bluuebunny/crossref_metadata_2025_split huggingface dataset:
All organic multiferroic magnetoelectric complexes with strong interfacial spin-dipole interaction
Authors: Yang Yuying , Chen Zhiyan , Lu Xiangqian , Hao Xiaotao , Qin Wei 
Published: August 2021

AbstractThe organic magnetoelectric complexes are beneficial for the development on flexible magnetoelectric devices in the future. In this work, we fabricated all organic multiferroic ferromagnetic/ferroelectric complexes to study magnetoelectric coupling at room temperature. Under the stimulus of external magnetic field, the localization of charge inside organic ferromagnets will be enhanced to affect spin–dipole interaction at organic multiferroic interfaces, where overall ferroelectric polarization is tuned to present an organic magnetoelectric coupling. Moreover, the magnetoelectric coupling of the organic ferromagnetic/ferroelectric complex is tightly dependent on incident light intensity. Decreasing light intensity, the dominated interfacial interaction will switch from spin–dipole to dipole–dipole interaction, which leads to the magnetoelectric coefficient changing from positive to negative in organic multiferroic magnetoelectric complexes.
Multivariate genome-wide covariance analyses of literacy, language and working memory skills reveal distinct etiologies
Authors: Shapland Chin Yang , Verhoef Ellen , Davey Smith George , Fisher Simon E. , Verhulst Brad , Dale Philip S. , St Pourcain Beate 
Published: August 2021

AbstractSeveral abilities outside literacy proper are associated with reading and spelling, both phenotypically and genetically, though our knowledge of multivariate genomic covariance structures is incomplete. Here, we introduce structural models describing genetic and residual influences between traits to study multivariate links across measures of literacy, phonological awareness, oral language, and phonological working memory (PWM) in unrelated UK youth (8–13 years,N = 6453). We find that all phenotypes share a large proportion of underlying genetic variation, although especially oral language and PWM reveal substantial differences in their genetic variance composition with substantial trait-specific genetic influences. Multivariate genetic and residual trait covariance showed concordant patterns, except for marked differences between oral language and literacy/phonological awareness, where strong genetic links contrasted near-zero residual overlap. These findings suggest differences in etiological mechanisms, acting beyond a pleiotropic set of genetic variants, and implicate variation in trait modifiability even among phenotypes that have high genetic correlations.
Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids
Authors: Jiang Xinyu , Song Qingxin , Ye Wenxue , Chen Z. Jeffrey 
Published: August 2021

AbstractDuring evolution successful allopolyploids must overcome ‘genome shock’ between hybridizing species but the underlying process remains elusive. Here, we report concerted genomic and epigenomic changes in resynthesized and natural Arabidopsis suecica (TTAA) allotetraploids derived from Arabidopsisthaliana (TT) and Arabidopsisarenosa (AA). A. suecica shows conserved gene synteny and content with more gene family gain and loss in the A and T subgenomes than respective progenitors, although A. arenosa-derived subgenome has more structural variation and transposon distributions than A. thaliana-derived subgenome. These balanced genomic variations are accompanied by pervasive convergent and concerted changes in DNA methylation and gene expression among allotetraploids. The A subgenome is hypomethylated rapidly from F1 to resynthesized allotetraploids and convergently to the T-subgenome level in natural A. suecica, despite many other methylated loci being inherited from F1 to all allotetraploids. These changes in DNA methylation, including small RNAs, in allotetraploids may affect gene expression and phenotypic variation, including flowering, silencing of self-incompatibility and upregulation of meiosis- and mitosis-related genes. In conclusion, concerted genomic and epigenomic changes may improve stability and adaptation during polyploid evolution.
Gradual evolution of allopolyploidy in Arabidopsis suecica
Authors: Burns Robin , Mandáková Terezie , Gunis Joanna , Soto-Jiménez Luz Mayela , Liu Chang , Lysak Martin A. , Novikova Polina Yu. , Nordborg Magnus 
Published: August 2021

AbstractMost diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of ‘genome shock’, such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution.
Community composition of aquatic fungi across the thawing Arctic
Authors: Kluge Mariana , Wurzbacher Christian , Wauthy Maxime , Clemmensen Karina Engelbrecht , Hawkes Jeffrey Alistair , Einarsdottir Karolina , Stenlid Jan , Peura Sari 
Published: August 2021

AbstractThermokarst activity at permafrost sites releases considerable amounts of ancient carbon to the atmosphere. A large part of this carbon is released via thermokarst ponds, and fungi could be an important organismal group enabling its recycling. However, our knowledge about aquatic fungi in thermokarstic systems is extremely limited. In this study, we collected samples from five permafrost sites distributed across circumpolar Arctic and representing different stages of permafrost integrity. Surface water samples were taken from the ponds and, additionally, for most of the ponds also the detritus and sediment samples were taken. All the samples were extracted for total DNA, which was then amplified for the fungal ITS2 region of the ribosomal genes. These amplicons were sequenced using PacBio technology. Water samples were also collected to analyze the chemical conditions in the ponds, including nutrient status and the quality and quantity of dissolved organic carbon. This dataset gives a unique overview of the impact of the thawing permafrost on fungal communities and their potential role on carbon recycling.
Mistaken identity may explain why male sea snakes (Aipysurus laevis, Elapidae, Hydrophiinae) “attack” scuba divers
Authors: Lynch Tim P. , Alford Ross A. , Shine Richard 
Published: August 2021

AbstractScuba-divers on tropical coral-reefs often report unprovoked “attacks” by highly venomous Olive sea snakes (Aipysurus laevis). Snakes swim directly towards divers, sometimes wrapping coils around the diver’s limbs and biting. Based on a focal animal observation study of free-ranging Olive sea snakes in the southern Great Barrier Reef, we suggest that these “attacks” are misdirected courtship responses. Approaches to divers were most common during the breeding season (winter) and were by males rather than by female snakes. Males also made repeated approaches, spent more time with the diver, and exhibited behaviours (such as coiling around a limb) also seen during courtship. Agitated rapid approaches by males, easily interpreted as “attacks”, often occurred after a courting male lost contact with a female he was pursuing, after interactions between rival males, or when a diver tried to flee from a male. These patterns suggest that “attacks” by sea snakes on humans result from mistaken identity during sexual interactions. Rapid approaches by females occurred when they were being chased by males. Divers that flee from snakes may inadvertently mimic the responses of female snakes to courtship, encouraging males to give chase. To prevent escalation of encounters, divers should keep still and avoid retaliation.
East Asian climate response to COVID-19 lockdown measures in China
Authors: Lee Sun-Seon , Chu Jung-Eun , Timmermann Axel , Chung Eui-Seok , Lee June-Yi 
Published: August 2021

AbstractThe COVID-19 pandemic caused disruptions of public life and imposed lockdown measures in 2020 resulted in considerable reductions of anthropogenic aerosol emissions. It still remains unclear how the associated short-term changes in atmospheric chemistry influenced weather and climate on regional scales. To understand the underlying physical mechanisms, we conduct ensemble aerosol perturbation experiments with the Community Earth System Model, version 2. In the simulations reduced anthropogenic aerosol emissions in February generate anomalous surface warming and warm-moist air advection which promotes low-level cloud formation over China. Although the simulated response is weak, it is detectable in some areas, in qualitative agreement with the observations. The negative dynamical cloud feedback offsets the effect from reduced cloud condensation nuclei. Additional perturbation experiments with strongly amplified air pollution over China reveal a nonlinear sensitivity of regional atmospheric conditions to chemical/radiative perturbations. COVID-19-related changes in anthropogenic aerosol emissions provide an excellent testbed to elucidate the interaction between air pollution and climate.
Physiological causes of transplantation shock on rice growth inhibition and delayed heading
Authors: Lee HyeonSeok , Hwang WoonHa , Jeong JaeHyeok , Yang SeoYeong , Jeong NamJin , Lee ChungKuen , Choi MyoungGoo 
Published: August 2021

AbstractTransplanting is an important rice cultivation method; however, transplanting shock commonly affects grain yield, and the mechanisms underlying the inhibition of growth, development, and delayed heading caused by transplanting shock have not yet been clearly elucidated. Here, we investigated the effects of seedling age, temperature, and root damage during transplanting on growth, development, and time to heading, both under artificially controlled and natural day length. Additionally, we investigated the impact of seedling root growth space and the potential mitigating effects of residual seed nutrients on young transplanted seedlings. The delay in heading in transplanted versus directly seeded plants was affected more by growth inhibition during the seedling period than by root damage during transplanting. However, root damage had an effect on the inhibition of leaf and tiller development, and the ratio of leaves to tillers increased because tiller development was inhibited more by transplanting shock compared with leaf development. Based on these findings, we propose factors reflecting the delay in growth due to transplanting shock that should be included for more accurate rice phenology modeling and suggest advantageous seeding conditions and transplanting methods for improved rice cultivation and yield in response to climate change.
Nearby contours abolish the binocular advantage
Authors: Lev Maria , Ding Jian , Polat Uri , Levi Dennis M. 
Published: August 2021

AbstractThat binocular viewing confers an advantage over monocular viewing for detecting isolated low luminance or low contrast objects, has been known for well over a century; however, the processes involved in combining the images from the two eyes are still not fully understood. Importantly, in natural vision, objects are rarely isolated but appear in context. It is well known that nearby contours can either facilitate or suppress detection, depending on their distance from the target and the global configuration. Here we report that at close distances collinear (but not orthogonal) flanking contours suppress detection more under binocular compared to monocular viewing, thus completely abolishing the binocular advantage, both at threshold and suprathreshold levels. In contrast, more distant flankers facilitate both monocular and binocular detection, preserving a binocular advantage up to about four times the detection threshold. Our results for monocular and binocular viewing, for threshold contrast discrimination without nearby flankers, can be explained by a gain control model with uncertainty and internal multiplicative noise adding additional constraints on detection. However, in context with nearby flankers, both contrast detection threshold and suprathreshold contrast appearance matching require the addition of both target-to-target and flank-to-target interactions occurring before the site of binocular combination. To test an alternative model, in which the interactions occur after the site of binocular combination, we performed a dichoptic contrast matching experiment, with the target presented to one eye, and the flanks to the other eye. The two models make very different predictions for abutting flanks under dichoptic conditions. Interactions after the combination site predict that the perceived contrast of the flanked target will be strongly suppressed, while interactions before the site predict the perceived contrast will be more or less veridical. The data are consistent with the latter model, strongly suggesting that the interactions take place before the site of binocular combination.
Human players manage to extort more than the mutual cooperation payoff in repeated social dilemmas
Authors: D’Arcangelo Chiara , Andreozzi Luciano , Faillo Marco 
Published: August 2021

AbstractSocial dilemmas are mixed-motive games. Although the players have a common interest in maintaining cooperation, each may try to obtain a larger payoff by cooperating less than the other. This phenomenon received increased attention after Press and Dyson discovered a class of strategies for the repeated prisoner’s dilemma (extortionate strategies) that secure for themselves a payoff that is never smaller, but can be larger, than the opponent’s payoff. We conducted an experiment to test whether humans adopt extortionate strategies when playing a social dilemma. Our results reveal that human subjects do try to extort a larger payoff from their opponents. However, they are only successful when extortionate strategies are part of a Nash equilibrium. In settings where extortionate strategies do not appear in any Nash equilibrium, attempts at extortion only result in a breakdown of cooperation. Our subjects recognized the different incentives implied by the two settings, and they were ready to “extort” the opponent when allowed to do so. This suggests that deviations from mutually cooperative equilibria, which are usually attributed to players’ impatience, coordination problems, or lack of information, can instead be driven by subjects trying to reach more favorable outcomes.
Structure activity relationships and the binding mode of quinolinone-pyrimidine hybrids as reversal agents of multidrug resistance mediated by P-gp
Authors: Laiolo Jerónimo , Lanza Priscila Ailin , Parravicini Oscar , Barbieri Cecilia , Insuasty Daniel , Cobo Justo , Vera D. Mariano Adolfo , Enriz Ricardo Daniel , Carpinella Maria Cecilia 
Published: August 2021

AbstractP-gp-associated multidrug resistance is a major impediment to the success of chemotherapy. With the aim of finding non-toxic and effective P-gp inhibitors, we investigated a panel of quinolin-2-one-pyrimidine hybrids. Among the active compounds, two of them significantly increased intracellular doxorubicin and rhodamine 123 accumulation by inhibiting the efflux mediated by P-gp and restored doxorubicin toxicity at nanomolar range. Structure–activity relationships showed that the number of methoxy groups, an optimal length of the molecule in its extended conformation, and at least one flexible methylene group bridging the quinolinone to the moiety bearing the pyrimidine favored the inhibitory potency of P-gp. The best compounds showed a similar binding pattern and interactions to those of doxorubicin and tariquidar, as revealed by MD and hybrid QM/MM simulations performed with the recent experimental structure of P-gp co-crystallized with paclitaxel. Analysis of the molecular interactions stabilizing the different molecular complexes determined by MD and QTAIM showed that binding to key residues from TMH 4–7 and 12 is required for inhibition.
Irrigation has a higher impact on soil bacterial abundance, diversity and composition than nitrogen fertilization
Authors: Li Haoran , Wang Hongguang , Jia Bin , Li Dongxiao , Fang Qin , Li Ruiqi 
Published: August 2021

AbstractThe aim of this study was to assess the effects of irrigation frequency and nitrogen fertilization rate on the abundance, diversity, and composition of soil bacteria in winter wheat. Irrigation, but not nitrogen fertilization, significantly affected the bacterial alpha diversity index. Among the 50 phyla obtained in these treatments, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Firmicutes were the predominant phyla. The LEfSe analysis of different treatments indicated that irrigation had a stronger effect on soil bacteria community composition than nitrogen fertilization. Moreover, the soil pH, moisture, available phosphorus (AP), and available potassium (AK) significantly correlated with the relative abundance of dominant bacteria at the phylum, genus, and operational taxonomic unit (OTU) levels. Overall, after three years of irrigation and fertilization treatments, the effect of irrigation on soil bacteria abundance, diversity, and composition of winter wheat was stronger than that of nitrogen fertilization, highlighting the importance of water availability for bacteria communities in semi-arid ecosystems. Inorganic and organic fertilizers should be applied in rotation.
Identifying volatile in vitro biomarkers for oral bacteria with proton-transfer-reaction mass spectrometry and gas chromatography–mass spectrometry
Authors: Roslund Kajsa , Lehto Markku , Pussinen Pirkko , Hartonen Kari , Groop Per-Henrik , Halonen Lauri , Metsälä Markus 
Published: August 2021

AbstractWe have measured the volatile fingerprints of four pathogenic oral bacteria connected to periodontal disease and dental abscess: Porphyromonas gingivalis (three separate strains), Prevotella intermedia, Prevotella nigrescens and Tannerella forsythia. Volatile fingerprints were measured in vitro from the headspace gas of the bacteria cultured on agar. Concrete identification of new and previously reported bacterial volatiles were performed by a combination of solid phase microextraction (SPME) and offline gas chromatography–mass spectrometry (GC–MS). We also studied the effect of the reduced electric field strength (E/N) on the fragmentation patterns of bacterial volatiles in online proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF-MS). We aimed to discover possible new biomarkers for the studied oral bacteria, as well as to validate the combination of GC–MS and PTR-MS for volatile analysis. Some of the most promising compounds produced include: 1-Methyl-1,2,3,4-tetrahydroisoquinoline (1MeTIQ), indole, and a cascade of sulphur compounds, such as methanethiol, dimethyl disulphide (DMDS) and dimethyl trisulphide (DMTS). We also found that several compounds, especially alcohols, aldehydes and esters, fragment significantly with the PTR-MS method, when high E/N values are used. We conclude that the studied oral bacteria can be separated by their volatile fingerprints in vitro, which could have importance in clinical and laboratory environments. In addition, using softer ionization conditions can improve the performance of the PTR-MS method in the volatile analysis of certain compounds.
Assessing the role of initial conditions in the local structural identifiability of large dynamic models
Authors: Joubert Dominique , Stigter J. D. , Molenaar Jaap 
Published: August 2021

AbstractStructural identifiabilityis a binary property that determines whether or notuniqueparameter values can, in principle, be estimated from error-free input–output data. The many papers that have been written on this topic collectively stress the importance of this a priori analysis in the model development process. The story however, often ends with a structurally unidentifiable model. This may leave a model developer with no plan of action on how to address this potential issue. We continue this model exploration journey by identifying one of the possible sources of a model’s unidentifiability: problematic initial conditions. It is well-known that certaininitial valuesmay result in the loss of local structural identifiability. Nevertheless, literature on this topic has been limited to the analysis of small toy models. Here, we present a systematic approach to detect problematic initial conditions of real-world systems biology models, that are usually not small. A model’s identifiability can often be reinstated by changing the value of such problematic initial conditions. This provides modellers an option to resolve the “unidentifiable model” problem. Additionally, a good understanding of which initial values should rather be avoided can be very useful during experimental design. We show how our approach works in practice by applying it to five models. First, two small benchmark models are studied to get the reader acquainted with the method. The first one shows the effect of a zero-valued problematic initial condition. The second one illustrates that the approach also yields correct results in the presence of input signals and that problematic initial conditions need not be zero-values. For the remaining three examples, we set out to identify key initial values which may result in the structuralunidentifiability. The third and fourth examples involve a systems biology Epo receptor model and a JAK/STAT model, respectively. In the final Pharmacokinetics model, of which its global structural identifiability has only recently been confirmed, we indicate that there are still sets of initial values for which this property does not hold.