Bridging big data in the ENIGMA consortium to combine non-equivalent cognitive measures
Not provided.
Science & Technology - Other Topics↗
Engineering topics
Anderson, Tim
Publications and source records attributed to Anderson, Tim.
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models
Abstract Background Sequence alignment lies at the heart of genome sequence annotation. While the BLAST suite of alignment tools has long held an important role in alignment-based sequence database search, greater sensitivity is achieved through the use of profile hidden Markov models (pHMMs). Here, we describe an FPGA hardware accelerator, called HAVAC, that targets a key bottleneck step (SSV) in the analysis pipeline of the popular pHMM alignment tool, HMMER. Results The HAVAC kernel calculates the SSV matrix at 1739 GCUPS on a $$\sim$$ ∼ $3000 Xilinx Alveo U50 FPGA accelerator card, $$\sim$$ ∼ 227× faster than the optimized SSV implementation in nhmmer . Accounting for PCI-e data transfer data processing, HAVAC is 65× faster than nhmmer’s SSV with one thread and 35× faster than nhmmer with four threads, and uses $$\sim$$ ∼ 31% the energy of a traditional high end Intel CPU. Conclusions HAVAC demonstrates the potential offered by FPGA hardware accelerators to produce dramatic speed gains in sequence annotation and related bioinformatics applications. Because these computations are performed on a co-processor, the host CPU remains free to simultaneously compute other aspects of the analysis pipeline.
59 BASIC BIOLOGICAL SCIENCES↗
Verbal Learning and Memory Deficits across Neurological and Neuropsychiatric Disorders: Insights from an ENIGMA Mega Analysis
Deficits in memory performance have been linked to a wide range of neurological and neuropsychiatric conditions. While many studies have assessed the memory impacts of individual conditions, this study considers a broader perspective by evaluating how memory recall is differentially associated with nine common neuropsychiatric conditions using data drawn from 55 international studies, aggregating 15,883 unique participants aged 15–90. The effects of dementia, mild cognitive impairment, Parkinson’s disease, traumatic brain injury, stroke, depression, attention-deficit/hyperactivity disorder (ADHD), schizophrenia, and bipolar disorder on immediate, short-, and long-delay verbal learning and memory (VLM) scores were estimated relative to matched healthy individuals. Random forest models identified age, years of education, and site as important VLM covariates. A Bayesian harmonization approach was used to isolate and remove site effects. Regression estimated the adjusted association of each clinical group with VLM scores. Memory deficits were strongly associated with dementia and schizophrenia (p < 0.001), while neither depression nor ADHD showed consistent associations with VLM scores (p > 0.05). Differences associated with clinical conditions were larger for longer delayed recall duration items. By comparing VLM across clinical conditions, this study provides a foundation for enhanced diagnostic precision and offers new insights into disease management of comorbid disorders.
Neurosciences & Neurology↗
An optimized FM-index library for nucleotide and amino acid search
Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.
59 BASIC BIOLOGICAL SCIENCES↗
CubeSat or Microsat Probabilistic + Analogies Cost Tool (COMPACT)
No abstract available
Mrozinksi, Joe↗
Hydrogen Research for Spaceport and Space-Based Applications: Hydrogen Sensors and Systems
The activities presented are a broad based approach to advancing key hydrogen related technologies in areas such as fuel cells, hydrogen production, and distributed sensors for hydrogen-leak detection, laser instrumentation for hydrogen-leak detection, and cryogenic transport and storage. Presented are the results from research projects, education and outreach activities, system and trade studies. The work will aid in advancing the state-of-the-art for several critical technologies related to the implementation of a hydrogen infrastructure. Activities conducted are relevant to a number of propulsion and power systems for terrestrial, aeronautics and aerospace applications. Sensor systems research was focused on hydrogen leak detection and smart sensors with adaptive feedback control for fuel cells. The goal was to integrate multifunction smart sensors, low-power high-efficiency wireless circuits, energy harvesting devices, and power management circuits in one module. Activities were focused on testing and demonstrating sensors in a realistic environment while also bringing them closer to production and commercial viability for eventual use in the actual operating environment.
Anderson, Tim↗
Hydrogen Research for Spaceport and Space-Based Applications: Hydrogen Production, Storage, and Transport
The activities presented are a broad based approach to advancing key hydrogen related technologies in areas such as fuel cells, hydrogen production, and distributed sensors for hydrogen-leak detection, laser instrumentation for hydrogen-leak detection, and cryogenic transport and storage. Presented are the results from research projects, education and outreach activities, system and trade studies. The work will aid in advancing the state-of-the-art for several critical technologies related to the implementation of a hydrogen infrastructure. Activities conducted are relevant to a number of propulsion and power systems for terrestrial, aeronautics and aerospace applications. Hydrogen storage and in-space hydrogen transport research focused on developing and verifying design concepts for efficient, safe, lightweight liquid hydrogen cryogenic storage systems. Research into hydrogen production had a specific goal of further advancing proton conducting membrane technology in the laboratory at a larger scale. System and process trade studies evaluated the proton conducting membrane technology, specifically, scale-up issues.
Anderson, Tim↗
Hydrogen Research for Spaceport and Space-Based Applications: Fuel Cell Projects
The activities presented are a broad based approach to advancing key hydrogen related technologies in areas such as fuel cells, hydrogen production, and distributed sensors for hydrogen-leak detection, laser instrumentation for hydrogen-leak detection, and cryogenic transport and storage. Presented are the results from research projects, education and outreach activities, system and trade studies. The work will aid in advancing the state-of-the-art for several critical technologies related to the implementation of a hydrogen infrastructure. Activities conducted are relevant to a number of propulsion and power systems for terrestrial, aeronautics and aerospace applications. Fuel cell research focused on proton exchange membranes (PEM), solid oxide fuel cells (SOFC). Specific technologies included aircraft fuel cell reformers, new and improved electrodes, electrolytes, interconnect, and seals, modeling of fuel cells including CFD coupled with impedance spectroscopy. Research was conducted on new materials and designs for fuel cells, along with using embedded sensors with power management electronics to improve the power density delivered by fuel cells. Fuel cell applications considered were in-space operations, aviation, and ground-based fuel cells such as; powering auxiliary power units (APUs) in aircraft; high power density, long duration power supplies for interplanetary missions (space science probes and planetary rovers); regenerative capabilities for high altitude aircraft; and power supplies for reusable launch vehicles.
Anderson, Tim↗
NASA Hydrogen Research for Spaceport and Space Based Applications
The activities presented are a broad based approach to advancing key hydrogen related technologies in areas such as hydrogen production, distributed sensors for hydrogen-leak detection, laser instrumentation for hydrogen-leak detection, and cryogenic transport and storage. Presented are the results form 15 research projects, education, and outreach activities, system and trade studies, and project management. The work will aid in advancing the state-of-the-art for several critical technologies related to the implementation of a hydrogen infrastructure. Activities conducted are relevant to a number of propulsion and power systems for terrestrial, aeronautics, and aerospace applications.
Anderson, Tim↗
NASA Hydrogen Research for Spaceport and Space Based Applications
Project management activities for this grant includes internal oversight, coordination and facilitation among research groups (internal to UF and external); system and/or trade studies to assist in evaluating and prioritizing new hydrogen production processes that may become available for potential research investigations; a technical and programmatic outreach activity; and formal reporting, including periodic technical reviews with the NASA team.
Anderson, Tim↗