bluuebunny/crossref_metadata_2025_split huggingface dataset:
A biosynthetic network for protoberberine production in Coptis chinensis
Authors: Wu Linrui , Zhao Binxin , Deng Zixin , Wang Bin , Yu Yi 
Published: December 2023

Abstract
Protoberberine alkaloids are a group of tetracyclic isoquinoline compounds known for their well-established antimicrobial and anti-inflammatory properties. The richness and diversity of protoberberine alkaloids accumulated in the Coptis genus necessitate a comprehensive examination of the biosynthetic machinery to understand their ecological significance. Here, from Coptis chinensis we identified CcCYP719A1, which could install a methylenedioxy bridge on either ring A or ring D of the protoberberine backbone, thus diverging metabolite flux towards the biosynthesis of various protoberberine components. We also obtained CcCYP719A2 and CcCYP719A3, which underwent positive selection after diverging from CcCYP719A1 and maintained specific catalytic activity on ring D. Further, we resolved the biosynthetic pathway of jatrorrhizine by identifying two demethylases, which could also modulate protoberberine composition by removing the C-3 methyl group and methylenedioxy bridge of ring D, allowing demethylated metabolites to be redirected into different routes. Moreover, we characterized 2-O-methyltransferase CcOMT1 and flavin-dependent oxidase CcTHBO, respectively responsible for the commonly observed 2-O-methylation and aromatic ring-C assembly in protoberberine alkaloids. Overall, this study reveals an interconnected metabolite network from which diverse protoberberine alkaloids originate. It provides valuable insights into the existence of undiscovered protoberberine components, and paves the way for the targeted production of desired protoberberine components for potential therapeutic development.
A Ca2+ sensor BraCBL1.2 involves in BraCRa-mediated clubroot resistance in Chinese cabbage
Authors: Piao Yinglan , Li Shizhen , Chen Yiduo , Zhao Sisi , Piao Zhongyun , Wang Haiping 
Published: December 2023

Abstract
Clubroot disease caused by Plasmodiophora brassicae (P. brassicae) severely threatens the cultivation of Cruciferous plants, especially Chinese cabbage. Recently, resistance genes in plants have been reported to encode for a Ca2+-permeable channel in the plasma membrane, which can mediate the cytosolic Ca2+ increase in plant cells upon pathogen attack. However, the downstream Ca2+ sensor and decoder are still unknown. In this study, we identified the virulent and avirulent P. brassicae isolates (Pbs) of two near isogenic lines, CR 3–2 and CS 3–2, with CR 3–2 harboring clubroot resistant gene BraCRa. The transcriptomic analysis was then conducted with CR 3–2 after inoculating with virulent isolate PbE and avirulent isolate Pb4. From the differentially expressed genes of transcriptomic data, we identified a Ca2+-sensor encoding gene, BraCBL1.2, that was highly induced in CR 3–2 during infection by Pb4 but not by PbE. Moreover, GUS histochemical staining and subcellular localization analysis revealed that BraCBL1.2 was specifically expressed in the root hair cells of Arabidopsis and encoded a putative Ca2+ sensor localized in the plasma membrane. We also developed an assay to investigate the BraCRa-mediated hypersensitive response (HR) in tobacco leaves. The results suggest that BraCBL1.2 is involved in the BraCRa-mediated plant ETI immune response against P. brassicae. In addition, we verified that overexpression of BraCBL1.2 enhanced clubroot resistance in Arabidopsis. Collectively, our data identified the involvement of a Ca2+ sensor in BraCRa-mediated clubroot resistance in Chinese cabbage, providing a theoretical basis for further research on the resistance of Chinese cabbage to P. brassicae.
Comprehensive dissection of variation and accumulation of free amino acids in tea accessions
Authors: Huang Rong , Wang Zhihua , Wen Weiwei , Yao Mingzhe , Liu Haoran , Li Fang , Zhang Shuran , Ni Dejiang , Chen Liang 
Published: December 2023

Abstract
Free amino acids (FAAs) positively determine the tea quality, notably theanine (Thea), endowing umami taste of tea infusion, which is the profoundly prevalent research in albino tea genetic resources. Therefore, 339 tea accessions were collected to study FAAs level for deciphering its variation and accumulation mechanism. Interestingly, alanine (Ala) and Thea which had the highest diversity index (H′) value among three varieties of Camellia sinensis (L.) O. Kuntze were significantly higher than wild relatives (P &lt; 0.05). The intraspecific arginine (Arg) and glutamine (Gln) contents in C. sinensis var. assamica were significantly lower than sinensis and pubilimba varieties. Moreover, the importance of interdependencies operating across FAAs and chlorophyll levels were highlighted via the cell ultrastructure, metabolomics, and transcriptome analysis. We then determined that the association between phytochrome interacting factor 1 (CsPIF1) identified by weighted gene co-expression network analysis (WGCNA) and Thea content. Intriguingly, transient knock-down CsPIF1 expression increased Thea content in tea plant, and the function verification of CsPIF1 in Arabidopsis also indicated that CsPIF1 acts as a negative regulator of Thea content by mainly effecting the genes expression related to Thea biosynthesis, transport, and hydrolysis, especially glutamate synthase (CsGOGAT), which was validated to be associated with Thea content with a nonsynonymous SNP by Kompetitive Allele-Specific PCR (KASP). We also investigated the interspecific and geographical distribution of this SNP. Taken together, these results help us to understand and clarify the variation and profile of major FAAs in tea germplasms and promote efficient utilization in tea genetic improvement and breeding.
Fertility education: recommendations for developing and implementing tools to improve fertility literacy
Authors: Martins Mariana V , Koert Emily , Sylvest Randi , Maeda Eri , Moura-Ramos Mariana , Hammarberg Karin , Harper Joyce 
Published: December 2023

AbstractMany recent societal trends have led to the need for fertility education, including the age at which individuals become parents, the development of new reproductive technologies, and family diversity. Fertility awareness has emerged as a concept very recently and is increasingly gaining recognition. However, fertility education is often neglected as there is no consensus on the appropriate content, target populations, or on who should provide it. This article attempts to provide an overview of the use of interventions to improve fertility education. We emphasize the importance of delivering evidence-based information on fertility and reproductive health through various methods while providing guidelines for their standardization and systematization. Recommendations are provided to aid the development and implementation of fertility education tools, including: the establishment of a comprehensive understanding of the target populations; the incorporation of theories of behavioural change; the inclusion of the users’ perspectives and the use of participatory research; and the use of specific guidelines for increasing engagement. By following these recommendations, it is expected that fertility education resources can contribute to improving fertility literacy, empowering individuals and couples to make informed reproductive decisions, and ultimately reducing the incidence of infertility and need for fertility treatment.
Subinhibitory effects of 2,4-diacetylphloroglucinol on filamentous fungus Aspergillus fumigatus
Authors: Stepanov Artyom A , Vasilchenko Anastasia V , Vasilchenko Alexey S 
Published: December 2023

Abstract

Aims
Aspergillus fungi are common members of the soil microbiota. Some physiological and structural characteristics of Aspergillus species make them important participants in soil ecological processes. In this study, we aimed to evaluate the impact of 2,4-diacetylphloroglucinol (2,4-DAPG), a common metabolite of soil and rhizosphere bacteria, on the physiology of Aspergillus fumigatus.

Methods and results
Integrated analysis using microscopy, spectrophotometry, and liquid chromatography showed the following effects of 2,4-DAPG on Aspergillus physiology. It was found that A. fumigatus in the biofilm state is resistant to high concentrations of 2,4-DAPG. However, experimental exposure led to a depletion of the extracellular polymeric substance, changes in the structure of the cell wall of the mycelium (increase in the content of α- and β-glucans, chitin, and ergosterol), and conidia (decrease in the content of DHN-melanin). 2,4-DAPG significantly reduced the production of mycotoxins (gliotoxin and fumagillin) but increased the secretion of proteases and galactosaminogalactan.

Conclusions
Overall, the data obtained suggest that 2,4-DAPG-producing Pseudomonas bacteria are unlikely to directly eliminate A. fumigatus fungi, as they exhibit a high level of resistance when in the biofilm state. However, at low concentrations, 2,4-DAPG significantly alters the physiology of aspergilli, potentially reducing the adaptive and competitive capabilities of these fungi.
Antibiofilm potential of nanonized eugenol againstPseudomonas aeruginosa
Authors: Ghosh Sourav , Sett Upasana , Pal Anabadya , Nandy Sanchita , Nandi Susmita , Chakrabarty Soumajit , Das Abhijit , Bandopadhyay Pathikrit , Basu Tarakdas 
Published: December 2023

AbstractAimsThe purpose of this study was to synthesize a nanoform of eugenol (an important phytochemical with various pharmacological potentials) and to investigate its antibiofilm efficacy on Pseudomonas aeruginosa biofilm.Methods and resultsColloidal suspension of eugenol-nanoparticles (ENPs) was synthesized by the simple ultrasonic cavitation method through the emulsification of hydrophobic eugenol into hydrophilic gelatin. Thus, the nanonization process made water-insoluble eugenol into water-soluble nano-eugenol, making the nanoform bioavailable. The size of the ENPs was 20–30 nm, entrapment efficiency of eugenol within gelatin was 80%, and release of eugenol from the gelatin cap was slow and sustained over 5 days. Concerning the clinically relevant pathogen P. aeruginosa, ENPs had higher antibiofilm (for both formation and eradication) activities than free eugenol. Minimal biofilm inhibitory concentration and minimal biofilm eradication concentration of ENP on P. aeruginosa biofilm were 2.0 and 4.0 mM, respectively. In addition, the measurement of P. aeruginosa biofilm biomass, biofilm thickness, amount of biofilm extra-polymeric substance, cell surface hydrophobicity, cell swarming and twitching efficiencies, cellular morphology, and biofilm formation in catheter demonstrated that the antibiofilm efficacy of nano-eugenol was 30%–40% higher than that of bulk eugenol.ConclusionThese results signify that future pharmacological and clinical studies are very much required to investigate whether ENPs can act as an effective drug against P. aeruginosa biofilm-mediated diseases. Thus, the problem of intrinsic antibiotic tolerance of biofilm-forming cells may be minimized by ENPs. Moreover, ENP may be used as a potential catheter-coating agent to inhibit pseudomonal colonization on catheter surfaces and, therefore, to reduce catheter-associated infections and complications.
Reference genome for the Mojave poppy bee (Perdita meconis), a specialist pollinator of conservation concern
Authors: Schweizer Rena M , Meidt Colleen G , Benavides Ligia R , Wilson Joseph S , Griswold Terry L , Sim Sheina B , Geib Scott M , Branstetter Michael G 
Published: December 2023

Abstract
The Mojave poppy bee, Perdita meconis Griswold (Hymenoptera: Anthophila: Andrenidae), is a species of conservation concern that is restricted to the eastern Mojave Desert of North America. It is a specialist pollinator of two poppy genera, Arctomecon and Argemone (Papaveraceae), and is being considered for listing under the US Endangered Species Act along with one of its pollinator hosts, the Las Vegas bearpoppy (Arctomecon californica). Here, we present a near chromosome-level genome of the Mojave poppy bee to provide a genomic resource that will aid conservation efforts and future research. We isolated DNA from a single, small (&lt;7 mm), male specimen collected using non-ideal preservation methods and then performed whole-genome sequencing using PacBio HiFi technology. After quality and contaminant filtering, the final draft genome assembly is 327 Mb, with an N50 length of 17.5 Mb. Annotated repetitive elements compose 37.3% of the genome, although a large proportion (24.87%) of those are unclassified repeats. Additionally, we annotated 18,245 protein-coding genes and 19,433 transcripts. This genome represents one of only a few genomes from the large bee family Andrenidae and one of only a few genomes for pollinator specialists. We highlight both the potential of this genome as a resource for future research, and how high-quality genomes generated from small, non-ideal (in terms of preservation) specimens could facilitate biodiversity genomics.
Leading with the trailing edge: facilitating patient choice for insulin products
Authors: Feldman Robin 
Published: December 2023

Abstract
Insulin prices have risen sharply, despite a century since its introduction. Against this backdrop, companies have discontinued dozens of insulin products. Discontinuation could relate to safety or effectiveness, or to the overwhelming benefits of newer products. On the other hand, discontinuation could suggest strategic behavior hampering competition and supporting prices. To test these theories, this project examined every insulin discontinuation, analyzing the role discontinuations play in insulin affordability. No evidence emerged of any discontinuation for safety or effectiveness. Rather, dozens of viable products were removed from the market, followed by more expensive versions, often with little or no clinical improvement. Insulin pens with a phone app may provide advantages, for example. However, for older patients, who may find the technology confusing, or for patients with budget constraints, the value proposition falters. Moreover, discontinuation blocks biosimilars from market entry because they cannot demonstrate biosimilarity without the drug. The problem exists for all biosimilars. If there are willing buyers and willing sellers of clinically effective products that are off-patent, entry should be facilitated. This article suggests a requirement that companies deposit samples at the time of FDA approval, laying the groundwork for later entry of trailing-edge products with clinically viable outcomes.
On the effects of photoionization feedback on second-generation star formation in globular clusters of different masses
Authors: Yaghoobi A , Rosdahl J , Calura F , Ataiee S 
Published: December 2023

ABSTRACT
We simulate the formation of second-generation (SG) stars in young clusters with masses of 105 and $10^6\, \mathrm{M}_{\odot }$ within $30\!-\!100\, \mathrm{Myr}$ after the formation of clusters. We assume the clusters move through a uniform interstellar medium with gas densities of 10−24 and $10^{-23}\, \mathrm{g\, cm}^{-3}$ and consider the stellar winds from asymptotic giant branch (AGB) stars, gas accretion on to the cluster, ram pressure, star formation, and photoionization feedback of our stellar systems including binary stars. We find that SG stars can be formed only within the $10^6\, \mathrm{M}_{\odot }$ cluster in the high-density simulation, where the cluster can accrete sufficient pristine gas from their surrounding medium, leading to efficient cooling required for the ignition of SG formation and sufficient dilution of the AGB ejecta. Hence, our results indicate that a denser environment is another requirement for the AGB scenario to explain the presence of multiple populations in globular clusters. On the other hand, the ionizing feedback becomes effective in heating the gas in our low-density simulations. As a result, the clusters cannot accumulate a considerable amount of pristine gas at their centre. The gas mass within the clusters in these simulations is similar to that in young massive clusters (YMCs). Hence, our studies can provide a possible reason for the lack of gas, star formation, and SG stars in YMCs. Our results indicate that the ionizing stellar feedback is not a severe problem for SG formation; rather, it can help the AGB scenario to account for some observables.
Preparing for low surface brightness science with the Vera C. Rubin Observatory: a comparison of observable and simulated intracluster light fractions
Authors: Brough Sarah , Ahad Syeda Lammim , Bahé Yannick M , Ellien Amaël , Gonzalez Anthony H , Jiménez-Teja Yolanda , Kimmig Lucas C , Martin Garreth , Martínez-Lombilla Cristina , Montes Mireia , Pillepich Annalisa , Ragusa Rossella , Remus Rhea-Silvia , Collins Chris A , Knapen Johan H , Mihos J Christopher 
Published: December 2023

ABSTRACT
Intracluster light (ICL) provides an important record of the interactions galaxy clusters have undergone. However, we are limited in our understanding by our measurement methods. To address this, we measure the fraction of cluster light that is held in the Brightest Cluster Galaxy and ICL (BCG+ICL fraction) and the ICL alone (ICL fraction) using observational methods (surface brightness threshold-SB, non-parametric measure-NP, composite models-CM, and multi-galaxy fitting-MGF) and new approaches under development (wavelet decomposition-WD) applied to mock images of 61 galaxy clusters (14 &lt;log10M200c/M⊙ &lt; 14.5) from four cosmological hydrodynamical simulations. We compare the BCG+ICL and ICL fractions from observational measures with those using simulated measures (aperture and kinematic separations). The ICL fractions measured by kinematic separation are significantly larger than observed fractions. We find the measurements are related and provide equations to estimate kinematic ICL fractions from observed fractions. The different observational techniques give consistent BCG+ICL and ICL fractions but are biased to underestimating the BCG+ICL and ICL fractions when compared with aperture simulation measures. Comparing the different methods and algorithms, we find that the MGF algorithm is most consistent with the simulations, and CM and SB methods show the smallest projection effects for the BCG+ICL and ICL fractions, respectively. The Ahad (CM), MGF, and WD algorithms are best set up to process larger samples; however, the WD algorithm in its current form is susceptible to projection effects. We recommend that new algorithms using these methods are explored to analyse the massive samples that Rubin Observatory’s Legacy Survey of Space and Time will provide.
Constraining the X-ray radiation origin of 3C 273 in the low state by polarization
Authors: Liu Mingjun , Zhang Wenda , Yuan Weimin 
Published: December 2023

ABSTRACT
3C 273 is one of the nearest high-luminosity quasars. Although classified as a blazar, 3C 273 also has some features in Seyferts, whose X-ray may originate from the corona. Since both jet and corona produce power-law spectra in X-ray, the spectrum cannot completely distinguish their contributions to 3C 273 in the low state. X-ray polarimetric observations provide the chance to constrain the X-ray radiation origin of 3C 273 in the low state. We perform general relativistic radiative transfer simulations with the code monk to compute the X-ray polarization in 2–10 keV from the jets, sphere coronae, and slab coronae for 3C 273. We find that the radiation from the jet in 2–10 keV has a larger polarization degree than that of the corona: the polarization degree in 2–10 keV from the corona is unpolarized, while these are 4.1 per cent–15.8 per cent for the jet with a vertical or radial magnetic field and ≤5.0 per cent for the jet with toroidal magnetic field. The X-ray polarization of the corona and jet is sensitive to optical depth and geometry, and the main driver for this dependence is the number of scatterings. These results show that X-ray polarization can effectively constrain the X-ray radiation origin of 3C 273 in the low state.
Stability and Ly α emission of Cold Stream in the Circumgalactic Medium: impact of magnetic fields and thermal conduction
Authors: Ledos Nicolas , Takasao Shinsuke , Nagamine Kentaro 
Published: December 2023

ABSTRACT
Cold streams of gas with temperatures around 104 K play a crucial role in the gas accretion on to high-redshift galaxies. The current resolution of cosmological simulations is insufficient to fully capture the stability and Ly α emission characteristics of cold stream accretion, underscoring the imperative need for conducting idealized high-resolution simulations. We investigate the impact of magnetic fields at various angles and anisotropic thermal conduction (TC) on the dynamics of radiatively cooling streams through a comprehensive suite of two-dimensional high-resolution simulations. An initially small magnetic field ($\sim 10^{-3} \, \mu\rm G$), oriented non-parallel to the stream, can grow significantly, providing stability against Kelvin–Helmholtz instabilities and reducing the Ly α emission by a factor of &lt;20 compared to the hydrodynamics case. With TC, the stream evolution can be categorized into three regimes: (1) the Diffusing Stream regime, where the stream diffuses into the surrounding hot circumgalactic medium; (2) the Intermediate regime, where TC diffuses the mixing layer, resulting in enhanced stabilization and reduced emissions; (3) the Condensing Stream regime, where the impact of magnetic field and TC on the stream’s emission and evolution becomes negligible. Extrapolating our findings to the cosmological context suggests that cold streams with a radius of $\le 1 \rm \, {\rm kpc}$ may fuel galaxies with cold metal-enriched magnetized gas ($B \sim 0.1\!-\!1 \, \mu \rm G$) for a longer time, leading to a broad range of Ly α luminosity signatures of $\sim 10^{37}\!-\!10^{41}\, \rm \, erg \, s^{-1}$.
Galaxy kinematics and mass estimates at z ∼ 1 from ionized gas and stars
Authors: Übler Hannah , Förster Schreiber Natascha M , van der Wel Arjen , Bezanson Rachel , Price Sedona H , D’Eugenio Francesco , Wisnioski Emily , Genzel Reinhard , Tacconi Linda J , Wuyts Stijn , Naab Thorsten , Lutz Dieter , Straatman Caroline M S , Shimizu Thomas Taro , Davies Ric , Liu Daizhong , Mendel Trevor 
Published: December 2023

ABSTRACT
We compare ionized gas and stellar kinematics of 16 star-forming galaxies (log (M⋆/M⊙) = 9.7–11.2, SFR =6 − 86 M⊙ yr−1) at z ∼ 1 using near-infrared integral field spectroscopy (IFS) of Hα emission from the KMOS3D (the K-band Multi-Object Spectrograph 3D) survey and optical slit spectroscopy of stellar absorption and gas emission from the LEGA-C (Large Early Galaxy Astrophysics Census) survey. Hα is dynamically colder than stars, with higher disc rotation velocities (by ∼45 per cent) and lower disc velocity dispersions (by a factor ∼2). This is similar to trends observed in the local Universe. We find higher rotational support for Hα relative to [O ii], potentially explaining systematic offsets in kinematic scaling relations found in the literature. Regarding dynamical mass measurements, for six galaxies with cumulative mass profiles from Jeans Anisotropic Multi-Gaussian Expansion (JAM) models the Hα dynamical mass models agree remarkably well out to ∼10 kpc for all but one galaxy (average $\Delta M_{\rm dyn}(R_{e,\rm F814W})\lt 0.1$ dex). Simpler dynamical mass estimates based on integrated stellar velocity dispersion are less accurate (standard deviation 0.24 dex). Differences in dynamical mass estimates are larger, for example, for galaxies with stronger misalignments of the Hα kinematic major axis and the photometric position angle, highlighting the added value of IFS observations for dynamics studies. The good agreement between the JAM and the dynamical models based on Hα kinematics at z ∼ 1 corroborates the validity of dynamical mass measurements from Hα IFS observations, which can be more easily obtained for higher redshift galaxies.