bluuebunny/crossref_metadata_2025 huggingface dataset:
What's in a Name? On the Use and Significance of the Term “Polar Vortex”
Authors: Manney Gloria L. , Butler Amy H. , Lawrence Zachary D. , Wargan Krzysztof , Santee Michelle L.
Published: May 2022

Mainstream and popular science media are rife with misunderstandings about what a “polar vortex” is. The term most aptly describes the stratospheric polar vortex, a single feature dominating the cool‐season circulation from ∼15–50 km. Regional jet stream variations dominate the tropospheric circulation, which is not well‐described as a polar vortex; indeed, there is no single consistent definition of a tropospheric polar vortex in the literature. Stratospheric polar vortex disturbances profoundly influence extreme weather events, including cold air outbreaks (CAOs). How the stratospheric polar vortex affects tropospheric jets, whose local excursions drive CAOs, is not fully understood. Public‐facing parts of publications describing research on this topic are not always clear about how the “polar vortex” is defined; greater clarity could improve communications both within the community and with non‐specialist audiences.
Simultaneous Detection of Signatures of Conjugate Photoelectrons in the Ionosphere and Thermosphere
Authors: Kil Hyosub , Paxton Larry J. , Schaefer Robert K.
Published: May 2022

We investigate the impact of conjugate photoelectrons (CPEs) on the topside (∼600 km altitude) ionosphere at low and midlatitudes using measurements of the ion temperature, density, and composition from the first Republic of China satellite during a period of the high to moderate solar activity (March 1999 to June 2004). Elevated ion temperatures and densities are observed in the dark Northern American‐Atlantic sector during the December solstice and in the Australian sector during the June solstice. The oxygen ion fraction and density are also elevated at these locations. These observations indicate that photoelectrons from the conjugate hemisphere heat the local ionospheric plasma. The morphology of the ion temperature in the winter hemisphere is well represented by the solar zenith angle in the sunlit conjugate hemisphere. The CPE hypothesis for the observed ionospheric heating is confirmed by coincident nighttime enhancements of the far ultraviolet airglow measured by the Global Ultraviolet Imager onboard the Thermosphere Ionosphere Mesosphere Energetics and Dynamics satellite.
Monthly to Decadal Variability of Mesoscale Stirring in the California Current System: Links to Upwelling, Climate Forcing, and Chlorophyll Transport
Authors: Giddings A. , Franks P. J. S. , Baumann‐Pickering S.
Published: May 2022

The California Current System (CCS) is a highly productive eastern boundary upwelling system. Cross‐shore transport is driven by horizontal stirring from mesoscale (and submesoscale) eddies, fronts, and filaments, which shift surface productivity away from the narrow upwelling zone inshore. Using an unprecedented 25‐year daily record of finite size Lyapunov exponents (FSLEs), we characterize the spatial and temporal patterns of mesoscale stirring in the entire CCS and quantify correlations of FSLEs with satellite‐measured chlorophyll a and climate indices. The annual cycle of mesoscale stirring is highly correlated with seasonal upwelling in the CCS, with bands of intense FSLE propagating to the west during the upwelling season. Annual cycles and interannual variability in FSLE intensity were most prominent to the north and inshore of the CCS, and weaker to the south and offshore. Interannual fluctuations in mesoscale stirring showed 3–12 month lagged responses to climate indices, with the CCS oscillating out of phase with waters west and north. Chlorophyll a is positively correlated with FSLE intensity in a meridional band 200–600 km offshore, consistent with the hypothesis that increased horizontal stirring increases the export of chlorophyll a to offshore waters. When mesoscale stirring intensifies during negative phases of the Pacific Decadal Oscillation and Ocean Niño index, we predict greater offshore transport of organic carbon. Our analyses underscore the predictability of annual and interannual cycles of mesoscale stirring and chlorophyll a fluxes in the CCS and their links with climate indices.
Evidence for Interhemispheric Mercury Exchange in the Pacific Ocean Upper Troposphere
Authors: Koenig Alkuin M. , Sonke Jeroen E. , Magand Olivier , Andrade Marcos , Moreno Isabel , Velarde Fernando , Forno Ricardo , Gutierrez René , Blacutt Luis , Laj Paolo , Ginot Patrick , Bieser Johannes , Zahn Andreas , Slemr Franz , Dommergue Aurélien
Published: May 2022

Even though anthropogenic mercury (Hg) emissions to the atmosphere are ∼2.5 times higher in the Northern Hemisphere (NH) than in the Southern Hemisphere (SH), atmospheric Hg concentrations in the NH are only ∼1.5 times higher than in the SH. Global Hg models attribute this apparent discrepancy to large SH oceanic Hg emissions or to interhemispheric exchange of Hg through the atmosphere. However, no observational data set exists to serve as a benchmark to validate whether these coarse‐resolution models adequately represent the complex dynamics of interhemispheric Hg exchange. During the 2015–2016 El Niño, we observed at mount Chacaltaya in the tropical Andes a ∼50% increase in ambient Hg compared to the year before, coinciding with a shift in synoptic transport pathways. Using this event as a case study, we investigate the impact of interhemispheric exchange on atmospheric Hg in tropical South America. We use HYSPLIT to link Hg observations to long‐range transport and find that the observed Hg increase relates strongly to air masses from the tropical Pacific upper troposphere (UT), a region directly impacted by interhemispheric exchange. Inclusion of the modeled seasonality of interhemispheric air mass exchange strengthens this relationship significantly. We estimate that interhemispheric exchange drives Hg seasonality in the SH tropical Pacific UT, with strongly enhanced Hg between July and October. We validate this seasonality with previously published aircraft Hg observations. Our results suggest that the transport of NH‐influenced air masses to tropical South America via the Pacific UT occurs regularly but became more detectable at Chacaltaya in 2015–2016 because of a westward shift in air mass origin.
On the Magnetosphere‐Ionosphere Coupling During the May 2021 Geomagnetic Storm
Authors: Piersanti M. , Del Moro D. , Parmentier A. , Martucci M. , Palma F. , Sotgiu A. , Plainaki C. , D’Angelo G. , Berrilli F. , Recchiuti D. , Papini E. , Giovannelli L. , Napoletano G. , Iuppa R. , Diego P. , Cicone A. , Mergé M. , De Donato C. , De Santis C. , Sparvoli R. , Ubertini P. , Battiston R. , Picozza P.
Published: May 2022

On 12 May 2021 the interplanetary doppelgänger of the 9 May 2021 coronal mass ejection impacted the Earth's magnetosphere, giving rise to a strong geomagnetic storm. This paper discusses the evolution of the various events linking the solar activity to the Earth's ionosphere with special focus on the effects observed in the circumterrestrial environment. We investigate the propagation of the interplanetary coronal mass ejection and its interaction with the magnetosphere—ionosphere system in terms of both magnetospheric current systems and particle redistribution, by jointly analyzing data from interplanetary, magnetospheric, and low Earth orbiting satellites. The principal magnetospheric current system activated during the different phases of the geomagnetic storm was correctly identified through the direct comparison between geosynchronous orbit observations and model predictions. From the particle point of view, we have found that the primary impact of the storm development is a net and rapid loss of relativistic electrons from the entire outer radiation belt. Our analysis shows no evidence for any short‐term recovery to pre‐storm levels during the days following the main phase. Storm effects also included a small Forbush decrease driven by the interplay between the interplanetary shock and subsequent magnetic cloud arrival.
A Repetitive Parameterization and Optimization Strategy for the Calibration of Complex and Computationally Expensive Process‐Based Models With Application to a 3D Water Quality Model of a Tropical Reservoir
Authors: Xia Wei , Shoemaker Christine Ann
Published: May 2022

Parameter calibration is critical for modeling, especially for current process‐based models that are complex with many chemical and biological processes and immeasurable model parameters. This analysis quantifies significant disadvantages of the traditional use of local or global sensitivity analysis (SA) for selecting calibration parameters of nonlinear, expensive models when there are a large number of constituents and parameters. We propose a new Repetitive parameterization and optimization (Rep‐OPT) strategy that uses multiple optimization steps; and between each optimization step, a modeler picks the parameters to be optimized in the next optimization step. The modeler picks the parameters in each iteration following a suggested set of steps that analyze which processes and parameters are related to the poorly fit constituents with the current parameter set. We successfully applied the Rep‐OPT strategy on a complex tropical water quality model with more than 91 parameters using real data. We demonstrate that expert knowledge with assistance of proposed postanalysis techniques (i.e., trade‐off analysis, component analysis, and mass‐balance analysis) can identify the right calibration parameters and obtain excellent model fit. In contrast, the traditional approach using SA with optimization (SA‐OPT) does not find the right calibration parameters for our data. The solution found by Rep‐OPT excellently improves manual solution by 32.7% in goodness‐of‐fit, and all calibrated constituents fit well to observations. The solution found by SA‐OPT using global SA improves manual solution by only 13.3%. Local sensitivity by SA‐OPT performs very poorly being 49.6% worse than manual solution.
Stronger Vertical Shear Leads to Earlier Secondary Eyewall Formation in Idealized Numerical Simulations
Authors: Liu Xinhang , Li Qingqing , Dai Yufan
Published: May 2022

Idealized numerical experiments show that stronger shear is more favorable for tropical cyclone secondary eyewall formation (SEF) than weaker shear amid a moist‐tropical environment when the shear magnitude is smaller than 15 m s−1. In particular, the larger the shear, the earlier the SEF occurs. A stationary banding complex (SBC) prevails before SEF in the large shear experiments, suggesting that SBCs are helpful in the SEF. Furthermore, a well‐organized stratiform sector is associated with the SBC. With increasing shear, the shear‐forced outflow also increases in the upper layers, transporting more moisture and icy particles outward from the inner core and favoring the development of the stratiform sector. The diabatic cooling of the stratiform sector strengthens the underlying descending radial inflow, forcing updrafts immediately outside the inner core. The subsequent axisymmetrization of the updrafts leads to SEF.
Completion of Global Ionospheric TEC Maps Using a Deep Learning Approach
Authors: Yang Ding , Fang Hanxian , Liu Zhendi
Published: May 2022

Total electron content (TEC) is an important parameter that describes the features of the ionosphere. The International GNSS Service (IGS) has been providing IGS Global TEC maps using analysis algorithms. However, collecting the completed data is difficult because of the lack of ground receivers, and the processing to obtain the completed IGS TEC maps is time‐consuming. The fast development of deep learning brings an effective way to solve these problems. Among the various deep learning methods, the generative adversarial network (GAN) exhibits great potential in recovering missing data. In this paper, we fill the missing data of the global IGS TEC maps using pix2pixhd, which is a novel deep learning method based on GAN. Differing from the traditional GAN, pix2pixhd has two generators and three discriminators. The network enhances the ability of our model to complete images with large‐scale missing areas. The result demonstrates that our model generates the ionospheric peak structures at low latitudes well, while behaving badly (the average correlation coefficient: 0.6857) around the edge of the ionospheric peak region. Comparing different scales of the missing data areas, our model has the best performance with 0%–15% missing data. With the large scale of missing data areas (30%–45% and >45%), the performance is still satisfactory. In addition, the completion effect of our model is slightly affected by geomagnetic and solar activity. Our work demonstrates a new possibility for the application of deep learning to a broader field of geosciences, particularly for problems of missing observational data.
Statistical Properties of Whistler‐Mode Hiss Waves in the Inner Radiation Belt
Authors: Yang Ling , Li Liuyuan , Cao Jinbin , Yu Jiang
Published: May 2022

Using the Van Allen Probes A and B observations from 01 January 2013 to 28 February 2018, we surveyed statistically the occurrence rate, intensity, and propagation properties of hiss waves in the inner radiation belt (1.1 < L ≤ 2). Like the outer plasmaspheric hiss (L > 2), the occurrence rate and amplitude of lower‐band hiss (<600 Hz) are higher in the dayside high‐L region (L > 1.3 and magnetic local time [MLT] = 6–20 hr) than the nightside (MLT ∼ 20–6 hr) and increase with enhanced substorm activities (AE increases). Furthermore, their peak power spectral densities are located nearly in the same band (∼200–500 Hz). The equatorward propagation of middle‐latitude hiss suggests that the lower‐band hiss waves in the inner radiation belt mostly originate from the outer plasmaspheric hiss at high latitudes. Although the outer plasmaspheric hiss is also a likely source of weak upper‐band hiss (≥600 Hz) in the dayside high‐L region (L > 1.3 and MLT = 6–20 hr), the intense upper‐band hiss waves mostly appear in the dayside low‐L region (L < 1.3) and most nightside regions. In the low‐L region, the amplitude of the upper‐band hiss has no obvious substorm dependence, and the average of its wave normal angles is comparable to that of lightning‐generated whistlers reported in the past.
Micro‐Scale Plasma Instabilities in the Interaction Region of the Solar Wind and the Martian Upper Atmosphere
Authors: Akbari Hassanali , Newman David , Fowler Christopher , Pfaff Robert , Andersson Laila , Malaspina David , Schwartz Steven , Ergun Robert , McFadden James , Mitchell David , Halekas Jasper , Rowland Douglas
Published: May 2022

We present results, obtained by several instruments onboard NASA’s Mars Atmosphere and Volatile Evolution (MAVEN) spacecraft, that show that the interaction region of the solar wind and the Martian upper atmosphere coincides with intense plasma wave activity. The turbulence region features nonlinear structures, identified as ion phase‐space holes and double layers, that emerge in the saturation phase of instabilities in the ion‐acoustic frequency range. One‐dimensional particle‐in‐cell simulations suggest that the waves and the nonlinear structures are very effective in coupling the flowing solar wind and the Martian plasma. Specifically, the simulations show that the magnetic field‐aligned component of the solar wind protons decelerates by about 20% in temporal and spatial scales of the orders of ∼100 ms and several kilometers, respectively. The results thus suggest that the waves may play an important role in the interaction region.
Mapping Magnetic Signals of Individual Magnetite Grains to Their Internal Magnetic Configurations Using Micromagnetic Models
Authors: Cortés‐Ortuño David , Fabian Karl , de Groot Lennart V.
Published: May 2022

Micromagnetic tomography (MMT) is a technique that combines X‐ray micro computed tomography and scanning magnetometry data to obtain information about the magnetic potential of individual grains embedded in a sample. Recovering magnetic signals of individual grains in natural and synthetic samples provides a new pathway to study the remanent magnetization that carries information about the ancient geomagnetic field and is the basis of all paleomagnetic studies. MMT infers the magnetic potential of individual grains by numerical inversion of surface magnetic measurements using spherical harmonic expansions. The magnetic potential of individual particles in principle is uniquely determined by MMT, not only by the dipole approximation, but also more complex, higher order, multipole moments. Here, we show that such complex magnetic information together with both particle shape and mineral properties severely constrains the internal magnetization structure of an individual grain. To this end, we apply a three dimensional micromagnetic model to predict the multipole signal from magnetization states of different local energy minima. We show that for certain grains it is even possible to uniquely infer the magnetic configuration from the inverted magnetic multipole moments. This result is crucial to discriminate single‐domain particles from grains in more complex configurations such as multi‐domain or vortex states. As a consequence, our investigation proves that by MMT it is feasible to select statistical ensembles of magnetic grains based on their magnetization states, which opens new possibilities to identify and characterize stable paleomagnetic recorders in natural samples.
Polymer-coated carbon nanotube hybrids with functional peptides for gene delivery into plant mitochondria
Authors: Law Simon Sau Yin , Liou Geoffrey , Nagai Yukiko , Giménez-Dejoz Joan , Tateishi Ayaka , Tsuchiya Kousuke , Kodama Yutaka , Fujigaya Tsuyohiko , Numata Keiji
Published: May 2022

The delivery of genetic material into plants has been historically challenging due to the cell wall barrier, which blocks the passage of many biomolecules. Carbon nanotube-based delivery has emerged as a promising solution to this problem and has been shown to effectively deliver DNA and RNA into intact plants. Mitochondria are important targets due to their influence on agronomic traits, but delivery into this organelle has been limited to low efficiencies, restricting their potential in genetic engineering. This work describes the use of a carbon nanotube-polymer hybrid modified with functional peptides to deliver DNA into intact plant mitochondria with almost 30 times higher efficiency than existing methods. Genetic integration of a folate pathway gene in the mitochondria displays enhanced plant growth rates, suggesting its applications in metabolic engineering and the establishment of stable transformation in mitochondrial genomes. Furthermore, the flexibility of the polymer layer will also allow for the conjugation of other peptides and cargo targeting other organelles for broad applications in plant bioengineering.
A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases
Authors: Rozman Grinberg Inna , Martínez-Carranza Markel , Bimai Ornella , Nouaïria Ghada , Shahid Saher , Lundin Daniel , Logan Derek T. , Sjöberg Britt-Marie , Stenmark Pål
Published: May 2022

Ribonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, an RNR-specific repressor, controls the transcription of RNR genes and, often, its own, in most bacteria and some archaea. NrdR senses the concentration of nucleotides through its ATP-cone, an evolutionarily mobile domain that also regulates the enzymatic activity of many RNRs, while a Zn-ribbon domain mediates binding to NrdR boxes upstream of and overlapping the transcription start site of RNR genes. Here, we combine biochemical and cryo-EM studies of NrdR from Streptomyces coelicolor to show, at atomic resolution, how NrdR binds to DNA. The suggested mechanism involves an initial dodecamer loaded with two ATP molecules that cannot bind to DNA. When dATP concentrations increase, an octamer forms that is loaded with one molecule each of dATP and ATP per monomer. A tetramer derived from this octamer then binds to DNA and represses transcription of RNR. In many bacteria — including well-known pathogens such as Mycobacterium tuberculosis — NrdR simultaneously controls multiple RNRs and hence DNA synthesis, making it an excellent target for novel antibiotics development.
PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction
Authors: Enghiad Behnam , Xue Pu , Singh Nilmani , Boob Aashutosh Girish , Shi Chengyou , Petrov Vassily Andrew , Liu Roy , Peri Siddhartha Suryanarayana , Lane Stephan Thomas , Gaither Emily Danielle , Zhao Huimin
Published: May 2022

Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor-intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error-free construction of plasmids with virtually any sequences in a high throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute (PfAgo)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments. PlasmidMaker should greatly expand the potential of synthetic biology.
Purine nucleotide depletion prompts cell migration by stimulating the serine synthesis pathway
Authors: Soflaee Mona Hoseini , Kesavan Rushendhiran , Sahu Umakant , Tasdogan Alpaslan , Villa Elodie , Djabari Zied , Cai Feng , Tran Diem H. , Vu Hieu S. , Ali Eunus S. , Rion Halie , O’Hara Brendan P. , Kelekar Sherwin , Hallett James Hughes , Martin Misty , Mathews Thomas P. , Gao Peng , Asara John M. , Manning Brendan D. , Ben-Sahra Issam , Hoxhaj Gerta
Published: May 2022

Purine nucleotides are necessary for various biological processes related to cell proliferation. Despite their importance in DNA and RNA synthesis, cellular signaling, and energy-dependent reactions, the impact of changes in cellular purine levels on cell physiology remains poorly understood. Here, we find that purine depletion stimulates cell migration, despite effective reduction in cell proliferation. Blocking purine synthesis triggers a shunt of glycolytic carbon into the serine synthesis pathway, which is required for the induction of cell migration upon purine depletion. The stimulation of cell migration upon a reduction in intracellular purines required one-carbon metabolism downstream of de novo serine synthesis. Decreased purine abundance and the subsequent increase in serine synthesis triggers an epithelial-mesenchymal transition (EMT) and, in cancer models, promotes metastatic colonization. Thus, reducing the available pool of intracellular purines re-routes metabolic flux from glycolysis into de novo serine synthesis, a metabolic change that stimulates a program of cell migration.
High capacity topological coding based on nested vortex knots and links
Authors: Kong Ling-Jun , Zhang Weixuan , Li Peng , Guo Xuyue , Zhang Jingfeng , Zhang Furong , Zhao Jianlin , Zhang Xiangdong
Published: May 2022

Optical knots and links have attracted great attention because of their exotic topological characteristics. Recent investigations have shown that the information encoding based on optical knots could possess robust features against external perturbations. However, as a superior coding scheme, it is also necessary to achieve a high capacity, which is hard to be fulfilled by existing knot-carriers owing to the limit number of associated topological invariants. Thus, how to realize the knot-based information coding with a high capacity is a key problem to be solved. Here, we create a type of nested vortex knot, and show that it can be used to fulfill the robust information coding with a high capacity assisted by a large number of intrinsic topological invariants. In experiments, we design and fabricate metasurface holograms to generate light fields sustaining different kinds of nested vortex links. Furthermore, we verify the feasibility of the high-capacity coding scheme based on those topological optical knots. Our work opens another way to realize the robust and high-capacity optical coding, which may have useful impacts on the field of information transfer and storage.
Structural anatomy of Protein Kinase C C1 domain interactions with diacylglycerol and other agonists
Authors: Katti Sachin S. , Krieger Inna V. , Ann Jihyae , Lee Jeewoo , Sacchettini James C. , Igumenova Tatyana I.
Published: May 2022

Diacylglycerol (DAG) is a versatile lipid whose 1,2-sn-stereoisomer serves both as second messenger in signal transduction pathways that control vital cellular processes, and as metabolic precursor for downstream signaling lipids such as phosphatidic acid. Effector proteins translocate to available DAG pools in the membranes by using conserved homology 1 (C1) domains as DAG-sensing modules. Yet, how C1 domains recognize and capture DAG in the complex environment of a biological membrane has remained unresolved for the 40 years since the discovery of Protein Kinase C (PKC) as the first member of the DAG effector cohort. Herein, we report the high-resolution crystal structures of a C1 domain (C1B from PKCδ) complexed to DAG and to each of four potent PKC agonists that produce different biological readouts and that command intense therapeutic interest. This structural information details the mechanisms of stereospecific recognition of DAG by the C1 domains, the functional properties of the lipid-binding site, and the identities of the key residues required for the recognition and capture of DAG and exogenous agonists. Moreover, the structures of the five C1 domain complexes provide the high-resolution guides for the design of agents that modulate the activities of DAG effector proteins.
A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs
Authors: Shue Yan Ting , Drainas Alexandros P. , Li Nancy Yanzhe , Pearsall Sarah M. , Morgan Derrick , Sinnott-Armstrong Nasa , Hipkins Susan Q. , Coles Garry L. , Lim Jing Shan , Oro Anthony E. , Simpson Kathryn L. , Dive Caroline , Sage Julien
Published: May 2022

The Notch pathway is a conserved cell-cell communication pathway that controls cell fate decisions. Here we sought to determine how Notch pathway activation inhibits the neuroendocrine cell fate in the lungs, an archetypal process for cell fate decisions orchestrated by Notch signaling that has remained poorly understood at the molecular level. Using intratumoral heterogeneity in small-cell lung cancer as a tractable model system, we uncovered a role for the transcriptional regulators REST and YAP as promoters of the neuroendocrine to non-neuroendocrine transition. We further identified the specific neuroendocrine gene programs repressed by REST downstream of Notch in this process. Importantly, we validated the importance of REST and YAP in neuroendocrine to non-neuroendocrine cell fate switches in both developmental and tissue repair processes in the lungs. Altogether, these experiments identify conserved roles for REST and YAP in Notch-driven inhibition of the neuroendocrine cell fate in embryonic lungs, adult lungs, and lung cancer.
Suppressing high-dimensional crystallographic defects for ultra-scaled DNA arrays
Authors: Chen Yahong , Yang Chaoyong , Zhu Zhi , Sun Wei
Published: May 2022

While DNA-directed nano-fabrication enables the high-resolution patterning for conventional electronic materials and devices, the intrinsic self-assembly defects of DNA structures present challenges for further scaling into sub-1 nm technology nodes. The high-dimensional crystallographic defects, including line dislocations and grain boundaries, typically lead to the pattern defects of the DNA lattices. Using periodic line arrays as model systems, we discover that the sequence periodicity mainly determines the formation of line defects, and the defect rate reaches 74% at 8.2-nm line pitch. To suppress high-dimensional defects rate, we develop an effective approach by assigning the orthogonal sequence sets into neighboring unit cells, reducing line defect rate by two orders of magnitude at 7.5-nm line pitch. We further demonstrate densely aligned metal nano-line arrays by depositing metal layers onto the assembled DNA templates. The ultra-scaled critical pitches in the defect-free DNA arrays may further promote the dimension-dependent properties of DNA-templated materials.
Quantum-limited determination of refractive index difference by means of entanglement
Authors: Reisner M. , Mazeas F. , Dauliat R. , Leconte B. , Aktas D. , Cannon R. , Roy P. , Jamier R. , Sauder G. , Kaiser F. , Tanzilli S. , Labonté L.
Published: May 2022

Shaping single-mode operation in high-power fibers requires a precise knowledge of the gain-medium optical properties. This requires precise measurements of the refractive index differences (Δn) between the core and the cladding of the fiber. We exploit a quantum optical method based on low-coherence Hong-Ou-Mandel interferometry to perform practical measurements of the refractive index difference using broadband energy-time entangled photons. The precision enhancement reached with this method is benchmarked with a classical method based on single photon interferometry. We show in classical regime an improvement by an order of magnitude of the precision compared to already reported classical methods. Strikingly, in the quantum regime, we demonstrate an extra factor of 4 on the precision enhancement, exhibiting a state-of-the-art Δnprecision of 6 × 10−7. This work sets the quantum photonics metrology as a powerful characterization tool that should enable a faster and reliable design of materials dedicated to light amplification.
Global cycling and climate effects of aeolian dust controlled by biological soil crusts
Authors: Rodriguez-Caballero E. , Stanelle T. , Egerer S. , Cheng Y. , Su H. , Canton Y. , Belnap J. , Andreae M. O. , Tegen I. , Reick C. H. , Pöschl U. , Weber B.
Published: May 2022

Biological soil crusts (biocrusts) cover ~12% of the global land surface. They are formed by an intimate association between soil particles, photoautotrophic and heterotrophic organisms, and they effectively stabilize the soil surface of drylands. Quantitative information on the impact of biocrusts on the global cycling and climate effects of aeolian dust, however, is not available. Here, we combine the currently limited experimental data with a global climate model to investigate the effects of biocrusts on regional and global dust cycling under current and future conditions. We estimate that biocrusts reduce the global atmospheric dust emissions by ~60%, preventing the release of ~0.7 Pg dust per year. Until 2070, biocrust coverage is expected to be severely reduced by climate change and land-use intensification. The biocrust loss will cause an increased dust burden, leading to a reduction of the global radiation budget of around 0.12 to 0.22 W m−2, corresponding to about 50% of the total direct forcing of anthropogenic aerosols. This biocrust control on dust cycling and its climate impacts have important implications for human health, biogeochemical cycling and the functioning of the ecosystems, and thus should be considered in the modelling, mitigation and management of global change.
Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration
Authors: Priya Sambhawa , Burns Michael B. , Ward Tonya , Mars Ruben A. T. , Adamowicz Beth , Lock Eric F. , Kashyap Purna C. , Knights Dan , Blekhman Ran
Published: May 2022

While gut microbiome and host gene regulation independently contribute to gastrointestinal disorders, it is unclear how the two may interact to influence host pathophysiology. Here we developed a machine learning-based framework to jointly analyse paired host transcriptomic (n = 208) and gut microbiome (n = 208) profiles from colonic mucosal samples of patients with colorectal cancer, inflammatory bowel disease and irritable bowel syndrome. We identified associations between gut microbes and host genes that depict shared as well as disease-specific patterns. We found that a common set of host genes and pathways implicated in gastrointestinal inflammation, gut barrier protection and energy metabolism are associated with disease-specific gut microbes. Additionally, we also found that mucosal gut microbes that have been implicated in all three diseases, such asStreptococcus, are associated with different host pathways in each disease, suggesting that similar microbes can affect host pathophysiology in a disease-specific manner through regulation of different host genes. Our framework can be applied to other diseases for the identification of host gene–microbiome associations that may influence disease outcomes.
Simulated carbon K edge spectral database of organic molecules
Authors: Shibata Kiyou , Kikumasa Kakeru , Kiyohara Shin , Mizoguchi Teruyasu
Published: May 2022

Here we provide a database of simulated carbon K (C-K) edge core loss spectra of 117,340 symmetrically unique sites in 22,155 molecules with no more than eight non-hydrogen atoms (C, O, N, and F). Our database contains C-K edge spectra of each carbon site and those of molecules along with their excitation energies. Our database is useful for analyzing experimental spectrum and conducting spectrum informatics on organic materials.
A global inventory of animal diversity measured in different grazing treatments
Authors: Barber-Cross Tianna , Filazzola Alessandro , Brown Charlotte , Dettlaff Margarete A. , Batbaatar Amgaa , Grenke Jessica S. J. , Peetoom Heida Isaac , Cahill James F.
Published: May 2022

Grazing by wild and domesticated grazers occurs within many terrestrial ecosystems worldwide, with positive and negative impacts on biodiversity. Management of grazed lands in support of biological conservation could benefit from a compiled dataset of animal biodiversity within and adjacent to grazed sites. In this database, we have assembled data from the peer-reviewed literature that included all forms of grazing, co-occurring species, and site information. We reviewed 3,489 published articles and found 245 studies in 41 countries that surveyed animal biodiversity co-occurring with grazers. We extracted 16,105 observations of animal surveys for over 1,200 species in all terrestrial ecosystems and on all continents except Antarctica. We then compiled 28 different grazing variables that focus on management systems, assemblages of grazer species, ecosystem characteristics, and survey type. Our database provides the most comprehensive summary of animal biodiversity patterns that co-occur with wild and domesticated grazers. This database could be used in future conservation initiatives and grazing management to enhance the prolonged maintenance of ecosystems and ecosystem services.
Cloud-based applications for accessing satellite Earth observations to support malaria early warning
Authors: Wimberly Michael C. , Nekorchuk Dawn M. , Kankanala Ramcharan R.
Published: May 2022

Malaria epidemics can be triggered by fluctuations in temperature and precipitation that influence vector mosquitoes and the malaria parasite. Identifying and monitoring environmental risk factors can thus provide early warning of future outbreaks. Satellite Earth observations provide relevant measurements, but obtaining these data requires substantial expertise, computational resources, and internet bandwidth. To support malaria forecasting in Ethiopia, we developed software for Retrieving Environmental Analytics for Climate and Health (REACH). REACH is a cloud-based application for accessing data on land surface temperature, spectral indices, and precipitation using the Google Earth Engine (GEE) platform. REACH can be implemented using the GEE code editor and JavaScript API, as a standalone web app, or as package with the Python API. Users provide a date range and data for 852 districts in Ethiopia are automatically summarized and downloaded as tables. REACH was successfully used in Ethiopia to support a pilot malaria early warning project in the Amhara region. The software can be extended to new locations and modified to access other environmental datasets through GEE.
Transcriptomic changes induced by applications of a commercial extract of Ascophyllum nodosum on tomato plants
Authors: Ali Omar , Ramsubhag Adesh , Daniram Benn Jr. Ramnarine Stephen , Jayaraman Jayaraj
Published: May 2022

Extracts of Ascophyllum nodosum are commonly used as commercial biostimulants in crop production. To further understand the seaweed extract-induced phenomena in plants, a transcriptomic study was conducted. RNA-seq differential gene expression analysis of tomato plants treated with a commercial A. nodosum extract formulation (Stimplex) revealed the up-regulation of 635 and down-regulation of 456 genes. Ontology enrichment analysis showed three gene categories were augmented, including biological processes, cellular components, and molecular functions. KEGG pathway analysis revealed that the extract had a strong influence on the expression of genes involved in carbon fixation, secondary metabolism, MAPK-signalling, plant hormone signal transduction, glutathione metabolism, phenylpropanoid and stilbenoid metabolism, and plant-pathogen interactions. qRT-PCR validation analysis using 15 genes established a strong correlation with the RNA sequencing results. The activities of defence enzymes were also significantly enhanced by seaweed extract treatment. Furthermore, AN-SWE treated tomato plants had significantly higher chlorophyll and growth hormone content and showed improved plant growth parameters and nutrient profiles than the control. It is postulated that seaweed extract-induced gene regulation was responsible for favourable plant responses that enabled better growth and tolerance to stress conditions. This study provides evidence at the transcriptomic level for the positive effects of foliar application of the Ascophyllum nodosum extract (Stimplex) observed in treated tomato plants.
Immunological profiles of the breast cancer microenvironment represented by tumor-infiltrating lymphocytes and PD-L1 expression
Authors: Hanamura Toru , Kitano Shigehisa , Kagamu Hiroshi , Yamashita Makiko , Terao Mayako , Tsuda Banri , Okamura Takuho , Kumaki Nobue , Hozumi Katsuto , Harada Naoki , Iwamoto Takayuki , Honda Chikako , Kurozumi Sasagu , Niikura Naoki
Published: May 2022

Tumor-infiltrating lymphocytes (TILs) and programmed cell death 1 ligand 1 (PD-L1) are established prognostic and predictive biomarkers for certain breast cancer subsets. However, their association with the immune response complexity is not fully understood. Therefore, we analyzed the association between the immune cell fractions in breast cancer tissues and histologically assessed TIL (hTIL) and PD-L1 (hPD-L1). Forty-five tumor and eighteen blood samples were collected from patients with breast cancer. Total leukocyte counts, frequency of 11 immune cell populations, and PD-L1 expression in each cell fraction were evaluated by flow cytometry. TILs and PD-L1 were assessed by hematoxylin and eosin staining and immunohistochemistry, respectively. A higher hTIL score showed association with increased leukocyte infiltration, higher CD4+ and CD8+ T cell proportions, and lower natural killer and natural killer T cell proportions. PD-L1 was highly expressed in nonclassical monocytes, monocyte/macrophages, myeloid-derived suppressor cells, myeloid dendritic cells, dendritic cells, and other lineages in tumors. hPD-L1 positivity reflected PD-L1 expression accurately in these fractions, as well as increased leukocyte infiltration in tumors. These results indicate that hTILs reflect differences in the immune responses in the tumor microenvironment, and certain immune cell fractions are favorably expressed in the PD-L1 pathway in breast cancer microenvironments.
Inducing respiratory complex I impairment elicits an increase in PGC1α in ovarian cancer
Authors: De Luise Monica , Sollazzo Manuela , Lama Eleonora , Coadă Camelia Alexandra , Bressi Licia , Iorio Maria , Cavina Beatrice , D’Angelo Luigi , Milioni Sara , Marchio Lorena , Miglietta Stefano , Coluccelli Sara , Tedesco Greta , Ghelli Anna , Lemma Silvia , Perrone Anna Myriam , Kurelac Ivana , Iommarini Luisa , Porcelli Anna Maria , Gasparre Giuseppe
Published: May 2022

Anticancer strategies aimed at inhibiting Complex I of the mitochondrial respiratory chain are increasingly being attempted in solid tumors, as functional oxidative phosphorylation is vital for cancer cells. Using ovarian cancer as a model, we show that a compensatory response to an energy crisis induced by Complex I genetic ablation or pharmacological inhibition is an increase in the mitochondrial biogenesis master regulator PGC1α, a pleiotropic coactivator of transcription regulating diverse biological processes within the cell. We associate this compensatory response to the increase in PGC1α target gene expression, setting the basis for the comprehension of the molecular pathways triggered by Complex I inhibition that may need attention as drawbacks before these approaches are implemented in ovarian cancer care.
Individualizing deep dynamic models for psychological resilience data
Authors: Köber Göran , Pooseh Shakoor , Engen Haakon , Chmitorz Andrea , Kampa Miriam , Schick Anita , Sebastian Alexandra , Tüscher Oliver , Wessa Michèle , Yuen Kenneth S. L. , Walter Henrik , Kalisch Raffael , Timmer Jens , Binder Harald
Published: May 2022

Deep learning approaches can uncover complex patterns in data. In particular, variational autoencoders achieve this by a non-linear mapping of data into a low-dimensional latent space. Motivated by an application to psychological resilience in the Mainz Resilience Project, which features intermittent longitudinal measurements of stressors and mental health, we propose an approach for individualized, dynamic modeling in this latent space. Specifically, we utilize ordinary differential equations (ODEs) and develop a novel technique for obtaining person-specific ODE parameters even in settings with a rather small number of individuals and observations, incomplete data, and a differing number of observations per individual. This technique allows us to subsequently investigate individual reactions to stimuli, such as the mental health impact of stressors. A potentially large number of baseline characteristics can then be linked to this individual response by regularized regression, e.g., for identifying resilience factors. Thus, our new method provides a way of connecting different kinds of complex longitudinal and baseline measures via individualized, dynamic models. The promising results obtained in the exemplary resilience application indicate that our proposal for dynamic deep learning might also be more generally useful for other application domains.
New approach to prepare cytocompatible 3D scaffolds via the combination of sodium hyaluronate and colloidal particles of conductive polymers
Authors: Truong Thanh Huong , Musilová Lenka , Kašpárková Věra , Jasenská Daniela , Ponížil Petr , Minařík Antonín , Korábková Eva , Münster Lukáš , Hanulíková Barbora , Mráček Aleš , Rejmontová Petra , Humpolíček Petr
Published: May 2022

Bio-inspired conductive scaffolds composed of sodium hyaluronate containing a colloidal dispersion of water-miscible polyaniline or polypyrrole particles (concentrations of 0.108, 0.054 and 0.036% w/w) were manufactured. For this purpose, either crosslinking with N-(3-dimethylaminopropyl-N-ethylcarbodiimide hydrochloride and N-hydroxysuccinimid or a freeze-thawing process in the presence of poly(vinylalcohol) was used. The scaffolds comprised interconnected pores with prevailing porosity values of ~ 30% and pore sizes enabling the accommodation of cells. A swelling capacity of 92–97% without any sign of disintegration was typical for all samples. The elasticity modulus depended on the composition of the scaffolds, with the highest value of ~ 50 kPa obtained for the sample containing the highest content of polypyrrole particles. The scaffolds did not possess cytotoxicity and allowed cell adhesion and growth on the surface. Using the in vivo-mimicking conditions in a bioreactor, cells were also able to grow into the structure of the scaffolds. The technique of scaffold preparation used here thus overcomes the limitations of conductive polymers (e.g. poor solubility in an aqueous environment, and limited miscibility with other hydrophilic polymer matrices) and moreover leads to the preparation of cytocompatible scaffolds with potentially cell-instructive properties, which may be of advantage in the healing of damaged electro-sensitive tissues.
A metamodel-based flexible insulin therapy for type 1 diabetes patients subjected to aerobic physical activity
Authors: Scharbarg Emeric , Greck Joachim , Le Carpentier Eric , Chaillous Lucy , Moog Claude H.
Published: May 2022

Patients with type 1 diabetes are subject to exogenous insulin injections, whether manually or through (semi)automated insulin pumps. Basic knowledge of the patient’s characteristics and flexible insulin therapy (FIT) parameters are then needed. Specifically, artificial pancreas-like closed-loop insulin delivery systems are some of the most promising devices for substituting for endogenous insulin secretion in type 1 diabetes patients. However, these devices require self-reported information such as carbohydrates or physical activity from the patient, introducing potential miscalculations and delays that can have life-threatening consequences. Here, we display a metamodel for glucose-insulin dynamics that is subject to carbohydrate ingestion and aerobic physical activity. This metamodel incorporates major existing knowledge-based models. We derive comprehensive and universal definitions of the underlying FIT parameters to form an insulin sensitivity factor (ISF). In addition, the relevance of physical activity modelling is assessed, and the FIT is updated to take physical exercise into account. Specifically, we cope with physical activity by using heart rate sensors (watches) with a fully automated closed insulin loop, aiming to maximize the time spent in the glycaemic range (75.5% in the range and 1.3% below the range for hypoglycaemia on a virtual patient simulator).These mathematical parameter definitions are interesting on their own, may be new tools for assessing mathematical models and can ultimately be used in closed-loop artificial pancreas algorithms or to extend distinguished FIT.