bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental legacy effects impact maize growth and microbiome assembly under drought stress
Authors: Swift Joel F. , Kolp Matthew R. , Carmichael Amanda , Ford Natalie E. , Hansen Paige M. , Sikes Benjamin A. , Kleiner Manuel , Wagner Maggie R. 
Published: April 2023

AbstractBackground and AimsAs the climate changes, plants and their associated microbiomes face greater water limitation and increased frequency of drought. Historical environmental patterns can leave a legacy effect on soil and root-associated microbiomes, but the impact of this conditioning on future drought performance is poorly understood. Precipitation gradients provide a means to assess these legacy effects.MethodsWe collected soil microbiomes from four native prairies across a steep precipitation gradient in Kansas, USA. Seedlings of twoZea maysgenotypes were inoculated with each soil microbiome in a factorial drought experiment. We investigated plant phenotypic and root microbiome responses to drought and modeled relationships between plant growth metrics and climatic conditions from the soil microbiome origin sites.ResultsDrought caused plants to accumulate shoot mass more slowly and achieve greater root/shoot mass ratios. Drought restructured the bacterial root-associated microbiome via depletion of Pseudomonadota and enrichment of Actinomycetota, whereas the fungal microbiome was largely unaffected. An environmental legacy effect on prairie soil microbiomes influenced plants’ drought responses: counterintuitively, prairie soil inocula from historically wetter locations increased shoot biomass under drought more than inocula from historically drier prairie soils.ConclusionWe demonstrated links between soil microbiome legacy effects and plant performance under drought, suggesting that future drying climates may condition soils to negatively impact plant performance.
Touching the (almost) untouchable: a minimally-invasive workflow for microbiological and biomolecular analyses of cultural heritage objects
Authors: Flocco Cecilia G. , Methner Anika , Burkart Franziska , Geppert Alicia , Overmann Jörg 
Published: April 2023

AbstractMicrobiological and biomolecular approaches to cultural heritage research have expanded the established research horizon -from the prevalent focus on the cultural object’s conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts on heritage objects in a global context of a changing climate. Standard microbiology and molecular biology methods were developed for other materials, specimens, disciplines and contexts. Although they could in principle be applied to cultural heritage research, certain characteristics common to several heritage objects – such as uniqueness, fragility, high value and restricted access, demand tailored approaches. In addition, samples from heritage objects often yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology that addresses these material limitations and operational hurdles along all procedural steps are needed. Here were propose a step-by-step standardized laboratory and bioinformatic workflow to analyse the microbiome of cultural heritage objects. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining modularity and flexibility to adapt and/or upscale the proposed workflow to heritage artefacts of a more robust nature or larger dimensions. We hope this review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.
Neural signatures of automatic repetition detection in temporally regular and jittered acoustic sequences
Authors: Ringer Hanna , Schröger Erich , Grimm Sabine 
Published: April 2023

AbstractDetection of repeating patterns within continuous sound streams is crucial for efficient auditory perception. Previous studies demonstrated a remarkable sensitivity of the human auditory system to periodic repetitions in randomly generated sounds. Automatic repetition detection was reflected in different EEG markers, including sustained activity, neural synchronisation, and event-related responses to pattern occurrences. The current study investigated how listeners’ attention and the temporal regularity of a sound modulate repetition perception, and how this influence is reflected in different EEG markers that were previously suggested to subserve dissociable functions. We reanalysed data of a previous study in which listeners were presented with random acoustic sequences with and without repetitions of a certain sound segment. Repeating patterns occurred either regularly or with a temporal jitter within the sequences, and participants’ attention was directed either towards or away from the auditory stimulation. Across both regular and jittered sequences during both attention and in-attention, pattern repetitions led to increased sustained activity throughout the sequence, evoked a characteristic positivity-negativity complex in the event-related potential, and enhanced inter-trial phase coherence of low-frequency oscillatory activity time-locked to repeating pattern onsets. While regularity only had a minor (if any) influence, attention significantly strengthened pattern repetition perception, which was consistently reflected in all three EEG markers. These findings suggest that the detection of pattern repetitions within continuous sounds relies on a flexible mechanism that is robust against in-attention and temporal irregularity, both of which typically occur in naturalistic listening situations. Yet, attention to the auditory input can enhance processing of repeating patterns and improve repetition detection.
The potential effects of tree planting on allergenic pollen production in New York City
Authors: Katz Daniel S.W. 
Published: April 2023

AbstractTree selection decisions affect urban pollen production but the overall importance of tree planting to airborne pollen concentrations remains poorly understood. A synthesis of existing data and available literature could inform tree -planting decisions and potentially help reduce future airborne pollen concentrations. This is especially relevant for the many cities that are considering tree planting campaigns, such as New York City. Here, I examine which allergenically -important tree taxa could be most influenced by municipal tree selectio n decisions in New York City by comparing tree species abundance from a representative plot-based city-wide tree survey with a street tree inventory. I then estimate pollen production from several allergenic tree taxa by combining these tree datasets with allometric equations of pollen production as a function of tree size. Pollen production is also compared to several years of airborne pollen measurements. The potential effect of a proposed planting campaign is estimated over time by combining growth rate equations with pollen production equations. Several tree genera are especially important producers of allergenic pollen in New York City, includingQuercus, Platanus, Morus, andBetula; these taxa also comprise 71% of airborne pollen measured and 93% of estimated pollen production (107 quadrillion pollen grains ; however pollen production could not be estimated for all taxa).Platanus×acerifoliais predominantly a street tree, indicating that previous municipal planting decisions have resulted in its current abundance (it accounts for 34% of total street tree basal area and has an estimated annual pollen production of almost 30 quadrillion grains) and will determine its future abundance. In contrast,MorusandBetulaare uncommon as street trees, indicating that municipal tree planting campaigns are unlikely to substantially affect their pollen production rates in NYC.Quercuswas the largest estimated producer of pollen in NYC (62 quadrillion pollen grains) and accounted for almost 25% of airborne pollen co llected, but its very high abundance outside of street trees suggest that the relative effect of planting trees in this genus will be relatively small. Overall, this study demonstrates how tree planting decisions can have important and long-lasting consequences for allergenic pollen production in certain circumstances, suggesting that pollen allergenicity should be considered in future tree selection decisions.
An improved genome assembly of the saguaro cactus (Carnegiea gigantea(Engelm.) Britton & Rose)
Authors: Copetti Dario , Búrquez Alberto , Shimizu Kentaro K. , Wing Rod A. , Sanderson Michael J. , Wojciechowski Martin F. 
Published: April 2023

AbstractWe present an improved genome assembly of the saguaro cactus (Carnegiea gigantea(Engelm.) Britton & Rose), obtained by incorporating long-read PacBio data to the existing short reads. The assembly improves in terms of total size, contiguity, and accuracy, allowing to extend the range of sequence analyses beyond the single-gene scale. Consequently, the assembly is 16% larger and has 20% more genes, expanding the resources for a neglected yet very remarkable plant family such as Cactaceae.Species taxonomyEukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Cactoideae; Echinocereeae; Carnegiea gigantea (Engelm.) Britton & Rose) (also known as saguaro cactus) (NCBI txid: 171969).
Egocentric cues influence the spatial memory of landmark configurations for memory-guided actions
Authors: Forster Pierre-Pascal , Fiehler Katja , Karimpur Harun 
Published: April 2023

AbstractAllocentric and egocentric reference frames are used to determine the spatial position of action targets in reference to objects in the environment, i.e., landmarks (allocentric), or the observer (egocentric). Previous research investigated reference frames in isolation, for example, by shifting landmarks relative to the target and asking participants to reach to the remembered target location. Systematic reaching errors were found in the direction of the landmark shift and used as a proxy for allocentric spatial coding. Here we examined the interaction of both allocentric and egocentric reference frames by shifting the landmarksas well asthe observer. We asked participants to encode a 3D configuration of balls, and to reproduce this configuration from memory after a short delay followed by a landmark or observer shift. We also manipulated the number of landmarks to test its effect on the use of allocentric and egocentric reference frames. Shifting the observer resulted in larger configurational errors. In addition, an increase in the number of landmarks led to a stronger reliance on allocentric cues and a weaker contribution of egocentric cues. In sum, our results highlight the important role of egocentric cues for allocentric spatial coding in the context of memory-guided actions.New & NoteworthyObjects in our environment are coded relative to each other (allocentrically) and are thought to serve as independent and reliable cues (landmarks) in the context of unreliable egocentric signals. Contrary to this assumption, we demonstrate that egocentric cues alter the spatial memory of landmark configurations, which could reflect recently discovered interactions between allocentric and egocentric neural processing pathways. Further, additional landmarks lead to a higher contribution of allocentric and a lower contribution of egocentric cues.
G2GSnake: A Snakemake workflow for host-pathogen genomic association studies
Authors: Xu Zhi Ming , Naret Olivier , Fellay Jacques 
Published: April 2023

AbstractSummaryJoint analyses of paired host and pathogen genome sequences have the potential to enhance our understanding of host-pathogen interactions. A systematic approach to conduct such a joint analysis is through a “genome-to-genome” (G2G) association study, which involves testing for associations between all host and pathogen genetic variants. Significant associations reveal host genetic factors that might drive pathogen variation, highlighting biological mechanisms likely to be involved in host control and pathogen escape. Here, we present a Snakemake workflow that allows researchers to conduct G2G studies in a reproducible and scalable manner. In addition, we have developed an intuitive R Shiny application that generates custom summaries of the results, enabling users to derive relevant insights.Availability and implementationG2GSnake is freely available at:https://github.com/zmx21/G2GSnakeunder the MIT license.
Defective pgsA contributes to increased membrane fluidity and cell wall thickening in S. aureus with high-level daptomycin resistance
Authors: Freeman Christian D. , Hansen Tayte , Urbauer Ramona , Wilkinson Brian J. , Singh Vineet K. , Hines Kelly M. 
Published: April 2023

ABSTRACTDaptomycin is a membrane-targeting last-resort antimicrobial therapeutic for the treatment of infections caused by methicillin- and/or vancomycin-resistantStaphylococcus aureus. In the rare event of failed daptomycin therapy, the source of resistance is often attributable to mutations directly within the membrane phospholipid biosynthetic pathway ofS. aureusor in the regulatory systems that control cell envelope response and membrane homeostasis. Here we describe the structural changes to the cell envelope in a daptomycin-resistant isolate ofS. aureusstrain N315 that has acquired mutations in the genes most commonly reported associated with daptomycin-resistance:mprF,yycG, andpgsA. In addition to the decreased phosphatidylglycerol (PG) levels that are the hallmark of daptomycin-resistance, the mutant with high-level daptomycin resistance had increased branched-chain fatty acids (BCFAs) in its membrane lipids, increased membrane fluidity, and increased cell wall thickness. However, the successful utilization of isotope-labeled straight-chain fatty acids (SCFAs) in lipid synthesis suggested that the aberrant BCFA:SCFA ratio arose from upstream alteration in fatty acid synthesis rather than a structural preference in PgsA. RT-qPCR studies revealed that expression of pyruvate dehydrogenase (pdhB) was suppressed in the daptomycin-resistant isolate, which is known to increase BCFA levels. While complementation with an additional copy ofpdhBhad no effect, complementation of thepgsAmutation resulted in increased PG formation, reduction in cell wall thickness, restoration of normal BCFA levels, and increased daptomycin susceptibility. Collectively, these results demonstrate thatpgsAcontributes to daptomycin resistance through its influence on membrane fluidity and cell wall thickness, in addition to phosphatidylglycerol levels.IMPORTANCEThe cationic lipopeptide antimicrobial daptomycin has become an essential tool for combating infections withStaphylococcus aureusthat display reduced susceptibility to β-lactams or vancomycin. Since daptomycin’s activity is based on interaction with the negatively charged membrane ofS. aureus, routes to daptomycin-resistance occur through mutations in the lipid biosynthetic pathway surrounding phosphatidylglycerols and the regulatory systems that control cell envelope homeostasis. Therefore, there are many avenues to achieve daptomycin resistance and several different, and sometimes contradictory, phenotypes of daptomycin-resistantS. aureus,including both increased and decreased cell wall thickness and membrane fluidity. This study is significant because it demonstrates the unexpected influence of a lipid biosynthesis gene,pgsA, on membrane fluidity and cell wall thickness inS. aureuswith high-level daptomycin resistance.
COP9 Signalosome Promotes Neointimal Hyperplasia via Deneddylation and CSN5-Mediated Nuclear Export
Authors: Giri Samiksha , Suo Chao , Pardi Ruggero , Fishbein Gregory A. , Rezvani Khosrow , Chen Yabing , Wang Xuejun 
Published: April 2023

ABSTRACTBACKGROUNDNeointimal hyperplasia (NH) is a common pathological response to vascular injury and mediated primarily by vascular smooth muscle cell (VSMC) migration and proliferation. The COP9 signalosome (CSN) is formed by 8 canonical subunits (CSN1 through CSN8) with its deneddylation activity residing in CSN5. Each or some of CSN subunits may have deneddylation-independent function. Despite strong evidence linking the CSN to cell cycle regulation in cancer cells, the role of the CSN in vascular biology remains obscure.METHODSNeointimal CSN5 expression in the lung tissue of pulmonary hypertension (PAH) patients was assessed with immunohistochemistry. Adult mice with smooth muscle cell-restricted CSN5 knockout (CSN5-SMKO) or CSN8 hypomorphism (CSN8-hypo) and cultured mouse VSMCs were studied to determine the role and governing mechanisms of the CSN in NH. NH was induced by ligation of the left common carotid artery (LCCA) and PDGF-BB stimulation was used to mimic the vascular injury in cell cultures.RESULTSRemarkably higher CSN5 levels were detected in the neointimal VSMCs of the pulmonary arteries of human PAH. LCCA ligation induced NH and significantly increased the mRNA and protein levels of CSN subunits in the LCCA wall of adult wild type mice. CSN5-SMKO impaired Cullin deneddylation and the nuclear export of p27 in vessel walls and markedly inhibited VSMC proliferation in mice. On the contrary, CSN8-hypo significantly exacerbated NH and VSMC proliferationin vivoandin cellulo.Cytoplasmic CSN5 mini-complexes and the nuclear export of p27 were significantly increased in CSN8-hypo mouse vessels and cultured CSN8-hypo VSMCs. Nuclear export inhibition with leptomycin attenuated the PDGF-BB-induced increases in VSMC proliferation in both CSN8-hypo and control VSMCs. Further, genetically disabling CSN5 nuclear export but not disabling CSN5 deneddylase activity suppressed the hyperproliferation and restored p27 nuclear localization in CSN8 hypomorphic VSMCs. Interestingly, CSN deneddylase inhibition by CSN5i-3 did not alter the hyperproliferation of cultured CSN8-hypo VSMCs but suppressed wild type VSMC proliferationin celluloandin vivoand blocked neointimal formation in wild type mice.CONCLUSIONThe CSN promotes VSMC proliferation and NH in injured vessels through deneddylation activity and CSN5-mediated nuclear export.
De-novo genome assembly of the invasive mosquito speciesAedes japonicusandAedes koreicus
Authors: Catapano Paolo L. , Falcinelli Monica , Damiani Claudia , Cappelli Alessia , Koukouli Despoina , Rossi Paolo , Ricci Irene , Napolioni Valerio , Favia Guido 
Published: April 2023

AbstractRecently, two invasiveAedesmosquito species,Ae. japonicusandAe. koreicus, are circulating in several European countries posing potential health risks to humans and animals. Vector control is the main option to prevent mosquito-borne diseases, and an accurate genome sequence of these mosquitoes is essential to better understand their biology and to develop effective control strategies. Here, we present a de novo genome assembly of theAe. japonicus(Ajap1) andAe. koreicus(Akor1) based on a hybrid approach that combines Oxford Nanopore long reads and Illumina short reads data. Their quality was ascertained using various metrics. Masking of repetitive elements, gene prediction and functional annotation was performed. Sequence analysis revealed a very high presence of repetitive DNA and, among others, thermal adaptation genes and insecticide-resistance genes. The RNA sequencing analysis of larvae and adults ofAe. koreicusandAe. japonicusexposed to different temperatures revealed genes showing a thermal-dependent activation. The assembly of Akor1 and Ajap1 genomes constitutes the first updated collective knowledge of the genomes of both mosquito species, providing the possibility to understand key mechanisms of their biology such as the ability to adapt to harsh climates and to develop insecticide-resistance mechanisms.
Interspecies generation of functional muscle stem cells
Authors: Domenig Seraina A. , Lenardič Ajda , Zvick Joel , Tarnowska-Sengül Monika , Bundschuh Nicola , Bacchin Giada , Ghosh Adhideb , Bar-Nur Ori 
Published: April 2023

AbstractSatellite cells, the stem cells of skeletal muscle tissue, hold a prodigious regeneration capacity. However, low satellite cell yield from autologous or donor-derived muscles precludes adoption of satellite cell transplantation for the treatment of muscle diseases including Duchenne muscular dystrophy (DMD). To address this limitation, here we investigated whether sufficient quantity of satellite cells can be produced in allogeneic or xenogeneic animal hosts. First, we report on exclusive satellite cell production in intraspecies mouse chimeras by injection of CRISPR/Cas9-corrected DMD-induced pluripotent stem cells (iPSCs) into blastocysts carrying an ablation system of host Pax7+ satellite cells. Additionally, injection of genetically-corrected DMD-iPSCs into rat blastocysts produced interspecies rat-mouse chimeras harboring mouse muscle stem cells that efficiently restored dystrophin expression in DMD mice. This study thus provides a proof-of-principle for the generation of therapeutically-competent stem cells between divergent species, raising the possibility of procuring human stem cells in large animals for regenerative medicine purposes.
Porosity-dependent impact study of a plate with Winkler-Pasternak elastic foundations reinforced with agglomerated CNTs
Authors: Ranjbar-Roeintan Mehdi 
Published: April 2023

Purpose
The purpose of this article is to investigate the porosity-dependent impact study of a plate with Winkler–Pasternak elastic foundations reinforced with agglomerated carbon nanotubes (CNTs).

Design/methodology/approach
Based on the first-order shear deformation plate theory, the strain energy related to elastic foundations is added to system strain energy. Using separation of variables and Lagrangian generalized equations, the nonlinear and time-dependent motion equations are extracted.

Findings
Verification examples are fulfilled to prove the precision and effectiveness of the presented model. The impact outputs illustrate the effects of various distribution of CNTs porosity functions along the plate thickness direction, Winkler–Pasternak elastic foundations and different boundary conditions on the Hertz contact law, the plate center displacement, impactor displacement and impactor velocity.

Originality/value
This paper investigates the effect of Winkler–Pasternak elastic foundations on the functionally graded porous plate reinforced with agglomerated CNTs under impact loading.
Reward interdependence and project professionals' knowledge hiding: the moderating role of knowledge attributes
Authors: Min Min , Zhang Zhen 
Published: April 2023

PurposeBased on interdependence theory, the authors investigated the effect of reward interdependence (RI) on project professionals' knowledge hiding and examined the moderating role of knowledge tacitness (KT) and complexity, in the context of new product development (NPD) teams.Design/methodology/approachThe authors conducted a time-lagged study in the context of NPD teams and collected data from a sample of 231 NPD professionals in China.FindingsThe study's findings indicate that RI was negatively associated with knowledge hiding. Knowledge tacitness negatively moderated the relation between RI and knowledge hiding. In contrast, the moderating effect of knowledge complexity (KC) was not significant.Practical implicationsTo reduce NPD professionals' knowledge hiding, organizations should not only design incentive plans that cultivate interpersonal relatedness but also address the drawbacks (decreased effectiveness of group rewards) resulting from KT.Originality/valueThe authors' paper provides novel insights into the inconsistent understanding of organizational rewards' effectiveness in managing knowledge withholding by demonstrating the differentiated effects of individual and group rewards on knowledge hiding as well as the differential contingent roles of knowledge attributes.