BACKGROUND & AIMS Some patients with irritable bowel syndrome with diarrhea (IBS-D) have intestinal hyperpermeability, which contributes to their diarrhea and abdominal pain. MicroRNA 29 (MIR29) regulates intestinal permeability in patients with IBS-D. We investigated and searched for targets of MIR29 and investigated the effects of disrupting Mir29 in mice. METHODS We investigated expression MIR29A and B in intestinal biopsies collected during endoscopy from patients with IBS (n = 183) and without IBS (controls) (n = 36). Levels were correlated with disease phenotype. We also generated and studied Mir29−/− mice, in which expression of Mir29a and b, but not c, is lost. Colitis was induced by administration of 2,4,6-trinitrobenzenesulfonic acid; intestinal tissues were collected and permeability was assessed. Microarray analysis was performed using tissues from Mir29−/− mice. Changes in levels of target genes were measured in human colonic epithelial cells and small intestinal epithelial cells after knockdown of MIR29 with anti-MIRs. RESULTS Intestinal tissues from patients with IBS-D (but not IBS with constipation or controls) had increased levels of MIR29A and B, but reduced levels of Claudin-1 (CLDN1) and nuclear factor-κB–repressing factor (NKRF). Induction of colitis and water avoidance stress increased levels of Mir29a and Mir29b and intestinal permeability in wild-type mice; these increased intestinal permeability in colons of far fewer Mir29−/− mice. In microarray and knockdown experiments, MIR29A and B were found to reduce levels of NKRF and CLDN1 messenger RNA, and alter levels of other messenger RNAs that regulate intestinal permeability. CONCLUSIONS Based on experiments in knockout mice and analyses of intestinal tissue samples from patients with IBS-D, MIR29 targets and reduces expression of CLDN1 and NKRF to increase intestinal permeability. Strategies to block MIR29 might be developed to restore intestinal permeability in patients with IBS-D.

Global Retinoblastoma Study Group IMPORTANCE Early diagnosis of retinoblastoma, the most common intraocular cancer, can save both a child's life and vision. However, anecdotal evidence suggests that many children across the world are diagnosed late. To our knowledge, the clinical presentation of retinoblastoma has never been assessed on a global scale.OBJECTIVES To report the retinoblastoma stage at diagnosis in patients across the world during a single year, to investigate associations between clinical variables and national income level, and to investigate risk factors for advanced disease at diagnosis. DESIGN, SETTING, AND PARTICIPANTSA total of 278 retinoblastoma treatment centers were recruited from June 2017 through December 2018 to participate in a cross-sectional analysis of treatment-naive patients with retinoblastoma who were diagnosed in 2017. MAIN OUTCOMES AND MEASURESAge at presentation, proportion of familial history of retinoblastoma, and tumor stage and metastasis. RESULTSThe cohort included 4351 new patients from 153 countries; the median age at diagnosis was 30.5 (interquartile range, 18.3-45.9) months, and 1976 patients (45.4%) were female. Most patients (n = 3685 [84.7%]) were from low-and middle-income countries (LMICs). Globally, the most common indication for referral was leukocoria (n = 2638 [62.8%]), followed by strabismus (n = 429 [10.2%]) and proptosis (n = 309 [7.4%]). Patients from high-income countries (HICs) were diagnosed at a median age of 14.1 months, with 656 of 666 (98.5%) patients having intraocular retinoblastoma and 2 (0.3%) having metastasis. Patients from low-income countries were diagnosed at a median age of 30.5 months, with 256 of 521 (49.1%) having extraocular retinoblastoma and 94 of 498 (18.9%) having metastasis. Lower national income level was associated with older presentation age, higher proportion of locally advanced disease and distant metastasis, and smaller proportion of familial history of retinoblastoma. Advanced disease at diagnosis was more common in LMICs even after adjusting for age (odds ratio for low-income countries vs upper-middle-income countries and HICs, 17.92 [95% CI,, and for lower-middle-income countries vs upper-middle-income countries and HICs, 5.74 [95% CI,). CONCLUSIONS AND RELEVANCEThis study is estimated to have included more than half of all new retinoblastoma cases worldwide in 2017. Children from LMICs, where the main global retinoblastoma burden lies, presented at an older age with more advanced disease and demonstrated a smaller proportion of familial history of retinoblastoma, likely because many do not reach a childbearing age. Given that retinoblastoma is curable, these data are concerning and mandate intervention at national and international levels. Further studies are needed to investigate factors, other than age at presentation, that may be associated with advanced disease in LMICs.

Background & Aims Little is known about the prevalence and burden of undiagnosed celiac disease in individuals younger than 50 years old. We determined the prevalence and morbidity of undiagnosed celiac disease in individuals younger than 50 years in a community. Methods We tested sera from 31,255 residents of Olmsted County, Minnesota (younger than 50 years old) without a prior diagnosis of celiac disease assay using an assay for immunoglobulin A (IgA) against tissue transglutaminase (tTG); in subjects with positive test results, celiac disease was confirmed using an assay for endomysial IgA. We performed a nested case–control study to compare the proportion of comorbidities between undiagnosed cases of celiac disease and age- and sex-matched seronegative controls (1:2). Medical records were abstracted to identify potential comorbidities. Results We identified 338 of 30,425 adults with positive results from both serologic tests. Based on this finding, we estimated the prevalence of celiac disease to be 1.1% (95% CI, 1.0%–1.2%); 8 of 830 children tested positive for IgA against tTG (1.0%, 95% CI, 0.4%–1.9%). No typical symptoms or classic consequences of diagnosed celiac disease (diarrhea, anemia, or fracture) were associated with undiagnosed celiac disease. Undiagnosed celiac disease was associated with increased rates of hypothyroidism (odds ratio, 2.2; P<.01) and lower than average level of cholesterol (P=.03) and ferritin (P=.01). During a median follow-up period of 6.3 years, the cumulative incidence of subsequent diagnosis with celiac disease at 5 years after testing was 10.8% in persons with undiagnosed celiac disease vs 0.1% in seronegative persons (P<.01). Celiac disease status was not associated with overall survival. Conclusions Based on serologic tests of a community population for celiac disease, we estimated the prevalence of undiagnosed celiac disease to be 1%. Undiagnosed celiac disease appeared to be clinically silent and remained undetected, but long-term outcomes have not been determined.

Coronavirus disease 2019 (Covid-19) is a predominantly respiratory illness caused by the SARS-CoV-2 virus. Data regarding prognostic factors are currently scarce given the novelty of the disease. Prognostic information would aid clinicians in managing patients, who are often left without data-driven guidelines to make important clinical decisions. It is known that lymphocytopenia, defined as an absolute lymphocyte count (ALC) < 1000 cells/µL, occurs in Covid-19 and may correlate with increased disease severity 1-5 ; indeed, lymphocytopenia is a common systemic manifestation of many viral illnesses 6 ; in particular, other coronaviruses like Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV) have been demonstrated to cause lymphocytopenia. 2 However, few studies have examined whether lymphocytopenia found at the time of admission to the hospital is helpful in understanding the disease course. Here, we set out to study a cohort of patients admitted to the hospital diagnosed with Covid-19 to determine whether lymphocytopenia, found at the time of admission to the hospital, was associated with disease severity and other clinical outcomes.

Classification of the amounts and types of lower order structural elements in proteins is a prerequisite to effective comparisons between protein folds. In an effort to provide an additional vehicle for fold comparison, we present an alternative classification scheme whereby protein folds are represented in statistical thermodynamic terms in such a way as to illuminate the energetic building blocks within protein structures. The thermodynamic relationship is examined between amino acid sequences and the conformational ensembles for a database of 159 Homo sapiens protein structures ranging from 50 to 250 amino acids. Using hierarchical clustering, it is shown through fold-recognition experiments that (1) eight thermodynamic environmental descriptors sufficiently accounts for the energetic variation within the native state ensembles of the H. sapiens structural database, (2) an amino acid library of only six residue types is sufficient to encode >90% of the thermodynamic information required for fold specificity in the entire database, and (3) structural resolution of the statistically derived environments reveals sequential cooperative segments throughout the protein, which are independent of secondary structure. As the first level of thermodynamic organization in proteins, these segments represent the thermodynamic counterpart to secondary structure.Keywords: native state ensemble; sequential cooperative segments; fold recognition; protein structure prediction; position-specific thermodynamics; protein stabilityThe ability to define a protein fold in terms of elementary units or building blocks is the cornerstone to effective structure comparison. By cataloging the frequency and length of these building blocks within each fold, similarities and differences can be noted and quantitatively evaluated. Indeed such classification schemes as structural classification of proteins (SCOP;Murzin et al. 1995) and families of structurally similar proteins (FSSP; Holm and Sander 1996) have proven invaluable as a means of comparing and contrasting folds. A hallmark feature of traditional descriptions of fold space is that the building blocks are described in terms of structural attributes. For example, each position in a protein is part of a primary structural unit (e.g., ␣-helix, ␤-sheet, etc.), each structural unit is, in turn, part of a higher order structural motif (e.g., ␣/␤), and the motifs are arranged to form unique folds. Although structural descriptions of fold space have proven to be effective in fold recognition as well as homology studies (Bowie et al. 1991;Godzik and Skolnick 1992;Jones et al. 1992;Bryant and Lawrence 1993;Defay and Cohen 1996;Huang et al. 1996;Rost et al. 1997;Kelley et al. 2000;Mallick et al. 2002), such approaches do not account (at least not explicitly) for the well-known experimental observation that proteins display regional differences in conformational heterogeneity, even under native conditions (Wuthrich 1989;Bai and Englander 1996). This

To investigate the relationship between an amino acid sequence and its corresponding protein fold, a database of thermodynamic stability information was assembled as a function of residue type from 81 nonhomologous proteins. This information was obtained using the COREX algorithm, which computes an ensemble-based description of the native state of proteins. Dissection of the COREX stability constant into its fundamental energetic components resulted in 12 thermodynamic environments describing the tertiary architecture of protein folds. Because of the observation that residue types partitioned unequally between these environments, it was hypothesized that thermodynamic environments contained energetic information that connected sequence to fold. To test the significance of this hypothesis, the thermodynamic stability information was incorporated into a three-dimensional-to-one-dimensional scoring matrix, and simple fold recognition experiments were performed in a manner such that information about the fold target was never included in the scoring. For 60 out of 81 fold targets, the correct sequence for the target scored in the top 5% of 3858 decoy sequences, with Z-scores ranging from 1.76 to 12.23. Furthermore, a scoring matrix assembled from the residues of 40 nonhomologous all-␣ proteins was used to thread sequences against 12 nonhomologous all-␤ protein targets. In 10 of 12 cases, sequences known to adopt the native all-␤ structure scored in the top 5% of 3858 decoy sequences, with Z-scores ranging from 1.99 to 7.94. These results indicate that energetic information encoded by thermodynamic environments represents a fundamental property of proteins that underlies classifications based on secondary structure.

An amino acid sequence, in the context of the solvent environment, contains all of the thermodynamic information necessary to encode a three-dimensional protein structure. To investigate the relationship between an amino acid sequence and its corresponding protein fold, a database of thermodynamic stability information was assembled that spanned 2951 residues from 44 nonhomologous proteins. This information was obtained using the COREX algorithm, which computes an ensemble-based description of the native state of a protein. It was observed that amino acid types partitioned unequally into high, medium, and low thermodynamic stability environments. Furthermore, these distributions were reproducible and were significantly different than those expected from random partitioning. To assess the structural importance of the distributions, simple fold-recognition experiments were performed based on a 3D-1D scoring matrix containing only COREX residue stability information. This procedure was able to recover amino acid sequences corresponding to correct target structures more effectively than scoring matrices derived from randomized data. High-scoring sequences were often aligned correctly with their corresponding target profiles, suggesting that calculated thermodynamic stability profiles have the potential to encode sequence information. As a control, identical fold-recognition experiments were performed on the same database of proteins using DSSP secondary structure information in the scoring matrix, instead of COREX residue stability information. The comparable performance of both approaches suggested that COREX residue stability information and secondary structure information could be of equivalent utility in more sophisticated fold-recognition techniques. The results of this work are a consequence of the idea that amino acid sequences fold not into single, rigidly stable structures but rather into thermodynamic ensembles best represented by a timeaveraged structure.

Position-specific denatured-state thermodynamics were determined for a database of human proteins by use of an ensemble-based model of protein structure. The results of modeling denatured protein in this manner reveal important sequence-dependent thermodynamic properties in the denatured ensembles as well as fundamental differences between the denatured and native ensembles in overall thermodynamic character. The generality and robustness of these results were validated by performing fold-recognition experiments, whereby sequences were matched with their respective folds based on amino acid propensities for the different energetic environments in the protein, as determined through cluster analysis. Correlation analysis between structure and energetic information revealed that sequence segments destined for beta-sheet in the final native fold are energetically more predisposed to a broader repertoire of states than are sequence segments destined for alpha-helix. These results suggest that within the subensemble of mostly unstructured states, the energy landscapes are dominated by states in which parts of helices adopt structure, whereas structure formation for sequences destined for beta-strand is far less probable. These results support a framework model of folding, which suggests that, in general, the denatured state has evolutionarily evolved to avoid low-energy conformations in sequences that ultimately adopt beta-strand. Instead, the denatured state evolved so that sequence segments that ultimately adopt alpha-helix and coil will have a high intrinsic structure formation capability, thus serving as potential nucleation sites.