bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Three Methodologies for Removal of Random‐Noise‐Induced Biases From Second‐Order Statistical Parameters of Lidar and Radar Measurements
Authors: Jandreau Jackson , Chu Xinzhao 
Published: December 2021

AbstractRandom‐noise‐induced biases are inherent issues to the accurate derivation of second‐order statistical parameters (e.g., variances, fluxes, energy densities, and power spectra) from lidar and radar measurements. We demonstrate here for the first time an altitude‐interleaved method for eliminating such biases, following the original proposals by Gardner and Chu (2020, https://doi.org/10.1364/ao.400375) who demonstrated a time‐interleaved method. Interleaving in altitude bins provides two statistically independent samples over the same time period and nearly the same altitude range, thus enabling the replacement of variances that include the noise‐induced biases with covariances that are intrinsically free of such biases. Comparing the interleaved method with previous variance subtraction (VS) and spectral proportion (SP) methods using gravity wave potential energy density calculated from Antarctic lidar data and from a forward model, this study finds the accuracy and precision of each method differing in various conditions, each with its own strengths and weakness. VS performs well in high‐SNR, yet its accuracy fails at lower‐SNR as it often yields negative values. SP is accurate and precise under high‐SNR, remaining accurate in worse conditions than VS would, yet develops a positive bias under low‐SNR. The interleaved method is accurate in all SNRs but requires a large number of samples to drive random‐noise terms in covariances toward zero and to compensate for the reduced precision due to the splitting of return signals. Therefore, selecting the proper bias removal/elimination method for actual signal and sample conditions is crucial in utilizing lidar/radar data, as neglecting this can conceal trends or overstate atmospheric variability.
Seismic Attenuation at the Equatorial Mid‐Atlantic Ridge Constrained by Local Rayleigh Wave Analysis From the PI‐LAB Experiment
Authors: Saikia Utpal , Rychert Catherine A. , Harmon Nicholas , Michael Kendall J. 
Published: December 2021

AbstractThe ocean lithosphere represents a simple realisation of the tectonic plate, offering a unique opportunity to better understand its physical and chemical properties in relationship to those of the underlying asthenosphere. While seismic velocity is frequently used to image the plate, seismic attenuation (Qμ−1) offers an important complimentary observation. We use fundamental mode Rayleigh waves from 17 local, M > 4.2 earthquakes recorded at stations located on 0–80 My old lithosphere near the equatorial Mid‐Atlantic Ridge. We determine the attenuation coefficient () for periods between 15 and 40 s and invert for 1‐D average shear wave quality factor values () and shear wave velocity (Vs). We find values of 175 ± 16 at 50 km depth, decreasing to 90 ± 15 at greater than 60 km. Comparison of our and Vs measurements to previous observations from oceanic settings shows agreement in terms of higher and Vs in the lithosphere in comparison to the asthenosphere. The observations from oceanic settings are in general agreement with the laboratory predictions for ‐Vs relationships for thermal models. However, a small amount of partial melt (1%) is required to explain several previous observations. Our result also compares favorably to previous observations of lithospheric and asthenospheric attenuation with respect to frequency. Melt is not required for the 1‐D average of our study area, consistent with previous electromagnetic and seismic imaging that suggested melt in punctuated and/or thin channel anomalies rather than over broad regions of the mantle.
Induced Magnetic Fields and Plasma Motions in the Inner Part of the Martian Magnetosphere
Authors: Dubinin E. , Fraenz M. , Modolo R. , Pätzold M. , Tellmann S. , Vaisberg O. , Shuvalov S. , Zelenyi L. , Chai L. , Wei Y. , McFadden J. , DiBraccio G. , Espley J. 
Published: December 2021

AbstractAnalysis of Mars Atmosphere and Volatile Evolution (MAVEN)/Supra‐Thermal And Thermal Ion Composition observations in the Martian upper atmosphere, bounded at higher altitudes by the shocked solar wind, shows that the draping of interplanetary magnetic field penetrates down to low altitudes (∼200−250 km) and governs dynamics of the ionosphere. The upper ionospheric plasma is driven into motion flowing around Mars similar to the shocked solar wind in the adjacent magnetosheath. Such a fluid‐like motion is accompanied by ion acceleration caused by the bending of the magnetic field, leading to ion extraction and finally to ion pickup. Extraction of ions and their acceleration produces a recoil effect of the bulk ionosphere in the opposite direction. This provides a strong asymmetry in ion dynamics in two different hemispheres, accompanied by wrapping of the magnetic field lines around Mars and respective reconnection.
Mesoscale and Submesoscale Shelf‐Ocean Exchanges Initialize an Advective Marine Heatwave
Authors: Chen Ke , Gawarkiewicz Glen , Yang Jiayan 
Published: December 2021

AbstractObservations and high‐resolution numerical modeling are used to investigate the dynamical processes related to the initiation of an advective Marine Heatwave in the Middle Atlantic Bight of the Northwest Atlantic continental shelf. Both the observations and the model identify two significant cross‐shelf intrusions in November 2016 and January 2017, with the latter inducing large‐magnitude water mass anomalies across the shelf. Model prognostic fields reveal the importance of the combination of cyclonic eddies or ringlets and upwelling‐favorable winds in producing the large‐distance cross‐shelf penetration and temperature/salinity anomalies. The cyclonic eddies in close proximity to the shelfbreak set up local along‐isobath pressure gradients and provide favorable conditions for the intensification of the shelfbreak front, both processes driving cross‐isobath intrusions of warm, salty offshore water onto the outer continental shelf. Subsequently, strong and persistent upwelling‐favorable winds drive a rapid, bottom intensified cross‐shelf penetration in January 2017 composed of the anomalous water mass off the shelfbreak. The along‐shelf settings including realistic representation of bathymetric features are essential in the characteristics of the cross‐shelf penetration. The results highlight the importance of smaller scale cyclonic eddies and the intricacy of the interplay between multiple processes to drive significant cross‐shelf events.
Ice and Supercooled Liquid Water Distributions Over the Southern Ocean Based on In Situ Observations and Climate Model Simulations
Authors: Yang Ching An , Diao Minghui , Gettelman Andrew , Zhang Kai , Sun Jian , McFarquhar Greg , Wu Wei 
Published: December 2021

AbstractThree climate models are evaluated using in situ airborne observations from the Southern Ocean Clouds, Radiation, Aerosol Transport Experimental Study (SOCRATES) campaign. The evaluation targets cloud phases, microphysical properties, thermodynamic conditions, and aerosol indirect effects from −40°C to 0°C. Compared with 580‐s averaged observations (i.e., 100 km horizontal scale), the Community Atmosphere Model version 6 (CAM6) shows the most similar result for cloud phase frequency distribution and allows more liquid‐containing clouds below −10°C compared with its predecessor—CAM5. The Energy Exascale Earth System Model (E3SM) underestimates (overestimates) ice phase frequencies below (above) −20°C. CAM6 and E3SM show liquid and ice water contents (i.e., LWC and IWC) similar to observations from −25°C to 0°C, but higher LWC and lower IWC than observations at lower temperatures. Simulated in‐cloud RH shows higher minimum values than observations, possibly restricting ice growth during sedimentation. As number concentrations of aerosols larger than 500 nm (Na500) increase, observations show increases of LWC, IWC, liquid, and ice number concentrations (Nliq, Nice). Number concentrations of aerosols larger than 100 nm (Na100) only show positive correlations with LWC and Nliq. From −20°C to 0°C, higher aerosol number concentrations are correlated with lower glaciation ratio and higher cloud fraction. From −40°C to −20°C, large aerosols show positive correlations with glaciation ratio. CAM6 shows small increases of LWC and Nliqwith Na500and Na100. E3SM shows small increases of Nicewith Na500. Overall, CAM6 and E3SM underestimate aerosol indirect effects on ice crystals and supercooled liquid droplets over the Southern Ocean.
Sex differences in neuronal systems function and behaviour: beyond a single diagnosis in autism spectrum disorders
Authors: Williams Olivia O. F. , Coppolino Madeleine , Perreault Melissa L. 
Published: December 2021

AbstractAutism spectrum disorder (ASD) is a complex neurodevelopmental disorder that is associated with functional brain alterations that underlie the expression of behaviour. Males are diagnosed up to four times more than females, and sex differences have been identified in memory, cognitive flexibility, verbal fluency, and social communication. Unfortunately, there exists a lack of information on the sex-dependent mechanisms of ASD, as well as biological markers to distinguish sex-specific symptoms in ASD. This can often result in a standardized diagnosis for individuals across the spectrum, despite significant differences in the various ASD subtypes. Alterations in neuronal connectivity and oscillatory activity, such as is observed in ASD, are highly coupled to behavioural states. Yet, despite the well-identified sexual dimorphisms that exist in ASD, these functional patterns have rarely been analyzed in the context of sex differences or symptomology. This review summarizes alterations in neuronal oscillatory function in ASD, discusses the age, region, symptom and sex-specific differences that are currently observed across the spectrum, and potential targets for regulating neuronal oscillatory activity in ASD. The need to identify sex-specific biomarkers, in order to facilitate specific diagnostic criteria and allow for more targeted therapeutic approaches for ASD will also be discussed.
Targeting of histone methyltransferase DOT1L plays a dual role in chemosensitization of retinoblastoma cells and enhances the efficacy of chemotherapy
Authors: Mao Yu , Sun Yu , Wu Zhixuan , Zheng Jingzhi , Zhang Jianing , Zeng Jiaqi , Lee Chunsik , Kim Jong Kyong 
Published: December 2021

AbstractAberrant and exclusive expression of chromatin regulators in retinoblastoma (RB) in contrast to terminally differentiated normal retina presents a unique opportunity of selective targeting for RB. However, precise roles of these chromatin regulators in RB development and their potential as therapeutic targets have not been defined thoroughly. Here, we report that targeting of disruptor of telomeric silencing 1-like (DOT1L), a histone H3K79 methyltransferase, sensitizes RB cells to chemotherapeutic drugs by impairing the DNA damage response and thereby potentiating apoptosis while it is largely inefficacious as a single-agent therapy. Moreover, we identified high mobility group AT-hook 2 (HMGA2) as a novel DOT1L target gene in RB cells and found that its aberrant expression is dependent on DOT1L. As HMGA2 depletion reduced CHK1 phosphorylation during DNA damage response and augmented the drug sensitivity in RB cells, our results suggested that DOT1L targeting has a dual role in chemosensitization of RB cells by directly interfering with the immediate involvement of DOT1L in early DNA damage response upon genotoxic insults and also by downregulating the expression of HMGA2 as a rather late effect of DOT1L inhibition. Furthermore, we provide the first preclinical evidence demonstrating that combined therapy with a DOT1L inhibitor significantly improves the therapeutic efficacy of etoposide in murine orthotopic xenografts of RB by rendering the response to etoposide more potent and stable. Taken together, these results support the therapeutic benefits of DOT1L targeting in combination with other chemotherapeutic agents in RB, with mechanistic insights into how DOT1L targeting can improve the current chemotherapy in an RB cell-selective manner.
A turquoise fluorescence lifetime-based biosensor for quantitative imaging of intracellular calcium
Authors: van der Linden Franka H. , Mahlandt Eike K. , Arts Janine J. G. , Beumer Joep , Puschhof Jens , de Man Saskia M. A. , Chertkova Anna O. , Ponsioen Bas , Clevers Hans , van Buul Jaap D. , Postma Marten , Gadella Theodorus W. J. , Goedhart Joachim 
Published: December 2021

AbstractThe most successful genetically encoded calcium indicators (GECIs) employ an intensity or ratiometric readout. Despite a large calcium-dependent change in fluorescence intensity, the quantification of calcium concentrations with GECIs is problematic, which is further complicated by the sensitivity of all GECIs to changes in the pH in the biological range. Here, we report on a sensing strategy in which a conformational change directly modifies the fluorescence quantum yield and fluorescence lifetime of a circular permutated turquoise fluorescent protein. The fluorescence lifetime is an absolute parameter that enables straightforward quantification, eliminating intensity-related artifacts. An engineering strategy that optimizes lifetime contrast led to a biosensor that shows a 3-fold change in the calcium-dependent quantum yield and a fluorescence lifetime change of 1.3 ns. We dub the biosensor Turquoise Calcium Fluorescence LIfeTime Sensor (Tq-Ca-FLITS). The response of the calcium sensor is insensitive to pH between 6.2–9. As a result, Tq-Ca-FLITS enables robust measurements of intracellular calcium concentrations by fluorescence lifetime imaging. We demonstrate quantitative imaging of calcium concentrations with the turquoise GECI in single endothelial cells and human-derived organoids.
Small molecule modulation of the Drosophila Slo channel elucidated by cryo-EM
Authors: Raisch Tobias , Brockmann Andreas , Ebbinghaus-Kintscher Ulrich , Freigang Jörg , Gutbrod Oliver , Kubicek Jan , Maertens Barbara , Hofnagel Oliver , Raunser Stefan 
Published: December 2021

AbstractSlowpoke (Slo) potassium channels display extraordinarily high conductance, are synergistically activated by a positive transmembrane potential and high intracellular Ca2+ concentrations and are important targets for insecticides and antiparasitic drugs. However, it is unknown how these compounds modulate ion translocation and whether there are insect-specific binding pockets. Here, we report structures of Drosophila Slo in the Ca2+-bound and Ca2+-free form and in complex with the fungal neurotoxin verruculogen and the anthelmintic drug emodepside. Whereas the architecture and gating mechanism of Slo channels are conserved, potential insect-specific binding pockets exist. Verruculogen inhibits K+ transport by blocking the Ca2+-induced activation signal and precludes K+ from entering the selectivity filter. Emodepside decreases the conductance by suboptimal K+ coordination and uncouples ion gating from Ca2+ and voltage sensing. Our results expand the mechanistic understanding of Slo regulation and lay the foundation for the rational design of regulators of Slo and other voltage-gated ion channels.
RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation
Authors: Poetz Fabian , Corbo Joshua , Levdansky Yevgen , Spiegelhalter Alexander , Lindner Doris , Magg Vera , Lebedeva Svetlana , Schweiggert Jörg , Schott Johanna , Valkov Eugene , Stoecklin Georg 
Published: December 2021

AbstractThe CCR4-NOT complex acts as a central player in the control of mRNA turnover and mediates accelerated mRNA degradation upon HDAC inhibition. Here, we explored acetylation-induced changes in the composition of the CCR4-NOT complex by purification of the endogenously tagged scaffold subunit NOT1 and identified RNF219 as an acetylation-regulated cofactor. We demonstrate that RNF219 is an active RING-type E3 ligase which stably associates with CCR4-NOT via NOT9 through a short linear motif (SLiM) embedded within the C-terminal low-complexity region of RNF219. By using a reconstituted six-subunit human CCR4-NOT complex, we demonstrate that RNF219 inhibits deadenylation through the direct interaction of the α-helical SLiM with the NOT9 module. Transcriptome-wide mRNA half-life measurements reveal that RNF219 attenuates global mRNA turnover in cells, with differential requirement of its RING domain. Our results establish RNF219 as an inhibitor of CCR4-NOT-mediated deadenylation, whose loss upon HDAC inhibition contributes to accelerated mRNA turnover.
A different perspective for nonphotochemical quenching in plant antenna complexes
Authors: Cignoni Edoardo , Lapillo Margherita , Cupellini Lorenzo , Acosta-Gutiérrez Silvia , Gervasio Francesco Luigi , Mennucci Benedetta 
Published: December 2021

AbstractLight-harvesting complexes of plants exert a dual function of light-harvesting (LH) and photoprotection through processes collectively called nonphotochemical quenching (NPQ). While LH processes are relatively well characterized, those involved in NPQ are less understood. Here, we characterize the quenching mechanisms of CP29, a minor LHC of plants, through the integration of two complementary enhanced-sampling techniques, dimensionality reduction schemes, electronic calculations and the analysis of cryo-EM data in the light of the predicted conformational ensemble. Our study reveals that the switch between LH and quenching state is more complex than previously thought. Several conformations of the lumenal side of the protein occur and differently affect the pigments’ relative geometries and interactions. Moreover, we show that a quenching mechanism localized on a single chlorophyll-carotenoid pair is not sufficient but many chlorophylls are simultaneously involved. In such a diffuse mechanism, short-range interactions between each carotenoid and different chlorophylls combined with a protein-mediated tuning of the carotenoid excitation energies have to be considered in addition to the commonly suggested Coulomb interactions.
Population-based estimates of breast cancer risk for carriers of pathogenic variants identified by gene-panel testing
Authors: Southey Melissa C. , Dowty James G. , Riaz Moeen , Steen Jason A. , Renault Anne-Laure , Tucker Katherine , Kirk Judy , James Paul , Winship Ingrid , Pachter Nicholas , Poplawski Nicola , Grist Scott , Park Daniel J. , Pope Bernard J. , Mahmood Khalid , Hammet Fleur , Mahmoodi Maryam , Tsimiklis Helen , Theys Derrick , Rewse Amanda , Willis Amanda , Morrow April , Speechly Catherine , Harris Rebecca , Sebra Robert , Schadt Eric , Lacaze Paul , McNeil John J. , Giles Graham G. , Milne Roger L. , Hopper John L. , Nguyen-Dumont Tú 
Published: December 2021

AbstractPopulation-based estimates of breast cancer risk for carriers of pathogenic variants identified by gene-panel testing are urgently required. Most prior research has been based on women selected for high-risk features and more data is needed to make inference about breast cancer risk for women unselected for family history, an important consideration of population screening. We tested 1464 women diagnosed with breast cancer and 862 age-matched controls participating in the Australian Breast Cancer Family Study (ABCFS), and 6549 healthy, older Australian women enroled in the ASPirin in Reducing Events in the Elderly (ASPREE) study for rare germline variants using a 24-gene-panel. Odds ratios (ORs) were estimated using unconditional logistic regression adjusted for age and other potential confounders. We identified pathogenic variants in 11.1% of the ABCFS cases, 3.7% of the ABCFS controls and 2.2% of the ASPREE (control) participants. The estimated breast cancer OR [95% confidence interval] was 5.3 [2.1–16.2] for BRCA1, 4.0 [1.9–9.1] for BRCA2, 3.4 [1.4–8.4] for ATM and 4.3 [1.0–17.0] for PALB2. Our findings provide a population-based perspective to gene-panel testing for breast cancer predisposition and opportunities to improve predictors for identifying women who carry pathogenic variants in breast cancer predisposition genes.
Capillary flow of liquids in open microchannels: overview and recent advances
Authors: Kolliopoulos Panayiotis , Kumar Satish 
Published: December 2021

AbstractCapillary flow is the spontaneous wicking of liquids in narrow spaces without the assistance of external forces. Examples of capillary flow can be found in numerous applications ranging from controlling and transporting fuel in spacecrafts to printed electronics manufacturing. Open rectangular microchannels often appear in these applications, with the lack of a top resulting in a complex free-surface morphology and evaporation. Here, we present a brief overview of this topic and discuss some recent advances.
Quasi-particle interference of the van Hove singularity in Sr2RuO4
Authors: Kreisel A. , Marques C. A. , Rhodes L. C. , Kong X. , Berlijn T. , Fittipaldi R. , Granata V. , Vecchione A. , Wahl P. , Hirschfeld P. J. 
Published: December 2021

AbstractThe single-layered ruthenate Sr2RuO4 is one of the most enigmatic unconventional superconductors. While for many years it was thought to be the best candidate for a chiral p-wave superconducting ground state, desirable for topological quantum computations, recent experiments suggest a singlet state, ruling out the original p-wave scenario. The superconductivity as well as the properties of the multi-layered compounds of the ruthenate perovskites are strongly influenced by a van Hove singularity in proximity of the Fermi energy. Tiny structural distortions move the van Hove singularity across the Fermi energy with dramatic consequences for the physical properties. Here, we determine the electronic structure of the van Hove singularity in the surface layer of Sr2RuO4 by quasi-particle interference imaging. We trace its dispersion and demonstrate from a model calculation accounting for the full vacuum overlap of the wave functions that its detection is facilitated through the octahedral rotations in the surface layer.
Education shapes the structure of semantic memory and impacts creative thinking
Authors: Denervaud Solange , Christensen Alexander P. , Kenett Yoed. N. , Beaty Roger E. 
Published: December 2021

AbstractEducation is central to the acquisition of knowledge, such as when children learn new concepts. It is unknown, however, whether educational differences impact not only what concepts children learn, but how those concepts come to be represented in semantic memory—a system that supports higher cognitive functions, such as creative thinking. Here we leverage computational network science tools to study hidden knowledge structures of 67 Swiss schoolchildren from two distinct educational backgrounds—Montessori and traditional, matched on socioeconomic factors and nonverbal intelligence—to examine how educational experience shape semantic memory and creative thinking. We find that children experiencing Montessori education show a more flexible semantic network structure (high connectivity/short paths between concepts, less modularity) alongside higher scores on creative thinking tests. The findings indicate that education impacts how children represent concepts in semantic memory and suggest that different educational experiences can affect higher cognitive functions, including creative thinking.