FAIRness and Usability for Open-access Omics Data Systems

Omics data sharing is crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the FAIRness of NASAs GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omics data domain, using 14 FAIRness metrics. The range of overall FAIRness scores was 6-12 (out of 14), average 10.1, and standard deviation 2.4. The range of Pass ratings for the metrics was 29-79%, Partial Pass 0-21%, and Fail 7-50%. The systems we evaluated performed the best in the areas of data findability and accessibility, and worst in the area of data interoperability. Reusability of metadata, in particular, was frequently not well supported. We relate our experiences implementing semantic integration of omics data from some of the assessed systems for federated querying and retrieval functions, given their shortcomings in data interoperability. Finally, we propose two new principles that Big Data system developers, in particular, should consider for maximizing data accessibility

Self-recording portable soil penetrometer

A lightweight portable penetrometer for testing soil characteristics is described. The penetrometer is composed of a handle, data recording, and probe components detachably joined together. The data recording component has an easily removed recording drum which rotates according to the downward force applied on the handle, and a stylus means for marking the drum along its height according to the penetration depth of probe into the soil

β-Cell failure in type 2 diabetes: a case of asking too much of too few?

The islet in type 2 diabetes (T2DM) is characterized by a deficit in β-cells, increased β-cell apoptosis, and extracellular amyloid deposits derived from islet amyloid polypeptide (IAPP). In the absence of longitudinal studies, it is unknown if the low β-cell mass in T2DM precedes diabetes onset (is a risk factor for diabetes) or develops as a consequence of the disease process. Although insulin resistance is a risk factor for T2DM, most individuals who are insulin resistant do not develop diabetes. By inference, an increased β-cell workload results in T2DM in some but not all individuals. We propose that the extent of the β-cell mass that develops during childhood may underlie subsequent successful or failed adaptation to insulin resistance in later life. We propose that a low innate β-cell mass in the face of subsequent insulin resistance may expose β-cells to a burden of insulin and IAPP biosynthetic demand that exceeds the cellular capacity for protein folding and trafficking. If this threshold is crossed, intracellular toxic IAPP membrane permeant oligomers (cylindrins) may form, compromising β-cell function and inducing β-cell apoptosis

The Potential of In-Space Research on Liquefaction Phenomena and Related Soil Behavior

Because the constitutive laws for soils are governed mainly by interparticle friction, all aspects of their mechanical behavior depend strongly on gravitational body forces. This fact poses serious limitations on the formulation of a materially objective soil constitutive theory, based on experimentation performed on earth. In particular, the presence of the earth\u27s gravity prohibits the design of controlled experiments to properly simulate a variety of critical phenomena associated with the dynamic response of soils to seismic excitation in a very low effective confining stress field. For these reasons, the advent of the space age and, more specifically, the capabilities of the Space Shuttle-Spacelab for several day experimentation by trained specialists in a shirt-sleeve, laboratory- controlled environment, under essentially zero-gravity conditions, could offer invaluable opportunities for developing a quantitative understanding of fundamental aspects of soil behavior during and after an earthquake, which, in turn, could result in significant technological advances in geotechnical earthquake engineering

FAIRness and Usability for Open-Access Omics Data Systems

Omics data sharing is especially crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the "FAIRness" of NASA's GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omics data domain, using 14 FAIRness metrics. 14 metrics. The range of Pass ratings was 29-79% of the 14 metrics, Partial Pass 0-21%, and Fail 7-50%. The range of overall FAIRness scores was 5-12 (out of 14). The systems we evaluated performed the best in the areas of data findability and accessibility, and worst in the area of data interoperability. We propose two new principles that Big Data systems, in particular, should consider for increasing data accessibility. We relate our experiences implementing semantic integration of omics data from several systems for the federated querying and retrieval functions of the GLDS, given the shortcomings in data interoperability of these systems

Hypoxia and muscle maintenance regulation: implications for chronic respiratory disease

PURPOSE OF REVIEW: Muscle wasting and impaired muscle oxidative metabolism are common extrapulmonary features of chronic respiratory failure (CRF) that significantly increase disease burden. This review aims to address the question whether hypoxia, an obvious consequence of this disease, actually plays a causal role in these muscle impairments. RECENT FINDINGS: In experimental models, a causal role for hypoxia in muscle atrophy and metabolic impairments has clearly been shown. Although the hypoxia-inducible factors and nuclear factor kappa B are putative mediators of these hypoxia-induced alterations, their true involvement remains to be proven. Molecular signatures of disrupted regulation of muscle mass and oxidative metabolism observed in these experimental models also have been shown in muscles of patients suffering from CRF, suggestive of but not conclusive for a causal role of hypoxia. Therapies, including but not restricted to those aimed at alleviating hypoxia, have been shown to partially but not completely restore muscle mass and oxidative capacity in CRF patients, which may imply an additive effect of nutritional modulation of substrate metabolism. SUMMARY: Although hypoxia clearly affects skeletal muscle maintenance, it remains to be confirmed whether and by which underlying molecular mechanisms hypoxia is causally involved in CRF-related muscle atrophy and impaired oxidative capacity

β-cell dysfunctional ERAD/ubiquitin/proteasome system in type 2 diabetes mediated by islet amyloid polypeptide-induced UCH-L1 deficiency.

ObjectiveThe islet in type 2 diabetes is characterized by β-cell apoptosis, β-cell endoplasmic reticulum stress, and islet amyloid deposits derived from islet amyloid polypeptide (IAPP). Toxic oligomers of IAPP form intracellularly in β-cells in humans with type 2 diabetes, suggesting impaired clearance of misfolded proteins. In this study, we investigated whether human-IAPP (h-IAPP) disrupts the endoplasmic reticulum-associated degradation/ubiquitin/proteasome system.Research design and methodsWe used pancreatic tissue from humans with and without type 2 diabetes, isolated islets from h-IAPP transgenic rats, isolated human islets, and INS 832/13 cells transduced with adenoviruses expressing either h-IAPP or a comparable expression of rodent-IAPP. Immunofluorescence and Western blotting were used to detect polyubiquitinated proteins and ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1) protein levels. Proteasome activity was measured in isolated rat and human islets. UCH-L1 was knocked down by small-interfering RNA in INS 832/13 cells and apoptosis was evaluated.ResultsWe report accumulation of polyubiquinated proteins and UCH-L1 deficiency in β-cells of humans with type 2 diabetes. These findings were reproduced by expression of oligomeric h-IAPP but not soluble rat-IAPP. Downregulation of UCH-L1 expression and activity to reproduce that caused by h-IAPP in β-cells induced endoplasmic reticulum stress leading to apoptosis.ConclusionsOur results indicate that defective protein degradation in β-cells in type 2 diabetes can, at least in part, be attributed to misfolded h-IAPP leading to UCH-L1 deficiency, which in turn further compromises β-cell viability

NASA's GeneLab Phase II: Federated Search and Data Discovery

GeneLab is currently being developed by NASA to accelerate 'open science' biomedical research in support of the human exploration of space and the improvement of life on earth. Phase I of the four-phase GeneLab Data Systems (GLDS) project emphasized capabilities for submission, curation, search, and retrieval of genomics, transcriptomics and proteomics ('omics') data from biomedical research of space environments. The focus of development of the GLDS for Phase II has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics

NASA's GeneLab: An Integrated Omics Data Commons and Workbench

GeneLab (http://genelab.nasa.gov) is a NASA initiative designed to accelerate open science biomedical research in support of the human exploration of space and the improvement of life on earth. The GeneLab Data Systems (GLDS) were developed to help investigators corroborate findings from omics (genomics, transcriptomics, proteomics, and metabolomics) assays and translate them into systems biology knowledge and, eventually, therapeutics, including countermeasures to support life in space. Phase I of the project (completed) emphasized developing key capabilities for submission, curation, storage, search, and retrieval of omics data from biomedical research in and of space environments. The development focus for Phase II (completed) was federated data search and retrieval of these kinds of data from other open-access repositories. The last phase of the project (in work) entails developing an omics analysis tool set, and a portal to visualize processed omics data, emphasizing integration with the data repository and search functions developed during the prior phases. The final product will be an open-access system where users can individually or collaboratively publish, search, integrate, analyze, and visualize omics data

NASA's GeneLab: An Integrated Omics Data Commons and Workbench

GeneLab (http://genelab.nasa.gov) is a NASA initiative designed to accelerate "open science" biomedical research in support of the human exploration of space and the improvement of life on earth. The GeneLab Data Systems (GLDS) were developed to help investigators corroborate findings from "omics" (genomics, transcriptomics, proteomics, and metabolomics) assays and translate them into systems biology knowledge and, eventually, therapeutics, including countermeasures to support life in space. Phase I of the project (completed) emphasized developing key capabilities for submission, curation, storage, search, and retrieval of omics data from biomedical research in and of space environments. The development focus for Phase II (completed) was federated data search and retrieval of these kinds of data from other open-access repositories. The last phase of the project (in work) entails developing an omics analysis tool set, and a portal to visualize processed omics data, emphasizing integration with the data repository and search functions developed during the prior phases. The final product will be an open-access system where users can individually or collaboratively publish, search, integrate, analyze, and visualize omics data