bluuebunny/crossref_metadata_2025_split huggingface dataset:
Box Model Intercomparison of Cloud Chemistry
Authors: Barth Mary C. , Ervens Barbara , Herrmann Hartmut , Tilgner Andreas , McNeill V. Faye , Tsui William Gang , Deguillaume Laurent , Chaumerliac Nadine , Carlton Annmarie , Lance Sara M. 
Published: October 2021

AbstractChemical processes in clouds and fogs can substantially alter atmospheric oxidant budgets and lead to aerosol mass formation. However, many regional and global models do not include detailed aqueous‐phase chemical mechanisms due to the (a) lack of complete understanding of the chemical processes and (b) computational burden of adding constituents. Current gas‐aqueous chemistry 0‐dimensional models were evaluated in a cloud‐chemistry box model intercomparison based on a mid‐September 2016 cloud chemistry event at Whiteface Mountain, New York. Multiphase mechanisms in the five participating models ranged from those appropriate for 3‐d models to highly complex with thousands of reactions. This study focused on oxidant levels in both phases and aqueous‐phase sulfate and organic acid formation. Comparison of gas‐phase‐only chemistry gives very similar oxidant predictions at night but shows significant differences during daytime with the hydroxyl radical (OH) variability of about an order of magnitude. The variability in the model results increases substantially with aqueous chemistry due to different Henry's Law constants, aqueous‐phase reaction rate constants, and chemical mechanisms. Using a prescribed liquid water content and pH value of 4.5, modeled aqueous OH, aldehyde, and organic acid concentrations differ by over an order of magnitude in daytime. Simulations were also conducted at a pH = 5.1, predicted variable pH, and with added transition metal ion chemistry. While we compare predicted and measured inorganic anions and water‐soluble organic carbon, we cannot do so for aqueous‐phase oxidant concentrations due to the lack of measurements. We highlight a need for recommended equilibrium and aqueous‐phase rate constants.
Improving Constraints on Planetary Interiors With PPs Receiver Functions
Authors: Kim D. , Lekić V. , Irving J. C. E. , Schmerr N. , Knapmeyer‐Endrun B. , Joshi R. , Panning M. P. , Tauzin B. , Karakostas F. , Maguire R. , Huang Q. , Ceylan S. , Khan A. , Giardini D. , Wieczorek M. A. , Lognonné P. , Banerdt W. B. 
Published: October 2021

AbstractSeismological constraints obtained from receiver function (RF) analysis provide important information about the crust and mantle structure. Here, we explore the utility of the free‐surface multiple of the P‐wave (PP) and the corresponding conversions in RF analysis. Using earthquake records, we demonstrate the efficacy of PPs‐RFs before illustrating how they become especially useful when limited data is available in typical planetary missions. Using a transdimensional hierarchical Bayesian deconvolution approach, we compute robust P‐to‐S (Ps)‐ and PPs‐RFs with InSight recordings of five marsquakes. Our Ps‐RF results verify the direct Ps converted phases reported by previous RF analyses with increased coherence and reveal other phases including the primary multiple reverberating within the uppermost layer of the Martian crust. Unlike the Ps‐RFs, our PPs‐RFs lack an arrival at 7.2 s lag time. Whereas Ps‐RFs on Mars could be equally well fit by a two‐ or three‐layer crust, synthetic modeling shows that the disappearance of the 7.2 s phase requires a three‐layer crust, and is highly sensitive to velocity and thickness of intra‐crustal layers. We show that a three‐layer crust is also preferred by S‐to‐P (Sp)‐RFs. While the deepest interface of the three‐layer crust represents the crust‐mantle interface beneath the InSight landing site, the other two interfaces at shallower depths could represent a sharp transition between either fractured and unfractured materials or thick basaltic flows and pre‐existing crustal materials. PPs‐RFs can provide complementary constraints and maximize the extraction of information about crustal structure in data‐constrained circumstances such as planetary missions.
Rotating Shallow Water Flow Under Location Uncertainty With a Structure‐Preserving Discretization
Authors: Brecht Rüdiger , Li Long , Bauer Werner , Mémin Etienne 
Published: October 2021

AbstractWe introduce a physically relevant stochastic representation of the rotating shallow water equations. The derivation relies mainly on a stochastic transport principle and on a decomposition of the fluid flow into a large‐scale component and a noise term that models the unresolved flow components. As for the classical (deterministic) system, this scheme, referred to as modeling under location uncertainty (LU), conserves the global energy of any realization and provides the possibility to generate an ensemble of physically relevant random simulations with a good trade‐off between the model error representation and the ensemble's spread. To maintain numerically the energy conservation feature, we combine an energy (in space) preserving discretization of the underlying deterministic model with approximations of the stochastic terms that are based on standard finite volume/difference operators. The LU derivation, built from the very same conservation principles as the usual geophysical models, together with the numerical scheme proposed can be directly used in existing dynamical cores of global numerical weather prediction models. The capabilities of the proposed framework is demonstrated for an inviscid test case on the f‐plane and for a barotropically unstable jet on the sphere.
Unmanned Aerial Vehicles in Hydrology and Water Management: Applications, Challenges, and Perspectives
Authors: Acharya Bharat Sharma , Bhandari Mahendra , Bandini Filippo , Pizarro Alonso , Perks Matthew , Joshi Deepak Raj , Wang Sheng , Dogwiler Toby , Ray Ram L. , Kharel Gehendra , Sharma Sadikshya 
Published: October 2021

AbstractThe hydrologic sciences and water resources management have long depended on a combination of in situ measurements and remotely sensed data for research and regulatory purposes. In situ measurements are constrained in their spatial distribution by both logistics and costs. Satellite‐ and manned aircraft‐based remote sensing provide spatially broad data, but often of a coarse resolution. Furthermore, all these data collection methods are often limited in their ability to respond to specific short‐term events when the data and imagery could inform real‐time assessment and decision‐making, especially during and immediately after natural disasters. Researchers and regulators are increasingly using unmanned aerial vehicles (UAVs) to fill these gaps in both spatial and temporal data resolution. UAVs are often more cost‐effective than traditional remote sensing or in situ data collection methodologies and the availability of new advancements in UAV design, power supply, payload capacity, and sensors has been driving rapid innovations in their use in the hydrological sciences. This in‐depth review explores these UAV technologies and how they are being employed for on‐demand and cost‐effective characterization, monitoring, assessment, and modeling of soil and water resources. Our discussion addresses both key opportunities and challenges in surface water and groundwater studies, land‐atmosphere interaction studies, water management in agriculture and forestry, ecosystem monitoring, and hydrological modeling.
Effect of inoculum size and antibiotics on bacterial traveling bands in a thin microchannel defined by optical adhesive
Authors: Liu Yang , Lehnert Thomas , Gijs Martin A. M. 
Published: October 2021

AbstractPhenotypic diversity in bacterial flagella-induced motility leads to complex collective swimming patterns, appearing as traveling bands with transient locally enhanced cell densities. Traveling bands are known to be a bacterial chemotactic response to self-generated nutrient gradients during growth in resource-limited microenvironments. In this work, we studied different parameters of Escherichia coli (E. coli) collective migration, in particular the quantity of bacteria introduced initially in a microfluidic chip (inoculum size) and their exposure to antibiotics (ampicillin, ciprofloxacin, and gentamicin). We developed a hybrid polymer-glass chip with an intermediate optical adhesive layer featuring the microfluidic channel, enabling high-content imaging of the migration dynamics in a single bacterial layer, i.e., bacteria are confined in a quasi-2D space that is fully observable with a high-magnification microscope objective. On-chip bacterial motility and traveling band analysis was performed based on individual bacterial trajectories by means of custom-developed algorithms. Quantifications of swimming speed, tumble bias and effective diffusion properties allowed the assessment of phenotypic heterogeneity, resulting in variations in transient cell density distributions and swimming performance. We found that incubation of isogeneic E. coli with different inoculum sizes eventually generated different swimming phenotype distributions. Interestingly, incubation with antimicrobials promoted bacterial chemotaxis in specific cases, despite growth inhibition. Moreover, E. coli filamentation in the presence of antibiotics was assessed, and the impact on motility was evaluated. We propose that the observation of traveling bands can be explored as an alternative for fast antimicrobial susceptibility testing.
Positive feedback between ROS and cis-axis of PIASxα/p38α-SUMOylation/MK2 facilitates gastric cancer metastasis
Authors: Wang Qian , Xu Ci , Fan Qiang , Yuan Haihua , Zhang Xin , Chen Biying , Cai Renjie , Zhang Yanjie , Lin Moubin , Xu Ming 
Published: October 2021

AbstractMAPK/p38 is an important mammalian signaling cascade that responds to a variety of intracellular or extracellular stimuli, such as reactive oxygen species (ROS), and participates in numerous physiological and pathological processes. However, the biological function of p38 in different tumors, and even at different stages of the same tumor, remains elusive. To further understand the regulatory mechanism of p38 and oxidative stress in the occurrence and development of gastric cancer, we report SUMOylation as a novel post-translational modification occurring on lysine 152 of MAPK14/p38α through immunoprecipitation and series of pull-down assays in vitro and in vivo. Importantly, we determine that p38α-SUMOylation functions as an authentic sensor and accelerator of reactive oxygen species generation via interaction with and activation of MK2 in the nucleus, and the ROS accumulation, in turn, promotes the SUMOylation of p38α by stabilizing the PIASxα protein. This precise regulatory mechanism is exploited by gastric cancer cells to create an internal environment for survival and, ultimately, metastasis. This study reveals novel insights into p38α-SUMOylation and its association with the intracellular oxidative stress response, which is closely related to the processes of gastric cancer. Furthermore, the PIASxα/p38α-SUMOylation/MK2 cis-axis may serve as a desirable therapeutic target in gastric cancer as targeting PIASxα, MK2, or a specific peptide region of p38α may reconcile the aberrant oxidative stress response in gastric cancer cells.
Approaching the ultimate superconducting properties of (Ba,K)Fe2As2 by naturally formed low-angle grain boundary networks
Authors: Iida Kazumasa , Qin Dongyi , Tarantini Chiara , Hatano Takafumi , Wang Chao , Guo Zimeng , Gao Hongye , Saito Hikaru , Hata Satoshi , Naito Michio , Yamamoto Akiyasu 
Published: October 2021

AbstractThe most effective way to enhance the dissipation-free supercurrent in the presence of a magnetic field for type II superconductors is to introduce defects that act as artificial pinning centers (APCs) for vortices. For instance, the in-field critical current density of doped BaFe2As2 (Ba122), one of the most technologically important Fe-based superconductors, has been improved over the last decade by APCs created by ion irradiation. The technique of ion irradiation has been commonly implemented to determine the ultimate superconducting properties. However, this method is rather complicated and expensive. Here, we report a surprisingly high critical current density and strong pinning efficiency close to the crystallographic c-axis for a K-doped Ba122 epitaxial thin film without APCs, achieving performance comparable to ion-irradiated K-doped Ba122 single crystals. Microstructural analysis reveals that the film is composed of columnar grains with widths of approximately 30–60 nm. The grains are rotated around the b- (or a-) axis by 1.5° and around the c-axis by −1°, resulting in the formation of low-angle grain boundary networks. This study demonstrates that the upper limit of in-field properties reached in ion-irradiated K-doped Ba122 is achievable by grain boundary engineering, which is a simple and industrially scalable manner.
Sympathetic cooling of positrons to cryogenic temperatures for antihydrogen production
Authors: Baker C. J. , Bertsche W. , Capra A. , Cesar C. L. , Charlton M. , Mathad A. Cridland , Eriksson S. , Evans A. , Evetts N. , Fabbri S. , Fajans J. , Friesen T. , Fujiwara M. C. , Grandemange P. , Granum P. , Hangst J. S. , Hayden M. E. , Hodgkinson D. , Isaac C. A. , Johnson M. A. , Jones J. M. , Jones S. A. , Jonsell S. , Kurchaninov L. , Madsen N. , Maxwell D. , McKenna J. T. K. , Menary S. , Momose T. , Mullan P. , Olchanski K. , Olin A. , Peszka J. , Powell A. , Pusa P. , Rasmussen C. Ø. , Robicheaux F. , Sacramento R. L. , Sameed M. , Sarid E. , Silveira D. M. , Stutter G. , So C. , Tharp T. D. , Thompson R. I. , van der Werf D. P. , Wurtele J. S. 
Published: October 2021

AbstractThe positron, the antiparticle of the electron, predicted by Dirac in 1931 and discovered by Anderson in 1933, plays a key role in many scientific and everyday endeavours. Notably, the positron is a constituent of antihydrogen, the only long-lived neutral antimatter bound state that can currently be synthesized at low energy, presenting a prominent system for testing fundamental symmetries with high precision. Here, we report on the use of laser cooled Be+ ions to sympathetically cool a large and dense plasma of positrons to directly measured temperatures below 7 K in a Penning trap for antihydrogen synthesis. This will likely herald a significant increase in the amount of antihydrogen available for experimentation, thus facilitating further improvements in studies of fundamental symmetries.
The flashfm approach for fine-mapping multiple quantitative traits
Authors: Hernández N. , Soenksen J. , Newcombe P. , Sandhu M. , Barroso I. , Wallace C. , Asimit J. L. 
Published: October 2021

AbstractJoint fine-mapping that leverages information between quantitative traits could improve accuracy and resolution over single-trait fine-mapping. Using summary statistics, flashfm (flexible and shared information fine-mapping) fine-maps signals for multiple traits, allowing for missing trait measurements and use of related individuals. In a Bayesian framework, prior model probabilities are formulated to favour model combinations that share causal variants to capitalise on information between traits. Simulation studies demonstrate that both approaches produce broadly equivalent results when traits have no shared causal variants. When traits share at least one causal variant, flashfm reduces the number of potential causal variants by 30% compared with single-trait fine-mapping. In a Ugandan cohort with 33 cardiometabolic traits, flashfm gave a 20% reduction in the total number of potential causal variants from single-trait fine-mapping. Here we show flashfm is computationally efficient and can easily be deployed across publicly available summary statistics for signals in up to six traits.
Hedgehog artificial macrophage with atomic-catalytic centers to combat Drug-resistant bacteria
Authors: Long Yanping , Li Ling , Xu Tao , Wu Xizheng , Gao Yun , Huang Jianbo , He Chao , Ma Tian , Ma Lang , Cheng Chong , Zhao Changsheng 
Published: October 2021

AbstractPathogenic drug-resistant bacteria represent a threat to human health, for instance, the methicillin-resistant Staphylococcus aureus (MRSA). There is an ever-growing need to develop non-antibiotic strategies to fight bacteria without triggering drug resistance. Here, we design a hedgehog artificial macrophage with atomic-catalytic centers to combat MRSA by mimicking the “capture and killing” process of macrophages. The experimental studies and theoretical calculations reveal that the synthesized materials can efficiently capture and kill MRSA by the hedgehog topography and substantial generation of •O2− and HClO with its Fe2N6O catalytic centers. The synthesized artificial macrophage exhibits a low minimal inhibition concentration (8 μg/mL Fe-Art M with H2O2 (100 μM)) to combat MRSA and rapidly promote the healing of bacteria-infected wounds on rabbit skin. We suggest that the application of this hedgehog artificial macrophage with “capture and killing” capability and high ROS-catalytic activity will open up a promising pathway to develop antibacterial materials for bionic and non-antibiotic disinfection strategies.
Characterisation of factors contributing to the performance of nonwoven fibrous matrices as substrates for adenovirus vectored vaccine stabilisation
Authors: Dulal Pawan , Gharaei Robabeh , Berg Adam , Walters Adam A. , Hawkins Nicholas , Claridge Tim D. W. , Kowal Katarzyna , Neill Steven , Ritchie Adam J. , Ashfield Rebecca , Hill Adrian V. S. , Tronci Giuseppe , Russell Stephen J. , Douglas Alexander D. 
Published: October 2021

AbstractAdenovirus vectors offer a platform technology for vaccine development. The value of the platform has been proven during the COVID-19 pandemic. Although good stability at 2–8 °C is an advantage of the platform, non-cold-chain distribution would have substantial advantages, in particular in low-income countries. We have previously reported a novel, potentially less expensive thermostabilisation approach using a combination of simple sugars and glass micro-fibrous matrix, achieving excellent recovery of adenovirus-vectored vaccines after storage at temperatures as high as 45 °C. This matrix is, however, prone to fragmentation and so not suitable for clinical translation. Here, we report an investigation of alternative fibrous matrices which might be suitable for clinical use. A number of commercially-available matrices permitted good protein recovery, quality of sugar glass and moisture content of the dried product but did not achieve the thermostabilisation performance of the original glass fibre matrix. We therefore further investigated physical and chemical characteristics of the glass fibre matrix and its components, finding that the polyvinyl alcohol present in the glass fibre matrix assists vaccine stability. This finding enabled us to identify a potentially biocompatible matrix with encouraging performance. We discuss remaining challenges for transfer of the technology into clinical use, including reliability of process performance.
Significance of genetic modifiers of hemoglobinopathies leading towards precision medicine
Authors: Hariharan Priya , Gorivale Manju , Sawant Pratibha , Mehta Pallavi , Nadkarni Anita 
Published: October 2021

AbstractHemoglobinopathies though a monogenic disorder, show phenotypic variability. Hence, understanding the genetics underlying the heritable sub-phenotypes of hemoglobinopathies, specific to each population, would be prognostically useful and could inform personalized therapeutics. This study aimed to evaluate the role of genetic modifiers leading to higher HbF production with cumulative impact of the modifiers on disease severity. 200 patients (100 β-thalassemia homozygotes, 100 Sickle Cell Anemia), and 50 healthy controls were recruited. Primary screening followed with molecular analysis for confirming the β-hemoglobinopathy was performed. Co-existing α-thalassemia and the polymorphisms located in 3 genetic loci linked to HbF regulation were screened. The most remarkable result was the association of SNPs with clinically relevant phenotypic groups. The γ-globin gene promoter polymorphisms [− 158 C → T, + 25 G → A],BCL11A rs1427407 G → T, − 3 bp HBS1L-MYB rs66650371 and rs9399137 T → C polymorphisms were correlated with higher HbF, in group that has lower disease severity score (P < 0.00001), milder clinical presentation, and a significant delay in the age of the first transfusion. Our study emphasizes the complex genetic interactions underlying the disease phenotype that may be a prognostic marker for predicting the clinical severity and assist in disease management.
Polariton condensation in an organic microcavity utilising a hybrid metal-DBR mirror
Authors: McGhee Kirsty E. , Putintsev Anton , Jayaprakash Rahul , Georgiou Kyriacos , O’Kane Mary E. , Kilbride Rachel C. , Cassella Elena J. , Cavazzini Marco , Sannikov Denis A. , Lagoudakis Pavlos G. , Lidzey David G. 
Published: October 2021

AbstractWe have developed a simplified approach to fabricate high-reflectivity mirrors suitable for applications in a strongly-coupled organic-semiconductor microcavity. Such mirrors are based on a small number of quarter-wave dielectric pairs deposited on top of a thick silver film that combine high reflectivity and broad reflectivity bandwidth. Using this approach, we construct a microcavity containing the molecular dye BODIPY-Br in which the bottom cavity mirror is composed of a silver layer coated by a SiO2 and a Nb2O5 film, and show that this cavity undergoes polariton condensation at a similar threshold to that of a control cavity whose bottom mirror consists of ten quarter-wave dielectric pairs. We observe, however, that the roughness of the hybrid mirror—caused by limited adhesion between the silver and the dielectric pair—apparently prevents complete collapse of the population to the ground polariton state above the condensation threshold.
Multi-omics analysis of m6A modification-related patterns based on m6A regulators and tumor microenvironment infiltration in lung adenocarcinoma
Authors: Wu Xincheng , Bai Zhengping 
Published: October 2021

AbstractEpigenetic modifications, especially N6-methyladenosine (m6A) modification, play a key role in tumor microenvironment (TME) infiltration. However, the regulatory role of m6A modification in the TME of lung adenocarcinoma (LUAD) remains unclear. A total of 2506 patients with LUAD were included in the analysis and divided into different groups according to distinct m6A modification-related patterns based on 23 m6A regulators. A comprehensive analysis was performed to explore TME infiltration in different m6A modification-related patterns. Principal component analysis was performed to obtain the m6Ascore and to quantify m6A modification-related patterns in different individuals. Three distinct m6A modification-related patterns were identified by 23 m6A regulators. The pathway enrichment analysis showed that m6Acluster-A was associated with immune activation; m6Acluster-B was associated with carcinogenic activation; m6Acluster-C was prominently related to substance metabolism. M6Acluster-A was remarkably rich in TME-infiltrating immune cells and patients with this pattern showed a survival advantage. The m6Ascore could predict TME infiltration, tumor mutation burden (TMB), the effect of tumor immunotherapy, and the prognosis of patients in LUAD. High m6Ascore was characterized by increased TME infiltration, reduced TMB, and survival advantage. Patients with a high m6Ascore exhibited significantly improved clinical response to anti-cytotoxic T lymphocyte antigen-4 (anti-CTLA4) immunotherapy. This study explored the regulatory mechanisms of TME infiltration in LUAD. The comprehensive analysis of m6A modification-related patterns may contribute to the development of individualized immunotherapy and the improvement of the overall effectiveness of immunotherapy for LUAD patients.