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.

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.

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.

Self-Reported Barriers to Healthcare Access for Rheumatoid Arthritis Patients in Rural and Northern Saskatchewan: A Mixed Methods Study

OBJECTIVES

The aim of the present study was to identify potential barriers for access to medical and allied health services from the perspective of rural and Northern Saskatchewan rheumatoid arthritis (RA) patients.

METHODS

A total of 100 adults with established RA, residing in rural and Northern Saskatchewan, were recruited from two rheumatology practices. Structured interviews with standardized scripts solicited patient perspectives on appointment waiting times, travel required to access medical services and satisfaction with healthcare provision. Thematic analysis was employed for qualitative data.

RESULTS

Patients-reported concerns regarding waiting time for their first rheumatology appointment. There was reduced access to allied health professionals, with only 53% of the participants having seen a physiotherapist (PT), and only 26% an occupational therapist (OT). Patients had similar driving distances to their family physician, PT, pharmacy and laboratory services but commuted significantly further for rheumatologist and OT services. There were high levels of satisfaction with their rheumatologist and family physician appointments (8.96 and 8.04 on a ten-point scale). Patients with longer travel times had higher satisfaction with their health care appointments: Patients who travelled one, two and more than two hours had satisfaction scores of 0.93, 0.88 and 1.32 points higher on a ten-point scale (p < 0.03).

CONCLUSIONS

Access to medical services is a concern for this population. Patients were dissatisfied with the waiting time for their first specialist appointment and with decreased access to allied health professionals. Patients travelling longer distances were more satisfied with their health care provider's care, suggesting that good patient-care giver relationships helped to ameliorate the difficulties of travelling to their appointments. Copyright © 2016 John Wiley & Sons, Ltd.

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.

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.

Rapid progressive extramedullary plasmacytoma in the orbit

BACKGROUND

Plasma cell tumors of the orbit are uncommon and mostly the first manifestation of a multiple myeloma (MM). Primary extramedullary plasmacytoma (EMP) of the orbit is exceedingly rare and only a few cases have been reported so far. Differentiation of an EMP from a MM is important, since 9.5 years have been reported as the mean survival of EMP, compared with a mean survival of 3 to 4 years for multiple myeloma.

HISTORY AND SIGNS

A 68-year-old man presented with a history of rapid progressive extramedullary plasmacytoma in the right orbit, increasing in size within a few weeks. MR imaging revealed an intraorbital mass measuring 5.2 x 4.7 x 3 cm. The earlier performed biopsy was positive for plasmacytoma of the lambda light chain type. Systemic work-up was negative for further tumor spread.

THERAPY AND OUTCOME

Irradiation (a maximum of 80 Gy) and several chemotherapy cycles showed no effect. Exenteration with sparing of the upper and lower lid skin was performed. The residual defect was covered by a Thiersch graft. Although the orbit had been irradiated with the maximal dose, the Thiersch graft healed well.

CONCLUSION

Normally, EMP is slow to increase in size. In our patient, marked growth of tumor was noted within one week. One underlying reason is the poorly differentiated, blastic morphology leading to this rapid tumor growth. However, particular molecular features, like a t(4;14), could not be demonstrated.

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.

Strategies for the development of a peptide computer

MOTIVATION

We devise a computational model using protein-protein interactions.

RESULTS

Peptide-antibody interactions can be used to perform a large number of small logical operations in parallel. We show for example how a sequence of operations can be used to compare the number of occurrences of an element in two sets and how to estimate the number of occurrences of an element in a set. Similar to DNA-computing, these techniques could in principle be extended to solve instances of NP-complete problems. We give as an example a procedure to solve examples of the satisfiability problem.

Significance of saliva for the denture-wearing population

This paper summarises a series of studies already published in German and presents new data related to the aetiology of the 'dry mouth' and its associated problems.

AIMS

To study factors affecting mucous and serous salivary gland secretion, the aetiology of the 'dry mouth' and its associated problems, causative factors for hyposalivation and it's treatment.

SETTING

Two university dental hospitals.

SUBJECTS

587 denture wearers and 521 control subjects, and autopsy material.

INTERVENTIONS

Exercise, chewing, water, oestrogen, pilocarpine, and anetholtrithion therapy, biopsy of the minor glands.

MAIN OUTCOME MEASURES

Palatal secretion (PAL, microL/cm2/min) and parotid salivary flow (PAR), subjective complaints and clinical findings.

RESULTS

Resting flow rates for PAL between 0 and 65 microliters/cm2/min were seen in every age group. The flow rates of PAR (0 to 3.7 ml/10 min) were not correlated with PAL. Most patients with a resting flow rate of PAL < or = 6.0 microliters/cm2 suffer from a 'dry mouth' and Burning Mouth Syndrome (BMS) or oral dysaesthesia (OD) with or without chronic lesions of the oral mucosa. Etiological factors for the incidence of reduced PAL and associated problems include xerostomic drugs, oestrogen deficiency, radiotherapy, thyroid dysfunction, smoking or continuous wearing of complete upper dentures. PAL also correlated with the retention of upper complete dentures. PAL was correlated with the water content of epithelial tissues. PAL and PAR were both increased by drinking ample fluid, improving their circulation by physical exercises, chewing intensively, or taking oestrogens, pilocarpine, anetholtrithion.

CONCLUSIONS

Variation in palatal salivary secretion occurs and is clinically important.

Body image, perceived pubertal timing, and adolescent mental health

PURPOSE

To examine the impact of gender, racial-ethnic group, and perceived pubertal timing on body image and adolescent mental health.

METHOD

A three-stage, area probability sample was selected which included 877 teens (13-18 years) with diverse social and demographic characteristics. Interviews in English or Spanish were conducted in person. The content emphasized emotional distress and problematic behavior, exposure to social stressors, coping resources and behaviors, and socioeconomic and demographic characteristics of the adolescent and his or her family.

RESULTS

Girls were more depressed and had lower self-esteem than boys, but not after controlling for body image. Hispanics were more depressed and had lower self-esteem than other racial-ethnic groups, a difference that remained when controlling for body image. African-Americans had the most positive body image, a finding that could not be attributed to higher self-esteem or fewer depressive symptoms. The impact of perceived pubertal timing on body image varied considerably by gender and across racial-ethnic group.

CONCLUSIONS

Negative feelings about their bodies contribute to the higher prevalence of depressive symptomatology and lower self-esteem among girls. African-Americans appear to take pride in their bodies in a manner that sets them apart from other teenagers, suggesting they hold a different ideal. Relative to teenagers of other racial-ethnic backgrounds, Hispanics may be at elevated risk for mental health problems.

Demographic and health characteristics of heavy marijuana smokers in Los Angeles County

The demographic, life-style, and self-reported health characteristics of a convenience sample of 207 male and 70 female, non-Hispanic White, heavy marijuana users in Los Angeles County were compared with those of more representative county and national samples. Consistent with other researchers' findings, heavy marijuana users were found to differ significantly in living arrangements, job stability, and income. Heavy marijuana users did not differ in completed education, self-reported physical health, or use of alcohol and cigarettes. Heavy marijuana users were less likely to be married than nonusers, but reported the same number of close friends with whom they interacted more frequently than same-aged comparison groups. Our findings suggest that heavy marijuana users are not homogeneous, and that female users differ significantly from male users.

Anticonvulsant and antipunishment effects of toluene

Toluene can have striking acute behavioral effects and is subject to abuse by inhalation. To determine if its actions resemble those of drugs used in the treatment of anxiety ("anxiolytics"), two sets of experiments were undertaken. Inasmuch as prevention of pentylenetetrazol-induced convulsions is an identifying property of this class of agents, we first demonstrated that pretreatment with injections of toluene delayed the onset of convulsive signs and prevented the tonic extension phase of the convulsant activity in a dose-related manner. Injections of another alkyl benzene, m-xylene, were of comparable potency to toluene. Inhalation of toluene delayed the time to death after pentylenetetrazol injection in a manner related to the duration and concentration of exposure; at lower convulsant doses, inhalation of moderate concentrations (EC50, 1311 ppm) prevented death. Treatment with a benzodiazepine receptor antagonist (Ro 15-1788) failed to reduce the anticonvulsant activity of inhaled toluene. Anxiolytics also attenuate the reduction in response rate produced by punishment with electric shock. Toluene increased rates of responding suppressed by punishment when responding was maintained under a multiple fixed-interval fixed-interval punishment schedule of reinforcement. Distinct antipunishment effects were observed after 2 hr of exposure to 1780 and 3000 ppm of toluene; the rate-increasing effects of toluene were related to concentration and to time after the termination of exposure. Thus, toluene and m-xylene resemble in several respects clinically useful drugs such as the benzodiazepines.

Failure of prostaglandin inhibition to attenuate the tolerance to hemorrhage in domestic chicken

Domestic fowl have been shown to have the ability to withstand severe hemorrhage. Recent studies in mammals have suggested that prostaglandin hormones may be beneficial during hemorrhagic shock. It has been reported that chickens have high circulating levels of prostaglandins. Anesthetized chickens were stressed by the removal of 45% of the their estimated total blood volume. When compared to controls, neither prostaglandin inhibition with indomethacin or meclofenamate decreased the ability of these animals to tolerate hemorrhage. Changes in mean arterial pressure following hemorrhage were not altered by prostaglandin inhibition. These data demonstrate that prostaglandins are not responsible for the tolerance to hemorrhage observed in domestic fowl.

The mandibular dental arch: part III. Buccal expansion

The tendency toward relapse in intercuspid width has been examined with those cases having final intercuspid width less than 27 mm showing significantly less relapse than those cases with final intercuspid width of 28 mm or more. The point of contact between the cuspid and first premolar has been introduced as a key point on the arch, determining arch width. An individualized norm has been derived for this measurement as a function of the patient's tooth size, facial pattern, and other variables based upon stable normal occlusions in treated cases. Those cases expanded to a dimension exceeding the norm by more than 1 mm showed a greater propensity toward relapse. The group following the norm was significantly more stable than the over- and underexpansion groups at the .025 significance level. An individual norm for intermolar width based upon the patient's facial pattern (using frontal and lateral X-rays) has been established. Cases showing relapse showed considerably less space between the lower molar and the JAG plane, and greater lower face height than stable cases. The results show that the space available for the permanent dentition can be estimated in advance of treatment based on the patient's own skeletal measurements, thus minimizing unnecessary extractions, relapse, and extended treatment time due to errors in diagnosis.