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At least 1,783 records · Page 99

Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verifi cation using targeted mass spectrometry methods.

Ellis, Matthew↗

Development of a Full-Scale Connected U-Net for Reflectivity Inpainting in Spaceborne Radar Blind Zones

CloudSat’s Cloud Profiling Radar is a valuable tool for remotely monitoring high-latitude snowfall, but its ability to observe hydrometeor activity near the Earth’s surface is limited by a radar blind zone caused by ground clutter contamination. This study presents the development of a deeply supervised U-Net-style convolutional neural network to predict cold season reflectivity profiles within the blind zone at two Arctic locations. The network learns to predict the presence and intensity of near-surface hydrometeors by coupling latent features encoded in blind zone-aloft clouds with additional context from collocated atmospheric state variables (i.e., temperature, specific humidity, and wind speed). Results show that the U-Net predictions outperform traditional linear extrapolation methods, with low mean absolute error, a 38% higher Sørensen–Dice coefficient, and vertical reflectivity distributions 60% closer to observed values. The U-Net is also able to detect the presence of near-surface cloud with a critical success index (CSI) of 72% and cases of shallow cumuliform snowfall and virga with 18% higher CSI values compared to linear methods. An explainability analysis shows that reflectivity information throughout the scene, especially at cloud edges and at the 1.2-km blind zone threshold, along with atmospheric state variables near the tropopause, are the most significant contributors to model skill. This surface-trained generative inpainting technique has the potential to enhance current and future remote sensing precipitation missions by providing a better understanding of the nonlinear relationship between blind zone reflectivity values and the surrounding atmospheric state.

54 ENVIRONMENTAL SCIENCES↗

How Would the Twenty-First-Century Warming Influence Pacific Decadal Variability and Its Connection to North American Rainfall: Assessment Based on a Revised Procedure for the IPO/PDO

Decadal climate variability of sea surface temperature (SST) over the Pacific Ocean can be characterized by interdecadal Pacific oscillation (IPO) or Pacific decadal oscillation (PDO) based on empirical orthogonal function (EOF) analysis. Although the procedures to derive the IPO and PDO indices differ in their regional focuses and filtering methods to remove interannual variability, the IPO and PDO are highly correlated in time and are often used interchangeably. Studies have shown that the IPO and PDO conjointly (IPO/PDO for conciseness) play a vital role in modulating the pace of global warming. It is less clear, however, how externally forced global warming may, in turn, affect the IPO/PDO. One obstacle to revealing this effect is that the conventional definitions of the IPO/PDO fail to account for the spatial heterogeneity of the background warming trend, which causes the IPO/PDO to be conflated with the warming trend, especially for the twenty-first-century simulation when the forced change is likely to be more dominant. Using a large-ensemble simulation in the Community Earth System Model, version 1 (CESM1), it is shown here that a better practice of detrending prior to EOF analysis is to remove the local and nonlinear trend, defined as the ensemble-mean time series at each grid box (or simply as the quadratic fit of the local time series if such an ensemble is not available). The revised IPO/PDO index is purely indicative of internal decadal variability. In the twenty-first-century warmer climate, the IPO/PDO has a weaker amplitude in space, a higher frequency in time, and a muted impact on global and North American temperature and rainfall.

54 ENVIRONMENTAL SCIENCES↗

The Amazonian Low-Level Jet and Its Connection to Convective Cloud Propagation and Evolution

In this work, we describe the existence of an Amazonian low-level jet (ALLJ) that can affect the propagation and life cycle of convective systems from the northeast coast of South America into central Amazonia. Horizontal winds from reanalysis were analyzed during March–April–May (MAM) of the two years (2014–15) of the GoAmazon2014/5 field campaign. Convective system tracking was performed using GOES-13 infrared imagery and classified into days with high and weak convective activity. The MAM average winds show a nocturnal enhancement of low-level winds starting near the coast in the early evening and reaching 1600 km inland by late morning. Mean 3-hourly wind speeds maximize at 9–10 m s -1 near 900 hPa, but individual days can have nighttime low-level winds exceeding 12 m s -1 . Based on objective low-level wind criteria, the ALLJ is present 10%–40% of the time over the Amazon during MAM depending on the location and time of day. The evolution of the ALLJ across the Amazon impacts the frequency of occurrence of cloud clusters and the intensity of the moisture flux. In addition, the ALLJ is associated with the enhancement of northeasterly flow in the midtroposphere during active convective days, when vertical momentum transport may be occurring in the organized cloud clusters. During the weakly active convective period, the ALLJ is weaker near the coast but stronger across the central Amazon and appears to be linked more directly with the South American low-level jet.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum entanglement distribution coexisting with high-rate, broadband classical optical communications over a real-world fiber connecting remote, synchronized nodes

Compatibility with existing classical network infrastructure offers a scalable path towards deploying large-scale quantum networks. Here, we demonstrate O-band polarization-encoded quantum entanglement distribution over an installed 24.4-km fiber while coexisting with a state-of-the-art fully loaded C-band classical communications line system and a picosecond-level precision L-band synchronization signal. The classical system carries two 800-Gbps channels while the remainder of the C-band is filled with amplified spontaneous emission, as is standard for such state-of-the-art communications systems. We examine the spontaneous Raman scattering spectrum generated from this broadband C-band light and offer insights into wavelength allocation for O-band quantum channels. Optimal wavelength selection and narrow filtering enable well-preserved Bell state fidelity when coexisting with 21.4-dBm aggregate launch power across the C-band suitable for 36-Tbps transmission. To the best of our knowledge, this is the first implementation of entanglement-based quantum communications between two remote nodes coexisting with independent classical communications traffic. We demonstrate coexistence of quantum entanglement with ultra-high power levels and record classical bandwidth, offering promise for real-world entanglement-based networking integrated within high-capacity communications infrastructure.

Talcott, Gina M. [Northwestern U.] (ORCID:00000002↗

A novel framework for increasing research transparency: Exploring the connection between diversity and innovation

A split sample/dual method research protocol is demonstrated to increase transparency while reducing the probability of false discovery. We apply the protocol to examine whether diversity in ownership teams increases or decreases the likelihood of a firm reporting a novel innovation using data from the 2018 United States Census Bureau’s Annual Business Survey. Transparency is increased in three ways: 1) all specification testing and identifying potentially productive models is done in an exploratory subsample that 2) preserves the validity of hypothesis test statistics fromde novoestimation in the holdout confirmatory sample with 3) all findings publicly documented in an earlier registered report and in this journal publication. Bayesian estimation procedures that leverage information from the exploratory stage included in the confirmatory stage estimation replace traditional frequentist null hypothesis significance testing. In addition to increasing statistical power by using information from the full sample, Bayesian methods directly estimate a probability distribution for the magnitude of an effect, allowing much richer inference. Estimated magnitudes of diversity along academic discipline, race, ethnicity, and foreign-born status dimensions are positively associated with innovation. A maximally diverse ownership team on these dimensions would be roughly six times more likely to report new-to-market innovation than a homophilic team.

Science & Technology - Other Topics↗

Connecting Geomechanical Properties with Potential for Proppant Embedment and Production Decline for the Emerging Caney Shale, Oklahoma

The Caney Shale is emerging as a target for hydrocarbon production, creating opportunities to study rock mechanical origins of observed/anticipated challenges to effective and sustained stimulation. Here we examine five subunits within the Caney, two of which are dubbed “ductile” and three of which are dubbed “reservoir” rock types. The “ductile” versus “reservoir” identification is initially based on elastic properties ascertained from well logs. By comparing core-based mechanical tests, it is found nominally ductile and reservoir layers do not differ in terms of brittleness, but instead the nominally ductile layers tend to be weaker and more prone to creep deformation compared to the nominally more brittle reservoir layers. This difference in mechanical properties is shown to generate higher susceptibility to proppant embedment in the weaker and more creep-prone layers. Specifically, over a 5-year period, the creep is expected to have little impact on reservoir layers but is predicted to reduce propped fracture aperture by a factor of 2 in the ductile layers.

Benge, Margaret↗

High and low dose radiation effects on mammary adenocarcinoma cells – an epigenetic connection

The successful treatment of cancer, including breast cancer, depends largely on radiation therapy and proper diagnostics. The effect of ionizing radiation on cells and tissues depends on the radiation dose and energy level, but there is insufficient evidence concerning how tumor cells respond to the low and high doses of radiation that are often used in medical diagnostic and treatment modalities. The purpose of this study was to investigate radiation-induced gene expression changes in the MCF7 breast adenocarcinoma cell line. Using microarray technology tools, we were able to screen the differential gene expressions profiles between various radiation doses applied to MCF-7 cells. Here, we report the substantial alteration in the expression level of genes after high-dose treatment. In contrast, no dramatic gene expression alterations were noticed after the application of low and medium doses of radiation. In response to a high radiation dose, MCF-7 cells exhibited down-regulation of biological pathways such as cell cycle, DNA replication, and DNA repair and activation of the p53 pathway. Similar dose-dependent responses were seen on the epigenetic level, which was tested by a microRNA expression analysis. MicroRNA analysis showed dose-dependent radiation-induced microRNA expression alterations that were associated with cell cycle arrest and cell death. An increased rate of apoptosis was determined by an Annexin V assay. The results of this study showed that high doses of radiation affect gene expression genetically and epigenetically, leading to alterations in cell cycle, DNA replication, and apoptosis.

59 BASIC BIOLOGICAL SCIENCES↗

Lattice regularization of reduced Kähler-Dirac fermions and connections to chiral fermions

We show how a path integral for reduced Kähler-Dirac fermions suffers from a phase ambiguity associated with the fermion measure that is an analog of the measure problem seen for chiral fermions. However, unlike the case of chiral symmetry, a doubler free lattice action exists which is invariant under the corresponding onsite symmetry. This allows for a clear diagnosis and solution to the problem using mirror fermions resulting in a unique gauge invariant measure. By introducing an appropriate set of Yukawa interactions which are consistent with ’t Hooft anomaly cancellation we conjecture the mirrors can be decoupled from low energy physics. Moreover, the minimal such Kähler-Dirac mirror model yields a light sector which corresponds, in the flat space continuum limit, to the Pati-Salam GUT model.

Physics↗

DIS physics at the EIC and LHeC and connections to the future LHC and $\nu$A programs

Deeply-inelastic scattering (DIS) stands to enter a golden age with the prospect of precision programs at the Electron-Ion Collider (EIC) and Large Hadron-electron Collider (LHeC). While these programs will be of considerable importance to resolving longstanding issues in (non)perturbative QCD as well as hadronic and nuclear structure, they will also have valuable implications for a wider range of physics at the Energy and Intensity Frontiers, including at the High-Luminosity LHC (HL-LHC) and future \nu A ν A facilities. In this plenary contribution, we highlight a number of salient examples of the potential HEP impact from the complementary EIC and LHeC programs drawn from their respective Yellow Report and Whitepaper. Interested readers are encouraged to consult the extensive studies and literature from which these examples are taken for more detail.

Hobbs, Timothy↗