bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Representation of Clouds in the Atmospheric Component LMDZ6A of the IPSL‐CM6A Earth System Model
Authors: Madeleine Jean‐Baptiste , Hourdin Frédéric , Grandpeix Jean‐Yves , Rio Catherine , Dufresne Jean‐Louis , Vignon Etienne , Boucher Olivier , Konsta Dimitra , Cheruy Frédérique , Musat Ionela , Idelkadi Abderrahmane , Fairhead Laurent , Millour Ehouarn , Lefebvre Marie‐Pierre , Mellul Lidia , Rochetin Nicolas , Lemonnier Florentin , Touzé‐Peiffer Ludovic , Bonazzola Marine 
Published: September 2020

AbstractThe cloud parameterizations of the LMDZ6A climate model (the atmospheric component of the IPSL‐CM6 Earth system model) are entirely described, and the global cloud distribution and cloud radiative effects are evaluated against the CALIPSO‐CloudSat and CERES observations. The cloud parameterizations in recent versions of LMDZ favor an object‐oriented approach for convection, with two distinct parameterizations for shallow and deep convection and a coupling between convection and cloud description through the specification of the subgrid‐scale distribution of water. Compared to the previous version of the model (LMDZ5A), LMDZ6A better represents the low‐level cloud distribution in the tropical belt, and low‐level cloud reflectance and cover are closer to the PARASOL and CALIPSO‐GOCCP observations. Mid‐level clouds, which were mostly missing in LMDZ5A, are now better represented globally. The distribution of cloud liquid and ice in mixed‐phase clouds is also in better agreement with the observations. Among identified deficiencies, low‐level cloud covers are too high in mid‐latitude to high‐latitude regions, and high‐level cloud covers are biased low globally. However, the cloud global distribution is significantly improved, and progress has been made in the tuning of the model, resulting in a radiative balance in close agreement with the CERES observations. Improved tuning also revealed structural biases in LMDZ6A, which are currently being addressed through a series of new physical and radiative parameterizations for the next version of LMDZ.
A Warm, Stratified, and Restricted Labrador Sea Across the Middle Eocene and Its Climatic Optimum
Authors: Cramwinckel Marlow J. , Coxall Helen K. , Śliwińska Kasia K. , Polling Marcel , Harper Dustin T. , Bijl Peter K. , Brinkhuis Henk , Eldrett James S. , Houben Alexander J. P. , Peterse Francien , Schouten Stefan , Reichart Gert‐Jan , Zachos James C. , Sluijs Appy 
Published: September 2020

AbstractSeveral studies indicate that North Atlantic Deep Water (NADW) formation might have initiated during the globally warm Eocene (56–34 Ma). However, constraints on Eocene surface ocean conditions in source regions presently conducive to deep water formation are sparse. Here we test whether ocean conditions of the middle Eocene Labrador Sea might have allowed for deep water formation by applying (organic) geochemical and palynological techniques, on sediments from Ocean Drilling Program (ODP) Site 647. We reconstruct a long‐term sea surface temperature (SST) drop from ~30°C to ~27°C between 41.5 to 38.5 Ma, based on TEX86. Superimposed on this trend, we record ~2°C warming in SST associated with the Middle Eocene Climatic Optimum (MECO; ~40 Ma), which is the northernmost MECO record as yet, and another, likely regional, warming phase at ~41.1 Ma, associated with low‐latitude planktic foraminifera and dinoflagellate cyst incursions. Dinoflagellate cyst assemblages together with planktonic foraminiferal stable oxygen isotope ratios overall indicate low surface water salinities and strong stratification. Benthic foraminifer stable carbon and oxygen isotope ratios differ from global deep ocean values by 1–2‰ and 2–4‰, respectively, indicating geographic basin isolation. Our multiproxy reconstructions depict a consistent picture of relatively warm and fresh but also highly variable surface ocean conditions in the middle Eocene Labrador Sea. These conditions were unlikely conducive to deep water formation. This implies either NADW did not yet form during the middle Eocene or it formed in a different source region and subsequently bypassed the southern Labrador Sea.
The Visual Complexity of Coronal Mass Ejections Follows the Solar Cycle
Authors: Jones S. R. , Scott C. J. , Barnard L. A. , Highfield R. , Lintott C. J. , Baeten E. 
Published: September 2020

AbstractThe Heliospheric Imagers on board National Aeronautics and Space Administration (NASA)'s twin STEREO spacecraft show that coronal mass ejections (CMEs) can be visually complex structures. To explore this complexity, we created a citizen science project with the U.K. Science Museum, in which participants were shown pairs of CME images and asked to decide which image in each pair appeared the most “complicated.” A Bradley‐Terry model was then applied to these data to rank the CMEs by their “complicatedness,” or “visual complexity.” This complexity ranking revealed that the annual average visual complexity values follow the solar activity cycle, with a higher level of complexity being observed at the peak of the cycle. The average complexity of CMEs observed by STEREO‐A was also found to be significantly higher than those observed by STEREO‐B. Visual complexity was found to be associated with CME size and brightness, but our results suggest that complexity may be influenced by the scale‐sizes of structure in the CMEs.
Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer
Authors: Cho Jae-Won , Hong Min Hee , Ha Sang-Jun , Kim Young-Joon , Cho Byoung Chul , Lee Insuk , Kim Hye Ryun 
Published: September 2020

AbstractAlthough approved programmed cell death protein (PD)-1 inhibitors show durable responses, clinical benefits to these agents are only seen in one-third of patients in most cancer types. Therefore, strategies for improving the response to PD-1 inhibitor for treating various cancers including non-small cell lung cancer (NSCLC) are urgently needed. Compared with genome and transcriptome, tumor DNA methylome in anti-PD-1 response was relatively unexplored. We compared the pre-treatment methylation status ofcis-regulatory elements between responders and non-responders to treatment with nivolumab or pembrolizumab using the Infinium Methylation EPIC Array, which can profile ~850,000 CpG sites, including ~350,000 CpG sites located in enhancer regions. Then, we analyzed differentially methylated regions overlapping promoters (pDMRs) or enhancers (eDMRs) between responders and non-responders to PD-1 inhibitors. We identified 1007 pDMRs and 607 eDMRs associated with the anti-PD-1 response. We also identified 1109 and 1173 target genes putatively regulated by these pDMRs and eDMRs, respectively. We found that eDMRs contribute to the epigenetic regulation of the anti-PD-1 response more than pDMRs. Hypomethylated pDMRs of Cytohesin 1 Interacting Protein (CYTIP) and TNF superfamily member 8 (TNFSF8) were more predictive than programmed cell death protein ligand 1 (PD-L1) expression for anti-PD-1 response and progression-free survival (PFS) and overall survival (OS) in a validation cohort, suggesting their potential as predictive biomarkers for anti-PD-1 immunotherapy. The catalog of promoters and enhancers differentially methylated between responders and non-responders to PD-1 inhibitors presented herein will guide the development of biomarkers and therapeutic strategies for improving anti-PD-1 immunotherapy in NSCLC.
Disease severity dictates SARS-CoV-2-specific neutralizing antibody responses in COVID-19
Authors: Chen Xiangyu , Pan Zhiwei , Yue Shuai , Yu Fei , Zhang Junsong , Yang Yang , Li Ren , Liu Bingfeng , Yang Xiaofan , Gao Leiqiong , Li Zhirong , Lin Yao , Huang Qizhao , Xu Lifan , Tang Jianfang , Hu Li , Zhao Jing , Liu Pinghuang , Zhang Guozhong , Chen Yaokai , Deng Kai , Ye Lilin 
Published: September 2020

AbstractCOVID-19 patients exhibit differential disease severity after SARS-CoV-2 infection. It is currently unknown as to the correlation between the magnitude of neutralizing antibody (NAb) responses and the disease severity in COVID-19 patients. In a cohort of 59 recovered patients with disease severity including severe, moderate, mild, and asymptomatic, we observed the positive correlation between serum neutralizing capacity and disease severity, in particular, the highest NAb capacity in sera from the patients with severe disease, while a lack of ability of asymptomatic patients to mount competent NAbs. Furthermore, the compositions of NAb subtypes were also different between recovered patients with severe symptoms and with mild-to-moderate symptoms. These results reveal the tremendous heterogeneity of SARS-CoV-2-specific NAb responses and their correlations to disease severity, highlighting the needs of future vaccination in COVID-19 patients recovered from asymptomatic or mild illness.
Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens
Authors: Vesga Pilar , Flury Pascale , Vacheron Jordan , Keel Christoph , Croll Daniel , Maurhofer Monika 
Published: September 2020

Abstract
Pseudomonas protegens shows a high degree of lifestyle plasticity since it can establish both plant-beneficial and insect-pathogenic interactions. While P. protegens protects plants against soilborne pathogens, it can also invade insects when orally ingested leading to the death of susceptible pest insects. The mechanism whereby pseudomonads effectively switch between lifestyles, plant-beneficial or insecticidal, and the specific factors enabling plant or insect colonization are poorly understood. We generated a large-scale transcriptomics dataset of the model P. protegens strain CHA0 which includes data from the colonization of wheat roots, the gut of Plutella xylostella after oral uptake and the Galleria mellonella hemolymph after injection. We identified extensive plasticity in transcriptomic profiles depending on the environment and specific factors associated to different hosts or different stages of insect infection. Specifically, motor-activity and Reb toxin-related genes were highly expressed on wheat roots but showed low expression within insects, while certain antimicrobial compounds (pyoluteorin), exoenzymes (a chitinase and a polyphosphate kinase), and a transposase exhibited insect-specific expression. We further identified two-partner secretion systems as novel factors contributing to pest insect invasion. Finally, we use genus-wide comparative genomics to retrace the evolutionary origins of cross-kingdom colonization.
Rare and common vertebrates span a wide spectrum of population trends
Authors: Daskalova Gergana N. , Myers-Smith Isla H. , Godlee John L. 
Published: September 2020

AbstractThe Earth’s biota is changing over time in complex ways. A critical challenge is to test whether specific biomes, taxa or types of species benefit or suffer in a time of accelerating global change. We analysed nearly 10,000 abundance time series from over 2000 vertebrate species part of the Living Planet Database. We integrated abundance data with information on geographic range, habitat preference, taxonomic and phylogenetic relationships, and IUCN Red List Categories and threats. We find that 15% of populations declined, 18% increased, and 67% showed no net changes over time. Against a backdrop of no biogeographic and phylogenetic patterning in population change, we uncover a distinct taxonomic signal. Amphibians were the only taxa that experienced net declines in the analysed data, while birds, mammals and reptiles experienced net increases. Population trends were poorly captured by species’ rarity and global-scale threats. Incorporation of the full spectrum of population change will improve conservation efforts to protect global biodiversity.
Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems
Authors: Bellas Christopher M. , Schroeder Declan C. , Edwards Arwyn , Barker Gary , Anesio Alexandre M. 
Published: September 2020

AbstractBacteriophage genomes rapidly evolve via mutation and horizontal gene transfer to counter evolving bacterial host defenses; such arms race dynamics should lead to divergence between phages from similar, geographically isolated ecosystems. However, near-identical phage genomes can reoccur over large geographical distances and several years apart, conversely suggesting many are stably maintained. Here, we show that phages with near-identical core genomes in distant, discrete aquatic ecosystems maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants. By repeatedly reconstructing the core and flexible regions of phage genomes from different metagenomes, we show a pool of homologous gene variants co-exist for each module in each location, however, the dominant variant shuffles independently in each module. These results suggest that in a natural community, recombination is the largest contributor to phage diversity, allowing a variety of host recognition receptors and genes to counter bacterial defenses to co-exist for each phage.
Printing accuracy tracking with 2D optical microscopy and super-resolution metamaterial-assisted 1D terahertz spectroscopy
Authors: Zhuldybina Mariia , Ropagnol Xavier , Bois Chloé , Zednik Ricardo J. , Blanchard François 
Published: September 2020

AbstractPrintable electronics is a promising manufacturing technology for the potential production of low-cost flexible electronic devices, ranging from displays to active wear. It is known that rapid printing of conductive ink on a flexible substrate is vulnerable to several sources of variation during the manufacturing process. However, this process is still not being subjected to a quality control method that is both non-invasive and in situ. To address this issue, we propose controlling the printing accuracy by monitoring the spatial distribution of the deposited ink using terahertz (THz) waves. The parameters studied are the printing speed of an industrial roll-to-roll press with flexography printing units and the pre-calibration compression, or expansion factor, for a pattern printed on a flexible plastic substrate. The pattern, which is carefully selected, has Babinet’s electromagnetic transmission properties in the THz frequency range. To validate our choice, we quantified the geometric variations of the printed pattern by visible microscopy and compared its accuracy using one-dimensional THz spectroscopy. Our study shows a remarkable agreement between visible microscopic observation of the printing performance and the signature of the THz transmission. Notably, under specific conditions, one-dimensional (1D) THz information from a resonant pattern can be more accurate than two-dimensional (2D) microscopy information. This result paves the way for a simple strategy for non-invasive and contactless in situ monitoring of printable electronics production.
Enhanced laser action from smart fabrics made with rollable hyperbolic metamaterials
Authors: Lin Hung-I , Wang Chun-Che , Shen Kun-Ching , Shalaginov Mikhail Y. , Roy Pradip Kumar , Bera Krishna Prasad , Kataria Monika , Paul Inbaraj Christy Roshini , Chen Yang-Fang 
Published: September 2020

AbstractRollable photonic devices that can adapt to freeform surfaces with reduced dimensions while maintaining their original functionalities are highly desirable. Among photonic devices, metamaterials with hyperbolic dispersion in momentum space, defined as hyperbolic metamaterial (HMM), possess a large photonic density of states that has been proven to boost light-matter interaction. However, these devices are mainly developed on rigid substrates, restricting their functionalities. Here, we present the attempt to integrate flexible and rollable HMMs consisting of polymer and metal multilayers on paper substrate. Quite interestingly, this design enables to exhibit high photonic density of states and scattering efficiency to enhance stimulated emission and induce pronounced laser action. The flexible and rollable HMM structure remains well its functionalities on freeform surfaces with curvature radius of 1 mm, and can withstand repeated bending without performance degradation. The intensity of laser action is enhanced by 3.5 times as compared to the flat surface. We anticipate that this flexible and rollable HMM structure can serve as a diverse platform for flexible photonic technologies, such as light-emitting devices, wearable optoelectronics, and optical communication.
Functional brain networks in the schizophrenia spectrum and bipolar disorder with psychosis
Authors: van Dellen Edwin , Börner Corinna , Schutte Maya , van Montfort Simone , Abramovic Lucija , Boks Marco P. , Cahn Wiepke , van Haren Neeltje , Mandl René , Stam Cornelis J. , Sommer Iris 
Published: September 2020

AbstractPsychotic experiences have been proposed to lie on a spectrum, ranging from subclinical experiences to treatment-resistant schizophrenia. We aimed to characterize functional connectivity and brain network characteristics in relation to the schizophrenia spectrum and bipolar disorder with psychosis to disentangle neural correlates to psychosis. Additionally, we studied antipsychotic medication and lithium effects on network characteristics. We analyzed functional connectivity strength and network topology in 487 resting-state functional MRI scans of individuals with schizophrenia spectrum disorder (SCZ), bipolar disorder with a history of psychotic experiences (BD), treatment-naïve subclinical psychosis (SCP), and healthy controls (HC). Since differences in connectivity strength may confound group comparisons of brain network topology, we analyzed characteristics of the minimum spanning tree (MST), a relatively unbiased backbone of the network. SCZ and SCP subjects had a lower connectivity strength than BD and HC individuals but showed no differences in network topology. In contrast, BD patients showed a less integrated network topology but no disturbances in connectivity strength. No differences in outcome measures were found between SCP and SCZ, or between BD patients that used antipsychotic medication or lithium and those that did not. We conclude that functional networks in patients prone to psychosis have different signatures for chronic SCZ patients and SCP compared to euthymic BD patients, with a limited role for medication. Connectivity strength effects may have confounded previous studies, as no functional network alterations were found in SCZ after strict correction for connectivity strength.
Dynamic control of heat flow using a spin-chain ladder cuprate film and an ionic liquid
Authors: Terakado Nobuaki , Nara Yoshinori , Machida Yuki , Takahashi Yoshihiro , Fujiwara Takumi 
Published: September 2020

AbstractDynamic control of heat flow for applications in thermal management has attracted much interest in fields such as electronics and thermal engineering. Spin-chain ladder cuprates are promising materials to realize dynamic control of heat flow, since their magnon thermal conductivity is sensitive to the hole density in the spin ladders, which can be dynamically controlled by an external field. Here, we demonstrate the electric control of heat flow using a polycrystalline cuprate film and an ionic liquid. The results showed that a voltage application to the interface causes imperfectly recoverable decreases in both the thermal conductance of the film and the peak due to magnons in the Raman spectra. This result may be attributed to an increase in the hole density in the spin ladders. This report highlights that magnon thermal conduction has potential for the development of advanced thermal management applications.
Carbohydrate knowledge, dietary guideline awareness, motivations and beliefs underlying low-carbohydrate dietary behaviours
Authors: Churuangsuk Chaitong , Lean Michael E. J. , Combet Emilie 
Published: September 2020

AbstractTo explore the factors (including knowledge and attitude) influencing the decision to follow a low-carbohydrate diet (LCD) or not in a sample of the UK population. An online questionnaire was distributed electronically to adults who had either followed LCD or not (February–December 2019). Demographics and self-reported “LCD-status” (current, past and non-follower) were collected. Multivariable linear regression was used with carbohydrate knowledge, dietary guideline agreement and theory of planned behaviour (TPB) constructs (all as predictors) to explain the intention to follow a LCD (outcome). Respondents (n = 723, 71% women, median age 34; 85% white-ethnicity) were either following (n = 170, 24%) or had tried a LCD in the preceding 3 months (n = 184, 25%). Current followers had lower carbohydrate knowledge scores (1–2 point difference, scale − 11 to 11) than past and non-followers. A majority of current LCD followers disagreed with the EatWell guide recommendations “Base meals on potatoes, bread, rice and pasta, or other starchy carbohydrates. Choose whole grains where possible” (84%) and “Choose unsaturated oils and spreads and eat in small amounts such as vegetable, rapeseed, olive and sunflower oils” (68%) compared to past (37%, 10%, respectively) and non-followers (16%, 8%, respectively). Weight-loss ranked first as a motivation, and the internet was the most influencial source of information about LCDs. Among LCD-followers, 71% reported ≥ 5% weight loss, and over 80% did not inform their doctor, nurse, or dietitian about following a diet. Approximately half of LCD followers incorporated supplements to their diets (10% used multivitamin/mineral supplements), despite the restrictive nature of the diet. TPB constructs, carbohydrate knowledge, and guideline agreement explained 60% of the variance for the intention to follow a LCD. Attitude (std-β = 0.60), perceived behavioural control (std-β = 0.24) and subjective norm (std-β = 0.14) were positively associated with the intention to follow a LCD, while higher knowledge of carbohydrate, and agreeing with national dietary guidelines were both inversely associated (std-β = − 0.09 and − 0.13). The strongest primary reason behind UK adults’ following a LCD is to lose weight, facilitated by attitude, perceived behavioural control and subjective norm. Higher knowledge about carbohydrate and agreement with dietary guidelines are found among people who do not follow LCDs.
Using the transient trajectories of an optically levitated nanoparticle to characterize a stochastic Duffing oscillator
Authors: Flajšmanová Jana , Šiler Martin , Jedlička Petr , Hrubý František , Brzobohatý Oto , Filip Radim , Zemánek Pavel 
Published: September 2020

AbstractWe propose a novel methodology to estimate parameters characterizing a weakly nonlinear Duffing oscillator represented by an optically levitating nanoparticle. The method is based on averaging recorded trajectories with defined initial positions in the phase space of nanoparticle position and momentum and allows us to study the transient dynamics of the nonlinear system. This technique provides us with the parameters of a levitated nanoparticle such as eigenfrequency, damping, coefficient of nonlinearity and effective temperature directly from the recorded transient particle motion without any need for external driving or modification of an experimental system. Comparison of this innovative approach with a commonly used method based on fitting the power spectrum density profile shows that the proposed complementary method is applicable even at lower pressures where the nonlinearity starts to play a significant role and thus the power spectrum density method predicts steady state parameters. The technique is applicable also at low temperatures and extendable to recent quantum experiments. The proposed method is applied on experimental data and its validity for one-dimensional and three-dimensional motion of a levitated nanoparticle is verified by extensive numerical simulations.