bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preliminary study of BF/C2 on immune mechanism of grass carp against GCRV infection
Authors: Wei Yuling , Xiao Yu , Liu Qiaolin , Du Zongjun , Xiao Tiaoyi 
Published: July 2024

AbstractBF/C2 is a crucial molecule in the coagulation complement cascade pathway and plays a significant role in the immune response of grass carp through the classical, alternative, and lectin pathways during GCRV infection. In vivo experiments demonstrated that the mRNA expression levels of BF/C2 (A, B) in grass carp positively correlated with GCRV viral replication at various stages of infection. Excessive inflammation leading to death coincided with peak levels of BF/C2 (A, B) mRNA expression and GCRV viral replication. Correspondingly, BF/C2 (A, B) recombinant protein, CIK cells and GCRV co-incubation experiments yielded similar findings. Therefore, 3 h (incubation period) and 9 h (death period) were selected as critical points for this study. Transcriptome sequencing analysis revealed significant differences in the expression of BF/C2A and BF/C2B during different stages of CIK infection with GCRV and compared to the blank control group (PBS). Specifically, the BF/C2A_3 and BF/C2A_9 groups exhibited 2729 and 2228 differentially expressed genes (DEGs), respectively, with 1436 upregulated and 1293 downregulated in the former, and 1324 upregulated and 904 downregulated in the latter. The BF/C2B_3 and BF/C2B_9 groups showed 2303 and 1547 DEGs, respectively, with 1368 upregulated and 935 downregulated in the former, and 818 upregulated and 729 downregulated in the latter. KEGG functional enrichment analysis of these DEGs identified shared pathways between BF/C2A and PBS groups at 3 and 9 h, including the C-type lectin receptor signaling pathway, protein processing in the endoplasmic reticulum, Toll-like receptor signaling pathway, Salmonella infection, apoptosis, tight junction, and adipocytokine signaling pathway. Additionally, the BF/C2B groups at 3 and 9 h shared pathways related to protein processing in the endoplasmic reticulum, glycolysis/gluconeogenesis, and biosynthesis of amino acids. The mRNA levels of these DEGs were validated in cellular models, confirming consistency with the sequencing results. In addition, the mRNA expression levels of these candidate genes (mapk1, il1b, rela, nfkbiab, akt3a, hyou1, hsp90b1, dnajc3a et al.) in the head kidney, kidney, liver and spleen of grass carp immune tissue were significantly different from those of the control group by BF/C2 (A, B) protein injection in vivo. These candidate genes play an important role in the response of BF/C2 (A, B) to GCRV infection and it also further confirmed that BF/C2 (A, B) of grass carp plays an important role in coping with GCRV infection.
Comparative transcriptomic profiles of Paulownia catalpifolia under different degrees of chilling stress during the seedling stage
Authors: Liu Baojun , Su Jiang , Fu Chuanming , Xian Kanghua , He Jinxiang , Huang Ningzhen 
Published: July 2024

Abstract
Background
Paulownia, an ecologically and economically valuable plant species native to China, is notable for its excellent timber quality and strong adaptability. Among them, Paulownia catalpifolia displays the ability to survive in cold climate, a trait associated with northern China. Yet, the molecular information for its cold-tolerance has not been explored. This study was to investigate the changes in physiological indices and transcript levels of P. catalpifolia following cold exposure, which could provide evidence for revealing whether there were differences in the genetic basis of inducing physiological perturbations between moderate low temperature (MLT) and extreme low temperature (ELT).

Results
The detection of physiological indices under diverse degrees of chilling stress showed similar patterns of alteration. Enhanced accumulation of osmoregulatory substances, such as soluble sugar and soluble protein, were more conducive under ELT compared to MLT in P. catalpifolia. Moreover, we observed leaf wilting symptoms distinctly after exposure to ELT for 48 h, while this effect was not obvious after MLT exposure for 48 h. Comparative transcriptomic analysis between MLT and ELT demonstrated 13,688 differentially expressed genes (DEGs), most of them appeared after 12 h and 48 h of treatment. GO and KEGG analyses elucidated prominent enrichment in aromatic-L-amino-acid decarboxylase activity term and carbohydrate metabolism pathways. Therefore, it was speculated that the DEGs involved in the above processes might be related to the difference in the contents of soluble protein and soluble sugar between MLT and ELT. Time series clustering analyses further highlighted several key genes engaged in the ‘Glycosyltransferases’, ‘Galactose metabolism’ and ‘Starch and sucrose metabolism’ pathways as well as the ‘tyrosine decarboxylase activity’ term. For instance, cellulose synthase-like A (CLSA2/9), raffinose synthase (RafS2), β-amylase (BAM1) and tyrosine/DOPA decarboxylase (TYDC1/2/5) genes, diverging in their expression trends between MLT and ELT, might significantly affect the soluble sugar and soluble protein abundance within P. catalpifolia.

Conclusion
Between MLT and ELT treatments, partial overlaps in response pathways of P. catalpifolia were identified, while several genes regulating the accumulation of osmotic adjustment substances had disparate expression patterns. These findings could provide a novel physiological and molecular perspective for P. catalpifolia to adapt to complex low temperature habitats.
Genome sequencing of Elaeocarpus spp. stem blight pathogen Pseudocryphonectria elaeocarpicola reveals potential adaptations to colonize woody bark
Authors: Yang Yuchen , Xiong Dianguang , Zhao Danyang , Huang Huayi , Tian Chengming 
Published: July 2024

Abstract
Background
Elaeocarpus spp. stem blight, caused by Pseudocryphonectria elaeocarpicola, is a destructive disease, which will significantly reduce the productivity and longevity of Elaeocarpus spp. plants, especially in the Guangdong Province of China. However, few information is available for P. elaeocarpicola. To unravel the potential adaptation mechanism of stem adaptation, the whole genome of P. elaeocarpicola was sequenced by using the DNBSEQ and PacBio platforms.

Results
P. elaeocarpicola harbors 44.49 Mb genome with 10,894 predicted coding genes. Genome analysis revealed that the P. elaeocarpicola genome encodes a plethora of pathogenicity-related genes. Analysis of carbohydrate-active enzymes (CAZymes) revealed a rich variety of enzymes participated in plant cell wall degradation, which could effectively degrade cellulose, hemicellulose and xyloglucans in the plant cell wall and promote the invasion of the host plant. There are 213 CAZyme families found in P. elaeocarpicola, among which glycoside hydrolase (GH) family has the largest number, far exceeding other tested fungi by 53%. Besides, P. elaeocarpicola has twice as many genes encoding chitin and cellulose degradation as Cryphonectria parasitica, which belong to the same family. The predicted typical secreted proteins of P. elaeocarpicola are numerous and functional, including many known virulence effector factors, indicating that P. elaeocarpicola has great potential to secrete virulence effectors to promote pathogenicity on host plants. AntiSMASH revealed that the genome encoded 61 secondary metabolic gene clusters including 86 secondary metabolic core genes which was much higher than C. parasitica (49). Among them, two gene cluster of P. elaeocarpicola, cluster12 and cluster52 showed 100% similarity with the mycotoxins synthesis clusters from Aspergillus steynii and Alternaria alternata, respectively. In addition, we annotated cytochrome P450 related enzymes, transporters, and transcription factors in P. elaeocarpicola, which are important virulence determinants of pathogenic fungi.

Conclusions
Taken together, our study represents the first genome assembly for P. elaeocarpicola and reveals the key virulence factors in the pathogenic process of P. elaeocarpicola, which will promote our understanding of its pathogenic mechanism. The acquired knowledge lays a foundation for further exploration of molecular interactions with the host and provide target for management strategies in future research.
Genomic analysis reveals the association of KIT and MITF variants with the white spotting in swamp buffaloes
Authors: Dai Dongmei , Sari Eka Meutia , Si Jingfang , Ashari Hidayat , Dagong Muhammad Ihsan Andi , Pauciullo Alfredo , Lenstra Johannes A. , Han Jianlin , Zhang Yi 
Published: July 2024

Abstract
Background
Swamp-type buffaloes with varying degrees of white spotting are found exclusively in Tana Toraja, South Sulawesi, Indonesia, where spotted buffalo bulls are highly valued in accordance with the Torajan customs. The white spotting depigmentation is caused by the absence of melanocytes. However, the genetic variants that cause this phenotype have not been fully characterized. The objective of this study was to identify the genomic regions and variants responsible for this unique coat-color pattern.

Results
Genome-wide association study (GWAS) and selection signature analysis identified MITF as a key gene based on the whole-genome sequencing data of 28 solid and 39 spotted buffaloes, while KIT was also found to be involved in the development of this phenotype by a candidate gene approach. Alternative candidate mutations included, in addition to the previously reported nonsense mutation c.649 C > T (p.Arg217*) and splice donor mutation c.1179 + 2T > A in MITF, a nonsense mutation c.2028T > A (p.Tyr676*) in KIT. All these three mutations were located in the genomic regions that were highly conserved exclusively in Indonesian swamp buffaloes and they accounted largely (95%) for the manifestation of white spotting. Last but not the least, ADAMTS20 and TWIST2 may also contribute to the diversification of this coat-color pattern.

Conclusions
The alternative mutations identified in this study affect, at least partially and independently, the development of melanocytes. The presence and persistence of such mutations may be explained by significant financial and social value of spotted buffaloes used in historical Rambu Solo ceremony in Tana Toraja, Indonesia. Several de novo spontaneous mutations have therefore been favored by traditional breeding for the spotted buffaloes.
Evaluating genomic inbreeding of two Chinese yak (Bos grunniens) populations
Authors: Chen Shi-Yi , Luo Zhihao , Jia Xianbo , Zhou Junkun , Lai Song-Jia 
Published: July 2024

Abstract
Background
Yaks are a vital livestock in the Qinghai-Tibetan Plateau area for providing food products, maintaining sustainable ecosystems, and promoting cultural heritage. Because of uncontrolled mating, it is impossible to estimate inbreeding level of yak populations using the pedigree-based approaches. With the aims to accurately evaluate inbreeding level of two Chinese yak populations (Maiwa and Jiulong), we obtained genome-wide single nucleotide polymorphisms (SNPs) by DNA sequencing and calculated five SNP-by-SNP estimators ($$\:{F}_{HOM}$$, $$\:{F}_{L\&H}$$, $$\:{F}_{VR1}$$, $$\:{F}_{VR2}$$, and $$\:{F}_{YAN}$$), as well as two segment-based estimators of runs of homozygosity (ROH, $$\:{F}_{ROH}$$) and homozygous-by-descent (HBD, $$\:{F}_{HBD}$$). Functional implications were analyzed for the positional candidate genes located within the related genomic regions.

Results
A total of 151,675 and 190,955 high-quality SNPs were obtained from 71 Maiwa and 30 Jiulong yaks, respectively. Jiulong had greater genetic diversity than Maiwa in terms of allele frequency and nucleotide diversity. The two populations could be genetically distinguished by principal component analysis, with the mean differentiation index (Fst) of 0.0054. The greater genomic inbreeding levels of Maiwa yaks were consistently supported by all five SNP-by-SNP estimators. Based on simple proportion of homozygous SNPs ($$\:{F}_{HOM}$$), a lower inbreeding level was indicated by three successfully sequenced old leather samples that may represent historical Maiwa yaks about five generations ago. There were 3304 ROH detected among all samples, with mean and median length of 1.97 Mb and 1.0 Mb, respectively. A total of 94 HBD segments were found among all samples, whereas 92 of them belonged to the shortest class with the mean length of 10.9 Kb. Based on the estimates of $$\:{F}_{ROH}$$ and $$\:{F}_{HBD}$$, however, there was no difference in inbreeding level between Maiwa and Jiulong yaks. Within the genomic regions with the significant Fst or enriched by ROH, we found several candidate genes and pathways that have been reported to be related to diverse production traits in farm animals.

Conclusions
We successfully evaluated the genomic inbreeding level of two Chinese yak populations. Although different estimators resulted in inconsistent conclusions on their genomic inbreeding levels, our results may be helpful to implement the genetic conservation and utilization programs for the two yak populations.
Mining key genes associated with phosphorus deficiency through genome-wide identification and characterization of cucumber SPX family genes
Authors: Li Jialin , Hu Linyue , Luan Qianqian , Zhang Jingdan , Feng Xueru , Li Hongmei , Wang Zenghui , He Wenxing 
Published: July 2024

Abstract
Background
Proteins harboring the SPX domain are crucial for the regulation of phosphate (Pi) homeostasis in plants. This study aimed to identify and analyze the entire SPX gene family within the cucumber genome.

Results
The cucumber genome encompassed 16 SPX domain-containing genes, which were distributed across six chromosomes and categorized into four distinct subfamilies: SPX, SPX-MFS, SPX-EXS and SPX-RING, based on their structure characteristics. Additionally, gene duplications and synteny analysis were conducted for CsSPXs, revealing that their promoter regions were enriched with a variety of hormone-responsive, biotic/abiotic stress and typical P1BS-related elements. Tissue expression profiling of CsSPX genes revealed that certain members were specifically expressed in particular organs, suggesting essential roles in cucumber growth and development. Under low Pi stress, CsSPX1 and CsSPX2 exhibited a particularly strong response to Pi starvation. It was observed that the cucumber cultivar Xintaimici displayed greater tolerance to low Pi compared to black-spined cucumber under low Pi stress conditions. Protein interaction networks for the 16 CsSPX proteins were predicted, and yeast two-hybrid assay revealed that CsPHR1 interacted with CsSPX2, CsSPX3, CsSPX4 and CsSPX5, implying their involvement in the Pi signaling pathway in conjunction with CsPHR1.

Conclusion
This research lays the foundation for further exploration of the function of the CsSPX genes in response to low Pi stress and for elucidating the underlying mechanism.
Designing a model of emergency medical services preparedness in response to mass casualty incidents: a mixed-method study
Authors: Saadatmand Vahid , Ahmadi Marzaleh Milad , Shokrpour Nasrin , Abbasi Hamid Reza , Peyravi Mahmoud Reza 
Published: July 2024

Abstract
Background
Emergency medical services preparedness in mass casualty incidents is one of the most important concerns in emergency systems. A mass casualty incident is a sudden event with several injured individuals that overwhelms the local health care system. This study aimed to identify and validate the components of emergency medical services readiness in mass casualty incidents which ultimately led to designing a conceptual model.

Methods
This research was an explanatory mixed-method study conducted in five consecutive stages in Iran between November 2021 and September 2023. First, a systematic review was carried out to extract the components of emergency medical services preparedness in mass casualty incidents based on the PRISMA guideline. Second, a qualitative study was designed to explore the preparedness components through in-depth semi-structured interviews and analyzed using the content analysis approach. Third, the integration of the components extracted from the two stages of the systematic review and qualitative study was done by an expert panel. Fourth, the obtained components were validated using the Delphi technique. Two rounds were done in the Delphi phase. Finally, the conceptual model of emergency medical services preparedness in mass casualty incidents was designed by a panel of experts.

Results
10 articles were included in the systematic review stage and sixteen main components were extracted and classified into four categories. In the second stage, thirteen components were extracted from the qualitative study and classified into five categories. Then, the components of the previous two phases were integrated into the panel of experts and 23 components were identified. After validation with the Delphi technique, 22 components were extracted. Lastly, the final components were examined by the panel of experts, and the conceptual schematic of the model was drawn.

Conclusions
It is necessary to have an integrated framework and model of emergency medical service readiness in the planning and management of mass casualty incidents. The components and the final model of this research were obtained after the systematic scientific steps, which can be used as a scheme to improve emergency medical service preparedness in response to mass casualty incidents.
Leveraging community health workers for COVID-19 response in Democratic Republic of Congo, Nigeria, Senegal, and Uganda: roles, barriers, and facilitators
Authors: Namuhani Noel , Babirye Ziyada , Monje Fred , Salawu Mobolaji M. , Bosonkie Marc , Bello Segun , Kabwama Steven N. , Egbende Landry , Bamgboye Eniola A. , Tusubira Andrew , Kashiya Yves , Kizito Susan , Afolabi Rotimi Felix , Adebowale Ayo S. , Dairo Magbagbeola David , Diallo Issakha , Leye Mamadou M. M. , Ndiaye Youssou , Fall Mane , Bassoum Oumar , Seck Ibrahima , Fawole Olufunmilayo I. , Mapatano Mala Ali , Ndejjo Rawlance , Wanyenze Rhoda K. , Kiwanuka Suzanne N. 
Published: July 2024

Abstract
Background
The Corona Virus Disease 2019 (COVID-19) pandemic overwhelmed health systems and disrupted the delivery of health services globally. Community Health Workers (CHWs) play a critical role in linking communities to health systems, supporting the prevention and control of diseases in many low- and middle-income countries. However, their roles, barriers, and facilitators in the response and control of the COVID-19 pandemic have not been well documented. We described the roles of CHWs in the COVID-19 response, including the barriers and facilitators.

Methods
A cross-sectional study design was used to assess the COVID-19 response in the Democratic Republic of Congo (DRC), Nigeria, Senegal, and Uganda. This involved 110 key informant interviews with policymakers, health facility managers, district health managers, and CHWs to understand the role of CHWs in the COVID 19 response, selected purposively. The total sample size was based on information saturation in each of the countries. A document review on the COVID-19 response was also conducted. We searched Google, Google Scholar, and PubMed for published and grey literature. Data from the selected documents were extracted into a Google master matrix in MS Excel and analyzed thematically.

Results
In COVID-19 Control, CHWs supported community-based surveillance, contact tracing, risk communication, community mobilization, and home-based care. To support the continuity of other non-COVID-19 services, the CHWs conducted community mobilization, sensitizations, outreaches, referrals, and patient follow-ups. CHWs were challenged by movement restrictions, especially in the initial stages of the lockdown, inadequate PPE, increased workload, low allowances, and motivation. CHW were facilitated by trainings, the development of guidelines, development partners’ support/funding, and the provision of personal protective equipment (PPE) and tools.

Conclusion
CHWs supported both the COVID-19 control and continuity of non-COVID-19 health care during the COVID-19 pandemic. CHWs are a critical resource that must be adequately supported to build resilient health systems.
Clinical and physiological risk factors contributing to the restricted mobility in older adults: a longitudinal analysis
Authors: Jiang Xin , Tan Huiying , Ren Huixia , Zhou Huiting , Chen Jingmei , Wang Zhen , Guo Yi , Zhou Junhong 
Published: July 2024

Abstract
Background
Mobility limitations (e.g., using wheelchair) have been closely linked to diminished functional independence and quality of life in older adults. The regulation of mobility is pertaining to multiple neurophysiologic and sociodemographic factors. We here aimed to characterize the relationships of these factors to the risk of restricted mobility in older adults.

Methods
In this longitudinal study, 668 older adults with intact mobility at baseline completed the baseline assessments of clinical characteristics, cognitive function, sleep quality, activities of daily living (ADL), walking performance, beat-to-beat blood pressure, and structural MRI of the brain. Then 506 of them (mean age = 70.7 ± 7.5 years) responded to the follow-up interview on the mobility limitation (as defined by if using wheelchair, cane, or walkers, or being disabled and lying on the bed) after 18 ± 3.5 months. Logistic regression analyses were performed to examine the relationships between the baseline characteristics and the follow-up mobility restriction.

Results
At baseline, compared to intact-mobility group (n = 475), restricted-mobility group (n = 31) were older, with lower score of ADL and the Montreal Cognitive Assessment (MoCA), greater score of Pittsburgh Sleep Quality Index (PSQI), poorer cardio- and cerebral vascular function, and slower walking speeds (ps < 0.05). The logistic regression analysis demonstrated that participants who were with history of falls, uncontrolled-hypertension, and/or greater Fazekas scale (odds ratios (ORs):1.3 ~ 13.9, 95% confidence intervals (CIs) = 1.1 ~ 328.2), walked slower, and/or with lower ADL score (ORs: 0.0026 ~ 0.9; 95%CI: 0.0001 ~ 0.99) at baseline, would have significantly greater risk of restricted mobility (p < 0.05; VIFs = 1.2 ~ 1.9).

Conclusions
These findings provide novel profile of potential risk factors, including vascular characteristics, psycho-cognitive and motor performance, for the development of restricted mobility in near future in older adults, ultimately helping the design of appropriate clinical and rehabilitative programs for mobility in this population.