bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing liquid fermentation for Wolfiporia cocos: gene expression and biosynthesis of pachymic acid and mycelial biomass
Authors: Noushahi Hamza Armghan , Khan Aamir Hamid , Khan Hamza Ali , Kiedrzyński Marcin , Akbar Adnan , Shahzad Raheel , Koerniati Sri , Alrefaei Abdulwahed Fahad , Shu Shaohua 
Published: June 2024

Abstract
Wolfiporia cocos, a versatile fungus acclaimed for its nutritional and therapeutic benefits in Traditional Chinese Medicine, holds immense potential for pharmaceutical and industrial applications. In this study, we aimed to optimize liquid fermentation techniques and culture medium composition to maximize mycelial biomass (MB) yield, pachymic acid (PA) concentration, and overall PA production. Additionally, we investigated the molecular basis of our findings by quantifying the expression levels of genes associated with PA and MB biosynthesis using quantitative real-time polymerase chain reaction. Under the optimized fermentation conditions, significant results were achieved, with maximum MB reaching 6.68 g l−1, PA content peaking at 1.25 mg g−1, and a total PA yield of 4.76 g l−1. Notably, among the four examined genes, squalene monooxygenase, exhibited enhanced expression at 0.06 ratio under the optimized conditions. Furthermore, within the realm of carbohydrate-active enzymes, the glycoside hydrolases 16 family displayed elevated expression levels at 21 ratios, particularly during MB production. This study enhances understanding of genetic mechanism governing MB and PA production in W. cocos, highlighting the roles of squalene monooxygenase and glycoside hydrolases 16 carbohydrate-active enzymes.
WISE2MBH: a scaling-based algorithm for probing supermassive black hole masses through WISE catalogues
Authors: Hernández-Yévenes J , Nagar N , Arratia V , Jarrett T H 
Published: June 2024

ABSTRACT
Supermassive Black Holes (SMBHs) are commonly found at the centres of massive galaxies. Estimating their masses (MBH) is crucial for understanding galaxy-SMBH co-evolution. We present WISE2MBH, an efficient algorithm that uses cataloged Wide-field Infrared Survey Explorer (WISE) magnitudes to estimate total stellar mass (M*) and scale this to bulge mass (MBulge), and MBH, estimating the morphological type (TType) and bulge fraction (B/T) in the process. WISE2MBH uses scaling relations from the literature or developed in this work, providing a streamlined approach to derive these parameters. It also distinguishes QSOs from galaxies and estimates the galaxy TType using WISE colours with a relation trained with galaxies from the 2MASS Redshift Survey. WISE2MBH performs well up to z ∼ 0.5 thanks to K-corrections in magnitudes and colours. WISE2MBH MBH estimates agree very well with those of a selected sample of local galaxies with MBH measurements or reliable estimates: a Spearman score of ∼0.8 and a RMSE of ∼0.63 were obtained. When applied to the ETHER sample at z ≤ 0.5, WISE2MBH provides ∼1.9 million MBH estimates (78.5 per cent new) and ∼100 thousand upper limits. The derived local black hole mass function (BHMF) is in good agreement with existing literature BHMFs. Galaxy demographic projects, including target selection for the Event Horizon Telescope, can benefit from WISE2MBH for up-to-date galaxy parameters and MBH estimates. The WISE2MBH algorithm is publicly available on GitHub.
Simultaneous retrieval of orbital phase resolved JWST/MIRI emission spectra of the hot Jupiter WASP-43b: evidence of water, ammonia, and carbon monoxide
Authors: Yang Jingxuan , Hammond Mark , Piette Anjali A A , Blecic Jasmina , Bell Taylor J , Irwin Patrick G J , Parmentier Vivien , Tsai Shang-Min , Barstow Joanna K , Crouzet Nicolas , Kreidberg Laura , Mendonça João M , Taylor Jake , Baeyens Robin , Ohno Kazumasa , Teinturier Lucas , Nixon Matthew C 
Published: June 2024

ABSTRACT
Spectroscopic phase curves of hot Jupiters measure their emission spectra at multiple orbital phases, thus enabling detailed characterization of their atmospheres. Precise constraints on the atmospheric composition of these exoplanets offer insights into their formation and evolution. We analyse four phase-resolved emission spectra of the hot Jupiter WASP-43b, generated from a phase curve observed with the Mid-Infrared Instrument/Low Resolution Spectrometer onboard the JWST, to retrieve its atmospheric properties. Using a parametric 2D temperature model and assuming a chemically homogeneous atmosphere within the observed pressure region, we simultaneously fit the four spectra to constrain the abundances of atmospheric constituents, thereby yielding more precise constraints than previous work that analysed each spectrum independently. Our analysis reveals statistically significant evidence of NH$_3$ (4$\sigma$) in a hot Jupiter’s emission spectra for the first time, along with evidence of H$_2$O (6.5$\sigma$), CO (3.1$\sigma$), and a non-detection of CH$_4$. With our abundance constraints, we tentatively estimate the metallicity of WASP-43b at 0.6$-6.5\times$ solar and its C/O ratio at 0.6$-$0.9. Our findings offer vital insights into the atmospheric conditions and formation history of WASP-43b by simultaneously constraining the abundances of carbon, oxygen, and nitrogen-bearing species.
The FLAMINGO project: galaxy clusters in comparison to X-ray observations
Authors: Braspenning Joey , Schaye Joop , Schaller Matthieu , McCarthy Ian G , Kay Scott T , Helly John C , Kugel Roi , Elbers Willem , Frenk Carlos S , Kwan Juliana , Salcido Jaime , van Daalen Marcel P , Vandenbroucke Bert 
Published: June 2024

ABSTRACT
Galaxy clusters are important probes for both cosmology and galaxy formation physics. We test the cosmological, hydrodynamical FLAMINGO (Full-hydro large-scale structure simulations with all-sky mapping for the interpretation of next generation observations) simulations by comparing to observations of the gaseous properties of clusters measured from X-ray observations. FLAMINGO contains unprecedented numbers of massive galaxy groups ($\gt 10^6$) and clusters ($\gt 10^5$) and includes variations in both cosmology and galaxy formation physics. We predict the evolution of cluster scaling relations as well as radial profiles of the temperature, density, pressure, entropy, and metallicity for different masses and redshifts. We show that the differences between volume-, and X-ray-weighting of particles in the simulations, and between cool- and non-cool-core samples, are similar in size as the differences between simulations for which the stellar and AGN (active galactic nucleus) feedback has been calibrated to produce significantly different gas fractions. Compared to thermally driven AGN feedback, kinetic jet feedback calibrated to produce the same gas fraction at $R_{\rm 500c}$ yields a hotter core with higher entropies and lower densities, which translates into a smaller fraction of cool-core clusters. Stronger feedback, calibrated to produce lower gas fractions and hence lower gas densities, results in higher temperatures, entropies, and metallicities, but lower pressures. The scaling relations and thermodynamic profiles show almost no evolution with respect to self-similar expectations, except for the metallicity decreasing with redshift. We find that the temperature, density, pressure, and entropy profiles of clusters in the fiducial FLAMINGO simulation are in excellent agreement with observations, while the metallicities in the core are too high.
Radio continuum emission from a tidal dwarf galaxy
Authors: Moncada-Cuadri Blanca M , Lisenfeld Ute , Querejeta Miguel , Mundell Carole 
Published: June 2024

ABSTRACT
Tidal dwarf galaxies (TDGs) form in the debris of galaxy mergers, making them ideal testbeds for investigating star formation in an extreme environment. We present radio continuum EVLA observations spanning 1–2 GHz of the interacting system Arp 94, which contains the TDG J1023+1952. We detect extended radio continuum emission from the disc of the TDG’s putative parent galaxy, the spiral NGC 3227. The TDG lies in front of the spiral disc, partially overlapping in projection. This challenging alignment complicates the separation of the respective contributions of radio emission from the TDG and disc. However, we show that the radio continuum appears more prominent around the TDG’s location, suggesting the detection of emission from the TDG. Quantifying this argument, we derive an upper limit of 2.2 mJy for the whole TDG’s emission. Our derived inband spectral index map of the system generally shows the expected behaviour of combined thermal and synchrotron radio emission in a galaxy disc, except for a region at the periphery of the disc and the TDG with a flat spectrum (spectral index $\sim$−0.4) unrelated to regions with high H $\alpha$ emission. We speculate that at this location – which coincides with the intersection of faint tidal tails – the collision of gas clouds produces shocks which re-accelerate cosmic ray electrons, and thereby enhance the radio emission. Overall, this study provides new insights about the Arp 94 system and expands the sample of TDGs studied at radio frequencies, with only two confirmed detections so far.
Extension of semi-analytic kilonova model and the application in multicolour light curves fitting
Authors: Gong Hong-Yu , Wei Da-Ming , Jin Zhi-Ping , Fan Yi-Zhong 
Published: June 2024

ABSTRACT
Observations of AT2017gfo, the counterpart of the double neutron star merger, confirmed the existence of kilonovae that are suggested to originate from the decay of the very heavy elements. However, the different simplified assumptions used in analytical and semi-analytical models can lead to a variety of fitting results. Previous semi-analytical models have assumed a grey body because of the challenge in calculating the detailed opacity of ejecta and to save the calculation time. However, the variation of opacity with wavelength cannot be ignored when calculating the multicolour flux. Though numerical simulations can calculate kilonova details, they require an excessive amount of time for data modelling. In this work, we propose an extension of previous semi-analytical models by not assuming the grey-body opacity and constant thermalization efficiency assumptions. We demonstrate that the impact of opacity changing with wavelength is non-negligible and then introduce an empirical analytical opacity in optical and near-infrared bands to calculate multicolour light curves of kilonovae with a three-dimensional, three-component model. Additionally, we consider the evolution of thermalization efficiency at later times, enabling application of our model to both the early and later phases of kilonovae. To enable efficient fitting of models with many parameters (23 parameters in the case of double neutron star merger), a quick method based on the greedy algorithm is developed. We can well reproduce the infrared/optical/ultraviolet observations of AT2017gfo. This model can also be extended to black-hole and neutron star mergers as well.
Chemical compositions of semiregular variable red giants
Authors: Pozhath Ramya , Lambert David L 
Published: June 2024

ABSTRACT
A sample of warm, low-level semiregular variables chosen from the General Catalogue of Variable Stars is studied for their chemical compositions by analysing high-resolution optical spectra. The abundance ratios from Na/Fe to Eu/Fe displayed by these and previously analysed semiregular variables are quite similar to ratios displayed by normal red giants across the Galactic thin and thick discs and halo populations in the solar neighbourhood, suggesting from this perspective that the variables may be among the more photometrically active red giants.
Empirical calibration for helium abundance determinations in active galactic nuclei
Authors: Dors O L , Almeida G C , Oliveira C B , Flury S R , Riffel R , Riffel R A , Cardaci M V , Hägele G F , Ilha G S , Krabbe A C , Arellano-Córdova K Z , Santos P C , Morais I N 
Published: June 2024

ABSTRACT
For the first time, a calibration between the He i$\lambda 5876$/H $\beta$ emission line ratio and the helium abundance y = 12 + log(He/H) for Narrow line regions of Seyfert 2 Active Galactic Nuclei is proposed. In this context, observational data (taken from the SDSS-DR15 and from the literature) and direct abundance estimates (via the $T_{\rm e}$-method) for a sample of 65 local ($z \: \lt \: 0.2$) Seyfert 2 nuclei are considered. The resulting calibration estimates the y abundance with an average uncertainty of 0.02 dex. Applying our calibration to spectroscopic data containing only strong emission lines, it yields a helium abundance distribution similar to that obtained via the $T_{\rm e}$-method. Some cautions must be considered to apply our calibration for Seyfert 2 nuclei with high values of electron temperature (${\gtrsim} 20\, 000$ K) or ionization parameter ($\log U \ \gt\ {-}2.0$).
Engineering spacer specificity of the Cre/loxP system
Authors: Hoersten Jenna , Ruiz-Gómez Gloria , Paszkowski-Rogacz Maciej , Gilioli Giorgio , Guillem-Gloria Pedro Manuel , Lansing Felix , Pisabarro M Teresa , Buchholz Frank 
Published: June 2024

Abstract
Translational research on the Cre/loxP recombination system focuses on enhancing its specificity by modifying Cre/DNA interactions. Despite extensive efforts, the exact mechanisms governing Cre discrimination between substrates remains elusive. Cre recognizes 13 bp inverted repeats, initiating recombination in the 8 bp spacer region. While literature suggests that efficient recombination proceeds between lox sites with non-loxP spacer sequences when both lox sites have matching spacers, experimental validation for this assumption is lacking. To fill this gap, we investigated target site variations of identical pairs of the loxP 8 bp spacer region, screening 6000 unique loxP-like sequences. Approximately 84% of these sites exhibited efficient recombination, affirming the plasticity of spacer sequences for catalysis. However, certain spacers negatively impacted recombination, emphasizing sequence dependence. Directed evolution of Cre on inefficiently recombined spacers not only yielded recombinases with enhanced activity but also mutants with reprogrammed selective activity. Mutations altering spacer specificity were identified, and molecular modelling and dynamics simulations were used to investigate the possible mechanisms behind the specificity switch. Our findings highlight the potential to fine-tune site-specific recombinases for spacer sequence specificity, offering a novel concept to enhance the applied properties of designer-recombinases for genome engineering applications.
Concerted action of ataxin-2 and PABPC1-bound mRNA poly(A) tail in the formation of stress granules
Authors: Yamagishi Ryota , Inagaki Hiroto , Suzuki Jun , Hosoda Nao , Sugiyama Haruka , Tomita Kazunori , Hotta Takashi , Hoshino Shin-ichi 
Published: June 2024

Abstract
Stress induces global stabilization of the mRNA poly(A) tail (PAT) and the assembly of untranslated poly(A)-tailed mRNA into mRNPs that accumulate in stress granules (SGs). While the mechanism behind stress-induced global PAT stabilization has recently emerged, the biological significance of PAT stabilization under stress remains elusive. Here, we demonstrate that stress-induced PAT stabilization is a prerequisite for SG formation. Perturbations in PAT length impact SG formation; PAT shortening, achieved by overexpressing mRNA deadenylases, inhibits SG formation, whereas PAT lengthening, achieved by overexpressing their dominant negative mutants or downregulating deadenylases, promotes it. PABPC1, which specifically binds to the PAT, is crucial for SG formation. Complementation analyses reveal that the PABC/MLLE domain of PABPC1, responsible for binding PAM2 motif-containing proteins, plays a key role. Among them, ataxin-2 is a known SG component. A dominant-negative approach reveals that the PAM2 motif of ataxin-2 is essential for SG formation. Notably, ataxin-2 increases stress sensitivity, lowering the threshold for SG formation, probably by promoting the aggregation of PABPC1-bound mRNA. The C-terminal region is responsible for the self-aggregation of ataxin-2. These findings underscore the critical roles of mRNA PAT, PABPC1 and ataxin-2 in SG formation and provide mechanistic insights into this process.
YY1 is involved in homologous recombination inhibition at guanine quadruplex sites in human cells
Authors: Cui Xinyu , Zhang Chengwen , Fu Chunqing , Hu Jinglei , Li Tengjiao , Li Lin 
Published: June 2024

Abstract
Homologous recombination (HR) is a key process for repairing DNA double strand breaks and for promoting genetic diversity. However, HR occurs unevenly across the genome, and certain genomic features can influence its activity. One such feature is the presence of guanine quadruplexes (G4s), stable secondary structures widely distributed throughout the genome. These G4s play essential roles in gene transcription and genome stability regulation. Especially, elevated G4 levels in cells deficient in the Bloom syndrome helicase (BLM) significantly enhance HR at G4 sites, potentially threatening genome stability. Here, we investigated the role of G4-binding protein Yin Yang-1 (YY1) in modulating HR at G4 sites in human cells. Our results show that YY1’s binding to G4 structures suppresses sister chromatid exchange after BLM knockdown, and YY1’s chromatin occupancy negatively correlates with the overall HR rate observed across the genome. By limiting RAD51 homolog 1 (RAD51) access, YY1 preferentially binds to essential genomic regions, shielding them from excessive HR. Our findings unveil a novel role of YY1–G4 interaction, revealing novel insights into cellular mechanisms involved in HR regulation.
Are non-practising entities opportunistic? Evidence from litigation of standard essential patents
Authors: Love Brian J , Helmers Christian 
Published: June 2024

Abstract
Are non-practising entities (NPEs)—firms that specialize in the enforcement of patent rights rather than the commercialization of patented technologies—more likely than other patent enforcers to behave opportunistically? To explore this question, we construct measures of opportunistic conduct by patent enforcers and document the presence or absence of these behaviours in a subset of US patent cases in which opportunism is especially likely to occur: cases that assert standard essential patents (SEPs). Our results suggest heterogeneity across different opportunistic behaviours. NPEs are more likely to exploit the SEP-declaration process and the SEP market’s lack of transparency, while practising entities (PEs) are more likely to pursue bans on the sale and importation of their products. We additionally present evidence that opportunism can affect case outcomes. Declaration and market-related opportunism are associated with a higher rate of settlement in NPE cases relative to PE cases.
Guideline-Concordant Therapy for Community-Acquired Pneumonia in the Hospitalized Population: A Systematic Review and Meta-analysis
Authors: Seo Chanhee , Corrado Mario , Lim Rachel , Thornton Christina S 
Published: June 2024

Abstract

Background
A commonly used guideline for community-acquired pneumonia (CAP) is the joint American Thoracic Society and Infectious Diseases Society of America practice guideline. We aimed to investigate the effect of guideline-concordant therapy in the treatment of CAP.

Methods
We systematically searched MEDLINE, Embase, CENTRAL, Web of Science, and Scopus from 2007 to December 2023. We screened citations, extracted data, and assessed risk of bias in duplicate. Primary outcomes were mortality rates, intensive care unit (ICU) admission, and length of stay. Secondary outcomes were guideline adherence, readmission, clinical cure rate, and adverse complications. We performed random-effect meta-analysis to estimate the overall effect size and assessed heterogeneity using the I2 statistics.

Results
We included 17 observational studies and 82 240 patients, of which 10 studies were comparative and pooled in meta-analysis. Overall guideline adherence rate was 65.2%. Guideline-concordant therapy was associated with a statistically significant reduction in 30-day mortality rate (crude odds ratio [OR], 0.49 [95% confidence interval .34–.70; I2 = 60%]; adjusted OR, 0.49 [.37–.65; I2 = 52%]) and in-hospital mortality rate (crude OR, 0.63 [.43–.92]; I2 = 61%). Due to significant heterogeneity, we could not assess the effect of guideline-concordant therapy on length of stay, ICU admission, readmission, clinical cure rate, and adverse complications.

Conclusions
In hospitalized patients with CAP, guideline-concordant therapy was associated with a significant reduction in mortality rate compared with nonconcordant therapy; however, there was limited evidence to support guideline-concordant therapy for other clinical outcomes. Future studies are needed to assess the clinical efficacy and safety of current guideline recommendations.
Clinical outcomes of image-guided therapies in patients with adrenocortical carcinoma: a tertiary referral center retrospective study
Authors: Chahla Brenda , Pal Koustav , Balderrama-Brondani Vania , Yaylaci Feyza , Campbell Matthew T , Sheth Rahul A , Habra Mouhammed Amir 
Published: June 2024

Abstract

Background
Image-guided therapies (IGTs) are commonly used in oncology, but their role in adrenocortical carcinoma (ACC) is not well defined.

Materials and Methods
A retrospective review of patients with ACC treated with IGTs. We assessed response to therapy using RECIST v1.1, time to next line of systemic therapy, disease control rate (DCR), local tumor progression-free survival (LTPFS), and complications of IGTs (based on the Common Terminology Criteria for Adverse Events [CTCAE] version 5.0).

Results
Our cohort included 26 patients (median age 56 years [range 38-76]; n = 18 female) who had 51 IGT sessions to treat 86 lesions. IGTs modalities included cryoablation (n = 49), microwave ablation (n = 21), combined microwave and bland trans-arterial embolization (n = 8), bland trans-arterial embolization alone (n = 3), radio-embolization (n = 3), and radiofrequency ablation (n = 2). DCR was 81.4% (70 out of 86), of which 66.3% of tumors showed complete response, 18.6% showed progressive disease, 8.1% showed partial response, and 7.0% showed stable disease. LTPFS rates were 73% and 63% at 1 and 2 years, respectively. Fourteen lesions underwent re-ablation for incomplete response on initial treatment. Sixteen patients (61.5%) received new systemic therapy following IGTs, with a median time to systemic therapy of 12.5 months (95% CI: 8.6 months upper limit not reached). There was 1 reported CTCAE grade 3 adverse event (biloma) following IGT.

Conclusions
IGT use in properly selected patients with ACC is safe and associated with prolonged disease control and delay in the need for systemic therapy.
Light quality induces a shift in coccosphere morphology in Scyphosphaera apsteinii
Authors: Chauhan Nishant , Barton Samuel , Zarkogiannis Stergios , Rickaby Rosalind E M 
Published: June 2024

Abstract
The coccolithophore Schyphosphaera apsteinii produces distinct coccolith morphotypes and offers a unique insight into coccolith calcification, as the number of lopadoliths per cell increases under low light intensities. This study employs S. apsteinii to investigate the acclimated impact of light intensity and wavelength on cell physiology and coccosphere morphology. Our findings reveal a marked increase in lopadolith production when grown under reduced light intensity, with lower growth rates, higher chlorophyll concentration and elevated net photosynthetic rates. Reduced blue-light also caused an increase in lopadolith numbers, elevated chlorophyll concentrations and net photosynthetic rates. Conversely, such responses are less pronounced under reduced red-light. Moreover, reduced blue- and red-light treatments exhibited enhanced growth rates compared to the light-replete control, despite a reduction in light intensity. Our findings suggest that changes in light quality cause a shift in the coccosphere morphology, affecting cell physiology and potentially aiding light harvesting in S. apsteinii.