bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tradeoffs between phage resistance and nitrogen fixation drive the evolution of genes essential for cyanobacterial heterocyst functionality
Authors: Kolan Dikla , Cattan-Tsaushu Esther , Enav Hagay , Freiman Zohar , Malinsky-Rushansky Nechama , Ninio Shira , Avrani Sarit 
Published: January 2024

Abstract
Harmful blooms caused by diazotrophic (nitrogen-fixing) Cyanobacteria are becoming increasingly frequent and negatively impact aquatic environments worldwide. Cyanophages (viruses infecting Cyanobacteria) can potentially regulate cyanobacterial blooms, yet Cyanobacteria can rapidly acquire mutations that provide protection against phage infection. Here, we provide novel insights into cyanophage:Cyanobacteria interactions by characterizing the resistance to phages in two species of diazotrophic Cyanobacteria: Nostoc sp. and Cylindrospermopsis raciborskii. Our results demonstrate that phage resistance is associated with a fitness tradeoff by which resistant Cyanobacteria have reduced ability to fix nitrogen and/or to survive nitrogen starvation. Furthermore, we use whole-genome sequence analysis of 58 Nostoc-resistant strains to identify several mutations associated with phage resistance, including in cell surface-related genes and regulatory genes involved in the development and function of heterocysts (cells specialized in nitrogen fixation). Finally, we employ phylogenetic analyses to show that most of these resistance genes are accessory genes whose evolution is impacted by lateral gene transfer events. Together, these results further our understanding of the interplay between diazotrophic Cyanobacteria and their phages and suggest that a tradeoff between phage resistance and nitrogen fixation affects the evolution of cell surface-related genes and of genes involved in heterocyst differentiation and nitrogen fixation.
Effects of Guizhi and Erxian Decoction on menopausal hot flashes: insights from the gut microbiome and metabolic profiles
Authors: Zong Yun , Mao Ting , Yao Peixun , Liang Jingtao , Lai Yawei , Chen Zhenyue , Chen Siyang , Huang Lei , Guo Yong , Zhu Min , Zhao Jingbing , Liu Yaqian , Li Yanfang , Guo Kaixin , Tang Hui , Ke Xuehong , Zhou Ying 
Published: January 2024

AbstractAimsTo examine the influence of GED on the gut microbiota and metabolites using a bilateral ovariectomized (OVX) rat model. We tried to elucidate the underlying mechanisms of GED in the treatment of menopausal hot flashes.Methods and results16S rRNA sequencing, metabonomics, molecular biological analysis, and fecal microbiota transplantation (FMT) were conducted to elucidate the mechanisms by which GED regulates the gut microbiota. GED significantly reduced OVX-induced hot flashes and improved disturbances in the gut microbiota metabolites. Moreover, FMT validated that the gut microbiota can trigger hot flashes, while GED can alleviate hot flash symptoms by modulating the composition of the gut microbiota. Specifically, GED upregulated the abundance of Blautia, thereby increasing l(+)-ornithine levels for the treatment of menopausal hot flashes. Additionally, GED affected endothelial nitric oxide synthase and heat shock protein 70 (HSP70) levels in the hypothalamic preoptic area by changing the gut microbiota composition.ConclusionsOur study illuminated the underlying mechanisms by which GED attenuated the hot flashes through modulation of the gut microbiota and explored the regulatory role of the gut microbiota on HSP70 expression in the preoptic anterior hypothalamus, thereby establishing a foundation for further exploration of the role of the gut–brain axis in hot flashes.
Forecasting the population development of within-season insect crop pests in sub-Saharan Africa: the Pest Risk Information Service
Authors: Day Charlotte , Murphy Sean T , Styles Jon , Taylor Bryony , Beale Tim , Holland William , Williams Frances , Shaw Andy , Finegold Cambria , Oronje MaryLucy , Oppong-Mensah Birgitta , Phiri Noah , Lowry Alyssa , Finch Elizabeth A , Mahony Josephine , Wood Suzy , Durocher-Granger Léna , Chacha Duncan , Maczey Norbert , Gonzalez-Moreno Pablo , Thomas Sarah E , Beeken Joe , Lewis Jane , Saldana Gerado Lopez , Duah Solomon , Bundi Mary , Wasilwa Lusike , Amata Ruth , Musila Ruth , Mutisya Daniel , Gitonga Christine K , Kalama Patrick , Nyasani Johnson O , Matimelo Matthews , Mgomba Henry , Gaitu Christopher , Ocloo Christopher , Adjei-Mensah Isaac , Ohene-Mensah Godfried , Nboyine Jerry Asalma , Susuwele Blessings 
Published: January 2024

Abstract
Smallholder farmers are the mainstay of the agricultural economies of sub-Saharan Africa (SSA), where they produce several crops, predominantly centered on maize. Smallholder productivity remains limited resulting from a range of confounding factors, but a primary cause is loss from pests and diseases, particularly insects. To improve productivity, recommendations for the mitigation of crop loss globally include early-warning and management systems for in-season indigenous pests. There are many early-warning systems in temperate regions; however, such systems are poorly established in Africa. This is in part due to the need for a combination of pest modeling, data handling and dissemination infrastructure, capacity, and resource provision. While each of these components is progressing in Africa, the means to successfully deploy such systems remain limited. To bridge this, the development of the Pest Risk Information Service (PRISE) began in 2017 for farmers in SSA. Implemented in Kenya, Ghana, Malawi, and Zambia, PRISE developed temperature-driven phenology models for major maize, bean, and tomato pests. Using downscaled and processed Earth Observation data to drive the models, PRISE partnered with African national agencies to communicate pre- and in-season pest alerts that forecast the time to act against key insect pests. Alerts were designed to be integrated into country-specific Good Agricultural Practice (GAP) recommendations to provide a complementary package to agricultural stakeholders. End line studies with farmers showed that those who received information about the target crops including PRISE pest forecasts, generally reported better outcomes in terms of reduced losses and increased incomes compared with farmers who did not.
Energetic particles in the central starburst, disc, and halo of NGC253
Authors: Rephaeli Yoel , Sadeh Sharon 
Published: January 2024

ABSTRACT
Detailed modelling of the spectro-spatial distributions of energetic electrons and protons in galactic discs and haloes of starburst galaxies (SBGs) is needed in order to follow their interactions with the magnetized interstellar medium and radiation fields, determine their radiative yields, and for estimating their residual spectral densities in intergalactic environments. We have developed a semi-analytical approach for calculating the particle spectro-spatial distributions in the disc and halo based on a diffusion model for particle propagation from acceleration sites in the central SB and disc regions, including all their relevant interaction modes. Important overall normalization of our models is based on previous modelling of the Galactic disc (with the galprop code), scaled to the higher star-formations rate in NGC253, and on spatially resolved radio measurements of the central SB and disc. These provide the essential input for determining the particle distributions and their predicted radiative yields in the outer disc and inner halo for a range of values of the key parameters that affect diffusion rate and energy losses. Results of our work clearly indicate that quantitative description of non-thermal emission in SBGs has to be based on modelling of the particle distributions in the entire disc, not just the central SB region.
On the sensitivity of weak gravitational lensing to the cosmic expansion function
Authors: Schmidt Christian F , Bartelmann Matthias 
Published: January 2024

ABSTRACT
We analyse the functional derivative of the cosmic-shear power spectrum $C_\ell ^\gamma$ with respect to the cosmic expansion function. Our interest in doing so is two-fold: (i) In view of attempts to detect minor changes of the cosmic expansion function that may be due to a possibly time-dependent dark-energy density, we wish to know how sensitive the weak-lensing power spectrum is to changes in the expansion function. (ii) In view of recent empirical determinations of the cosmic expansion function from distance measurements, independent of specific cosmological models, we wish to find out how uncertainties in the expansion function translate to uncertainties in the cosmic-shear power spectrum. We find the following answers: relative changes of the expansion function are amplified by the cosmic-shear power spectrum by a factor ≈2–6, weakly depending on the scale factor where the change is applied, and the current uncertainty of one example for an empirically determined expansion function translates to a relative uncertainty of the cosmic-shear power spectrum of $\approx 10~{{\ \rm per\ cent}}$.
Hyperonic uncertainties in neutron stars, mergers, and supernovae
Authors: Kochankovski Hristijan , Ramos Angels , Tolos Laura 
Published: January 2024

ABSTRACT
In this work, we delve into the temperature-dependent Equation of State (EoS) of baryonic matter within the framework of the FSU2H* hadronic model, which comprehensively incorporates hyperons and is suitable for relativistic simulations of neutron star mergers and supernovae. To assess the impact of the uncertainties in the hyperonic sector on astrophysical observables, we introduce two additional models, namely FSU2H*L (FSU2H*-Lower) and FSU2H*U(FSU2H*-Upper). These models cover the entire spectrum of variability of hyperonic potentials, as derived from experimental data. Our investigations reveal that these uncertainties extend their influence not only to the relative abundances of various particle species but also to the EoS itself and, consequently, have an impact on the global properties of both cold and hot neutron stars. Notably, their effects become more pronounced at large temperatures, owing to the increased presence of hyperons. These findings have direct implications for the outcomes of relativistic simulations of neutron star mergers and supernovae, emphasizing the need of accounting for hyperonic uncertainties to ensure the accuracy and reliability of such simulations in astrophysical contexts.
New-generation maximum entropy method: a Lagrangian-based algorithm for dynamic reconstruction of interferometric data
Authors: Mus Alejandro , Martí-Vidal Ivan 
Published: January 2024

ABSTRACT
Imaging interferometric data in radio astronomy requires the use of non-linear algorithms that rely on different assumptions on the source structure and may produce non-unique results. This is especially true for very long baseline interferometry (VLBI) observations, where the sampling of Fourier space is very sparse. A basic tenet in standard VLBI imaging techniques is to assume that the observed source structure does not evolve during the observation. However, the recent VLBI results of the supermassive black hole at our Galactic Centre (Sagittarius A*), recently reported by the Event Horizon Telescope Collaboration, require the development of dynamic imaging algorithms, since it exhibits variability at minute time-scales. In this paper, we introduce a new non-convex optimization problem that extends the standard maximum entropy method (MEM), for reconstructing intra-observation dynamical images from interferometric data that evolve in every integration time. We present a rigorous mathematical formalism to solve the problem via the primal–dual approach. We build a Newton strategy and we give its numerical complexity. We also give a strategy to iteratively improve the obtained solution and, finally, we define a novel figure of merit to evaluate the quality of the recovered solution. Then, we test the algorithm, called the new-generation MEM (ngMEM), in different synthetic data sets, with increasing difficulty. Finally, we compare it with another well-established dynamical imaging method. Within this comparison, we have identified a significant improvement of the ngMEM reconstructions. Moreover, the evaluation of the integration time evolution scheme and the time contribution showed that this method can play a crucial role in obtaining good dynamic reconstructions.
Can radial temperature profiles be inferred using NH3 (1, 1) and (2, 2) observations?
Authors: Estalella Robert , Palau Aina , Busquet Gemma 
Published: January 2024

ABSTRACT
A number of works infer radial temperature profiles of envelopes surrounding young stellar objects using several rotational transitions in a pixel-by-pixel or azimuthally averaged basis. However, in many cases the assumption that the rotational temperature is constant along the line of sight is made, while this is not the case when a partially resolved envelope, assumed to be spherically symmetric, is used to obtain values of temperature for different projected radii. This kind of analysis (homogeneous analysis) is intrinsically inconsistent. By using a spherical envelope model to interpret NH3 (1,1) and (2,2) observations, we tested how robust it is to infer radial temperature profiles of an envelope. The temperature and density of the model envelope are power laws of radius, but the density can be flat for an inner central part. The homogeneous analysis was applied to obtain radial temperature profiles, and resulted that for small projected radii, where the optical depth of the lines is high, the homogeneous temperature can be much higher than the actual envelope temperature. In general, for larger projected radii, both the temperature and the temperature power-law index can be underestimated by as much as 40 per cent, and 0.15, respectively. We applied this study to the infrared dark cloud G14.225–0.506 for which the radial temperature profile was previously derived from the dust emission at submillimetre wavelengths and the spectral energy distribution. As expected, the homogeneous analysis underestimated both the temperature and the temperature power-law index.
Modified pustulotic arthro-osteitis diagnostic guidance 2022 – Modified Sonozaki criteria – Secondary publication
Authors: Tsuji Shigeyoshi , Okubo Yukari , Kishimoto Mitsumasa , Taniguchi Yoshinori , Ishihara Yoko , Tamura Masao , Kobayashi Satomi , Watanabe Rei , Takakubo Yuya , Tomita Tetsuya 
Published: January 2024

ABSTRACT
The concept of pustulotic arthro-osteitis (PAO) was first reported by Sonozaki et al. in 1979, with diagnostic criteria (Sonozaki criteria) proposed in 1981. These criteria have served as the gold standard for PAO diagnosis for over 40 years. In recent years, there has been an increasing emphasis on maximizing the quality of life of patients with PAO. This is achieved by striving for clinical remission, structural remission, and functional remission through early diagnosis and appropriate therapeutic intervention from an early stage. This article is an English translation of a summary of the ‘Modified PAO Diagnostic Guidance 2022ʹ, edited by the Japan Ministry of Health, Labour and Welfare’s Research Group on improvement of medical standard and quality of life of patients with spondyloarthritis and related diseases represented by ankylosing spondylitis and the Japan Spondyloarthritis Society. This guidance is intended to be helpful to both Japanese and global communities in rheumatology and spondyloarthritis.
Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling
Authors: Bivehed Erik , Hellman Björn , Wenson Leonie , Stenerlöw Bo , Söderberg Ola , Heldin Johan 
Published: January 2024

Abstract
In the comet assay, tails are formed after single-cell gel electrophoresis if the cells have been exposed to genotoxic agents. These tails include a mixture of both DNA single-strand breaks (SSBs) and double-strand breaks (DSBs). However, these two types of strand breaks cannot be distinguished using comet assay protocols with conventional DNA stains. Since DSBs are more problematic for the cells, it would be useful if the SSBs and DSBs could be differentially identified in the same comet. In order to be able to distinguish between SSBs and DSBs, we designed a protocol for polymerase-assisted DNA damage analysis (PADDA) to be used in combination with the Flash comet protocol, or on fixed cells. By using DNA polymerase I to label SSBs and terminal deoxynucleotidyl transferase to label DSBs with fluorophore-labelled nucleotides. Herein, TK6-cells or HaCat cells were exposed to either hydrogen peroxide (H2O2), ionising radiation (X-rays) or DNA cutting enzymes, and then subjected to a comet protocol followed by PADDA. PADDA offers a wider detection range, unveiling previously undetected DNA strand breaks.
Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing
Authors: Xiong Xiong , Chen Hengye , Zhang Qifan , Liu Yangying , Xu Chenhuan 
Published: January 2024

Abstract
Hemi-methylated cytosine dyads widely occur on mammalian genomic DNA, and can be stably inherited across cell divisions, serving as potential epigenetic marks. Previous identification of hemi-methylation relied on harsh bisulfite treatment, leading to extensive DNA degradation and loss of methylation information. Here we introduce Mhemi-seq, a bisulfite-free strategy, to efficiently resolve methylation status of cytosine dyads into unmethylation, strand-specific hemi-methylation, or full-methylation. Mhemi-seq reproduces methylomes from bisulfite-based sequencing (BS-seq & hpBS-seq), including the asymmetric hemi-methylation enrichment flanking CTCF motifs. By avoiding base conversion, Mhemi-seq resolves allele-specific methylation and associated imprinted gene expression more efficiently than BS-seq. Furthermore, we reveal an inhibitory role of hemi-methylation in gene expression and transcription factor (TF)–DNA binding, and some displays a similar extent of inhibition as full-methylation. Finally, we uncover new hemi-methylation patterns within Alu retrotransposon elements. Collectively, Mhemi-seq can accelerate the identification of DNA hemi-methylation and facilitate its integration into the chromatin environment for future studies.
Survivability of amorphous ice in comets depends on the latent heat of crystallization of impure water ice
Authors: Arakawa Sota , Wakita Shigeru 
Published: January 2024

Abstract
Comets are believed to have amorphous rather than crystalline ice at the epoch of their accretion. Cometary ice contains some impurities that govern the latent heat of ice crystallization, Lcry. However, it is still controversial whether the crystallization process is exothermic or endothermic. In this study, we perform one-dimensional simulations of the thermal evolution of kilometer-sized comets and investigate the effect of the latent heat. We find that the depth at which amorphous ice can survive significantly depends on the latent heat of ice crystallization. Assuming the cometary radius of 2 km, the depth of the amorphous ice mantle is approximately 100 m when the latent heat is positive (i.e., the exothermic case with Lcry = +9 × 104 J kg−1). In contrast, when we consider the impure ice representing the endothermic case with Lcry = −9 × 104 J kg−1, the depth of the amorphous ice mantle could exceed 1 km. Although our numerical results indicate that these depths depend on the size and the accretion age of comets, the depth in a comet with the negative latent heat is a few to several times larger than in the positive case for a given comet size. This work suggests that the spatial distribution of the ice crystallinity in a comet nucleus depends on the latent heat, which can be different from the previous estimates assuming pure water ice.
On the Kinematics of (p, pX) Knockout Reactions in Normal and Inverse Kinematics
Authors: Uesaka Tomohiro 
Published: January 2024

Abstract
An overview of the kinematics of (p, pX) knockout reactions is given. Consistent descriptions of the kinematical quantities for normal and inverse kinematics are provided. Starting from the kinematics of p–X elastic scatterings, which are elementary processes of the (p, pX) knockout reactions, the effects of the separation energy of the knocked-out particle SX, its in-nucleus momentum $\vec{k}_{F}$, and a momentum transfer q are investigated. These three quantities are called “knockout feature quantities” in this article. The main conclusions are as follows: SX dependences of the (p, pX) kinematics are mainly through changes in the p–X center-of-momentum energy $\sqrt{s_{pX}}$ for which no difference exists between normal and inverse kinematics. The effects of longitudinal-to-the-beam component of $\vec{k}_{F}$ cause a significant difference between normal and inverse kinematics through changes in βpX and $\sqrt{s_{pX}}$. On the other hand, the transverse to the beam component of $\vec{k}_{F}$ changes energy sharing between the scattered proton and the knocked-out particle in both normal and inverse kinematics.
Efficacy of baricitinib in patients with moderate-to-severe rheumatoid arthritis up to 6.5 years of treatment: results of a long-term study
Authors: Caporali Roberto , Taylor Peter C , Aletaha Daniel , Sanmartí Raimon , Takeuchi Tsutomu , Mo Daojun , Haladyj Ewa , Bello Natalia , Zaremba-Pechmann Liliana , Fang Ying , Dougados Maxime 
Published: January 2024

Abstract

Objectives
To evaluate the long-term efficacy of once-daily baricitinib 4 mg or 2 mg in patients with active rheumatoid arthritis who had inadequate response (IR) to MTX, csDMARDs or bDMARDs.

Methods
Data from three completed phase III studies—RA-BEAM (MTX-IR), RA-BUILD (csDMARD-IR) and RA-BEACON (bDMARD-IR)—and one completed long-term extension study (RA-BEYOND) were analysed up to 6.5 years [340 weeks (RA-BEAM) and 336 weeks (RA-BUILD and RA-BEACON)]. Low disease activity (LDA) [Simplified Disease Activity Index (SDAI) ≤11], clinical remission (SDAI ≤3.3) and physical function [Health Assessment Questionnaire Disability Index (HAQ-DI) ≤0.5] were the main outcomes assessed. Completer and non-responder imputation (NRI) analyses were conducted on each population.

Results
At week 340 or 336, LDA was achieved in 37%/83% of MTX-IR, 35%/83% of csDMARD-IR and 23%/73% of bDMARD-IR patients treated with baricitinib 4 mg, assessed by NRI/completer analyses, respectively. Remission was achieved in 20%/40% of MTX-IR, 13%/32% of csDMARD-IR and 9%/30% of bDMARD-IR patients treated with baricitinib 4 mg, assessed by NRI/completer analyses, respectively. HAQ-DI ≤0.5 was reached in 31%/51% of MTX-IR, 25%/46% of csDMARD-IR and 24%/38% of bDMARD-IR patients treated with baricitinib 4 mg, assessed by NRI/completer analyses, respectively.

Conclusion
Treatment with baricitinib 4 mg or 2 mg demonstrated efficacy up to 6.5 years with maintained LDA/remission results across SDAI, CDAI and DAS28-hsCRP consistent with previously reported data, and was well tolerated.

Trial registration
United States National Library of Medicine clinical trials database www.clinicaltrials.gov; RA-BEYOND; NCT01885078.