Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications.

The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI's capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.

Twenty Years After Enactment of the Organ Transplant Law in Japan: Why Are There Still So Few Deceased Donors?

BACKGROUND: Twenty years have passed since the 1997 enactment of the Organ Transplant Law in Japan, but the number of deceased donors remains extremely low. In this study we examine why deceased donation has continued to remain so infrequent. METHODS: This investigation was a secondary analysis of published data from the Japan Organ Transplant Network, 2016 Fact Book of Organ Transplantation in Japan, and International Registry on Organ Donation and Transplantation. RESULTS: In the past 20 years, donation intent declarations, knowledge, and respect for family member's wishes have increased, whereas resistance toward transplantation has decreased. Despite this, the traditional perspective on corpses of gotai manzoku (ie, the soul cannot be put to rest without being physically intact and without defect), the family-centricism, and reward-seeking altruism have not changed much. Living organ transplants have alleviated the organ deficiency somewhat, and the law requiring family consent seems to have contributed to the observed small increase in deceased donors. CONCLUSION: The number of deceased donors is unlikely to increase suddenly. However, 8 strategies are proposed to increase the number of deceased donors, including: increasing the number of donor procurement coordinators and establishing a training system; increasing the number of organ procurement facilities; creating hub transplant centers and training transplant surgeons; implementing radical reform in public education; reducing workload and improving education of emergency physicians, neurosurgeons, and pediatricians; revisiting the stringent standards of brain-death determination; revisiting the registration process; and considering development of a Japanese version of organ procurement organizations as well as revisions to the Organ Transplant Law. The Japanese government and academic societies must work together to increase the number of deceased donors in Japan.

Histological parameters to evaluate intestinal health on broilers challenged with Eimeria and Clostridium perfringens with or without enramycin as growth promoter.

The maintenance of integrity of the gastrointestinal tract is an important aspect for animal productivity, since it is able to absorb nutrients more efficiently and serves as a barrier against microorganisms. To control agents detrimental to intestinal integrity, growth-promoting antibiotics (AGP) are used, which reduce the number of toxin-producing microorganisms in the intestinal lumen, acting as anti-inflammatory agents. There is a demand for restriction of use of AGP in animal feed, but there are few studies showing what parameters we should observe to search for alternative additives. The aim of this study was to establish histological parameters that explain the effect of enramycin as growth promoter on intestinal health in broilers challenged with Eimeria and Clostridium perfringens. The zootechnical performance and the histology by I See Inside (ISI) methodology were evaluated on liver and ileum samples. Chickens challenged without AGP have the worst BWG, FCR, and histological ISI score (ISI score 9) in the ileum compared to non-challenged (ISI score 5). The use of enramycin on challenged group significantly minimized the ISI score in the ileum at 21 and 28 d (ISI score 7.4 and 8.0, respectively) compared with the challenged group not fed with enramycin (ISI score 9.2 and 9.9, respectively), associated with reduced lamina propria thickness and inflammatory cell infiltration. We suggest these 2 histological parameters as a standard to compare products for gut health.

Interval timing errors in a patient with thalamic chronotaraxis.

Thalamic chronotaraxis is an isolated disorientation of time caused by the damage of thalamus, especially the mediodorsal nucleus. We performed interval timing trials on a patient with this phenomenon. Based on the results of those trials and compared to the previous reports, thalamic chronotaraxis of our case might be due to the disfunction of the dorsolateral prefrontal cortex caused by the right thalamic infarction.

Comparison of MR Imaging and Dual-Energy CT for the Evaluation of Cartilage Invasion by Laryngeal and Hypopharyngeal Squamous Cell Carcinoma.

BACKGROUND AND PURPOSE: Dual-energy CT can distinguish iodine-enhanced tumors from nonossified cartilage and has been investigated for evaluating cartilage invasion in patients with laryngeal and hypopharyngeal squamous cell carcinomas. In this study, we compared the diagnostic accuracy of MR imaging and of a combination of weighted-average and iodine overlay dual-energy CT images in detecting cartilage invasion by laryngeal and hypopharyngeal squamous cell carcinomas, in particular thyroid cartilage invasion. MATERIALS AND METHODS: Fifty-five consecutive patients who underwent 3T MR imaging and 128-slice dual-energy CT for preoperative initial staging of laryngeal or hypopharyngeal squamous cell carcinomas were included. Two blinded observers evaluated laryngeal cartilage invasion on MR imaging and dual-energy CT using a combination of weighted-average and iodine-overlay images. Pathologic findings of surgically resected specimens were used as the reference standard for evaluating sensitivity, specificity, and the areas under the receiver operating characteristic curve of both modalities for cartilage invasion by each type of cartilage and for all cartilages together. Sensitivity and specificity were compared using the McNemar test and generalized linear mixed models. RESULTS: Dual-energy CT showed higher specificity than MR imaging for diagnosing all cartilage together (84% for MR imaging versus 98% for dual-energy CT, P < .004) and for thyroid cartilage (64% versus 100%, P < .001), with a similar average area under the curve (0.94 versus 0.95, P = .70). The sensitivity did not differ significantly for all cartilages together (97% versus 81%, P = .16) and for thyroid cartilage (100% versus 89%, P = .50), though there was a trend toward increased sensitivity with MR imaging. CONCLUSIONS: Dual-energy CT showed higher specificity and acceptable sensitivity in diagnosing laryngeal cartilage invasion compared with MR imaging.

Outcomes following autologous hematopoietic stem cell transplant for patients with relapsed Wilms' tumor: a CIBMTR retrospective analysis.

Despite the marked improvement in the overall survival (OS) for patients diagnosed with Wilms' tumor (WT), the outcomes for those who experience relapse have remained disappointing. We describe the outcomes of 253 patients with relapsed WT who received high-dose chemotherapy (HDT) followed by autologous hematopoietic stem cell transplant (HCT) between 1990 and 2013, and were reported to the Center for International Blood and Marrow Transplantation Research. The 5-year estimates for event-free survival (EFS) and OS were 36% (95% confidence interval (CI); 29-43%) and 45% (95 CI; 38-51%), respectively. Relapse of primary disease was the cause of death in 81% of the population. EFS, OS, relapse and transplant-related mortality showed no significant differences when broken down by disease status at transplant, time from diagnosis to transplant, year of transplant or conditioning regimen. Our data suggest that HDT followed by autologous HCT for relapsed WT is well tolerated and outcomes are similar to those reported in the literature. As attempts to conduct a randomized trial comparing maintenance chemotherapy with consolidation versus HDT followed by stem cell transplant have failed, one should balance the potential benefits with the yet unknown long-term risks. As disease recurrence continues to be the most common cause of death, future research should focus on the development of consolidation therapies for those patients achieving complete response to therapy.

A novel mutation in the RSPO4 gene in a patient with autosomal recessive anonychia.

The Wnt signalling pathway is a major pathway involved in the embryogenic development of the various organs of the body. Appropriate signalling in this pathway relies on the proper functioning of several proteins including the R-spondin family of proteins. Deactivating mutations in R-spondin 4 are associated with anonychia. We present the case of a 26-year-old man presenting with anonychia of the 20 nails, which had been present since birth. Using genetic studies, we identified a novel nonsense mutation, c.164-165TC>AA, characterized by two consecutive mismatch bases. To our knowledge, this mutation is the first to be reported in R-spondin 4 in a Lebanese population. Evaluating new patients with anonychia provides fruitful clinical and molecular findings.

Effect of aflatoxin experimental ingestion and Eimeira vaccine challenges on intestinal histopathology and immune cellular dynamic of broilers: applying an Intestinal Health Index.

The present study evaluated the effect of aflatoxin B1 and Eimeria vaccine challenges and their interaction on intestinal morphology, applying the morphometric index "I See Inside" (ISI). Immune cellular response and broiler chicken performance were also studied. A total of 240 broiler chickens were divided in a 2 × 2 factorial arrangement with 4 treatments, T1: Control diet and no challenge (CON), T2: Aflatoxin B1 (AFLA), T3: Control diet and Eimeria challenge (COC), and T4: Aflatoxin B1 and Eimeria challenge (AFLA+COC). The mathematical morphometric index ISI was applied to evaluate macro and microscopic alterations. Samples of liver and jejunum were analyzed for macrophages, CD4+, and CD8+ cells counting by immunohistochemistry at 7, 14, and 21 d of age. Chickens challenged with Eimeria presented higher ISI of macroscopic alterations associated to Eimeria lesion at the medium small intestine, lower body weight gain (BWG) and feed intake (FI), and worse feed conversion ratio compared to non-challenged birds. Both Eimeria and aflatoxin challenges modulated the immune cells in the jejunum and liver, generally increasing the number of macrophages, CD4+, and CD8+ cells in relation to the control group. Birds from COC and COC+AFLA groups presented higher ISI histological score in the jejunum at 7 and 14 d of age compared to the CON and AFLA groups. The reduction of FI and BWG was correlated to high histological ISI and resulted in a high presence of immune cells in tissues, suggesting immune response demand. The histological ISI had statistical correlation to broiler performance.

A prognostic model predicting autologous transplantation outcomes in children, adolescents and young adults with Hodgkin lymphoma.

Autologous hematopoietic cell transplantation (AutoHCT) is a potentially curative treatment modality for relapsed/refractory Hodgkin lymphoma (HL). However, no large studies have evaluated pretransplant factors predictive of outcomes of AutoHCT in children, adolescents and young adults (CAYA, age <30 years). In a retrospective study, we analyzed 606 CAYA patients (median age 23 years) with relapsed/refractory HL who underwent AutoHCT between 1995 and 2010. The probabilities of PFS at 1, 5 and 10 years were 66% (95% confidence interval (CI): 62-70), 52% (95% CI: 48-57) and 47% (95% CI: 42-51), respectively. Multivariate analysis for PFS demonstrated that at the time of AutoHCT patients with Karnofsky/Lansky score ⩾90, no extranodal involvement and chemosensitive disease had significantly improved PFS. Patients with time from diagnosis to first relapse of <1 year had a significantly inferior PFS. A prognostic model for PFS was developed that stratified patients into low-, intermediate- and high-risk groups, predicting for 5-year PFS probabilities of 72% (95% CI: 64-80), 53% (95% CI: 47-59) and 23% (95% CI: 9-36), respectively. This large study identifies a group of CAYA patients with relapsed/refractory HL who are at high risk of progression after AutoHCT. Such patients should be targeted for novel therapeutic and/or maintenance approaches post-AutoHCT.

Inverse estimation of radon flux distribution for East Asia using measured atmospheric radon concentration.

In this study, the (222)Rn flux density distribution at surface was estimated in East Asia with the Bayesian synthesis inversion using measurement data and a long-range atmospheric (222)Rn transport model. Surface atmospheric (222)Rn concentrations measured at Hateruma Island in January 2008 were used. The estimated (222)Rn flux densities were generally higher than the prior ones. The area-weighted mean (222)Rn flux density for East Asia in January 2008 was estimated to be 44.0 mBq m(-2) s(-1). The use of the estimated (222)Rn flux density improved the discrepancy of the model-calculated concentrations with the measurements at Hateruma Island.