bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sources of Subseasonal‐To‐Seasonal Predictability of Atmospheric Rivers and Precipitation in the Western United States
Authors: Huang Huanping , Patricola Christina M. , Bercos‐Hickey Emily , Zhou Yang , Rhoades Alan , Risser Mark D. , Collins William D. 
Published: March 2021

AbstractAtmospheric rivers (ARs) account for a large portion of winter precipitation in the western US. To evaluate the sources of AR and precipitation predictability at subseasonal‐to‐seasonal timescales, we examine the relationships between two climate modes, the El Niño/Southern Oscillation (ENSO) and Madden‐Julian oscillation (MJO), and winter hydroclimate in the western US. Our analysis uses a large ensemble of the Weather Research and Forecast (WRF) model simulations from 1981 to 2017, facilitating the assessment of uncertainty in climate mode‐AR relationship due to climate variability and short length of observations. Over the North Pacific basin, we find ENSO‐related latitudinal shifts of ARs, but ENSO has little effect on basin‐wide averaged AR frequency. Over the western US, there is some uncertainty in the ENSO‐AR connection due to the impacts of ENSO indices and datasets. However, extreme El Niño events defined by the ENSO longitude index are consistently linked to increased landfalling AR activity. The MJO can lead to significantly enhanced or suppressed landfalling AR activity in the large‐ensembles, depending on the phase of MJO and time lag, while observations are too short in length to robustly show this signal. ENSO substantially modulates the MJO‐AR relationship, triggering variegated responses of landfalling ARs and AR precipitation in La Niña and El Niño years. Our findings highlight the need to evaluate concurrent effects of different climate modes on ARs and precipitation, and may shed light on a path toward more accurate subseasonal‐to‐seasonal prediction of ARs and precipitation over the western US.
Legacy Effects Following Fire on Surface Energy, Water and Carbon Fluxes in Mature Amazonian Forests
Authors: de Oliveira Gabriel , Brunsell Nathaniel A. , Chen Jing M. , Shimabukuro Yosio E. , Mataveli Guilherme A. V. , dos Santos Carlos A. C. , Stark Scott C. , de Lima Andre , Aragao Luiz E. O. C. 
Published: March 2021

AbstractThe ongoing deforestation process in Amazonia has led to intensified forest fires in the region, particularly in Brazil, after more than a decade of effective forest conservation policy. This study aims to investigate the recovery of two mature sub‐montane ombrophile Amazonian forests affected by fire in terms of energy, water and carbon fluxes utilizing remote sensing (MODIS) and climate reanalysis data (GLDAS). These two forest plots, mainly composed of Manilkara spp. (Maçaranduba), Protium spp. (Breu) (∼30 m), Bertholletia excelsa (Castanheira) and Dinizia excelsa Ducke (Angelim‐Pedra) (∼50 m), occupy areas of 100.5 and 122.1 km2 and were subject to fire on the same day, on September 12, 2010. The fire significantly increased land surface temperature (0.8°C) and air temperature (1.2°C) in the forests over a 3 years interval. However, the forests showed an ability to recover their original states in terms of coupling between the carbon and water cycles comparing the 3‐year periods before and after the fires. Results from a wavelet analysis showed an intensification in annual and seasonal fluctuations, and in some cases (e.g., daily net radiation and evapotrasnspiration) sub‐annual fluctuation. We interpreted these changes to be consistent with overall intensification of the coupling of energy balance components and drivers imposed by climate and solar cycle seasonality, as well as faster time scale changes, consistent with a shift toward greater forest openness and consequent reduction in the interception of incoming solar radiation by the canopy.
A Framework for Modeling Rock Glaciers and Permafrost at the Basin‐Scale in High Alpine Catchments
Authors: Pruessner L. , Huss M. , Phillips M. , Farinotti D. 
Published: March 2021

AbstractSince rock glaciers are believed to be more resilient to climate change, water stores therein may become important water reservoirs in future, in particular in dry regions, which currently rely on glacial runoff. In order to estimate and evaluate the future runoff potential from permafrost and rock glaciers, distributed runoff models suitable for high Alpine catchments are needed. An extension to the distributed Glacier Evolution and Runoff Model (GERM) to include permafrost and rock glaciers in Alpine catchments is presented here, and compared to the established one dimensional (1D) physics‐based model SNOWPACK. The new permafrost component introduced to GERM treats permafrost as discreet depth layers in a 1D column for all grid cells, which have bulk thermal properties calculated from their constituents (ice, water, air, and solid component). The temperature evolution is computed using heat conduction and latent heat exchanges, modified by ventilation effects. Finally, we infer water runoff from permafrost degradation. Ground temperature variations calculated by both models are compared to borehole measurements at three Alpine sites and similar performances are found. Differences between the models are present in the amplitude of seasonal ground temperature variations, with SNOWPACK having a tendency to slightly overestimate them, while GERM underestimates them.
Prediction of Dynamic Plasmapause Location Using a Neural Network
Authors: Guo Deyu , Fu Song , Xiang Zheng , Ni Binbin , Guo Yingjie , Feng Minghang , Guo Jianguang , Hu Zejun , Gu Xudong , Zhu Jianan , Cao Xing , Wang Qi 
Published: March 2021

AbstractAs a common boundary layer that distinctly separates the regions of high‐density plasmasphere and low‐density plasmatrough, the plasmapause is essential to comprehend the dynamics and variability of the inner magnetosphere. Using the machine learning framework PyTorch and high‐quality Van Allen Probes data set, we develop a neural network model to predict the global dynamic variation of the plasmapause location, along with the identification of 6,537 plasmapause crossing events during the period from 2012 to 2017. To avoid the overfitting and optimize the model generalization, 5,493 events during the period from September 2012 to December 2015 are adopted for division into the training set and validation set in terms of the 10‐fold cross‐validation method, and the remaining 1,044 events are used as the test set. The model parameterized by only AE or Kp index can reproduce the plasmapause locations similar to those modeled using all five considered solar wind and geomagnetic parameters. Model evaluation on the test set indicates that our neural network model is capable of predicting the plasmapause location with the lowest RMSE. Our model can also produce a smooth magnetic local time variation of the plasmapause location with good accuracy, which can be incorporated into global radiation belt simulations and space weather forecasts under a variety of geomagnetic conditions.
Uncertainty Analysis and Identification of Key Parameters Controlling Bacteria Transport Within a Riverbank Filtration Scenario
Authors: Knabe Dustin , Guadagnini Alberto , Riva Monica , Engelhardt Irina 
Published: March 2021

AbstractManaged aquifer recharge through bank filtration is an important method to produce sustainable drinking water. Yet, water quality related to transport of pathogens (bacteria and viruses) into groundwater systems from surface waters can be a matter of concern, especially in urbanized regions. Based on a 1‐year monitoring campaign, a reactive transport model was developed for bacteria transport at a riverbank filtration site located in Germany. The model allows simulating advective‐dispersive transport and relies on the colloid filtration theory to mimic attachment and detachment of bacteria to and from the sediment in addition to inactivation, straining and blocking of bacteria. Due to the complexity of the investigated processes, the reactive transport model is characterized by a high level of parametrization, encompassing parameters driving flow as well as solute and colloid transport. A global sensitivity analysis has been applied to identify the most relevant model parameters with respect to piezometric pressure heads, groundwater temperature, and concentrations of chloride, oxygen, coliforms, and Escherichia coli. The model has been calibrated within a stochastic framework, to provide model parameter estimates and to quantify their uncertainty. Our results suggest that bacteria transport models are highly sensitive to inactivation coefficients, straining coefficients, and bacteria size. Permeability of the colmation layer at the riverbank is a key factor for bacteria transport through its influence on residence times. Seasonal variability of boundary conditions, especially anoxic aquifer conditions in the summer and high groundwater flow velocities during flooding periods, resulted in a reduction of inactivation and increased bacteria concentrations at observation wells.
Deriving Melt Rates at a Complex Ice Shelf Base Using In Situ Radar: Application to Totten Ice Shelf
Authors: Vaňková Irena , Cook Sue , Winberry J. Paul , Nicholls Keith W. , Galton‐Fenzi Benjamin K. 
Published: March 2021

AbstractA phase‐sensitive radar (ApRES) was deployed on Totten Ice Shelf to provide the first in situ basal melt estimate at this dynamic East Antarctic ice shelf. Observations of internal ice dynamics at tidal time scales showed that early arrivals from off‐nadir reflectors obscure the true depth of the ice shelf base. Using the observed tidal deformation, the true base was found to lie at 1,910–1,950‐m depth, at 350–400 m greater range than the first reflection from an ice‐ocean interface. The robustness of the basal melt rate estimate was increased by using multiple basal reflections over the radar footprint, yielding a melt rate of 22 ± 2.1 m a−1. The ApRES estimate is over 40% lower than the three existing satellite estimates covering Totten Ice Shelf. This difference in basal melt is dynamically significant and highlights the need for independent melt rate estimates using complementary instrumentation and techniques that rely on different sets of assumptions.
Treatment-free remission following frontline nilotinib in patients with chronic phase chronic myeloid leukemia: 5-year update of the ENESTfreedom trial
Authors: Radich Jerald P. , Hochhaus Andreas , Masszi Tamás , Hellmann Andrzej , Stentoft Jesper , Casares María Teresa Gómez , García-Gutiérrez J. Valentín , Conneally Eibhlin , le Coutre Philipp D. , Gattermann Norbert , Martino Bruno , Saussele Susanne , Giles Francis J. , Ross David M. , Aimone Paola , Li Sai , Titorenko Ksenia , Saglio Giuseppe 
Published: March 2021

AbstractThe ENESTfreedom trial assessed the feasibility of treatment-free remission (TFR) in patients with chronic myeloid leukemia in chronic phase (CML-CP) following frontline nilotinib treatment. Results for long-term outcomes after a 5-year follow-up are presented herein. Patients who had received ≥2 years of frontline nilotinib therapy and achieved MR4.5underwent a 1-year nilotinib treatment consolidation phase before attempting TFR. At the 5-year data cut-off, 81/190 patients entering the TFR phase (42.6%) were still in TFR, with 76 (40.0%) in MR4.5. Patients who lost major molecular response (MMR) entered a treatment re-initiation phase; 90/91 patients entering this phase (98.9%) regained MMR and 84/91 patients (92.3%) regained MR4.5. The Kaplan–Meier estimated treatment-free survival rate at 5 years was 48.2%. No disease progression or CML-related deaths were reported. Whereas the incidence of adverse events (AEs) declined from 96 weeks following the start of TFR, an increase in AE frequency was observed for patients in the treatment re-initiation phase. Low Sokal risk score,BCR-ABL1ISlevels at 48 weeks of TFR and stable MR4.5response for the first year of TFR were associated with higher TFR rates. Overall, these results support the efficacy and safety of attempting TFR following upfront nilotinib therapy of >3 years in patients with CML-CP.
Demonstration of an integrated nanophotonic chip-scale alkali vapor magnetometer using inverse design
Authors: Sebbag Yoel , Talker Eliran , Naiman Alex , Barash Yefim , Levy Uriel 
Published: March 2021

AbstractRecently, there has been growing interest in the miniaturization and integration of atomic-based quantum technologies. In addition to the obvious advantages brought by such integration in facilitating mass production, reducing the footprint, and reducing the cost, the flexibility offered by on-chip integration enables the development of new concepts and capabilities. In particular, recent advanced techniques based on computer-assisted optimization algorithms enable the development of newly engineered photonic structures with unconventional functionalities. Taking this concept further, we hereby demonstrate the design, fabrication, and experimental characterization of an integrated nanophotonic-atomic chip magnetometer based on alkali vapor with a micrometer-scale spatial resolution and a magnetic sensitivity of 700 pT/√Hz. The presented platform paves the way for future applications using integrated photonic–atomic chips, including high-spatial-resolution magnetometry, near-field vectorial imaging, magnetically induced switching, and optical isolation.
Metabolomic analyses of COVID-19 patients unravel stage-dependent and prognostic biomarkers
Authors: Danlos François-Xavier , Grajeda-Iglesias Claudia , Durand Sylvère , Sauvat Allan , Roumier Mathilde , Cantin Delphine , Colomba Emeline , Rohmer Julien , Pommeret Fanny , Baciarello Giulia , Willekens Christophe , Vasse Marc , Griscelli Frank , Fahrner Jean-Eudes , Goubet Anne-Gaëlle , Dubuisson Agathe , Derosa Lisa , Nirmalathasan Nitharsshini , Bredel Delphine , Mouraud Séverine , Pradon Caroline , Stoclin Annabelle , Rozenberg Flore , Duchemin Jérôme , Jourdi Georges , Ellouze Syrine , Levavasseur Françoise , Albigès Laurence , Soria Jean-Charles , Barlesi Fabrice , Solary Eric , André Fabrice , Pène Frédéric , Ackerman Félix , Mouthon Luc , Zitvogel Laurence , Marabelle Aurélien , Michot Jean-Marie , Fontenay Michaela , Kroemer Guido 
Published: March 2021

AbstractThe circulating metabolome provides a snapshot of the physiological state of the organism responding to pathogenic challenges. Here we report alterations in the plasma metabolome reflecting the clinical presentation of COVID-19 patients with mild (ambulatory) diseases, moderate disease (radiologically confirmed pneumonitis, hospitalization and oxygen therapy), and critical disease (in intensive care). This analysis revealed major disease- and stage-associated shifts in the metabolome, meaning that at least 77 metabolites including amino acids, lipids, polyamines and sugars, as well as their derivatives, were altered in critical COVID-19 patient’s plasma as compared to mild COVID-19 patients. Among a uniformly moderate cohort of patients who received tocilizumab, only 10 metabolites were different among individuals with a favorable evolution as compared to those who required transfer into the intensive care unit. The elevation of one single metabolite, anthranilic acid, had a poor prognostic value, correlating with the maintenance of high interleukin-10 and -18 levels. Given that products of the kynurenine pathway including anthranilic acid have immunosuppressive properties, we speculate on the therapeutic utility to inhibit the rate-limiting enzymes of this pathway including indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase.
Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution
Authors: Zhang Shuyuan , Qiao Shuyuan , Yu Jinfang , Zeng Jianwei , Shan Sisi , Tian Long , Lan Jun , Zhang Linqi , Wang Xinquan 
Published: March 2021

AbstractIn recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. All three receptor-binding domains (RBDs) of these two spike trimers are in the “down” conformation, indicating they are more prone to adopt the receptor-binding inactive state. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. We further identified critical residues in the RBD underlying different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes. These results collectively indicate that tight RBD–ACE2 binding and efficient RBD conformational sampling are required for the evolution of SARS-CoV-2 to gain highly efficient infection.
Flexible and high-performance electrochromic devices enabled by self-assembled 2D TiO2/MXene heterostructures
Authors: Li Ran , Ma Xiaoyuan , Li Jianmin , Cao Jun , Gao Hongze , Li Tianshu , Zhang Xiaoyu , Wang Lichao , Zhang Qinghong , Wang Gang , Hou Chengyi , Li Yaogang , Palacios Tomás , Lin Yuxuan , Wang Hongzhi , Ling Xi 
Published: March 2021

AbstractTransition metal oxides (TMOs) are promising electrochromic (EC) materials for applications such as smart windows and displays, yet the challenge still exists to achieve good flexibility, high coloration efficiency and fast response simultaneously. MXenes (e.g. Ti3C2Tx) and their derived TMOs (e.g. 2D TiO2) are good candidates for high-performance and flexible EC devices because of their 2D nature and the possibility of assembling them into loosely networked structures. Here we demonstrate flexible, fast, and high-coloration-efficiency EC devices based on self-assembled 2D TiO2/Ti3C2Tx heterostructures, with the Ti3C2Tx layer as the transparent electrode, and the 2D TiO2 layer as the EC layer. Benefiting from the well-balanced porosity and connectivity of these assembled nanometer-thick heterostructures, they present fast and efficient ion and electron transport, as well as superior mechanical and electrochemical stability. We further demonstrate large-area flexible devices which could potentially be integrated onto curved and flexible surfaces for future ubiquitous electronics.
An extended APOBEC3A mutation signature in cancer
Authors: Langenbucher Adam , Bowen Danae , Sakhtemani Ramin , Bournique Elodie , Wise Jillian F. , Zou Lee , Bhagwat Ashok S. , Buisson Rémi , Lawrence Michael S. 
Published: March 2021

AbstractAPOBEC mutagenesis, a major driver of cancer evolution, is known for targeting TpC sites in DNA. Recently, we showed that APOBEC3A (A3A) targets DNA hairpin loops. Here, we show that DNA secondary structure is in fact an orthogonal influence on A3A substrate optimality and, surprisingly, can override the TpC sequence preference. VpC (non-TpC) sites in optimal hairpins can outperform TpC sites as mutational hotspots. This expanded understanding of APOBEC mutagenesis illuminates the genomic Twin Paradox, a puzzling pattern of closely spaced mutation hotspots in cancer genomes, in which one is a canonical TpC site but the other is a VpC site, and double mutants are seen only in trans, suggesting a two-hit driver event. Our results clarify this paradox, revealing that both hotspots in these twins are optimal A3A substrates. Our findings reshape the notion of a mutation signature, highlighting the additive roles played by DNA sequence and DNA structure.
Harmonized and high-quality datasets of aerosol optical depth at a US continental site, 1997–2018
Authors: Kassianov Evgueni , Cromwell Erol , Monroe Justin , Riihimaki Laura D. , Flynn Connor , Barnard Jaime , Michalsky Joseph J. , Hodges Gary , Shi Yan , Comstock Jennifer M. 
Published: March 2021

AbstractAerosol optical depth (AOD) characterizes the aerosol burden in the atmosphere, while its wavelength dependence is a sign of particle size. Long-term records of wavelength-resolved AOD with high quality and suitable continuity are required for climate change assessment. Typically, climate-related studies use AOD products provided by several, and perhaps different, ground-based instruments. The measurements from these instruments often have different accuracy and temporal resolution. To preserve the advantages of these products (high quality) and to reduce their disadvantages (patchy records), we generate a merged dataset obtained from four instruments deployed at a US continental site in which a nearly-continuous AOD record is found at two wavelengths (500 and 870 nm) with high quality and high temporal resolution (1-min) for a 21-yr period (1997–2018). The combined dataset addresses: (1) varying data quality and resolution mismatch of the individual AOD records, and (2) the uncertainty of the merged AOD and its relevance for user-specified needs. The generated dataset will be beneficial for a wide range of applications including aerosol-radiation interactions.
Forager and farmer evolutionary adaptations to malaria evidenced by 7000 years of thalassemia in Southeast Asia
Authors: Vlok Melandri , Buckley Hallie R. , Miszkiewicz Justyna J. , Walker Meg M. , Domett Kate , Willis Anna , Trinh Hiep H. , Minh Tran T. , Nguyen Mai Huong T. , Nguyen Lan Cuong , Matsumura Hirofumi , Wang Tianyi , Nghia Huu T. , Oxenham Marc F. 
Published: March 2021

AbstractThalassemias are inherited blood disorders that are found in high prevalences in the Mediterranean, Southeast Asia and the Pacific. These diseases provide varying levels of resistance to malaria and are proposed to have emerged as an adaptive response to malaria in these regions. The transition to agriculture in the Holocene has been suggested to have influenced the selection for thalassemia in the Mediterranean as land clearance for farming encouraged interaction between Anopheles mosquitos, the vectors for malaria, and human groups. Here we document macroscopic and microscopic skeletal evidence for the presence of thalassemia in both hunter-gatherer (Con Co Ngua) and early agricultural (Man Bac) populations in northern Vietnam. Firstly, our findings demonstrate that thalassemia emerged prior to the transition to agriculture in Mainland Southeast Asia, from at least the early seventh millennium BP, contradicting a long-held assumption that agriculture was the main driver for an increase in malaria in Southeast Asia. Secondly, we describe evidence for significant malarial burden in the region during early agriculture. We argue that the introduction of farming into the region was not the initial driver of the selection for thalassemia, as it may have been in other regions of the world.