bluuebunny/crossref_metadata_2025 huggingface dataset:
A generalised Dickman distribution and the number of species in a negative binomial process model
Authors: Ipsen Yuguang , Maller Ross A. , Shemehsavar Soudabeh
Published: July 2021

We derive the large-sample distribution of the number of species in a version of Kingman’s Poisson–Dirichlet model constructed from an$\alpha$-stable subordinator but with an underlying negative binomial process instead of a Poisson process. Thus it depends on parameters$\alpha\in (0,1)$from the subordinator and$r>0$from the negative binomial process. The large-sample distribution of the number of species is derived as sample size$n\to\infty$. An important component in the derivation is the introduction of a two-parameter version of the Dickman distribution, generalising the existing one-parameter version. Our analysis adds to the range of Poisson–Dirichlet-related distributions available for modeling purposes.
A class of solvable multidimensional stopping problems in the presence of Knightian uncertainty
Authors: Alvarez E. Luis H. R. , Christensen Sören
Published: July 2021

We investigate the impact of Knightian uncertainty on the optimal timing policy of an ambiguity-averse decision-maker in the case where the underlying factor dynamics follow a multidimensional Brownian motion and the exercise payoff depends on either a linear combination of the factors or the radial part of the driving factor dynamics. We present a general characterization of the value of the optimal timing policy and the worst-case measure in terms of a family of explicitly identified excessive functions generating an appropriate class of supermartingales. In line with previous findings based on linear diffusions, we find that ambiguity accelerates timing in comparison with the unambiguous setting. Somewhat surprisingly, we find that ambiguity may lead to stationarity in models which typically do not possess stationary behavior. In this way, our results indicate that ambiguity may act as a stabilizing mechanism.
Forum on Jon Butler's God in Gotham: The Miracle of Religion in Modern Manhattan: Introductory Remarks
Authors: McGreevy John
Published: July 2021

Jon Butler's God in Gotham: The Miracle of Religion in Modern Manhattan is not a book, Butler would be the first to tell us, that anyone should have expected to read (or write). The equation of Manhattan with modernity and modernity with secularization has long been hardwired into the scholarly and popular imagination. Butler wants to disrupt these circuits. It is not that Manhattan was not secular but rather that religion flourished there beyond all expectations between the late nineteenth century and 1960.
God in Gotham? Really?
Authors: Butler Jon
Published: July 2021

The generous, warm-hearted comments about God in Gotham from Wallace Best, Deborah Dash Moore, and Thomas Tweed, plus John McGreevy's introduction, do, indeed, please its author. I am relieved that no one said I should have remained a colonialist or that the book merely replicates what others have said. But the writing of history never ends, and their comments open fascinating avenues for deeper explorations of religion in the seemingly inhospitable atmosphere of modern urban life. If God in Gotham is succeeded by multiple new books and articles that turn its arguments and conclusions in different and even opposite directions, hallelujah! History moves on. Our books are just markers along the way.
Muslims in Medieval Inquisitorial Thought: Nicolau Eymeric and His Contexts
Authors: Bailey Michael D.
Published: July 2021

This article analyzes the scant treatment of Muslims in medieval inquisitorial thought, focusing mainly on the late fourteenth-century Aragonese inquisitor Nicolau Eymeric'sDirectorium inquisitorum(1376). It argues for four contexts in which to understand his engagement with Islam. First, as background, is a longstanding Christian (although not inquisitorial) tradition categorizing Islam as a heresy, with which he did not substantially engage. Second is his own goal to extend inquisitorial authority to new subjects, in which he drew on previous inquisitorial thought about Jews. The third involves conflicts between church officials and the Crown of Aragon about jurisdiction over non-Christian subjects. The fourth centers on the supposition that he did not view Muslims living within Christendom as an especially covert or insidious threat requiring special investigation to uncover, which speaks to how he and other inquisitors viewed their role and the nature of the threats they aimed to counter. In broad terms, this article contributes to our understanding of one important way in which medieval Christianity engaged with other religions. It also provides a basis for understanding later developments in early modern Europe.
Is Swedish more beautiful than Danish? Matched guise investigations with unknown languages
Authors: Hilton Nanna H. , Gooskens Charlotte , Schüppert Anja , Tang Chaoju
Published: July 2021

Are some languages universally seen as beautiful? And if so, what are the linguistic traits that make some languages sound more pleasing than others? This paper addresses these two questions. We do so with results from two listener experiments that use speech samples from a bilingual Danish–Swedish speaker in a matched guise test, where the listeners are ‘previously unexposed’ students from central China. Our results indicate that listeners from Central China with no previous exposure find Swedish more pleasing sounding than Danish. This finding provides evidence that there could be features of language that sound more beautiful to listeners cross-culturally. In a follow-up experiment we remove the intonation contours of the speech to see whether this prosodic trait plays a role for evaluations. The results show that the difference in evaluations between Swedish and Danish disappears when both speech samples are monotonised. We discuss the importance of our findings for language attitudes research.
Ground-dwelling spider families and forest structure variables for monitoring ecologically sustainable logging operations
Authors: Alcalde Ana Sofía , Politi Natalia , Rodríguez-Artigas Sandra , Corronca José Antonio , Rivera Luis Osvaldo
Published: July 2021

Approximately 80% of neotropical forests are subject to unsustainable economic practices, such as logging. Spiders are a megadiverse taxonomic group with a particularly great diversity in forest ecosystems and could help indicate the sustainability of logging operations. At six sites at 400–700 m altitude in the piedmont forest of north-western Argentina, spiders collected using pitfall traps and forest structure and spider assemblage structure variables were quantified in order to examine the association between them and to identify indicator spider families. Logging changes forest structure and seems to generate an unsuitable habitat for spiders associated with mature forests. The family taxonomic level is a good surrogate for spider morphospecies. The Mysmenidae, Nemesiidae, Theridiidae, Pholcidae, Hahniidae and Tetragnathidae families were associated with upper canopy cover of 20% or more and with more than two dead fallen trees per 0.1 ha and >15 live trees per 0.1 ha, found in unlogged forests. Bearing in mind that the piedmont forest of north-western Argentina is being logged in the absence of sustainability criteria, we suggest including spiders in monitoring schemes to complement the information obtained from more readily used groups, such as charismatic vertebrates.
An investigation of machine translation output quality and the influencing factors of source texts
Authors: Lee Sangmin-Michelle
Published: July 2021

The use of machine translation (MT) in the academic context has increased in recent years. Hence, language teachers have found it difficult to ignore MT, which has led to some concerns. Among the concerns, its accuracy has become a major factor that shapes language teachers’ pedagogical decision to use MT in their language classrooms. Despite the urgency of the issue, studies on MT output quality in foreign language education remain scarce. Moreover, as MT is advancing every year, updated studies are imperative. Therefore, the present study investigated the quality of MT outputs (Google Translate) from Korean to English by comparing it with the English-translated texts of intermediate English as a foreign language students. The study also examined the factors within the source texts that affect the quality of MT outputs. Five trained evaluators examined multiple aspects of MT output samples (N = 104) and students’ English texts (N = 104), including mechanics, vocabulary, grammar, and context. The results showed that both texts were equally comprehensible, but MT outperformed the students in most aspects under investigation. The study further found that only two factors in the source texts – punctuation and sentence complexity – influenced MT output quality, whereas lexical and grammatical accuracy, lexical diversity, and contextual understanding did not affect it. Based on the results, the study presents classroom implications for using MT for educational purposes.
Evaluation of primary care services in Hungary: a comprehensive description of provision, professional competences, cooperation, financing, and infrastructure, based on the findings of the Hungarian-arm of the QUALICOPC study
Authors: Rurik Imre , Nánási Anna , Jancsó Zoltán , Kalabay László , Lánczi Levente István , Móczár Csaba , Semanova Csilla , Schmidt Péter , Torzsa Péter , Ungvári Tímea , Kolozsvári László Róbert
Published: July 2021

Background:

Primary health care provision in terms of quality, equity, and costs are different by countries. The Quality and Costs of Primary Care (QUALICOPC) study evaluated these domains and parameters in 35 countries, using uniformized method with validated questionnaires filled out by family physicians/general practitioners (GPs).

This paper aims to provide data of the Hungarian-arm of the QUALICOPC study and to give an overview about the recent Hungarian primary care (PC) system.

Methods:

The questionnaires were completed in 222 Hungarian GP practices, delivered by fieldworkers, in a geographically representative distribution. Descriptive analysis was performed on the data.

Findings:

Financing is based mostly on capitation, with additional compensatory elements and minor financial incentives. The gate-keeping function is weak. The communication between GPs and specialists is often insufficient. The number of available devices and equipment are appropriate. Single-handed practices are predominant. Appointment instead of queuing is a new option and is becoming more popular, mainly among better-educated and urban patients. GPs are involved in the management of almost all chronic condition of all generations. Despite the burden of administrative tasks, half of the GPs estimate their job as still interesting, burn-out symptoms were rarely found. Among the evaluated process indicators, access, continuity, comprehensiveness, and coordination were rated as satisfactory, together with equity among health outcome indicators. Financing is insufficient; therefore, many GPs are involved in additional income-generating activities. The old age of the GPs and the lack of the younger GPs generation contributes to a shortage in manpower. Cooperation and communication between different levels of health care provision should be improved, focusing better on community orientation and on preventive services. Financing needs continuous improvement and appropriate incentives should be implemented. There is a need for specific PC-oriented guidelines to define properly the tasks and competences of GPs.
Quasi‐Stationary Intense Rainstorms Spread Across Europe Under Climate Change
Authors: Kahraman Abdullah , Kendon Elizabeth J. , Chan Steven C. , Fowler Hayley J.
Published: July 2021

Under climate change, increases in precipitation extremes are expected due to higher atmospheric moisture. However, the total precipitation in an event also depends on the condensation rate, precipitation efficiency, and duration. Here, a new approach following an “ingredients‐based methodology” from severe weather forecasting identifies important aspects of the heavy precipitation response to climate change, relevant from an impacts perspective and hitherto largely neglected. Using 2.2 km climate simulations, we show that a future increase in precipitation extremes across Europe occurs, not only because of higher moisture and updraft velocities, but also due to slower storm movement, increasing local duration. Environments with extreme precipitation potential are 7× more frequent than today by 2100, while the figure for quasi‐stationary ones is 11× (14× for land). We find that a future reduction in storm speeds, possibly through Arctic Amplification, could enhance event accumulations and flood risk beyond expectations from studies focusing on precipitation rates.
When Betelgeuse Won’t Explode, You Need a Big Telescope to Prove It
Authors: Cartier Kimberly
Published: July 2021

Thanks to last-minute telescope time, researchers pieced together the sequence of events that caused Betelgeuse’s Great Dimming last year.
How Does LCL Height Influence Deep Convective Updraft Width?
Authors: Mulholland J. P. , Peters J. M. , Morrison H.
Published: July 2021

Previous studies have hypothesized that the width of deep convection should positively scale with lifting condensation level (LCL) height. To evaluate this hypothesis, we analyzed idealized large‐eddy simulations with varying LCL heights and initial warm bubble widths in unsheared environments with comparable convective available potential energy. For a given initial warm bubble width, simulations with higher LCLs result in wider, deeper, and stronger cloudy updrafts compared to simulations with lower LCLs. Rising dry thermals in higher LCL simulations experience longer residence times within the sub‐cloud layer, and consequently entrain more conditionally unstable air and grow wider before reaching the LCL. The resulting cloudy updrafts are wider, deeper, and have faster vertical velocities because of a reduction in entrainment‐driven dilution of buoyancy, relative to lower LCL simulations. These results confirm the hypothesized positive relationship between LCL height and deep convective updraft width, and provide a physical explanation for this relationship.
Uncertainty of Tropical Cyclone Wind Radii on Sea Surface Temperature Cooling
Authors: Pun Iam‐Fei , Knaff John A. , Sampson Charles R.
Published: July 2021

The sea surface temperature (SST) beneath a tropical cyclone (TC) is of great importance to its dynamics; therefore, understanding and accurately estimating the magnitude of SST cooling is of vital importance. Existing studies have explored important influences on SST of TC translation speed, maximum surface winds, ocean thermal condition, and ocean stratification. But the influence of the TC wind radii (or collectively called the TC size) on SST has been largely overlooked. In this study, we assess the influence of wind radii uncertainty on SST cooling by a total of 15,983 numerical simulations for the western North Pacific during the 2014–2018 seasons. Results show a 6%–20% SST cooling error induced using wind radii from the Joint Typhoon Warning Center official forecast and a 35%–40% SST cooling error using wind radii from the operational runs of the Hurricane Weather Research and Forecasting (HWRF) model. Our results indicate that SST cooling is most sensitive to the radius of 64 kt winds (R64) due to its effects on the integrated kinetic energy of the TC and subsequent mixing of the ocean surface layer. It is also found that the correlation between SST cooling induced by the TC and its size is 0.49, which is the highest among all the parameters tested. This suggests that it is extremely important to get TC size correct in order to predict the SST cooling response, which then impacts TC evolution in numerical weather prediction models.
DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.)
Authors: Yin Liqin , Zhu Zhendong , Huang Liangjun , Luo Xuan , Li Yun , Xiao Chaowen , Yang Jin , Wang Jisheng , Zou Qiong , Tao Lanrong , Kang Zeming , Tang Rong , Wang Maolin , Fu Shaohong
Published: July 2021

Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (Brassica napus). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome ofB. napus. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation inB. napusmight be partially regulated byMET1. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formedBrassicapolyploids.
Conductivity of the phloem in mango (Mangifera indica L.)
Authors: Barceló-Anguiano Miguel , Hormaza José I. , Losada Juan M.
Published: July 2021

Mango (Mangifera indica L., Anacardiaceae), the fifth most consumed fruit worldwide, is one of the most important fruit crops in tropical regions, but its vascular anatomy is quite unexplored. Previous studies examined the xylem structure in the stems of mango, but the anatomy of the phloem has remained elusive, leaving the long-distance transport of photoassimilates understudied. We combined fluorescence and electron microscopy to evaluate the structure of the phloem tissue in the tapering branches of mango trees, and used this information to describe the hydraulic conductivity of its sieve tube elements following current models of fluid transport in trees. We revealed that the anatomy of the phloem changes from current year branches, where it was protected by pericyclic fibres, to older ones, where the lack of fibres was concomitant with laticiferous canals embedded in the phloem tissue. Callose was present in the sieve plates, but also in the walls of the phloem sieve cells, making them discernible from other phloem cells. A scaling geometry of the sieve tube elements—including the number of sieve areas and the pore size across tapering branches—resulted in an exponential conductivity towards the base of the tree. These evaluations in mango fit with previous measurements of the phloem architecture in the stems of forest trees, suggesting that, despite agronomic management, the phloem sieve cells scale with the tapering branches. The pipe model theory applied to the continuous tubing system of the phloem appears as a good approach to understand the hydraulic transport of photoassimilates in fruit trees.
VqMYB154 promotes polygene expression and enhances resistance to pathogens in Chinese wild grapevine
Authors: Jiang Changyue , Wang Dan , Zhang Jie , Xu Yan , Zhang Chaohong , Zhang Jianxia , Wang Xiping , Wang Yuejin
Published: July 2021

Resveratrol plays a crucial phytoalexin role in the grapevine and is beneficial to human health. However, the molecular mechanism of resveratrol accumulation in the enhancement of disease resistance is unclear. Here, we report that the transcription factor VqMYB154 from Vitis quinquangularis accession Danfeng-2 is strongly expressed under artificial inoculation with Uncinula necator and regulates resveratrol accumulation. Unlike its homolog, VqMYB154 has a pathogen-induced promoter and responds to stimulation by U. necator, Pseudomonas syringae, and other treatments. Yeast one-hybrid and GUS activity assays confirmed that VqMYB154 can activate the stilbene synthase genes VqSTS9, VqSTS32, and VqSTS42 by directly binding to their promoters. Overexpression of VqMYB154 in grape leaves resulted in activation of the stilbene pathway, upregulation of STS genes, and accumulation of stilbenoids. In addition, heterologous overexpression of VqMYB154 in Arabidopsis activated resistance-related genes and resulted in greater programmed cell death and accumulation of reactive oxygen species, which led to resistance against P. syringae. These results suggest that the transcription factor VqMYB154 from V. quinquangularis accession Danfeng-2 participates in the regulatory mechanism that improves the biosynthesis and accumulation of stilbenes and enhances resistance to disease in grapevine.
Evolution of the MLO gene families in octoploid strawberry (Fragaria ×ananassa) and progenitor diploid species identified potential genes for strawberry powdery mildew resistance
Authors: Tapia Ronald R , Barbey Christopher R , Chandra Saket , Folta Kevin M , Whitaker Vance M , Lee Seonghee
Published: July 2021

Powdery mildew (PM) caused by Podosphaera aphanis is a major fungal disease of cultivated strawberry. Mildew Resistance Locus O (MLO) is a gene family described for having conserved seven-transmembrane domains. Induced loss-of-function in specific MLO genes can confer durable and broad resistance against PM pathogens. However, the genomic structure and potential role of MLO genes for PM resistance have not been characterized yet in the octoploid cultivated strawberry. In the present study, MLO gene families were characterized in four diploid progenitor species (Fragaria vesca, F. iinumae, F. viridis, and F. nipponica) and octoploid cultivated (Fragaria ×ananassa) strawberry, and potential sources of MLO-mediated susceptibility were identified. Twenty MLO sequences were identified in F. vesca and 68 identified in F. ×ananassa. Phylogenetic analysis divided diploid and octoploid strawberry MLO genes into eight different clades, in which three FveMLO (MLO10, MLO17, and MLO20) and their twelve orthologs of FaMLO were grouped together with functionally characterized MLO genes conferring PM susceptibility. Copy number variations revealed differences in MLO composition among homoeologous chromosomes, supporting the distinct origin of each subgenome during the evolution of octoploid strawberry. Dissecting genomic sequence and structural variations in candidate FaMLO genes revealed their potential role associated with genetic controls and functionality in strawberry against PM pathogen. Furthermore, the gene expression profiling and RNAi silencing of putative FaMLO genes in response to the pathogen indicate the function in PM resistance. These results are a critical first step in understanding the function of strawberry MLO genes and will facilitate further genetic studies of PM resistance in cultivated strawberry.
Antagonism between abscisic acid and gibberellin regulates starch synthesis and corm development in Gladiolus hybridus
Authors: Li Jingru , Seng Shanshan , Li Donglei , Zhang Fengqin , Liu Yixuan , Yao Ting , Liang Jiahui , Yi Mingfang , Wu Jian
Published: July 2021

Understanding corm development in flower bulbs is of importance for securing the quality of cut flowers and propagation of commercial stocks. Gladiolus is one of the most popular bulb plants worldwide. Its corm development is characterized by starch accumulation. Previous research has shown that phytohormones (especially gibberellin (GA)) are involved in tuber development. However, the relationship between abscisic acid (ABA)/GA and starch during corm development remains unclear. To gain deeper insights into the biological process of corm development, we performed a detailed anatomical characterization of different stages of corm development and analyzed phytohormone levels. Our study showed that corm development is linked to hormones (ABA and GA) and carbohydrates (sucrose and starch). Exogenous hormone treatment and silencing of endogenous hormone biosynthesis genes indicated that ABA positively regulates corm development, while GA acts as an antagonist of ABA function. A sucrose synthase gene (GhSUS2) was shown to be involved in the antagonism between ABA and GA. GhSUS2 was upregulated by ABA and downregulated by GA. The increase in the transcript level of GhSUS2 coincided with the development of corm/cormels. Silencing of GhSUS2 repressed corm development and starch accumulation. In conclusion, we propose that GhSUS2, an essential enzyme in sucrose degradation, is differentially regulated by ABA and GA and controls corm development in Gladiolus.
Evaluation of ambient mass spectrometry tools for assessing inherent postharvest pepper quality
Authors: Mason Tyler J. , Bettenhausen Harmonie M. , Chaparro Jacqueline M. , Uchanski Mark E. , Prenni Jessica E.
Published: July 2021

Horticulturists are interested in evaluating how cultivar, environment, or production system inputs can affect postharvest quality. Ambient mass spectrometry approaches enable analysis of minimally processed samples under ambient conditions and offer an attractive high-throughput alternative for assessing quality characteristics in plant products. Here, we evaluate direct analysis in real time (DART-MS) mass spectrometry and rapid evaporative ionization-mass spectrometry (REIMS) to assess quality characteristics in various pepper (Capsicum annuum L.) cultivars. DART-MS exhibited the ability to discriminate between pod colors and pungency based on chemical fingerprints, while REIMS could distinguish pepper market class (e.g., bell, lunchbox, and popper). Furthermore, DART-MS analysis resulted in the putative detection of important bioactive compounds in human diet such as vitamin C, p-coumaric acid, and capsaicin. The results of this study demonstrate the potential for these approaches as accessible and reliable tools for high throughput screening of pepper quality.
Copper(I)-catalysed site-selective C(sp3)–H bond chlorination of ketones, (E)-enones and alkylbenzenes by dichloramine-T
Authors: Jin Jianwen , Zhao Yichao , Kyne Sara Helen , Farshadfar Kaveh , Ariafard Alireza , Chan Philip Wai Hong
Published: July 2021

Strategies that enable intermolecular site-selective C–H bond functionalisation of organic molecules provide one of the cornerstones of modern chemical synthesis. In chloroalkane synthesis, such methods for intermolecular site-selective aliphatic C–H bond chlorination have, however, remained conspicuously rare. Here, we present a copper(I)-catalysed synthetic method for the efficient site-selective C(sp3)–H bond chlorination of ketones, (E)-enones and alkylbenzenes by dichloramine-T at room temperature. A key feature of the broad substrate scope is tolerance to unsaturation, which would normally pose an immense challenge in chemoselective aliphatic C–H bond functionalisation. By unlocking dichloramine-T’s potential as a chlorine radical atom source, the product site-selectivities achieved are among the most selective in alkane functionalisation and should find widespread utility in chemical synthesis. This is exemplified by the late-stage site-selective modification of a number of natural products and bioactive compounds, and gram-scale preparation and formal synthesis of two drug molecules.
Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex
Authors: Minegishi Katsura , Rothé Benjamin , Komatsu Kaoru R. , Ono Hiroki , Ikawa Yayoi , Nishimura Hiromi , Katoh Takanobu A. , Kajikawa Eriko , Sai Xiaorei , Miyashita Emi , Takaoka Katsuyoshi , Bando Kana , Kiyonari Hiroshi , Yamamoto Tadashi , Saito Hirohide , Constam Daniel B. , Hamada Hiroshi
Published: July 2021

Molecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examined how the fluid flow induces Dand5 mRNA decay. We found that the first 200 nucleotides in the 3′ untranslated region (3′-UTR) of Dand5 mRNA are necessary and sufficient for the left-sided decay and to mediate the response of a 3′-UTR reporter transgene to Ca2+, the cation channel Pkd2, the RNA-binding protein Bicc1 and their regulation by the flow direction. We show that Bicc1 preferentially recognizes GACR and YGAC sequences, which can explain the specific binding to a conserved GACGUGAC motif located in the proximal Dand5 3′-UTR. The Cnot3 component of the Ccr4-Not deadenylase complex interacts with Bicc1 and is also required for Dand5 mRNA decay at the node. These results suggest that Ca2+ currents induced by leftward fluid flow stimulate Bicc1 and Ccr4-Not to mediate Dand5 mRNA degradation specifically on the left side of the node.
High-resolution characterization of gene function using single-cell CRISPR tiling screen
Authors: Yang Lu , Chan Anthony K. N. , Miyashita Kazuya , Delaney Christopher D. , Wang Xi , Li Hongzhi , Pokharel Sheela Pangeni , Li Sandra , Li Mingli , Xu Xiaobao , Lu Wei , Liu Qiao , Mattson Nicole , Chen Kevin Yining , Wang Jinhui , Yuan Yate-Ching , Horne David , Rosen Steven T. , Soto-Feliciano Yadira , Feng Zhaohui , Hoshii Takayuki , Xiao Gang , Müschen Markus , Chen Jianjun , Armstrong Scott A. , Chen Chun-Wei
Published: July 2021

Identification of novel functional domains and characterization of detailed regulatory mechanisms in cancer-driving genes is critical for advanced cancer therapy. To date, CRISPR gene editing has primarily been applied to defining the role of individual genes. Recently, high-density mutagenesis via CRISPR tiling of gene-coding exons has been demonstrated to identify functional regions in genes. Furthermore, breakthroughs in combining CRISPR library screens with single-cell droplet RNA sequencing (sc-RNAseq) platforms have revealed the capacity to monitor gene expression changes upon genetic perturbations at single-cell resolution. Here, we present “sc-Tiling,” which integrates a CRISPR gene-tiling screen with single-cell transcriptomic and protein structural analyses. Distinct from other reported single-cell CRISPR screens focused on observing gene function and gene-to-gene/enhancer-to-gene regulation, sc-Tiling enables the capacity to identify regulatory mechanisms within a gene-coding region that dictate gene activity and therapeutic response.
Binding of guide piRNA triggers methylation of the unstructured N-terminal region of Aub leading to assembly of the piRNA amplification complex
Authors: Huang Xiawei , Hu Hongmiao , Webster Alexandre , Zou Fan , Du Jiamu , Patel Dinshaw J. , Sachidanandam Ravi , Toth Katalin Fejes , Aravin Alexei A. , Li Sisi
Published: July 2021

PIWI proteins use guide piRNAs to repress selfish genomic elements, protecting the genomic integrity of gametes and ensuring the fertility of animal species. Efficient transposon repression depends on amplification of piRNA guides in the ping-pong cycle, which in Drosophila entails tight cooperation between two PIWI proteins, Aub and Ago3. Here we show that post-translational modification, symmetric dimethylarginine (sDMA), of Aub is essential for piRNA biogenesis, transposon silencing and fertility. Methylation is triggered by loading of a piRNA guide into Aub, which exposes its unstructured N-terminal region to the PRMT5 methylosome complex. Thus, sDMA modification is a signal that Aub is loaded with piRNA guide. Amplification of piRNA in the ping-pong cycle requires assembly of a tertiary complex scaffolded by Krimper, which simultaneously binds the N-terminal regions of Aub and Ago3. To promote generation of new piRNA, Krimper uses its two Tudor domains to bind Aub and Ago3 in opposite modification and piRNA-loading states. Our results reveal that post-translational modifications in unstructured regions of PIWI proteins and their binding by Tudor domains that are capable of discriminating between modification states is essential for piRNA biogenesis and silencing.
Serine-linked PARP1 auto-modification controls PARP inhibitor response
Authors: Prokhorova Evgeniia , Zobel Florian , Smith Rebecca , Zentout Siham , Gibbs-Seymour Ian , Schützenhofer Kira , Peters Alessandra , Groslambert Joséphine , Zorzini Valentina , Agnew Thomas , Brognard John , Nielsen Michael L. , Ahel Dragana , Huet Sébastien , Suskiewicz Marcin J. , Ahel Ivan
Published: July 2021

Poly(ADP-ribose) polymerase 1 (PARP1) and PARP2 are recruited and activated by DNA damage, resulting in ADP-ribosylation at numerous sites, both within PARP1 itself and in other proteins. Several PARP1 and PARP2 inhibitors are currently employed in the clinic or undergoing trials for treatment of various cancers. These drugs act primarily by trapping PARP1 on damaged chromatin, which can lead to cell death, especially in cells with DNA repair defects. Although PARP1 trapping is thought to be caused primarily by the catalytic inhibition of PARP-dependent modification, implying that ADP-ribosylation (ADPr) can counteract trapping, it is not known which exact sites are important for this process. Following recent findings that PARP1- or PARP2-mediated modification is predominantly serine-linked, we demonstrate here that serine ADPr plays a vital role in cellular responses to PARP1/PARP2 inhibitors. Specifically, we identify three serine residues within PARP1 (499, 507, and 519) as key sites whose efficient HPF1-dependent modification counters PARP1 trapping and contributes to inhibitor tolerance. Our data implicate genes that encode serine-specific ADPr regulators, HPF1 and ARH3, as potential PARP1/PARP2 inhibitor therapy biomarkers.
Structural basis of the activation of c-MET receptor
Authors: Uchikawa Emiko , Chen Zhiming , Xiao Guan-Yu , Zhang Xuewu , Bai Xiao-chen
Published: July 2021

The c-MET receptor is a receptor tyrosine kinase (RTK) that plays essential roles in normal cell development and motility. Aberrant activation of c-MET can lead to both tumors growth and metastatic progression of cancer cells. C-MET can be activated by either hepatocyte growth factor (HGF), or its natural isoform NK1. Here, we report the cryo-EM structures of c-MET/HGF and c-MET/NK1 complexes in the active state. The c-MET/HGF complex structure reveals that, by utilizing two distinct interfaces, one HGF molecule is sufficient to induce a specific dimerization mode of c-MET for receptor activation. The binding of heparin as well as a second HGF to the 2:1 c-MET:HGF complex further stabilize this active conformation. Distinct to HGF, NK1 forms a stable dimer, and bridges two c-METs in a symmetrical manner for activation. Collectively, our studies provide structural insights into the activation mechanisms of c-MET, and reveal how two isoforms of the same ligand use dramatically different mechanisms to activate the receptor.
Xanthomonas effector XopR hijacks host actin cytoskeleton via complex coacervation
Authors: Sun He , Zhu Xinlu , Li Chuanxi , Ma Zhiming , Han Xiao , Luo Yuanyuan , Yang Liang , Yu Jing , Miao Yansong
Published: July 2021

The intrinsically disordered region (IDR) is a preserved signature of phytobacterial type III effectors (T3Es). The T3E IDR is thought to mediate unfolding during translocation into the host cell and to avoid host defense by sequence diversification. Here, we demonstrate a mechanism of host subversion via the T3E IDR. We report that the Xanthomonas campestris T3E XopR undergoes liquid-liquid phase separation (LLPS) via multivalent IDR-mediated interactions that hijack the Arabidopsis actin cytoskeleton. XopR is gradually translocated into host cells during infection and forms a macromolecular complex with actin-binding proteins at the cell cortex. By tuning the physical-chemical properties of XopR-complex coacervates, XopR progressively manipulates multiple steps of actin assembly, including formin-mediated nucleation, crosslinking of F-actin, and actin depolymerization, which occurs through competition for actin-depolymerizing factor and depends on constituent stoichiometry. Our findings unravel a sophisticated strategy in which bacterial T3E subverts the host actin cytoskeleton via protein complex coacervation.
A regulatory network involving Rpo, Gac and Rsm for nitrogen-fixing biofilm formation by Pseudomonas stutzeri
Authors: Shang Liguo , Yan Yongliang , Zhan Yuhua , Ke Xiubin , Shao Yahui , Liu Yaqun , Yang Hua , Wang Shanshan , Dai Shuling , Lu Jiasi , Yan Ning , Yang Zhimin , Lu Wei , Liu Zhu , Chen Shanchun , Elmerich Claudine , Lin Min
Published: July 2021

Biofilm and nitrogen fixation are two competitive strategies used by many plant-associated bacteria; however, the mechanisms underlying the formation of nitrogen-fixing biofilms remain largely unknown. Here, we examined the roles of multiple signalling systems in the regulation of biofilm formation by root-associated diazotrophicP. stutzeriA1501. Physiological analysis, construction of mutant strains and microscale thermophoresis experiments showed that RpoN is a regulatory hub coupling nitrogen fixation and biofilm formation by directly activating the transcription ofpslA, a major gene involved in the synthesis of the Psl exopolysaccharide component of the biofilm matrix andnifA, the transcriptional activator ofnifgene expression. Genetic complementation studies and determination of the copy number of transcripts by droplet digital PCR confirmed that the regulatory ncRNA RsmZ serves as a signal amplifier to trigger biofilm formation by sequestering the translational repressor protein RsmA away frompslAandsadCmRNAs, the latter of which encodes a diguanylate cyclase that synthesises c-di-GMP. Moreover, RpoS exerts a braking effect on biofilm formation by transcriptionally downregulating RsmZ expression, while RpoS expression is repressed posttranscriptionally by RsmA. These findings provide mechanistic insights into how the Rpo/Gac/Rsm regulatory networks fine-tune nitrogen-fixing biofilm formation in response to the availability of nutrients.
Teaching solid mechanics to artificial intelligence—a fast solver for heterogeneous materials
Authors: Mianroodi Jaber Rezaei , H. Siboni Nima , Raabe Dierk
Published: July 2021

We propose a deep neural network (DNN) as a fast surrogate model for local stress calculations in inhomogeneous non-linear materials. We show that the DNN predicts the local stresses with 3.8% mean absolute percentage error (MAPE) for the case of heterogeneous elastic media and a mechanical contrast of up to factor of 1.5 among neighboring domains, while performing 103 times faster than spectral solvers. The DNN model proves suited for reproducing the stress distribution in geometries different from those used for training. In the case of elasto-plastic materials with up to 4 times mechanical contrast in yield stress among adjacent regions, the trained model simulates the micromechanics with a MAPE of 6.4% in one single forward evaluation of the network, without any iteration. The results reveal an efficient approach to solve non-linear mechanical problems, with an acceleration up to a factor of 8300 for elastic-plastic materials compared to typical solvers.
Statistical learning occurs during practice while high-order rule learning during rest period
Authors: Quentin Romain , Fanuel Lison , Kiss Mariann , Vernet Marine , Vékony Teodóra , Janacsek Karolina , Cohen Leonardo G. , Nemeth Dezso
Published: July 2021

Knowing when the brain learns is crucial for both the comprehension of memory formation and consolidation and for developing new training and neurorehabilitation strategies in healthy and patient populations. Recently, a rapid form of offline learning developing during short rest periods has been shown to account for most of procedural learning, leading to the hypothesis that the brain mainly learns during rest between practice periods. Nonetheless, procedural learning has several subcomponents not disentangled in previous studies investigating learning dynamics, such as acquiring the statistical regularities of the task, or else the high-order rules that regulate its organization. Here we analyzed 506 behavioral sessions of implicit visuomotor deterministic and probabilistic sequence learning tasks, allowing the distinction between general skill learning, statistical learning, and high-order rule learning. Our results show that the temporal dynamics of apparently simultaneous learning processes differ. While high-order rule learning is acquired offline, statistical learning is evidenced online. These findings open new avenues on the short-scale temporal dynamics of learning and memory consolidation and reveal a fundamental distinction between statistical and high-order rule learning, the former benefiting from online evidence accumulation and the latter requiring short rest periods for rapid consolidation.
How young children integrate information sources to infer the meaning of words
Authors: Bohn Manuel , Tessler Michael Henry , Merrick Megan , Frank Michael C.
Published: July 2021

Before formal education begins, children typically acquire a vocabulary of thousands of words. This learning process requires the use of many different information sources in their social environment, including their current state of knowledge and the context in which they hear words used. How is this information integrated? We specify a developmental model according to which children consider information sources in an age-specific way and integrate them via Bayesian inference. This model accurately predicted 2–5-year-old children’s word learning across a range of experimental conditions in which they had to integrate three information sources. Model comparison suggests that the central locus of development is an increased sensitivity to individual information sources, rather than changes in integration ability. This work presents a developmental theory of information integration during language learning and illustrates how formal models can be used to make a quantitative test of the predictive and explanatory power of competing theories.
Nonlinear second-order photonic topological insulators
Authors: Kirsch Marco S. , Zhang Yiqi , Kremer Mark , Maczewsky Lukas J. , Ivanov Sergey K. , Kartashov Yaroslav V. , Torner Lluis , Bauer Dieter , Szameit Alexander , Heinrich Matthias
Published: July 2021

Higher-order topological insulators are a novel topological phase beyond the framework of conventional bulk–boundary correspondence1,2. In these peculiar systems, the topologically non-trivial boundary modes are characterized by a co-dimension of at least two3,4. Despite several promising preliminary considerations regarding the impact of nonlinearity in such systems5,6, the flourishing field of experimental higher-order topological insulator research has thus far been confined to the linear evolution of topological states. As such, the observation of the interplay between nonlinearity and the dynamics of higher-order topological phases in conservative systems remains elusive. Here we experimentally demonstrate nonlinear higher-order topological corner states. Our photonic platform enables us to observe nonlinear topological corner states as well as the formation of solitons in such topological structures. Our work paves the way towards the exploration of topological properties of matter in the nonlinear regime, and may herald a new class of compact devices that harnesses the intriguing features of topology in an on-demand fashion.
Eight soybean reference genome resources from varying latitudes and agronomic traits
Authors: Chu Jeffrey Shih-Chieh , Peng Bo , Tang Kuanqiang , Yi Xingxing , Zhou Huangkai , Wang Huan , Li Guang , Leng Jiantian , Chen Nansheng , Feng Xianzhong
Published: July 2021

Comparative analysis of multiple reference genomes representing diverse genetic backgrounds is critical for understanding the role of key alleles important in domestication and genetic breeding of important crops such as soybean. To enrich the genetic resources for soybean, we describe the generation, technical assessment, and preliminary genomic variation analysis of eight de novo reference-grade soybean genome assemblies from wild and cultivated accessions. These resources represent soybeans cultured at different latitudes and exhibiting different agronomical traits. Of these eight soybeans, five are from new accessions that have not been sequenced before. We demonstrate the usage of these genomes to identify small and large genomic variations affecting known genes as well as screening for genic PAV regions for identifying candidates for further functional studies.
Phytotoxic effects of invasive Ageratina adenophora on two native subtropical shrubs in Nepal
Authors: Darji Tej Bahadur , Adhikari Barsha , Pathak Seeta , Neupane Shristi , Thapa Lal B. , Bhatt Tara Datt , Pant Ramesh Raj , Pant Gunanand , Pal Khadka Bahadur , Bishwakarma Kiran
Published: July 2021

The response of native plants to allelopathic interference of invasive species may differ from species to species. In this study, the phytotoxic effects ofAgeratina adenophorawere tested on two native shrubs (Osbeckia stellataandElsholtzia blanda) of Nepal. Both the shrubs were grown in pots under treatments ofA. adenophorafresh leaves and root leachates, and litter. Then, the seedling length and biomass were compared among the treatments. The results show thatA. adenophoralitter has stimulatory effects but the leachates from fresh leaves and root are phytotoxic to the growth and development of native shrubs. Infrared Spectroscopy (IR) analysis confirmed the presence of O–H (Hydroxyl), N–H (Amines), C≡C (Alkynes), and C–H stretching (Aromatic) or C–O–C stretching (Ethers) in the leachates representing harmful allelochemicals. The invaded soil byA. adenophorahad low pH and a high amount of organic matter, total nitrogen, phosphorus, and potassium than the uninvaded soil. The results indicate that the nativeO. stellataandE. blandaare harmed byA. adenophorain nature by leaching of allelochemicals and probably by reducing the soil pH. Overall, this study has provided valuable insights regarding the effects ofA. adenophorainvasion on native shrubs and revealing the potential mechanism of its invasiveness.