bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct domain regions of NIN and NLP1 mediate symbiotic and nitrate signalling in Medicago truncatula
Authors: Wang Jiang , Fu Mengdi , Luo Zhenpeng , Liu Jing , Xie Fang 
Published: February 2025

Abstract
Nodule Inception (NIN) and NIN-like protein 1 (NLP1), both belonging to the RWP-RK type transcription factors, play critical roles in plant development. Specifically, NIN is pivotal in facilitating root nodule symbiosis in nitrogen-starved conditions, while NLP1 coordinates nodulation in response to nitrate level. In this study, we conducted domain swapping experiments between NIN and NLP1 in Medicago truncatula to elucidate the functional significance of their respective domains. The findings reveal that the C-terminal regions, including the RWP-RK and PB1 domains of NIN, can substitute for those of NLP1, whereas reciprocal substitution does not yield equivalent outcomes. Moreover, our results emphasize the critical role of PB1-mediated interactions in the activity of NLP1, a feature not essential for NIN. Additionally, the N-terminal segment, conserved in NLPs but containing deletions or mutations in NIN, is essential for the proper functioning of both NIN and NLP1. Collectively, our research indicates evolutionary divergence of NIN from ancestral NLPs, suggesting specific adaptations that have enabled NIN as a central regulator in root nodulation processes.
Mitigation of Losses
Authors: Zeller Bruno 
Published: February 2025

Abstract
This chapter discusses the duty of a party relying on the breach of contract to mitigate the losses. Mitigation is a principle that is an obligation in the common law but not clearly defined in civil law. In arbitration practices, mitigation has become a general principle of international trade. The United Nations Convention on Contracts for the International Sale of Goods (CISG) has incorporated the doctrine of mitigation specifically into Article 77, but the rule is also reflected in Articles 85 and 86, which are concerned with the preservation of the goods after a breach. The idea behind Article 77 is that the plaintiff cannot recover damages that he could have avoided but at the same time is obliged to return the goods in the similar or same state he received them.
Multiband flux and spectral variability study of the flaring activity in BL Lacertae during its 2020 outburst
Authors: Agarwal Aditi , Agrawal V , Zola S , Jana Swarnendu , Bisht M S , Raj A , Kouprianov V , Reichart Daniel E , Caton D B , Dawidson James W 
Published: February 2025

ABSTRACT
In this work, we present the results of recent quasi-simultaneous multiband optical observations (in BVRI) of the blazar BL Lacertae over diverse time-scales. For this study, the source was observed from 2020 September–October using six different telescopes around the world, collecting $\sim$5800 photometric image frames in BVRI. The source displays many episodes of significant intraday variability, and the amplitude increases with the brightness of the target. Moreover, the object also showed significant variability on a short-term basis, with flux variability amplitudes of 85.6 per cent, 78.9 per cent, 93.4 per cent, and 67.6 per cent in B, V, R, and I passbands, respectively. The colour–magnitude analysis of the source displays dominantly bluer-when-brighter behaviour on both intraday and short time-scales, which can be attributed to the energetic processes in the jet. Correlation analysis points towards a strong correlation between optical bands with no firmly detectable time lags. Moreover, we also performed a periodicity search using the Lomb–Scargle and weighted wavelet Z-transform methods and found plausible indications of the presence of quasi-periodicity in the blazar. We also generated spectral energy distributions for nights with quasi-simultaneous observations in all four bands and found the spectral index to range from 2.9–3.2, which can be ascribed to a strong jet contribution. We discuss the results within the framework of prospective source intrinsic and extrinsic scenarios.
Into the Mystic: the MUSE view of the ionized gas in the Mystic Mountains in Carina
Authors: Reiter Megan , McLeod Anna F , Itrich Dominika , Klaassen Pamela D 
Published: February 2025

ABSTRACT
We present optical integral field unit observations of the Mystic Mountains, a dust pillar complex in the centre of the Carina Nebula that is heavily irradiated by the nearby young massive cluster Trumpler 14. With the continuous spatial and spectral coverage of data from the Multi-Unit Spectroscopic Explorer (MUSE), we measure the physical properties in the ionized gas including the electron density and temperature, excitation, and ionization. MUSE also provides an excellent view of the famous jets HH 901, 902, and 1066, revealing them to be high-density, low-ionization outflows despite the harsh environment. HH 901 shows spatially extended [C i] emission tracing the rapid dissociation of the photoevaporating molecular outflow in this highly irradiated source. We compute the photoevaporation rate of the Mystic Mountains and combine it with recent Atacama Large Millimeter Array observations of the cold molecular gas to estimate the remaining lifetime of the Mystic Mountains and the corresponding shielding time for the embedded protostars. The longest remaining lifetimes are for the smallest structures, suggesting that they have been compressed by ionizing feedback. Our data do not suggest that star formation in the Mystic Mountains has been triggered but it does point to the role that ionization-driven compression may play in enhancing the shielding of embedded stars and discs. Planet formation models suggest that the shielding time is a strong determinant of the mass and orbital architecture of planets, making it important to quantify in high-mass regions like Carina that represent the type of environment where most stars form.
MeerKLASS L-band deep-field intensity maps: entering the H i dominated regime
Authors:   MeerKLASS Collaboration, Barberi-Squarotti Matilde , Bernal José L , Bull Philip , Camera Stefano , Carucci Isabella P , Chen Zhaoting , Cunnington Steven , Engelbrecht Brandon N , Fonseca José , Grainge Keith , Irfan Melis O , Li Yichao , Mazumder Aishrila , Paul Sourabh , Pourtsidou Alkistis , Santos Mario G , Spinelli Marta , Wang Jingying , Witzemann Amadeus , Wolz Laura 
Published: February 2025

ABSTRACT
We present results from MeerKAT single-dish H i intensity maps, the final observations to be performed in L-band in the MeerKAT Large Area Synoptic Survey (MeerKLASS) campaign. The observations represent the deepest single-dish H i intensity maps to date, produced from 41 repeated scans over $236\, \deg ^2$, providing 62 h of observational data for each of the 64 dishes before flagging. By introducing an iterative self-calibration process, the estimated thermal noise of the reconstructed maps is limited to ${\sim }\, 1.21$ mK ($1.2\, \times$ the theoretical noise level). This thermal noise will be subdominant relative to the H i fluctuations on large scales ($k\, {\lesssim }\, 0.15\, h\, \text{Mpc}^{-1}$), which demands upgrades to power spectrum analysis techniques, particularly for covariance estimation. In this work, we present the improved MeerKLASS analysis pipeline, validating it on both a suite of mock simulations and a small sample of overlapping spectroscopic galaxies from the Galaxy And Mass Assembly (GAMA) survey. Despite only overlapping with ${\sim }\, 25~{{\ \rm per\ cent}}$ of the MeerKLASS deep field, and a conservative approach to covariance estimation, we still obtain a ${\gt }\, 4\, \sigma$ detection of the cross-power spectrum between the intensity maps and the 2269 galaxies at the narrow redshift range $0.39\, {\lt }\, z\, {\lt }\, 0.46$. We briefly discuss the H i autopower spectrum from these data, the detection of which will be the focus of follow-up work. For the first time with MeerKAT single-dish intensity maps, we also present evidence of H i emission from stacking the maps onto the positions of the GAMA galaxies.
An examination of large-scale galactic effects on molecular cloud properties in NGC 628: the significant impact of tidal effects from neighbouring material on the evolution of molecular clouds
Authors: Zhou J W , Dib Sami 
Published: February 2025

ABSTRACT
The physical factors that influence the development of molecular cloud’s density contrast are connected to those that affect star formation in the galaxy. For NGC 628 (M74), the proportion of high- and low-density contrast clouds initially increases with the distance to the galactic centre ($R_{G}$) and then keeps relatively stable. Spiral arms, bubbles, and magnetic fields are not responsible for the variations in density contrast observed among molecular clouds. The effects of shear and tides calculated from the galactic rotation curve consistently decrease as $R_{G}$ increases, and the shear effect can be neglected. We further studied the tidal effects of the neighbouring material on each cloud using the tidal tensor analysis and the pixel-by-pixel computation, after combining molecular gas, atomic gas, and stellar mass surface density maps. When $R_{\rm G} \lt $ 4 kpc, the tidal strengths derived from the pixel-by-pixel computation decrease as $R_{\rm G}$ increases, and then remains relatively constant when $R_{\rm G} \gt $ 4 kpc. This aligns well with the dependence of the proportion of high- and low-density contrast clouds on $R_{\rm G}$. Therefore, the tidal effects of neighbouring material have a significant impact on the development of molecular cloud’s density contrast. A key factor contributing to the low star formation rate in the galactic centre is the excessive tidal influences from neighbouring material on molecular clouds, which hinder the gravitational collapse within these clouds, resulting in low density contrasts. The tidal effects from neighbouring material may also be a significant contributing factor to the slowing down of a pure free-fall gravitational collapse for gas structures on galaxy-cloud scales revealed in our previous works by velocity gradient measurements.
Neural infalling cloud equations (NICE): increasing the efficacy of subgrid models and scientific equation discovery using neural ODEs and symbolic regression
Authors: Tan Brent 
Published: February 2025

ABSTRACT
Galactic systems are inherently multiphase, and understanding the roles and interactions of the various phases is key towards a more complete picture of galaxy formation and evolution. For instance, these interactions play a pivotal role in the cycling of baryons which fuels star formation. The transport and dynamics of cold clouds in their surrounding hot environment are governed by complex small-scale processes (such as the interplay of turbulence and radiative cooling) that determine how the phases exchange mass, momentum, and energy. Large-scale models thus require subgrid prescriptions in the form of models validated on small-scale simulations, which often take the form of coupled differential equations. In this work, we explore using neural ordinary differential equations (ODEs) which embed neural networks as terms in the model to capture an uncertain physical process. We then apply symbolic regression to potentially discover new insights into the physics of cloud–environment interactions. We test this on both generated mock data and actual simulation data. We also extend the neural ODE to include a secondary neural term. We show that neural ODEs in tandem with symbolic regression can be used to enhance the accuracy and efficiency of subgrid models, and/or discover the underlying equations to improve generality and scientific understanding. We highlight the potential of this scientific machine learning approach as a natural extension to the traditional modelling paradigm, both for the development of semi-analytical models and for physically interpretable equation discovery in complex non-linear systems.
Antinuclear antibodies staining patterns and titres in juvenile idiopathic arthritis
Authors: Sener Seher , Batu Ezgi Deniz , Aliyev Emil , Basaran Ozge , Saribas Zeynep , Bilginer Yelda , Sener Burcin , Ozen Seza 
Published: February 2025

ABSTRACT

Objectives
In our study, we evaluated the antinuclear antibodies (ANA) staining patterns and titres in juvenile idiopathic arthritis (JIA) patients.

Methods
JIA patients were retrospectively assessed. ANA was identified by using indirect immunofluorescence assay on HEp-2 cells, with a positivity threshold set at a titre of ≥1/100.

Results
Eight hundred-five patients were evaluated [oligoarticular JIA (n = 396), enthesitis-related arthritis (n = 195), polyarticular JIA (n = 132), systemic JIA (n = 53), psoriatic arthritis (n = 20), and unclassified JIA (n = 9)]. The most frequently observed ANA nuclear staining patterns were AC-4/5 (fine or large speckled) in 29.7% of patients and AC-1 (homogeneous) in 25.9%. The most common ANA cytoplasmic staining pattern was AC-19 (dense, fine speckled) (17.6%). Most systemic and unclassified JIA patients were ANA negative. The most frequently detected ANA titre in oligoarticular JIA and enthesitis-related arthritis patients was 1/160 (P = .026 and P = .018, respectively), while in psoriatic arthritis patients, it was 1/320 (P &lt; .001). In addition, uveitis and inflammatory bowel disease were most frequently associated with AC-4/5 & AC-19 patterns and an ANA titre of 1/160 (all P &lt; .001).

Conclusions
Our study showed that many JIA subtypes and JIA-related comorbidities were associated with the AC-4/5, AC-1, and AC-19 ANA patterns. However, multicentre studies in larger cohorts are needed to generalize these results.
Breakthrough herpes zoster following recombinant zoster vaccinations in a rheumatoid arthritis patient receiving a Janus kinase inhibitor: A case report and literature review
Authors: Nagata Shunya , Yokogawa Naoto 
Published: February 2025

ABSTRACT
The recombinant zoster vaccine (RZV) is immunologically and clinically effective in immunosuppressed patients. Though rheumatoid arthritis (RA) and the Janus kinase inhibitor (JAKi) increase the risk of herpes zoster (HZ) infection, breakthrough cases in which a HZ infection followed RZV administration are rare. We report herein a 63-year-old female patient with seropositive RA who experienced a HZ infection despite receiving the RZV. She had been receiving tocilizumab, methotrexate, and low-dose prednisolone until tocilizumab was switched to upadacitinib 4 weeks after two RZV administrations, which resulted in 63 weeks’ remission. Her current admission was for a painful rash consisting of blisters and erythema on the right nasal alar and lips corresponding to the right V2 segment of the trigeminal nerve. HZ was diagnosed and treated for 7 days with intravenous acyclovir, which alleviated the symptoms. JAKi can suppress a range of immunogenic mechanisms which underlie the efficacy of the RZV. The present patient was expected to respond favourably to the RZV because JAKi had not been administered prior to the vaccinations; however, the later start of JAKi therapy caused a breakthrough HZ infection. Immunocompromised patients have a higher risk of severe HZ, including the disseminated form, but breakthrough cases are relatively rare. The RZV is recommended as prophylaxis against HZ as well as means of mitigating its severity when it does occur.
The structure of the MutL-CTD:processivity-clamp complex provides insight regarding strand discrimination in non-methyl-directed DNA mismatch repair
Authors: Nirwal Shivlee , Jha Ritika , Narayanan Naveen , Sharma Minakshi , Kulkarni Dhananjaya S , Sharma Dalchand , Babu Amith S , Suthar Dhiraj K , Rao Desirazu N , Nair Deepak T 
Published: February 2025

Abstract
Many prokaryotes, including members of the Neisseria species, lack MutH and cannot employ methyl-directed DNA mismatch repair (MMR). The nick on the daughter strand is created by the endonuclease activity present in the C-terminal domain (CTD) of the MutL homodimer. MutL-CTD is known to interact with the processivity-clamp. The crystal structure of the homodimeric MutL-CTD from Neisseria (NgoL-CTD) in complex with homodimeric processivity-clamp (Nβ-Clamp) shows that each NgoL-CTD monomer binds to a Nβ-Clamp monomer through the conserved motif III (517QHLLIP522). The structure and allied biochemical studies plus in vivo growth assays conducted with wild-type (wt) plus mutant proteins shows that the endonuclease dimer sits transversely across the C-terminal face of the Nβ-Clamp ring. The comparison of the structure with that of the partial prokaryotic replisome suggests that the relative orientation of DNA, Nβ-Clamp, and NgoL-CTD may direct the daughter strand towards one of the active sites in endonuclease homodimer. Nicking assays conducted with wt and mutant NgoL-CTD in the presence and absence of Nβ-Clamp support this inference. Overall, our studies posit that strand discrimination in non-methyl-directed MMR is achieved through a structural strategy involving the β-Clamp which is distinct from the chemical strategy employed in prokaryotes like Escherichia coli.
Crossovers are regulated by a conserved and disordered synaptonemal complex domain
Authors: Neves Ana Rita Rodrigues , Čavka Ivana , Rausch Tobias , Köhler Simone 
Published: February 2025

Abstract
During meiosis, the number and distribution of crossovers (COs) must be precisely regulated through CO assurance and interference to prevent chromosome missegregation and genomic instability in the progeny. Here we show that this regulation of COs depends on a disordered and conserved domain within the synaptonemal complex (SC). This domain is located at the C-terminus of the central element protein SYP-4 in Caenorhabditis elegans. While not necessary for synapsis, the C-terminus of SYP-4 is crucial for both CO assurance and interference. Although the SYP-4 C-terminus contains many potential phosphorylation sites, we found that phosphorylation is not the primary regulator of CO events. Instead, we discovered that nine conserved phenylalanines are required to recruit a pro-CO factor predicted to be an E3 ligase and regulate the physical properties of the SC. We propose that this conserved and disordered domain plays a crucial role in maintaining the SC in a state that allows transmitting signals to regulate CO formation. While the underlying mechanisms remain to be fully understood, our findings align with existing models suggesting that the SC plays a critical role in determining the number and distribution of COs along chromosomes, thereby safeguarding the genome for future generations.
DNA replication dynamics are associated with genome composition in Plasmodium species
Authors: Totañes Francis Isidore Garcia , Chapman Sarah E , Rai Subash Kumar , Jones Mathew J K , Boemo Michael A , Merrick Catherine J 
Published: February 2025

Abstract
Plasmodium species have variable genome compositions: many have an A/T content &gt;80%, while others are similar in composition to human cells. Here, we made a direct comparison of DNA replication dynamics in two Plasmodium species whose genomes differ by ∼20% A/T content. This yielded fundamental insights into how DNA composition may affect replication. The highly A/T-biased genome of Plasmodium falciparum showed unusual replication dynamics that were not observed in the more balanced Plasmodium knowlesi—which had dynamics more like those of human cell lines. Replication forks moved 50% slower in P. falciparum than in P. knowlesi. In P. falciparum, replication forks slowed down over the course of S-phase, whereas in P. knowlesi, fork speed increased as in human cells. Furthermore, in both P. knowlesi and human cells, replication forks were strikingly slowed by sequences of particularly high A/T bias, but in P. falciparum, although replication forks were inherently slow, they were not particularly slow in such biased sequences. Thus, the replisome of P. falciparum may have evolved alongside its extremely biased genome, making it unusually robust to sequence bias. Since several antimalarial drugs act to stall DNA replication, this study may have implications for the effectiveness of, and development of, antimalarial therapies.
Current state and future prospects of Horizontal Gene Transfer detection
Authors: Wijaya Andre Jatmiko , Anžel Aleksandar , Richard Hugues , Hattab Georges 
Published: February 2025

Abstract
Artificial intelligence (AI) has been shown to be beneficial in a wide range of bioinformatics applications. Horizontal Gene Transfer (HGT) is a driving force of evolutionary changes in prokaryotes. It is widely recognized that it contributes to the emergence of antimicrobial resistance (AMR), which poses a particularly serious threat to public health. Many computational approaches have been developed to study and detect HGT. However, the application of AI in this field has not been investigated. In this work, we conducted a review to provide information on the current trend of existing computational approaches for detecting HGT and to decipher the use of AI in this field. Here, we show a growing interest in HGT detection, characterized by a surge in the number of computational approaches, including AI-based approaches, in recent years. We organize existing computational approaches into a hierarchical structure of computational groups based on their computational methods and show how each computational group evolved. We make recommendations and discuss the challenges of HGT detection in general and the adoption of AI in particular. Moreover, we provide future directions for the field of HGT detection.
Single cobalt atoms with unconventional dynamic coordination mechanism for selective ammonia sensor
Authors: Li Yuejiao , Li Yaguang , Shi Yushu , Gao Jianmei , Lu Jianmin , Wang Chao , Chang Junyu , Wang Zhenming , Yang Yangyue , Yang Bing , Feng Liang , Fu Qiang , Bao Xinhe , Wu Zhong-Shuai 
Published: February 2025

ABSTRACT
Developing gas sensors that can simultaneously achieve high sensitivity and selectivity for the detection of a single-type gas remains a significant challenge. Herein we demonstrate cobalt (Co) single atoms with an unconventional dynamically changing coordination structure that could be used as NH3-sensing material with superior sensitivity and selectivity. According to the steric effect of 2-methylimidazole (2MI) molecules and carbonyl groups on graphene, the Co single atom is evolved into a bidentate coordinated structure (Co-2MI-G). In-situ characterization and theoretical simulation reveal that the sensing mechanism of Co-2MI-G is the specific chemical adsorption between unsaturated coordinated Co single atoms and NH3 molecules, causing a reversible switching of coordination number from 2 to 4, a valence state transfer from Co2+ to Co3+ of Co single atoms, and a band-gap width from 0.14 eV to 0.50 eV. Consequently, the Co-2MI-G-based gas sensor presents a sensing response of 67.598% for 1 ppm NH3 and a limit of detection of 2.67 ppb, at least 1.8 times higher than that of state-of-the-art NH3 sensors, together with robust stability and reproducibility. This work provides an innovative perspective on utilizing single atoms for ultra-selective gas sensing by coordination regulation.