Surveying Current Practices in the Use of Gadolinium-Based Contrast Agents for Routine Brain Magnetic Resonance Imaging in the Evaluation of Isolated Growth Hormone Deficiency Among U.S. Pediatric Endocrinologists.

INTRODUCTION: This survey investigates brain MRI practices for isolated GHD among Pediatric Endocrine Society (PES) members, focusing on gadolinium-based contrast agents (GBCAs) versus non-contrast MRI. METHODS: A 15-question survey was distributed to 1,553 PES members, capturing data on GBCA usage, non-contrast imaging access, and awareness of gadolinium retention. RESULTS: 85% of respondents routinely order brain MRIs for isolated GHD, with 60% using GBCAs. Most respondents have access to high-resolution non-contrast imaging, though 54% are unaware of gadolinium retention risks. CONCLUSION: High-resolution non-contrast MRI demonstrates diagnostic efficacy, suggesting a shift away from GBCAs in clinic practice for isolated GHD. The survey forms the basis to update PES guidelines in the evaluation of isolated GHD.

Enzyme Kinetics Analysis: An online tool for analyzing enzyme initial rate data and teaching enzyme kinetics.

Enzymes are nature's catalysts, mediating chemical processes in living systems. The study of enzyme function and mechanism includes defining the maximum catalytic rate and affinity for substrate/s (among other factors), referred to as enzyme kinetics. Enzyme kinetics is a staple of biochemistry curricula and other disciplines, from molecular and cellular biology to pharmacology. However, because enzyme kinetics involves concepts rarely employed in other areas of biology, it can be challenging for students and researchers. Traditional graphical analysis was replaced by computational analysis, requiring another skill not core to many life sciences curricula. Computational analysis can be time-consuming and difficult in free software (e.g., R) or require costly software (e.g., GraphPad Prism). We present Enzyme Kinetics Analysis (EKA), a web-tool to augment teaching and learning and streamline EKA. EKA is an interactive and free tool for analyzing enzyme kinetic data and improving student learning through simulation, built using R and RStudio's ShinyApps. EKA provides kinetic models (Michaelis-Menten, Hill, simple reversible inhibition models, ternary-complex, and ping-pong) for users to fit experimental data, providing graphical results and statistics. Additionally, EKA enables users to input parameters and create data and graphs, to visualize changes to parameters (e.g., K M or number of measurements). This function is designed for students learning kinetics but also for researchers to design experiments. EKA (enzyme-kinetics.shinyapps.io/enzkinet_webpage/) provides a simple, interactive interface for teachers, students, and researchers to explore enzyme kinetics. It gives researchers the ability to design experiments and analyze data without specific software requirements.

Deciphering m6A dynamics at a single-base level during planarian anterior-posterior axis specification.

Background: The establishment of the anterior-posterior (A-P) axis is a crucial step during tissue repair and regeneration. Despite the association reported recently of N6-methyladenosine (m6A) with regeneration, the mechanism underlying the regulation of m6A in A-P axis specification during regeneration remains unknown. Herein, we deciphered the m6A landscape at a single-base resolution at multiple time points during A-P axis regeneration and constructed the de novo transcriptome assembly of the Dugesia japonica planarian. Results: Immunofluorescence staining and comparative analysis revealed that m6A is widespread across the planarian and dynamically regulated during regeneration along the A-P axis, exhibiting a strong spatiotemporal feature. The resulting datasets of m6A-modified genes identified 80 anterior-specific genes and 13 posterior-specific genes, respectively. In addition, we showed that YTHDC1 serves as the primary m6A reader to be involved in the m6A-mediated specification of A-P axis during regeneration in Dugesia japonica planarian. Conclusions: Our study provides an RNA epigenetic explanation for the specification of the A-P axis during tissue regeneration in planarian.

The chronic stress risk phenotype mirrored in the human retina as a neurodegenerative condition.

The brain is the key organ that orchestrates the stress response which translates to the retina. The retina is an extension of the brain and retinal symptoms in subjects with neurodegenerative diseases substantiated the eye as a window to the brain. The retina is used in this study to determine whether chronic stress reflects neurodegenerative signs indicative of neurodegenerative conditions. A three-year prospective cohort (n = 333; aged 46 ± 9 years) was stratified into stress-phenotype cases (n = 212) and controls (n = 121) by applying the Malan stress-phenotype index. Neurodegenerative risk markers included ischemia (astrocytic S100 calcium-binding protein B/S100B); 24-h blood pressure, proteomics; inflammation (tumor-necrosis-factor-α/TNF-α); neuronal damage (neuron-specific-enolase); anti-apoptosis of retinal-ganglion-cells (beta-nerve-growth-factor), astrocytic activity (glial-fibrillary-acidic-protein); hematocrit (viscosity) and retinal follow-up data [vessels; stress-optic-neuropathy]. Stress-optic-neuropathy risk was calculated from two indices: a newly derived diastolic-ocular-perfusion-pressure cut-point ≥68 mmHg relating to the stress-phenotype; combined with an established cup-to-disk ratio cut-point ≥0.3. Higher stress-optic-neuropathy (39% vs. 17%) and hypertension (73% vs. 16%) prevalence was observed in the stress-phenotype cases vs. controls. Elevated diastolic-ocular-perfusion-pressure, indicating hypoperfusion, was related to arterial narrowing and trend for ischemia increases in the stress-phenotype. Ischemia in the stress-phenotype at baseline, follow-up and three-year changes was related to consistent inflammation (TNF-α and cytokine-interleukin-17-receptor-A), neuron-specific-enolase increases, consistent apoptosis (chitinase-3-like protein 1, low beta-nerve-growth-factor), glial-fibrillary-acidic-protein decreases, elevated viscosity, vein widening as risk marker of endothelial dysfunction in the blood-retinal barrier, lower vein count, and elevated stress-optic-neuropathy. The stress-phenotype and related neurodegenerative signs of ongoing brain ischemia, apoptosis and endothelial dysfunction compromised blood-retinal barrier permeability and optic nerve integrity. In fact, the stress-phenotype could identify persons at high risk of neurodegeneration to indicate a neurodegenerative condition.

Systematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing.

N6-methyladenosine (m6A) has been increasingly recognized as a new and important regulator of gene expression. To date, transcriptome-wide m6A detection primarily relies on well-established methods using next-generation sequencing (NGS) platform. However, direct RNA sequencing (DRS) using the Oxford Nanopore Technologies (ONT) platform has recently emerged as a promising alternative method to study m6A. While multiple computational tools are being developed to facilitate the direct detection of nucleotide modifications, little is known about the capabilities and limitations of these tools. Here, we systematically compare ten tools used for mapping m6A from ONT DRS data. We find that most tools present a trade-off between precision and recall, and integrating results from multiple tools greatly improve performance. Using a negative control could improve precision by subtracting certain intrinsic bias. We also observed variation in detection capabilities and quantitative information among motifs, and identified sequencing depth and m6A stoichiometry as potential factors affecting performance. Our study provides insight into the computational tools currently used for mapping m6A based on ONT DRS data and highlights the potential for further improving these tools, which may serve as the basis for future research.

High-precision mapping reveals rare N6-deoxyadenosine methylation in the mammalian genome.

N6-deoxyadenosine methylation (6mA) is the most widespread type of DNA modification in prokaryotes and is also abundantly distributed in some unicellular eukaryotes. However, 6mA levels are remarkably low in mammals. The lack of a precise and comprehensive mapping method has hindered more advanced investigations of 6mA. Here, we report a new method MM-seq (modification-induced mismatch sequencing) for genome-wide 6mA mapping based on a novel detection principle. We found that modified DNA bases are prone to form a local open region that allows capture by antibody, for example, via a DNA breathing or base-flipping mechanism. Specified endonuclease or exonuclease can recognize the antibody-stabilized mismatch-like structure and mark the exact modified sites for sequencing readout. Using this method, we examined the genomic positions of 6mA in bacteria (E. coli), green algae (C. reinhardtii), and mammalian cells (HEK239T, Huh7, and HeLa cells). In contrast to bacteria and green algae, human cells possess a very limited number of 6mA sites which are sporadically distributed across the genome of different cell types. After knocking out the RNA m6A methyltransferase METTL3 in mouse ES cells, 6mA becomes mostly diminished. Our results imply that rare 6mA in the mammalian genome is introduced by RNA m6A machinery via a non-targeted mechanism.

Obesity, but not glycemic control, predicts liver steatosis in children with type 1 diabetes.

OBJECTIVE: Nonalcoholic fatty liver disease (NAFLD), the most common liver disease in children, is strongly associated with obesity and insulin resistance. Although type 1 diabetes (T1D) is characterized by insulin deficiency, increasing obesity rates among children with T1D is a major risk factor for NAFLD in this patient population. Predisposing factors for NAFLD in children with T1D are not known. STUDY DESIGN: This is a cross-sectional study comparing children with T1D across the range of body mass index (BMI) to the BMI-matched obese group without T1D. Hepatic steatosis was semi-quantitatively measured via the vibration-controlled transient elastogram (VCTE) method. Linear regression analysis was performed to assess the relationship between controlled-attenuated parameter (CAP) scores and clinical parameters. Receiver-operator curve (ROC) analysis was used to evaluate the diagnostic performance of several clinical parameters against NAFLD status determined via CAP. RESULTS: Two-thirds of subjects with obesity had CAP scores suggestive of NAFLD, while 16 % (n = 6) of T1D patients without obesity had elevated CAP. Obese subjects were different from non-obese subjects in many laboratory and clinical characteristics, regardless of T1D status. CAP score was significantly associated with BMI, HDL-Cholesterol (HDL-c), and HbA1c in all subjects as well as the T1D-only subgroup. Among subjects with obesity only, age, HDL-cand ALT were the most significant predictors. Diagnostic performance of BMI, HDL-c, and BMI/HDL ratio were in the good to the excellent range for predicting NAFLD among all subjects, while performance varied for T1D-only or obesity-only groups. CONCLUSION: The clinical and imaging findings of children with T1D and obesity are comparable to non-diabetic children with a similar degree of obesity. Obesity is the major risk factor for NAFLD in pediatric T1D. BMI, HDL-c, and BMI/HDL ratio may be helpful markers to determine further workup for NAFLD in children with T1D, particularly those with obesity.

Capillaric field effect transistors.

Controlling fluid flow in capillaric circuits is a key requirement to increase their uptake for assay applications. Capillary action off-valves provide such functionality by pushing an occluding bubble into the channel using a difference in capillary pressure. Previously, we utilized the binary switching mode of this structure to develop a powerful set of fundamental fluidic valving operations. In this work, we study the transistor-like qualities of the off-valve and provide evidence that these structures are in fact functionally complementary to electronic junction field effect transistors. In view of this, we propose the new term capillaric field effect transistor to describe these types of valves. To support this conclusion, we present a theoretical description, experimental characterization, and practical application of analog flow resistance control. In addition, we demonstrate that the valves can also be reopened. We show modulation of the flow resistance from fully open to pinch-off, determine the flow rate-trigger channel volume relationship and demonstrate that the latter can be modeled using Shockley's equation for electronic transistors. Finally, we provide a first example of how the valves can be opened and closed repeatedly.

Evaluating a standardized protocol for the management of diabetes insipidus in pediatric neurosurgical patients.

OBJECTIVES: Central diabetes insipidus (DI) is a known complication following surgical resection of a suprasellar mass. There are limited data analyzing the outcomes of a standardized protocol for the management of postoperative DI in the pediatric population. We sought to fill this gap and hypothesized that utilizing a standardized protocol for fluid management (3-bag system) would reduce serum sodium fluctuations in the postoperative period after suprasellar surgery. METHODS: A retrospective chart review was performed. Patients were identified with the following criteria: age ≤ 18 years, undergoing a surgical procedure for suprasellar mass that also had postoperative DI. The primary outcome was the variability in serum sodium during the first 48 h and between 48 and 120 h postoperatively. RESULTS: There were 21 encounters pre-protocol and 22 encounters post-protocol for neurosurgical procedures. Use of the standardized protocol was associated with a lower range of sodium within 48 h postoperatively (p=0.065) and 83% lower odds of hypernatremia (Na>150 mmol/L) within 48 h postoperatively (CI 0.039-0.714) after controlling for age, gender, and prior DI diagnosis. History of DI conferred a lower risk of hypernatremia as well as less sodium fluctuation within 48 h postoperatively. Younger patients, those <9.7 years of age were associated with increased risk of hyponatremia and greater sodium fluctuations during the postoperative period. CONCLUSIONS: In patients with postoperative DI after suprasellar surgery, using a standardized protocol for fluid management (3-bag system) appears to reduce serum sodium variability in the first 48 h after surgery.