bluuebunny/crossref_metadata_2025_split huggingface dataset:
A proposed newTombusviridaegenus featuring extremely long 5’ untranslated regions and a luteo/polerovirus-like gene block
Authors: Lozier Zachary , Hill Lilyahna , Semmann Elizabeth , Miller W. Allen 
Published: June 2024

SummaryTombusviridaeis a large family of single-stranded, positive-sense RNA plant viruses with uncapped, non-polyadenylated genomes encoding 5-7 open reading frames (ORFs). Previously, we discovered, by high-throughput sequencing of maize and teosinte RNA, a novel genome of a virus we call Maize-associated tombusvirus (MaTV). Here we determined the precise termini of the MaTV genome by using 5’ and 3’ rapid amplification of cDNA ends (RACE). In GenBank, we discovered eleven other nearly complete viral genomes with MaTV-like genome organizations and related RNA-dependent RNA polymerase (RdRp) sequences. These genomes came from diverse plant, fungal, invertebrate and vertebrate organisms, and some have been found in multiple organisms across the globe. The available 5’ untranslated regions (UTRs) of these genomes are remarkably long: at least 438 to 727 nucleotides (nt), in contrast to those of other tombusvirids, which are <150 nt. Moreover these UTRs contain 6 to 12 AUG triplets that are unlikely to be start codons, because - with the possible exception of MaTV - there are no large or conserved ORFs in the 5’ UTRs. Such features suggest an internal ribosome entry site (IRES), but we found no conserved secondary structures. In the 50 nt upstream of and adjacent to the ORF1 start codon, the 5’ UTR was cytosine-rich and guanosine-poor. As in most tombusvirids, ORF2 (RdRp gene) appears to be translated by in-frame ribosomal readthrough of the ORF1 stop codon. Indeed, in all twelve genomes we identified RNA structures known in other tombusviruses to facilitate this readthrough. ORF5 is predicted to be translated by readthrough of the ORF3 (coat protein gene) stop codon as in genusLuteovirus. The resulting readthrough domains are highly divergent. ORF4 overlaps with ORF3 and may initiate with a non-AUG start codon. We also found no obvious 3’ cap-independent translation elements, which are present in other tombusvirids. The twelve genomes diverge sufficiently from other tombusvirids to warrant classification in a new genus. Because they contain two leaky stop codons and a potential leaky start codon, we propose to name this genusRimosavirus(rimosa= leaky in Latin).
Single and combined effect of salinity, heat, cold, and drought in Arabidopsis at metabolomics and photosynthetic levels
Authors: Secomandi Elena , De Gregorio Marco Armando , Castro-Cegrí Alejandro , Lucini Luigi 
Published: June 2024

ABSTRACTEnsuring food security is one of the main challenges related to a growing global population under climate change conditions. The increasing soil salinity levels, drought, heatwaves, and late chilling severely threaten crops and often co-occur in field conditions. This work aims to provide deeper insight into the impact of single vs combined abiotic stresses at the growth, biochemical and photosynthetic levels inArabidopsis thalianaL. By studying single and combined stresses, stress interactions and synergic effects have been highlighted. Lower photosynthetic efficiency was recorded from the beginning in all the conditions that included salinity. Consistently, membrane stability and ROS production, combined with a targeted metabolomic quantification of glycine, GABA, proline, and glycine-betaine molecular markers, highlighted the hierarchically stronger impact of salinity and its combinations on plant biochemistry. Untargeted metabolomics coupled with multivariate statistics pointed out distinct metabolic reprogramming triggered by the different stress conditions, either alone or in combination, differentiating the impact of salinity, drought, and their combination with cold and heat. These results contribute to delving into the impact of various stress combinations, hierarchically highlighting the stress-specific effects and pointing out different interactions.HIGHLIGHTSCombined stresses highlighted synergic and stronger impact on Arabidopsis secondary metabolism, redox imbalance and photosynthetic performance compared to individual stresses. Overall, salinity and its combination were the most impactful.
Development, validation and application of an LC-MS/MS method quantifying free forms of the micronutrients queuine and queuosine in human plasma using a surrogate matrix approach
Authors: Pan Xiaobei , Chandrasekaran Swathine , Woodside Jayne V. , Riedel-Heller Steffi G. , Scherer Martin , Wagner Michael , Ramirez Alfredo , Green Brian D. 
Published: June 2024

AbstractQueuosine (Q) is a hypermodified 7-deaza-guanosine nucleoside exclusively synthesized by bacteria. This micronutrient and its respective nucleobase form queuine (q) are salvaged by humans either from gut microflora, or digested food. Depletion of Q-tRNA in human or mouse cells causes protein misfolding that triggers endoplasmic reticular stress and activation of the unfolded protein responses. In vivo, this reduces neuronal architecture of the mouse brain affecting learning and memory. Herein, a sensitive method for quantifying free q and Q in human blood was developed, optimised and validated.After evaluating q/Q extraction efficiency in several different solid-phase sorbents, Bond Elut PBA (phenylboronic acid) cartridges were found to have the highest extraction recovery for q (82%) and Q (71%) from pooled human plasma. PBS with 4% BSA was used as surrogate matrix for method development and validation. An LC-MS/MS method was validated across the concentration range of 0.0003 – 1 µM for both q and Q, showing excellent: linearity (r2= 0.997 (q) and r2= 0.998 (Q)), limit of quantification (0.0003 µM), accuracy (100.39% - 125.71%) and precision (CV% < 15.68%). In a sampling of healthy volunteers (n = 44) there was no significant difference in q levels between male (n = 14; mean = 0.0068 µM) and female (n = 30; mean = 0.0080 µM) participants (p = 0.50). Q was not detected in human plasma. This validated method can now be used to further our understanding of the role of q/Q in nutrition, physiology and pathology.
Magnesium modulates phospholipid metabolism to promote bacterial phenotypic resistance to antibiotics
Authors: Li Hui , Yang Jun , Kuang Su-fang , Fu Huan-zhe , Lin Hui-ying , Peng Bo 
Published: June 2024

AbstractNon-inheritable antibiotic or phenotypic resistance ensures bacterial survival during antibiotic treatment. However, exogenous factors promoting phenotypic resistance are poorly defined. Here, we demonstrate thatVibrio alginolyticusare recalcitrant to killing by a broad spectrum of antibiotics under high magnesium. Functional metabolomics demonstrated that magnesium modulates fatty acid biosynthesis by increasing saturated fatty acid biosynthesis while decreasing unsaturated fatty acid production. Exogenous supplementation of unsaturated and saturated fatty acids increased and decreased bacterial susceptibility to antibiotics, respectively, confirming the role of fatty acids in antibiotic resistance. Functional lipidomics revealed that glycerophospholipid metabolism is the major metabolic pathway remodeled by magnesium, where phosphatidylethanolamine (PE) biosynthesis is reduced and phosphatidylglycerol (PG) production is increased. This process alters membrane composition, increasing membrane polarization, and decreasing permeability and fluidity, thereby reducing antibiotic uptake byV. alginolyticus. These findings suggest the presence of a previously unrecognized metabolic mechanism by which bacteria escape antibiotic killing through the use of an environmental factor.
Dynamic HSF2 regulation drives breast cancer progression by steering the balance between proliferation and invasion
Authors: Pessa Jenny C. , Paavolainen Oona , Puustinen Mikael C. , Hästbacka Hendrik S. E. , Da Silva Alejandro J. , Pihlström Sandra , Gramolelli Silvia , Boström Pia , Hartiala Pauliina , Peuhu Emilia , Joutsen Jenny , Sistonen Lea 
Published: June 2024

ABSTRACTPhenotypic plasticity is a hallmark of breast carcinogenesis that facilitates the acquisition of invasive propertiesviaepithelial-mesenchymal transition (EMT). Transforming growth factor-beta (TGF-β), a key EMT-inducing cytokine, drives pro-metastatic gene programs through downstream transcription factors. Among mammalian stress-protective transcription factors, heat shock factor 2 (HSF2) has been associated with cancer progression, but the mechanisms regulating HSF2 expression and activity are unknown. Here, we demonstrate that TGF-β stimulation downregulates HSF2 to enable activation of an invasive phenotype. Remarkably, ectopic expression of HSF2 in breast cancer cells inhibited TGF-β-mediated effects on gene expression and cellular properties. By using bothin vitrocell models andin vivozebrafish xenografts, we found that a temporal downregulation of HSF2 is a prerequisite for EMT activation, while ectopically sustained HSF2 promotes rapid cell proliferation and survival. Analyses of human patient tissues corroborated our results by showing that HSF2 is dynamically regulated during breast cancer progression. Specifically, HSF2 expression and nuclear co-localization with the proliferation marker Ki67 are dramatically increased already in ductal carcinomain situ. Altogether, our findings expand the pathological landscape of HSF2, demonstrating that dynamic regulation of HSF2 is an inherent property of malignant progression and characterizes the distinct stages of breast cancer.
The Aggregated Gut Viral Catalogue (AVrC): A Unified Resource for Exploring the Viral Diversity of the Human Gut
Authors: Galperina Anastasia , Lugli Gabriele Andrea , Milani Christian , De Vos Willem M. , Ventura Marco , Salonen Anne , Hurwitz Bonnie , Ponsero Alise J. 
Published: June 2024

AbstractDespite the growing interest in the role of the gut virome in human health and disease, identifying viral sequences from human gut metagenomes remains computationally challenging due to underrepresentation of viral genomes in reference databases. Several recent large-scale efforts have mined human gut metagenomes to establish viral sequence catalogues, using varied computational tools and quality control criteria. However, there has been no consistent comparison of these catalogues’ quality, diversity, and completeness, nor unification into a comprehensive resource. Here, we systematically surveyed nine previously published human gut viral catalogues, assessing their quality and the overlap of the viral sequences retrieved. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy. We further expanded representation by mining 7,867 infant gut metagenomes, retrieving 1,205,739 additional putative viral sequences. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Detailed annotations were generated for sequence quality, taxonomy, predicted lifestyle, and putative host. The AVrC reveals the gut virome’s substantial unexplored diversity, providing a pivotal resource for viral discovery. The AVrC is accessible as a relational database and through a web interface allowing customized querying and subset retrieval, enabling streamlined utilization by the research community and future expansions as novel data becomes available.Author summaryThe human gut is home to a vast array of viruses, collectively known as the gut virome, which play a crucial role in human health and disease. Recently, several research groups aiming at providing an overview of the Human gut viral diversity, have created catalogues of viral sequences found in the human gut by analyzing a large number of fecal samples from different individuals. In this study, we compared nine of these existing catalogues and found that there was surprisingly little overlap between them, with 82% of the viral sequences being unique to a single catalogue. To further expand the available data, we analyzed nearly 8,000 additional fecal samples from infants. By combining all this ressources, we created a unified resource called the Aggregated Gut Viral Catalogue (AVrC), which contains more than a million distinct viral sequences, representing nearly 450,000 different viral species. This catalogue, which is easily accessible to the scientific community through a user-friendly web interface, provides a valuable tool for exploring the vast diversity of the human gut virome and its potential implications for human health.
An efficient method for visualizing the plaques ofBdellovibrio bacteriovorus
Authors: Zhao Qian , Xu Jiangong , Zhu Kui 
Published: June 2024

ABSTRACTBdellovibrio bacteriovoruspreys upon other Gram-negative bacteria. This obligate predator is recognized as a living antibiotic to control the rising problem of antibiotic resistance. Plaque forming units (PFU) counting is commonly used to determine the viable numbers ofB. bacteriovorus. However, nearly 3-days incubation is always necessary for getting the single, obvious plaques on the double layer agar plate. This time-consuming procedure greatly impedes the purification and enumeration efficiency ofB. bacteriovorus. In this work, we evaluated the advantages of fluorescent prey on the plaque visualization of the predator. Our study reveals that plaques of theB. bacteriovorushave already formed before they could be monitored by eyes on the double layer agar plate. The regular single plaques are easily observed under the enhanced background of fluorescent prey lawn in 1.5 days, reducing nearly half of the time consumption in the purification and enumeration ofB. bacteriovorus. In addition, it also provides some paradigms for modeling and testing the subtle predation process on the solid medium.IMPORTANCEThe viability of predatorBdellovibrio bacteriovorusis typically suggested by the lysis of the prey bacteria on the double layer agar plate. However, long period incubation is necessary to get single obvious plaques ofB. bacteriovorus. Here, we found that plaques are already generated before it can be monitored by eyes. The plaques are obvious on the enhanced background of the double layer agar plate in the presence of fluorescent prey under UV light. We confirmed that the utilization of fluorescence labeled prey bacteria reduces the time spent on the isolation, purification, and enumeration of the predatorB. bacteriovoruson the double layer agar plate.
Tensing Flipper: Photosensitized manipulation of membrane tension, lipid phase separation and raft protein sorting in biological membranes
Authors: Torra Joaquim , Campelo Felix , Garcia-Parajo Maria F. 
Published: June 2024

ABSTRACTThe lateral organization of proteins and lipids in the plasma membrane is fundamental to regulating a wide range of cellular processes. Compartmentalized ordered membrane domains enriched with specific lipids, often termed lipid rafts, have been shown to modulate the physicochemical and mechanical properties of membranes and to drive protein sorting. Novel methods and tools enabling the visualization, characterization and/or manipulation of membrane compartmentalization are crucial to link the properties of the membrane with cell functions. Flipper, a commercially-available fluorescent membrane tension probe, has become a reference tool for quantitative membrane tension studies in living cells. Here, we report on a so far unidentified property of Flipper, namely, its ability to photosensitize singlet oxygen (1O2) under blue light when embedded into lipid membranes. This in turn results in the production of lipid hydroperoxides that increase membrane tension and trigger phase separation. In biological membranes, the photo-induced segregated domains retain the sorting ability of intact phase-separated membranes, directing raft and non-raft proteins into ordered and disordered regions, respectively, in contrast to radical-based photo-oxidation reactions that disrupt raft protein partitioning. The dual tension reporting and photosensitizing abilities of Flipper enable simultaneous visualization and manipulation of the mechanical properties and lateral organization of membranes, providing a powerful tool to optically control lipid raft formation and to explore the interplay between membrane biophysics and cell function.
Integrable symplectic maps with a polygon tessellation
Authors: Zolkin T. , Kharkov Y. , Nagaitsev S. 
Published: June 2024

Identifying integrable dynamics remains a formidable challenge, and despite centuries of research, only a handful of examples are known to date. In this article, we explore a distinct form of area-preserving (symplectic) mappings derived from the stroboscopic Poincaré cross section of a kicked rotator—an oscillator subjected to an external force periodically switched on in short pulses. The significance of this class of problems extends to various applications in physics and mathematics, including particle accelerators, crystallography, and studies of chaos. Notably, Suris's theorem constrains the integrability within this category of mappings, outlining potential scenarios with analytic invariants of motion. In this paper, we challenge the assumption of the analyticity of the invariant by exploring piecewise linear transformations on a torus (T2) and associated systems on the plane (R2), incorporating arithmetic quasiperiodicity and discontinuities. Introducing a new automated technique, we discovered previously unknown scenarios featuring polygonal invariants that form perfect tessellations and, moreover, fibrations of the plane or torus. This work reveals a novel category of planar tilings characterized by discrete symmetries that emerge from the invertibility of transformations and are intrinsically linked to the presence of integrability. Our algorithm relies on the analysis of the Poincaré rotation number and its piecewise monotonic nature for integrable cases, contrasting with the noisy behavior in the case of chaos, thereby allowing for clear separation. Some of the newly discovered systems exhibit the peculiar behavior of “integrable diffusion,” characterized by infinite and quasirandom hopping between tiles while being confined to a set of invariant segments. Finally, through the implementation of a smoothening procedure, all mappings can be generalized to quasi-integrable scenarios with suppressed volume occupied by chaotic trajectories, thereby opening doors to potential practical applications.

Published by the American Physical Society
2024
GIWAXS experimental methods at the NFPS-BL17B beamline at Shanghai Synchrotron Radiation Facility
Authors: Zhu Zhongjie , Lu Lanlu , Li Chunyu , Xiao Qingjie , Wu Tingting , Tang Jianchao , Gu Yijun , Bao Kangwen , Zhang Yupu , Jiang Luozhen , Liu Yang , Zhang Weizhe , Zhou Shuyu , Qin Wenming 
Published: June 2024

The BL17B beamline at the Shanghai Synchrotron Radiation Facility was first designed as a versatile high-throughput protein crystallography beamline and one of five beamlines affiliated to the National Facility for Protein Science in Shanghai. It was officially opened to users in July 2015. As a bending magnet beamline, BL17B has the advantages of high photon flux, brightness, energy resolution and continuous adjustable energy between 5 and 23 keV. The experimental station excels in crystal screening and structure determination, providing cost-effective routine experimental services to numerous users. Given the interdisciplinary and green energy research demands, BL17B beamline has undergone optimization, expanded its range of experimental methods and enhanced sample environments for a more user-friendly testing mode. These methods include single-crystal X-ray diffraction, powder crystal X-ray diffraction, wide-angle X-ray scattering, grazing-incidence wide-angle X-ray scattering (GIWAXS), and fully scattered atom pair distribution function analysis, covering structure detection from crystalline to amorphous states. This paper primarily presents the performance of the BL17B beamline and the application of the GIWAXS methodology at the beamline in the field of perovskite materials.
Category–level drivers of the market share–rank power law relationship
Authors: Bae Young Han , Gruca Thomas S. , Lim Hyunwoo , Russell Gary J. 
Published: June 2024

Purpose
This paper aims to analyze variations in the parameters of the market share–rank power law across consumer packaged goods (CPG) categories.

Design/methodology/approach
The authors use a two-level hierarchical linear model to examine the relationships between category-level variables and the parameters of the market share–rank power law in 790 CPG categories.

Findings
The slope of the market share–rank power law is shallower – indicating more equal market shares – in categories of high importance to retailers and those with high levels of promotional activity or high-volume purchases. Higher levels of market share inequality are associated with categories with high overall prices.

Research limitations/implications
To the best of the authors’ knowledge, this is the first research to show the systematic influence of category characteristics on the relationship between brands’ market shares and their ranks, thus, identifying a key moderator for this important empirical generalization in marketing.

Practical implications
While market leadership may be a desirable goal for many brands, the corresponding market share at the top brand does vary. Moreover, the share premium for being number one in the category (gap between the top and other highly ranked brands) can be greatly affected by retailers’ strategies. In addition, the slope of the power law has desirable qualities as a measure of market concentration. However, the empirical study shows that category characteristics must be considered when analyzing differences in concentration across categories or time.

Originality/value
While other studies document variations in the market share–rank power law relationship, to the best of the authors’ knowledge, this is the first that models these variations as a function of observable category characteristics. The comprehensive nature of the data demonstrates the universality of the market share–rank power law relationship across CPG categories in the USA.
A comparative analysis of supply chain management between Portugal and Ireland
Authors: Dominique-Ferreira Sérgio , Brophy Richard , Prentice Catherine 
Published: June 2024

PurposeThis study investigates how insurance intermediaries in Portugal and Ireland evaluate supply chain management (SCM) practices within the insurance industry, specifically focusing on potential regional variations in their assessments.Design/methodology/approachA comparative research design was employed, collecting data through surveys administered to insurance brokers in Portugal and Ireland. These countries were chosen due to their well-developed intermediary-based insurance markets.FindingsThe results show that some dimensions of supply chain management are significantly different between Portugal and Ireland. Nevertheless, the insurance brokers from the two countries also share similar views on key aspects of supply chain management.Practical implicationsThis study offers valuable insights for insurance industry management, particularly regarding the dynamics of the insurer-intermediary relationship and the importance of catering to intermediary needs. The findings also highlight potential areas for European Union policy consideration, such as addressing potential asymmetries within the insurance sector across member states.Social implicationsImproved relationships and collaboration within the insurance supply chain can lead to enhanced access to insurance products and more tailored services for consumers.Originality/valueThis research addresses two key gaps in the literature. Firstly, it examines the insurer-intermediary relationship from the intermediary perspective, a viewpoint often neglected in prior research. Secondly, the study investigates and confirms the existence of regional variations in insurance SCM practices across two European countries.