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Data for The utility of transfer learning to improve the performance of deep learning in axon segmentation

The utility of transfer learning to improve the performance of deep learning in axon segmentation Data Data: All the input and labeled volumes tf-logs: Tensorflow logs, view with command "tensorboard --logdir [name of folder]" Model Weights: model_weights: the argument list under variable combo indicate 1) no oversampling, 2) no rotation, 3) no learn scheduler, and 4) flipping on all three dimensions, and the additional values indicate 5) elastic deformation percentage, 6) rotate deformation percentage, 7) layer setting , 8) learning rate, and 9) training/validation/test data division suffix (leave '' if not using suffix). Results: Output from inference segment_total_results_validation_final: All validation results and calculations segment_total_results: All test results and calculations Authors The modified code was created for a paper by: Marjolein Oostrom, Michael A. Muniak, Rogene Eichler West, Sarah Akers, Paritosh Pande, Moses Obiri, Wei Wang, Kasey Bowyer, Zhuhao Wu, Lisa Bramer, Tianyi Mao, Bobbie Jo Webb-Robertson The work is adapted from Github TrailMap, which was created by Albert Pun and Drew Friedmann Acknowledgments MO, RMEW, SA, MO, LB, BJWR were supported by the Laboratory Directed Research and Development at Pacific Northwest National Laboratory (PNNL), a Department of Energy facility operated by Battelle under contract DE-AC05-76RLO01830. WW, KB, and ZW were supported in part by a NIH/BRAIN Initiative Grant RF1MH128969. MAM and TM were supported by two NIH/BRAIN Initiative Grants R01NS104944, RF1MH120119 and NIH R01NS081071. This research is affiliated with the Pacific northwest bioMedical Innovation Co-laboratory (PMedIC) collaboration between OHSU and PNNL.

Oostrom, Marjolein T↗

USSR Space Life Sciences Digest, issue 1

The first issue of the bimonthly digest of USSR Space Life Sciences is presented. Abstracts are included for 49 Soviet periodical articles in 19 areas of aerospace medicine and space biology, published in Russian during the first quarter of 1985. Translated introductions and table of contents for nine Russian books on topics related to NASA's life science concerns are presented. Areas covered include: botany, cardiovascular and respiratory systems, cybernetics and biomedical data processing, endocrinology, gastrointestinal system, genetics, group dynamics, habitability and environmental effects, health and medicine, hematology, immunology, life support systems, man machine systems, metabolism, musculoskeletal system, neurophysiology, perception, personnel selection, psychology, radiobiology, reproductive system, and space biology. This issue concentrates on aerospace medicine and space biology.

Hooke, L. R.↗

Assessments of Physiology and Cognition in Hybrid-Reality Environments (APACHE)

NASA is planning to return to the Moon in the mid-2020s as a stepping stone to Mars missions in the 2030s. Spacewalks, or extravehicular activities (EVAs), performed on the Moon and Mars will differ in a variety of ways from those that have been performed in decades past. NASA has identified multiple risks to human health and performance associated with a crewed mission to Mars, especially those associated with exploration EVAs which are expected to be a primary mission activity. Crew may be expected to conduct up to 24 hours of EVA per person per week, where the likelihood of injury and/or mental mistakes are increased compared to ground-based training or current microgravity EVAs and the consequences of which can be catastrophic. Current test environments for exploration EVA research and technology development are large, costly facilities that are limited in their availability or capabilities. Spacesuit testing in a reduced gravity environment such as NASA’s Neutral Buoyancy Laboratory, while a good representation of the crew’s physical workload during exploration EVAs, typically has small datasets and is difficult to integrate physiological sensors or other types of crew performance measures. Meanwhile, scientific field-based testing such as NASA’s Desert Research and Technology Studies offers an operationally relevant environment for exploration EVAs, particularly for cognitive workload, but is also limited by small datasets, lack of a pressurized spacesuit, and obtrusive measures. The limitations of current analogs for exploration EVAs identify a need for a new test environment that can approximate both the physical and cognitive demands associated with exploration EVAs to enable rapid, controlled, and repeatable evaluations of human health and performance risks of exploration missions. In response, the Human Physiology, Performance, Protection, and Operations Laboratory (H-3PO) at NASA Johnson Space Center has developed a hybrid reality exploration EVA analog named the Assessments of Physiology And Cognition in Hybrid-reality Environments (APACHE) to address these limitations using a combination of virtual, physical, and hybrid reality techniques. The APACHE facility resides at NASA Johnson Space Center and serves as a large “sandbox” for EVA research and simulation. At its center is a roughly 15x20ft space surrounded by a 14” tall sandbox partially filled with lunar regolith simulant to emulate the physical feeling of walking on a planetary surface and to allow for simulated geology operations. Nearby, a curved passive treadmill (Skillmill Connect, Technogym, Fairfield, NJ) and an omnidirectional treadmill (Infinadeck, Infinadeck, Rocklin, CA) are included to enable exploration of these large virtual environments while also imposing the physical demands, representative timelines, and cognitive burdens required to navigate and traverse these distances during exploration EVA. A 6DOF motion platform is used to simulate rover operations and supports various human performance evaluations and associated risks. Lastly, APACHE can support two extravehicular (EV) crewmembers working in tandem. A computer workstation is located nearby and also supports an intravehicular (IV) crewmember as part of a full mission simulation. The IV crewmember has direct video and audio communication with the EV crew in VR to provide operational and procedural support. The software used in APACHE was created by the JSC Engineering Directorate, in partnership with Buendea, powered by a custom Unreal Engine 5 (UE5.3, Epic Games) project. APACHE currently utilizes the HTC Vive Pro Eye in a wireless configuration for VR simulations. There are two virtual environments that subjects can explore within APACHE, a Lunar and Martian surface. The virtual Lunar surface was created from LIDAR data of the Lunar South Pole to create roughly 16 sq km of explorable terrain. The virtual Martian surface contains roughly 400 sq km of explorable terrain derived from Mars Reconnaissance Orbiter LIDAR data of the Jezero Crater. The immersion and related cognitive burdens of conducting a planetary EVA is simulated through a series of EVA-relevant tasks performed in the VR environment, using these high-fidelity visual representations. Additionally, APACHE includes biosensor driven informatics, such as real-time heart rate monitoring and/or derived values from model simulations, for active monitoring by the EV crew and added cognitive demand. A “Wizard of Oz” control panel enables test operators to activate contingency events such as simulated spacesuit malfunctions, loss of communications, and/or limited visibility. Embedded performance measures such as accuracy, completeness, and execution time have been developed for various exploration tasks to objectively quantify crew performance during an EVA and compare impacts to performance when different environmental stressors, both physical and cognitive, are added to or removed from the simulation. Additionally, validated cognitive and operational performance measures such as the Digit Symbol Substitution Task have been recreated and embedded in VR for direct and relatively unobtrusive measurement of motor perception. The APACHE environment currently supports multiple research studies at NASA. Examples include the CHAPEA project, a series of simulated year-long missions on Mars by a 4-person crew; and the CO2 Contingency Walk Back Study, an investigation of elevated CO2 exposure on crew performance during a contingency EVA scenario. APACHE also provides a test environment to support the development of the Crew State and Risk Model, which is a collection of individualized, mathematical models of crew physical and cognitive state; and the Personalized EVA Informatics and Decision Support system, an operational tool for flight controllers, and eventually a self-reliant Martian crew, to make biomedically-informed decisions in real-time to optimize the EVA planning and execution with respect to crew health and performance. Some technical challenges associated with developing the APACHE environment, as well as current limitations, include VR limitless natural walking with a hybrid spacesuit simulator, optimizing performance for wireless PC VR streaming while maintaining a high degree of visual fidelity, and the integration of various physiological (metabolic masks) and psychometric (eye tracking) sensors with the VR headset.

Human Performance↗

Injectable and implantable cellular-scale electronic devices

Provided are implantable or surface mounted biomedical devices and related methods for interfacing with a target tissue. The devices have a substrate and device component supported by the substrate. The components of the device are specially configured and packaged to be ultra-thin and mechanically compliant. In particular, device thicknesses are less than 1 mm and have lateral dimensions between about 1 m and 10 mm, depending on the application. Delivery substrates may be incorporated to assist with device implantation and handling. The devices can be shaped to provide injection in a minimally invasive manner, thereby avoiding unnecessary tissue damage and providing a platform for long-term implantation for interfacing with biological tissue.

36 MATERIALS SCIENCE↗

The surface stress of biomedical silicones is a stimulant of cellular response

Silicones are commonly used for lubrication of syringes, encapsulation of medical devices, and fabrication of surgical implants. While silicones are generally viewed as relatively inert to the cellular milieu, they can mediate a variety of inflammatory responses and other deleterious effects, but the mechanisms underlying the bioactivity of silicones remain unresolved. Here, we report that silicone liquids and gels have high surface stresses that can strongly resist deformation at cellular length scales. Biomedical silicones, including syringe lubricants and fillings from FDA-approved breast implants, readily adsorb matrix proteins and activate canonical rigidity sensing pathways through their surface stresses. In 3D culture models, liquid silicone droplets support robust cellular adhesion and the formation of multinucleated monocyte-derived cell masses that recapitulate phenotypic aspects of granuloma formation in the foreign body response. Together, our findings implicate surface stress as a cellular stimulant that should be considered in application of silicones for biomedical purposes.

60 APPLIED LIFE SCIENCES↗

Mesoporous Thin Film Architectures: Addressing Material Demands through Molecular Self-Assembly

Mesoporous thin films spark interest across a wide range of disciplines due to their tunable nanostructures, large internal surface areas, and strong compatibility with planar optical, electronic, and microfluidic devices. While attention in the porous materials community has shifted toward macroporous or disordered nanoporous systems, a resurgence in mesoporous thin film research is underway, driven by new molecular self-assembly methods, advanced materials chemistry, and improved characterization techniques. The integration of high-χN block copolymer design, kinetically persistent micelle templating, and postdeposition processing protocols now allows control over structural parameters such as pore size, wall thickness, porosity, and connectivity. These advances have overcome many of the thermodynamic and processing constraints that previously limited widespread adoption. Rather than serving only as high-surface-area supports, mesoporous thin films are engineered as active interfaces where responsive chemistries and nanoscale confinement act in tandem. Embedding switchable ligands, thermoresponsive polymers, redox mediators, or ion-selective groups directly within the pore walls enables real-time control over transport, optical, and electrochemical properties. These capabilities open up new directions in adaptive coatings, gated membranes, and fast-response biosensors. To further expand their functional scope, mesoporous films are integrated into hierarchical and multicomponent architectures. Techniques such as triblock terpolymer templating, crack-directed assembly, and nanoimprint lithography allow for control over spatial organization on the micron and submicron scale and pore system orientation. This enables programmable anisotropy, enhanced molecular diffusion, and wavelength-selective photonic behavior, essential for next-generation sensing, catalysis, and energy applications. Such structural and functional complexity requires equally sophisticated characterization. Multimodal and in situ techniques can track material dynamics under operational conditions. Recent progress includes extended-range ellipsometric porosimetry (EP) for hierarchical architectures, vacuum EP for interface energetics, time-resolved EP for diffusion kinetics, and correlative AFM-SAXS mapping. The introduction of advanced neutron-based spectroscopies, particularly quasielastic neutron scattering (QENS), promises to provide real-time access to ion transport dynamics and segmental motion under nanoscale confinement, offering a path toward deeper mechanistic understanding of structure-performance correlations in mesoporous systems. This Account reflects the technical advances made and the interdisciplinary collaborations that have shaped our collective vision. The particular dimensions of mesopores enable us to subtly tune interactions at the molecular, interfacial, and mesoscopic levels that permit us to harness nanoconfinement. What emerges is a versatile, modular platform capable of chemical gating, energy transduction, and sensing with a level of tunability unmatched by other porous materials. We highlight critical challenges including the need for more robust large-area processing, a deeper understanding of dynamic behavior under cycling, and better integration with device-level architectures. Our strategies support the transition of mesoporous thin films into active high-performance components in next-generation energy, environmental, and biomedical systems.

oxides↗

A Lakehouse Architecture for the Management and Analysis of Heterogeneous Data for Biomedical Research and Mega-biobanks

Data Lakehouse is a new paradigm in data architectures that embodies and integrates already established concepts for the systematic management of disparate, large-scale data – a data lake for heterogeneous data management, use of open standards for high-performance querying, and systematic maintenance of the data "freshness". In addition to being a new concept, the data lakehouse is also still a conceptual construct. Many projects that use the lakehouse require maturing, empirical studies, and specific implementations. In this paper, we present our implementation of the data lakehouse concept in a biomedical research and health data analytics domain, and we discuss the implementation of some unique and novel features such as support for specialized access controls in support of HIPAA regulation and IRB protocols, and support for the FAIR standard.

Begoli, Edmon↗

Evaluation of dual-tip micromanometers during 21-day implantation in goats

Investigative research efforts using a cardiovascular model required the determination of central circulatory haemodynamic and arterial system parameters for the evaluation of cardiovascular performance. These calculations required continuous beat-to-beat measurement of pressure within the four chambers of the heart and great vessels. Sensitivity and offset drift, longevity, and sources of error for eight 3F dual-tipped micromanometers were determined during 21 days of implantation in goats. Subjects were instrumented with pairs of chronically implanted fluid-filled access catheters in the left and right ventricles, through which dual-tipped (test) micromanometers were chronically inserted and single-tip (standard) micromanometers were acutely inserted. Acutely inserted sensors were calibrated daily and measured pressures were compared in vivo to the chronically inserted sensors. Comparison of the pre- and post-gain calibration of the chronically inserted sensors showed a mean sensitivity drift of 1.0 +/- 0.4% (99% confidence, n = 9 sensors) and mean offset drift of 5.0 +/- 1.5 mmHg (99% confidence, n = 9 sensors). Potential sources of error for these drifts were identified, and included measurement system inaccuracies, temperature drift, hydrostatic column gradients, and dynamic pressure changes. Based upon these findings, we determined that these micromanometers may be chronically inserted in high-pressure chambers for up to 17 days with an acceptable error, but should be limited to acute (hours) insertions in low-pressure applications.

Non-NASA Center↗

NEEMO - NASA's Extreme Environment Mission Operations: On to a NEO

During NEEMO missions, a crew of six Aquanauts lives aboard the National Oceanic and Atmospheric Administration (NOAA) Aquarius Underwater Laboratory the world's only undersea laboratory located 5.6 km off shore from Key Largo, Florida. The Aquarius habitat is anchored 62 feet deep on Conch Reef which is a research only zone for coral reef monitoring in the Florida Keys National Marine Sanctuary. The crew lives in saturation for a week to ten days and conducts a variety of undersea EVAs (Extra Vehicular Activities) to test a suite of long-duration spaceflight Engineering, Biomedical, and Geoscience objectives. The crew also tests concepts for future lunar exploration using advanced navigation and communication equipment in support of the Constellation Program planetary exploration analog studies. The Astromaterials Research and Exploration Science (ARES) Directorate and Behavioral Health and Performance (BHP) at NASA/Johnson Space Center (JSC), Houston, Texas support this effort to produce a high-fidelity test-bed for studies of human planetary exploration in extreme environments as well as to develop and test the synergy between human and robotic curation protocols including sample collection, documentation, and sample handling. The geoscience objectives for NEEMO missions reflect the requirements for Lunar Surface Science outlined by the LEAG (Lunar Exploration Analysis Group) and CAPTEM (Curation and Analysis Planning Team for Extraterrestrial Materials) white paper [1]. The BHP objectives are to investigate best meas-ures and tools for assessing decrements in cogni-tive function due to fatigue, test the feasibility study examined how teams perform and interact across two levels, use NEEMO as a testbed for the development, deployment, and evaluation of a scheduling and planning tool. A suite of Space Life Sciences studies are accomplished as well, ranging from behavioral health and performance to immunology, nutrition, and EVA suit design results of which will directly support the investigation of open questions and operational concepts that will enable NASA to continue its plan for planetary exploration.

Bell, M. S.↗

Enabling Space Biological Knowledge Discovery Through Image and Video Data Sharing

Increased biomedical risks associated with deep space crewed missions (cis-Lunar, Mars transit/surface) require development of health countermeasures, novel ecosystem support, risk modeling, and fundamental space biological knowledge discovery. Molecular-omics, physiological-phenotypic-behavioral, and environmental-radiation telemetry data from space biological and health studies are needed for reuse by scientists to address these tasks. The data as well as space-relevant biospecimens are being made more findable, accessible, interoperable, and reusable through NASA’s Open Science Data Repository (OSDR). This new OSDR umbrella grouping includes NASA GeneLab, the NASA Ames Life Sciences Data Archive (ALSDA), and the NASA Biological Institutional Scientific Collection. The OSDR system design appropriately handles metadata and processed-tabular results from ALSDA studies collected from space experiments. But raw and processed ALSDA bioimage and video datasets require an expansion of OSDR’s data architecture to handle ingestion, curation, and egress. The academic-industry bioimaging field saw a scientific renaissance in the past several years through leveraging open-source software, international collaborations, machine learning, and other open science/programming approaches. As crewed missions and more biological experiments are on the deep space horizon, OSDR is embracing data stewardship through listening to feedback from subject matter experts and designing an expanded architecture which is appropriate for NASA’s goals to enable analysis and reuse of bioimaging and video data for the public science community.Discovery Through Image and Video Data Sharing

space biology↗

Empowering Women in Biomedical Informatics: Pivoting for Success in the Post-Pandemic World

The COVID-19 pandemic and the isolation measures implemented to contain its spread have exacerbated pre-existing barriers to advancement for women in biomedical informatics. In 2020, the Women in AMIA (WIA) Networking, Mentoring, and Lifecycle Committee administered a survey to identify resources and needs to assist women in informatics. Part of this survey identified several factors impacted by the pandemic: 1) work-life boundaries disappeared and caring for family while working from home became increasingly challenging; 2) isolation, stress and safety of well-being was heightened during the pandemic impacting physical and mental health; 3) diverse working environment and modality brought unforeseen challenges in collaborations and unified communications. These challenges present an opportunity for promoting career development for women professionals in biomedical informatics. This WIA-sponsored panel brings together leaders in the field to highlight their personal experiences and strategies to support women professionals.

Dua, Prerna↗

Do plasma melatonin concentrations decline with age?

PURPOSE: Numerous reports that secretion of the putative sleep-promoting hormone melatonin declines with age have led to suggestions that melatonin replacement therapy be used to treat sleep problems in older patients. We sought to reassess whether the endogenous circadian rhythm of plasma melatonin concentration changes with age in healthy drug-free adults. METHODS: We analyzed the amplitude of plasma melatonin profiles during a constant routine in 34 healthy drug-free older subjects (20 women and 14 men, aged 65 to 81 years) and compared them with 98 healthy drug-free young men (aged 18 to 30 years). RESULTS: We could detect no significant difference between a healthy and drug-free group of older men and women as compared to one of young men in the endogenous circadian amplitude of the plasma melatonin rhythm, as described by mean 24-hour average melatonin concentration (70 pmol/liter vs 73 pmol/liter, P = 0.97), or the duration (9.3 hours vs 9.1 hours, P = 0.43), mean (162 pmol/liter vs 161 pmol/liter, P = 0.63), or integrated area (85,800 pmol x min/liter vs 86,700 pmol x min/liter, P = 0.66) of the nocturnal peak of plasma melatonin. CONCLUSION: These results do not support the hypothesis that reduction of plasma melatonin concentration is a general characteristic of healthy aging. Should melatonin replacement therapy or melatonin supplementation prove to be clinically useful, we recommend that an assessment of endogenous melatonin be carried out before such treatment is used in older patients.

Non-NASA Center↗

Commercial investigation results for the generic bioprocessing apparatus flown on United States Microgravity Laboratory-1

The Generic Bioprocessing Apparatus (BPA) payload was developed by BioServe to support the commercial flight development needs of our specialized consortia comprised of business, academic, and government entities. The consortia have commitments to explore commercial opportunities in bioprocessing, biomedical models, and closed agricultural systems. In addition, some members of BioServe have interests in the development and/or qualification of enabling flight hardware used in life sciences space flight testing. Some business and academic entities have interests in more than one of these consortia. To aid in payload development, flight, and analysis, each consortium member contributes resources ranging from proprietary expertise and materials, to hardware and cash. Professionals from business, academia, and government often interact with each other via graduate research assistants who do much of the 'hands-on' payload preparation and subsequent data analyses. The GBA supported research, testing, and development activities for each different BioServe consortium. It produced an environment in which professionals from diverse backgrounds came together with a single focus. And, it provided a truly novel learning environment for a youthful new cadre of space professionals committed to the exploration of commercial opportunities presented by space. Since the GBA supported a large number of different experiments, this paper briefly describes the payload characteristics and the essential operations of the payload. A summary of the experiments is presented. Finally, a few of the experiments are described in detail highlighting some novel effects of space flight on life science systems. Portions of the reported work have or will appear in appropriate archival journals as cited in the bibliography. In several instances, data collected from USML-1 have been supplemented with related data collected on more recent STS missions.

Stodieck, Louis S.↗

Life sciences utilization of Space Station Freedom

Space Station Freedom will provide the United States' first permanently manned laboratory in space. It will allow, for the first time, long term systematic life sciences investigations in microgravity. This presentation provides a top-level overview of the planned utilization of Space Station Freedom by NASA's Life Sciences Division. The historical drivers for conducting life sciences research on a permanently manned laboratory in space as well as the advantages that a space station platform provides for life sciences research are discussed. This background information leads into a description of NASA's strategy for having a fully operational International Life Sciences Research Facility by the year 2000. Achieving this capability requires the development of the five discipline focused 'common core' facilities. Once developed, these facilities will be brought to the space station during the Man-Tended Capability phase, checked out and brought into operation. Their delivery must be integrated with the Space Station Freedom manifest. At the beginning of Permanent Manned Capability, the infrastructure is expected to be completed and the Life Sciences Division's SSF Program will become fully operational. A brief facility description, anticipated launch date and a focused objective is provided for each of the life sciences facilities, including the Biomedical Monitoring and Countermeasures (BMAC) Facility, Gravitational Biology Facility (GBF), Gas Grain Simulation Facility (GGSF), Centrifuge Facility (CF), and Controlled Ecological Life Support System (CELSS) Test Facility. In addition, hardware developed by other NASA organizations and the SSF International Partners for an International Life Sciences Research Facility is also discussed.

Chambers, Lawrence P.↗

Effects of prolonged bed rest on the total peripheral resistance baroreflex

Orthostatic intolerance following prolonged exposure to microgravity continues to be a primary concern of the human space program. Reduced autonomic tone has been demonstrated to contribute to this phenomenon, and the heart rate baroreflex, in particular, has been repeatedly shown to be impaired. However, only the works of Yelle et al. have attempted to address the role of the total peripheral resistance (TPR) baroreflex, a potentially more significant contributor to blood pressure regulation. We applied a previously developed method for estimating the static gains of both the arterial and cardiopulmonary TPR baroreflexes to data obtained before and after 16-day bed rest. Reductions in the estimated static gains of the arterial (statistically significant) and cardiopulmonary TPR baroreflexes were found after bed rest. This study supports the works of Yelle et al, which imply that the TPR baroreflex is reduced after spaceflight.

Non-NASA Center↗

Compression under a mechanical counter pressure space suit glove

Background: Current gas-pressurized space suits are bulky stiff shells severely limiting astronaut function and capability. A mechanical counter pressure (MCP) space suit in the form of a tight elastic garment could dramatically improve extravehicular activity (EVA) dexterity, but also be advantageous in safety, cost, mass and volume. The purpose of this study was to verify that a prototype MCP glove exerts the design compression of 200 mmHg, a pressure similar to the current NASA EVA suit. Methods: Seven male subjects donned a pressure measurement array and MCP glove on the right hand, which was placed into a partial vacuum chamber. Average compression was recorded on the palm, the bottom of the middle finger, the top of the middle finger and the dorsum of the hand at pressures of 760 (ambient), 660 and 580 mmHg. The vacuum chamber was used to simulate the pressure difference between the low breathing pressure of the current NASA space suits (approximately 200 mmHg) and an unprotected hand in space. Results: At ambient conditions, the MCP glove compressed the dorsum of the hand at 203.5 +/- 22.7 mmHg, the bottom of the middle finger at 179.4 +/- 16.0 mmHg, and the top of the middle finger at 183.8 +/- 22.6 mmHg. The palm compression was significantly lower (59.6 +/- 18.8 mmHg, p<0.001). There was no significant change in glove compression with the chamber pressure reductions. Conclusions: The MCP glove compressed the dorsum of the hand and middle finger at the design pressure.

NASA Discipline Life Sciences Technologies↗