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At least 397 records · Page 22

Smoking-related microRNAs and mRNAs in human peripheral blood mononuclear cells

Teenager smoking is of great importance in public health. Functional roles of microRNAs have been documented in smoke-induced gene expression changes, but comprehensive mechanisms of microRNA-mRNA regulation and benefits remained poorly understood. We conducted the Teenager Smoking Reduction Trial (TSRT) to investigate the causal association between active smoking reduction and whole-genome microRNA and mRNA expression changes in human peripheral blood mononuclear cells (PBMC). A total of 12 teenagers with a substantial reduction in smoke quantity and a decrease in urine cotinine/creatinine ratio were enrolled in genomic analyses. In Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA), differentially expressed genes altered by smoke reduction were mainly associated with glucocorticoid receptor signaling pathway. The integrative analysis of microRNA and mRNA found eleven differentially expressed microRNAs negatively correlated with predicted target genes. CD83 molecule regulated by miR-4498 in human PBMC, was critical for the canonical pathway of communication between innate and adaptive immune cells. Our data demonstrated that microRNAs could regulate immune responses in human PBMC after habitual smokers quit smoking and support the potential translational value of microRNAs in regulating disease-relevant gene expression caused by tobacco smoke. - Highlights: • We conducted a smoke reduction trial program and investigated the causal relationship between smoke and gene regulation. • MicroRNA and mRNA expression changes were examined in human PBMC. • MicroRNAs are important in regulating disease-causal genes after tobacco smoke reduction.

60 APPLIED LIFE SCIENCES↗

Evidence for Field-Dependent Charge Separation Caused by Mixed Phases in Polymer–Fullerene Organic Solar Cells

As organic photovoltaic performance approaches 20% efficiencies, causal structure–performance relationships must be established for devices to realize theoretical limits and become commercially competitive. Here, we reveal evidence of a causal relationship between mixed donor–acceptor interfaces and charge generation in polymer–fullerene solar cells. To do this, we combine a holistic loss analysis of device performance with quantitative synchrotron X-ray nanocharacterization to identify a >98% anticorrelation between field-dependent geminate recombination and nanodomain purity. Importantly, our analysis eliminates other possible explanations of the performance trends, a requirement to establish causality. The unprecedented granular level of our analysis also separates field-dependent and field-independent recombination at the interface, where we find for the first time that this system is free of field-independent recombination, a loss channel that plagues high-performance systems, including those with non-fullerene acceptors. Furthermore, this result broadens the case that minimizing mixed phases to promote sharp interfaces between pure aggregated domains is the ideal nanostructure for realizing theoretical efficiency limits of organic photovoltaics.

30 DIRECT ENERGY CONVERSION↗

Potential Vorticity Dynamics Explain How Extratropical Oceans and the Arctic Modulate Wintertime Land–Temperature Variations

Temperature variations across the continental northern hemisphere at the interdecadal scale are thought to be remotely modulated by oceanic internal climate variability and the Arctic. Nevertheless, further elucidating the dynamics is essential for clarifying ongoing debates. We show that potential vorticity (PV) dynamics provide a concise explanation for these teleconnections. Our findings demonstrate that extratropical oceans and the Arctic can remotely modulate the wintertime continental temperature variations by stimulating PV anomalies, which are constrained by climatological PV gradients and jet streams. A causal explanation includes anomalous temperature and precipitation over oceans and the Arctic inducing local PV anomalies via diabatic heating. Subsequently, meridional and downstream advection distributes the anomalous PV to remote land regions where the climatological PV gradients are strong, that is, involving PV fronts, as well as jet streams; therefore, PV fronts and jet streams jointly indicate land regions that are largely and frequently impacted. However, land can also modulate other regions through the same mechanism when variations over land occur in advance. Clear causality depends on which factor is independent, while interactions among those regions may convolute the causality, thereby causing further debates.

54 ENVIRONMENTAL SCIENCES↗

Testing Hidden Assumptions of Representativeness in Reach-Scale Studies of Hyporheic Exchange

Field studies of hyporheic exchange in mountain systems are often conducted using short study reaches and a limited number of observations. It is common practice to assume these study reaches represent hyporheic exchange at larger scales or different sites and to infer general relationships among potential causal mechanisms from the limited number of observations. However, these assumptions of representativeness are rarely tested. In this study, we develop numerical models from four segments of mountain streams in different geomorphologic settings and extract shorter reaches to test how representative exchange metrics are in shorter reaches compared to their reference segments. We also map the locations of the representative reaches to determine if a pattern exists based on location. Finally, we compare variance of these shorter within-site reaches to 29 additional reaches across the same basin to understand the impacts of inferring causal mechanisms, for example, the expectation that wide and narrow valley bottoms will yield different hyporheic exchange patterns. Our results show that the location and length strategy of the study reach must be considered before assuming an exchange metric to be representative of anything other than the exact segment studied. Further, it is necessary to quantify within and between site variations before making causal inferences based on observable characteristics, such as valley width or stream morphology. Our findings have implications for future field practices and how those practices are translated into models.

54 ENVIRONMENTAL SCIENCES↗

Targeted seed EMS mutagenesis reveals a basic helix–loop–helix transcription factor underlying male sterility in sorghum

Abstract Forward genetic screens of mutant populations are fundamental for functional genomics studies. However, isolating independent mutant alleles to molecularly identify causal genes is challenging in species recalcitrant to genetic manipulation. Here, we demonstrate that classic seed ethyl methanesulfonate (EMS) mutagenesis coupled with genome sequencing can overcome this limitation in sorghum. We used this method to generate new mutant alleles of sorghum MALE STERILE 8 (MS8) and identified the causal locus for the ms8 phenotype as Sobic.004G270900, which encodes the sorghum ortholog of maize bhlh122, a basic helix–loop–helix (bHLH) transcription factor required for male fertility in maize. Bulked segregant analysis mapped ms8-1 to a region on chromosome 4 containing Sobic.004G270900. Seeds from heterozygous MS8/ms8-1 plants were mutagenized and screened for chimeric inflorescences containing sectors with white, sterile anthers resembling the ms8-1 homozygous phenotype. DNA sequencing of sterile and fertile sectors from a single chimeric inflorescence revealed two mutations in Sobic.004G270900 within the sterile sector, but not the fertile sector. Isolation of this loss-of-function allele (ms8-2) established Sobic.004G270900 as the causative locus for male sterility in the ms8 mutant. We generated additional alleles of MS8 in a different genetic background using CRISPR/Cas9-based gene editing, where deletions in Sobic.004G270900 also resulted in male sterility. Our work identified a gene underlying male sterility in sorghum and provides a novel and straightforward genetic tool for researchers who lack access to advanced transformation facilities to validate gene candidates. Unlike gene editing, no prior knowledge of candidate genes is required for targeted seed EMS mutagenesis to aid identification of causal loci.

Genetics & Heredity↗

Relaxed Bell inequalities with arbitrary measurement dependence for each observer

Bell's inequality was originally derived under the assumption that experimenters are free to select detector settings independently of any local “hidden variables” that might affect the outcomes of measurements on entangled particles. This assumption has come to be known as “measurement independence” (also referred to as “freedom of choice” or “settings independence”). For a two-setting, two-outcome Bell test, we derive modified Bell inequalities that relax measurement independence, for either or both observers, while remaining locally causal. We describe the loss of measurement independence for each observer using the parameters M 1 and M 2 , as defined by Hall in 2010, and also by a more complete description that adds two new parameters, which we call M 1 ^ and M 2 ^ , deriving a modified Bell inequality for each description. These “relaxed” inequalities subsume those considered in previous work as special cases, and quantify how much the assumption of measurement independence needs to be relaxed in order for a locally causal model to produce a given violation of the standard Bell-Clauser-Horne-Shimony-Holt (Bell-CHSH) inequality. We demonstrate that both relaxed Bell inequalities are tight bounds on the CHSH parameter by constructing locally causal models that saturate them. For any given Bell inequality violation, the new two-parameter and four-parameter models each require significantly less mutual information between the hidden variables and measurement settings than previous models. We conjecture that the new models, with optimal parameters, require the minimum possible mutual information for a given Bell violation. We also argue that, contrary to various claims in the literature, relaxing freedom of choice need not imply superdeterminism.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Exploring theoretical uncertainties in the hydrodynamic description of relativistic heavy-ion collisions

We explore theoretical uncertainties in the hydrodynamic description of relativistic heavy-ion collisions by examining the full nonlinear causality conditions and quantifying the second-order transport coefficients' role on flow observables. The causality conditions impose physical constraints on the maximum allowed values of inverse Reynolds numbers during the hydrodynamic evolution. Including additional second-order gradient terms in the Denicol-Niemi-Molnár-Rischke (DNMR) theory significantly shrinks the casual regions compared to those in the Israel-Stewart hydrodynamics. For Au + Au collisions, we find the variations of flow observables are small with and without imposing the necessary causality conditions, suggesting a robust extraction of the quark-gluon plasma's transport coefficients in previous model-to-data comparisons. However, sizable sensitivity is present in small p + Au collisions, which poses challenges to study the small systems' collectivity.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Complementarity for a dynamical black hole

Black hole complementarity posits that the interior of a black hole is not independent from its Hawking radiation. This leads to an apparent violation of causality: the interior can be acausally affected by operators acting solely on the radiation. We argue that this perspective is misleading and that the black hole interior must be viewed as existing in the causal past of the Hawking radiation, despite the fact that they are spacelike separated in the semiclassical description. Consequently, no operation on the Hawking radiation—no matter how complex—can affect the experience of an infalling observer. The black hole interior and the radiation only appear spacelike separated in the semiclassical description because an infalling observer’s ability to access complex information is limited; the chaotic dynamics on the horizon, as viewed from the exterior, then converts any effect caused by such an observer to information in the Hawking radiation which cannot be accessed at the semiclassical level. We arrive at the picture described above by considering a unitary exterior description in which the flow of information is strictly causal, which we extend to apply throughout the entire history of black hole evolution, including its formation. This description uses the stretched event horizon as an inner edge of spacetime, on which the information inside is holographically encoded. We argue that the global spacetime picture arises from coarse graining over black hole microstates, and discuss its relationship with the exterior description.

79 ASTRONOMY AND ASTROPHYSICS↗

MO-G-BRE-08: Taxonomy of Corrective Actions in Radiotherapy

Purpose: Various causal taxonomies have been developed for healthcare incidents and for radiation therapy in particular. The causal analysis of incidents leads to corrective actions which can also be organized into a taxonomy. Such a corrective action classification system would provide information about the situational context, the action type, and the leverage of the action in order to detect patterns in the corrective actions frequently employed in radiation therapy. It would also provide practical guidance to the radiation therapy community for determining the appropriateness and potential effectiveness of proposed corrective actions. Materials: A review of causal analysis reports and corrective action plans was conducted using the following sources: US NRC medical event reports, IAEA reports, ROSIS submissions, US Veterans Health Administration reports, and singleincident report sources. The corrective actions presented in the published sources were then mapped onto four corrective action taxonomy prototypes: role-based, safety-context-based, responsibility-based, and hierarchy of hazard control. The resulting corrective action taxonomy was then validated through use of the published sources. Results: The responsibility-based taxonomy and hierarchy of hazard taxonomy provided more intuitive and sensible categories than the role-based taxonomy or the safety-context taxonomy. The most frequent corrective actions were added safety barriers, training, process standardization, and development of a quality improvement program where one was lacking. Conclusion: Published corrective action statements in radiation therapy emphasize what to do more so than whom the recipient is or which process step is affected. The hierarchy of hazard taxonomy provides a suitable framework for radiation therapy and has the advantage of providing insight into the likelihood that a particular corrective action will mitigate the recurrence of the error it was meant to correct. This information would be useful to medical center administration, safety personnel, and regulators who must assess the projected efficacy of corrective actions. Derek Brown is a director of TreatSafely, LLC.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Analysis of 2016 Occurrence Reports Involving Electrical Energy

The 04100 Center Director requested an analysis of 2016 occurrence reports (ORs) involving electrical energy be performed to facilitate learning through use of performance assurance methodologies. Preliminarily, 11 reportable events were identified for review; however, this population was updated to 12 during the review. Appendix 1 includes the analysis protocol and a listing of the ORs reviewed. The Team completed its review at the end of October 2016. At that time, causal analysis and associated corrective action information was available for eight events. Elements of this analysis included determining the following: common weaknesses that contributed to electrical events; the quality of causal analysis products with the goal of providing sustainable long-term corrective actions; and how learning from issues, causes, and corrective actions from prior similar events is incorporated into causal analyses for today’s events. As used in this report, the term “trends” was used as a catalyst to determine categories of events for deeper analysis. The content of ORs is important. The information in an OR for a past event can be useful in addressing today’s issues because it provides information on systemic issues that were found and past actions addressing those issues. The effectiveness of those actions as viewed from today’s vantage point is useful input to the determination of corrective actions for current problems. Additionally, as a means of communication to DOE and NNSA, ORs provide a measure of Sandia’s maturity in understanding problems and their solutions.

42 ENGINEERING↗

Holographic Space-Time and Quantum Information

The formalism of Holographic Space-time (HST) is a translation of the principles of Lorentzian geometry into the language of quantum information. Intervals along time-like trajectories, and their associated causal diamonds, completely characterize a Lorentzian geometry. The Bekenstein-Hawking-Gibbons-’t Hooft-Jacobson-Fischler-Susskind-Bousso Covariant Entropy Principle, equates the logarithm of the dimension of the Hilbert space associated with a diamond to one quarter of the area of the diamond’s holographic screen, measured in Planck units. The most convincing argument for this principle is Jacobson’s derivation of Einstein’s equations as the hydrodynamic expression of this entropy law. In that context, the null energy condition (NEC) is seen to be the analog of the local law of entropy increase. The quantum version of Einstein’s relativity principle is a set of constraints on the mutual quantum information shared by causal diamonds along different time-like trajectories. The implementation of this constraint for trajectories in relative motion is the greatest unsolved problem in HST. The other key feature of HST is its claim that, for non-negative cosmological constant or causal diamonds much smaller than the asymptotic radius of curvature for negative c.c., the degrees of freedom localized in the bulk of a diamond are constrained states of variables defined on the holographic screen. This principle gives a simple explanation of otherwise puzzling features of BH entropy formulae, and resolves the firewall problem for black holes in Minkowski space. It motivates a covariant version of the CKN [1] bound on the regime of validity of quantum field theory (QFT) and a detailed picture of the way in which QFT emerges as an approximation to the exact theory

tensor network↗

Efficiently Computable Limits on EPR Pair Generation in Quantum Broadcast Channels

We investigate the generation of EPR pairs between three observers in a general causally structured setting, where communication occurs via a noisy quantum broadcast channel. The most general quantum codes for this setup take the form of tripartite quantum channels. Since the receivers are constrained by causal ordering, additional temporal relationships naturally emerge between the parties. These causal constraints enforce intrinsic no-signalling conditions on any tripartite operation, ensuring that it constitutes a physically realizable quantum code for a quantum broadcast channel. We analyze these constraints and, more broadly, characterize the most general quantum codes for communication over such channels. We examine the capabilities of codes that are fully no-signalling among the three parties, positive partial transpose (PPT)-preserving, or both, and derive simple semidefinite programs to compute the achievable entanglement fidelity. We then establish a hierarchy of semidefinite programming converse bounds -- both weak and strong -- for the capacity of quantum broadcast channels for EPR pair generation, in both one-shot and asymptotic regimes. Notably, in the special case of a point-to-point channel, our strong converse bound recovers and strengthens existing results. Finally, we demonstrate how the PPT-preserving codes we develop can be leveraged to construct PPT-preserving entanglement combing schemes, and vice versa.

FOS: Physical sciences↗

Opportunistic experiments to constrain aerosol effective radiative forcing

Aerosol–cloud interactions (ACIs) are considered to be the most uncertain driver of present-day radiative forcing due to human activities. The nonlinearity of cloud-state changes to aerosol perturbations make it challenging to attribute causality in observed relationships of aerosol radiative forcing. Using correlations to infer causality can be challenging when meteorological variability also drives both aerosol and cloud changes independently. Natural and anthropogenic aerosol perturbations from well-defined sources provide “opportunistic experiments” (also known as natural experiments) to investigate ACI in cases where causality may be more confidently inferred. These perturbations cover a wide range of locations and spatiotemporal scales, including point sources such as volcanic eruptions or industrial sources, plumes from biomass burning or forest fires, and tracks from individual ships or shipping corridors. We review the different experimental conditions and conduct a synthesis of the available satellite datasets and field campaigns to place these opportunistic experiments on a common footing, facilitating new insights and a clearer understanding of key uncertainties in aerosol radiative forcing. Cloud albedo perturbations are strongly sensitive to background meteorological conditions. Strong liquid water path increases due to aerosol perturbations are largely ruled out by averaging across experiments. Opportunistic experiments have significantly improved process-level understanding of ACI, but it remains unclear how reliably the relationships found can be scaled to the global level, thus demonstrating a need for deeper investigation in order to improve assessments of aerosol radiative forcing and climate change.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nonlinear plants, factorizations and stable feedback systems

For nonlinear plants represented by causal maps defined over extended spaces, right factorization and normalized right-coprime factorization concepts are discussed in terms of well-posed stable feedback systems. This setup covers continuous-time, discrete-time, time-invariant or time-varying input-output maps. The nonlinear maps are factored in terms of causal bounded-input bounded-output stable maps. In factored form, all instabilities of the original map are represented by the inverse of a causal stable `denominator' map. The existence of maps with right factorizations and normalized right-coprime factorizations is shown using a well-posed stable unity-feedback system. In the case where one of the subsystems has a normalized right-coprime factorization, the stability of the feedback system is equivalent to the stability of the pseudostate map.

Desoer, Charles A.↗

Predictions of Substorms and Intensifications Following Northward Turnings of the IMF

Substorms are often observed to occur at the end of intervals of Southward interplanetary magnetic field (IMF), i.e. following the northward turning. Despite the significant correlation between northward turning and substorms, no direct causal relationship between northward turnings and substorms has been demonstrated. Assuming such a causal relationship, we predict that substorms will occur within a particular interval following the observation of a northward turning in the IMF. We observe 16 northward turnings following steady, southward IMF in data taken by the WIND spacecraft magnetic field instrument (MFI). To ensure that the northward turning was observed at the magnetosphere, we require that the northward turning also be observed by instruments on either one of Geotail or IMP-8 while the separation of the second spacecraft from WIND was more that 10 R(sub E). These two-spacecraft observations also allow us to predict more accurately the arrival time of the northward turning at the Earth. Of the predictions substorms, 10 predictions were clearly successful to within +/- 12 min. Five predictions failed, but the failures reveal clear shortcomings in the criteria for a northward turning that we correct. The failures were caused by an increase in the absolute value of B(sub YGSM) simultaneous with the northward turning in 3 cases, and a weak southward IMF preceding the northward turning in 2 cases. The final northward turning arrived in the recovery phase of an ongoing substorm, and resulted in unusual auroral activity. The implication of the predictability of substorms following sharp northward turnings is that the postulated causal relationship between northward turnings and substorm onset exists. The effect of increases in the absolute value of B(sub YGSM) to negate the triggering ability of northward turnings suggests that the triggering mechanism involves sharp reductions in the magnetospheric convection electric field.

Blanchard, G. T.↗

The Role of Instability Waves in Predicting Jet Noise

There has been an ongoing debate about the role of linear instability waves in the prediction of jet noise. Parallel mean flow models, such as the one proposed by Lilley, usually neglect these waves because they cause the solution to become infinite. The resulting solution is then non-causal and can, therefore, be quite different from the true causal solution for the chaotic flows being considered here. The present paper solves the relevant acoustic equations for a non-parallel mean flow by using a vector Green s function approach and assuming the mean flow to be weakly non-parallel, i.e., assuming the spread rate to be small. It demonstrates that linear instability waves must be accounted for in order to construct a proper causal solution to the jet noise problem. . Recent experimental results (e.g., see Tam, Golebiowski, and Seiner,1996) show that the small angle spectra radiated by supersonic jets are quite different from those radiated at larger angles (say, at 90deg) and even exhibit dissimilar frequency scalings (i.e., they scale with Helmholtz number as opposed to Strouhal number). The present solution is (among other things )able to explain this rather puzzling experimental result.

Goldstein, M. E.↗

Development and Testing of Data Mining Algorithms for Earth Observation

The new algorithms developed under this project included a principled procedure for classification of objects, events or circumstances according to a target variable when a very large number of potential predictor variables is available but the number of cases that can be used for training a classifier is relatively small. These "high dimensional" problems require finding a minimal set of variables -called the Markov Blanket-- sufficient for predicting the value of the target variable. An algorithm, the Markov Blanket Fan Search, was developed, implemented and tested on both simulated and real data in conjunction with a graphical model classifier, which was also implemented. Another algorithm developed and implemented in TETRAD IV for time series elaborated on work by C. Granger and N. Swanson, which in turn exploited some of our earlier work. The algorithms in question learn a linear time series model from data. Given such a time series, the simultaneous residual covariances, after factoring out time dependencies, may provide information about causal processes that occur more rapidly than the time series representation allow, so called simultaneous or contemporaneous causal processes. Working with A. Monetta, a graduate student from Italy, we produced the correct statistics for estimating the contemporaneous causal structure from time series data using the TETRAD IV suite of algorithms. Two economists, David Bessler and Kevin Hoover, have independently published applications using TETRAD style algorithms to the same purpose. These implementations and algorithmic developments were separately used in two kinds of studies of climate data: Short time series of geographically proximate climate variables predicting agricultural effects in California, and longer duration climate measurements of temperature teleconnections.

Glymour, Clark↗

Opportunistic Experiments to Constrain Aerosol Effective Radiative Forcing

Aerosol-cloud interactions (ACI) are considered to be the most uncertain driver of present-day radiative forcing due to human activities. The non-linearity of cloud-state changes to aerosol perturbations make it challenging to attribute causality in observed relationships of aerosol radiative forcing. Using correlations to infer causality can be challenging when meteorological variability also drives both aerosol and cloud changes independently. Natural and anthropogenic aerosol perturbations from well defined sources provide ‘opportunistic experiments’ (also known as natural experiments) to investigate ACI in cases where causality may be more confidently inferred. These perturbations cover a wide range of locations and spatio-temporal scales, including point sources such as volcanic eruptions or industrial sources, plumes from biomass burning or forest fires, and tracks from individual ships or shipping corridors.We review the different experimental conditions and conduct a synthesis of the available satellite data sets and field campaigns to place these opportunistic experiments on a common footing, facilitating new insights and a clearer understanding of key uncertainties in aerosol radiative forcing. Cloud albedo perturbations are strongly sensitive to background meteorological conditions. Strong liquid water path increases due to aerosol perturbations are largely ruled out by averaging across experiments. Opportunistic experiments have significantly improved process-level understanding of ACI, but it remains unclear how reliably the relationships found can be scaled to the global level, thus demonstrating a need for deeper investigation in order to improve assessments of aerosol radiative forcing and climate change.

Matthew W Christensen↗