bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anatomically resolved oscillatory bursts orchestrate visual thalamocortical activity during naturalistic stimulus viewing
Authors: Meyerolbersleben Lukas S. , Sirota Anton , Busse Laura 
Published: August 2024

SUMMARYNatural vision involves encoding of complex visual input, which engages a plethora of interacting circuit mechanisms. In the mammalian forebrain, one signature of such interacting circuit mechanisms is fast oscillatory dynamics, which can be reflected in the local field potential (LFP). We here used data from the Allen Neuropixels Visual Coding project to show that local visual features in naturalistic stimuli induce retinotopically specific V1 oscillations in various frequency bands. These LFP oscillations occurred in bursts, were localized to specific V1 layers, and were associated with phase coupling of V1 translaminar spiking, pointing to feature-specific circuit motifs. Finally, we discovered that these visually-induced circuit motifs occurred across a range of stimuli, suggesting that they might constitute general routes for feature-specific information flow. Together, our analyses demonstrate visually-induced, fast oscillations, which likely reflect the operation of distinct mesoscale circuits for the differential and multiplexed coding of complex visual input and feature-specific thalamo-cortical information propagation.
Single-stranded DNA drives σ subunit loading onto RNA polymerase to unlock initiation-competent conformations
Authors: Vishwakarma Rishi Kishore , Marechal Nils , Morichaud Zakia , Blaise Mickaël , Margeat Emmanuel , Brodolin Konstantin 
Published: August 2024

ABSTRACTInitiation of transcription requires the formation of the “open” promoter complex (RPo). For this, the σ subunit of bacterial RNA polymerase (RNAP) binds to the non-template strand of the -10 element sequence of promoters and nucleates DNA unwinding. This is accompanied by a cascade of conformational changes on RNAP the mechanics of which remains elusive. Here, using single-molecule Förster resonance energy transfer and cryo-electron microscopy, we explored the conformational landscape of RNAP from the human pathogenMycobacterium tuberculosisupon binding to a single-stranded DNA fragment that includes the -10 element sequence (-10 ssDNA). We found that like the transcription activator RbpA, -10 ssDNA induced σ subunit loading onto the DNA/RNA channels of RNAP. This triggered RNAP clamp closure and unswiveling that are required for RPo formation and RNA synthesis initiation. Our results reveal a mechanism of ssDNA-guided RNAP maturation and identify the σ subunit as a regulator of RNAP conformational dynamics
Enhanced Maturity and Functionality of Vascularized Human Liver Organoids through 3D Bioprinting and Pillar Plate Culture
Authors: Lekkala Vinod Kumar Reddy , Shrestha Sunil , Al Qaryoute Ayah , Dhinoja Sanchi , Acharya Prabha , Raheem Abida , Jagadeeswaran Pudur , Lee Moo-Yeal 
Published: August 2024

AbstractLiver tissues, composed of hepatocytes, cholangiocytes, stellate cells, Kupffer cells, and sinusoidal endothelial cells, are differentiated from endodermal and mesodermal germ layers. By mimicking the developmental process of the liver, various differentiation protocols have been published to generate human liver organoids (HLOs)in vitrousing induced pluripotent stem cells (iPSCs). However, HLOs derived solely from the endodermal germ layer often encounter technical hurdles, such as insufficient maturity and functionality, limiting their utility for disease modeling and hepatotoxicity assays. To overcome this, we separately differentiated EpCAM+endodermal progenitor cells (EPCs) and mesoderm-derived vascular progenitor cells (VPCs) from the same human iPSC line. These cells were then mixed in BME-2 matrix and concurrently differentiated into vascular human liver organoids (vHLOs). Remarkably, vHLOs exhibited significantly higher maturity than vasculature-free HLOs, as demonstrated by increased coagulation factor secretion, albumin secretion, drug-metabolizing enzyme (DME) expression, and bile acid transportation. To enhance assay throughput and miniaturize vHLO culture, we 3D bioprinted expandable HLOs (eHLOs) in BME-2 matrix on a pillar plate platform derived from EPCs and VPCs and compared with HLOs derived from endoderm alone. Compared to HLOs cultured in a 50 μL BME-2 matrix dome in a 24-well plate, vHLOs cultured on the pillar plate exhibited superior maturity, likely due to enhanced nutrient and signaling molecule diffusion. The integration of physiologically relevant patterned liver organoids with the unique pillar plate platform enhanced the capabilities for high-throughput screening and disease modeling.
Multi-scale dynamics influence the division potential of stomatal lineage ground cells inArabidopsis
Authors: Fung Hannah F. , Amador Gabriel O. , Dale Renee , Gong Yan , Vollbrecht Macy , Erberich Joel M. , Mair Andrea , Bergmann Dominique C. 
Published: August 2024

AbstractDuring development, many precursor lineages are flexible, producing variable numbers and types of progeny cells. What factors determine whether a precursor cell differentiates or retains the capacity to divide? Here, we leverage the developmental flexibility of the stomatal lineage ground cell (SLGC) inArabidopsisleaves as a model for how flexible decisions are regulated. Using a quantitative approach that combines long-term live imaging and statistical modeling, we discover that cell size is a strong predictor of SLGC behaviour: larger SLGCs divide less often than smaller cells. We propose that cell size is linked to division behaviour at multiple spatial scales. At the neighbourhood scale, cell size correlates with the strength of cell-cell signaling, which affects the rate at which SPEECHLESS (SPCH), a division-promoting transcription factor, is degraded. At the subcellular scale, cell size correlates with nuclear size, which modulates the concentration of SPCH in the nucleus. Our work shows how initial differences in SPCH levels are canalized by nuclear size and cell-cell signaling to inform the behaviour of a flexible cell type.
Insecticide resistance and population structure of the invasive malaria vector,Anopheles stephensi, from Fiq, Ethiopia
Authors: Samake Jeanne N. , Yared Solomon , Hassen Mussie Abdosh , Zohdy Sarah , Carter Tamar E. 
Published: August 2024

AbstractAnopheles stephensiinvasion in Ethiopia poses a risk of increased malaria disease burden in the region. Thus, understanding the insecticide resistance profile and population structure of the recently detectedAn. stephensi population in Fiq, Ethiopia, is critical to inform vector control to stop the spread of this invasive malaria species in the country. Following entomological surveillance forAn. stephensiin Fiq, Somali region, Ethiopia, we confirmed the presence ofAn. stephensimorphologically and molecularly in Fiq. Characterization of larval habitats and insecticide susceptibility tests revealed that FiqAn. stephensiis most often found in artificial containers and is resistant to most adult insecticides tested (organophosphates, carbamates, pyrethroids) except for pirimiphos-methyl and PBO-pyrethroids. However, the immature larval stage was susceptible to temephos. Further comparative genomic analyses with previousAn. stephensi populations from Ethiopia using 1,704 biallelic SNPs revealed genetic relatedness between FiqAn. stephensiand east-central EthiopiaAn. stephensipopulations, particularly JigjigaAn. stephensi. Our findings of the insecticide resistance profile, coupled with the likely source population of FiqAn. stephensi, can inform vector control strategies against this malaria vector in Fiq and Jigjiga to limit further spread out of these two locations to other parts of the country and continent.
Digital marketing ecosystems and global market expansion: current state and future research agenda
Authors: Nim Nandini , Pedada Kiran , Hewett Kelly 
Published: August 2024

PurposeThis article aims to provide greater clarity regarding the conceptualization and critical role of digital marketing ecosystems for the global expansion of multinational enterprises (MNEs) and offer novel research directions to prompt future research.Design/methodology/approachThe authors first review the marketing literature related to marketing ecosystems, highlighting the evolution of this body of work across a range of domains such as services, innovation and new product development, communications and marketing strategy more broadly. Next, two case examples of MNEs whose global expansion efforts have been supported by their marketing ecosystems are used to highlight the role of marketing ecosystems in global market expansion. Finally, novel research directions are offered to prompt future research and provide greater insight into this emerging area.FindingsThe case examples we examine yield important insights into the role of marketing ecosystems for MNEs expanding from emerging markets (EMs) to developed markets (DMs). EM-MNEs such as TEMU face more communication and payment ecosystem challenges while opening their supply chain to DMs. Contrary to EM-MNEs, DM-MNEs face institutional and sociocultural challenges that require different marketing ecosystem orchestration approaches.Originality/valueMarketing ecosystems can provide MNEs with greater multinational flexibility, enabling them to adapt their global strategies to navigate increasing complexities in global markets, such as trends toward increased protectionism and geopolitical disruptions. However, there is surprisingly little research addressing this issue.
Potential drivers of differences in breeding phenology as a component of life history strategies among coexisting species
Authors: Martin Thomas E. , Lloyd Penn 
Published: August 2024

Abstract

Breeding phenology can have strong demographic consequences. Yet, the reasons why coexisting animal species differ in breeding phenology have received little attention.
We tested selection pressures that underlie life history variation, such as age‐specific mortality, diet, and body size to explain breeding phenology of 16 coexisting songbird species in arid shrubland in South Africa.
The average start and end dates for the earliest and latest species differed by 1.5 months, with a gradient among remaining species. Nest predation risk generally increased through the season, although species differed in seasonal patterns. Species with lower annual adult mortality, greater seasonal increases in nest predation, and greater nest predation rates had earlier start and stop dates, thereby reducing demographic risks. Species with higher adult mortality had larger brood sizes that require more food and they bred later when food was more abundant. Evolved timing of breeding thereby reflected risk management and food availability related to longevity and brood size.
These factors may place unrecognized constraints on within‐species responses to climate change. Given the importance of phenology for fitness, phenology should be integrated as a core life history trait in future theory, and evolutionary constraints need to be considered in responses to climate change.

Read the free Plain Language Summary for this article on the Journal blog.
Entomopathogenic Bacillus cereus impairs the fitness of the spotted‐wing drosophila, Drosophila suzukii
Authors: He Nana , Zhou Shaojie , Zhou Chuanming , Yang Weikang , Zhang Sheng , Yan Deqiang , Ji Xiaowen , Liu Wei 
Published: August 2024

AbstractDrosophila suzukii is a notorious pest which causes devastating damage to thin‐skinned fruits, and the larvae feed on the fruit, causing extensive agricultural economic loss. The current application of insecticides to manage this pest results in serious resistance and environmental hazards, so an alternative strategy for D. suzukii biocontrol is urgently needed. Here, we reported that entomopathogenic Bacillus cereus has the potential to biocontrol D. suzukii. We isolated and identified the bacterial strain, B. cereus H1, that was detrimental to the fitness of both D. suzukii progenies and parents. D. suzukii was robustly repelled to depositing eggs on the halves with metabolites of B. cereus H1. Both males and females of D. suzukii were susceptible to B. cereus H1. B. cereus H1 significantly arrested larval development with at least 40% lethal larvae. The median lethal time (LT50) of males and females of D. suzukii challenged with B. cereus H1 was 3 and 2 d, respectively. Moreover, B. cereus H1 disrupted the intestinal integrity and pH value of D. suzukii and resulted in an increase in bacterial load of guts and hemolymph. Mechanistically, infection of B. cereus H1 led to the activation of the dual oxidase (DUOX)‐ROS‐Jun N‐terminal kinase (JNK) pathway. The findings showed that the entomopathogen B. cereus H1 could potentially act as a biological control agent against D. suzukii, advancing fundamental concepts of integrated pest management programs against D. suzukii.
Modeling of moisture content during baking with different approaches for effective diffusivity and evaluation of quality variables in baked potato slices
Authors: Pacheco‐Plata Felícitas , Gutiérrez‐Dorado Roberto , Iribe‐Salazar Rosalina , Carrazco‐Escalante Marco , Caro‐Hernández Olivia , Camacho‐Hernández Leticia , Vázquez‐López Yessica , Cronin Kevin , Caro‐Corrales José 
Published: August 2024

AbstractBaking is a healthier alternative to frying, since texture, color, smell, and flavor are developed, without adding oil. The objective was to estimate the moisture content in potato slices, during baking using Fick's law of diffusion to model internal moisture transport and to assess the impact on quality attributes. Moisture transport kinetics were examined at three baking temperatures of 120, 130, and 140°C. Fick's law was employed to estimate average moisture content using different methods: considering both a constant (method of slopes by subperiods, MSS; and method of successive approximations, MSA) and a variable (represented as a quadratic function of time, QFT) behavior of effective diffusivity (De). Three quality variables were analyzed: water activity (aw, dew point hygrometry), total color difference (∆E, colorimetry), and fracturability (F, universal testing machine). The diffusivity estimated with the time‐varying De method provided a more realistic description of moisture migration during baking. The aw, ∆E, and F for baked potato slices ranged from 0.234 to 0.276, 17.9 to 24.6, and 5.20 to 5.49 N, respectively. These attributes imply improved stability and extended shelf life, showing typical colors and texture changes for baked snacks. These changes are linked to variations in diffusivity, influenced by the size and quantity of micropores within the food structure. This study could allow an accurate prediction of mass transfer by considering variable De, facilitating the optimization of baking conditions.Practical ApplicationThe analysis of the moisture content using Fick's law, considering a time‐varying diffusivity, enables the optimization of the baking process for foods. This helps minimize the occurrence of defective products.
The rootstock modifies the arbuscular mycorrhizal community of the root system, while the influence of the scion is limited in grapevines
Authors: Lailheugue Vincent , Darriaut Romain , Tran Joseph , Morel Marine , Marguerit Elisa , Lauvergeat Virginie 
Published: August 2024

AbstractUnderstanding the effects of grapevine rootstock and scion genotypes on arbuscular mycorrhizal fungi (AMF), as well as the roles of these fungi in plant development, could provide new avenues for adapting viticulture to climate change and reducing agrochemical inputs. The root colonization of 10 rootstock/scion combinations was studied using microscopy and metabarcoding approaches and linked to plant development phenotypes. The AMF communities were analysed using 18S rRNA gene sequencing. The 28S rRNA gene was also sequenced for some combinations to evaluate whether the method changed the results. Root colonization indexes measured by microscopy were not significantly different between genotypes. Metabarcoding analyses showed an effect of the rootstock genotype on the β‐diversity and the enrichment of several taxa with both target genes, as well as an effect on the Chao1 index with the 18S rRNA gene. We confirm that rootstocks recruit different AMF communities when subjected to the same pedoclimatic conditions, while the scion has little or no effect. Significant correlations were observed between AMF community composition and grapevine development, suggesting that AMF have a positive effect on plant growth. Given these results, it will be important to define consensus methods for studying the role of these beneficial micro‐organisms in vineyards.
Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity
Authors: Mongiardino Koch Nicolás , Milla Carmona Pablo 
Published: August 2024

Abstract

Much of our understanding of the history of life hinges upon time calibration, the process of assigning absolute times to cladogenetic events. Bayesian approaches to time‐scaling phylogenetic trees have dramatically grown in complexity, and depend today upon numerous methodological choices. Arriving at objective justifications for all of these is difficult and time‐consuming. Thus, divergence times are routinely inferred under only one or a handful of parametric conditions, often times chosen arbitrarily. Progress towards building robust biological timescales necessitates the development of better methods to visualize and quantify the sensitivity of results to these decisions.

Here, we present an R package that assists in this endeavour through the use of chronospaces, that is, graphical representations summarizing variation in the node ages contained in time‐calibrated trees. We further test this approach by estimating divergence times for three empirical datasets—spanning widely differing evolutionary timeframes—using the software PhyloBayes.

Our results reveal large differences in the impact of many common methodological decisions, with the choice of clock (uncorrelated vs autocorrelated) and loci having strong effects on inferred ages. Other decisions have comparatively minor consequences, including the use of the computationally intensive site‐heterogeneous model CAT‐GTR, whose effect might only be discernible for exceedingly old divergences (e.g. the deepest eukaryote nodes).

The package chronospace implements a range of graphical and analytical tools that assist in the exploration of sensitivity and the prioritization of computational resources in the inference of divergence times.
Prescribed burning beneficial or neutral for native herbaceous vegetation in an invader dominated commercially grazed savanna
Authors: Radford Ian J. , Abbott Brett N. , Nicholas David M. , Whiteman Lindsay , Grice Anthony C. 
Published: August 2024

AbstractPrescribed burning is frequently used in savanna vegetation in Australia and worldwide. In north‐east Queensland savanna burning has been proposed for the control of woody weeds including Cryptostegia grandiflora (rubbervine), an invasive shrub/vine of riparian savanna. However, burning as a management tool can have non‐target impacts on ecosystems, particularly where associated with additional invasive species, such as the exotic stoloniferous grass species Bothriochloa pertusa (Indian couch). For this reason, an experiment was established to test for non‐target impacts of prescribed burning on herbaceous vegetation. The experiment consisted of wet and dry season burning, and single and double burning treatments during a 4 year study. Annual herbaceous surveys were conducted, both before treatments applied, and then annually. We addressed alternative hypotheses, that (i) burning would exacerbate grazing impacts resulting in negative outcomes for native herbaceous vegetation, or alternatively (ii) burning would be neutral or beneficial to native herbaceous assemblages due to savanna co‐evolution with fire. Burning treatments resulted in subtle but beneficial responses for native herbaceous vegetation. Native legume biomass, percent composition and percent frequency, and forb species richness, increased 4–5 months following wet season burning with above average rainfall. There was a delayed (8–18 months) positive response of burning (both wet and dry season) in percent composition of native grazing sensitive perennial grasses. There was a slight short‐term decline in introduced perennial grass percent composition and biomass following treatment. Results were consistent with predominantly positive or neutral responses to prescribed burning. There was no evidence to support the hypothesis that invaded native savanna herbaceous assemblages declined with burning treatment applications. These results are discussed in relation to other savanna studies in northern Australia and to the role of fire in the maintenance of herbaceous vegetation in savanna biomes.
Double cropping as an adaptation to climate change in the United States
Authors: Gammans Matthew , Mérel Pierre , Ortiz‐Bobea Ariel 
Published: August 2024

AbstractA warming climate expands the frost‐free season, plausibly allowing for increased cropping intensity in temperate regions. This paper assesses the potential of multiple cropping to offset the projected negative effects of climate change on agricultural yields in the United States. We use cross‐sectional variation in observed land cover, soil characteristics, and climate to estimate farmers' propensity to double‐crop winter wheat with soybeans. Our estimates imply that under current economic conditions, a 3°C warming would result in an increase of 2.1 percentage points in the share of current soybean area double cropped, primarily driven by expansions in cooler regions. A fixed‐effects panel model of county yields further indicates that yields of double‐cropped soybeans are about 12% lower than those of single‐cropped soybeans. Accounting for changes in cropping intensity and attendant effects on soybean yields, we project that at current prices, a 3°C warming would induce a shift in cropping intensity that increases revenue from soy systems by 1.3% overall, offsetting only a small fraction of the revenue impacts of predicted yield declines.
Impact of steroid hormone levels on estradiol‐mediated regulation of cytochrome P450 2B6 compared to 1B1 in breast cancer cells
Authors: Hoffmann Marco , Müller Julian Peter , Maurer Jochen , Folliot Anne‐Marie , Yamoune Sabrina , Stingl Julia Carolin 
Published: August 2024

AbstractPharmacogenetic variants of the steroid hormone‐metabolizing enzyme cytochrome P450 2B6 (CYP2B6) were reported to be associated with breast cancer (BC) risk and prognosis. CYP2B6 expression is inducible by estradiol (E2) but induction was demonstrated only under steroid hormone‐deprived medium conditions. Physiological conditions, however, even under endocrinological BC treatment, do not correspond to complete steroid hormone depletion. The aim of this study was to investigate the E2‐mediated CYP2B6 and CYP1B1 regulation under various steroid hormone conditions, including physiological concentrations, in human oestrogen receptor positive (T47D, MCF‐7) and negative (MDA‐MB‐231) BC cell lines. We confirm that steroid‐deprived pre‐cultivation led to CYP2B6 upregulation in T47D, but not in MCF‐7. However, when pre‐cultivated with steroid‐containing medium CYP2B6 was downregulated in T47D and MCF‐7, while the addition of physiological E2 concentrations to steroid‐deprived medium resulted in a downregulation in T47D. In contrast, CYP1B1 was never downregulated in any culture condition. Thus, we show that E2‐mediated CYP2B6 regulation in BC cells depends on steroid hormone exposure in a cell line‐specific manner. Our data indicates the importance of being careful with conclusions drawn from CYP2B6 induction findings in vitro, as we demonstrate potential influences of hormonal changes on CYP2B6 expression, which could impact steroid hormone homeostasis and, consequently, BC risk.