were excluded. Group A consisted of 354 patients who received an oral dose of sulodexide twice a day for 7 days before scheduled sclerotherapy; the treatment then continued for 3 months. Group B consisted of 366 patients who received the standard sclerotherapy protocol. Polidocanol was used as the sclerosing agent, and 20 to 30 mm Hg compression stockings were used in both groups for 7 days. Control photographs were taken, and a follow-up examination took place after 1 month and 3 months. Computer software was used to analyze the treated area for incidence of hyperpigmentation, total area of hyperpigmentation, skin tone increase in the hyperpigmented area, vein disappearance, and incidence of major bleeding. The sample size was calculated to give a statistical power of 80%. Student t-test and the χ2 test were used for comparative analyses, as appropriate. The level of significance was set at P < .05. RESULTS: A total of 609 patients completed the 3-month follow-up: 312 in group A and 297 in group B. After 1 month, the incidence of hyperpigmentation was 8.7% in group A and 14.8% in group B (P = .01). Group A developed an average area of hyperpigmentation of 10.7% compared with 18.2% in group B (P = .01), and the skin tone of the hyperpigmented area was lower in group A than in group B (P = .02). However, the latter difference was not significant after 3 months. The overall vein disappearance rate was similar in both groups. CONCLUSIONS: Our analysis shows that by adding a venoactive drug (sulodexide) to the standard sclerotherapy protocol, the occurrence of hyperpigmentation is reduced without affecting the desired therapeutic vein elimination response.

Cardiac Sarcoidosis: A Clinical Overview.

Cardiac sarcoidosis (CS) with clinical manifestation occurs in about 5-8% of patients with sarcoidosis. CS may be clinically suspected by the presence of ventricular arrhythmia, conduction abnormalities, and heart failure (HF). However, 20%-25% of patients may present with silent CS, having asymptomatic cardiac involvement. The diagnosis of CS is based on findings from nuclear studies, cardiac magnetic resonance, and extra-cardiac tissue biopsy. Due to the inflammatory nature of the disease, immunosuppressive medications are a cornerstone of therapy. The treatment also includes recommended HF medical therapies. Since CS patients are at risk of sudden cardiac death resulting from progression of cardiac dysfunction or the presence of scar originating from fatal arrhythmias, implantable cardioverter-defibrillators should be considered, with special indication beyond accepted recommendations in HF. In CS, the extent of left ventricular dysfunction is the most important mortality predictor. Heart transplant or mechanical circulatory support may represent life saving strategies in selective CS patients.

The Agreement Between an iPad Visual Field App and Humphrey Frequency Doubling Technology in Visual Field Screening at Health Fairs.

PRECIS: This is the first exploratory study demonstrating the promising potential of app-based visual fields testing in a low-resource health fair setting for community screening of high-risk Latino adults. PURPOSE: To compare the "Visual Fields Easy" (VFE) iPad application against the Humphrey Frequency Doubling Technology (FDT) N-30-5 in detecting abnormal visual fields in a low-resource health fair setting. METHODS: Latinos aged 40 to 80 years were recruited at a health fair in Los Angeles, California, in November 2017. Both eyes were tested using VFE and FDT. To account for possible nested correlations between participants and eyes, linear mixed effects models were used to estimate the difference in test time and the association in percent of missed points. A Bland-Altman plot and receiver operator characteristic curve were constructed for further comparisons. RESULTS: Forty-five participants with a mean age of 58.5 years (SD=9.5 y) were recruited and both eyes were tested (90 eyes). VFE testing took on average 141 seconds longer per eye than FDT (95% confidence interval: 137-145 s), and FDT resulted in having 7.50% more missed points than VFE (95% confidence interval: 2.56%-12.43%, P=0.002). The Bland-Altman plot depicted reduced agreement with increasing average of percent of points missed. The sensitivity and specificity of VFE were 67% and 77%, respectively, with an area under the receiver operator characteristic curve of 0.71. CONCLUSIONS: In this exploratory study, VFE exhibited moderate discrimination for identifying Latino adults with abnormal visual fields compared with FDT. Agreement between FDT and VFE was greater for patients with mild-to-moderate visual field loss. Further software enhancements of app-based fields testing, in concert with other portable testing, represents promising screening methods for high-risk groups in resource-limited environments.

HLA Loci and Recurrence of Focal Segmental Glomerulosclerosis in Pediatric Kidney Transplantation.

Recurrent focal segmental glomerulosclerosis (FSGS) after kidney transplantation accounts for the majority of allograft failures in children with primary FSGS. Although current research focuses on FSGS pathophysiology, a common etiology and mechanisms of disease recurrence remain elusive. METHODS: We performed a retrospective review of the Scientific Registry of Transplant Recipients to determine the association of specific HLA recurrence of FSGS. Kidney transplants recipients under the age of 19 who were diagnosed with FSGS, who were transplanted after January 1, 2000, and who had complete HLA data were included in the study. We performed simple logistic regression on all HLA A, B, C, DR, and DQ represented in the dataset and FSGS recurrence and then determined those associated with recurrence using the Benjamini-Hochberg method for multiple comparisons. For those HLAs that were associated with recurrence, we further determined the effect of matching recipient and donor HLA with recurrence. RESULTS: HLA DR7, DR53, DQ2, DR52, and DQ7 were associated with increased or decreased risk of recurrent disease after transplantation. We identified a risk haplotype consisting of HLA-DR7, DR53, and DQ2 that was consistently associated with an increased risk of recurrence (odds ratio 1.91; 95% confidence interval, 1.44-2.54, P < 0.001). We also found that donor/recipient concordance for HLA-DQ7 was associated with a decreased risk of recurrence (odds ratio 0.42; 95% confidence interval, 0.37-0.53, P = 0.009). CONCLUSIONS: HLA profiles may be used for risk stratification of recurrence of FSGS in pediatric kidney transplant recipients and deserves further study.

Sulodexide in the Treatment of Patients with Early Stages of COVID-19: A Randomized Controlled Trial.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may induce several vascular endothelial-dependent systemic complications, and sulodexide has pleiotropic actions on the vascular endothelium, which may prove beneficial. We aimed to assess the effect of sulodexide when used within 3 days of coronavirus disease 2019 (COVID-19) clinical onset. We conducted a randomized placebo-controlled outpatient trial. To be included, patients must have been at high risk for severe clinical progression. Participants received sulodexide (oral 1,000 LRU/d) or placebo for 21 days. The primary endpoint was the need for hospital care. Also assessed were patients' need for supplemental oxygen as well as D-dimer and C-reactive protein (CRP) levels, thromboembolic events, major bleeding, and mortality. A total of 243 patients were included in the per-protocol analysis from June 5 to August 30, 2020. Of these, 124 received sulodexide and 119 received a placebo. Only 17.7% of the patients in the sulodexide group required hospitalization, compared with 29.4% in the placebo group (p = 0.03). This benefit persisted in the intention-to-treat analysis (15% in sulodexide group vs. 24% with placebo [p = 0.04]). With sulodexide, fewer patients required supplemental oxygen (30 vs. 42% [p = 0.05]). After 2 weeks, fewer patients had D-dimer levels >500 ng/dL (22 vs. 47% [p < 0.01]), and patients also had lower mean CRP levels (12.5 vs. 17.8 mg/dL [p < 0.01]). There were no between-group differences in thromboembolic events, major bleeding, or mortality. Treatment of COVID-19 patients with sulodexide, when provided within 3 days of clinical onset, improved their clinical outcomes. Although the results should be confirmed, sulodexide could be valuable in an outpatient setting.

Lamellar bone is an incremental tissue reconciling enamel rhythms, body size, and organismal life history.

Mammalian enamel formation is periodic, including fluctuations attributable to the daily biological clock as well as longer-period oscillations that enigmatically correlate with body mass. Because the scaling of bone mass to body mass is an axiom of vertebrate hard tissue biology, we consider that long-period enamel formation rhythms may reflect corresponding and heretofore unrecognized rhythms in bone growth. The principal aim of this study is to seek a rhythm in bone growth demonstrably related to enamel oscillatory development. Our analytical approach is based in morphology, using a variety of hard tissue microscopy techniques. We first ascertain the relationship among long-period enamel rhythms, the striae of Retzius, and body mass using a large sample of mammalian taxa. In addition, we test whether osteocyte lacuna density (a surrogate for rates of cell proliferation) in bone is correlated with mammalian body mass. Finally, using fluorescently labeled developing bone tissues, we investigate whether the bone lamella, a fundamental microanatomical unit of bone, relates to rhythmic enamel growth increments. Our results confirm a positive correlation between long-period enamel rhythms and body mass and a negative correlation between osteocyte density and body mass. We also confirm that lamellar bone is an incremental tissue, one lamella formed in the species-specific time dependency of striae of Retzius formation. We conclude by contextualizing our morphological research with a current understanding of autonomic regulatory control of the skeleton and body mass, suggesting a central contribution to the coordination of organismal life history and body mass.