bluuebunny/crossref_metadata_2025 huggingface dataset:
Social Comparisons for Following Health Recommendations and Their Relation to Worry and Intentions During COVID-19
Authors: Rose Jason P. , Edmonds Keith A.
Published: May 2021

Abstract. Background: During uncertain threatening situations, people make social comparisons that influence self-evaluations, inform decisions, and guide behavior. In 2019, an emerging infectious disease (COVID-19) became a pandemic and resulted in unparalleled public health recommendations (e.g., social distancing, wear masks in public). Aims: The current research examined people’s beliefs about how their own compliance to recommendations compared to others and explored the unique associations between social comparisons, worry, risk perceptions, and intentions for health-protective action. Method: An adult sample of US residents ( N = 452) completed an online, cross-sectional survey about their thoughts, feelings, and behaviors in the early stages of the COVID-19 pandemic. Results: First, participants reported better-than-average compliance beliefs. Second, comparative beliefs were positively (and uniquely) associated with intentions for future compliance-related behaviors and general risk-reduction behaviors (e.g., information seeking) – particularly for participants who viewed COVID-19 as threatening. Finally, the relation between comparative beliefs and intentions was indirect through worry (but not risk), though alternative models also achieved support. Limitations: Our findings are limited by our use of a cross-sectional design, methodological choices, and our lack of behavioral measures. Conclusions: Overall, results demonstrate that people are attentive to their comparative levels of compliance behaviors during an infectious disease pandemic. Results are discussed in terms of their theoretical implications and the relevance of social comparisons for self-protective action during a pandemic.
Cloud Process Coupling and Time Integration in the E3SM Atmosphere Model
Authors: Santos Sean Patrick , Caldwell Peter M. , Bretherton Christopher S.
Published: May 2021

In this study, we find significant sensitivity to the choice of time step for the Energy Exascale Earth System Model's atmospheric component, leading to large decreases in the magnitude of cloud forcing when the time step is reduced to 10 s. Reducing the time step size for the microphysics increases precipitation, leading to a drying of the atmosphere and an increase in surface evaporation. This effect is amplified when the microphysics is substepped together with other cloud physics processes. Coupling the model's dynamics and physics more frequently reduces cloud fraction at lower altitudes, while producing more cloud liquid at higher altitudes. Reducing the deep convection time step also reduces low cloud mass and cloud fraction. Together, these results suggest that cloud physics in a global circulation model can depend strongly on time step and, in particular, on the frequency with which cloud‐related processes are coupled with each other and with the model dynamics.
Understanding the Information Content in the Hierarchy of Model Development Decisions: Learning From Data
Authors: Gharari Shervan , Gupta Hoshin V. , Clark Martyn P. , Hrachowitz Markus , Fenicia Fabrizio , Matgen Patrick , Savenije Hubert H. G.
Published: May 2021

Process‐based hydrological models seek to represent the dominant hydrological processes in a catchment. However, due to unavoidable incompleteness of knowledge, the construction of “fidelius” process‐based models depends largely on expert judgment. We present a systematic approach that treats models as hierarchical assemblages of hypotheses (conservation principles, system architecture, process parameterization equations, and parameter specification), which enables investigating how the hierarchy of model development decisions impacts model fidelity. Each model development step provides information that progressively changes our uncertainty (increases, decreases, or alters) regarding the input‐state‐output behavior of the system. Following the principle of maximum entropy, we introduce the concept of “minimally restrictive process parameterization equations—MR‐PPEs,” which enables us to enhance the flexibility with which system processes can be represented, and to thereby investigate the important role that the system architectural hypothesis (discretization of the system into subsystem elements) plays in determining model behavior. We illustrate and explore these concepts with synthetic and real‐data studies, using models constructed from simple generic buckets as building blocks, thereby paving the way for more‐detailed investigations using sophisticated process‐based hydrological models. We also discuss how proposed MR‐PPEs can bridge the gap between current process‐based modeling and machine learning. Finally, we suggest the need for model calibration to evolve from a search over “parameter spaces” to a search over “function spaces.”
Physics‐Based Analytical Model of the Planetary Bow Shock Position and Shape
Authors: Kotova G. , Verigin M. , Gombosi T. , Kabin K. , Slavin J. , Bezrukikh V.
Published: May 2021

In studies of physical processes near planetary bow shocks, empirical models of the latter are usually used. While computational magneto‐hydrodynamics (MHD) or kinetic models of bow shocks are often more accurate, their computationally extensive nature limits their applicability to routine analysis of large volumes of data. We suggest an analytical model of the bow shock position based on MHD calculations and accurate analytical solutions. The analytical expressions for the bow shock position and shape include the following parameters: The distance of the bow shock nose point from the planet, radii of curvature and bluntnesses of the shock surface at this point and a parameter describing the transition to the asymptotic downstream slope of the shock. It is shown that for an analytical description of the surface of the shock, it is sufficient to approximate its radius of curvature and bluntness in two perpendicular planes. Another parameter used in this model is the bow shock skewing angle, appearing when the interplanetary magnetic field directed at an angle with respect to the solar wind velocity. This parameter naturally vanishes when the magnetic field of the solar wind is directed either parallel or perpendicular to the velocity vector. The exact analytical solution for the asymptotic downstream slope of the MHD Mach cone is modified to take into account the skewing angle of the bow shock.
Determining the Sources and Transport of Brown Carbon Using Radionuclide Tracers and Modeling
Authors: Jiang Hongxing , Li Jun , Sun Rong , Liu Guoqing , Tian Chongguo , Tang Jiao , Cheng Zhineng , Zhu Sanyuan , Zhong Guangcai , Ding Xiang , Zhang Gan
Published: May 2021

The isotope tracer technique plays a key role in identifying the sources and atmospheric processes affecting pollution. The sources of brown carbon (BrC) at Guangzhou during 2017–2018 were characterized by positive matrix factorization with radiocarbon isotope constraints and multiple linear regression analysis. The primary emission factors of fossil fuel combustion (FF) and biomass burning (BB) accounted for 34% and 27% of dissolved BrC absorption at λ = 365 nm (Abs365), respectively. The total mean light absorption contributed by secondary sources was 39%. The FF‐origin Abs365 changed insignificantly throughout the year and was dominant in the summer monsoon period, whereas the Abs365 from BB and secondary nitrate formation increased and contributed larger fractions during the winter monsoon period. Transported BrC was estimated using an index of 7Be/(7Be + n210Pb). Higher values were generally accompanied by lower Abs365, whereas lower values were associated with higher Abs365, indicating that BrC absorption of aerosols transported from the upper‐atmosphere is lower than that of aerosols transported near the surface. Based on the positive correlations between 210Pb and Abs365 and non‐fossil dissolved organic carbon in the winter monsoon period, we estimated that the contribution of invasive BrC (include ground and upper‐atmosphere level) to total absorption during the period of elevated BrC was ∼50%. The transported BrC was likely related to BB organic aerosols and secondary nitrate formation processes. This study supports radionuclides as a novel method for characterizing the sources and transport of BrC that can be applied in future atmospheric research.
Transitions in symbiosis: evidence for environmental acquisition and social transmission within a clade of heritable symbionts
Authors: Drew Georgia C , Budge Giles E , Frost Crystal L , Neumann Peter , Siozios Stefanos , Yañez Orlando , Hurst Gregory D D
Published: May 2021

A dynamic continuum exists from free-living environmental microbes to strict host-associated symbionts that are vertically inherited. However, knowledge of the forces that drive transitions in symbiotic lifestyle and transmission mode is lacking. Arsenophonus is a diverse clade of bacterial symbionts, comprising reproductive parasites to coevolving obligate mutualists, in which the predominant mode of transmission is vertical. We describe a symbiosis between a member of the genus Arsenophonus and the Western honey bee. The symbiont shares common genomic and predicted metabolic properties with the male-killing symbiont Arsenophonus nasoniae, however we present multiple lines of evidence that the bee Arsenophonus deviates from a heritable model of transmission. Field sampling uncovered spatial and seasonal dynamics in symbiont prevalence, and rapid infection loss events were observed in field colonies and laboratory individuals. Fluorescent in situ hybridisation showed Arsenophonus localised in the gut, and detection was rare in screens of early honey bee life stages. We directly show horizontal transmission of Arsenophonus between bees under varying social conditions. We conclude that honey bees acquire Arsenophonus through a combination of environmental exposure and social contacts. These findings uncover a key link in the Arsenophonus clades trajectory from free-living ancestral life to obligate mutualism, and provide a foundation for studying transitions in symbiotic lifestyle.
Imaging beta-amyloid (Aβ) burden in the brains of middle-aged individuals with alcohol-use disorders: a [11C]PIB PET study
Authors: Flanigan Margaret R. , Royse Sarah K. , Cenkner David P. , Kozinski Katelyn M. , Stoughton Clara J. , Himes Michael L. , Minhas Davneet S. , Lopresti Brian , Butters Meryl A. , Narendran Rajesh
Published: May 2021

No in vivo human studies have examined the prevalence of Alzheimer’s disease (AD) neuropathology in individuals with alcohol-use disorder (AUD), although recent research suggests that a relationship between the two exists. Therefore, this study used Pittsburgh Compound-B ([11C]PiB) PET imaging to test the hypothesis that AUD is associated with greater brain amyloid (Aβ) burden in middle-aged adults compared to healthy controls. Twenty healthy participants (14M and 6F) and 19 individuals with AUD (15M and 4F), all aged 40–65 years, underwent clinical assessment, MRI, neurocognitive testing, and positron emission tomography (PET) imaging. Global [11C]PiB standard uptake value ratios (SUVRs), cortical thickness, gray matter volumes (GMVs), and neurocognitive function in subjects with AUD were compared to healthy controls. These measures were selected because they are considered markers of risk for future AD and other types of neurocognitive dysfunction. The results of this study showed no significant differences in % global Aβ positivity or subthreshold Aβ loads between AUD and controls. However, relative to controls, we observed a significant 6.1% lower cortical thickness in both AD-signature regions and in regions not typically associated with AD, lower GMV in the hippocampus, and lower performance on tests of attention as well as immediate and delayed memory in individuals with AUD. This suggest that Aβ accumulation is not greater in middle-aged individuals with AUD. However, other markers of neurodegeneration, such as impaired memory, cortical thinning, and reduced hippocampal GMV, are present. Further studies are needed to elucidate the patterns and temporal staging of AUD-related pathophysiology and cognitive impairment. Imaging β-amyloid in middle age alcoholics as a mechanism that increases their risk for Alzheimer’s disease; Registration Number: NCT03746366.
Leaf nutrient content and transcriptomic analyses of endive (Cichorium endivia) stressed by downpour-induced waterlog reveal a gene network regulating kestose and inulin contents
Authors: Testone Giulio , Sobolev Anatoly Petrovich , Mele Giovanni , Nicolodi Chiara , Gonnella Maria , Arnesi Giuseppe , Biancari Tiziano , Giannino Donato
Published: May 2021

Endive (Cichorium endiviaL.), a vegetable consumed as fresh or packaged salads, is mostly cultivated outdoors and known to be sensitive to waterlogging in terms of yield and quality. Phenotypic, metabolic and transcriptomic analyses were used to study variations in curly- (‘Domari’, ‘Myrna’) and smooth-leafed (‘Flester’, ‘Confiance’) cultivars grown in short-term waterlog due to rainfall excess before harvest. After recording loss of head weights in all cultivars (6-35%), which was minimal in ‘Flester’, NMR untargeted profiling revealed variations as influenced by genotype, environment and interactions, and included drop of total carbohydrates (6–50%) and polyols (3–37%), gain of organic acids (2–30%) and phenylpropanoids (98–560%), and cultivar-specific fluctuations of amino acids (−37 to +15%). The analysis of differentially expressed genes showed GO term enrichment consistent with waterlog stress and included the carbohydrate metabolic process. The loss of sucrose, kestose and inulin recurred in all cultivars and the sucrose-inulin route was investigated by covering over 50 genes of sucrose branch and key inulin synthesis (fructosyltransferases) and catabolism (fructan exohydrolases) genes. The lowered expression of a sucrose gene subset together with that ofSUCROSE:SUCROSE-1-FRUCTOSYLTRANSFERASE(1-SST) may have accounted for sucrose and kestose contents drop in the leaves of waterlogged plants. Two anti-correlated modules harbouring candidate hub-genes, including1-SST, were identified by weighted gene correlation network analysis, and proposed to control positively and negatively kestose levels. In silico analysis further pointed at transcription factors of GATA, DOF, WRKY types as putative regulators of1-SST.
Genetic regulators of leaf size in Brassica crops
Authors: Karamat Umer , Sun Xiaoxue , Li Na , Zhao Jianjun
Published: May 2021

Leaf size influences plant development and biomass and is also an important agricultural trait in Brassica crops, in which leaves are the main organ produced for consumption. Leaf size is determined by the coordinated regulation of cell proliferation and cell expansion during leaf development, and these processes are strictly controlled by various integrated signals from the intrinsic regulatory network and the growth environment. Understanding the molecular mechanism of leaf size control is a prerequisite for molecular breeding for crop improvement purposes. Although research on leaf size control is just beginning in Brassica, recent studies have identified several genes and QTLs that are important in leaf size regulation. These genes have been proposed to influence leaf growth through different pathways and mechanisms, including phytohormone biosynthesis and signaling, transcription regulation, small RNAs, and others. In this review, we summarize the current findings regarding the genetic regulators of leaf size in Brassica and discuss future prospects for this research.
Chromatin accessibility and translational landscapes of tea plants under chilling stress
Authors: Wang Pengjie , Jin Shan , Chen Xuejin , Wu Liangyu , Zheng Yucheng , Yue Chuan , Guo Yongchun , Zhang Xingtan , Yang Jiangfan , Ye Naixing
Published: May 2021

Plants have evolved regulatory mechanisms at multiple levels to regulate gene expression in order to improve their cold adaptability. However, limited information is available regarding the stress response at the chromatin and translational levels. Here, we characterize the chromatin accessibility, transcriptional, and translational landscapes of tea plants in vivo under chilling stress for the first time. Chilling stress significantly affected both the transcription and translation levels as well as the translation efficiency of tea plants. A total of 3010 genes that underwent rapid and independent translation under chilling stress were observed, and they were significantly enriched in the photosynthesis-antenna protein and phenylpropanoid biosynthesis pathways. A set of genes that were significantly responsive to cold at the transcription and translation levels, including four (+)-neomenthol dehydrogenases (MNDs) and two (E)-nerolidol synthases (NESs) arranged in tandem on the chromosomes, were also found. We detected potential upstream open reading frames (uORFs) on 3082 genes and found that tea plants may inhibit the overall expression of genes by enhancing the translation of uORFs under chilling stress. In addition, we identified distal transposase hypersensitive sites (THSs) and proximal THSs and constructed a transcriptional regulatory network for tea plants under chilling stress. We also identified 13 high-confidence transcription factors (TFs) that may play a crucial role in cold regulation. These results provide valuable information regarding the potential transcriptional regulatory network in plants and help to clarify how plants exhibit flexible responses to chilling stress.
Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution
Authors: Chen Hongguo , Zeng Xiangling , Yang Jie , Cai Xuan , Shi Yumin , Zheng Riru , Wang Zhenqi , Liu Junyi , Yi Xinxin , Xiao Siwei , Fu Qiang , Zou Jingjing , Wang Caiyun
Published: May 2021

Osmanthus fragransis a well-known ornamental plant that has been domesticated in China for 2500 years. More than 160 cultivars have been found during this long period of domestication, and they have subsequently been divided into four cultivar groups, including the Yingui, Jingui, Dangui, and Sijigui groups. These groups provide a set of materials to study genetic evolution and variability. Here, we constructed a reference genome ofO. fragrans‘Liuyejingui’ in the Jingui group and investigated its floral color traits and domestication history by resequencing a total of 122 samples, including 119O. fragransaccessions and three otherOsmanthusspecies, at an average sequencing depth of 15×. The population structure analysis showed that these 119 accessions formed an apparent regional cluster. The results of linkage disequilibrium (LD) decay analysis suggested that varieties with orange/red flower color in the Dangui group had undergone more artificial directional selection; these varieties had the highest LD values among the four groups, followed by the Sijigui, Jingui, and Yingui groups. Through a genome-wide association study, we further identified significant quantitative trait loci and genomic regions containing several genes, such as ethylene-responsive transcription factor 2 and Arabidopsis pseudoresponse regulator 2, that are positively associated with petal color. Moreover, we found a frameshift mutation with a 34-bp deletion in the first coding region of the carotenoid cleavage dioxygenase 4 gene. This frameshift mutation existed in at least one site on both alleles in all varieties of the Dangui group. The results from this study shed light on the genetic basis of domestication in woody plants, such asO. fragrans.
Transcriptomic and epigenomic remodeling occurs during vascular cambium periodicity in Populus tomentosa
Authors: Chen Bo , Xu Huimin , Guo Yayu , Grünhofer Paul , Schreiber Lukas , Lin Jinxing , Li Ruili
Published: May 2021

Trees in temperate regions exhibit evident seasonal patterns, which play vital roles in their growth and development. The activity of cambial stem cells is the basis for regulating the quantity and quality of wood, which has received considerable attention. However, the underlying mechanisms of these processes have not been fully elucidated. Here we performed a comprehensive analysis of morphological observations, transcriptome profiles, the DNA methylome, and miRNAs of the cambium inPopulus tomentosaduring the transition from dormancy to activation. Anatomical analysis showed that the active cambial zone exhibited a significant increase in the width and number of cell layers compared with those of the dormant and reactivating cambium. Furthermore, we found that differentially expressed genes associated with vascular development were mainly involved in plant hormone signal transduction, cell division and expansion, and cell wall biosynthesis. In addition, we identified 235 known miRNAs and 125 novel miRNAs. Differentially expressed miRNAs and target genes showed stronger negative correlations than other miRNA/target pairs. Moreover, global methylation and transcription analysis revealed that CG gene body methylation was positively correlated with gene expression, whereas CHG exhibited the opposite trend in the downstream region. Most importantly, we observed that the number of CHH differentially methylated region (DMR) changes was the greatest during cambium periodicity. Intriguingly, the genes with hypomethylated CHH DMRs in the promoter were involved in plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interactions during vascular cambium development. These findings improve our systems-level understanding of the epigenomic diversity that exists in the annual growth cycle of trees.
CsTCPs regulate shoot tip development and catechin biosynthesis in tea plant (Camellia sinensis)
Authors: Yu Shuwei , Li Penghui , Zhao Xuecheng , Tan Mangmang , Ahmad Muhammad Zulfiqar , Xu Yujie , Tadege Million , Zhao Jian
Published: May 2021

The growth of leaves and biosynthesis of characteristic secondary metabolites are critically important for tea production and quality control. However, little is known about the coordinated regulation of leaf development and catechin biosynthesis in tea plants. Here, we reported that TCP TFs are involved in both catechin biosynthesis and leaf development. An integrated analysis of catechin profiling and CsTCP expression in different tissues of plants under various environmental conditions at different developmental stages indicated significant correlations between the transcript levels of CIN-type TCPs and catechin production. CIN-type CsTCP3 and CsTCP4 and PCF-type CsTCP14 interacted with the MYB-bHLH-WD40 repeat (MBW) complex by forming a CsTCP3-CsTT8 heterodimer and modulating the transactivation activity of the promoters of anthocyanin synthase (CsANS1) and anthocyanidin reductase (CsANR1). Four types of microRNA/target modules, miR319b/CsTCP3-4, miR164b/CsCUC, miR396/CsGRF-GIF, and miR165b/HD-ZIPIII ones, were also identified and characterized for their functions in the regulation of the development of tea plant shoot tips and leaf shape. The results of these modules were reflected by their different expression patterns in developing buds and leaves that had distinctly different morphologies in three different tea plant varieties. Their roles in the regulation of catechin biosynthesis were also further verified by manipulation of microRNA319b (miR319b), which targets the transcripts of CsTCP3 and CsTCP4. Thus, CsTCPs represent at least one of these important groups of TFs that can integrate tea plant leaf development together with secondary metabolite biosynthesis. Our study provides new insight into shoot tip development and catechin production in tea plants and lays a foundation for further mechanistic understanding of the regulation of tea plant leaf development and secondary metabolism.
Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome
Authors: Wang Pengjie , Yu Jiaxin , Jin Shan , Chen Shuai , Yue Chuan , Wang Wenling , Gao Shuilian , Cao Hongli , Zheng Yucheng , Gu Mengya , Chen Xuejin , Sun Yun , Guo Yuqiong , Yang Jiangfan , Zhang Xingtan , Ye Naixing
Published: May 2021

Tea plants (Camellia sinensis) are commercially cultivated in >60 countries, and their fresh leaves are processed into tea, which is the most widely consumed beverage in the world. Although several chromosome-level tea plant genomes have been published, they collapsed the two haplotypes and ignored a large number of allelic variations that may underlie important biological functions in this species. Here, we present a phased chromosome-scale assembly for an elite oolong tea cultivar, “Huangdan”, that is well known for its high levels of aroma. Based on the two sets of haplotype genome data, we identified numerous genetic variations and a substantial proportion of allelic imbalance related to important traits, including aroma- and stress-related alleles. Comparative genomics revealed extensive structural variations as well as expansion of some gene families, such as terpene synthases (TPSs), that likely contribute to the high-aroma characteristics of the backbone parent, underlying the molecular basis for the biosynthesis of aroma-related chemicals in oolong tea. Our results uncovered the genetic basis of special features of this oolong tea cultivar, providing fundamental genomic resources to study evolution and domestication for the economically important tea crop.
The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative
Authors: Barrera-Redondo Josué , Sánchez-de la Vega Guillermo , Aguirre-Liguori Jonás A. , Castellanos-Morales Gabriela , Gutiérrez-Guerrero Yocelyn T. , Aguirre-Dugua Xitlali , Aguirre-Planter Erika , Tenaillon Maud I. , Lira-Saade Rafael , Eguiarte Luis E.
Published: May 2021

Despite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.
CsbZIP1-CsMYB12 mediates the production of bitter-tasting flavonols in tea plants (Camellia sinensis) through a coordinated activator–repressor network
Authors: Zhao Xuecheng , Zeng Xiangsheng , Lin Ning , Yu Shuwei , Fernie Alisdair R. , Zhao Jian
Published: May 2021

Under high light conditions or UV radiation, tea plant leaves produce more flavonols, which contribute to the bitter taste of tea; however, neither the flavonol biosynthesis pathways nor the regulation of their production are well understood. Intriguingly, tea leaf flavonols are enhanced by UV-B but reduced by shading treatment. CsFLS, CsUGT78A14, CsMYB12, and CsbZIP1 were upregulated by UV-B radiation and downregulated by shading. CsMYB12 and CsbZIP1 bound to the promoters of CsFLS and CsUGT78A14, respectively, and activated their expression individually. CsbZIP1 positively regulated CsMYB12 and interacted with CsMYB12, which specifically activated flavonol biosynthesis. Meanwhile, CsPIF3 and two MYB repressor genes, CsMYB4 and CsMYB7, displayed expression patterns opposite to that of CsMYB12. CsMYB4 and CsMYB7 bound to CsFLS and CsUGT78A14 and repressed their CsMYB12-activated expression. While CsbZIP1 and CsMYB12 regulated neither CsMYB4 nor CsMYB7, CsMYB12 interacted with CsbZIP1, CsMYB4, and CsMYB7, but CsbZIP1 did not physically interact with CsMYB4 or CsMYB7. Finally, CsPIF3 bound to and activated CsMYB7 under shading to repress flavonol biosynthesis. These combined results suggest that UV activation and shading repression of flavonol biosynthesis in tea leaves are coordinated through a complex network involving CsbZIP1 and CsPIF3 as positive MYB activators and negative MYB repressors, respectively. The study thus provides insight into the regulatory mechanism underlying the production of bitter-tasting flavonols in tea plants.
Molecular and clinical determinants of response and resistance to rucaparib for recurrent ovarian cancer treatment in ARIEL2 (Parts 1 and 2)
Authors: Swisher Elizabeth M. , Kwan Tanya T. , Oza Amit M. , Tinker Anna V. , Ray-Coquard Isabelle , Oaknin Ana , Coleman Robert L. , Aghajanian Carol , Konecny Gottfried E. , O’Malley David M. , Leary Alexandra , Provencher Diane , Welch Stephen , Chen Lee-may , Wahner Hendrickson Andrea E. , Ma Ling , Ghatage Prafull , Kristeleit Rebecca S. , Dorigo Oliver , Musafer Ashan , Kaufmann Scott H. , Elvin Julia A. , Lin Douglas I. , Chambers Setsuko K. , Dominy Erin , Vo Lan-Thanh , Goble Sandra , Maloney Lara , Giordano Heidi , Harding Thomas , Dobrovic Alexander , Scott Clare L. , Lin Kevin K. , McNeish Iain A.
Published: May 2021

ARIEL2 (NCT01891344) is a single-arm, open-label phase 2 study of the PARP inhibitor (PARPi) rucaparib in relapsed high-grade ovarian carcinoma. In this post hoc exploratory biomarker analysis of pre- and post-platinum ARIEL2 samples, RAD51C and RAD51D mutations and high-level BRCA1 promoter methylation predict response to rucaparib, similar to BRCA1/BRCA2 mutations. BRCA1 methylation loss may be a major cross-resistance mechanism to platinum and PARPi. Genomic scars associated with homologous recombination deficiency are irreversible, persisting even as platinum resistance develops, and therefore are predictive of rucaparib response only in platinum-sensitive disease. The RAS, AKT, and cell cycle pathways may be additional modulators of PARPi sensitivity.
Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii
Authors: Luo Tao , Xu Peng , Zhang Yangyi , Porter Jessica L. , Ghanem Marwan , Liu Qingyun , Jiang Yuan , Li Jing , Miao Qing , Hu Bijie , Howden Benjamin P. , Fyfe Janet A. M. , Globan Maria , He Wencong , He Ping , Wang Yiting , Liu Houming , Takiff Howard E. , Zhao Yanlin , Chen Xinchun , Pan Qichao , Behr Marcel A. , Stinear Timothy P. , Gao Qian
Published: May 2021

Mycobacterium kansasii can cause serious pulmonary disease. It belongs to a group of closely-related species of non-tuberculous mycobacteria known as the M. kansasii complex (MKC). Here, we report a population genomics analysis of 358 MKC isolates from worldwide water and clinical sources. We find that recombination, likely mediated by distributive conjugative transfer, has contributed to speciation and on-going diversification of the MKC. Our analyses support municipal water as a main source of MKC infections. Furthermore, nearly 80% of the MKC infections are due to closely-related M. kansasii strains, forming a main cluster that apparently originated in the 1900s and subsequently expanded globally. Bioinformatic analyses indicate that several genes involved in metabolism (e.g., maintenance of the methylcitrate cycle), ESX-I secretion, metal ion homeostasis and cell surface remodelling may have contributed to M. kansasii’s success and its ongoing adaptation to the human host.
Responses of plant diversity to precipitation change are strongest at local spatial scales and in drylands
Authors: Korell Lotte , Auge Harald , Chase Jonathan M. , Harpole W. Stanley , Knight Tiffany M.
Published: May 2021

Mitigating and adapting to climate change requires an understanding of the magnitude and nature by which climate change will influence the diversity of plants across the world’s ecosystems. Experiments can causally link precipitation change to plant diversity change, however, these experiments vary in their methods and in the diversity metrics reported, making synthesis elusive. Here, we explicitly account for a number of potentially confounding variables, including spatial grain, treatment magnitude and direction and background climatic conditions, to synthesize data across 72 precipitation manipulation experiments. We find that the effects of treatments with higher magnitude of precipitation manipulation on plant diversity are strongest at the smallest spatial scale, and in drier environments. Our synthesis emphasizes that quantifying differential responses of ecosystems requires explicit consideration of spatial grain and the magnitude of experimental manipulation. Given that diversity provides essential ecosystem services, especially in dry and semi-dry areas, our finding that these dry ecosystems are particular sensitive to projected changes in precipitation has important implications for their conservation and management.
Nonequilibrium charge-density-wave order beyond the thermal limit
Authors: Maklar J. , Windsor Y. W. , Nicholson C. W. , Puppin M. , Walmsley P. , Esposito V. , Porer M. , Rittmann J. , Leuenberger D. , Kubli M. , Savoini M. , Abreu E. , Johnson S. L. , Beaud P. , Ingold G. , Staub U. , Fisher I. R. , Ernstorfer R. , Wolf M. , Rettig L.
Published: May 2021

The interaction of many-body systems with intense light pulses may lead to novel emergent phenomena far from equilibrium. Recent discoveries, such as the optical enhancement of the critical temperature in certain superconductors and the photo-stabilization of hidden phases, have turned this field into an important research frontier. Here, we demonstrate nonthermal charge-density-wave (CDW) order at electronic temperatures far greater than the thermodynamic transition temperature. Using time- and angle-resolved photoemission spectroscopy and time-resolved X-ray diffraction, we investigate the electronic and structural order parameters of an ultrafast photoinduced CDW-to-metal transition. Tracking the dynamical CDW recovery as a function of electronic temperature reveals a behaviour markedly different from equilibrium, which we attribute to the suppression of lattice fluctuations in the transient nonthermal phonon distribution. A complete description of the system’s coherent and incoherent order-parameter dynamics is given by a time-dependent Ginzburg-Landau framework, providing access to the transient potential energy surfaces.
Sex differences in fear memory consolidation via Tac2 signaling in mice
Authors: Florido A. , Velasco E. R. , Soto-Faguás C. M. , Gomez-Gomez A. , Perez-Caballero L. , Molina P. , Nadal R. , Pozo O. J. , Saura C. A. , Andero R.
Published: May 2021

Memory formation is key for brain functioning. Uncovering the memory mechanisms is helping us to better understand neural processes in health and disease. Moreover, more specific treatments for fear-related disorders such as posttraumatic stress disorder and phobias may help to decrease their negative impact on mental health. In this line, the Tachykinin 2 (Tac2) pathway in the central amygdala (CeA) has been shown to be sufficient and necessary for the modulation of fear memory consolidation. CeA-Tac2 antagonism and its pharmacogenetic temporal inhibition impair fear memory in male mice. Surprisingly, we demonstrate here the opposite effect of Tac2 blockade on enhancing fear memory consolidation in females. Furthermore, we show that CeA-testosterone in males, CeA-estradiol in females and Akt/GSK3β/β-Catenin signaling both mediate the opposite-sex differential Tac2 pathway regulation of fear memory.
Consequences of spatial patterns for coexistence in species-rich plant communities
Authors: Wiegand Thorsten , Wang Xugao , Anderson-Teixeira Kristina J. , Bourg Norman A. , Cao Min , Ci Xiuqin , Davies Stuart J. , Hao Zhanqing , Howe Robert W. , Kress W. John , Lian Juyu , Li Jie , Lin Luxiang , Lin Yiching , Ma Keping , McShea William , Mi Xiangcheng , Su Sheng-Hsin , Sun I-Fang , Wolf Amy , Ye Wanhui , Huth Andreas
Published: May 2021

Ecology cannot yet fully explain why so many tree species coexist in natural communities such as tropical forests. A major difficulty is linking individual-level processes to community dynamics. We propose a combination of tree spatial data, spatial statistics and dynamical theory to reveal the relationship between spatial patterns and population-level interaction coefficients and their consequences for multispecies dynamics and coexistence. Here we show that the emerging population-level interaction coefficients have, for a broad range of circumstances, a simpler structure than their individual-level counterparts, which allows for an analytical treatment of equilibrium and stability conditions. Mechanisms such as animal seed dispersal, which result in clustering of recruits that is decoupled from parent locations, lead to a rare-species advantage and coexistence of otherwise neutral competitors. Linking spatial statistics with theories of community dynamics offers new avenues for explaining species coexistence and calls for rethinking community ecology through a spatial lens.
Customized depolarization spatial patterns with dynamic retardance functions
Authors: Marco David , López-Morales Guadalupe , Sánchez-López María del Mar , Lizana Ángel , Moreno Ignacio , Campos Juan
Published: May 2021

In this work we demonstrate customized depolarization spatial patterns by imaging a dynamical time-dependent pixelated retarder. A proof-of-concept of the proposed method is presented, where a liquid–crystal spatial light modulator is used as a spatial retarder that emulates a controlled spatially variant depolarizing sample by addressing a time-dependent phase pattern. We apply an imaging Mueller polarimetric system based on a polarization camera to verify the effective depolarization effect. Experimental validation is provided by temporal integration on the detection system. The effective depolarizance results are fully described within a simple graphical approach which agrees with standard Mueller matrix decomposition methods. The potential of the method is discussed by means of three practical cases, which include non-reported depolarization spatial patterns, including exotic structures as a spirally shaped depolarization pattern.
All-metal wideband metasurface for near-field transformation of medium-to-high gain electromagnetic sources
Authors: Lalbakhsh Ali , Afzal Muhammad U. , Hayat Touseef , Esselle Karu P. , Mandal Kaushik
Published: May 2021

Electromagnetic (EM) metasurfaces are essential in a wide range of EM engineering applications, from incorporated into antenna designs to separate devices like radome. Near-field manipulators are a class of metasurfaces engineered to tailor an EM source’s radiation patterns by manipulating its near-field components. They can be made of all-dielectric, hybrid, or all-metal materials; however, simultaneously delivering a set of desired specifications by an all-metal structure is more challenging due to limitations of a substrate-less configuration. The existing near-field phase manipulators have at least one of the following limitations; expensive dielectric-based prototyping, subject to ray tracing approximation and conditions, narrowband performance, costly manufacturing, and polarization dependence. In contrast, we propose an all-metal wideband phase correcting structure (AWPCS) with none of these limitations and is designed based on the relative phase error extracted by post-processing the actual near-field distributions of any EM sources. Hence, it is applicable to any antennas, including those that cannot be accurately analyzed with ray-tracing, particularly for near-field analysis. To experimentally verify the wideband performance of the AWPCS, a shortened horn antenna with a large apex angle and a non-uniform near-field phase distribution is used as an EM source for the AWPCS. The measured results verify a significant improvement in the antenna’s aperture phase distribution in a large frequency band of 25%.
Rbm24 displays dynamic functions required for myogenic differentiation during muscle regeneration
Authors: Grifone Raphaëlle , Saquet Audrey , Desgres Manon , Sangiorgi Claudia , Gargano Caterina , Li Zhenlin , Coletti Dario , Shi De-Li
Published: May 2021

Skeletal muscle has a remarkable capacity of regeneration after injury, but the regulatory network underlying this repair process remains elusive. RNA-binding proteins play key roles in the post-transcriptional regulation of gene expression and the maintenance of tissue homeostasis and plasticity. Rbm24 regulates myogenic differentiation during early development, but its implication in adult muscle is poorly understood. Here we show that it exerts multiple functions in muscle regeneration. Consistent with its dynamic subcellular localization during embryonic muscle development, Rbm24 also displays cytoplasm to nucleus translocation during C2C12 myoblast differentiation. In adult mice, Rbm24 mRNA is enriched in slow-twitch muscles along with myogenin mRNA. The protein displays nuclear localization in both slow and fast myofibers. Upon injury, Rbm24 is rapidly upregulated in regenerating myofibers and accumulates in the myonucleus of nascent myofibers. Through satellite cell transplantation, we demonstrate that Rbm24 functions sequentially to regulate myogenic differentiation and muscle regeneration. It is required for myogenin expression at early stages of muscle injury and for muscle-specific pre-mRNA alternative splicing at late stages of regeneration. These results identify Rbm24 as a multifaceted regulator of myoblast differentiation. They provide insights into the molecular pathway orchestrating the expression of myogenic factors and muscle functional proteins during regeneration.
Elastocaloric-effect-induced adiabatic magnetization in paramagnetic salts due to the mutual interactions
Authors: Squillante Lucas , Mello Isys F. , Seridonio Antonio C. , de Souza Mariano
Published: May 2021

The temperature change under adiabatic stress, i.e., the elastocaloric effect, is a well-understood phenomenon and of particular interest due to its potential application in alternative ways for refrigeration. Here, we demonstrate that in the regime of low-temperatures (a few mK) real paramagnets can be magnetized when compressed adiabatically without applied magnetic field. Such adiabatic magnetization is a genuine many-body problem, stemming from the inherent dipolar mutual interactions between adjacent magnetic moments. We showcase experimental setups to carry out adiabatic magnetization and thus to access such a subtle effect. Perspectives of further investigations by controlling the mutual interactions in Bose–Einstein condensates in magnetic insulators and dipolar spin-ice systems via the adiabatic increase of temperature are also presented. Yet, we discuss the connection between the elastic Grüneisen parameter and the shift on the critical temperature of second-order phase transitions under adiabatic stress, as well as its connection with the Ehrenfest relation.
Prevalence and predictive factors of osteoporosis in Thai systemic sclerosis
Authors: Chuealee Wiriya , Foocharoen Chingching , Mahakkanukrauh Ajanee , Suwannaroj Siraphop , Pongchaiyakul Chatlert , Nanagara Ratanavadee
Published: May 2021

Systemic sclerosis (SSc) is recognized as a chronic inflammatory disease and several SSc-associated factors may increase the risk of osteoporosis and its related fractures. To determine the prevalence and predictive factors of osteoporosis in Thai SSc, a cross-sectional study was designed in adult SSc patients at Scleroderma clinic, Khon Kaen University Hospital. The prevalence of osteoporosis with the 95% confidence interval (CI) were determined and the odds ratio (OR) with 95%CI were assessed the clinical association with osteoporosis. A total of 205 SSc patients were recruited with the female to male ratio of 2.7:1. The majority of cases were diffuse SSc subset (83.4%) with a disease duration < 5 years (62.9%). The overall prevalence of osteoporosis was 29.3% (95%CI 23.1–36.0). After an age adjusted analysis, the respective prevalence of osteoporosis at lumbar spine (LS) in women and men was 26.3% and 10%, while the prevalence of osteoporosis at the femoral neck (FN) in women and men was 11% and 2.1%. Low BMI (≤ 18.5 kg/m2) and menopause were associated with osteoporosis at both the LS and FN. Using multivariate analysis, low BMI and menopause were associated with osteoporosis at LS (OR 7.78 and 5.32, respectively), while low BMI was also associated with osteoporosis at LS in pre-menopausal women. In conclusion, the prevalence of osteoporosis in Thai SSc was 29.3%. Osteoporosis at the LS is more common than FN in both men and women. Low BMI was associated with osteoporosis in overall SSc and pre-menopausal women, while only menopause was associated with osteoporosis at the FN.
Mitigation of bacterial spot disease induced biotic stress in Capsicum annuum L. cultivars via antioxidant enzymes and isoforms
Authors: Ramzan Musarrat , Sana Sundas , Javaid Nida , Shah Anis Ali , Ejaz Samina , Malik Waqas Nazir , Yasin Nasim Ahmad , Alamri Saud , Siddiqui Manzer H. , Datta Rahul , Fahad Shah , Tahir Nazia , Mubeen Sidra , Ahmed Niaz , Ali Muhammad Arif , El Sabagh Ayman , Danish Subhan
Published: May 2021

Bacterial spot, caused by a group ofXanthomonads(Xanthomonasspp.), is a devastating disease. It can adversely affect theCapsicum annumproductivity. Scientists are working on the role of antioxidants to meet this challenge. However, research is lacking on the role of antioxidant enzymes and their isoforms in the non-compatible pathogen and host plant interaction and resistance mechanisms incapsicumvarieties. The present study was conducted to ascertain the defensive role of antioxidant enzymes and their isoforms in chilli varieties Hybrid, Desi, Serrano, Padron, and Shehzadi against bacterial spot disease-inducedXanthomonassp. The seedlings were inoculated with bacterial pathogen @ 107 CFU/mL, and samples were harvested after regular intervals of 24 h for 4 days followed by inoculation. Total plant proteins were extracted in phosphate buffer and quantified through Bradford assay. The crude protein extracts were analyzed through quantitative enzymatic assays in order to document activity levels of various antioxidant enzymes, including peroxidase (POD), Catalase (CAT), Ascorbate peroxidase (APX), and Superoxide dismutase (SOD). Moreover, the profiles appearance of these enzymes and their isoforms were determined using native polyacrylamide gel electrophoresis (PAGE) analysis. These enzymes exhibited maximum activity in Hybrid (HiR) cultivar followed by Desi (R), Serrano (S), Padron, and Shehzadi (HS). Both the number of isoforms and expression levels were higher in highly resistant cultivars compared to susceptible and highly susceptible cultivars. The induction of POD, CAT, and SOD occurs at the early stages of growth in resistantCapsicumcultivars. At the same time, APX seems to make the second line of antioxidant defense mechanisms. We found that modulating antioxidant enzymes and isoforms activity at the seedling stage was an important mechanism for mitigating plant growth inhibition in the resistant ones.