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- Jin, X. J., et al.
(author)
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Functional Roles of Poly(ADP-Ribose) in Stress Granule Formation and Dynamics
- 2021
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In: Frontiers in Cell and Developmental Biology. - : Frontiers Media SA. - 2296-634X. ; 9
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Research review (peer-reviewed)abstract
- Stress granules (SGs) are highly dynamic cytoplasmic foci formed in response to stress. The formation of SGs is reported to be regulated by diverse post-translational protein modifications (PTMs). Among them, ADP-ribosylation is of emerging interest due to its recently identified roles in SG organization. In this review, we summarized the latest advances on the roles of poly(ADP-ribose) (PAR) in the regulation of SG formation and dynamics, including its function in modulating nucleocytoplasmic trafficking and SG recruitment of SG components, as well as its effects on protein phase separation behavior. Moreover, the functional role of PAR chain diversity on dynamic of SG composition is also introduced. Potential future developments on investigating global ADP-ribosylation networks, individual roles of different PARPs, and interactions between ADP-ribosylation and other PTMs in SGs are also discussed.
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- Kim, Jongyul, et al.
(author)
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LineFS: Efficient SmartNIC Offload of a Distributed File System with Pipeline Parallelism
- 2021
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In: ACM SIGOPS 28th Symposium on Operating Systems Principles. - New York, NY, USA : ACM.
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Conference paper (peer-reviewed)abstract
- In multi-tenant systems, the CPU overhead of distributed file systems (DFSes) is increasingly a burden to application performance. CPU and memory interference cause degraded and unstable application and storage performance, in particular for operation latency. Recent client-local DFSes for persistent memory (PM) accelerate this trend. DFS offload to SmartNICs is a promising solution to these problems, but it is challenging to fit the complex demands of a DFS onto simple SmartNIC processors located across PCIe.We present LineFS, a SmartNIC-offloaded, high-performance DFS with support for client-local PM. To fully leverage the SmartNIC architecture, we decompose DFS operations into execution stages that can be offloaded to a parallel datapath execution pipeline on the SmartNIC. LineFS offloads CPU-intensive DFS tasks, like replication, compression, data publication, index and consistency management to a Smart-NIC. We implement LineFS on the Mellanox BlueField Smart-NIC and compare it to Assise, a state-of-the-art PM DFS. LineFS improves latency in LevelDB up to 80% and throughput in Filebench up to 79%, while providing extended DFS availability during host system failures.
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- Akiyama, Kazunori, et al.
(author)
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First M87 Event Horizon Telescope Results. III. Data Processing and Calibration
- 2019
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In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 875:1
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Journal article (peer-reviewed)abstract
- We present the calibration and reduction of Event Horizon Telescope (EHT) 1.3 mm radio wavelength observations of the supermassive black hole candidate at the center of the radio galaxy M87 and the quasar 3C 279, taken during the 2017 April 5-11 observing campaign. These global very long baseline interferometric observations include for the first time the highly sensitive Atacama Large Millimeter/submillimeter Array (ALMA); reaching an angular resolution of 25 μas, with characteristic sensitivity limits of ∼1 mJy on baselines to ALMA and ∼10 mJy on other baselines. The observations present challenges for existing data processing tools, arising from the rapid atmospheric phase fluctuations, wide recording bandwidth, and highly heterogeneous array. In response, we developed three independent pipelines for phase calibration and fringe detection, each tailored to the specific needs of the EHT. The final data products include calibrated total intensity amplitude and phase information. They are validated through a series of quality assurance tests that show consistency across pipelines and set limits on baseline systematic errors of 2% in amplitude and 1° in phase. The M87 data reveal the presence of two nulls in correlated flux density at ∼3.4 and ∼8.3 Gλ and temporal evolution in closure quantities, indicating intrinsic variability of compact structure on a timescale of days, or several light-crossing times for a few billion solar-mass black hole. These measurements provide the first opportunity to image horizon-scale structure in M87.
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- Akiyama, Kazunori, et al.
(author)
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First M87 Event Horizon Telescope Results. IV. Imaging the Central Supermassive Black Hole
- 2019
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In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 875:1
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Journal article (peer-reviewed)abstract
- We present the first Event Horizon Telescope (EHT) images of M87, using observations from April 2017 at 1.3 mm wavelength. These images show a prominent ring with a diameter of similar to 40 mu as, consistent with the size and shape of the lensed photon orbit encircling the "shadow" of a supermassive black hole. The ring is persistent across four observing nights and shows enhanced brightness in the south. To assess the reliability of these results, we implemented a two-stage imaging procedure. In the first stage, four teams, each blind to the others' work, produced images of M87 using both an established method (CLEAN) and a newer technique (regularized maximum likelihood). This stage allowed us to avoid shared human bias and to assess common features among independent reconstructions. In the second stage, we reconstructed synthetic data from a large survey of imaging parameters and then compared the results with the corresponding ground truth images. This stage allowed us to select parameters objectively to use when reconstructing images of M87. Across all tests in both stages, the ring diameter and asymmetry remained stable, insensitive to the choice of imaging technique. We describe the EHT imaging procedures, the primary image features in M87, and the dependence of these features on imaging assumptions.
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- Farah, Haneen, et al.
(author)
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Drivers’ Decision Making of Overtaking Strategies of Cyclists on Rural Roads–A Driving Simulator Experiment
- 2019
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Conference paper (other academic/artistic)abstract
- Cyclists’ involvement in road crashes has not been improving with the same magnitude as other modes of transport. Especially, the interactions between cyclists and motorized traffic can end up with the most severe types of crashes. To improve the safety of these interactions, a thorough understanding of road users’ decisions and behaviours is first needed. In this study, the authors focus on drivers’ overtaking manoeuvres of cyclists on rural roads. The main objective of this study is to develop a model that can predict drivers’ decisions whether to perform a flying or an accelerative overtaking manoeuvre when approaching a cyclist in the presence of oncoming traffic. A driving simulator study was designed to collect trajectory data of the overtaking vehicle, cyclist, and oncoming traffic. Drivers’ characteristics data was collected using surveys. In total, 37 drivers participated, each of them performing 7 overtaking manoeuvres. Out of 259 overtaking manoeuvres, 168 were flying and 91 were accelerative. Two binary logistic regression models were developed and estimated. In the two models, the time-to-collision and the driver’s speed significantly affect the decision on the overtaking manoeuvre type. In the first model, the correlations among the observations of the same driver were captured through the drivers’ characteristics. In the second model, these correlations were captured through a driver specific error term. The overall performance is 87.7% and 94.9% for the first and second models, respectively. In the paper the authors discuss the usability of each model for policy making, system design, and system evaluation.
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- Godbolt, Alison K., et al.
(author)
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Disorders of consciousness : Preliminary data supports added value of extended behavioural assessment
- 2012
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In: Brain Injury. - : Informa UK Limited. - 0269-9052 .- 1362-301X. ; 26:2, s. 188-193
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Journal article (peer-reviewed)abstract
- Background: The use of validated behavioural assessment scales in assessment of patients with Disorders of Consciousness (DOC) is well established. However, there is little evidence to guide decisions on total time spent in behavioural assessment. Objective: To assess whether brief behavioural assessment was as effective as extended behavioural assessment in detecting non-vegetative behaviours. Methods: Consecutive patients with suspected DOC were assessed with two standardized instruments: Coma Recovery Scale Revised (CRS-R) and Sensory Modality Assessment and Rehabilitation Technique (SMART). Assessors were blinded to results from the other scale at the point of assessment. Two administrations of CRS-R together took 50-60 minutes ('brief' assessment). One complete SMART assessment took 600 minutes ('extended' assessment). Patients were classified as being in a vegetative state (VS) or minimally conscious state (MCS)/emerged from minimally conscious state (EMCS), following brief and extended assessment. Results: Ten patients were assessed. Brief and extended assessment yielded the same diagnostic category (VS or MCS) for six patients and different categories for four, with extended assessment detecting higher level behaviours. Conclusions: Brief behavioural assessment was not as effective as extended assessment in detecting non-vegetative behaviours. Total time spent in behavioural assessment is likely important. Further studies and clearer clinical guidance are needed.
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- Liu, Yingxin, et al.
(author)
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Nanoscale Assembly of Cellulose Nanocrystals during Drying and Redispersion
- 2018
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In: ACS Macro Letters. - : American Chemical Society (ACS). - 2161-1653. ; 7:2, s. 172-177
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Journal article (peer-reviewed)abstract
- We have followed the structural evolution during evaporation-induced self-assembly of sulfonated cellulose nanocrystal (CNC) in the presence of H+ and Li+ counterions by small-angle X-ray scattering. Drying of CNC-H dispersions results in ordered films that could not be readily redispersed, while the CNC-Li films were disordered and prone to reswelling and redispersion. The scaling of the separation distance (d) between CNC particles and the particle concentration (c) shows that the CNC-H dispersions display a unidimensional contraction of the nematic structure (d alpha c(-1)) during drying, while the CNC-Li dispersions consolidate isotropically (d alpha c(-1/3)), which is characteristic for hydrogels with no preferential orientation. Temporal evolution of the structure factor and complementary dynamic light-scattering measurements show that CNC-Li is more aggregated than CNC-H during evaporation-induced assembly. Insights on the structural evolution during CNC assembly and redispersion can promote development of novel and optimized processing routes of nanocellulose-based materials.
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