bluuebunny/crossref_metadata_2025_split huggingface dataset:
Principal Component Analysis of Ground Level Enhancement of Cosmic Ray Events
Authors: Ugwoke R. E. , Ubachukwu A. A. , Urama J. O. , Okike O. , Alhassan J. A. , Chukwude A. E. 
Published: February 2023

Abstract
We applied principal component analysis (PCA) to the study of five ground level enhancements (GLEs) of cosmic ray (CR) events. The nature of the multivariate data involved makes PCA a useful tool for this study. A subroutine program written and implemented in the R software environment generated interesting principal components. Analysis of the results shows that the method can distinguish between neutron monitors (NMs) that observed Forbush decreases from those that observed GLEs at the same time. The PCA equally assigned NMs with identical signal counts with the same correlation factor (r) and those with close r values equally have a close resemblance in their CR counts. The results further indicate that while NMs that have the same time of peak may not have the same r, most NMs that had the same r also had the same time of peak. Analyzing the second principal components yielded information on the differences between NMs having opposite but the same or close values of r. NMs that had the same r equally had the tendency of being close in latitude.
Tutorial: multiphoton microscopy to advance neuroscience research
Authors: Hernández Iván Coto , Yau Jenny , Rishøj Lars , Cui Nanke , Minderler Steven , Jowett Nate 
Published: February 2023

Abstract
Multiphoton microscopy (MPM) employs ultrafast infrared lasers for high-resolution deep three-dimensional imaging of live biological samples. The goal of this tutorial is to provide a practical guide to MPM imaging for novice microscopy developers and life-science users. Principles of MPM, microscope setup, and labeling strategies are discussed. Use of MPM to achieve unprecedented imaging depth of whole mounted explants and intravital imaging via implantable glass windows of the mammalian nervous system is demonstrated.
Effect of annealing temperature on microstructures and mechanical properties of a hot-rolled Ti-6Al-4V-0.5Ni-0.5Nb alloy for offshore applications
Authors: Yao X J , Yao S Y , Qin C H , Wang Y F , Tang W , Yu Y 
Published: February 2023

Abstract
Titanium alloys have been increasingly used for downhole tubular and components for corrosive oil wells due to their combination of strength, density, and corrosion resistance. The present study investigated the effect of annealing temperature on microstructures and mechanical properties of a Ti-6Al-4V-0.5Ni-0.5Nb alloy developed for oil well application. The α/β- and β-rolled Ti-6Al-4V-0.5Ni-0.5Nb alloy plates were subjected to annealing at different temperatures ranging from 750 to 900 °C and held for 1 h, and the microstructure and mechanical properties were evaluated. The experimental results show that the developed alloy exhibited both high strength and ductility than that of the conventional Ti-6Al-4V alloy. The α/β- and β-rolled alloy after annealing exhibited bimodal structures and provided well-balanced strength, ductility, and impact toughness, high strength of 950−1000 MPa, elongation of 17%−18%, and impact toughness of 90−120 J cm−2. From a mechanical viewpoint, the new alloy after appropriate annealing is suitable for oil well applications.
Single-point spin Chern number in a supercell framework
Authors: Favata Roberta , Marrazzo Antimo 
Published: February 2023

Abstract
We present an approach for the calculation of the

Z

2

topological invariant in non-crystalline two-dimensional quantum spin Hall insulators. While topological invariants were originally mathematically introduced for crystalline periodic systems, and crucially hinge on tracking the evolution of occupied states through the Brillouin zone, the introduction of disorder or dynamical effects can break the translational symmetry and imply the use of larger simulation cells, where the k-point sampling is typically reduced to the single Γ-point. Here, we introduce a single-point formula for the spin Chern number that enables to adopt the supercell framework, where a single Hamiltonian diagonalisation is performed. Inspired by the work of Prodan (2009 Phys. Rev. B 80 125327), our single-point approach allows to calculate the spin Chern number even when the spin operator

s
ˆ

z

does not commute with the Hamiltonian, as in the presence of Rashba spin–orbit coupling. We validate our method on the Kane–Mele model, both pristine and in the presence of Anderson disorder. Finally, we investigate the disorder-driven transition from the trivial phase to the topological state known as topological Anderson insulator. Beyond disordered systems, our approach is particularly useful to investigate the role of defects, to study topological alloys and in the context of ab-initio molecular dynamics simulations at finite temperature.
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes
Authors: Srivastava Mansi , Dukeshire Matthew R , Mir Quoseena , Omoru Okiemute Beatrice , Manzourolajdad Amirhossein , Janga Sarath Chandra 
Published: February 2023

Abstract
Long-range ribonucleic acid (RNA)–RNA interactions (RRI) are prevalent in positive-strand RNA viruses, including Beta-coronaviruses, and these take part in regulatory roles, including the regulation of sub-genomic RNA production rates. Crosslinking of interacting RNAs and short read-based deep sequencing of resulting RNA–RNA hybrids have shown that these long-range structures exist in severe acute respiratory syndrome coronavirus (SARS-CoV)-2 on both genomic and sub-genomic levels and in dynamic topologies. Furthermore, co-evolution of coronaviruses with their hosts is navigated by genetic variations made possible by its large genome, high recombination frequency and a high mutation rate. SARS-CoV-2’s mutations are known to occur spontaneously during replication, and thousands of aggregate mutations have been reported since the emergence of the virus. Although many long-range RRIs have been experimentally identified using high-throughput methods for the wild-type SARS-CoV-2 strain, evolutionary trajectory of these RRIs across variants, impact of mutations on RRIs and interaction of SARS-CoV-2 RNAs with the host have been largely open questions in the field. In this review, we summarize recent computational tools and experimental methods that have been enabling the mapping of RRIs in viral genomes, with a specific focus on SARS-CoV-2. We also present available informatics resources to navigate the RRI maps and shed light on the impact of mutations on the RRI space in viral genomes. Investigating the evolution of long-range RNA interactions and that of virus–host interactions can contribute to the understanding of new and emerging variants as well as aid in developing improved RNA therapeutics critical for combating future outbreaks.
Molecular phylogenetics of Maranta (Marantaceae: Zingiberales): non-monophyly and support for a wider circumscription
Authors: Fernandes Geysla Da Costa , Luna Naédja K , Fraga Elmary , Barros Maria Claudene , Chase Mark W , Pessoa Edlley M 
Published: February 2023

Abstract
Neotropical Maranta has repeatedly emerged as non-monophyletic in molecular phylogenetic studies, but no taxonomic changes have been proposed due to previous weak support for the main clades and overall sparse taxonomic sampling. Our study includes a phylogenetic hypothesis strictly based on molecular evidence, using nuclear ribosomal (nrITS) and plastid (rps16, trnL-F and rpl32-trnL) markers for Maranta and allied genera. Thirty-two species from eight genera were sampled, and maximum likelihood (ML) and Bayesian inference (BI) analyses were carried out. Non-ambiguous indels were scored in both analyses to test their contribution to internal support. Our results confirm that Maranta, as previously delimited, is non-monophyletic, with species of Hylaeanthe, Myrosma and Koernickanthe nested among clades of Maranta. The combined BI analysis without indels was the best resolved, and inclusion of indels increased support only for terminal clades. The sampled species comprise two sister clades, one with Maranta + Hylaeanthe + Myrosma + Koernickanthe and the other with Ctenanthe + Saranthe + Stromanthe. The infrageneric classification proposed by Schumann for Maranta (M. subgenera Maranta and Calateastrum) is partially corroborated by our results, but the remaining subgenera need to be further studied. Based on our strongly supported phylogenetic results, we revise the taxonomy of these genera, expanding the limits of Maranta. We propose two new combinations and a new name for Hylaeanthe in Maranta.
Contribution of the stereoscopic representation of motion-in-depth during visually guided feedback control
Authors: Wang Xiaolu , Liang Haowen , Li Le , Zhou Jianying , Song Rong 
Published: February 2023

AbstractConsiderable studies have focused on the neural basis of visually guided tracking movement in the frontoparallel plane, whereas the neural process in real-world circumstances regarding the influence of binocular disparity and motion-in-depth (MID) perception is less understood. Although the role of stereoscopic versus monoscopic MID information has been extensively described for visual processing, its influence on top-down regulation for motor execution has not received much attention. Here, we orthogonally varied the visual representation (stereoscopic versus monoscopic) and motion direction (depth motion versus bias depth motion versus frontoparallel motion) during visually guided tracking movements, with simultaneous functional near-infrared spectroscopy recordings. Results show that the stereoscopic representation of MID could lead to more accurate movements, which was supported by specific neural activity pattern. More importantly, we extend prior evidence about the role of frontoparietal network in brain–behavior relationship, showing that occipital area, more specifically, visual area V2/V3 was also robustly involved in the association. Furthermore, by using the stereoscopic representation of MID, it is plausible to detect robust brain–behavior relationship even with small sample size at low executive task demand. Taken together, these findings highlight the importance of the stereoscopic representation of MID for investigating neural correlates of visually guided feedback control.
An adaptive bounded-confidence model of opinion dynamics on networks
Authors: Kan Unchitta , Feng Michelle , Porter Mason A 
Published: February 2023

AbstractIndividuals who interact with each other in social networks often exchange ideas and influence each other’s opinions. A popular approach to study the spread of opinions on networks is by examining bounded-confidence models (BCMs), in which the nodes of a network have continuous-valued states that encode their opinions and are receptive to other nodes’ opinions when they lie within some confidence bound of their own opinion. In this article, we extend the Deffuant–Weisbuch (DW) model, which is a well-known BCM, by examining the spread of opinions that coevolve with network structure. We propose an adaptive variant of the DW model in which the nodes of a network can (1) alter their opinions when they interact with neighbouring nodes and (2) break connections with neighbours based on an opinion tolerance threshold and then form new connections following the principle of homophily. This opinion tolerance threshold determines whether or not the opinions of adjacent nodes are sufficiently different to be viewed as ‘discordant’. Using numerical simulations, we find that our adaptive DW model requires a larger confidence bound than a baseline DW model for the nodes of a network to achieve a consensus opinion. In one region of parameter space, we observe ‘pseudo-consensus’ steady states, in which there exist multiple subclusters of an opinion cluster with opinions that differ from each other by a small amount. In our simulations, we also examine the roles of early-time dynamics and nodes with initially moderate opinions for achieving consensus. Additionally, we explore the effects of coevolution on the convergence time of our BCM.
Invasive ant learning is not affected by seven potential neuroactive chemicals
Authors: Galante Henrique , Czaczkes Tomer J 
Published: February 2023

Abstract
Argentine ants Linepithema humile are one of the most damaging invasive alien species worldwide. Enhancing or disrupting cognitive abilities, such as learning, has the potential to improve management efforts, for example by increasing preference for a bait, or improving ants’ ability to learn its characteristics or location. Nectar-feeding insects are often the victims of psychoactive manipulation, with plants lacing their nectar with secondary metabolites such as alkaloids and non-protein amino acids which often alter learning, foraging, or recruitment. However, the effect of neuroactive chemicals has seldomly been explored in ants. Here, we test the effects of seven potential neuroactive chemicals—two alkaloids: caffeine and nicotine; two biogenic amines: dopamine and octopamine, and three nonprotein amino acids: β-alanine, GABA and taurine—on the cognitive abilities of invasive L. humile using bifurcation mazes. Our results confirm that these ants are strong associative learners, requiring as little as one experience to develop an association. However, we show no short-term effect of any of the chemicals tested on spatial learning, and in addition no effect of caffeine on short-term olfactory learning. This lack of effect is surprising, given the extensive reports of the tested chemicals affecting learning and foraging in bees. This mismatch could be due to the heavy bias towards bees in the literature, a positive result publication bias, or differences in methodology.
Bacterial communities of Antarctic lichens explored by gDNA and cDNA 16S rRNA gene amplicon sequencing
Authors: Woltyńska Aleksandra , Gawor Jan , Olech Maria A , Górniak Dorota , Grzesiak Jakub 
Published: February 2023

Abstract
Recently, lichens came once more into the scientific spotlight due to their unique relations with prokaryotes. Several temperate region lichen species have been thoroughly explored in this regard yet, the information on Antarctic lichens and their associated bacteriobiomes is somewhat lacking. In this paper, we assessed the phylogenetic structure of the whole and active fractions of bacterial communities housed by Antarctic lichens growing in different environmental conditions by targeted 16S rRNA gene amplicon sequencing. Bacterial communities associated with lichens procured from a nitrogen enriched site were very distinct from the communities isolated from lichens of a nitrogen depleted site. The former were characterized by substantial contributions of Bacteroidetes phylum members and the elusive Armatimonadetes. At the nutrient-poor site the lichen-associated bacteriobiome structure was unique for each lichen species, with chlorolichens being occupied largely by Proteobacteria. Lichen species with a pronounced discrepancy in diversity between the whole and active fractions of their bacterial communities had the widest ecological amplitude, hinting that the nonactive part of the community is a reservoir of latent stress coping mechanisms. This is the first investigation to make use of targeted metatranscriptomics to infer the bacterial biodiversity in Antarctic lichens.
SsrA and SmpB have multifaceted physiological roles in the black rot pathogenXanthomonas campestris pathovar campestris
Authors: Lo Hsueh-Hsia , Liao Chao-Tsai , Li Chih-En , Chang Hsiao-Ching , Hsiao Yi-Min 
Published: February 2023

AbstractSsrA and SmpB are known to play important roles in translational quality control and are essential for virulence in many human and animal pathogenic bacteria. The physiological roles and contribution of SsrA and SmpB to plant pathogen are unclear. Here, we present evidence to show that ssrA and smpB are involved in pathogenesis of Xanthomonas campestris pathovar campestris, the cause of black rot diseases in crucifers. The ssrA and smpB mutants exhibited defects in bacterial attachment, cell motility, and extracellular enzyme activity. The mutation of ssrA and smpB also resulted in a reduction in temperature tolerance. These altered phenotypes of the ssrA and smpB mutants could be complemented to wild-type levels by the intact ssrA and smpB genes. This is the first demonstration of the roles of SsrA and SmpB in phytopathogen.
Epsilon-poly-l-lysine increases disease resistance of citrus against postharvest green mold by activating amino acid metabolism and phenolic compounds biosynthesis
Authors: Zhang Xiong , Deng Qian , Wang Wenjun , Zhang Hongyan , Chen Ou , Zeng Kaifang 
Published: February 2023

AbstractAs a famous fruit worldwide, citrus is susceptible to green mold caused by Penicillium digitatum, which causes large economic losses every year. ε-Poly-l-lysine (ε-PL) is a novel preservative with strong inhibitory effects on fungi, and has the capacity to induce disease resistance in fruit, but the mechanism has been reported rarely, especially in citrus. In the present study, 800 μg/mL ε-PL and P. digitatum spores were inoculated in two different wounds on the citrus pericarp at an interval of 24 h. The results revealed that ε-PL inhibited that the development of green mold without direct contact with P. digitatum, indicating that the disease resistance of citrus was activated. Transcriptome analysis revealed that ε-PL activated amino acid metabolism and phenylpropanoid biosynthesis. Besides, the accumulation of glutamic acid, proline, arginine, serine, lysine, phenylalanine, and tyrosine were changed during storage. In phenylpropanoid biosynthesis, ε-PL increased phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), and 4-coumarate:coenzyme A ligase (4CL) activities and total phenolic and flavonoid contents. Importantly, among these phenolic compounds, ε-PL promoted the accumulation of individual phenolic compounds including ferulic acid, chlorogenic acid, p-coumaric acid, caffeic acid, gallic acid, catechins, epicatechin, and narirutin. In conclusion, ε-PL enhanced the resistance of citrus through amino acid metabolism and accumulation of phenolic compounds. These results improved the knowledge of the mechanism of ε-PL–induced disease resistance and provided a fresh theoretical basis for the use of ε-PL in postharvest citrus preservation.
Mitonuclear Interactions and the Origin of Macaque Societies
Authors: Zhu Jianlong , Evans Ben J 
Published: February 2023

AbstractIn most eukaryotes, aerobic respiration requires interactions between autosomally encoded genes (Ninteract genes) and mitochondrial DNA, RNA, and protein. In species where females are philopatric, contrasting distributions of genetic variation in mitochondrial and nuclear genomes create variation in mitonuclear interactions that may be subject to natural selection. To test this expectation, we turned to a group with extreme female philopatry: the macaque monkeys. We examined four genomic data sets from (1) wild caught and (2) captive populations of rhesus macaque, which is the most widely distributed nonhuman primate, and (3) the stump-tailed macaque and (4) a subspecies of longtail macaque, both of whose mitochondrial DNA is introgressed from a highly diverged ancestor. We identified atypically long runs of homozygosity, low polymorphism, high differentiation, and/or rapid protein evolution associated with Ninteract genes compared with non-Ninteract genes. These metrics suggest a subset of Ninteract genes were independently subject to atypically pervasive natural selection in multiple species. These findings suggest that natural selection on mitonuclear interactions could have influenced several aspects of macaque societies including species diversity, ecological breadth, female-biased adult sex ratio and demography, sexual dimorphism, and mitonuclear phylogenomics.
Development of homozygous tetraploid potato and whole genome doubling-induced the enrichment of H3K27ac and potentially enhanced resistance to cold-induced sweetening in tubers
Authors: Guo Hongwei , Zhou Min , Zhang Guoyan , He Li , Yan Caihong , Wan Min , Hu Jianjun , He Wei , Zeng Deying , Zhu Bo , Zeng Zixian 
Published: February 2023

AbstractPolyploid plants typically display advantages on some agronomically important traits over their diploid counterparts. Extensive studies have shown genetic, transcriptomic, and epigenetic dynamics upon polyploidization in multiple plant species. However, few studies have unveiled those alternations imposed only by ploidy level, without any interference from heterozygosity. Cultivated potato is highly heterozygous. Thus, in this study, we developed two homozygous autotetraploid lines and one homozygous diploid line in parallel from a homozygous diploid potato. We confirmed their ploidy levels using chloroplast counting and karyotyping. Oligo-FISH and genome re-sequencing validated that these potato lines are nearly homozygous. We investigated variations in phenotypes, transcription, and histone modifications between two ploidies. Both autotetraploid lines produced larger but fewer tubers than the diploid line. Interestingly, each autotetraploid line displayed ploidy-related differential expression for various genes. We also discovered a genome-wide enrichment of H3K27ac in genic regions upon whole-genome doubling (WGD). However, such enrichment was not associated with the differential gene expression between two ploidies. The tetraploid lines may exhibit better resistance to cold-induced sweetening (CIS) than the diploid line in tubers, potentially regulated through the expression of CIS-related key genes, which seems to be associated with the levels of H3K4me3 in cold-stored tubers. These findings will help to understand the impacts of autotetraploidization on dynamics of phenotypes, transcription, and histone modifications, as well as on CIS-related genes in response to cold storage.
Characteristics of photosynthesis and vertical canopy architecture of citrus trees under two labor-saving cultivation modes using unmanned aerial vehicle (UAV)-based LiDAR data in citrus orchards
Authors: Dian Yuanyong , Liu Xiaoyang , Hu Lei , Zhang Jinzhi , Hu Chungen , Liu Yongzhong , Zhang Jinxin , Zhang Wenbo , Hu Qingqing , Zhang Yahao , Fang Yanni , Zhou Jingjing 
Published: February 2023

AbstractAnalyzing and comparing the effects of labor-saving cultivation modes on photosynthesis, as well as studying their vertical canopy architecture, can improve the tree structure of high-quality and high-yield citrus and selection of labor-saving cultivation modes. The photosynthesis of 1080 leaves of two labor-saving cultivation modes (wide-row and narrow-plant mode and fenced mode) comparing with the traditional mode were measured, and nitrogen content of all leaves and photosynthetic nitrogen use efficiency (PNUE) were determined. Unmanned aerial vehicle (UAV)-based light detection and ranging (LiDAR) data were used to assess the vertical architecture of three citrus cultivation modes. Results showed that for the wide-row and narrow-plant and traditional modes leaf photosynthetic CO2 assimilation rate, stomatal conductance, and transpiration rate of the upper layer were significantly higher than those of the middle layer, and values of the middle layer were markedly higher than those of the lower layer. In the fenced mode, a significant difference in photosynthetic factors between the upper and middle layers was not observed. A vertical canopy distribution had a more significant effect on PNUE in the traditional mode. Leaves in the fenced mode had distinct photosynthetic advantages and higher PNUE. UAV-based LiDAR data effectively revealed the differences in the vertical canopy architecture of citrus trees by enabling calculating the density and height percentile of the LiDAR point cloud. The point cloud densities of three cultivation modes were significantly different for all LiDAR density slices, especially at higher canopy heights. The labor-saving modes, particularly the fenced mode, had significantly higher height percentile data.