NexusLIMS: A Laboratory Information Management System for Shared-Use Electron Microscopy Facilities.

This work introduces NexusLIMS, an electron microscopy laboratory information management system designed and implemented by the Office of Data and Informatics and the Materials Science and Engineering Division at NIST for a multi-user electron microscopy co-op facility. NexusLIMS comprises network infrastructure, shared information technology resources, a custom software package to harvest and extract experimental information and construct experimental metadata records, and an intuitive web-based user-facing interface for searching, browsing, and examining research data. These metadata records conform to the Nexus Experiment schema, which is introduced in this work. The NexusLIMS suite of tools requires minimal input and adjustments to user behavior, instead relying on existing organizational procedures and the collection of information from a multitude of sources to construct a complete picture and record of a research experiment. The underlying infrastructure and design considerations for a multi-user data management system are discussed. The core codebase for NexusLIMS is made publicly available alongside this work, and its modular design encourages the adaptation of the presented methods at other research organizations.

Laboratory Information Management Systems for Electron Microscopy: Evaluation of the 4CeeD Data Curation Platform.

An evaluation of the feasibility and the requirements associated with a facility-wide deployment of a laboratory information management system (LIMS) at an electron microscopy facility was conducted. 4CeeD, an open-source LIMS, was selected for the focus study. This report summarizes data infrastructure prerequisites, critical and desirable features, and lessons learned from using and interacting with 4CeeD, and broader LIMS adoption recommendations for this facility.

Lack of junctional adhesion molecule (JAM)-B ameliorates experimental autoimmune encephalomyelitis.

In multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE) autoaggressive CD4+ T cells cross the blood-brain barrier (BBB) and cause neuroinflammation. Therapeutic targeting of CD4+ T-cell trafficking into the CNS by blocking α4-integrins has proven beneficial for the treatment of MS but comes with associated risks, probably due to blocking CD8+ T cell mediated CNS immune surveillance. Our recent observations show that CD8+ T cells also rely on α4ß1-integrins to cross the BBB. Besides vascular cell adhesion molecule-1 (VCAM-1), we identified junctional adhesion molecule-B (JAM-B) as a novel vascular α4ß1-integrin ligand involved in CD8+ T-cell migration across the BBB. This prompted us to investigate, if JAM-B also mediates CD4+ T-cell migration across the BBB. We first ensured that encephalitogenic T cells can bind to JAM-B in vitro and next compared EAE pathogenesis in JAM-B-/- C57BL/6J mice and their wild-type littermates. Following immunization with MOGaa35-55 peptide, JAM-B-/- mice developed ameliorated EAE compared to their wild-type littermates. At the same time, we isolated higher numbers of CD45+ infiltrating immune cells from the CNS of JAM-B-/- C57BL/6J mice suffering from EAE. Immunofluorescence staining revealed that the majority of CD45+ inflammatory cells accumulated in the leptomeningeal and perivascular spaces of the CNS behind the BBB but do not gain access to the CNS parenchyma. Trapping of CNS inflammatory cells was not due to increased inflammatory cell proliferation. Neither a loss of BBB integrity or BBB polarity potentially affecting local chemokine gradients nor a lack of focal gelatinase activation required for CNS parenchymal immune cell entry across the glia limitans could be detected in JAM-B-/- mice. Lack of a role for JAM-B in the effector phase of EAE was supported by the observation that we did not detect any role for JAM-B in EAE pathogenesis, when EAE was elicited by in vitro activated MOG aa35-55-specific CD4+ effector T cells. On the other hand, we also failed to demonstrate any role of JAM-B in in vivo priming, proliferation or polarization of MOGaa35-55-specific CD4+ T cells in peripheral immune organs. Finally, our study excludes expression of and thus a role for JAM-B on peripheral and CNS infiltrating myeloid cells. Taken together, although endothelial JAM-B is not required for immune cell trafficking across the BBB in EAE, in its absence accumulation of inflammatory cells mainly in CNS leptomeningeal spaces leads to amelioration of EAE.

Contemporaneous sample data tracking for the generation of genome edited cell lines.

It is difficult to capture the large numbers of steps and details that often characterize research in the biomedical sciences. We present an approach that is based on commercial spreadsheet software so it is easily adaptable by the experimentalist. The approach is designed to be compatible with an experimentalist's workflow and allows the capture in real time of detailed information associated, in this use case, with laboratory actions involved in the process of editing, enriching and isolating clonal gene-edited pluripotent stem cell (PSC) lines. Intuitive features and flexibility allow an experimentalist without extensive programming knowledge to modify spreadsheets in response to changes in protocols and to perform simple queries. The experimental details are collated in a table format from which they can be exported in open standard formats (e.g., Extensible Markup Language (XML) or Comma Separated Values (CSV) for ingestion into a data repository supporting interoperability with other applications. We demonstrate a sample- and file-naming convention that enables the automated creation of file directory folders with human readable semantic titles within a local file system. These operations facilitate the local organization of documentation and data for each cell line derived from each transfection in designated folder/file locations. This approach is generalizable to experimental applications beyond this use case.

Building Open Access to Research (OAR) Data Infrastructure at NIST.

As a National Metrology Institute (NMI), the USA National Institute of Standards and Technology (NIST) scientists, engineers and technology experts conduct research across a full spectrum of physical science domains. NIST is a non-regulatory agency within the U.S. Department of Commerce with a mission to promote U.S. innovation and industrial competitiveness by advancing measurement science, standards, and technology in ways that enhance economic security and improve our quality of life. NIST research results in the production and distribution of standard reference materials, calibration services, and datasets. These are generated from a wide range of complex laboratory instrumentation, expert analyses, and calibration processes. In response to a government open data policy, and in collaboration with the broader research community, NIST has developed a federated Open Access to Research (OAR) scientific data infrastructure aligned with FAIR (Findable, Accessible, Interoperable, Reusable) data principles. Through the OAR initiatives, NIST's Material Measurement Laboratory Office of Data and Informatics (ODI) recently released a new scientific data discovery portal and public data repository. These science-oriented applications provide dissemination and public access for data from across the broad spectrum of NIST research disciplines, including chemistry, biology, materials science (such as crystallography, nanomaterials, etc.), physics, disaster resilience, cyberinfrastructure, communications, forensics, and others. NIST's public data consist of carefully curated Standard Reference Data, legacy high valued data, and new research data publications. The repository is thus evolving both in content and features as the nature of research progresses. Implementation of the OAR infrastructure is key to NIST's role in sharing high integrity reproducible research for measurement science in a rapidly changing world.

Delivery of immunoglobulin G antibodies to the rat nervous system following intranasal administration: Distribution, dose-response, and mechanisms of delivery.

The intranasal route has been hypothesized to circumvent the blood-brain and blood-cerebrospinal fluid barriers, allowing entry into the brain via extracellular pathways along olfactory and trigeminal nerves and the perivascular spaces (PVS) of cerebral blood vessels. We investigated the potential of the intranasal route to non-invasively deliver antibodies to the brain 30 min following administration by characterizing distribution, dose-response, and mechanisms of antibody transport to and within the brain after administering non-targeted radiolabeled or fluorescently-labeled full length immunoglobulin G (IgG) to normal adult female rats. Intranasal [125I]-IgG consistently yielded highest concentrations in the olfactory bulbs, trigeminal nerves, and leptomeningeal blood vessels with their associated PVS. Intranasal delivery also resulted in significantly higher [125I]-IgG concentrations in the CNS than systemic (intra-arterial) delivery for doses producing similar endpoint blood concentrations. Importantly, CNS targeting significantly increased with increasing dose only with intranasal administration, yielding brain concentrations that ranged from the low-to-mid picomolar range with tracer dosing (50 µg) up to the low nanomolar range at higher doses (1 mg and 2.5 mg). Finally, intranasal pre-treatment with a previously identified nasal permeation enhancer, matrix metalloproteinase-9, significantly improved intranasal [125I]-IgG delivery to multiple brain regions and further allowed us to elucidate IgG transport pathways extending from the nasal epithelia into the brain using fluorescence microscopy. The results show that it may be feasible to achieve therapeutic levels of IgG in the CNS, particularly at higher intranasal doses, and clarify the likely cranial nerve and perivascular distribution pathways taken by antibodies to reach the brain from the nasal mucosae.

Integrating ecosystem services into risk management decisions: case study with Spanish citrus and the insecticide chlorpyrifos.

The European regulatory system for the approval of pesticides includes a thorough evaluation of risks to the environment and is designed to be protective of ecosystems. However, a decision to ban an agrochemical could also potentially have a negative impact on the value of ecosystem services, if resulting changes in crop management are damaging to ecosystems or result in negative socio-economic impacts. To support regulatory decision-making, consideration of ecosystem services to identify best environmental management options could be a way forward. There is generally a growing trend for the consideration of ecosystem services in decision making. Ecosystems provide the conditions for growing food, regulate water and provide wildlife habitats; these, amongst others, are known as ecosystem services. The objectives of this case study were to bring a holistic approach to decision making by valuing the environmental, social and economic benefits derived from the use of chlorpyrifos in Valencian citrus production. Spanish growers harvest between 5 and 6 milliont of citrus annually, worth an estimated €5 to 7 billion in food markets throughout Europe. The approach highlighted the potential for unintended negative consequences of regulatory decisions if the full context is not considered. In this study, rather than a regulatory restriction, the best option was the continued use of chlorpyrifos together with vegetated conservation patches as refuges for non-target insects. The conservation patches offset potential insecticidal impacts to insects whilst maintaining citrus production, farm income and the amenity value of the citrus landscape of Valencia. This was an initial proof-of-concept study and illustrates the importance of a wider perspective; other cases may have different outcomes depending on policies, the pesticide, crop scenarios, farm economics and the region.