FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research.

The FaceBase Consortium was established by the National Institute of Dental and Craniofacial Research in 2009 as a 'big data' resource for the craniofacial research community. Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community on the FaceBase Hub website. The Hub has developed numerous visualization and analysis tools designed to promote integration of multidisciplinary data while remaining dedicated to the FAIR principles of data management (findability, accessibility, interoperability and reusability) and providing a faceted search infrastructure for locating desired data efficiently. Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here. FaceBase 3 now welcomes contributions of data on craniofacial and dental development in humans, model organisms and cell lines. Collectively, the FaceBase Consortium, along with other NIH-supported data resources, provide a continuously growing, dynamic and current resource for the scientific community while improving data reproducibility and fulfilling data sharing requirements.

Conserved and Divergent Features of Human and Mouse Kidney Organogenesis.

Human kidney function is underpinned by approximately 1,000,000 nephrons, although the number varies substantially, and low nephron number is linked to disease. Human kidney development initiates around 4 weeks of gestation and ends around 34-37 weeks of gestation. Over this period, a reiterative inductive process establishes the nephron complement. Studies have provided insightful anatomic descriptions of human kidney development, but the limited histologic views are not readily accessible to a broad audience. In this first paper in a series providing comprehensive insight into human kidney formation, we examined human kidney development in 135 anonymously donated human kidney specimens. We documented kidney development at a macroscopic and cellular level through histologic analysis, RNA in situ hybridization, immunofluorescence studies, and transcriptional profiling, contrasting human development (4-23 weeks) with mouse development at selected stages (embryonic day 15.5 and postnatal day 2). The high-resolution histologic interactive atlas of human kidney organogenesis generated can be viewed at the GUDMAP database (www.gudmap.org) together with three-dimensional reconstructions of key components of the data herein. At the anatomic level, human and mouse kidney development differ in timing, scale, and global features such as lobe formation and progenitor niche organization. The data also highlight differences in molecular and cellular features, including the expression and cellular distribution of anchor gene markers used to identify key cell types in mouse kidney studies. These data will facilitate and inform in vitro efforts to generate human kidney structures and comparative functional analyses across mammalian species.

OH Radical as a Probe of the Spin Polarizability in 1- and 2-Naphthol.

The relative yields for addition of the OH radical at the various positions of 1- and 2-naphthol provide a measure of the spin polarizability in the naphthols. The observed yields show that addition occurs predominantly at the naphthol positions that are conjugated with the OH substituent. They also show that the electronic structures of the naphthols are significantly affected by a concerted interaction between the OH substituent and the unsubstituted ring and that this effect is somewhat greater when the OH substituent is adjacent to the naphthol bridge. The yields for addition at the different naphthol positions correlate with the local spin polarizabilities at reactive carbons in the naphthol. The spin polarizability may be a general property governing the reactivity of closed-shell molecules with radicals.

A flexible, open, decentralized system for digital pathology networks.

High-resolution digital imaging is enabling digital archiving and sharing of digitized microscopy slides and new methods for digital pathology. Collaborative research centers, outsourced medical services, and multi-site organizations stand to benefit from sharing pathology data in a digital pathology network. Yet significant technological challenges remain due to the large size and volume of digitized whole slide images. While information systems do exist for managing local pathology laboratories, they tend to be oriented toward narrow clinical use cases or offer closed ecosystems around proprietary formats. Few solutions exist for networking digital pathology operations. Here we present a system architecture and implementation of a digital pathology network and share results from a production system that federates major research centers.

MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses.

Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase ( www.facebase.org , https://doi.org/10.25550/3-HXMC ) and GitHub ( https://github.com/jaydevine/MusMorph ).

Making Common Fund data more findable: catalyzing a data ecosystem.

The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes of Health Common Fund without requiring that data owners move, reformat, or rehost those data. This system is centered on a catalog that integrates detailed descriptions of biomedical datasets from individual Common Fund Programs' Data Coordination Centers (DCCs) into a uniform metadata model that can then be indexed and searched from a centralized portal. This Crosscut Metadata Model (C2M2) supports the wide variety of data types and metadata terms used by individual DCCs and can readily describe nearly all forms of biomedical research data. We detail its use to ingest and index data from 11 DCCs.

Tricuspid valve repair with the Cardioband system: two-year outcomes of the multicentre, prospective TRI-REPAIR study.

AIMS: Tricuspid regurgitation (TR) is associated with high morbidity and mortality rates with limited treatment options. We report one- and two-year outcomes of the Cardioband tricuspid valve reconstruction system in the treatment of ≥moderate functional TR in the TRI-REPAIR study. METHODS AND RESULTS: Thirty patients were enrolled in this single-arm, multicentre, prospective study. Patients were evaluated as having ≥moderate, symptomatic functional TR and deemed inoperable due to unacceptable surgical risk. Clinical, functional, and echocardiographic data were prospectively collected up to two years (mean duration 604±227 days). At baseline, 83% were in NYHA Class III-IV, and the mean LVEF was 58%. Technical success was 100%. At two years, there were eight deaths. Echocardiography showed a significant reduction in septolateral annular diameter of 16% (p=0.006) and 72% of patients (p=0.016) with ≤moderate TR grade; 82% of patients were in NYHA Class I-II (p=0.002). Six-minute walk distance and KCCQ score improved by 73 m (p=0.058) and 14 points (p=0.046), respectively. CONCLUSIONS: These results demonstrate that the Cardioband tricuspid system showed favourable results in patients with symptomatic, ≥moderate functional TR. Annular reduction and TR severity reduction remained significant and sustained at two years. Patients experienced improvements in quality of life and exercise capacity. ClinicalTrials.gov Identifier: NCT02981953.

Absorption spectrum, mass spectrometric properties, and electronic structure of 1,2-benzoquinone.

Absorption spectrophotometric and mass spectrometric properties of 1,2-benzoquinone, prepared in aqueous solution by the hexachloroiridate(IV) oxidation of catechol and isolated by HPLC, are reported. Its absorption spectrum has a broad moderately intense band in the near UV with an extinction coefficient of 1370 M(-1)cm(-1) at its 389 nm maximum. The oscillator strength of this band contrasts with those of the order-of-magnitude stronger approximately 250 nm bands of most 1,4-benzoquinones. Gaussian analysis of its absorption spectrum indicates that it also has modestly intense higher energy bands in the 250-320 nm region. In atmospheric pressure mass spectrometric studies 1,2-benzoquinone exhibits very strong positive and negative mass 109 signals that result from the addition of protons and hydride ions in APCI and ESI ion sources. It is suggested that the hydride adduct is formed as the result of the highly polar character of ortho-quinone. On energetic collision the hydride adduct loses an H atom to produce the 1,2-benzosemiquinone radical anion. The present studies also show that atmospheric pressure mass spectral patterns observed for catechol are dominated by signals of 1,2-benzoquinone resulting from oxidation of catechol in the ion sources. Computational studies of the electronic structures of 1,2-benzoquinone, its proton and hydride ion adducts, and 1,2-benzosemiquinone radical anion are reported. These computational studies show that the structures of the proton and hydride adducts are similar and indicate that the hydride adduct is the proton adduct of a doubly negatively charged 1,2-benzoquinone. The contrast between the properties of 1,2- and 1,4-benzoquinone provides the basis for considerations on the effects of conjugation in aromatic systems.

Towards Co-Evolution of Data-Centric Ecosystems.

Database evolution is a notoriously difficult task, and it is exacerbated by the necessity to evolve database-dependent applications. As science becomes increasingly dependent on sophisticated data management, the need to evolve an array of database-driven systems will only intensify. In this paper, we present an architecture for data-centric ecosystems that allows the components to seamlessly co-evolve by centralizing the models and mappings at the data service and pushing model-adaptive interactions to the database clients. Boundary objects fill the gap where applications are unable to adapt and need a stable interface to interact with the components of the ecosystem. Finally, evolution of the ecosystem is enabled via integrated schema modification and model management operations. We present use cases from actual experiences that demonstrate the utility of our approach.

Toward FAIR Knowledge Turns in Bioinformatics.

Sharing of bioinformatics data within research communities holds the promise of facilitating more rapid discovery, yet the volume of data is growing at a pace exponentially greater than what traditional biocuration can support. We present here an approach that we have used to empower data producing researchers to curate high quality shared data that is ready for reuse and re-analysis.

Globus MEDICUS - federation of DICOM medical imaging devices into healthcare Grids.

The Digital Imaging and Communications in Medicine (DICOM) standard defines Radiology medical device interoperability and image data exchange between modalities, image databases - Picture Archiving and Communication Systems (PACS) - and image review end-points. However the scope of DICOM and PACS technology is currently limited to the trusted and static environment of the hospital. In order to meet the demand for ad-hoc tele-radiology and image guided medical procedures within the global healthcare enterprise, a new technology must provide mobility, security, flexible scale of operations, and rapid responsiveness for DICOM medical devices and subsequently medical image data. Grid technology, an informatics approach to securely federate independently operated computing, storage, and data management resources at the global scale over public networks, meets these core requirements. Here we present an approach to federate DICOM and PACS devices for large-scale medical image workflows within a global healthcare enterprise. The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing) project uses the standards-based Globus Toolkit Grid infrastructure to vertically integrate a new service for DICOM devices - the DICOM Grid Interface Service (DGIS). This new service translates between DICOM and Grid operations and thus transparently extends DICOM to Globus based Grid infrastructure. This Grid image workflow paradigm has been designed to provide not only solutions for global image communication, but fault-tolerance and disaster recovery using Grid data replication technology. Actual use-case of 40 MEDICUS Grid connected international hospitals of the Childerns Oncology Group and the Neuroblastoma Cancer Foundation and further clinical applications are discussed. The open-source Globus MEDICU http://dev.globus.org/wiki/Incubator/MEDICUS.

ERMrest: A Collaborative Data Catalog with Fine Grain Access Control.

Creating and maintaining an accurate description of data assets and the relationships between assets is a critical aspect of making data findable, accessible, interoperable, and reusable (FAIR). Typically, such metadata are created and maintained in a data catalog by a curator as part of data publication. However, allowing metadata to be created and maintained by data producers as the data is generated rather then waiting for publication can have significant advantages in terms of productivity and repeatability. The responsibilities for metadata management need not fall on any one individual, but rather may be delegated to appropriate members of a collaboration, enabling participants to edit or maintain specific attributes, to describe relationships between data elements, or to correct errors. To support such collaborative data editing, we have created ERMrest, a relational data service for the Web that enables the creation, evolution and navigation of complex models used to describe and structure diverse file or relational data objects. A key capability of ERMrest is its ability to control operations down to the level of individual data elements, i.e. fine-grained access control, so that many different modes of data-oriented collaboration can be supported. In this paper we introduce ERMrest and describe its fine-grained access control capabilities that support collaborative editing. ERMrest is in daily use in many data driven collaborations and we describe a sample policy that is based on a common biocuration pattern.

Experiences with Deriva: An Asset Management Platform for Accelerating eScience.

The pace of discovery in eScience is increasingly dependent on a scientist's ability to acquire, curate, integrate, analyze, and share large and diverse collections of data. It is all too common for investigators to spend inordinate amounts of time developing ad hoc procedures to manage their data. In previous work, we presented Deriva, a Scientific Asset Management System, designed to accelerate data driven discovery. In this paper, we report on the use of Deriva in a number of substantial and diverse eScience applications. We describe the lessons we have learned, both from the perspective of the Deriva technology, as well as the ability and willingness of scientists to incorporate Scientific Asset Management into their daily workflows.

A neuroinformatics of brain modeling and its implementation in the Brain Operation Database BODB.

We present principles for an integrated neuroinformatics framework which makes explicit how models are grounded on empirical evidence, explain (or not) existing empirical results and make testable predictions. The new ontological framework makes explicit how models bring together structural, functional, and related empirical observations. We emphasize schematics of the model's operation linked to summaries of empirical data (SEDs) used in both the design and testing of the model, with tests comparing SEDs to summaries of simulation results (SSRs) from the model. We stress the importance of protocols for models as well as experiments. We complement the structural ontology of nested brain structures with a functional ontology of Brain Operating Principles (BOPs) for observed neural function and an ontological framework for grounding models in empirical data. We present an implementation of this ontological framework in the Brain Operation Database (BODB), an environment in which modelers and experimentalists can work together by making use of their shared empirical data, models and expertise.

Enabling collaborative research using the Biomedical Informatics Research Network (BIRN).

OBJECTIVE: As biomedical technology becomes increasingly sophisticated, researchers can probe ever more subtle effects with the added requirement that the investigation of small effects often requires the acquisition of large amounts of data. In biomedicine, these data are often acquired at, and later shared between, multiple sites. There are both technological and sociological hurdles to be overcome for data to be passed between researchers and later made accessible to the larger scientific community. The goal of the Biomedical Informatics Research Network (BIRN) is to address the challenges inherent in biomedical data sharing. MATERIALS AND METHODS: BIRN tools are grouped into 'capabilities' and are available in the areas of data management, data security, information integration, and knowledge engineering. BIRN has a user-driven focus and employs a layered architectural approach that promotes reuse of infrastructure. BIRN tools are designed to be modular and therefore can work with pre-existing tools. BIRN users can choose the capabilities most useful for their application, while not having to ensure that their project conforms to a monolithic architecture. RESULTS: BIRN has implemented a new software-based data-sharing infrastructure that has been put to use in many different domains within biomedicine. BIRN is actively involved in outreach to the broader biomedical community to form working partnerships. CONCLUSION: BIRN's mission is to provide capabilities and services related to data sharing to the biomedical research community. It does this by forming partnerships and solving specific, user-driven problems whose solutions are then available for use by other groups.

Determination of the spectroscopic properties and chromatographic sensitivities of substituted quinones by hexachlorate(IV) oxidation of hydroquinones.

HPLC studies of the oxidation of substituted hydroquinones show that the corresponding quinones can, in most cases, be produced quantitatively by two electron transfer to hexachloroiridate(IV). As a consequence the chromatographic and spectroscopic properties of substituted quinones that are not readily available can be determined without the necessity of preparation of an isolatable sample. Absorption spectra and extinction coefficients of bromoquinone, chloroquinone, hydroxyquinone and carboxyquinone anion at pH 7 are reported as illustrative examples. All have intense absorption bands at approximately 250nm that are characteristic of quinones. Oxidation of carboxyhydroquinone at low pH is, however, anomalous in that a hydroxylated carboxyquinone is produced as the result of four electron transfer to hexachloroiridate.

Hydroxyl radical as a probe of the charge distribution in aromatics: phenol.

Initial radiation chemical yields of 1.48 (2), 0.24 (2), and 2.01 molecules per 100 eV of absorbed energy are reported for addition of *OH radical to each of the ortho, meta, and para positions of phenol. These yields represent 91% of the yield of 5.96 expected for *OH addition to 5 mM phenol and are in general agreement with other previous measurements. Pulse radiolysis experiments show that phenoxy radical is produced in a yield of approximately 0.42 as a result of addition of *OH at phenol's ipso position. The total of these yields (5.84) accounts for the addition of virtually all of the expected *OH radicals. The relative yields for addition to the ortho, meta, and para positions provide a measure of the charge distribution in phenol that correlates quite well with the unpaired spin distribution in phenoxyl radical. This correlation indicates that the OH substituent similarly affects the charge distribution on the aromatic ring of phenol and the unpaired spin distribution in the phenoxyl radical.

Concerted effects of substituents in the reaction of .OH radicals with aromatics: the cresols.

The concerted effects of hydroxyl and methyl substituents in controlling the site of .OH radical attack on aromatics in aqueous solutions are explored using the cresols as typical examples. The distributions of dihydroxytoluenes produced in the radiolysis of aqueous solutions of the cresols containing ferricyanide as a radical oxidant were examined by capillary electrophoretic and liquid chromatographic methods. Because .OH is a strong electrophile, it adds preferentially at the electron-rich sites of an aromatic ring. As a result, the observed distributions of dihydroxytoluenes reflect the charge distributions in the cresols. It is shown that in the case of m-cresol the hydroxyl substituent has a dominant ortho-para directing effect similar to that observed for phenol. In o- and p-cresol, this effect is modified, indicating that the methyl substituent has a significant effect on the electronic structure of those cresols. Correlation of the charge distribution in the cresols indicated by the observed distribution of dihydroxytoluenes with the unpaired spin distribution in the corresponding methylphenoxyl radicals demonstrates that the electronic structures of o- and p-cresol and their corresponding phenoxyl radicals are similarly affected by hydroxyl and methyl substitution. Addition of .OH at the methyl-substituted positions of o- and p-cresol to produce o- and p-dienone is also reported. The observation of these dienones demonstrates that addition of .OH at the ipso positions of alkylated aromatics can be of considerable importance. Mass spectrometric studies show that these dienones have relatively higher proton affinities than their isomeric analogues.