bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Modified Evaporation Model Indicates That the Effects of Air Warming on Global Drying Trends Have Been Overestimated
Authors: Liu Meixian , Xu Xianli , Scanlon Bridget R. , Sun Alexander Y. , Wang Kelin 
Published: November 2021

AbstractPotential evapotranspiration (PET) is a key input to hydrologic models simulating the atmospheric water demand. Thus, uncertainties in PET would result in considerable uncertainty in model outputs. Among numerous PET algorithms, the Penman‐Monteith equation (PM equation) is most widely used because of its clear physical basis and acceptable estimation. However, PM equation has a physical limitation resulting from the linear approximation of the saturation water vapor pressure differences between the evaporation surface and the surrounding air, which can affect markedly the responses of PET to air warming. By considering a modified PM‐type evaporation model, we revisited the global drying trends based on the widely used Palmer Drought Severity Index (PDSI). We demonstrate that the studies, which based on the classic PM equation, often overestimate the effects of air warming on global drying trends. Particularly, the PET_PM (PET calculated using the classic PM equation) driven PDSI, overestimates global mean drought‐affected areas by 60%, drought intensity by 65%, and drought duration by 35% on average over the globe, and tends to overestimate drying trends in areas that are drying and underestimate wetting trends in areas that are becoming wetter.
Isotopic Evidence for the High Contribution of Wintertime Photochemistry to Particulate Nitrate Formation in Northern China
Authors: Zhang Zhongyi , Jiang Zhuang , Guan Hui , Liang Yue , Zheng Nengjian , Guo Wei 
Published: November 2021

AbstractStable isotopic constraint and observationally coupled atmospheric chemistry model are two robust means to identify the oxidation mechanisms for atmospheric particulate nitrate (NO3−) production. However, large discrepancies between the two approaches have been noted in the heavily polluted environments of North China Plain (NCP). Herein, daily PM2.5samples (n = 418) were collected at five urban cities across NCP during the winter of 2017–2018; the ionic species (e.g., NO3−and methanesulfonic acid: MSA) and the dual‐isotopic signatures of NO3−were quantified. In this study, we revisited the O isotopic signatures of atmospheric O‐bearing molecules, especially that of OH radical in accordance with the up‐to‐date field measurements conducted in NCP regions. In brief, the δ18O‐OH was determined by the competition between the OH loss reaction rate and its isotopic equilibration reaction with H2O. Our improved isotopic results suggested that the daytime OH oxidation pathway was as important as the nocturnal channels in wintertime nitrate production in NCP (46.4% vs. 53.6%), whereas the exceedingly high loadings of NO3−in haze days were attributed to the heterogeneous chemistry of N2O5hydrolysis. Chemical analysis also confirmed the importance of active photochemistry in secondary components production, as the MSA (a photooxidation product) linearly correlated with the NO3−(R2 = 0.86,p < 0.05). Our preliminary results compared well with the recent model simulations (e.g., sophisticated 3D model and observationally constraint model). To alleviate the winter haze in NCP, future emission regulations should aim to reduce the photochemical oxidants, particularly their precursors of NOxand VOCs simultaneously.
The Influence of Three‐Dimensional Topography on Turbulent Flow Structures Over Dunes in Unidirectional Flows
Authors: Hardy R. J. , Best J. L. , Marjoribanks T. I. , Parsons D. R. , Ashworth P. J. 
Published: November 2021

AbstractDunes are the most prevalent bedform present in sand‐bedded rivers and their morphology typically comprises multiple scales of three‐dimensional topography. However, our understanding of flow over dunes is predicated largely on two‐dimensional models, a condition which is rare in nature. Here, we present results of Large Eddy Simulations over a static, three‐dimensional dune field, using a two‐ and three‐ dimensional topographic realisation, to investigate the interaction between bed topography and turbulent flow structures. We show that flow over two‐dimensional bedforms increases the velocity over the stoss slope and reduces the size of the leeside separation zone as compared to 3D topography. Flow over three‐dimensional bedforms generates twice as many vortices as over two‐dimensional bedforms, and these vortices are longer, wider and taller than flow over their two‐dimensional counterparts. Turbulence is dominated by hairpin‐shaped vortices and Kelvin‐Helmholtz instabilities that interact with the bed in the brink point region of the dune crest and down the lee slope, and generate high shear stresses for long durations. These results are used to propose a new conceptual model showing the differences between flow over two‐ and three‐dimensional bedforms. The findings highlight how the size, morphology and stacking of coherent flow structures into larger flow superstructures may be critical in sediment entrainment, and may dictate the relationship between event duration and magnitude that drives sediment impulses at the bed. This will ultimately lead to an increased in the three‐dimensionality of bedform morphology.
Hydrogeomorphic Recovery and Temporal Changes in Rainfall Thresholds for Debris Flows Following Wildfire
Authors: Hoch Olivia J. , McGuire Luke A. , Youberg Ann M. , Rengers Francis K. 
Published: November 2021

AbstractWildfire‐induced changes to soil and vegetation promote runoff‐generated debris flows in steep watersheds. Postfire debris flows are most commonly observed in steep watersheds during the first wet season following a wildfire, but it is unclear how long the elevated threat of debris flow persists and why debris‐flow potential changes in recovering burned areas. This work quantifies how rainfall intensity‐duration (ID) thresholds for debris‐flow initiation change with time since burning and provides a mechanistic explanation for these changes. We constrained a hydrologic model using field and remotely sensed measurements of soil‐infiltration capacity, vegetation cover, runoff, and debris‐flow activity. We applied this model to estimate rainfall ID thresholds for debris‐flow initiation within three burned areas in the southwestern United States over a postfire recovery period of three to four years. Modeling suggests ID thresholds are lowest immediately following the fire (below a one‐year recurrence interval [RI] storm) and increase with time, such that a 10‐ to 25‐year RI storm would be required to generate a debris flow after three years of recovery. Modeled changes in rainfall ID thresholds result from increases in soil infiltration capacity, canopy interception, hydraulic roughness, and median grain size of sediment entrained in an incipient debris flow. The relative importance of each of these factors varied among our three sites. Results improve our ability to assess temporal changes in postfire debris‐flow potential, highlight how site‐specific factors may alter the persistence of postfire debris‐flow hazards, and provide additional constraints on the timescale of recovery following wildfire.
Cancer drivers and clonal dynamics in acute lymphoblastic leukaemia subtypes
Authors: Studd James B. , Cornish Alex J. , Hoang Phuc H. , Law Philip , Kinnersley Ben , Houlston Richard 
Published: November 2021

AbstractTo obtain a comprehensive picture of composite genetic driver events and clonal dynamics in subtypes of paediatric acute lymphoblastic leukaemia (ALL) we analysed tumour-normal whole genome sequencing and expression data from 361 newly diagnosed patients. We report the identification of both structural drivers, as well as recurrent non-coding variation in promoters. Additionally we found the transcriptional profile of histone gene cluster 1 and CTCF altered tumours shared hallmarks of hyperdiploid ALL suggesting a ‘hyperdiploid like’ subtype. ALL subtypes are driven by distinct mutational processes with AID mutagenesis being confined to ETV6-RUNX1 tumours. Subclonality is a ubiquitous feature of ALL, consistent with Darwinian evolution driving selection and expansion of tumours. Driver mutations in B-cell developmental genes (IKZF1, PAX5, ZEB2) tend to be clonal and RAS/RTK mutations subclonal. In addition to identifying new avenues for therapeutic exploitation, this analysis highlights that targeted therapies should take into account composite mutational profile and clonality.
Circ_0058106 promotes proliferation, metastasis and EMT process by regulating Wnt2b/β-catenin/c-Myc pathway through miR-185-3p in hypopharyngeal squamous cell carcinoma
Authors: Li Ce , Li Wenming , Cao Shengda , Xu Jianing , Qian Ye , Pan Xinliang , Lei Dapeng , Wei Dongmin 
Published: November 2021

AbstractHypopharyngeal squamous cell carcinoma (HSCC) accounts 95% of hypopharyngeal cancer, which is characterized by high early metastasis rate and poor prognosis. It is reported that circular RNA is involved in the occurrence and development of cancer; however, the role of circRNA in hypopharyngeal cancer has little been investigated. We performed hypopharyngeal carcinoma circRNA microarray and qRT-PCR verification. The results showed circ_0058106 expression level was significantly upregulated in tumor tissues than in corresponding normal tissues. We found that circ_0058106 upregulation promoted proliferation, migration and invasion of HSCC cells, while knockdown of circ_0058106 inhibited proliferation, migration and invasion of HSCC cells both in vitro and in vivo. Bioinformatics predicted circ_0058106 may interact with miR-185-3p. We verified circ_0058106 directly bound miR-185-3p and downregulated miR-185-3p expression by using dual-luciferase reporter assay and qRT-PCR. Moreover, we proved circ_0058106 promoted HSCC cells tumorigenesis and EMT process by regulating Wnt2b/β-catenin/c-Myc pathway via miR-185-3p. In conclusion, our findings firstly confirmed the carcinogenic effect of circ_0058106 in promoting HSCC cells tumorigenesis, metastasis, invasion and EMT process by regulating Wnt2b/β-catenin/c-Myc pathway through sponging miR-185-3p, indicating that circ_0058106 may be a new therapeutic target and prognostic marker for HSCC.
Mid-lateral cerebellar complex spikes encode multiple independent reward-related signals during reinforcement learning
Authors: Sendhilnathan Naveen , Ipata Anna , Goldberg Michael E. 
Published: November 2021

AbstractAlthough the cerebellum has been implicated in simple reward-based learning recently, the role of complex spikes (CS) and simple spikes (SS), their interaction and their relationship to complex reinforcement learning and decision making is still unclear. Here we show that in a context where a non-human primate learned to make novel visuomotor associations, classifying CS responses based on their SS properties revealed distinct cell-type specific encoding of the probability of failure after the stimulus onset and the non-human primate’s decision. In a different context, CS from the same cerebellar area also responded in a cell-type and learning independent manner to the stimulus that signaled the beginning of the trial. Both types of CS signals were independent of changes in any motor kinematics and were unlikely to instruct the concurrent SS activity through an error based mechanism, suggesting the presence of context dependent, flexible, multiple independent channels of neural encoding by CS and SS. This diversity in neural information encoding in the mid-lateral cerebellum, depending on the context and learning state, is well suited to promote exploration and acquisition of wide range of cognitive behaviors that entail flexible stimulus-action-reward relationships but not necessarily motor learning.
Lysine acetylation regulates the interaction between proteins and membranes
Authors: Okada Alan K. , Teranishi Kazuki , Ambroso Mark R. , Isas Jose Mario , Vazquez-Sarandeses Elena , Lee Joo-Yeun , Melo Arthur Alves , Pandey Priyatama , Merken Daniel , Berndt Leona , Lammers Michael , Daumke Oliver , Chang Karen , Haworth Ian S. , Langen Ralf 
Published: November 2021

AbstractLysine acetylation regulates the function of soluble proteins in vivo, yet it remains largely unexplored whether lysine acetylation regulates membrane protein function. Here, we use bioinformatics, biophysical analysis of recombinant proteins, live-cell fluorescent imaging and genetic manipulation of Drosophila to explore lysine acetylation in peripheral membrane proteins. Analysis of 50 peripheral membrane proteins harboring BAR, PX, C2, or EHD membrane-binding domains reveals that lysine acetylation predominates in membrane-interaction regions. Acetylation and acetylation-mimicking mutations in three test proteins, amphiphysin, EHD2, and synaptotagmin1, strongly reduce membrane binding affinity, attenuate membrane remodeling in vitro and alter subcellular localization. This effect is likely due to the loss of positive charge, which weakens interactions with negatively charged membranes. In Drosophila, acetylation-mimicking mutations of amphiphysin cause severe disruption of T-tubule organization and yield a flightless phenotype. Our data provide mechanistic insights into how lysine acetylation regulates membrane protein function, potentially impacting a plethora of membrane-related processes.
Network analysis reveals rare disease signatures across multiple levels of biological organization
Authors: Buphamalai Pisanu , Kokotovic Tomislav , Nagy Vanja , Menche Jörg 
Published: November 2021

AbstractRare genetic diseases are typically caused by a single gene defect. Despite this clear causal relationship between genotype and phenotype, identifying the pathobiological mechanisms at various levels of biological organization remains a practical and conceptual challenge. Here, we introduce a network approach for evaluating the impact of rare gene defects across biological scales. We construct a multiplex network consisting of over 20 million gene relationships that are organized into 46 network layers spanning six major biological scales between genotype and phenotype. A comprehensive analysis of 3,771 rare diseases reveals distinct phenotypic modules within individual layers. These modules can be exploited to mechanistically dissect the impact of gene defects and accurately predict rare disease gene candidates. Our results show that the disease module formalism can be applied to rare diseases and generalized beyond physical interaction networks. These findings open up new venues to apply network-based tools for cross-scale data integration.
Four-band non-Abelian topological insulator and its experimental realization
Authors: Jiang Tianshu , Guo Qinghua , Zhang Ruo-Yang , Zhang Zhao-Qing , Yang Biao , Chan C. T. 
Published: November 2021

AbstractVery recently, increasing attention has been focused on non-Abelian topological charges, e.g., the quaternion group Q8. Different from Abelian topological band insulators, these systems involve multiple entangled bulk bandgaps and support nontrivial edge states that manifest the non-Abelian topological features. Furthermore, a system with an even or odd number of bands will exhibit a significant difference in non-Abelian topological classification. To date, there has been scant research investigating even-band non-Abelian topological insulators. Here, we both theoretically explore and experimentally realize a four-band PT (inversion and time-reversal) symmetric system, where two new classes of topological charges as well as edge states are comprehensively studied. We illustrate their difference in the four-dimensional (4D) rotation sense on the stereographically projected Clifford tori. We show the evolution of the bulk topology by extending the 1D Hamiltonian onto a 2D plane and provide the accompanying edge state distributions following an analytical method. Our work presents an exhaustive study of four-band non-Abelian topological insulators and paves the way towards other even-band systems.
Monovalent lanthanide(I) in borozene complexes
Authors: Li Wan-Lu , Chen Teng-Teng , Chen Wei-Jia , Li Jun , Wang Lai-Sheng 
Published: November 2021

AbstractLanthanide (Ln) elements are generally found in the oxidation state +II or +III, and a few examples of +IV and +V compounds have also been reported. In contrast, monovalent Ln(+I) complexes remain scarce. Here we combine photoelectron spectroscopy and theoretical calculations to study Ln-doped octa-boron clusters (LnB8−, Ln = La, Pr, Tb, Tm, Yb) with the rare +I oxidation state. The global minimum of the LnB8−species changes fromCstoC7vsymmetry accompanied by an oxidation-state change from +III to +I from the early to late lanthanides. All theC7v-LnB8−clusters can be viewed as a monovalent Ln(I) coordinated by a η8-B82−doubly aromatic ligand. The B73−, B82−, and B9−series of aromatic boron clusters are analogous to the classical aromatic hydrocarbon molecules, C5H5−, C6H6, and C7H7+, respectively, with similar trends of size and charge state and they are named collectively as “borozenes”. Lanthanides with variable oxidation states and magnetic properties may be formed with different borozenes.
Co-evolution based machine-learning for predicting functional interactions between human genes
Authors: Stupp Doron , Sharon Elad , Bloch Idit , Zitnik Marinka , Zuk Or , Tabach Yuval 
Published: November 2021

AbstractOver the next decade, more than a million eukaryotic species are expected to be fully sequenced. This has the potential to improve our understanding of genotype and phenotype crosstalk, gene function and interactions, and answer evolutionary questions. Here, we develop a machine-learning approach for utilizing phylogenetic profiles across 1154 eukaryotic species. This method integrates co-evolution across eukaryotic clades to predict functional interactions between human genes and the context for these interactions. We benchmark our approach showing a 14% performance increase (auROC) compared to previous methods. Using this approach, we predict functional annotations for less studied genes. We focus on DNA repair and verify that 9 of the top 50 predicted genes have been identified elsewhere, with others previously prioritized by high-throughput screens. Overall, our approach enables better annotation of function and functional interactions and facilitates the understanding of evolutionary processes underlying co-evolution. The manuscript is accompanied by a webserver available at: https://mlpp.cs.huji.ac.il.
Type VI secretion system mutations reduced competitive fitness of classical Vibrio cholerae biotype
Authors: Kostiuk Benjamin , Santoriello Francis J. , Diaz-Satizabal Laura , Bisaro Fabiana , Lee Kyung-Jo , Dhody Anna N. , Provenzano Daniele , Unterweger Daniel , Pukatzki Stefan 
Published: November 2021

AbstractThe gram-negative bacterium Vibrio cholerae is the causative agent of the diarrhoeal disease cholera and is responsible for seven recorded pandemics. Several factors are postulated to have led to the decline of 6th pandemic classical strains and the rise of El Tor biotype V. cholerae, establishing the current 7th pandemic. We investigated the ability of classical V. cholerae of the 2nd and 6th pandemics to engage their type six secretion system (T6SS) in microbial competition against non-pandemic and 7th pandemic strains. We report that classical V. cholerae underwent sequential mutations in T6SS genetic determinants that initially exposed 2nd pandemic strains to microbial attack by non-pandemic strains and subsequently caused 6th pandemic strains to become vulnerable to El Tor biotype V. cholerae intraspecific competition. The chronology of these T6SS-debilitating mutations agrees with the decline of 6th pandemic classical strains and the emergence of 7th pandemic El Tor V. cholerae.
Screening of cashmere fineness-related genes and their ceRNA network construction in cashmere goats
Authors: Hui Taiyu , Zheng Yuanyuan , Yue Chang , Wang Yanru , Bai Zhixian , Sun Jiaming , Cai Weidong , Zhang Xinjiang , Bai Wenlin , Wang Zeying 
Published: November 2021

AbstractCompetitive endogenous RNA (ceRNA) is a transcript that can be mutually regulated at the post-transcriptional level by competing shared miRNAs. The ceRNA network connects the function of protein-encoded mRNA with the function of non-coding RNA, such as microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). However, compared with the ceRNA, the identification and combined analysis of lncRNAs, mRNAs, miRNAs, and circRNAs in the cashmere fineness have not been completed. Using RNA-seq technology, we first identified the miRNAs presented in Liaoning Cashmere Goat (LCG) skin, and then analyzed the mRNAs, lncRNAs, circRNAs expressed in LCG and Inner Mongolia cashmere goat (MCG) skin. As a result, 464 known and 45 new miRNAs were identified in LCG skin. In LCG and MCG skin, 1222 differentially expressed mRNAs were identified, 170 differentially expressed lncRNAs and 32 differentially expressed circRNAs were obtained. Then, qRT-PCR was used to confirm further the representative lncRNAs, mRNAs, circRNAs and miRNAs. In addition, miRanda predicted the relationships of ceRNA regulatory network among lncRNAs, circRNAs, miRNAs and mRNAs, the potential regulatory effects were investigated by Go and KEGG analysis. Through the screening and analysis of the results, the ceRNA network regulating cashmere fineness was constructed. LncRNA MSTRG14109.1 and circRNA452 were competed with miRNA-2330 to regulated the expression of TCHH, KRT35 and JUNB, which may provide a potential basis for further research on the process of regulating the cashmere fineness.
Evaluation of antimicrobial activities of plant aqueous extracts against Salmonella Typhimurium and their application to improve safety of pork meat
Authors: Gavriil Alkmini , Zilelidou Evangelia , Papadopoulos Angelis-Evangelos , Siderakou Danae , Kasiotis Konstantinos M. , Haroutounian Serkos A. , Gardeli Chrysavgi , Giannenas Ilias , Skandamis Panagiotis N. 
Published: November 2021

AbstractNine odorless laboratory-collected hydro-distilled aqueous extracts (basil, calendula, centrifuged oregano, corn silk, laurel, oregano, rosemary, spearmint, thyme) and one industrial steam-distilled oregano hydrolate acquired as by-products of essential oils purification were screened for their in vitro antimicrobial activity against three Salmonella Typhimurium strains (4/74, FS8, FS115) at 4 and 37 °C. Susceptibility to the extracts was mainly plant- and temperature-dependent, though strain dependent effects were also observed. Industrial oregano hydrolate eliminated strains immediately after inoculation, exhibiting the highest antimicrobial potential. Hydro-distilled extracts eliminated/reduced Salmonella levels during incubation at 4 °C. At 37 °C, oregano, centrifuged oregano, thyme, calendula and basil were bactericidal while spearmint, rosemary and corn silk bacteriostatic. A strain-dependent effect was observed for laurel. The individual or combined effect of marinades and edible coatings prepared of industrial hydrolate and hydro-distilled oregano extracts with or without oregano essential oil (OEO) was tested in pork meat at 4 °C inoculated with FS8 strain. Lower in situ activity was observed compared to in vitro assays. Marinades and edible coatings prepared of industrial oregano hydrolate + OEO were the most efficient in inhibiting pathogen. Marination in oregano extract and subsequent coating with either 50% oregano extract + OEO or water + OEO enhanced the performance of oregano extract. In conclusion, by-products of oregano essential oil purification may be promising alternative antimicrobials to pork meat stored under refrigeration when applied in the context of multiple hurdle approach.