bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics reveals putative copper tolerance genes in a Fusarium oxysporum strain
Authors: Ragasa Lorenz Rhuel P , Cuomo Christina A , del Rosario Ricardo C H , Velarde Michael C 
Published: November 2024

Abstract
Copper has been widely used as a main component in fungicides due to its versatility and effectivity. However, copper contamination from the environment creates selective pressure for the emergence of copper-tolerant pathogenic fungal strains that may proliferate and further cause damage to important agricultural crops. Although some studies focused on specific cellular mechanisms of copper tolerance, comprehensive genomic data are lacking. Here, we examined the genes potentially involved in copper tolerance by conducting a comparative analysis of newly sequenced genomes of 2 Fusarium oxysporum strains, IB-SN1W (copper-tolerant) and Foc-3429 (copper-sensitive), with other Fusarium species. Whole-genome assembly and annotation identified 10 core chromosomes shared between the 2 strains. Protein prediction revealed 16,894 and 15,420 protein-coding genes for IB-SN1W and Foc-3429, respectively. There are 388 unique genes in IB-SN1W not found in Foc-3429, potentially contributing to copper tolerance. Furthermore, the identification of synteny between the 2 strains, including the analysis of orthologous genes within the Fusarium genus, confirmed the presence of accessory chromosomes that are specific to IB-SN1W, accounting for 13% of the genome. These accessory chromosomes consist of genes associated with cation transporter activity, vacuole, copper oxidases, and copper transporters which shed light on the potential mechanism of copper tolerance in this strain. Additionally, a region within an accessory chromosome contains a high density of copper-related genes, raising the possibility that horizontal transfer of these chromosomes may contribute to copper tolerance.
Imaging moveout in acoustic factorized orthorhombic media
Authors: Galtung Kristoffer Tesdal , Stovas Alexey 
Published: November 2024

SUMMARY
In velocity model building using full waveform inversion, diving waves are a source of the low-frequency information needed to update the low- to intermediate wavenumber components in the velocity model. Because full waveform inversion is a highly nonlinear optimization problem attempting to fit the information from the whole wavefield, it is prone to get stuck in local minimums and experience cycle skipping if the initial model does not contain accurate enough information about the low-wavenumbers to constrain the kinematics. Such initial velocity models will typically be estimated using alternative inversion methods that only apply information from parts of the wavefield in the forward modelling and recorded data. In migration velocity analysis, the unfocusing of the image, caused by inconsistency in the kinematics of reflected waves, is measured and is used to update the velocity model by applying differential semblance optimization. The same concept is applicable when using information from diving waves. For diving waves, little is known about the focusing behaviour, also known as imaging moveout, especially in the presence of azimuthal anisotropy, such as orthorhombic anisotropy, which is a good approximation for volcanic plains and sedimentary basins. Obtaining more knowledge about the focusing behaviour of diving waves for this type of anisotropy may help when choosing parameters to invert during inversion that yield a low trade-off between the parameters. Here, we derive approximate series-based equations describing the imaging moveout of diving qP waves in acoustic factorized orthorhombic anisotropic media. Due to the complexity of the analytical solutions for diving wave properties in such models, we find a vertical transverse isotropic type of simplification that manages to conserve the curvature and horizontal velocity of the diving qP wave. The accuracy of the simplified expressions is compared to the exact form and found to yield small errors. To verify the validity of the derived equations for imaging moveout, we compare the generated surfaces with images containing the shape of the unfocusing obtained using reverse time migration, showing a good fit. Of the anisotropic parameters defining the acoustic factorized orthorhombic model, the $\epsilon _1$ and $\epsilon _2$ parameters have the largest influence on the shape of the surface. The anelliptical parameters are shown only to induce minimal changes. Our method to obtain the series expressions describing the imaging moveout in the acoustic factorized orthorhombic model is also applicable to higher symmetry special cases of orthorhombic anisotropy by setting appropriate conditions. Here, this is demonstrated by additionally finding an approximate series expression describing the imaging moveout in acoustic factorized vertical transversely isotropic media, yielding a good match with the image obtained from reverse time migration.
Transcription factors MdEIL1 and MdHY5 integrate ethylene and light signaling to promote chlorophyll degradation in mature apple peels
Authors: Li Li-Xian , Yang San-Kui , Fang Yue , Wu Zhi-Meng , Ma Hua-Ying , Wang Shuo , Li Dan , Feng Shou-Qian 
Published: November 2024

Abstract
Although it is well-established that ethylene and light stimulate the process of chlorophyll degradation in mature apple peels, there is still a need for further exploration of the molecular mechanisms that regulate this process. This study identified MdEIL1 and MdHY5 as promoters of the chlorophyll degradation pathway in apple peels, activated by ethylene and light. Physiological and molecular tests demonstrated that MdEIL1 and MdHY5 are responsible for activating the expression of genes associated with chlorophyll degradation, including MdERF17, MdNYC1, MdPPH and MdPAO. Furthermore, the interaction between MdEIL1 and MdHY5 proteins enhances their regulatory activity on the target gene MdERF17. Moreover, MdEIL1 binds to the promoter of MdHY5, resulting in the upregulation of its expression, which is further enhanced in the presence of the MdEIL1-MdHY5 protein complex. These findings indicate that MdEIL1-MdHY5 module acts as positive regulator mediating ethylene and light signals that promote chlorophyll degradation in apple peels.
Feasibility, safety and quality of complex mitral valve repair in the early phase of a robotic surgery programme
Authors: Kobayashi Kei , Guo Yizhan , Rubino Thomas E , Ramirez Luis E , Waterford Stephen D , Sultan Ibrahim , Morell Victor D , Bonatti Johannes 
Published: November 2024

Abstract

OBJECTIVES
To evaluate the feasibility, safety and quality of robotic-assisted mitral valve repair in complex versus non-complex cases during the early phase of a programme.

METHODS
Since the programme launch in September 2021 until February 2024, 100 patients underwent robotic-assisted mitral valve repair. Of them, 21 patients had complex repairs, while 79 had non-complex repairs. The median age was 58 years for complex cases and 61 years for non-complex cases (P = 0.36).

RESULTS
Bileaflet prolapse was significantly more prevalent in the complex group (52.4% vs 12.7%, P &lt; 0.001). Neochord placement (61.9% vs 13.9%, P &lt; 0.001) and commissuroplasty (28.6% vs 5.1%, P = 0.005) were more frequent in the complex group. The complex group had longer cardiopulmonary bypass times (161 vs 141 min, P &lt; 0.001), aortic cross-clamp times (123 vs 102 min, P &lt; 0.001) and leaflet repair times (43 vs 24 min, P &lt; 0.001). Second pump runs were required more often for complex cases (23.8% vs 3.8%, P = 0.01). All patients left the operating room with residual mitral regurgitation of mild or less. Fewer complex patients were extubated in the operating room (42.9% vs 70.9%, P = 0.02), yet hospital stay was similar (4 vs 4 days, P = 0.56). There were no significant differences in postoperative adverse events. There were no differences in mitral regurgitation of mild or less 4 weeks post-surgery (95.2% vs 98.7%, P = 0.47).

CONCLUSIONS
Complex mitral valve repair can be safely and effectively performed with robotic assistance, even in the early phase of a programme. Despite longer operative and ventilation times in the complex group, hospital stay and postoperative adverse events remained similar.
Transitive Phrasal Verbs in English–Chinese Learners’ Dictionaries: A Syntactic Perspective
Authors: Zhao Dan 
Published: November 2024

Abstract
This article explores the treatment of transitive phrasal verbs (TPVs) in English–Chinese learners’ dictionaries (ECLDs). Despite the syntactic and semantic complexities of TPVs, research on the systematic treatment of TPVs in ECLDs has been limited. By annotating syntactic structures, ECLDs can present the semantic and pragmatic characteristics of TPVs more accurately and assist learners in using appropriate syntactic structures to communicate deeper meanings in language output. Phrasal verbs (PVs) are a category of verb combinations with distinct syntactic structures, functioning as single-word lexical verbs despite being multiword verbs in form. A test administered to intermediate and advanced English learners revealed that Chinese EFL learners made frequent mistakes in using PVs, reflecting the confusion and uncertainty surrounding these structures. This paper presents a comparison of the different classifications of multiword verbs present in ECLDs, arguing that these variations have only further muddied the waters with relation to PVs. Based on an analysis of the unique syntactic features of PVs, it proposes that ECLDs can enhance English learners’ understanding of TPVs through the systematic use of tables, annotations, and examples.
Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous bacterial phylum Patescibacteriota phyl. nov.
Authors: Dutkiewicz Zuzanna , Singleton Caitlin M , Sereika Mantas , Villada Juan C , Mussig Aaron J , Chuvochina Maria , Albertsen Mads , Schulz Frederik , Woyke Tanja , Nielsen Per H , Hugenholtz Philip , Rinke Christian 
Published: November 2024

Abstract
Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities, and dependence on other prokaryotic hosts. Despite the prevalence of the name Ca. Patescibacteria in the scientific literature, it is not officially recognized under the International Code of Nomenclature of Prokaryotes and lacks a nomenclatural type. Here, we rectify this situation by describing two closely related circular metagenome-assembled genomes and by proposing one of them (ABY1TS) to serve as the nomenclatural type for the species Patescibacterium danicumTS gen. nov., sp. nov. according to the rules of the SeqCode. Rank-normalized phylogenomic inference confirmed the stable placement of P. danicumTS in the Ca. Patescibacteria class ABY1. Based on these results, we propose Patescibacterium gen. nov. to serve as the type genus for associated higher taxa, including the phylum Patescibacteriota phyl. nov. We complement our proposal with a genomic characterization, metabolic reconstruction, and biogeographical analysis of Patescibacterium. Our results confirm small genome sizes (&lt;1 Mbp), low GC content (&gt;36%), and the occurrence of long gene coding insertions in the 23S rRNA sequences, along with reduced metabolic potential, inferred symbiotic lifestyle, and a global distribution. In summary, our proposal will provide nomenclatural stability to the fourth-largest phylum in the bacterial domain.
Low-calorie and high-protein diet has diverse impacts on the muscle, bone, and bone marrow adipose tissues
Authors: Romano Beatriz Coimbra , de Araújo Iana Mizumukai , Ribeiro Mariana S P , Parreiras e Silva Luciana T , Dick-de-Paula Ingid , Fukada Sandra Y , Porto Felipe Manoel , Jorgetti Vanda , de Assis Pereira Francisco , Elias Lucila Leico Kagohara , de Paula Francisco José Albuquerque 
Published: November 2024

Abstract
The present study was designed to evaluate the influence of a high-protein diet under conditions of calorie restriction (CR) in the muscle, adipose tissue, bone, and marrow adipose tissue (MAT). It included three groups of 20 female Wistar Hannover rats, fed with the following diets for 8 wk: control group (C) fed with an AIN93M diet, CR group (R) fed with an AIN-93M diet modified to 30% CR, and CR + high-protein group (H) fed with an AIN-93M diet modified to 30% CR with 40% protein. Body composition was determined by DXA. The femur was used for histomorphometry and the estimation of adipocytes. Microcomputed tomography (μCT) was employed to analyze the bone structure. Hematopoietic stem cells from the bone marrow were harvested for osteoclastogenesis. Body composition revealed that the gain in lean mass surpassed the increase in fat mass only in the H group. Bone histomorphometry and μCT showed that a high-protein diet did not mitigate CR-induced bone deterioration. In addition, the number of bone marrow adipocytes and the differentiation of hematopoietic stem cells into osteoclasts were higher in H than in the other groups. These results indicated that under CR, a high-protein diet was beneficial for muscle mass. However, as the μCT scanning detected significant bone deterioration, this combined diet might accentuate the detrimental effect on the skeleton caused by CR. Remarkably, the H group rats exhibited greater MAT expansion and elevated hematopoietic stem cell differentiation into osteoclasts than the CR and control counterparts. These data suggest that a high protein may not be an appropriate strategy to preserve bone health under CR conditions.
Electromagnetic–thermal–mechanical coupling analysis of bent rotor straightening via electromagnetic induction heating
Authors: Cho Hwangki , Park Jun Su , Han You Sung , Xu Guanshui , Sohn Dongwoo 
Published: November 2024

Abstract
Rotors of steam turbines in power plants can be locally deformed by undesired situations, such as rubbing between the rotors and stationary parts. A straightening process is required to correct bending without causing additional damage because a rotor bending displacement of ∼0.15 mm can stop turbine unit operation. In this study, a numerical framework was established to simulate the straightening process using electromagnetic induction heating, which is straightforward and economical among the methods for straightening bent rotors. The straightening process involves complex coupling of electromagnetic, thermal, and mechanical phenomena. For efficiency, sequential coupling was used in the simulations, dividing the multiphysics phenomena into electromagnetic–thermal and thermal–mechanical fields. The temperature distributions resulting from electromagnetic induction heating were calculated through two-way coupling of the electromagnetic–thermal analysis. The thermal deformations of the rotors were obtained by solving the coupled equations for the thermal field obtained from the electromagnetic–thermal analysis and the mechanical field. Using the established numerical framework, the thermal–mechanical behaviors and straightening mechanisms of bent rotors were investigated. Furthermore, the effects of process parameters, including the direction of gravity and heating and cooling conditions, on the straightening performance were determined. Appropriate parameters were identified to achieve the desired straightening performance with final bending displacements of &lt;0.1 mm for bent rotors with initial bending displacements of 0.15–0.3 mm. For a rotor made of A182 F11 Class 2, the best straightening performance was obtained by heating the rotor to a maximum temperature of 650 °C for 20 h under insulation, followed by natural cooling. The simulation results revealed that the straightening performance can be improved when the rotor is rapidly heated to a high maximum temperature and cooled immediately, as long as the temperature conditions do not cause phase transformation or unintended plastic deformation of the bent rotors.
Tumor microtubes: A new potential therapeutic target for high-grade gliomas
Authors: Guo Yunzhu , Li Yangxin , Su Peng , Yan Min , Wang Ming , Li Shenjie , Xiang Wei , Chen Ligang , Dong Wei , Zhou Zhengjun , Zhou Jie 
Published: November 2024

Abstract
High-grade infiltrating gliomas are highly aggressive and fatal brain tumors that present significant challenges for research and treatment due to their complex microenvironment and tissue structure. Recent discovery of tumor microtubes (TMs) has provided new insights into how high-grade gliomas develop in the brain and resist treatment. TMs are unique, ultra-long, and highly functional membrane protrusions that form multicellular networks and play crucial roles in glioma invasiveness, drug resistance, recurrence, and heterogeneity. This review focuses on the different roles that TMs play in glioma cell communication, material transport, and tumor cell behavior. Specifically, non-connecting TMs primarily promote glioma invasiveness, likely related to their role in enhancing cell motility. On the other hand, interconnecting TMs form functional and communication networks by connecting with surrounding astrocytes and neurons, thereby promoting glioma malignancy. We summarize the factors that influence the formation of TMs in gliomas and current strategies targeting TMs. As the understanding of TMs advances, we are closer to uncovering whether they might be the long-sought Achilles’ heel of treatment-resistant gliomas. By delving deeper into TMs research, we hope to develop more effective therapeutic strategies for patients with malignant gliomas.
Machine learning applications to reveal the difference in Robinia pseudoacacia growth and its drivers on China’s Loess Plateau
Authors: Su Bingqian , Xu Wenlong , Su Zhuoxia , Shangguan Zhouping 
Published: November 2024

Abstract
The decline in tree growth has become a global issue. It is critically important to explore the factors affecting tree growth under the background of global climate change to understand tree growth models. A database was established based on Robinia pseudoacacia growth and its driving factors on China’s Loess Plateau. Linear regression and three machine learning methods, including support vector machine, random forest (RF) and gradient boosting machine were used to develop R. pseudoacacia growth models considering forest age, density, climate factors and topographic factors. The root mean square deviation method was adopted to quantitatively assess the relationship between tree growth and soil properties. The average tree height of R. pseudoacacia on the Loess Plateau was 8.8 ± 0.1 m, the average diameter at breast height (DBH) was 10.4 ± 0.1 cm and the average crown diameter was 3.2 ± 0.1 m. The RF model was a fast and effective machine learning method for predicting R. pseudoacacia growth, which showed the best simulation capability and could account for 67% of tree height variability and 55% of DBH variability. Model importance indicated that forest age and stand density were the main factors predicting R. pseudoacacia growth, followed by climate factors. The trade-off between R. pseudoacacia growth and soil properties revealed that soil texture and soil pH were the primary determinants of R. pseudoacacia growth in this region. Our synthesis provides a good framework for sustainable forest management in vulnerable ecological areas under future climate change.
Transgluteal approach for excision of pelvic lipoma causing sciatic pain
Authors: Gecheva Nia , Ilkov Petar , Uzunov Konstantin 
Published: November 2024

Abstract
Sciatic nerve pain, affecting 12%-27% of the general population, often arises from a myriad of etiologies due to the complex anatomy of the sciatic region. The intricate relationship between the sciatic nerve and surrounding structures in the pelvis poses significant challenges in both diagnosis and surgical management. We report two cases of adult female patients presenting with chronic sciatic pain, refractory to conservative treatment. Imaging studies, including magnetic resonance imaging and computed tomography, identified retroperitoneal lipomas exerting compressive effects on the sciatic nerve. Both patients underwent surgical excision of the lipomas via a transgluteal approach with complete resection of the benign tumors in both cases. The successful outcomes in these cases underscore the potential of the transgluteal approach as a novel and effective treatment strategy in the management of complex retroperitoneal tumors causing sciatic pain.
The salty emission of the intermediate-mass AGB star OH 30.1−0.7
Authors: Danilovich T , Richards A M S , Van de Sande M , Gottlieb C A , Millar T J , Karakas A I , Müller H S P , Justtanont K , Plane J M C , Etoka S , Wallström S H J , Decin L , Engels D , Groenewegen M A T , Kerschbaum F , Khouri T , de Koter A , Olofsson H , Paladini C , Stancliffe R J 
Published: November 2024

ABSTRACT
We analyse continuum and molecular emission, observed with Atacama Large Millimetre/submillimetre Array, from the dust-enshrouded intermediate-mass asymptotic giant branch (AGB) star OH 30.1−0.7. We find a secondary peak in the continuum maps, ‘feature B’, separated by 4.6 arcsec from the AGB star, which corresponds to a projected separation of $1.8\times 10^{4}$ au, placing a lower limit on the physical separation. This feature is most likely composed of cold dust and is likely to be ejecta associated with the AGB star, though we cannot rule out that it is a background object. The molecular emission we detect includes lines of CO, SiS, CS, $\mathrm{SO}_2$, NS, NaCl, and KCl. We find that the NS emission is off centre and arranged along an axis perpendicular to the direction of feature B, indicative of a UV-emitting binary companion (e.g. a G-type main sequence star or hotter), perhaps on an eccentric orbit, contributing to its formation. However, the NaCl and KCl emission constrain the nature of that companion to not be hotter than a late B-type main-sequence star. We find relatively warm emission arising from the inner wind and detect several vibrationally excited lines of SiS ($\upsilon =1$), NaCl (up to $\upsilon =4$), and KCl (up to $\upsilon =2$), and emission from low-energy levels in the mid to outer envelope, as traced by $\mathrm{SO}_2$. The CO emission is abruptly truncated around 3.5 arcsec or 14 000 au from the continuum peak, suggesting that mass loss at a high rate may have commenced as little as 2800 yr ago.
Functional and molecular insights into the role of Sae2 C-terminus in the activation of MRX endonuclease
Authors: Colombo Chiara Vittoria , Casari Erika , Gnugnoli Marco , Corallo Flavio , Tisi Renata , Longhese Maria Pia 
Published: November 2024

Abstract
The yeast Sae2 protein, known as CtIP in mammals, once phosphorylated at Ser267, stimulates the endonuclease activity of the Mre11-Rad50-Xrs2 (MRX) complex to cleave DNA ends that possess hairpin structures or protein blocks, such as the Spo11 transesterase or trapped topoisomerases. Stimulation of the Mre11 endonuclease by Sae2 depends on a Rad50–Sae2 interaction, but the mechanism by which this is achieved remains to be elucidated. Through genetic studies, we show that the absence of the last 23 amino acids from the Sae2 C-terminus specifically impairs MRX-dependent DNA cleavage events, while preserving the other Sae2 functions. Employing AlphaFold3 protein structure predictions, we found that the Rad50–Sae2 interface involves not only phosphorylated Ser267 but also the phosphorylated Thr279 residue and the C-terminus of Sae2. This region engages in multiple interactions with residues that are mutated in rad50-s mutants, which are known to be specifically defective in the processing of Spo11-bound DNA ends. These interactions are critical for stabilizing the association between Sae2 and Rad50, thereby ensuring the correct positioning of Mre11 in its active endonucleolytic state.