Microminiaturized Immunoassays Using Atomic Force Microscopy and Compositionally Patterned Antigen Arrays

This paper combines the topographic imaging capability of the atomic force microscope (AFM) with a compositionally patterned array of immobilized antigenic rabbit IgG on gold as an approach to performing immunoassays. The substrates are composed of micrometer-sized domains of IgG that are covalently linked to a photolithographically patterned array of a monolayer-based coupling agent. The immobilized coupling agent, which is prepared by the chemisorption of dithiobis(succinimidyl undecanoate) on gold, is separated by micrometer-sized grids of a monolayer formed from octadecanethiol (ODT). The strong hydrophobicity of the ODT adlayer, combined with the addition of the surfactant Tween 80 to the buffer solution that is used in forming the antibody−antigen pairs, minimizes the nonspecific adsorption of proteinaceous materials to the grid regions. This minimization allows the grids to function as a reference plane for the AFM detection of the height increase when a complementary antibody−antigen pair is formed. The advantageous features of this strategy, which include ease of sample preparation, an internal reference plane for the detection of topographic changes, and the potential for regeneration and reuse, are demonstrated using rabbit IgG as an immobilized antigen and goat anti-rabbit IgG as the complementary antibody. The prospects for further miniaturization are discussed

Real and Perceived Discordance in Physicians and U.S. Adults’ Beliefs Regarding the Causes and Controllability of Type 2 Diabetes

Discordance between physicians and patients’ health beliefs can impede health communication efforts. However, little research considers physicians’ perceptions of patient beliefs, despite the importance of perceptions in shaping communication. In the current work, we examine instances of actual and perceived discordance between physicians and U.S. adults’ beliefs regarding the causes and controllability of type 2 diabetes. 229 family physicians completed an online survey measuring their health beliefs and perceptions of their patients’ beliefs. Physicians’ responses were contrasted against beliefs from a national survey sample of 1,168 U.S. adults. T-tests assessed whether (a) physicians’ beliefs diverged from the national sample’s beliefs (actual discordance), (b) physicians perceived that their health beliefs diverged from their patients’ beliefs (perceived discordance), and (c) physicians’ perceptions of patient beliefs diverged from the national sample’s beliefs (accuracy of perceived discordance). Findings revealed evidence of actual discordance; compared to the national sample, physicians were more likely to attribute type 2 diabetes to genes (versus lifestyle factors) and perceived greater control over developing diabetes. Moreover, although physicians perceived discordance between their own and their patients’ beliefs, data from the national sample suggested that these gaps were less substantial than physicians expected. In particular, findings showed that physicians generally overestimated discordance, expecting that people would be less likely to (1) attribute the development of diabetes to lifestyle factors (versus genes), and (2) perceive control over developing diabetes, than was actually reported. Implications of actual and perceived discordance for effective health communication and patient education are discussed

ISSCR standards for the use of human stem cells in basic research.

The laboratory culture of human stem cells seeks to capture a cellular state as an in vitro surrogate of a biological system. For the results and outputs from this research to be accurate, meaningful, and durable, standards that ensure reproducibility and reliability of the data should be applied. Although such standards have been previously proposed for repositories and distribution centers, no widely accepted best practices exist for laboratory research with human pluripotent and tissue stem cells. To fill that void, the International Society for Stem Cell Research has developed a set of recommendations, including reporting criteria, for scientists in basic research laboratories. These criteria are designed to be technically and financially feasible and, when implemented, enhance the reproducibility and rigor of stem cell research

The OneOklahoma Cyberinfrastructure Initiative: A Model for Multi-institutional Collaboration

The OneOklahoma Cyberinfrastructure Initiative: A Model for Multi-institutional Collaboration A White Paper submitted by the OneOklahoma Cyberinfrastructure Initiative membership to the National Science Foundation Workshop on The Role of Regional Organizations in Improving Access to the National Computational Infrastructure The OneOklahoma Cyberinfrastructure Initiative (OneOCII) is a statewide all-inclusive advanced digital services collaboration that has been providing access to Cyberinfrastructure (CI) resources, as well as expertise and education, so far to over 100 institutions and organizations statewide (over 50 academic and almost 50 non-academic), including PhD-granting universities, primarily undergraduate institutions, community colleges, career techs and high schools, among them 10 Minority Serving Institutions (MSIs).The OneOklahoma Cyberinfrastructure Initiative OneOCIIN

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, management, and analysis. In this perspective, we present AnVIL, describe its ecosystem and interoperability with other platforms, and highlight how this platform and associated initiatives contribute to improved genomic data sharing efforts. The AnVIL is a federated cloud platform designed to manage and store genomics and related data, enable population-scale analysis, and facilitate collaboration through the sharing of data, code, and analysis results. By inverting the traditional model of data sharing, the AnVIL eliminates the need for data movement while also adding security measures for active threat detection and monitoring and provides scalable, shared computing resources for any researcher. We describe the core data management and analysis components of the AnVIL, which currently consists of Terra, Gen3, Galaxy, RStudio/Bioconductor, Dockstore, and Jupyter, and describe several flagship genomics datasets available within the AnVIL. We continue to extend and innovate the AnVIL ecosystem by implementing new capabilities, including mechanisms for interoperability and responsible data sharing, while streamlining access management. The AnVIL opens many new opportunities for analysis, collaboration, and data sharing that are needed to drive research and to make discoveries through the joint analysis of hundreds of thousands to millions of genomes along with associated clinical and molecular data types

Tropical Data: Approach and Methodology as Applied to Trachoma Prevalence Surveys

PURPOSE: Population-based prevalence surveys are essential for decision-making on interventions to achieve trachoma elimination as a public health problem. This paper outlines the methodologies of Tropical Data, which supports work to undertake those surveys. METHODS: Tropical Data is a consortium of partners that supports health ministries worldwide to conduct globally standardised prevalence surveys that conform to World Health Organization recommendations. Founding principles are health ministry ownership, partnership and collaboration, and quality assurance and quality control at every step of the survey process. Support covers survey planning, survey design, training, electronic data collection and fieldwork, and data management, analysis and dissemination. Methods are adapted to meet local context and needs. Customisations, operational research and integration of other diseases into routine trachoma surveys have also been supported. RESULTS: Between 29th February 2016 and 24th April 2023, 3373 trachoma surveys across 50 countries have been supported, resulting in 10,818,502 people being examined for trachoma. CONCLUSION: This health ministry-led, standardised approach, with support from the start to the end of the survey process, has helped all trachoma elimination stakeholders to know where interventions are needed, where interventions can be stopped, and when elimination as a public health problem has been achieved. Flexibility to meet specific country contexts, adaptation to changes in global guidance and adjustments in response to user feedback have facilitated innovation in evidence-based methodologies, and supported health ministries to strive for global disease control targets

Shear‐Wave Velocity Structure of Sediments on Cascadia's Continental Margin From Probabilistic Inversion of Seafloor Compliance Data

Abstract Several seismic techniques, both passive and active, exist for estimating the shear‐wave velocity VS structure of shallow sedimentary structures. In particular, passive compliance signals recorded by broadband ocean‐bottom seismometers (OBSs) can be used to invert for VS structure. While compliance‐based imaging studies have been carried out at several locations across the Cascadia Subduction Zone, such an approach has not been extensively applied to OBSs deployed on the continental shelf and slope. In this study, we measure compliance and coherence signals at 13 broadband OBSs deployed along Cascadia's continental shelf and upper slope. We then use a recently developed technique to probabilistically invert compliance signals for shallow VS structure that makes use of mixture density neural networks. Finally, we compare and contrast our inverted VS profiles and derived properties obtained using this method with previous studies focused on the properties of basin sediments