bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinship networks of seed exchange shape spatial patterns of plant virus diversity
Authors: Delêtre Marc , Lett Jean-Michel , Sulpice Ronan , Spillane Charles 
Published: July 2021

AbstractBy structuring farmers’ informal networks of seed exchange, kinship systems play a key role in the dynamics of crop genetic diversity in smallholder farming systems. However, because many crop diseases are propagated through infected germplasm, local seed systems can also facilitate the dissemination of seedborne pathogens. Here, we investigate how the interplay of kinship systems and local networks of germplasm exchange influences the metapopulation dynamics of viruses responsible for the cassava mosaic disease (CMD), a major threat to food security in Africa. Combining anthropological, genetic and plant epidemiological data, we analyzed the genetic structure of local populations of the African cassava mosaic virus (ACMV), one of the main causal agents of CMD. Results reveal contrasted patterns of viral diversity in patrilineal and matrilineal communities, consistent with local modes of seed exchange. Our results demonstrate that plant virus ecosystems have also a cultural component and that social factors that shape regional seed exchange networks influence the genetic structure of plant virus populations.
Mechanistic insight into bacterial entrapment by septin cage reconstitution
Authors: Lobato-Márquez Damián , Xu Jingwei , Güler Gizem Özbaykal , Ojiakor Adaobi , Pilhofer Martin , Mostowy Serge 
Published: July 2021

AbstractSeptins are cytoskeletal proteins that assemble into hetero-oligomeric complexes and sense micron-scale membrane curvature. During infection with Shigella flexneri, an invasive enteropathogen, septins restrict actin tail formation by entrapping bacteria in cage-like structures. Here, we reconstitute septin cages in vitro using purified recombinant septin complexes (SEPT2-SEPT6-SEPT7), and study how these recognize bacterial cells and assemble on their surface. We show that septin complexes recognize the pole of growing Shigella cells. An amphipathic helix domain in human SEPT6 enables septins to sense positively curved membranes and entrap bacterial cells. Shigella strains lacking lipopolysaccharide components are more efficiently entrapped in septin cages. Finally, cryo-electron tomography of in vitro cages reveals how septins assemble as filaments on the bacterial cell surface.
A multi-step nucleation process determines the kinetics of prion-like domain phase separation
Authors: Martin Erik W. , Harmon Tyler S. , Hopkins Jesse B. , Chakravarthy Srinivas , Incicco J. Jeremías , Schuck Peter , Soranno Andrea , Mittag Tanja 
Published: July 2021

AbstractCompartmentalization by liquid-liquid phase separation (LLPS) has emerged as a ubiquitous mechanism underlying the organization of biomolecules in space and time. Here, we combine rapid-mixing time-resolved small-angle X-ray scattering (SAXS) approaches to characterize the assembly kinetics of a prototypical prion-like domain with equilibrium techniques that characterize its phase boundaries and the size distribution of clusters prior to phase separation. We find two kinetic regimes on the micro- to millisecond timescale that are distinguished by the size distribution of clusters. At the nanoscale, small complexes are formed with low affinity. After initial unfavorable complex assembly, additional monomers are added with higher affinity. At the mesoscale, assembly resembles classical homogeneous nucleation. Careful multi-pronged characterization is required for the understanding of condensate assembly mechanisms and will promote understanding of how the kinetics of biological phase separation is encoded in biomolecules.
Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors
Authors: Cretu Constantin , Gee Patricia , Liu Xiang , Agrawal Anant , Nguyen Tuong-Vi , Ghosh Arun K. , Cook Andrew , Jurica Melissa , Larsen Nicholas A. , Pena Vladimir 
Published: July 2021

AbstractIntron selection during the formation of prespliceosomes is a critical event in pre-mRNA splicing. Chemical modulation of intron selection has emerged as a route for cancer therapy. Splicing modulators alter the splicing patterns in cells by binding to the U2 snRNP (small nuclear ribonucleoprotein)—a complex chaperoning the selection of branch and 3′ splice sites. Here we report crystal structures of the SF3B module of the U2 snRNP in complex with spliceostatin and sudemycin FR901464 analogs, and the cryo-electron microscopy structure of a cross-exon prespliceosome-like complex arrested with spliceostatin A. The structures reveal how modulators inactivate the branch site in a sequence-dependent manner and stall an E-to-A prespliceosome intermediate by covalent coupling to a nucleophilic zinc finger belonging to the SF3B subunit PHF5A. These findings support a mechanism of intron recognition by the U2 snRNP as a toehold-mediated strand invasion and advance an unanticipated drug targeting concept.
A tool for identifying green solvents for printed electronics
Authors: Larsen Christian , Lundberg Petter , Tang Shi , Ràfols-Ribé Joan , Sandström Andreas , Mattias Lindh E. , Wang Jia , Edman Ludvig 
Published: July 2021

AbstractThe emerging field of printed electronics uses large amounts of printing and coating solvents during fabrication, which commonly are deposited and evaporated within spaces available to workers. It is in this context unfortunate that many of the currently employed solvents are non-desirable from health, safety, or environmental perspectives. Here, we address this issue through the development of a tool for the straightforward identification of functional and “green” replacement solvents. In short, the tool organizes a large set of solvents according to their Hansen solubility parameters, ink properties, and sustainability descriptors, and through systematic iteration delivers suggestions for green alternative solvents with similar dissolution capacity as the current non-sustainable solvent. We exemplify the merit of the tool in a case study on a multi-solute ink for high-performance light-emitting electrochemical cells, where a non-desired solvent was successfully replaced by two benign alternatives. The green-solvent selection tool is freely available at: www.opeg-umu.se/green-solvent-tool.
Initiating polyketide biosynthesis by on-line methyl esterification
Authors: Li Pengwei , Chen Meng , Tang Wei , Guo Zhengyan , Zhang Yuwei , Wang Min , Horsman Geoff P. , Zhong Jin , Lu Zhaoxin , Chen Yihua 
Published: July 2021

AbstractAurantinins (ARTs) are antibacterial polyketides featuring a unique 6/7/8/5-fused tetracyclic ring system and a triene side chain with a carboxyl terminus. Here we identify the art gene cluster and dissect ART’s C-methyl incorporation patterns to study its biosynthesis. During this process, an apparently redundant methyltransferase Art28 was characterized as a malonyl-acyl carrier protein O-methyltransferase, which represents an unusual on-line methyl esterification initiation strategy for polyketide biosynthesis. The methyl ester bond introduced by Art28 is kept until the last step of ART biosynthesis, in which it is hydrolyzed by Art9 to convert inactive ART 9B to active ART B. The cryptic reactions catalyzed by Art28 and Art9 represent a protecting group biosynthetic logic to render the ART carboxyl terminus inert to unwanted side reactions and to protect producing organisms from toxic ART intermediates. Further analyses revealed a wide distribution of this initiation strategy for polyketide biosynthesis in various bacteria.
The synergistic interference effect of silica nanoparticles concentration and the wavelength of ELISA on the colorimetric assay of cell toxicity
Authors: Abbasi Fariba , Hashemi Hassan , Samaei Mohammad Reza , SavarDashtaki Amir , Azhdarpoor Abooalfazl , Fallahi Mohammad Javad 
Published: July 2021

AbstractThe 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay is the most common method for the determination of cell toxicity, but some factors limit the sensitivity of this method, such as pH. Less attention had been paid to the interference effect of optical and plasmonic properties of SiO2 nanoparticles (NPs) in the wavelength range assigned to MTT. This study investigated the synergistic interference effect of SiO2 NPs and wavelength on MTT assay for the first time. The examined variables included the type of SiO2 NPs concentrations (1, 10, and 100 mM) and different wavelengths (470, 490, 520, and 570 nm). The results showed that optical density (OD) increased (p < 0.05) when wavelength and the concentration of crystalline SiO2 NPs increased. So, the maximum OD at 10 and 100 mM were attributed to crystalline SiO2 NPs (p < 0.05) due to the functional group, whereas it was related to amorphous at 1 mM (p > 0.05). According to polynomial regression modeling (PRM), the maximum interference effect was predicted at crystalline SiO2 NPs and wavelength > 550 nm. Besides, the synergistic effects of SiO2 NPs, wavelength, and concentration of NPs had been a good fitting with first-order PRM. Thus, the concentration of SiO2 NPs had a confounder factor in colorimetric for MTT assay. The best artificial neural network (ANN) structure was related to the 3:7:1 network (Rall = 0.936, MSE = 0.0006, MAPE = 0.063). The correlation between the actual and predicted data was 0.88. As SiO2 NPs presence is an interfering factor in MTT assay concerning wavelength, it is suggested wavelength use with minimum confounding effect for MTT assay.
Elevated cellular PpIX potentiates sonodynamic therapy in a mouse glioma stem cell-bearing glioma model by downregulating the Akt/NF-κB/MDR1 pathway
Authors: Shono Kenji , Mizobuchi Yoshifumi , Yamaguchi Izumi , Nakajima Kohei , Fujiwara Yuri , Fujihara Toshitaka , Kitazato Keiko , Matsuzaki Kazuhito , Uto Yoshihiro , Sampetrean Oltea , Saya Hideyuki , Takagi Yasushi 
Published: July 2021

AbstractGlioblastoma (GBM) has high mortality rates because of extreme therapeutic resistance. During surgical resection for GBM, 5-aminolevulinic acid (5-ALA)-induced protoporphyrin IX (PpIX) fluorescence is conventionally applied to distinguish GBM. However, surgical intervention is insufficient for high invasive GBM. Sonodynamic therapy (SDT) combined with low-intensity ultrasonication (US) and PpIX, as a sonosensitizer, is an emerging and promising approach, although its efficacy is limited. Based on our previous study that down-regulation of multidrug resistant protein (MDR1) in GBM augmented the anti-tumor effects of chemotherapy, we hypothesized that elevation of cellular PpIX levels by down-regulation of MDR1 enhances anti-tumor effects by SDT. In high invasive progeny cells from mouse glioma stem cells (GSCs) and a GSC-bearing mouse glioma model, we assessed the anti-tumor effects of SDT with a COX-2 inhibitor, celecoxib. Down-regulation of MDR1 by celecoxib increased cellular PpIX levels, as well as valspodar, an MDR1 inhibitor, and augmented anti-tumor effects of SDT. MDR1 down-regulation via the Akt/NF-κB pathway by celecoxib was confirmed, using an NF-κB inhibitor, CAPÉ. Thus, elevation of cellar PpIX by down-regulation of MDR1 via the Akt/NF-κB pathway may be crucial to potentiate the efficacy of SDT in a site-directed manner and provide a promising new therapeutic strategy for GBM.
Validation of a self-report questionnaire for periodontitis in a Japanese population
Authors: Iwasaki Masanori , Usui Michihiko , Ariyoshi Wataru , Nakashima Keisuke , Nagai-Yoshioka Yoshie , Inoue Maki , Kobayashi Kaoru , Borgnakke Wenche S. , Taylor George W. , Nishihara Tatsuji 
Published: July 2021

AbstractWe aimed to assess the validity of the self-report questionnaire for periodontitis in a Japanese population. A Japanese 9-item self-report questionnaire, developed by translating English-version questions that were used to detect periodontitis, was validated against full-mouth clinically-assessed periodontitis in 949 Japanese adults (average age = 43.2 years). Multivariable logistic regression modeling was used to calculate the area under the receiver operating characteristic curve (AUC), wherein the periodontitis case definition of the Centers for Disease Control and Prevention/American Academy of Periodontology was considered the gold standard. Severe, moderate, and mild periodontitis were identified in 6.2%, 30.0%, and 6.7% of the study population, respectively. Self-reported oral health questions combined with socio-demographic and health-related variables had an AUC > 0.70 (range, 0.71–0.87) for any periodontitis category. Four oral health questions (“have gum disease,” “loose tooth,” “lost bone,” and “bleeding gums”) were selected in the parsimonious model for severe periodontitis. The periodontitis screening score generated by the responses to these four questions had an AUC, sensitivity, and specificity of 0.82, 73.1%, and 74.3%, respectively, where the cut-off was set at 2 points. In conclusion, a locally adapted version of the self-report questionnaire had an acceptable diagnostic capacity for the detection of periodontitis in this study population.
Genomic evolution of antimicrobial resistance in Escherichia coli
Authors: Leekitcharoenphon Pimlapas , Johansson Markus Hans Kristofer , Munk Patrick , Malorny Burkhard , Skarżyńska Magdalena , Wadepohl Katharina , Moyano Gabriel , Hesp Ayla , Veldman Kees T. , Bossers Alex ,   EFFORT Consortium, Graveland Haitske , van Essen Alieda , Battisti Antonio , Caprioli Andrea , Blaha Thomas , Hald Tine , Daskalov Hristo , Saatkamp Helmut W. , Stärk Katharina D. C. , Luiken Roosmarijn E. C. , Van Gompel Liese , Hansen Rasmus Borup , Dewulf Jeroen , Duarte Ana Sofia Ribeiro , Zając Magdalena , Wasyl Dariusz , Sanders Pascal , Gonzalez-Zorn Bruno , Brouwer Michael S. M. , Wagenaar Jaap A. , Heederik Dick J. J. , Mevius Dik , Aarestrup Frank M. 
Published: July 2021

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.
$$\mu PT$$ statistical ensemble: systems with fluctuating energy, particle number, and volume
Authors: Marzolino Ugo 
Published: July 2021

AbstractWithin the theory of statistical ensemble, the so-called $$\mu PT$$

μ
P
T

ensemble describes equilibrium systems that exchange energy, particles, and volume with the surrounding. General, model-independent features of volume and particle number statistics are derived. Non-analytic points of the partition function are discussed in connection with divergent fluctuations and ensemble equivalence. Quantum and classical ideal gases, and a model of Bose gas with mean-field interactions are discussed as examples of the above considerations.
A network approach to the five-facet model of mindfulness
Authors: Heeren Alexandre , Lannoy Séverine , Coussement Charlotte , Hoebeke Yorgo , Verschuren Alice , Blanchard M. Annelise , Chakroun-Baggioni Nadia , Philippot Pierre , Gierski Fabien 
Published: July 2021

AbstractDespite the large-scale dissemination of mindfulness-based interventions, debates persist about the very nature of mindfulness. To date, one of the dominant views is the five-facet approach, which suggests that mindfulness includes five facets (i.e., Observing, Describing, Nonjudging, Nonreactivity, and Acting with Awareness). However, uncertainty remains regarding the potential interplay between these facets. In this study, we investigated the five-facet model via network analysis in an unselected sample (n = 1704). We used two distinct computational network approaches: a Gaussian graphical model (i.e., undirected) and a directed acyclic graph, with each model determining the relations between the facets and their relative importance in the network. Both computational approaches pointed to the facet denoting Acting with Awareness as playing an especially potent role in the network system. Altogether, our findings offer novel data-driven clues for the field's larger quest to ascertain the very foundations of mindfulness.
Cascading effects of moth outbreaks on subarctic soil food webs
Authors: Calderón-Sanou Irene , Münkemüller Tamara , Zinger Lucie , Schimann Heidy , Yoccoz Nigel Gilles , Gielly Ludovic , Foulquier Arnaud , Hedde Mickael , Ohlmann Marc , Roy Mélanie , Si-Moussi Sara , Thuiller Wilfried 
Published: July 2021

AbstractThe increasing severity and frequency of natural disturbances requires a better understanding of their effects on all compartments of biodiversity. In Northern Fennoscandia, recent large-scale moth outbreaks have led to an abrupt change in plant communities from birch forests dominated by dwarf shrubs to grass-dominated systems. However, the indirect effects on the belowground compartment remained unclear. Here, we combined eDNA surveys of multiple trophic groups with network analyses to demonstrate that moth defoliation has far-reaching consequences on soil food webs. Following this disturbance, diversity and relative abundance of certain trophic groups declined (e.g., ectomycorrhizal fungi), while many others expanded (e.g., bacterivores and omnivores) making soil food webs more diverse and structurally different. Overall, the direct and indirect consequences of moth outbreaks increased belowground diversity at different trophic levels. Our results highlight that a holistic view of ecosystems improves our understanding of cascading effects of major disturbances on soil food webs.
Seasonality and landscape characteristics impact species community structure and temporal dynamics of East African butterflies
Authors: Schmitt Thomas , Ulrich Werner , Delic Andjela , Teucher Mike , Habel Jan Christian 
Published: July 2021

AbstractSpecies community structures respond strongly to habitat changes. These are either driven by nature or human activities. The biota of East African drylands responds highly sensitively to natural and anthropogenic impacts. Thus, seasonality strongly influences resource availability in a cyclic manner during the year, with cyclic appearance of the different developmental stages of invertebrates, while man-made landscape transformations profoundly and permanently modify habitat structures and, as a consequence, species communities. Butterflies are an excellent model group for the study of the effects of seasonality, and to test for biodiversity responses to anthropogenic activities such as habitat modification, degradation and destruction. We performed transect counts of adult butterflies in riparian forests and their adjoining areas, either dry savannahs with occasional pasturing (i.e. near-natural status) or farmland areas with fields, gardens and settlements (i.e. highly degraded status with lack of original vegetation). Transects were set along the river beds as well as at 250 m and 500 m distances parallel to these rivers, with eight transects per distance class and site (i.e. 48 transects in total). We recorded habitat structures for each transect. Counts were conducted during the dry and the rainy season, with 16 repetitions for each single transect, i.e. eight per season and transect. We compiled trait data on morphology, geographic distribution, ecology, behaviour, and life-history for all butterfly species encountered. Our results show higher species richness and numbers of individuals in farmland transects compared with the savannah region. Seasonal fluctuations of the detectable species abundances between the rainy and dry season were severe. These fluctuations were much more pronounced for the savannah than the farmland area, i.e. was buffered by human activities. Farmland and savannah support two distinct butterfly communities, with generalist species being more common in the farmland communities. Strict habitat associations were comparatively weak and typical dry savannah and riparian forest species were not clearly restricted to the near natural landscape.
Quasilinearization numerical technique for dual slip MHD Newtonian fluid flow with entropy generation in thermally dissipating flow above a thin needle
Authors: Khan Sohaib , Ali Farhad , Khan Waqar A. , Imtiaz Anees , Khan Ilyas , Abdeljawad Thabet 
Published: July 2021

AbstractIn the present article, we investigate the dual slip effect namely the velocity slip and thermal slip conditions on MHD flow past a thin needle. The entropy generation for the incompressible fluids that’s water and acetone that flowing above the thin needle is discussed. The energy dissipating term and the magnetic effect is included in the axial direction. The leading partial differential equations are transformed to ODE by an appropriate similarity transformation and solved using a numerical technique that is the Quasilinearization method. The terms for the rate of entropy generation, the Bejan number, and the irreversibility distribution ratio are discussed. Each dimensionless number is shown with velocity slip and also with the magnetic parameter is presented in graphical form. In the result, we conclude that the entropy generation rate is increasing with the increase in thermal slip parameter also some increasing effect is found as the size of the needle increases