Structured analysis and modeling of complex systems

The Aircrew Evaluation Sustained Operations Performance (AESOP) facility at Brooks AFB, Texas, combines the realism of an operational environment with the control of a research laboratory. In recent studies we collected extensive data from the Airborne Warning and Control Systems (AWACS) Weapons Directors subjected to high and low workload Defensive Counter Air Scenarios. A critical and complex task in this environment involves committing a friendly fighter against a hostile fighter. Structured Analysis and Design techniques and computer modeling systems were applied to this task as tools for analyzing subject performance and workload. This technology is being transferred to the Man-Systems Division of NASA Johnson Space Center for application to complex mission related tasks, such as manipulating the Shuttle grappler arm

Identification of hepatitis C virus core protein residues critical for the interaction with the cellular DEAD-Box Helicase DDX3 and their functional relevance

Hepatitis C virus (HCV) is a single-stranded RNA virus belonging to the Flaviviridae and infects approximately 170 million people worldwide. Unlike other known RNA viruses, HCV causes a persistent infection in the majority of infected people and can lead to cirrhosis of the liver and hepatocellular carcinoma. For these reasons, HCV is rightly classified as a major human pathogen. HCV core protein is believed to form, by analogy with other members of the Flaviviridae family, the nucleocapsid of the virus. As well as this, core has been shown to modulate many cellular processes via interactions with numerous host-cell proteins. One such protein shown to interact with HCV core is the DEAD-box RNA helicase DDX3. In cells expressing either HCV core alone, or as part of the full length HCV polyprotein, DDX3 is redistributed from its normal diffuse cytoplasmic localisation to lipid droplets where it colocalises with core. The cellular function of DDX3 is still unknown although it has been suggested to be involved in processes such as splicing, translation and RNA transport. The aim of this study was to investigate the role of DDX3 in the life cycle of HCV. This was aided by the recent discovery of a fully infectious HCV genotype 2a clone (strain JFH-1), allowing previously inaccessible aspects of the virus life cycle to be studied such as particle assembly and release. A library of HCV core mutants (residues 1-59 only) was produced by error-prone PCR and subsequently expressed in bacteria and analysed for their ability to bind bacterially expressed DDX3 using a rapid, high throughput ELISA screen. Six HCV core residues, conserved throughout all genotypes, were identified as being critical for interaction with DDX3. These residues were confirmed as being critical for the interaction by transfection of mutant core (together with E1 and E2 to ensure correct processing of core) into Huh7 cells. None of the 6 mutant core proteins were able to redistribute cellular DDX3. In order to study the effects of abolishing the core-DDX3 interaction in terms of a fully infectious HCV life cycle, the 6 critical residues were individually mutated to alanine in the cell culture infectious strain JFH-1 genome. All 6 mutant JFH-1 RNAs were capable of replication and being translated. Further investigation however, suggested that replication rate of mutant JFH-1 RNA was >50-fold lower than that of wild type JFH-1 RNA replication. Mutant core proteins colocalised with the lipid droplet marker ADRP, indicating correct subcellular localisation of the viral protein. Western-immunoblot analysis of mutant cores also confirmed that core proteins of same molecular weight to that of wild type core were produced, suggesting mutant cores were correctly processed. Of the 6 mutant JFH-1 clones analysed, 5 of them were capable of secreting infectious HCV particles that could subsequently infect naïve Huh7 cells, as detected by immunofluorescence and RT-PCR. However, one mutant, in which residue 33 of core had been changed from glycine to alanine, was initially unable to produce infectious particles. Upon passaging of cells electroporated with this mutant, infectious particles were eventually produced. The production of infectious particles consistently coincided with the presence of a second mutation in the surrounding area of the originally mutated residue 33. However, JFH-1 RNA containing both the mutation at residue 33 and the second identified mutation nearby, was unable to produce infectious particles upon electroporation, suggesting another lesion elsewhere in the HCV genome may also be required in order to overcome the effect of mutating residue 33. A recent report has indicated that DDX3 may be a nucleo-cytoplasmic shuttling protein, utilising the CRM1 export pathway. To confirm this, DDX3 localisation was analysed in the presence of the CRM1 inhibitor leptomycin B (LMB). In the absence of LMB, DDX3 was seen to have a diffuse cytoplasmic localisation while a small proportion was also seen in the nucleus. In the presence of LMB however, a build-up of DDX3 was seen in the nucleus, confirming that DDX3 uses the CRM1 pathway to shuttle from the nucleus to the cytoplasm. The results of this study indicate that the interaction of the cellular DEAD-box helicase DDX3 with core protein is not essential for the life cycle of HCV. It has been shown here however, that the replication rates of mutant HCV RNA are lower than that of wild type, suggesting that DDX3 may enhance either replication itself, or translation (which in turn provides the machinery required for viral RNA replication). Investigating this possibility is the subject of our future work. The identification of glycine 33 of core protein as being essential for production of infectious virus particles (without abolishing replication) will provide the basis for further studies on the production of infectious particles and the role that core protein plays in this process. The panel of JFH-1 core mutants will also be useful in studying the core-DDX3 interaction in a much wider context involving the role of DDX3 in normal cells. This study has uncovered important details regarding the interaction between core and DDX3 and, together with the reagents produced throughout this investigation, should enable further successful study into the role of DDX3 in the life cycle of HCV

Quantitative EEG as a Prognostic Tool in Suspected Anti-N-Methyl-D-Aspartate Receptor Antibody Encephalitis

PURPOSE: Anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis is a form of autoimmune encephalitis associated with EEG abnormalities. In view of the potentially severe outcomes, there is a need to develop prognostic tools to inform clinical management. The authors explored whether quantitative EEG was able to predict outcomes in patients with suspected anti-NMDAR encephalitis. METHODS: A retrospective, observational study was conducted of patients admitted to a tertiary clinical neuroscience center with suspected anti-NMDAR encephalitis. Peak power and peak frequency within delta (<4 Hz), theta (4-8 Hz), alpha (8 - 13 Hz), and beta (13-30 Hz) frequency bands were calculated for the first clinical EEG recording. Outcome was based on the modified Rankin Scale (mRS) score at 1 year after hospital discharge. Binomial logistic regression using backward elimination was performed with peak frequency and power, anti-NMDAR Encephalitis One-Year Functional Status score, age, and interval from symptom onset to EEG entered as predictors. RESULTS: Twenty patients were included (mean age 48.6 years, 70% female), of which 7 (35%) had a poor clinical outcome (mRS 2-6) at 1 year. There was no association between reported EEG abnormalities and outcome. The final logistic regression model was significant (χ2(1) = 6.35, P < 0.012) with peak frequency in the delta range (<4 Hz) the only retained predictor. The model explained 38% of the variance (Nagelkerke R2) and correctly classified 85% of cases. Higher peak frequency in the delta range was significantly associated (P = 0.04) with an increased likelihood of poor outcome. CONCLUSIONS: In this exploratory study, it was found that quantitative EEG on routinely collected EEG recordings in patients with suspected anti-NMDAR encephalitis was feasible. A higher peak frequency within the delta range was associated with poorer clinical outcome and may indicate anti-NMDAR-mediated synaptic dysfunction. Quantitative EEG may have clinical utility in predicting outcomes in patients with suspected NMDAR antibody encephalitis, thereby serving as a useful adjunct to qualitative EEG assessment; however, given the small sample size, replication in a larger scale is indicated

Embryonic Lethality, Liver Degeneration, and Impaired NF-κB Activation in IKK-β-Deficient Mice

AbstractIκB kinase-α and -β (IKK-α and IKK-β), the catalytic subunits of the IKK complex, phosphorylate IκB proteins on specific serine residues, thus targeting IκB for degradation and activating the transcription factor NF-κB. To elucidate the in vivo function of IKK-β, we generated IKK-β-deficient mice. The homozygous mouse embryo dies at ∼14.5 days of gestation due to liver degeneration and apoptosis. IKK-β-deficient embryonic fibroblasts have both reduced basal NF-κB activity and impaired cytokine-induced NF-κB activation. Similarly, basal and cytokine-inducible kinase activities of the IKK complex are greatly reduced in IKK-β-deficient cells. These results indicate that IKK-β is crucial for liver development and regulation of NF-κB activity and that IKK-α can only partially compensate for the loss of IKK-β

Physical principles for scalable neural recording

Simultaneously measuring the activities of all neurons in a mammalian brain at millisecond resolution is a challenge beyond the limits of existing techniques in neuroscience. Entirely new approaches may be required, motivating an analysis of the fundamental physical constraints on the problem. We outline the physical principles governing brain activity mapping using optical, electrical, magnetic resonance, and molecular modalities of neural recording. Focusing on the mouse brain, we analyze the scalability of each method, concentrating on the limitations imposed by spatiotemporal resolution, energy dissipation, and volume displacement. Based on this analysis, all existing approaches require orders of magnitude improvement in key parameters. Electrical recording is limited by the low multiplexing capacity of electrodes and their lack of intrinsic spatial resolution, optical methods are constrained by the scattering of visible light in brain tissue, magnetic resonance is hindered by the diffusion and relaxation timescales of water protons, and the implementation of molecular recording is complicated by the stochastic kinetics of enzymes. Understanding the physical limits of brain activity mapping may provide insight into opportunities for novel solutions. For example, unconventional methods for delivering electrodes may enable unprecedented numbers of recording sites, embedded optical devices could allow optical detectors to be placed within a few scattering lengths of the measured neurons, and new classes of molecularly engineered sensors might obviate cumbersome hardware architectures. We also study the physics of powering and communicating with microscale devices embedded in brain tissue and find that, while radio-frequency electromagnetic data transmission suffers from a severe power–bandwidth tradeoff, communication via infrared light or ultrasound may allow high data rates due to the possibility of spatial multiplexing. The use of embedded local recording and wireless data transmission would only be viable, however, given major improvements to the power efficiency of microelectronic devices

Quantum state preparation and macroscopic entanglement in gravitational-wave detectors

Long-baseline laser-interferometer gravitational-wave detectors are operating at a factor of 10 (in amplitude) above the standard quantum limit (SQL) within a broad frequency band. Such a low classical noise budget has already allowed the creation of a controlled 2.7 kg macroscopic oscillator with an effective eigenfrequency of 150 Hz and an occupation number of 200. This result, along with the prospect for further improvements, heralds the new possibility of experimentally probing macroscopic quantum mechanics (MQM) - quantum mechanical behavior of objects in the realm of everyday experience - using gravitational-wave detectors. In this paper, we provide the mathematical foundation for the first step of a MQM experiment: the preparation of a macroscopic test mass into a nearly minimum-Heisenberg-limited Gaussian quantum state, which is possible if the interferometer's classical noise beats the SQL in a broad frequency band. Our formalism, based on Wiener filtering, allows a straightforward conversion from the classical noise budget of a laser interferometer, in terms of noise spectra, into the strategy for quantum state preparation, and the quality of the prepared state. Using this formalism, we consider how Gaussian entanglement can be built among two macroscopic test masses, and the performance of the planned Advanced LIGO interferometers in quantum-state preparation

Searching for a Stochastic Background of Gravitational Waves with LIGO

The Laser Interferometer Gravitational-wave Observatory (LIGO) has performed the fourth science run, S4, with significantly improved interferometer sensitivities with respect to previous runs. Using data acquired during this science run, we place a limit on the amplitude of a stochastic background of gravitational waves. For a frequency independent spectrum, the new limit is $\Omega_{\rm GW} < 6.5 \times 10^{-5}$. This is currently the most sensitive result in the frequency range 51-150 Hz, with a factor of 13 improvement over the previous LIGO result. We discuss complementarity of the new result with other constraints on a stochastic background of gravitational waves, and we investigate implications of the new result for different models of this background.Comment: 37 pages, 16 figure

Search for gravitational wave bursts in LIGO's third science run

We report on a search for gravitational wave bursts in data from the three LIGO interferometric detectors during their third science run. The search targets subsecond bursts in the frequency range 100-1100 Hz for which no waveform model is assumed, and has a sensitivity in terms of the root-sum-square (rss) strain amplitude of hrss ~ 10^{-20} / sqrt(Hz). No gravitational wave signals were detected in the 8 days of analyzed data.Comment: 12 pages, 6 figures. Amaldi-6 conference proceedings to be published in Classical and Quantum Gravit

Revealing the progenitor of SN 2021zby through analysis of the TESSTESS shock-cooling light curve

We present early observations and analysis of the double-peaked Type IIb supernova (SN IIb) 2021zby. $TESS$ captured the prominent early shock cooling peak of SN 2021zby within the first $\sim$10 days after explosion with a 30-minute cadence. We present optical and near-infrared spectral series of SN 2021zby, including three spectra during the shock cooling phase. Using a multi-band model fit, we find that the inferred properties of its progenitor are consistent with a red supergiant or yellow supergiant, with an envelope mass of $\sim$0.3-3.0 M$_\odot$ and an envelope radius of $\sim$50-350$R_\odot$. These inferred progenitor properties are similar to those of other SNe IIb with double-peak feature, such as SNe 1993J, 2011dh, 2016gkg and 2017jgh. This study further validates the importance of the high cadence and early coverage in resolving the shape of the shock cooling light curve, while the multi-band observations, especially UV, is also necessary to fully constrain the progenitor properties.Comment: 12 pages, 5 figures, 2 tables, submitted to ApJ