Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine.

It is unclear why disease occurs in only a small proportion of persons carrying common risk alleles of disease susceptibility genes. Here we demonstrate that an interaction between a specific virus infection and a mutation in the Crohn's disease susceptibility gene Atg16L1 induces intestinal pathologies in mice. This virus-plus-susceptibility gene interaction generated abnormalities in granule packaging and unique patterns of gene expression in Paneth cells. Further, the response to injury induced by the toxic substance dextran sodium sulfate was fundamentally altered to include pathologies resembling aspects of Crohn's disease. These pathologies triggered by virus-plus-susceptibility gene interaction were dependent on TNFalpha and IFNgamma and were prevented by treatment with broad spectrum antibiotics. Thus, we provide a specific example of how a virus-plus-susceptibility gene interaction can, in combination with additional environmental factors and commensal bacteria, determine the phenotype of hosts carrying common risk alleles for inflammatory disease.

Lightness constancy in reality, in virtual reality, and on flat-panel displays.

Virtual reality (VR) displays are being used in an increasingly wide range of applications. However, previous work shows that viewers often perceive scene properties very differently in real and virtual environments and so realistic perception of virtual stimuli should always be a carefully tested conclusion, not an assumption. One important property for realistic scene perception is surface color. To evaluate how well virtual platforms support realistic perception of achromatic surface color, we assessed lightness constancy in a physical apparatus with real lights and surfaces, in a commercial VR headset, and on a traditional flat-panel display. We found that lightness constancy was good in all three environments, though significantly better in the real environment than on the flat-panel display. We also found that variability across observers was significantly greater in VR and on the flat-panel display than in the physical environment. We conclude that these discrepancies should be taken into account in applications where realistic perception is critical but also that in many cases VR can be used as a flexible alternative to flat-panel displays and a reasonable proxy for real environments.

ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery.

BACKGROUND: The growing power and ever decreasing cost of RNA sequencing (RNA-Seq) technologies have resulted in an explosion of RNA-Seq data production. Comparing gene expression values within RNA-Seq datasets is relatively easy for many interdisciplinary biomedical researchers; however, user-friendly software applications increase the ability of biologists to efficiently explore available datasets. RESULTS: Here, we describe ROGUE (RNA-Seq Ontology Graphic User Environment, https://marisshiny. RESEARCH: chop.edu/ROGUE/ ), a user-friendly R Shiny application that allows a biologist to perform differentially expressed gene analysis, gene ontology and pathway enrichment analysis, potential biomarker identification, and advanced statistical analyses. We use ROGUE to identify potential biomarkers and show unique enriched pathways between various immune cells. CONCLUSIONS: User-friendly tools for the analysis of next generation sequencing data, such as ROGUE, will allow biologists to efficiently explore their datasets, discover expression patterns, and advance their research by allowing them to develop and test hypotheses.

Limited Evidence for Use of a Black Race Modifier in eGFR Calculations: A Systematic Review.

BACKGROUND: Commonly used estimated glomerular filtration rate (eGFR) equations include a Black race modifier (BRM) that was incorporated during equation derivation. Race is a social construct, and a poorly characterized variable that is applied inconsistently in clinical settings. The BRM results in higher eGFR for any creatinine concentration, implying fundamental differences in creatinine production or excretion in Black individuals compared to other populations. Equations without inclusion of the BRM have the potential to detect kidney disease earlier in patients at the greatest risk of chronic kidney disease (CKD), but also has the potential to over-diagnose CKD or impact downstream clinical interventions. The purpose of this study was to use an evidence-based approach to systematically evaluate the literature relevant to the performance of the eGFR equations with and without the BRM and to examine the clinical impact of the use or removal. CONTENT: PubMed and Embase databases were searched for studies comparing measured GFR to eGFR in racially diverse adult populations using the Modification of Diet in Renal Disease or the 2009-Chronic Kidney Disease Epidemiology Collaboration-creatinine equations based on standardized creatinine measurements. Additionally, we searched for studies comparing clinical use of eGFR calculated with and without the BRM. Here, 8632 unique publications were identified; an additional 3 studies were added post hoc. In total, 96 studies were subjected to further analysis and 44 studies were used to make a final assessment. SUMMARY: There is limited published evidence to support the use of a BRM in eGFR equations.

Luminance calibration of virtual reality displays in Unity.

Virtual reality (VR) displays are an increasingly popular medium for experiments on visual perception. This presents the challenge of showing precisely controlled stimuli on devices that were not primarily designed for research. Here we describe methods for controlling stimulus luminance in VR experiments created in Unity using the Built-in Render Pipeline. We discuss the Gamma/Linear setting, measuring luminance in a VR headset, and using color grading in Unity's Post-Processing Stack to make stimulus luminance proportional to achromatic RGB value. We provide MATLAB code that uses luminance measurements from a VR headset to generate the lookup table that Unity requires for linearizing luminance. We emphasize that when creating experiments in this complex environment, it is important to experiment with the rendering process to confirm that stimuli are displayed as expected. We show results of several such tests and provide code as a starting point for readers who wish to run further tests related to their own research.

Fathers' Visitation of Very Low Birth Weight Infants in the Neonatal Intensive Care Unit during the First Week of Life.

OBJECTIVE: The perceived fragility of extremely preterm neonates may deter paternal visitation early during the neonatal intensive care unit (NICU) stay. We retrospectively analyzed the correlation between paternal visitation of very low birth weight (VLBW) infants in our NICU and sociodemographic characteristics. STUDY DESIGN: We identified inborn VLBW infants admitted to our NICU from 2017 to 2018. The rate of visit days in the first week of life was analyzed using Spearman's correlation and Poisson's regression. RESULTS: The analysis included 292 infants (median gestational age [GA]: 29 weeks), with fathers present on a median of 3 days of the first week of life. GA was not correlated with visitation (rho = -0.04). On multivariable regression, fathers visited less frequently if they did not live with the mother or if the mother lived 25 to 75 km from the hospital versus < 25 km. CONCLUSION: Fathers' visitation in our NICU was constrained by socioeconomic factors rather than VLBW infants' characteristics.

Implementation of point-of-care testing in a pediatric healthcare setting.

Point-of-care testing (POCT) refers to testing performed outside the clinical laboratory near the patient or at the site of patient care. This could be in critical care settings like the intensive care unit (ICU) and emergency department (ED) or primary care settings like physician offices where testing is performed by nonlaboratory personnel. POCT circumvents several steps in central laboratory testing including specimen transportation and processing resulting in faster turnaround times. Provider access to rapid test results at the site of patient care allows for prompt medical decision making which can lead to improved patient outcomes, operational efficiencies, patient satisfaction, and even cost savings in some cases. In addition to providing results rapidly, POCT devices have small specimen volume requirements compared to central laboratory tests making POCT particularly attractive for pediatric healthcare settings. The availability of published reports on the impact of POCT implementation in pediatric care are helpful resources when evaluating the clinical necessity of POCT prior to implementation. Even though several studies have shown advantages to implementing POCT in different pediatric settings, it is important to note that limitations exist that might limit the utilization of certain POCTs in some pediatric populations. So, it is important that these limitations and the analytical performance of a test are considered while keeping the target patient population in mind. Since POCTs are performed by non-laboratory staff who are not trained laboratory personnel, one challenge with POCT is maintaining regulatory compliance and quality assurance. It is therefore important that regulatory and quality assurance programs be put in place prior to implementing POCT in the pediatric hospital. With advances in POCT technology, most POCT devices have the capability to interface to the laboratory information system (LIS) and electronic medical record (EMR). POCT device interfacing allows for improved compliance to regulatory and quality assurance standards. Maintaining a cost efficient POCT program is becoming increasingly important as hospitals and healthcare systems are undergoing consolidation and harmonization. This includes assessing the clinical and operational benefit of POCT before implementation and inventory management to ensure minimal reagent wastage. This review discusses these different considerations when implementing POCT with a focus on the pediatric healthcare setting.

Impact of Hormone Therapy on Laboratory Values in Transgender Patients.

BACKGROUND: For transgender individuals taking hormone therapy (HT), data on laboratory values are limited, and the effects on laboratory values cannot be easily predicted. We evaluated the impact on common laboratory analytes in transgender individuals before and after initiation of HT. METHODS: We conducted a retrospective chart review of transgender patients identified at transgender-specific clinics at an urban county hospital and community clinic. Laboratory data were collected on hormone concentrations, hematologic parameters, electrolytes, lipids, and liver and renal markers before and after initiation of HT. RESULTS: We identified 183 transgender women (TW) and 119 transgender men (TM) for whom laboratory data were available. In all, 87 TW and 62 TM had baseline laboratory data, and data were also available for 133 TW and 89 TM on HT for >6 months. The most significant changes were seen in red blood cell count, hemoglobin concentration, hematocrit, and creatinine levels after >6 months of HT, which increased in TM and decreased in TW after HT (P < 0.005; d index > 0.6). Alkaline phosphatase, aspartate aminotransferase, and alanine aminotransferase levels increased in TM; however, the effect size was small (d index < 0.5). Calcium, albumin, and alkaline phosphatase levels significantly decreased in TW (P < 0.001; d > 0.6). Additionally, TM were found to have increased triglycerides and decreased HDL levels (P < 0.005; d > 0.6). CONCLUSIONS: Changes occur in several common laboratory parameters for patients on HT. Some laboratory values changed to match the gender identity, whereas others remained unchanged or were intermediate from the baseline values. These findings will help guide interpretation of laboratory test results in transgender patients taking HT.

Electrochemical impedance spectroscopy reveals a new mechanism based on competitive binding between Tris and protein on a conductive biomimetic polydopamine surface.

A novel mechanism was developed to study the interaction of mussel inspired polydopamine surfaces with bovine serum albumin using cyclic voltammetry and electrochemical impedance spectroscopy supplemented with XPS, IR spectroscopy, UV spectroscopy and atomic force microscopy. The polydopamine surfaces reveal different mechanisms that give a new insight into understanding the interaction with BSA under the variable conditions used for PDA preparation and BSA adsorption. The study provides an in-depth analysis of the orientations and interactions of BSA with polydopamine surfaces. The protein interaction behavior changed significantly in different environments including different pH values and concentrations of buffer and it revealed a competitive binding mechanism of protein binding. The study provides an outlook for studying the interaction of protein foulants with PDA, which should be carried out in nucleophilic buffers, while the covalent binding or immobilization of biomolecules to PDA surfaces should be carried out in non-nucleophilic buffer for higher efficiency.

Polydopamine films change their physicochemical and antimicrobial properties with a change in reaction conditions.

The morphology and physicochemical properties of polydopamine are not totally inherent and undergo changes with differing reaction conditions like the choice of solvent used for polymerization. The polymerisation of dopamine to polydopamine carried out in different solvents like sodium hydroxide, sodium bicarbonate, PBS and Tris leads to polydopamine with exceptionally different morphological and physicochemical features with each solvent. Additionally, the different physicochemical characteristics and morphologies bestow the polymer films with different extents of antimicrobial activity. Moreover, the findings supported by chemical evidence from X-ray photoelectron spectroscopy reveal that higher antibacterial activities were obtained against E. coli and S. aureus with polydopamine films prepared by Tris and NaOH solvent induced polymerization. The antibacterial activity observed in saline was found to be higher than that in PBS medium for both E. coli and S. aureus. The higher antibacterial activity of polydopamine films prepared in Tris and NaOH solvents was attributed to the covalent incorporation of -OH groups on the surface provided by nucleophilic Tris and NaOH solvents during the polymerisation process. The distinct physicochemical and morphological changes were supported by the results from contact angle measurements, FE-SEM, EDAX, AFM, and XPS analysis. The present finding provides insight into the different chemistry, morphologies and properties of the designed polydopamine films with controlled antibacterial/antifouling properties. Additionally, new insights into the mechanism of formation, physicochemical changes in morphology and properties of polydopamine coatings were revealed.

Lightness matching and perceptual similarity.

Lightness constancy is the ability to perceive surface reflectance correctly despite substantial changes in lighting intensity. A classic view is that lightness constancy is the result of a "discounting" of lighting intensity, and this continues to be a prominent view today. Logvinenko and Maloney (2006) have proposed an alternative approach to understanding lightness constancy, in which observers do not make explicit estimates of reflectance, and lightness constancy is instead based on a perceptual similarity metric that depends on both the reflectance and the illuminance of surfaces viewed under different lighting conditions. Here we compare these two views using a novel, free-adjustment reflectance-matching task. We test whether observers can match reflectance in a task where they are free to adjust both the illuminance and the reflectance of the match stimulus over a wide range. We find that observers can match reflectance under these conditions, which supports the view that observers make explicit estimates of reflectance. We also compare performance in this free adjustment task using physical objects and computer-rendered images as stimuli. We find that lightness constancy is good in both cases, but with some evidence of a glow-related artifact with computer-rendered stimuli.

Autophagy proteins control goblet cell function by potentiating reactive oxygen species production.

Delivery of granule contents to epithelial surfaces by secretory cells is a critical physiologic process. In the intestine, goblet cells secrete mucus that is required for homeostasis. Autophagy proteins are required for secretion in some cases, though the mechanism and cell biological basis for this requirement remain unknown. We found that in colonic goblet cells, proteins involved in initiation and elongation of autophagosomes were required for efficient mucus secretion. The autophagy protein LC3 localized to intracellular multi-vesicular vacuoles that were consistent with a fusion of autophagosomes and endosomes. Using cultured intestinal epithelial cells, we found that NADPH oxidases localized to and enhanced the formation of these LC3-positive vacuoles. Both autophagy proteins and endosome formation were required for maximal production of reactive oxygen species (ROS) derived from NADPH oxidases. Importantly, generation of ROS was critical to control mucin granule accumulation in colonic goblet cells. Thus, autophagy proteins can control secretory function through ROS, which is in part generated by LC3-positive vacuole-associated NADPH oxidases. These findings provide a novel mechanism by which autophagy proteins can control secretion.

Oncometabolites: A New Paradigm for Oncology, Metabolism, and the Clinical Laboratory.

BACKGROUND: Pediatric clinical laboratories commonly measure tricarboxylic acid cycle intermediates for screening, diagnosis, and monitoring of specific inborn errors of metabolism, such as organic acidurias. In the past decade, the same tricarboxylic acid cycle metabolites have been implicated and studied in cancer. The accumulation of these metabolites in certain cancers not only serves as a biomarker but also directly contributes to cellular transformation, therefore earning them the designation of oncometabolites. CONTENT: D-2-hydroxyglutarate, L-2-hydroxyglutarate, succinate, and fumarate are the currently recognized oncometabolites. They are structurally similar and share metabolic proximity in the tricarboxylic acid cycle. As a result, they promote tumorigenesis in cancer cells through similar mechanisms. This review summarizes the currently understood common and distinct biological features of these compounds. In addition, we will review the current laboratory methodologies that can be used to quantify these metabolites and their downstream targets. SUMMARY: Oncometabolites play an important role in cancer biology. The metabolic pathways that lead to the production of oncometabolites and the downstream signaling pathways that are activated by oncometabolites represent potential therapeutic targets. Clinical laboratories have a critical role to play in the management of oncometabolite-associated cancers through development and validation of sensitive and specific assays that measure oncometabolites and their downstream effectors. These assays can be used as screening tools and for follow-up to measure response to treatment, as well as to detect minimal residual disease and recurrence.

Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.

A coding polymorphism (Thr300Ala) in the essential autophagy gene, autophagy related 16-like 1 (ATG16L1), confers increased risk for the development of Crohn disease, although the mechanisms by which single disease-associated polymorphisms contribute to pathogenesis have been difficult to dissect given that environmental factors likely influence disease initiation in these patients. Here we introduce a knock-in mouse model expressing the Atg16L1 T300A variant. Consistent with the human polymorphism, T300A knock-in mice do not develop spontaneous intestinal inflammation, but exhibit morphological defects in Paneth and goblet cells. Selective autophagy is reduced in multiple cell types from T300A knock-in mice compared with WT mice. The T300A polymorphism significantly increases caspase 3- and caspase 7-mediated cleavage of Atg16L1, resulting in lower levels of full-length Atg16Ll T300A protein. Moreover, Atg16L1 T300A is associated with decreased antibacterial autophagy and increased IL-1ß production in primary cells and in vivo. Quantitative proteomics for protein interactors of ATG16L1 identified previously unknown nonoverlapping sets of proteins involved in ATG16L1-dependent antibacterial autophagy or IL-1ß production. These findings demonstrate how the T300A polymorphism leads to cell type- and pathway-specific disruptions of selective autophagy and suggest a mechanism by which this polymorphism contributes to disease.

Autophagy and intestinal homeostasis.

Nutrient absorption is the basic function that drives mammalian intestinal biology. To facilitate nutrient uptake, the host's epithelial barrier is composed of a single layer of cells. This constraint is problematic, as a design of this type can be easily disrupted. The solution during the course of evolution was to add numerous host defense mechanisms that can help prevent local and systemic infection. These mechanisms include specialized epithelial cells that produce a physiochemical barrier overlying the cellular barrier, robust and organized adaptive and innate immune cells, and the ability to mount an inflammatory response that is commensurate with a specific threat level. The autophagy pathway is a critical cellular process that strongly influences all these functions. Therefore, a fundamental understanding of the components of this pathway and their influence on inflammation, immunity, and barrier function will facilitate our understanding of homeostasis in the gastrointestinal tract.

Posterior Probability Matching and Human Perceptual Decision Making.

Probability matching is a classic theory of decision making that was first developed in models of cognition. Posterior probability matching, a variant in which observers match their response probabilities to the posterior probability of each response being correct, is being used increasingly often in models of perception. However, little is known about whether posterior probability matching is consistent with the vast literature on vision and hearing that has developed within signal detection theory. Here we test posterior probability matching models using two tools from detection theory. First, we examine the models' performance in a two-pass experiment, where each block of trials is presented twice, and we measure the proportion of times that the model gives the same response twice to repeated stimuli. We show that at low performance levels, posterior probability matching models give highly inconsistent responses across repeated presentations of identical trials. We find that practised human observers are more consistent across repeated trials than these models predict, and we find some evidence that less practised observers more consistent as well. Second, we compare the performance of posterior probability matching models on a discrimination task to the performance of a theoretical ideal observer that achieves the best possible performance. We find that posterior probability matching is very inefficient at low-to-moderate performance levels, and that human observers can be more efficient than is ever possible according to posterior probability matching models. These findings support classic signal detection models, and rule out a broad class of posterior probability matching models for expert performance on perceptual tasks that range in complexity from contrast discrimination to symmetry detection. However, our findings leave open the possibility that inexperienced observers may show posterior probability matching behaviour, and our methods provide new tools for testing for such a strategy.