bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes
Authors: Le Moan Alan , Stankowski Sean , Rafajlović Marina , Ortega-Martinez Olga , Faria Rui , Butlin Roger K , Johannesson Kerstin 
Published: April 2024

Abstract
Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to the completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the 2 ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for &gt; 1,000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, 2 of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species.
Faecal bacterial communities differ amongst discrete foraging populations of dugongs along the east Australian coast
Authors: Mikkelsen Deirdre , McGowan Alexandra M , Gibson Justine S , Lanyon Janet M , Horsman Sara , Seddon Jennifer M 
Published: April 2024

Abstract
Gut bacterial communities play a vital role in a host's digestion and fermentation of complex carbohydrates, absorption of nutrients, and energy harvest/storage. Dugongs are obligate seagrass grazers with an expanded hindgut and associated microbiome. Here, we characterised and compared the faecal bacterial communities of dugongs from genetically distinct populations along the east coast of Australia, between subtropical Moreton Bay and tropical Cleveland Bay. Amplicon sequencing of fresh dugong faecal samples (n=47) revealed Firmicutes (62%) dominating the faecal bacterial communities across all populations. Several bacterial genera (Bacteroides, Clostridium sensu stricto 1, Blautia and Polaribacter) were detected in samples from all locations, suggesting their importance in seagrass digestion. Principal coordinate analysis showed the three southern-most dugong populations having different faecal bacterial community compositions from northern populations. The relative abundances of the genera Clostridium sensu stricto 13 and dgA-11 gut group were higher, but Bacteroides was lower, in the southern dugong populations, compared to the northern populations, suggesting potential adaptive changes associated with location. This study contributes to our knowledge of the faecal bacterial communities of dugongs inhabiting Australian coastal waters. Future studies of diet selection in relation to seagrass availability throughout the dugong's range will help to advance our understanding of the roles that seagrass species may play in affecting the dugong's faecal bacterial community composition.
Surface loading on a self-gravitating, linear viscoelastic Earth: moving beyond Maxwell
Authors: Lau H C P 
Published: April 2024

SUMMARY
Constitutive laws are a necessary ingredient in calculations of glacial isostatic adjustment (GIA) or other surface loading problems (e.g. loading by ocean tides). An idealized constitutive law governed by the Maxwell viscoelastic model is widely used but increasing attention is being directed towards more intricate constitutive laws that, in particular, include transient rheology. In this context, transient rheology collectively refers to dissipative mechanisms activated in addition to creep modelled by the Maxwell viscoelastic model. Consideration of such viscoelastic models in GIA is in its infancy and to encourage their wider use, we present constitutive laws for several experimentally derived transient rheologies and outline a flexible method in which to incorporate them into geophysical problems, such as the viscoelastic deformation of the Earth induced by surface loading. To further motivate this need, we demonstrate, via the Love number collocation method, how predictions of crustal displacement depart significantly between Earth models that adopt only Maxwell viscoelasticity and those with transient rheology. Throughout this paper, we highlight the differences in terminology and emphases between the rock mechanics, seismology and GIA communities, which have perhaps contributed towards the relative scarcity in integrating this broader and more realistic class of constitutive laws within GIA. We focus on transient rheology since the associated deformation has been demonstrated to operate on timescales that range from hours to decades. With ice mass loss enhanced at similar timescales as a consequence of anthropogenically caused climate change, the ability to model GIA with more accurate constitutive laws is an important tool to investigate such problems.
Basic Remarks on Lagrangian Submanifolds of Hyperkähler Manifolds
Authors: Mboro René 
Published: April 2024

Abstract
This note presents basic restrictions on the topology of Lagrangian surfaces of hyper-Kähler $4$-folds and a remark on the interaction of a Lagrangian subvariety of a hyper-Kähler variety with a Lagrangian fibration of the latter.
The Macroeconomic Effects of EU Regional Structural Funds
Authors: Canova Fabio , Pappa Evi 
Published: April 2024

Abstract
We examine the macroeconomic effects of two EU regional structural funds. The European regional development fund (ERDF) has positive short term average consequences, but gains typically dissipate within 3 years. The European Social Fund has insignificant average short term effects, but the medium term effect is positive and economically important. There are regional heterogeneities in terms of location, level of development, EU tenure, Euro area membership, and national borders. The reaction of regional government expenditure to shocks in the structural funds accounts for the differences. The implications for the EU Recovery and Resilience Facility are discussed.
Responses of belowground bud bank density of geophytes to environmental perturbations: a meta-analysis
Authors: Fang Tao , Ye Duo , Gao Ju-Juan , Luo Fang-Li , Zhu Yao-Jun , Yu Fei-Hai 
Published: April 2024

Abstract
A belowground bud bank is a collection of asexual propagules produced by the underground storage organs of geophytes. Renewal through belowground bud banks is the main reproductive strategy of geophytes. The belowground bud bank density reflects the potential renewal capacity of geophyte communities. However, the effects of different perturbation regimes and habitats on the belowground bud bank density of geophytes are not comprehensively understood. Moreover, whether different types of belowground bud banks respond differently to perturbations is still unclear. For this meta-analysis, relevant papers on the effects of environmental perturbations on the belowground bud bank density of geophytes were systematically collected. The cumulative effect size of different perturbation regimes and habitats on belowground bud banks among different bud types was analyzed. Overall, the effect of environmental perturbations on belowground bud bank density was small, which may result from opposite or fluctuating responses of bud banks to different perturbations. Drought negatively affected bud bank density. Environmental perturbations decreased rhizome bud density but increased tiller bud density. In wetlands, perturbations decreased belowground bud bank density. However, no significant effect was found for other habitat types. In general, belowground bud banks of geophytes are highly resistant and resilient. Changes in belowground bud bank density depend on the type of perturbations, the habitats in which plants are distributed and the type of bud banks.
Effects of warming conditions on plant nitrogen–phosphorus stoichiometry and resorption of three plant species in alpine meadows on the Tibetan Plateau
Authors: Zheng Lang , Cao Xuan , Yang Zhiyong , Wang Hui , Zang Qiqi , Song Wenchen , Shen Miaogen , Xiao Chunwang 
Published: April 2024

Abstract
Global climate change is expected to have a significant impact on ecosystems worldwide, especially for alpine meadows which are considered as one of the most vulnerable components. However, the effects of global warming on the plant nitrogen–phosphorus stoichiometry and resorption in alpine meadows remain unclear. Therefore, to investigate the plant nitrogen–phosphorus stoichiometry and resorption in alpine meadows on the Qinghai-Tibet Plateau, we conducted an artificial warming study using open-top chambers (OTCs) over the 3 years of warming period. We selected three dominant species, four height types of OTCs (0.4, 0.6, 0.8 and 1 m) and four warming methods (year-round warming, winter warming, summer–autumn–winter warming and spring–summer–autumn warming in the experiment) in this experiment. In our study, soil temperature significantly increased with increasing the height of OCTs under the different warming methods. Kobresia pygmaea presented an increase in nitrogen (N) limitation and Kobresia humilis presented an increase in phosphorus (P) limitation with increasing temperature, while Potentilla saundersiana was insensitive to temperature changes in terms of nitrogen and phosphorus limitations. Both nitrogen resorption efficiency:phosphorus resorption efficiency and N:P trends in response to rising temperatures were in the same direction. The differential responses of the chemical stoichiometry of the three species to warming were observed, reflecting that the responses of nitrogen and phosphorus limitations to warming are multifaceted, and the grassland ecosystems may exhibit a certain degree of self-regulatory capability. Our results show that using chemical dosage indicators of a single dominant species to represent the nitrogen and phosphorus limitations of the entire ecosystem is inaccurate, and using N:P to reflect the nutritional limitations might have been somewhat misjudged in the context of global warming.
Improving transformation and regeneration efficiency in medicinal plants: insights from other recalcitrant species
Authors: Bennur Praveen Lakshman , O’Brien Martin , Fernando Shyama C , Doblin Monika S 
Published: April 2024

Abstract
Medicinal plants are integral to traditional medicine systems worldwide, being pivotal for human health. Harvesting plant material from natural environments, however, has led to species scarcity, prompting action to develop cultivation solutions that also aid conservation efforts. Biotechnological tools, specifically plant tissue culture and genetic transformation, offer solutions for sustainable, large-scale production and enhanced yield of valuable biomolecules. While these techniques are instrumental to the development of the medicinal plant industry, the challenge of inherent regeneration recalcitrance in some species to in vitro cultivation hampers these efforts. This review examines the strategies for overcoming recalcitrance in medicinal plants using a holistic approach, emphasizing the meticulous choice of explants (e.g. embryonic/meristematic tissues), plant growth regulators (e.g. synthetic cytokinins), and use of novel regeneration-enabling methods to deliver morphogenic genes (e.g. GRF/GIF chimeras and nanoparticles), which have been shown to contribute to overcoming recalcitrance barriers in agriculture crops. Furthermore, it highlights the benefit of cost-effective genomic technologies that enable precise genome editing and the value of integrating data-driven models to address genotype-specific challenges in medicinal plant research. These advances mark a progressive step towards a future where medicinal plant cultivation is not only more efficient and predictable but also inherently sustainable, ensuring the continued availability and exploitation of these important plants for current and future generations.
Biodegradation of aliphatic and aromatic hydrocarbons by bacteria isolated from Bahregan area
Authors: Shahidi Rizi Masumeh Sadat , Emtiazi Giti , Akhavan Sepahy Abbas 
Published: April 2024

Abstract
Environmental pollution with aromatic and aliphatic hydrocarbons caused by oil and petrochemical industries has very toxic and carcinogenic effects on living organisms and should be removed from the environment.
In this research, after analyzing the oil sludge of the Bahregan area, it was found that most aliphatic paraffin compounds are related to octadecane, most liquid aliphatic compounds are related to hexadecane, and most aromatic compounds are related to naphthalene, phenanthrene, fluoranthene, and anthracene. Then, we investigated the ability of native bacteria from this area, such as Thalassospira, Chromohalobacter, and a bacterial consortium, to biodegrade the dominant aromatic and aliphatic hydrocarbons found in oil sludge. The results of Gas Chromatography–Mass Spectrometry analysis showed that among the tested hydrocarbon sources, Thalassospira can completely remove octadecane and hexadecane, and Chromohalobacter can reduce hexadecane from 15.9 to 9.9%. The bacterial consortium can completely remove octadecane and reduce hexadecane from 15.9 to 5.1%, toluene from 25.6 to 0.6%, and phenanthrene from 12.93 to 6%.
According to the obtained results, the bacterial consortium effectively plays a role in the biodegradation of aromatic and aliphatic hydrocarbons, making it a viable solution for treating hydrocarbon pollutants in various environments.
Pathovars, occurrence, and characterization of plasmid-mediated quinolone resistance in diarrheal Escherichia coli isolated from farmers and farmed chickens in Tunisia and Nigeria
Authors: AL-GALLAS Nazek , Fadel Mohamed-Elamen , Altammar Khadijah A , Awadi Yasmin , Aissa Ridha Ben 
Published: April 2024

Abstract
The poultry industry is a very important agricultural and industrial sector in Tunisia and Nigeria, with little information about occurrence of diarrheagenic Escherichia coli in the farmers and chickens. This study aimed to detect the prevalence of diarrheal E. coli in humans and poultry and to investigate plasmid-mediated quinolone resistance (PMQR) genes in both countries. Seventy-four isolates of E. coli were studied; nine different virulence genes were screened by PCR. Serotyping was performed only for pathotypes as well as the determining of antibiotic resistance profiles against 21 antibiotics. PMQR genes were investigated by PCR. EAEC was the most abundant pathotype (37/74; 50%) in human and chicken isolates, whereas single EHEC and EPEC (1/74, 1.35%) pathotypes were detected in Tunisia and Nigeria, respectively. About 17 (45.95%) quinolones/fluoroquinolones-resistant isolates were detected, from which the following PMQR genes were detected: aac(6′)-Ib-cr (8/17, 47.05%), qepA (6/17, 35.29%), qnrA + qnrB (2/17, 11.76%), and qnrS gene (1/17, 5.88%). Our findings highlight high occurrence of EAEC pathotype in Tunisia and Nigeria, more frequent than EPEC and EHEC. Additionally, all E. coli pathotypes isolated from different sources (humans, poultry) showed resistance to several antibiotics, which are in use as therapeutic choices in Tunisia and Nigeria.
Taxonomy of Candida parapsilosis complex isolated from neonates and the role of Hsp90 inhibitors to enhanced the antifungal activity of micafungin
Authors: da Silva Carolina Maria , de Lima Neto Reginaldo Gonçalves , de Carvalho Ana Maria Rabelo , Macêdo Danielle Patrícia Cerqueira , de Azevedo Melo Analy Salles , Neves Rejane Pereira 
Published: April 2024

Abstract
Species from Candida parapsilosis complex are frequently found in neonatal candidemia. The antifungal agents to treat this infection are limited and the occurrence of low in vitro susceptibility to echinocandins such as micafungin has been observed. In this context, the chaperone Hsp90 could be a target to reduce resistance. Thus, the objective of this research was to identify isolates from the C. parapsilosis complex and verify the action of Hsp90 inhibitors associated with micafungin. The fungal identification was based on genetic sequencing and mass spectrometry. Minimal inhibitory concentrations were determined by broth microdilution method according to Clinical Laboratory and Standards Institute. The evaluation of the interaction between micafungin with Hsp90 inhibitors was realized using the checkerboard methodology. According to the polyphasic taxonomy, C. parapsilosis sensu stricto was the most frequently identified, followed by C. orthopsilosis and C. metapsilosis, and one isolate of Lodderomyces elongisporus was identified by genetic sequencing. The Hsp90 inhibitor geladanamycin associated with micafungin showed a synergic effect in 31.25% of the isolates, a better result was observed with radicicol, which shows synergic effect in 56.25% tested yeasts. The results obtained demonstrate that blocking Hsp90 could be effective to reduce antifungal resistance to echinocandins.
The S-PLUS Fornax Project (S+FP): SExtractor detection and measurement of nearby galaxies in large photometric surveys
Authors: Haack R F , Smith Castelli A V , Mendes de Oliveira C , Almeida-Fernandes F , Faifer F R , Lopes A R , Jaffe Y , Demarco R , Lima-Dias C , Lomelí-Nuñez L , Montaguth G P , Schoenell W , Ribeiro T , Kanaan A 
Published: April 2024

ABSTRACT
All-sky multiband photometric surveys represent a unique opportunity of exploring rich nearby galaxy clusters up to several virial radii, reaching the filament regions where pre-processing is expected to occur. These projects aim to tackle a large number of astrophysical topics, encompassing both the Galactic and extragalactic fields. In that sense, generating large catalogues with homogeneous photometry for both resolved and unresolved sources that might be interesting to achieve specific goals, imposes a compromise when choosing the set of parameters to automatically detect and measure such a plethora of objects. In this work, we present the acquired experience on studying the galaxy content of the Fornax cluster using large catalogues obtained by the Southern Photometric Local Universe Survey (S-PLUS). We realized that some Fornax bright galaxies are missed in the S-PLUS iDR4 catalogues. In addition, Fornax star-forming galaxies are included as multiple detections due to overdeblending. To solve those issues, we performed specific SExtractor runs to identify the proper set of parameters to recover as many Fornax galaxies as possible with confident photometry and avoiding duplications. From that process, we obtained new catalogues containing 12-band improved photometry for ∼ 3 × 106 resolved and unresolved sources in an area of ∼ 208 deg2 in the direction of the Fornax cluster. Together with identifying the main difficulties to carry out the study of nearby groups and clusters of galaxies using S-PLUS catalogues, we also share possible solutions to face issues that seem to be common to other ongoing photometric surveys.
H α reverberation mapping from broad-band photometry of dwarf type 1 Seyfert galaxy NGC 4395
Authors: Gu Huapeng , Wu Xue-Bing , Wen Yuhan , Ma Qinchun , Guo Hengxiao 
Published: April 2024

ABSTRACT
NGC 4395 is a dwarf type 1 Seyfert galaxy with a possible intermediate-mass black hole of several $\rm {10^4}$ solar masses in its centre. As a well-studied object, its broad-line region size has been measured via H $\rm {\alpha }$ time lag in numerous spectroscopic reverberation mapping (SRM) and narrow-band photometric reverberation mapping (PRM) campaigns. Here, we present its H $\rm {\alpha }$ time lag measurement using broad-band photometric data, with the application of our newly developed ICCF-Cut (Interpolation and Cross-Correlation Function - Cut) method as well as the javelin (Just Another Vehicle for Estimating Lags In Nuclei) and χ2 methods. Utilizing the minute-cadence multiband light curves obtained from the $\rm {2}$-m Faulkes Telescope North and $\rm {10.4}$-m Gran Telescopio Canarias telescopes in recent works, we measured its H $\rm {\alpha }$ lag as approximately 40–90 min from broad-band PRM. With the H $\rm {\alpha }$ emission line velocity dispersion, we calculated its central black hole mass as $M_{\rm BH} = (8\pm 4) \times 10^3\ \mathrm{ M}_{\rm \odot }$. These results are comparable with previous results obtained by narrow-band PRM and SRM, providing further support to an intermediate-mass black hole in NGC 4395. In addition, our study also validates the ICCF-Cut as an effective method for broad-band PRM, which holds the potential for widespread application in the era of large multi-epoch, high-cadence photometric surveys.
Characterizing tidal features around galaxies in cosmological simulations
Authors: Khalid A , Brough S , Martin G , Kimmig L C , Lagos C D P , Remus R -S , Martinez-Lombilla C 
Published: April 2024

ABSTRACT
Tidal features provide signatures of recent mergers and offer a unique insight into the assembly history of galaxies. The Vera C. Rubin Observatory’s Legacy Survey of Space and Time (LSST) will enable an unprecedentedly large survey of tidal features around millions of galaxies. To decipher the contributions of mergers to galaxy evolution it will be necessary to compare the observed tidal features with theoretical predictions. Therefore, we use cosmological hydrodynamical simulations NewHorizon, eagle, IllustrisTNG, and Magneticum to produce LSST-like mock images of z ∼ 0 galaxies (z ∼ 0.2 for NewHorizon) with $M_{\scriptstyle \star ,\text{ 30 pkpc}}\ge 10^{9.5}$ M$_{\scriptstyle \odot }$. We perform a visual classification to identify tidal features and classify their morphology. We find broadly good agreement between the simulations regarding their overall tidal feature fractions: $f_{{\small NewHorizon}}=0.40\pm 0.06$, $f_{{\small EAGLE}}=0.37\pm 0.01$, $f_{{\small TNG}}=0.32\pm 0.01$, and $f_{{\small Magneticum}}=0.32\pm 0.01$, and their specific tidal feature fractions. Furthermore, we find excellent agreement regarding the trends of tidal feature fraction with stellar and halo mass. All simulations agree in predicting that the majority of central galaxies of groups and clusters exhibit at least one tidal feature, while the satellite members rarely show such features. This agreement suggests that gravity is the primary driver of the occurrence of visually identifiable tidal features in cosmological simulations, rather than subgrid physics or hydrodynamics. All predictions can be verified directly with LSST observations.