bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record
Authors: Blanco-Melo Daniel , Campbell Matthew A. , Zhu Henan , Dennis Tristan P. W. , Modha Sejal , Lytras Spyros , Hughes Joseph , Gatseva Anna , Gifford Robert J. 
Published: May 2024

Abstract
Background
Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)—virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes.

Results
Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses.

Conclusions
We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.
Engineering non-conventional yeast Rhodotorula toruloides for ergothioneine production
Authors: Liu Ke , Xiang Gedan , Li Lekai , Liu Tao , Ke Jie , Xiong Liangbin , Wei Dongzhi , Wang Fengqing 
Published: May 2024

Abstract
Background
Ergothioneine (EGT) is a distinctive sulfur-containing histidine derivative, which has been recognized as a high-value antioxidant and cytoprotectant, and has a wide range of applications in food, medical, and cosmetic fields. Currently, microbial fermentation is a promising method to produce EGT as its advantages of green environmental protection, mild fermentation condition, and low production cost. However, due to the low-efficiency biosynthetic process in numerous cell factories, it is still a challenge to realize the industrial biopreparation of EGT. The non-conventional yeast Rhodotorula toruloides is considered as a potential candidate for EGT production, thanks to its safety for animals and natural ability to synthesize EGT. Nevertheless, its synthesis efficiency of EGT deserves further improvement.

Results
In this study, out of five target wild-type R. toruloides strains, R. toruloides 2.1389 (RT1389) was found to accumulate the highest EGT production, which could reach 79.0 mg/L at the shake flask level on the 7th day. To achieve iterative genome editing in strain RT1389, CRISPR-assisted Cre recombination (CACR) method was established. Based on it, an EGT-overproducing strain RT1389-2 was constructed by integrating an additional copy of EGT biosynthetic core genes RtEGT1 and RtEGT2 into the genome, the EGT titer of which was 1.5-fold increase over RT1389. As the supply of S-adenosylmethionine was identified as a key factor determining EGT production in strain RT1389, subsequently, a series of gene modifications including S-adenosylmethionine rebalancing were integrated into the strain RT1389-2, and the resulting mutants were rapidly screened according to their EGT production titers with a high-throughput screening method based on ergothionase. As a result, an engineered strain named as RT1389-3 was selected with a production titer of 267.4 mg/L EGT after 168 h in a 50 mL modified fermentation medium.

Conclusions
This study characterized the EGT production capacity of these engineered strains, and demonstrated that CACR and high-throughput screening method allowed rapid engineering of R. toruloides mutants with improved EGT production. Furthermore, this study provided an engineered RT1389-3 strain with remarkable EGT production performance, which had potential industrial application prospects.
Correlates of COVID-19 vaccine uptake among the forcibly displaced: evidence from Libya
Authors: Achore Meshack 
Published: May 2024

Abstract
Background
Vaccine hesitancy and refusal can hinder the control of infectious diseases such as coronavirus disease 2019 (COVID-19). Although forcibly displaced individuals are at high risk of contracting COVID-19, evidence shows that they are less likely to accept the COVID-19 vaccine. Given their predicament, the factors influencing vaccine uptake in the general population might differ vastly from those in displaced populations. Given the limited evidence on vaccine uptake from humanitarian settings, the current study examined the determinants of COVID-19 vaccine uptake among the forcibly displaced in Libya.

Methods
Data were extracted from the World Bank/United Nations High Commissioner for Refugees (UNHCR) microdata repository. Data were collected between April and July 2021 after the rollout of the first dose of the COVID-19 vaccine in Libya. Percentages, means, and standard deviations were used to quantify the distribution of the sample population. Logistic regression models were employed to identify factors influencing COVID-19 vaccine uptake.

Results
Odds ratios (ORs) with p values are used to present the regression analysis results. The study revealed that people unaffected by COVID-19 were less likely (OR = .71, 95%CI = 0.67–0.89) to accept the vaccine. Similarly, individuals with access to free COVID-19 vaccines were more likely to be vaccinated than those without free vaccines (OR = 38, 95%CI = 0.19–0.28). Finally, the results indicated that individuals were six times more likely to be vaccinated at mass vaccination sites ((OR = 6.31, 95%CI = 5.46- 7.94) and 1.92 times more likely to be vaccinated at local health centers (OR = 1.92, 95%CI = 0.1.72–3.11) than they were at hospitals and distant health facilities.

Conclusion
Implementing comprehensive mass vaccination venues, public education initiatives, and awareness campaigns regarding the importance of vaccination can decrease vaccine hesitancy among the forcibly displaced.
Effect of rice hull biochar treatment on net ecosystem carbon budget and greenhouse gas emissions in Chinese cabbage cultivation on infertile soil
Authors: Park Do-Gyun , Jeong Hyeon-Cheol , Jang Eun-Bin , Lee Jong-Mun , Lee Hyoung-Seok , Park Hye-Ran , Lee Sun-Il , Park Do-Gyun , Jang Eun-Bin , Oh Taek-Keun 
Published: May 2024

AbstractBiochar, with its potential to enhance soil fertility, sequester carbon, boost crop yields and reduce greenhouse gas emissions, offers a solution. Addressing the challenges posed by climate change is crucial for food security and agriculture. However, its widespread adoption in agriculture remains in its infancy. This study assessed the effects of rice hull biochar on cabbage production and greenhouse gas emissions, especially nitrous oxide (N2O). A trial, employing a randomized block design in triplicate was conducted from September 13 to November 23, 2022, where "Cheongomabi" cabbage was cultivated with N-P2O5-K2O fertilization at 32$$-$$
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7.8$$-$$
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19.8 kg 10a−1. Additional fertilizer was applied twice post-sowing. The Biochar application rates were control = 0 ton ha−1, B1 = 1 ton ha−1, B3 = 3 ton ha−1, and B5 = 5 ton ha−1. The aboveground biomass of autumn cabbage harvested 82 days after sowing was 2.40–2.70 kg plant−1 in the control and biochar treatments (B1, B3, and B5), with no significant differences (p > 0.05). Cumulative CO2 emissions during cultivation varied across treatment groups, with initial and cumulative emissions of 10.40–17.94 g m−2 day−1 and 3.63–4.43 ton ha−1, respectively. N2O emissions decreased with higher biochar application: reductions of 2.9%, 25.4%, and 41.1% in the B1, B3, and B5 treatments, respectively, compared to the control. The biochar application had no significant impact on yield but curbed soil emissions, Net ecosystem carbon balance during cabbage cultivation ranged from 0.42 to 3.41 ton ha−1 for the B1, B3, and B5 treatments, respectively, compared to control. Overall, the study underscores biochar’s role in mitigating emissions and boosting soil carbon during cabbage cultivation in fall.
Professional learning activity in and of teacher teams: multilevel assessment of how transformational leadership, goal interdependence, and collective efficacy affect information sharing
Authors: Oude Groote Beverborg Arnoud 
Published: May 2024

AbstractEngaging in learning with colleagues is paramount for teachers to enhance students’ learning. To be effective and sustainable, it requires engagement both by individual teachers as well as whole teams. Surprisingly however, research examining learning activity as a characteristic of individuals in teams and a property of teams, as well as their antecedents on both levels, is still scarce. This study examined how perceptions of transformational leadership, as mediated by goal interdependence and collective-efficacy, facilitate teachers’ engagement in information sharing, and whether effects are similar for individuals and teams. Questionnaire data were analyzed using multilevel structural equation modelling. Results showed that individual engagement in information sharing and individuals’ perceptions of goal interdependence were directly impacted by transformational leadership practices. Information sharing of teams, and collective efficacy, were impacted by consistent perceptions of goal interdependence. Teachers shape their learning amongst themselves in teams, with individual support from their leader.
Study on the photodegradation behaviors of thermal-aged silk
Authors: Gong Yuxuan , Zhou Guangzhao , Qiao Chengquan , Pan Yongkang 
Published: May 2024

Abstract
In museums, silk cultural relics are highly sensitive to light. However, lighting is inevitable due to the exhibition needs, despite any light would pose irreversible damage to silk. Although the solution of eliminating UV radiation was widely achieved in museum lighting environment, long-time accumulation of other light sources still would induce photodegradation of silk. This work therefore established the simulated light ageing experiments to assess the degradation behaviors of silk samples with different ageing degrees. The variation of color values and structure transformation of each sample group were determined by the means of scanning electron microscopy (SEM), colorimeter, Fourier Transform infrared spectroscopy (FTIR) and 13C CPMAS NMR. The results indicated that silk samples with different initial ageing degrees presented different discoloration tendency and structural variation in experimental lighting environment, suggesting the higher disordered structure makes the silk more vulnerable to light damage. It is of great significance to understand the long-time impacts of illumination on degraded silk and further provide methodology for predicting the duration of exhibited silk cultural relics.
Laboratory exploration of a novel method to protect silicate relics against salt efflorescence by directional induction of water
Authors: Li Qiang , Gao Ge , Yang Longkang , Huang Xiao , Luo Hongjie 
Published: May 2024

Abstract
Salt efflorescence is one of the critical problems for the preservation of immovable silicate relics. Salt efflorescence mainly comes from continuous cycles of crystallization/dissolution or hydration/dehydration of salts in confined pores in silicate relics. Many protocols have been developed in attempts to alleviate possible salt damages with minor success because of endless water and salt feed from underground. In this study, we propose and design a novel technique for salt damage prevention and protection of immovable relics. Materials with higher water-absorbing ability than matrix are applied to control the water and salt migration direction in simulated sand samples. The distribution of moisture content on the surface of sand is followed by hyperspectral imaging. It appears that water and salt molecules will preferentially transport towards positions containing higher water-absorbing material. Both organic and inorganic high water-absorbing materials show effective in controlling the water and salt migration direction, which provides a new approach for the prevention and protection of salt efflorescence in silicate cultural relics.
Examination of shallow and deep S-wave velocity structures from microtremor array measurements and receiver function analysis at strong-motion stations in Kathmandu basin, Nepal
Authors: Shigefuji Michiko , Takai Nobuo , Bijukchhen Subeg Man , Timsina Chintan , Bhattarai Mukunda 
Published: May 2024

AbstractThe Himalayan collision zone, where the Indian Plate subducts beneath the Eurasian Plate at a low angle, has caused many devastating earthquakes. The Kathmandu basin, situated in this region, is surrounded by mountains on all sides and is filled with distinct soft lake sediments with a highly undulating bedrock topography. The basin has been experiencing rapid urbanization, and the growing population in its major cities has increased the vulnerability to seismic risk during future earthquakes. Several strong-motion stations have recently been deployed in the Kathmandu basin. It is expected that the data captured by this strong-motion station array will further enhance our understanding of site amplification in sedimentary basins. Clear P-to-S converted waves have been observed in the strong-motion records. In this study, we investigate the medium boundary that generated these converted waves. First, we estimate the shallow velocity structures, which correspond to the topographic slopes or surface geology, beneath the strong-motion stations. We then apply a receiver function analysis to the strong-motion records. The receiver function indicates that the interface between the soft sediment and seismic bedrock serves as a boundary that generates converted waves. The obtained results can be used for tuning three-dimensional velocity structures.
Graphical Abstract
Laparoscopic transabdominal approach for resection of presacral epidermoid cyst in an obese man: a case report
Authors: Yoshida Naohiro , Nakamura Koki , Shigaki Takahiro , Fujiyoshi Kenji , Koushi Kenichi , Yoshida Takefumi , Isobe Taro , Mori Naoki , Sudo Tomoya , Sakai Hisamune , Hisaka Toru , Ishibashi Nobuya , Akiba Jun , Fujita Fumihiko 
Published: May 2024

Abstract
Background
Complete resection of presacral epidermoid cysts is recommended due to the potential for infection or malignancy. Transsacral and transabdominal approaches have been used to treat presacral tumors. However, there are no standard surgical approaches to resection. We present the case of a presacral epidermoid cyst in an obese male patient who underwent laparoscopic transabdominal resection.

Case presentation
A 44-year-old man was referred to our hospital for treatment of a cystic tumor on the pelvic floor. Contrast-enhanced computed tomography revealed a 45 × 40-mm tumor on the left ventral side of the rectum, right side of the ischial spine, dorsal side of the seminal vesicles, and in front of the 5th sacrum. Enhanced magnetic resonance imaging revealed a multilocular cystic tumor with high and low signal intensities on T2-weighted images. The tumor was diagnosed as an epidermoid cyst. We considered the transsacral or laparoscopic approach and decided to perform a laparoscopic-assisted transabdominal resection since the tumor was in front of away from the sacrum, and a transsacral approach would result in a larger scar due to poor visibility from the thickness of the buttocks. The entire tumor was safely resected under laparoscopic guidance, because the laparoscopic transabdominal approach can provide a good and magnified field of view even in a narrow pelvic cavity with small skin incisions, allowing safe resection of the pelvic organs, vessels, and nerves while observing the tumor contour.

Conclusions
The laparoscopic transabdominal approach is an effective method for treating presacral tumors in obese patients.
Dislocation-precipitate interactions in crystals: from the BKS model to collective dislocation dynamics
Authors: Laurson Lasse , Alava Mikko J. 
Published: May 2024

AbstractThe increase in the yield stress due to the presence of obstacles to dislocation motion such as precipitates is a multiscale phenomenon. The details on the nanoscale when an individual dislocation runs into a precipitate play an important role in determining plasticity on a macroscopic scale. The classical analysis of this phenomenon is due to Bacon, Kocks and Scattergood (BKS) from early 1970’s and has been followed by a large body of work both developing the theory and applying it to real experiments and their understanding. Beyond the microscopic details the next level of complexity is met in the micrometer scale when the physics of the yielding and the yield stress depend on two mechanisms: the dislocation-precipitate interaction, and the collective dynamics of the whole ensemble of dislocations in the volume. In this review we discuss the BKS relation and collective dislocation dynamics in precipitation-hardened crystals in the light of recent research, including large-scale discrete dislocation dynamics simulations, statistical physics ideas, and machine learning developments.
Effect of dietary seaweed Caulerpa racemosa on growth, biochemical, non-specific immunity, and disease resistance to Pseudomonas aeruginosa in Cirrhinus mrigala
Authors: Ragunath Cholaraj , Ramasubramanian Venkatachalam 
Published: May 2024

Abstract
Background
The green seaweed Caulerpa racemosa possesses highly potential elements in animal forages and human use since ancient times. The current study was designed to investigate the antioxidants, phytochemical properties of C. racemosa, as well as their effects on growth parameters, biochemical components, non-specific immunological parameters, and disease resistance to P. aeruginosa in Cirrhinus mrigala. The experimental group, divided into five groups as T1–T5. T2–T5, was given C. racemosa extract at concentrations of 0.5%, 2.5%, 4.5%, & 6.5% supplemented with basal diets. T1's group food is devoid of extract and acts as a control, and the trial lasted forty-five days.

Results
C. racemosa exhibited dose-dependent antioxidant activity. The highest levels of DPPH (61.21%), ABTS (70.55%), and H2O2 (66.55%) scavenging activities were obtained at 100 µg/ml 100 μg/ml. GC–MS analysis revealed phytoconstituents in the crude extract, such as palmitolinoleic acid, butanoic acid, arachidonate, linoleic acid, vaccenic acid, octadecenoic acid, trans-phytol, and eicosanoids. Among these different concentrations, 4.5% C. racemosa supplemented diet produced a significantly higher growth metrics of C. mrigala’s (WG, SGR, FCR), biochemical constituents, when compared to other concentrations. In a post-challenge trial, 4.5% C. racemosa extract meals increased C. mrigala SOD, CAT, non-specific immune response (lysozyme, NBT, phagocytic activity), and haematological (RBC, WBC, HCT & Hb) parameters when compared to other experiments.

Conclusions
The findings revealed that 4.5% of C. racemosa may be supplied in the diet of C. mrigala to regulate better survival growth performance and haematological parameters.
Impacts of inter-satellite links on the ECOM model performance for BDS-3 MEO satellites
Authors: Yang Chao , Guo Jing , Xu Xiaolong , Wang Longyu , Zhao Qile 
Published: May 2024

AbstractInter-satellite link (ISL) plays an essential role in current and future Global Navigation Satellite System (GNSS). In this study, we investigate the impact of ISL observations on precise orbit determination for BeiDou-3 Navigation Satellite System (BDS-3) Medium Earth Orbit (MEO) satellites based on different Extended CODE Orbit Models (ECOM). Thanks to the better observation geometry of the Ka-band ISL data compared to the L-band data for BDS-3 MEO satellites, the ISL solution substantially reduces Orbit Boundary Discontinuity (OBD) errors, except for C30, which suffers from unstable Ka-band hardware delay. From the external quality analysis, ISL significantly enhances the reliability of the orbit of MEO satellites manufactured by the China Academy of Space Technology (CAST). The standard deviation (STD) of the satellite laser ranging (SLR) residuals is approximately 2.5 cm, and the root mean square (RMS) is reduced by 10–23% compared to L-band solutions. Besides, the Sun-elongation angle dependent systematic error in SLR residuals nearly vanishes based on the reduced 5-parameter ECOM (ECOM1) or extended 7-parameter ECOM (ECOM2) with ISL data. This is because the ISL reduces the correlation between state parameters and solar radiation pressure (SRP) parameters as well as those among SRP parameters, leading to a more accurate estimation of both orbit and SRP perturbations, particularly those alongBdirection. This confirms that the deficiency of the SRP models for BDS-3 CAST satellites can be compensated by using better observation geometry from ISL data. On the other hand, for the satellite manufactured by Shanghai Engineering Center for Microsatellites (SECM), the ISL allows for a more accurate estimation of theBc1parameter in the ECOM1 model. This only reduces linear systematic error, possibly because the impact generated by the satellite bus cannot be entirely absorbed by theB-direction parameters.