3,349 results on '"Glenn, K."'
Search Results
2. Designing an all-flash Lustre file system for the 2020 NERSC Perlmutter system
- Author
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Lockwood, Glenn K, Lozinskiy, Kirill, Gerhardt, Lisa, Cheema, Ravi, Hazen, Damian, and Wright, Nicholas J
- Subjects
lustre ,architecture ,storage ,flash - Published
- 2024
3. New species of awl-head katydids, Cestrophorus and Acanthacara, from the Andes of Ecuador (Orthoptera, Conocephalinae, Cestrophorini)
- Author
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Braun, Holger, Morris, Glenn K, and Pensoft Publishers
- Subjects
bioacoustics ear fastigium montane sinusoid song s - Published
- 2022
4. Design and Implementation of Burst Buffer Over-Subscription Scheme for HPC Storage Systems
- Author
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Bang, Jiwoo, Sim, Alexander, Lockwood, Glenn K, Eom, Hyeonsang, and Sung, Hanul
- Subjects
Distributed Computing and Systems Software ,Information and Computing Sciences ,Resource management ,Supercomputers ,Memory management ,Hardware ,File systems ,Engines ,Writing ,Storage automation ,Publishing ,Burst buffer ,checkpoint ,demotion ,over-subscription ,parallel file system ,restart ,Engineering ,Technology ,Information and computing sciences - Abstract
Burst Buffer is widely used in supercomputer centers to bridge the performance gap between computational power and the high-performance I/O systems. The primary role of Burst Buffer is to temporarily absorb the bursty I/O and reduce the heavy access on Parallel File System (PFS). However, the job resource manager on High-Performance Computer (HPC) systems prefers to use a dedicated Burst Buffer allocation approach, which eventually leads to the severely underutilized Burst Buffer resource. To improve the efficiency of using the expensive Burst Buffer resource, we analyze the I/O patterns on Burst Buffer in depth. We propose Burst Buffer over-subscription allocation method, which improves Burst Buffer utilization by allowing each job to access Burst Buffer only during its I/O phases so that the jobs can overlap each other. Furthermore, we develop a new I/O congestion-Aware scheduler and a transparent data management system between Burst Buffer and PFS. Our approach also reduces the memory overhead and improves the data persistence of the data management system by adapting the persistent memory. With the proposed approach, not only the Burst Buffer utilization can be improved, but also HPC applications can achieve high I/O performance by exploiting the powerful Burst Buffer hardware capabilities. Experimental results show that BBOS can improve Burst Buffer utilization by up to 120% while more stable and higher checkpoint performance is guaranteed even under high I/O loads compared to other state-of-The-Art schedulers. Besides, our approach can improve the hit ratio of restart requests by up to 96.4% and provides up to 210% higher restart throughput on Burst Buffer.
- Published
- 2023
5. A Taxonomy of Error Sources in HPC I/O Machine Learning Models
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Isakov, Mihailo, Currier, Mikaela, del Rosario, Eliakin, Madireddy, Sandeep, Balaprakash, Prasanna, Carns, Philip, Ross, Robert B., Lockwood, Glenn K., and Kinsy, Michel A.
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Computer Science - Distributed, Parallel, and Cluster Computing ,Computer Science - Performance - Abstract
I/O efficiency is crucial to productivity in scientific computing, but the increasing complexity of the system and the applications makes it difficult for practitioners to understand and optimize I/O behavior at scale. Data-driven machine learning-based I/O throughput models offer a solution: they can be used to identify bottlenecks, automate I/O tuning, or optimize job scheduling with minimal human intervention. Unfortunately, current state-of-the-art I/O models are not robust enough for production use and underperform after being deployed. We analyze multiple years of application, scheduler, and storage system logs on two leadership-class HPC platforms to understand why I/O models underperform in practice. We propose a taxonomy consisting of five categories of I/O modeling errors: poor application and system modeling, inadequate dataset coverage, I/O contention, and I/O noise. We develop litmus tests to quantify each category, allowing researchers to narrow down failure modes, enhance I/O throughput models, and improve future generations of HPC logging and analysis tools.
- Published
- 2022
6. Eliciting the aboveground physiological regulation that underlies salinity tolerance in faba bean (Vicia faba L.)
- Author
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Tavakkoli, Ehsan, Watts-Williams, Stephanie J., Rengasamy, Pichu, and McDonald, Glenn K.
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- 2024
- Full Text
- View/download PDF
7. Should individuals with unilateral transtibial amputation carry a load on their intact or prosthetic side?
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Ardianuari, Satria, Cyr, Krista M., Neptune, Richard R., and Klute, Glenn K.
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- 2024
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8. The influence of load carriage and prosthetic foot type on individual muscle and prosthetic foot contributions to body support and propulsion
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Lefranc, Aude S., Klute, Glenn K., and Neptune, Richard R.
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- 2024
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- View/download PDF
9. Biliary complications after adult-to-adult living-donor liver transplantation: An international multicenter study of 3633 cases
- Author
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Li, Zhihao, Rammohan, Ashwin, Gunasekaran, Vasanthakumar, Hong, Suyoung, Chih-Yi Chen, Itsuko, Kim, Jongman, Hervera Marquez, Kris Ann, Hsu, Shih-Chao, Kirimker, Elvan Onur, Akamatsu, Nobuhisa, Shaked, Oren, Finotti, Michele, Yeow, Marcus, Genedy, Lara, Dutkowski, Philipp, Nadalin, Silvio, Boehnert, Markus U., Polak, Wojciech G., Bonney, Glenn K., Mathur, Abhishek, Samstein, Benjamin, Emond, Jean C., Testa, Giuliano, Olthoff, Kim M., Rosen, Charles B., Heimbach, Julie K., Taner, Timucin, Wong, Tiffany CL., Lo, Chung-Mau, Hasegawa, Kiyoshi, Balci, Deniz, Cattral, Mark, Sapisochin, Gonzalo, Selzner, Nazia, Jeng, Long-Bin, Broering, Dieter, Joh, Jae-Won, Chen, Chao-Long, Suh, Kyung-Suk, Rela, Mohamed, and Clavien, Pierre-Alain
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- 2024
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10. Assessment of aerosol persistence in ICUs via low-cost sensor network and zonal models
- Author
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Glenn, K., He, J., Rochlin, R., Teng, S., Hecker, J. G., and Novosselov, I.
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- 2023
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11. Multi-region sampling with paired sample sequencing analyses reveals sub-groups of patients with novel patient-specific dysregulation in Hepatocellular Carcinoma
- Author
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Jeon, Ah-Jung, Teo, Yue-Yang, Sekar, Karthik, Chong, Shay Lee, Wu, Lingyan, Chew, Sin-Chi, Chen, Jianbin, Kendarsari, Raden Indah, Lai, Hannah, Ling, Wen Huan, Kaya, Neslihan Arife, Lim, Jia Qi, Ramasamy, Adaikalavan, Oguz, Gokce, Chung, Alexander Yaw-Fui, Chan, Chung Yip, Cheow, Peng-Chung, Kam, Juinn Huar, Madhavan, Krishnakumar, Kow, Alfred, Ganpathi, Iyer Shridhar, Lim, Tony Kiat Hon, Leow, Wei-Qiang, Loong, Shihleone, Loh, Tracy Jiezhen, Wan, Wei Keat, Soon, Gwyneth Shook Ting, Pang, Yin Huei, Yoong, Boon Koon, Ong, Diana Bee-Lan, Lim, Jasmine, de Villa, Vanessa H., Cruz, Rouchelle D.dela, Chanwat, Rawisak, Thammasiri, Jidapa, Bonney, Glenn K., Goh, Brian K. P., Tucker-Kellogg, Greg, Foo, Roger Sik Yin, and Chow, Pierce K. H.
- Published
- 2023
- Full Text
- View/download PDF
12. Sagittal and transverse ankle angle coupling can influence prosthetic socket transverse plane moments
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Glenn K. Klute and Connor W. Mulcahy
- Subjects
prosthesis ,lower limb ,amputation ,residual limb ,torsion adapter ,transverse plane rotation adapter ,Other systems of medicine ,RZ201-999 ,Medical technology ,R855-855.5 - Abstract
IntroductionThe intact foot and ankle comprise a complex set of joints that allow rotation in multiple planes of motion. Some of these motions are coupled, meaning rotation in one plane induces motion in another. One such coupling is between the sagittal and transverse planes. For every step, plantar- and dorsi-flexion motion is coupled with external and internal rotation of the shank relative to the foot, respectively. There is no prosthetic foot available for prescription that mimics this natural coupling. The purpose of this study was to determine if a sagittal:transverse ankle angle coupling ratio exists that minimizes the peak transverse plane moment during prosthetic limb stance.MethodsA novel, torsionally active prosthesis (TAP) was used to couple sagittal and transverse plane motions using a 60-watt motor. An embedded controller generated transverse plane rotation trajectories proportional to sagittal plane ankle angles corresponding to sagittal:transverse coupling ratios of 1:0 (rigid coupling analogous to the standard-of-care), 6:1, 4:1, 3:1, and 2:1. Individuals with unilateral transtibial amputation were block randomized to walk in a straight line and in both directions around a 2 m circle at their self-selected speed with the TAP set at randomized coupling ratios. The primary outcome was the peak transverse plane moment, normalized to body mass, during prosthetic limb stance. Secondary outcomes included gait biomechanic metrics and a measure of satisfaction.ResultsEleven individuals with unilateral transtibial amputations participated in the study. The 6:1 coupling ratio resulted in reduced peak transverse plane moments in pairwise comparisons with 3:1 and 2:1 coupling ratios while walking in a straight line and with the prosthesis on the outside of the circle (p
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- 2024
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13. Racial and Ethnic Equity in Care for Hypertension and Diabetes in an Urban Indian Health Organization
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Moore, Kelly R., Schroeder, Emily B., Goodrich, Glenn K., Manson, Spero M., Malone, Allen S., Pieper, Lisa E., Son-Stone, Linda, Johnson, David, and Steiner, John F.
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- 2023
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14. Designing an all-flash Lustre file system for the 2020 NERSC Perlmutter system
- Author
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Lockwood, Glenn K, Lozinskiy, Kirill, Gerhardt, Lisa, Cheema, Ravi, Hazen, Damian, and Wright, Nicholas J
- Subjects
lustre ,architecture ,storage ,flash - Published
- 2021
15. Architecture and Performance of Perlmutter’s 35 PB ClusterStor E1000 All-Flash File System
- Author
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Lockwood, Glenn K, Chiusole, Alberto, Gerhardt, Lisa, Lozinskiy, Kirill, Paul, David, and Wright, Nicholas J
- Abstract
NERSC's newest system, Perlmutter, features a 35 PB all-flash Lustre file system built on HPE Cray ClusterStor E1000. We present its architecture, early performance figures, and performance considerations unique to this architecture. We demonstrate the performance of E1000 OSSes through low-level Lustre tests that achieve over 90% of the theoretical bandwidth of the SSDs at the OST and LNet levels. We also show end-to-end performance for both traditional dimensions of I/O performance (peak bulk-synchronous bandwidth) and non-optimal workloads endemic to production computing (small, incoherent I/Os at random offsets) and compare them to NERSC's previous system, Cori, to illustrate that Perlmutter achieves the performance of a burst buffer and the resilience of a scratch file system. Finally, we discuss performance considerations unique to all-flash Lustre and present ways in which users and HPC facilities can adjust their I/O patterns and operations to make optimal use of such architectures.
- Published
- 2021
16. Identifying Relative Changes in Social Risk Factors
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Xu, Stanley, Goodrich, Glenn K, Moore, Kelly R, Manson, Spero M, Gottlieb, Laura M, Hessler, Danielle, Schroeder, Emily B, and Steiner, John F
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Public Health ,Health Sciences ,Clinical Research ,Prevention ,Clinical Trials and Supportive Activities ,Zero Hunger ,Adolescent ,Adult ,Aged ,Cohort Studies ,Female ,Humans ,Hypertension ,Indigenous Peoples ,Male ,Middle Aged ,New Mexico ,Odds Ratio ,Prospective Studies ,Risk Factors ,Sociological Factors ,Urban Population ,social determinants of health ,cohort study ,food insecurity ,housing instability ,transportation barriers ,Public Health and Health Services ,Applied Economics ,Health Policy & Services ,Applied economics ,Health services and systems ,Policy and administration - Abstract
BackgroundIndividuals often report concurrent social risk factors such as food insecurity, unstable housing, and transportation barriers. Comparing relative changes between pairs of social risk factors may identify those that are more resistant to change.ObjectiveThe objective of this study was to develop a method to describe relative changes in pairs of social risk factors.Research designThis was a prospective cohort study.SubjectsParticipants in a randomized controlled trial of hypertension care in an Urban Indian Health Organization.MeasuresWe measured 7 social risk factors (housing, transportation, food, clothing, health care, utilities, and debts) at enrollment, 6, and 12 months among 295 participants in the trial. We hypothesized that pairwise comparisons could identify social risk factors that were less likely to change over time. We used conditional odds ratios (ORs) with 95% confidence intervals (CIs) to rank each pair.ResultsFood, clothing, health care, utilities, and debts had more changes between 0 and 6 months relative to housing (OR=2.3, 3.4, 4.7, 3.5, and 3.4, respectively; all 95% CI excluded 1.0). These same social risk factors also had more changes between baseline and 6 months relative to transportation (OR=2.8, 3.4, 4.9, 4.7, and 4.1, respectively; all 95% CI excluded 1.0). Changes in housing and transportation risk factors were comparable (OR=0.7, 95% CI: 0.4-1.4). Relative changes between 6 and 12 months were similar.ConclusionsHousing and transportation exhibited fewer relative changes than other social risk factors and might be more resistant to change. Awareness of the relationships between social risk factors can help define priorities for intervention.
- Published
- 2021
17. An empirical study of I/O separation for burst buffers in HPC systems
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Koo, Donghun, Lee, Jaehwan, Liu, Jialin, Byun, Eun-Kyu, Kwak, Jae-Hyuck, Lockwood, Glenn K, Hwang, Soonwook, Antypas, Katie, Wu, Kesheng, and Eom, Hyeonsang
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Data Management and Data Science ,Information and Computing Sciences ,Burst buffer ,Multi-streamed SSD ,I/O separation ,Stream-aware ,Evaluation ,Computer Software ,Distributed Computing ,Distributed computing and systems software - Abstract
To meet the exascale I/O requirements for the High-Performance Computing (HPC), a new I/O subsystem, Burst Buffer, based on solid state drives (SSD), has been developed. However, the diverse HPC workloads and the bursty I/O pattern cause severe data fragmentation that requires costly garbage collection (GC) and increases the number of bytes written to the SSD. To address this data fragmentation challenge, a new multi-stream feature has been developed for SSDs. In this work, we develop an I/O Separation scheme called BIOS to leverage this multi-stream feature to group the I/O streams based on the user IDs. We propose a stream-aware scheduling policy based on burst buffer pools in the workload manager, and integrate the BIOS with the workload manager to optimize the I/O separation scheme in burst buffer. We evaluate the proposed framework with a burst buffer I/O traces from Cori Supercomputer including a diverse set of applications. Experimental results show that the BIOS could improve the performance by 1.44x on average and reduce the Write Amplification Factor (WAF) by up to 1.20x. These demonstrate the potential benefits of the I/O separation scheme for solid state storage systems.
- Published
- 2021
18. Content and Performance of the MiniMUGA Genotyping Array: A New Tool To Improve Rigor and Reproducibility in Mouse Research
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Sigmon, John Sebastian, Blanchard, Matthew W, Baric, Ralph S, Bell, Timothy A, Brennan, Jennifer, Brockmann, Gudrun A, Burks, A Wesley, Calabrese, J Mauro, Caron, Kathleen M, Cheney, Richard E, Ciavatta, Dominic, Conlon, Frank, Darr, David B, Faber, James, Franklin, Craig, Gershon, Timothy R, Gralinski, Lisa, Gu, Bin, Gaines, Christiann H, Hagan, Robert S, Heimsath, Ernest G, Heise, Mark T, Hock, Pablo, Ideraabdullah, Folami, Jennette, J Charles, Kafri, Tal, Kashfeen, Anwica, Kulis, Mike, Kumar, Vivek, Linnertz, Colton, Livraghi-Butrico, Alessandra, Lloyd, KC Kent, Lutz, Cathleen, Lynch, Rachel M, Magnuson, Terry, Matsushima, Glenn K, McMullan, Rachel, Miller, Darla R, Mohlke, Karen L, Moy, Sheryl S, Murphy, Caroline EY, Najarian, Maya, O’Brien, Lori, Palmer, Abraham A, Philpot, Benjamin D, Randell, Scott H, Reinholdt, Laura, Ren, Yuyu, Rockwood, Steve, Rogala, Allison R, Saraswatula, Avani, Sassetti, Christopher M, Schisler, Jonathan C, Schoenrock, Sarah A, Shaw, Ginger D, Shorter, John R, Smith, Clare M, St. Pierre, Celine L, Tarantino, Lisa M, Threadgill, David W, Valdar, William, Vilen, Barbara J, Wardwell, Keegan, Whitmire, Jason K, Williams, Lucy, Zylka, Mark J, Ferris, Martin T, McMillan, Leonard, and de Villena, Fernando Pardo Manuel
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Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,Aetiology ,2.6 Resources and infrastructure (aetiology) ,Animals ,Female ,Genome-Wide Association Study ,Genotype ,Genotyping Techniques ,Male ,Mice ,Mice ,Inbred C57BL ,Oligonucleotide Array Sequence Analysis ,Polymorphism ,Genetic ,Reproducibility of Results ,Sex Determination Processes ,genetic QC ,genetic background ,substrains ,chromosomal sex ,genetic constructs ,diagnostic SNPs ,Developmental Biology ,Biochemistry and cell biology - Abstract
The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well-annotated genome, wealth of genetic resources, and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost-effective, informative, and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole-genome sequencing. Here, we describe the content and performance of a new iteration of the Mouse Universal Genotyping Array (MUGA), MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: (1) chromosomal sex determination, (2) discrimination between substrains from multiple commercial vendors, (3) diagnostic SNPs for popular laboratory strains, (4) detection of constructs used in genetically engineered mice, and (5) an easy-to-interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA, we genotyped 6899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays, both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived, and recombinant inbred lines. Here, we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, new markers that expand the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. We provide preliminary evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the relevant main stock. We conclude that MiniMUGA is a valuable platform for genetic QC, and an important new tool to increase the rigor and reproducibility of mouse research.
- Published
- 2020
19. A genomic enhancer signature associates with hepatocellular carcinoma prognosis
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Jeon, Ah-Jung, Anene-Nzelu, Chukwuemeka George, Teo, Yue-Yang, Chong, Shay Lee, Sekar, Karthik, Wu, Lingyan, Chew, Sin-Chi, Chen, Jianbin, Kendarsari, Raden Indah, Lai, Hannah, Ling, Wen Huan, Kaya, Neslihan Arife, Lim, Jia Qi, Chung, Alexander Yaw Fui, Cheow, Peng-Chung, Kam, Juinn Huar, Madhavan, Krishnakumar, Kow, Alfred, Ganpathi, Iyer Shridhar, Lim, Tony Kiat Hon, Leow, Wei-Qiang, Loong, Shihleone, Loh, Tracy Jiezhen, Wan, Wei Keat, Soon, Gwyneth Shook Ting, Pang, Yin Huei, Yoong, Boon Koon, Bee-Lan Ong, Diana, Lim, Jasmine, de Villa, Vanessa H., dela Cruz, Rouchelle D., Chanwat, Rawisak, Thammasiri, Jidapa, Bonney, Glenn K., Goh, Brian K.P., Foo, Roger Sik Yin, and Chow, Pierce Kah-Hoe
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- 2023
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20. UNOS Down-Staging Criteria for Liver Transplantation of Hepatocellular Carcinoma: Systematic Review and Meta-Analysis of 25 Studies
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Tan, Darren Jun Hao, Lim, Wen.Hui, Yong, Jie Ning, Ng, Cheng Han, Muthiah, Mark D., Tan, Eunice X., Xiao, Jieling, Lim, Snow Yunni, Pin Tang, Ansel Shao, Pan, Xin Hui, Kabir, Tousif, Bonney, Glenn K., Sundar, Raghav, Syn, Nicholas, Kim, Beom Kyung, Dan, Yock Young, Noureddin, Mazen, Loomba, Rohit, and Huang, Daniel Q.
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- 2023
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21. Biomechanical responses of individuals with transtibial amputation stepping on a coronally uneven and unpredictable surface
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Cyr, Krista M., Segal, Ava D., Neptune, Richard R., and Klute, Glenn K.
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- 2023
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22. BBOS: Efficient HPC Storage Management via Burst Buffer Over-Subscription
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Sung, Hanul, Bang, Jiwoo, Kim, Chungyong, Kim, Hyung-Sin, Sim, Alexander, Lockwood, Glenn K, and Eom, Hyeonsang
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Distributed Computing and Systems Software ,Information and Computing Sciences ,Burst Buffer ,PFS ,Over-subscription ,Checkpoint ,Restart ,Demotion - Abstract
To avoid access to PFS, dedicated BB allocation is preferred despite of severe BB underutilization. Recently, new all-flash HPC storage systems with integrated BB and PFS are proposed, which speed up access to PFS. For this reason, we adopt BB over-subscription allocation method by allowing HPC applications to use BB only for I/O phase for improving BB utilization. Unfortunately, BB over-subscription aggravates I/O interference and demotion overhead from BB to PFS, resulting in degraded performance. To minimize the performance degradation, we develop an I/O scheduler to prevent I/O congestion and a new transparent data management system based on checkpoint/restart characteristics of HPC applications. With the proposed approach, not only the BB utilization can be improved, but also high performance of applications is achieved. In our experiments, we find that BB utilization is improved at least 2.2x, and more stable and higher checkpoint performance is guaranteed compared to other approaches. Besides, we achieve up to 96.4% hit ratio of restart requests on BB and up to 3.1x higher restart performance than others.
- Published
- 2020
23. Multi-region sampling with paired sample sequencing analyses reveals sub-groups of patients with novel patient-specific dysregulation in Hepatocellular Carcinoma
- Author
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Ah-Jung Jeon, Yue-Yang Teo, Karthik Sekar, Shay Lee Chong, Lingyan Wu, Sin-Chi Chew, Jianbin Chen, Raden Indah Kendarsari, Hannah Lai, Wen Huan Ling, Neslihan Arife Kaya, Jia Qi Lim, Adaikalavan Ramasamy, Gokce Oguz, Alexander Yaw-Fui Chung, Chung Yip Chan, Peng-Chung Cheow, Juinn Huar Kam, Krishnakumar Madhavan, Alfred Kow, Iyer Shridhar Ganpathi, Tony Kiat Hon Lim, Wei-Qiang Leow, Shihleone Loong, Tracy Jiezhen Loh, Wei Keat Wan, Gwyneth Shook Ting Soon, Yin Huei Pang, Boon Koon Yoong, Diana Bee-Lan Ong, Jasmine Lim, Vanessa H. de Villa, Rouchelle D.dela Cruz, Rawisak Chanwat, Jidapa Thammasiri, Glenn K. Bonney, Brian K. P. Goh, Greg Tucker-Kellogg, Roger Sik Yin Foo, and Pierce K. H. Chow
- Subjects
Multi-region sampling ,Patient subgroups ,Personalized medicine ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background Conventional differential expression (DE) testing compares the grouped mean value of tumour samples to the grouped mean value of the normal samples, and may miss out dysregulated genes in small subgroup of patients. This is especially so for highly heterogeneous cancer like Hepatocellular Carcinoma (HCC). Methods Using multi-region sampled RNA-seq data of 90 patients, we performed patient-specific differential expression testing, together with the patients’ matched adjacent normal samples. Results Comparing the results from conventional DE analysis and patient-specific DE analyses, we show that the conventional DE analysis omits some genes due to high inter-individual variability present in both tumour and normal tissues. Dysregulated genes shared in small subgroup of patients were useful in stratifying patients, and presented differential prognosis. We also showed that the target genes of some of the current targeted agents used in HCC exhibited highly individualistic dysregulation pattern, which may explain the poor response rate. Discussion/conclusion Our results highlight the importance of identifying patient-specific DE genes, with its potential to provide clinically valuable insights into patient subgroups for applications in precision medicine.
- Published
- 2023
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24. Design and Implementation of Burst Buffer Over-Subscription Scheme for HPC Storage Systems
- Author
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Jiwoo Bang, Alexander Sim, Glenn K. Lockwood, Hyeonsang Eom, and Hanul Sung
- Subjects
Burst buffer ,checkpoint ,demotion ,over-subscription ,parallel file system ,restart ,Electrical engineering. Electronics. Nuclear engineering ,TK1-9971 - Abstract
Burst Buffer is widely used in supercomputer centers to bridge the performance gap between computational power and the high-performance I/O systems. The primary role of Burst Buffer is to temporarily absorb the bursty I/O and reduce the heavy access on Parallel File System (PFS). However, the job resource manager on High-Performance Computer (HPC) systems prefers to use a dedicated Burst Buffer allocation approach, which eventually leads to the severely underutilized Burst Buffer resource. To improve the efficiency of using the expensive Burst Buffer resource, we analyze the I/O patterns on Burst Buffer in depth. We propose Burst Buffer over-subscription allocation method, which improves Burst Buffer utilization by allowing each job to access Burst Buffer only during its I/O phases so that the jobs can overlap each other. Furthermore, we develop a new I/O congestion-aware scheduler and a transparent data management system between Burst Buffer and PFS. Our approach also reduces the memory overhead and improves the data persistence of the data management system by adapting the persistent memory. With the proposed approach, not only the Burst Buffer utilization can be improved, but also HPC applications can achieve high I/O performance by exploiting the powerful Burst Buffer hardware capabilities. Experimental results show that BBOS can improve Burst Buffer utilization by up to 120% while more stable and higher checkpoint performance is guaranteed even under high I/O loads compared to other state-of-the-art schedulers. Besides, our approach can improve the hit ratio of restart requests by up to 96.4% and provides up to 210% higher restart throughput on Burst Buffer.
- Published
- 2023
- Full Text
- View/download PDF
25. New species of awl-head katydids, Cestrophorus and Acanthacara , from the Andes of Ecuador (Orthoptera, Conocephalinae, Cestrophorini)
- Author
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Braun, Holger and Morris, Glenn K.
- Published
- 2022
26. The Influence of Multiple Pregnancies on Gait Asymmetry: A Case Study.
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Lefranc, Aude S., Klute, Glenn K., and Neptune, Richard R.
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GAIT in humans ,JOINT instability ,THIRD trimester of pregnancy ,POSTURAL balance ,PREGNANT women ,ACCIDENTAL falls ,DIAGNOSIS ,BODY movement ,WALKING ,SECOND trimester of pregnancy ,MULTIPLE pregnancy ,SPACE perception ,PELVIS ,GROUND reaction forces (Biomechanics) ,PREGNANCY - Abstract
Gait asymmetry is a predictor of fall risk and may contribute to increased falls during pregnancy. Previous work indicates that pregnant women experience asymmetric joint laxity and pelvic tilt during standing and asymmetric joint moments and angles during walking. How these changes translate to other measures of gait asymmetry remains unclear. Thus, the purpose of this case study was to determine the relationships between pregnancy progression, subsequent pregnancies, and gait asymmetry. Walking data were collected from an individual during 2 consecutive pregnancies during the second and third trimesters and 6 months postpartum of her first pregnancy and the first, second, and third trimesters and 6 months postpartum of her second pregnancy. Existing asymmetries in step length, anterior–posterior (AP) impulses, AP peak ground reaction forces, lateral impulses, and joint work systematically increased as her pregnancy progressed. These changes in asymmetry may be attributed to pelvic asymmetry, leading to asymmetric hip flexor and extensor length, or due to asymmetric plantar flexor strength, as suggested by her ankle work asymmetry. Relative to her first pregnancy, she had greater asymmetry in step length, step width, braking AP impulse, propulsive AP impulse, and peak braking AP ground reaction force during her second pregnancy, which may have resulted from increased joint laxity. [ABSTRACT FROM AUTHOR]
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- 2023
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27. List of contributors
- Author
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Allan, David, primary, Anderson, Donald D., additional, Arndt, Anton, additional, Arnold, John B., additional, Aubin, Patrick, additional, Barn, Ruth, additional, Behforootan, Sara, additional, Berardo-Cates, Alexander, additional, Bernasconi, Alessio, additional, Boe, David, additional, Braaksma, William, additional, Brockett, Claire, additional, Brunnquell, Christina L., additional, Bus, Sicco A., additional, Carniel, Emanuele Luigi, additional, Chatzistergos, Panagiotis, additional, Chawla, Sagar S., additional, Chockalingam, Nachiappan, additional, Chung, Christine B., additional, Conti, Matthew S., additional, Dalton, Brian H., additional, Davis, Irene S., additional, de Cesar Netto, Cesar, additional, Deland, Jonathan, additional, Donovan, Luke, additional, Eckel, Tobin, additional, Ellis, Scott J., additional, Finkenstaedt, Tim, additional, Fontanella, Chiara Giulia, additional, Freibott, Christina E., additional, Garfinkel, Jonathan H., additional, Golightly, Yvonne M., additional, Grantham, Aerie, additional, Greiner, Thomas M., additional, Greisberg, Justin K., additional, Hamill, Joseph, additional, Hannan, Marian T., additional, Hendry, Gordon, additional, Hillstrom, Howard J., additional, Hillstrom, Rajshree, additional, Hirsch, Bruce Elliot, additional, Hollander, Karsten, additional, Hurn, Sheree, additional, Iaquinto, Joseph M., additional, Kang, Gu Eon, additional, Kelly, Luke A., additional, Kiewiet, Nathan, additional, Klute, Glenn K., additional, Krzak, Joseph J., additional, Ledoux, William R., additional, Leslie, Morgan E., additional, Lintz, François, additional, Long, Jason T., additional, Lundberg, Arne, additional, Marconi, Dante, additional, Menz, Hylton B., additional, Mickle, Karen J., additional, Mifsud, Max, additional, Morgan, Oliver, additional, Naemi, Roozbeh, additional, Najafi, Bijan, additional, Natali, Arturo Nicola, additional, Norvell, Daniel C., additional, Paterson, Kade L., additional, Perez, Michael T., additional, Power, Geoffrey A., additional, Rajopadhye, Kalyani, additional, Redmond, Anthony, additional, Rombokas, Eric, additional, Rosenbaum, Dieter, additional, Russell Esposito, Elizabeth, additional, Sands, Andrew K., additional, Shawen, Scott, additional, Siriwanarangsun, Palanan, additional, Smith, Michelle D., additional, Song, Jinsup, additional, Stebbins, Julie, additional, Stone, Amanda, additional, Telfer, Scott, additional, Thorhauer, Eric, additional, Torp, Danielle, additional, Turner, Robert, additional, Wayne, Jennifer S., additional, Weir, Gillian, additional, Wilken, Jason, additional, and Woodburn, James, additional
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- 2023
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28. Prosthetic Feet
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Klute, Glenn K., primary
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- 2023
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29. Novel Benchmark for Adult-to-Adult Living-Donor Liver Transplantation. Integrating Eastern and Western Experiences
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Li, Zhihao, Rammohan, Ashwin, Gunasekaran, Vasanthakumar, Hong, Suyoung, Chen, Chih-Yi, Kim, Jongman, Hervera Marquez, Kris Ann, Hsu, Shih Chao, Kirimker, Onur, Akamatsu, Nobuhisa, Shaked, Oren, Finotti, Michele, Yeow, Marcus, Genedy, Lara, Dutkowski, Philipp, Nadalin, Silvio, Boehnert, Markus U., Polak, Wojciech G., Bonney, Glenn K., Mathur, Abhisek, Samstein, Benjamin, Emond, Jean C., Testa, Giuliano, Olthoff, Kim M., Rosen, Charles B., Heimbach, Julie K., Taner, Timucin, Wong, Tiffany CL., Lo, Chung-Mau, Hasegawa, Kiyoshi, Balci, Deniz, Cattral, Mark, Sapisochin, Gonzalo, Selzner, Nazia, Bin Jeng, Long, Broering, Dieter, Joh, Jae-Won, Chen, Chao-Long, Suk Suh, Kyung, Rela, Mohamed, and Clavien, Pierre-Alain
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- 2023
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30. A Taxonomy of Error Sources in HPC I/O Machine Learning Models.
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Mihailo Isakov, Mikaela Currier, Eliakin Del Rosario, Sandeep Madireddy, Prasanna Balaprakash, Philip H. Carns, Robert B. Ross, Glenn K. Lockwood, and Michel A. Kinsy
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- 2022
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31. Effect of an Asthma Exacerbation on Medication Adherence
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Cvietusa, Peter J., Goodrich, Glenn K., Shoup, Jo Ann, King, Diane K., and Bender, Bruce G.
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- 2023
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32. New species of awl-head katydids, Cestrophorus and Acanthacara, from the Andes of Ecuador (Orthoptera, Conocephalinae, Cestrophorini)
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Holger Braun and Glenn K. Morris
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Zoology ,QL1-991 - Abstract
The Cestrophorini are small katydids of Ecuador’s montane rainforest bearing a prominent awl-shaped fastigium verticis. They are unusual among Conocephalinae in lacking pre-tympanic ear chambers: their eardrums are exposed on their fore tibiae. There are presently two genera, Cestrophorus Redtenbacher, 1891 and Acanthacara Scudder, 1869. Awl-head habitat includes both climax forest and anthropogenically disturbed areas (e.g., pastures, roadsides) on lower slopes in the drainage of the volcanoes Aliso, Chiles and Tungurahua. At night, males perch on low vegetation and stridulate to attract females. To three extant species, we add a further seven, two in Cestrophorus and five in Acanthacara. Male calling songs were recorded and analyzed for all three Cestrophorus species and for three of the Acanthacara spp. We describe and discuss the waveforms of their sinusoid and transient sound pulses in time and frequency domains.
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- 2022
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33. Costs and Consequences of a Novel Emergency Department Sepsis Diagnostic Test: The IntelliSep Index
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Christopher S. Hollenbeak, PhD, Daniel J. Henning, MD, MPH, Glenn K. Geeting, MD, Nathan A. Ledeboer, PhD, Imran A. Faruqi, MD, Christi G. Pierce, DSc, MSHA, MBA, Christopher B. Thomas, MD, and Hollis R. O’Neal, Jr, MD, MS
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Medical emergencies. Critical care. Intensive care. First aid ,RC86-88.9 - Abstract
OBJECTIVES:. Sepsis causes 270,000 deaths and costs $38 billion annually in the United States. Most cases of sepsis present in the emergency department (ED), where rapid diagnosis remains challenging. The IntelliSep Index (ISI) is a novel diagnostic test that analyzes characteristics of WBC structure and provides a reliable early signal for sepsis. This study performs a cost-consequence analysis of the ISI relative to procalcitonin for early sepsis diagnosis in the ED. PERSPECTIVE:. U.S. healthcare system. SETTING:. Community hospital ED. METHODS:. A decision tree analysis was performed comparing ISI with procalcitonin. Model parameters included prevalence of sepsis, sensitivity and specificity of diagnostic tests (both ISI and procalcitonin), costs of hospitalization, and mortality rate stratified by diagnostic test result. Mortality and prevalence of sepsis were estimated from best available literature. Costs were estimated based on an analysis of a large, national discharge dataset, and adjusted to 2018 U.S. dollars. Outcomes included expected costs and survival. RESULTS:. Assuming a confirmed sepsis prevalence of 16.9% (adjudicated to Sepsis-3), the ISI strategy had an expected cost per patient of $3,849 and expected survival rate of 95.08%, whereas the procalcitonin strategy had an expected cost of $4,656 per patient and an expected survival of 94.98%. ISI was both less costly and more effective than procalcitonin, primarily because of fewer false-negative results. These results were robust in sensitivity analyses. CONCLUSIONS:. ISI was both less costly and more effective in preventing mortality than procalcitonin, primarily because of fewer false-negative results. The ISI may provide health systems with a higher-value diagnostic test in ED sepsis evaluation. Additional work is needed to validate these results in clinical practice.
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- 2023
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34. A genomic enhancer signature associates with hepatocellular carcinoma prognosis
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Ah-Jung Jeon, Chukwuemeka George Anene-Nzelu, Yue-Yang Teo, Shay Lee Chong, Karthik Sekar, Lingyan Wu, Sin-Chi Chew, Jianbin Chen, Raden Indah Kendarsari, Hannah Lai, Wen Huan Ling, Neslihan Arife Kaya, Jia Qi Lim, Alexander Yaw Fui Chung, Peng-Chung Cheow, Juinn Huar Kam, Krishnakumar Madhavan, Alfred Kow, Iyer Shridhar Ganpathi, Tony Kiat Hon Lim, Wei-Qiang Leow, Shihleone Loong, Tracy Jiezhen Loh, Wei Keat Wan, Gwyneth Shook Ting Soon, Yin Huei Pang, Boon Koon Yoong, Diana Bee-Lan Ong, Jasmine Lim, Vanessa H. de Villa, Rouchelle D. dela Cruz, Rawisak Chanwat, Jidapa Thammasiri, Glenn K. Bonney, Brian K.P. Goh, Roger Sik Yin Foo, and Pierce Kah-Hoe Chow
- Subjects
Epigenetics ,Multi-omics ,Hepatocellular carcinoma ,Cancer prognosis ,Personalised medicine ,Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Background & Aims: Lifestyle and environmental-related exposures are important risk factors for hepatocellular carcinoma (HCC), suggesting that epigenetic dysregulation significantly underpins HCC. We profiled 30 surgically resected tumours and the matched adjacent normal tissues to understand the aberrant epigenetic events associated with HCC. Methods: We identified tumour differential enhancers and the associated genes by analysing H3K27 acetylation (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-seq) and Hi-C/HiChIP data from the resected tumour samples of 30 patients with early-stage HCC. This epigenome dataset was analysed with previously reported genome and transcriptome data of the overlapping group of patients from the same cohort. We performed patient-specific differential expression testing using multiregion sequencing data to identify genes that undergo both enhancer and gene expression changes. Based on the genes selected, we identified two patient groups and performed a recurrence-free survival analysis. Results: We observed large-scale changes in the enhancer distribution between HCC tumours and the adjacent normal samples. Many of the gain-in-tumour enhancers showed corresponding upregulation of the associated genes and vice versa, but much of the enhancer and gene expression changes were patient-specific. A subset of the upregulated genes was activated in a subgroup of patients’ tumours. Recurrence-free survival analysis revealed that the patients with a more robust upregulation of those genes showed a worse prognosis. Conclusions: We report the genomic enhancer signature associated with differential prognosis in HCC. Findings that cohere with oncofoetal reprogramming in HCC were underpinned by genome-wide enhancer rewiring. Our results present the epigenetic changes in HCC that offer the rational selection of epigenetic-driven gene targets for therapeutic intervention or disease prognostication in HCC. Impact and Implications: Lifestyle and environmental-related exposures are the important risk factors of hepatocellular carcinoma (HCC), suggesting that tumour-associated epigenetic dysregulations may significantly underpin HCC. We profiled tumour tissues and their matched normal from 30 patients with early-stage HCC to study the dysregulated epigenetic changes associated with HCC. By also analysing the patients’ RNA-seq and clinical data, we found the signature genes – with epigenetic and transcriptomic dysregulation – associated with worse prognosis. Our findings suggest that systemic approaches are needed to consider the surrounding cellular environmental and epigenetic changes in HCC tumours.
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- 2023
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35. Understanding Data Motion in the Modern HPC Data Center
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Lockwood, Glenn K, Snyder, Shane, Byna, Suren, Carns, Philip, and Wright, Nicholas J
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Distributed Computing and Systems Software ,Information and Computing Sciences ,Clinical Research ,Affordable and Clean Energy ,data movement ,storage ,workflows - Abstract
The utilization and performance of storage, compute, and network resources within HPC data centers have been studied extensively, but much less work has gone toward characterizing how these resources are used in conjunction to solve larger scientific challenges. To address this gap, we present our work in characterizing workloads and workflows at a data-center-wide level by examining all data transfers that occurred between storage, compute, and the external network at the National Energy Research Scientific Computing Center over a three-month period in 2019. Using a simple abstract representation of data transfers, we analyze over 100 million transfer logs from Darshan, HPSS user interfaces, and Globus to quantify the load on data paths between compute, storage, and the wide-area network based on transfer direction, user, transfer tool, source, destination, and time. We show that parallel I/O from user jobs, while undeniably important, is only one of several major I/O workloads that occurs throughout the execution of scientific workflows. We also show that this approach can be used to connect anomalous data traffic to specific users and file access patterns, and we construct time-resolved user transfer traces to demonstrate that one can systematically identify coupled data motion for individual workflows.
- Published
- 2019
36. A Quantitative Approach to Architecting All-Flash Lustre File Systems
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Lockwood, Glenn K, Lozinskiy, Kirill, Gerhardt, Lisa, Cheema, Ravi, Hazen, Damian, and Wright, Nicholas J
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Information and Computing Sciences ,Architecture ,Lustre ,Flash ,Artificial Intelligence & Image Processing ,Information and computing sciences - Abstract
New experimental and AI-driven workloads are moving into the realm of extreme-scale HPC systems at the same time that high-performance flash is becoming cost-effective to deploy at scale. This confluence poses a number of new technical and economic challenges and opportunities in designing the next generation of HPC storage and I/O subsystems to achieve the right balance of bandwidth, latency, endurance, and cost. In this work, we present quantitative models that use workload data from existing, disk-based file systems to project the architectural requirements of all-flash Lustre file systems. Using data from NERSC’s Cori I/O subsystem, we then demonstrate the minimum required capacity for data, capacity for metadata and data-on-MDT, and SSD endurance for a future all-flash Lustre file system.
- Published
- 2019
37. Rational drug combination design in patient-derived avatars reveals effective inhibition of hepatocellular carcinoma with proteasome and CDK inhibitors
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Jhin Jieh Lim, Lissa Hooi, Yock Young Dan, Glenn K. Bonney, Lei Zhou, Pierce K.-H. Chow, Cheng Ean Chee, Tan Boon Toh, and Edward K.-H. Chow
- Subjects
Combination therapy ,Patient-derived xenograft ,Organoids ,Proteasome inhibitors ,CDK inhibitors ,Hepatocellular carcinoma ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background Hepatocellular carcinoma (HCC) remains difficult to treat due to limited effective treatment options. While the proteasome inhibitor bortezomib has shown promising preclinical activity in HCC, clinical trials of bortezomib showed no advantage over the standard-of-care treatment sorafenib, highlighting the need for more clinically relevant therapeutic strategies. Here, we propose that rational drug combination design and validation in patient-derived HCC avatar models such as patient-derived xenografts (PDXs) and organoids can improve proteasome inhibitor-based therapeutic efficacy and clinical potential. Methods HCC PDXs and the corresponding PDX-derived organoids (PDXOs) were generated from primary patient samples for drug screening and efficacy studies. To identify effective proteasome inhibitor-based drug combinations, we applied a hybrid experimental-computational approach, Quadratic Phenotypic Optimization Platform (QPOP) on a pool of nine drugs comprising proteasome inhibitors, kinase inhibitors and chemotherapy agents. QPOP utilizes small experimental drug response datasets to accurately identify globally optimal drug combinations. Results Preliminary drug screening highlighted the increased susceptibility of HCC PDXOs towards proteasome inhibitors. Through QPOP, the combination of second-generation proteasome inhibitor ixazomib (Ixa) and CDK inhibitor dinaciclib (Dina) was identified to be effective against HCC. In vitro and in vivo studies demonstrated the synergistic pro-apoptotic and anti-proliferative activity of Ixa + Dina against HCC PDXs and PDXOs. Furthermore, Ixa + Dina outperformed sorafenib in mitigating tumor formation in mice. Mechanistically, increased activation of JNK signaling mediates the combined anti-tumor effects of Ixa + Dina in HCC tumor cells. Conclusions Rational drug combination design in patient-derived avatars highlights the therapeutic potential of proteasome and CDK inhibitors and represents a feasible approach towards developing more clinically relevant treatment strategies for HCC.
- Published
- 2022
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38. Costs and Consequences of a Novel Emergency Department Sepsis Diagnostic Test: The IntelliSep Index
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Hollenbeak, Christopher S., Henning, Daniel J., Geeting, Glenn K., Ledeboer, Nathan A., Faruqi, Imran A., Pierce, Christi G., Thomas, Christopher B., and O’Neal, Hollis R., Jr
- Published
- 2023
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39. Acute exercise induces distinct quantitative and phenotypical T cell profiles in men with prostate cancer
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Erik D. Hanson, Samy Sakkal, Lauren C. Bates-Fraser, Shadney Que, Eunhan Cho, Guillaume Spielmann, Elif Kadife, John A. Violet, Claudio L. Battaglini, Lee Stoner, David B. Bartlett, Glenn K. McConell, and Alan Hayes
- Subjects
androgen deprivation therapy (ADT) ,exercise oncology ,exercise immunology ,conventional t cells (Tconv) ,unconventional t cells ,exercise induced immunosuppression ,Sports ,GV557-1198.995 - Abstract
BackgroundReduced testosterone levels can influence immune system function, particularly T cells. Exercise during cancer reduces treatment-related side effects and provide a stimulus to mobilize and redistribute immune cells. However, it is unclear how conventional and unconventional T cells (UTC) respond to acute exercise in prostate cancer survivors compared to healthy controls.MethodsAge-matched prostate cancer survivors on androgen deprivation therapy (ADT) and those without ADT (PCa) along with non-cancer controls (CON) completed ∼45 min of intermittent cycling with 3 min at 60% of peak power interspersed by 1.5 min of rest. Fresh, unstimulated immune cell populations and intracellular perforin were assessed before (baseline), immediately following (0 h), 2 h, and 24 h post-exercise.ResultsAt 0 h, conventional T cell counts increased by 45%–64% with no differences between groups. T cell frequency decreased by −3.5% for CD3+ and −4.5% for CD4+ cells relative to base at 0 h with CD8+ cells experiencing a delayed decrease of −4.5% at 2 h with no group differences. Compared to CON, the frequency of CD8+CD57+ cells was −18.1% lower in ADT. Despite a potential decrease in maturity, ADT increased CD8+perforin+ GMFI. CD3+Vα7.2+CD161+ counts, but not frequencies, increased by 69% post-exercise while CD3+CD56+ cell counts increased by 127% and were preferentially mobilized (+1.7%) immediately following the acute cycling bout. There were no UTC group differences. Cell counts and frequencies returned to baseline by 24 h.ConclusionFollowing acute exercise, prostate cancer survivors demonstrate normal T cell and UTC responses that were comparable to CON. Independent of exercise, ADT is associated with lower CD8+ cell maturity (CD57) and perforin frequency that suggests a less mature phenotype. However, higher perforin GMFI may attenuate these changes, with the functional implications of this yet to be determined.
- Published
- 2023
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40. Adapting to the Times: Combining Microlearning Videos and Twitter to Teach Surgical Technique
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Wakam, Glenn K., Palmon, Itai, Kulick, Alexandra A., Lark, Meghan, Sonnenday, Christopher J., and Waits, Seth A.
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- 2022
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41. Transition to Virtual Asthma Care During the COVID-19 Pandemic: An Observational Study
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Cvietusa, Peter J., Goodrich, Glenn K., Steiner, John F., Shoup, Jo Ann, King, Diane K., Ritzwoller, Debra P., Shetterly, Susan M., and Bender, Bruce G.
- Published
- 2022
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42. Rational drug combination design in patient-derived avatars reveals effective inhibition of hepatocellular carcinoma with proteasome and CDK inhibitors
- Author
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Lim, Jhin Jieh, Hooi, Lissa, Dan, Yock Young, Bonney, Glenn K., Zhou, Lei, Chow, Pierce K.-H., Chee, Cheng Ean, Toh, Tan Boon, and Chow, Edward K.-H.
- Published
- 2022
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43. Clinical translation of patient-derived tumour organoids- bottlenecks and strategies
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Foo, Malia Alexandra, You, Mingliang, Chan, Shing Leng, Sethi, Gautam, Bonney, Glenn K., Yong, Wei-Peng, Chow, Edward Kai-Hua, Fong, Eliza Li Shan, Wang, Lingzhi, and Goh, Boon-Cher
- Published
- 2022
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44. Trajectory of immune evasion and cancer progression in hepatocellular carcinoma
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Nguyen, Phuong H. D., Wasser, Martin, Tan, Chong Teik, Lim, Chun Jye, Lai, Hannah L. H., Seow, Justine Jia Wen, DasGupta, Ramanuj, Phua, Cheryl Z. J., Ma, Siming, Yang, Jicheng, Suthen, Sheena D/O, Tam, Wai Leong, Lim, Tony K. H., Yeong, Joe, Leow, Wei Qiang, Pang, Yin Huei, Soon, Gwyneth, Loh, Tracy Jiezhen, Wan, Wei Keat, Chan, Chung Yip, Cheow, Peng Chung, Toh, Han Chong, Kow, Alfred, Dan, Yock Young, Kam, Juinn Huar, Iyer, Shridhar, Madhavan, Krishnakumar, Chung, Alexander, Bonney, Glenn K., Goh, Brian K. P., Fu, Naiyang, Yu, Victor C., Zhai, Weiwei, Albani, Salvatore, Chow, Pierce K. H., and Chew, Valerie
- Published
- 2022
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45. Clinical translation of patient-derived tumour organoids- bottlenecks and strategies
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Malia Alexandra Foo, Mingliang You, Shing Leng Chan, Gautam Sethi, Glenn K. Bonney, Wei-Peng Yong, Edward Kai-Hua Chow, Eliza Li Shan Fong, Lingzhi Wang, and Boon-Cher Goh
- Subjects
Tumour ,Organoid ,Precision ,Medicine ,Three-Dimensional (3D) ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Abstract Multiple three-dimensional (3D) tumour organoid models assisted by multi-omics and Artificial Intelligence (AI) have contributed greatly to preclinical drug development and precision medicine. The intrinsic ability to maintain genetic and phenotypic heterogeneity of tumours allows for the reconciliation of shortcomings in traditional cancer models. While their utility in preclinical studies have been well established, little progress has been made in translational research and clinical trials. In this review, we identify the major bottlenecks preventing patient-derived tumour organoids (PDTOs) from being used in clinical setting. Unsuitable methods of tissue acquisition, disparities in establishment rates and a lengthy timeline are the limiting factors for use of PDTOs in clinical application. Potential strategies to overcome this include liquid biopsies via circulating tumour cells (CTCs), an automated organoid platform and optical metabolic imaging (OMI). These proposed solutions accelerate and optimize the workflow of a clinical organoid drug screening. As such, PDTOs have the potential for potential applications in clinical oncology to improve patient outcomes. If remarkable progress is made, cancer patients can finally benefit from this revolutionary technology.
- Published
- 2022
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46. Trajectory of immune evasion and cancer progression in hepatocellular carcinoma
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Phuong H. D. Nguyen, Martin Wasser, Chong Teik Tan, Chun Jye Lim, Hannah L. H. Lai, Justine Jia Wen Seow, Ramanuj DasGupta, Cheryl Z. J. Phua, Siming Ma, Jicheng Yang, Sheena D/O Suthen, Wai Leong Tam, Tony K. H. Lim, Joe Yeong, Wei Qiang Leow, Yin Huei Pang, Gwyneth Soon, Tracy Jiezhen Loh, Wei Keat Wan, Chung Yip Chan, Peng Chung Cheow, Han Chong Toh, Alfred Kow, Yock Young Dan, Juinn Huar Kam, Shridhar Iyer, Krishnakumar Madhavan, Alexander Chung, Glenn K. Bonney, Brian K. P. Goh, Naiyang Fu, Victor C. Yu, Weiwei Zhai, Salvatore Albani, Pierce K. H. Chow, and Valerie Chew
- Subjects
Science - Abstract
In order to design cancer immune therapies, it is important to understand how tumours evade the immune response that is mounted against them. Authors here analyse the distribution and properties of immune cells in hepatocellular carcinoma and describe a progressive tumour-immune co-evolution programme from early to late stage cancer.
- Published
- 2022
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47. Living donor hepatectomy in medium volume liver transplant centre has comparable outcomes to high volume centres: validation of donabedian quality assurance framework
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Yeow, Marcus Wei Xuan, Pang, Ning Q., Bonney, Glenn K., Madhavan, Krishnakumar, Kow, Wei Chieh Alfred, and Iyer, Shridhar Ganpathi
- Published
- 2022
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48. Changing Landscape of Open Offers in Liver Transplantation in the Machine Perfusion Era: Exposure, Equity, and Economics.
- Author
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Wehrle, Chase J., Gross, Abby, Fares, Sami, Kusakabe, Jiro, Calderon, Esteban, Shanmugarajah, Kumaran, Uysal, Melis, Fleischer, Christina M., Allkushi, Erlind, Schold, Jesse D., Khalil, Mazhar, Pita, Alejandro, Fujiki, Masato, Schlegel, Andrea, Miller, Charles, Hashimoto, Koji, and Wakam, Glenn K.
- Abstract
Background: Open offers (OOs) in liver transplantation (LT) result from bypassing the traditional allocation system. Little is known about the trends of OOs or the differences in donor/recipient characteristics compared to traditionally placed organs. We aim to quantify modern practices regarding OOs and understand NMP's impact, focusing on social determinants of health (SDH), cost, and graft‐associated risk. Methods: LTs from 1/1/2018 to 12/31/2023 at a single center were included. NMP was implemented on 10/1/2022. The CDC (centers for disease control)‐validated social vulnerability index (SVI) and donor risk index (DRI) were calculated. Comprehensive complications index (CCI), Clavien‐Dindo grades, patient and graft survival, and costs of transplantation were included. Results: 1162 LTs were performed; 193 (16.8%) from OOs. OOs were more common in the post‐NMP era (26.5% vs. 13.3%, p < 0.001). Pre‐NMP, patients receiving OOs had longer waitlist times (118 vs. 69 days, p < 0.001), lower MELDs (17 vs. 25 points, p < 0.001), and riskier grafts (DRI = 1.8 vs. 1.6, p = 0.004) compared to standard offers. Post‐NMP, recipients receiving OOs demonstrated no difference in waitlist time (27 vs. 20 days, p = 0.21) or graft risk (DRI = 2.03 vs. 2.23, p = 0.17). OO recipient MELD remained lower (16 vs. 22, p < 0.001). OO recipients were more socially vulnerable (SVI), pre‐NMP (0.41 vs. 0.36, p = 0.004), but less vulnerable after NMP (0.23 vs. 0.36, p = 0.019). Despite increased graft risk, pre‐NMP OO‐LTs were less expensive in the 90‐day global period ($154 939 vs. $178 970, p = 0.002) and the 180‐days pre‐/post‐LT ($208 807 vs. $228 091, p = 0.021). Cost trends remained similar with NMP. Conclusion: OOs are increasingly utilized and may be appealing due to demonstrated cost reductions even with NMP. Although most OO‐related metrics in our center remain similar before and after machine perfusion, programs should take caution that increasing use does not worsen organ access for socially vulnerable populations. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
49. Lifelong physiology of a former marathon world-record holder: the pros and cons of extreme cardiac remodeling.
- Author
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Foulkes, Stephen J., Haykowsky, Mark J., Kistler, Peter M., McConell, Glenn K., Trappe, Scott, Hargreaves, Mark, Costill, David L., and Gerche, Andre La
- Subjects
AEROBIC capacity ,CARDIAC magnetic resonance imaging ,LONG-distance runners ,CARDIAC output ,ATRIAL fibrillation ,ENDURANCE athletes ,EXERCISE tests - Abstract
In a 77-year-old former world-record-holding male marathoner (2:08:33.6), this study sought to investigate the impact of lifelong intensive endurance exercise on cardiac structure, function, and the trajectory of functional capacity (determined by maximal oxygen consumption, V̇ o
2max ) throughout the adult lifespan. As a competitive runner, our athlete (DC) reported performing up to 150–300 miles/wk of moderate-to-vigorous exercise and sustained 10–15 h/wk of endurance exercise after retirement from competition. DC underwent maximal cardiopulmonary exercise testing in 1970 (aged 27 yr), 1991 (aged 49 yr), and 2020 (aged 77 yr) to determine V̇ o2max . At his evaluation in 2020, DC also underwent comprehensive cardiac assessments including resting echocardiography, and resting and exercise cardiac magnetic resonance to quantify cardiac structure and function at rest and during peak supine exercise. DC's V̇ o2max showed minimal change from 27 yr (69.7 mL/kg/min) to 49 yr (68.1 mL/kg/min), although it eventually declined by 36% by the age of 77 yr (43.6 mL/kg/min). DC's V̇ o2max at 77 yr, was equivalent to the 50th percentile for healthy 20- to 29-yr-old males and 2.4 times the requirement for maintaining functional independence. This was partly due to marked ventricular dilatation (left-ventricular end-diastolic volume: 273 mL), which facilitates a large peak supine exercise stroke volume (200 mL) and cardiac output (22.2 L/min). However, at the age of 78 yr, DC developed palpitations and fatigue and was found to be in atrial fibrillation requiring ablation procedures to revert his heart to sinus rhythm. Overall, this life study of a world champion marathon runner exemplifies the substantial benefits and potential side effects of many decades of intense endurance exercise. NEW & NOTEWORTHY: This life study of a 77-yr-old former world champion marathon runner exemplifies the impact of lifelong high-volume endurance exercise on functional capacity (V̇ o2max equivalent to a 20- to 29-yr-old), partly due to extreme ventricular remodeling that facilitates a large cardiac output during exercise despite reduced maximal heart rate. Although it is possible that this extreme remodeling may contribute to developing atrial fibrillation, the net benefits of extreme exercise throughout this athlete's lifespan favor increased health span and expected longevity. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
50. New Challenges of Benchmarking All-Flash Storage for HPC.
- Author
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Glenn K. Lockwood, Alberto Chiusole, and Nicholas J. Wright
- Published
- 2021
- Full Text
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