bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineered Bacillus subtilis WB600/ZD prevents Salmonella Infantis-induced intestinal inflammation and alters the colon microbiota in a mouse model
Authors: Li Wei , Wang Xue , Chen Keyuan , Zhu Yaohong , Yang Guiyan , Jin Yipeng , Wang Jiufeng 
Published: February 2025

Abstract
Antimicrobial peptides (AMPs) are instrumental in maintaining intestinal homeostasis and have emerged as potential therapeutic candidates for ameliorating intestinal bacterial infections. However, the intrinsic instability associated with the in vivo delivery of AMPs constitutes a substantial impediment to their therapeutic efficacy in treating infections. In this study, we genetically modified Bacillus subtilis (B. subtilis) WB600 to express Zophobas atratus defensin (ZD), an antimicrobial peptide with broad-spectrum activity isolated from Zophobas atratus, for oral administration. This engineered strain effectively protects against Salmonella Infantis (S. Infantis) infection in mice. Pretreatment with WB600/ZD prevented NF-κB pathway activation induced by S. Infantis infection and increased expression of antioxidant and tight junction proteins, thus alleviating the severity of intestinal inflammation in both the jejunum and ileum (P < 0.01). Moreover, WB600/ZD pretreatment facilitated the growth of beneficial bacteria such as Lachnospiraceae, Butyricicoccus, Eubacterium_xylanophilum, and Clostridia_UCG-014 while decreasing the abundance of pathogenic bacteria such as Escherichia-Shigella and Salmonella (P < 0.05). In conclusion, this study underscores the protective effects of WB600/ZD on S. Infantis-induced intestinal inflammation, suggesting that oral delivery of B. subtilis WB600/ZD may be a promising prophylactic strategy for combating bacterial infections in the intestine.
Limited transmission of avian influenza viruses, avulaviruses, coronaviruses and Chlamydia sp. at the interface between wild birds and a free-range duck farm
Authors: Le Gall-Ladevèze Chloé , Vollot Benjamin , Hirschinger Julien , Lèbre Laëtitia , Aaziz Rachid , Laroucau Karine , Guérin Jean-Luc , Paul Mathilde , Cappelle Julien , Le Loc’h Guillaume 
Published: February 2025

Abstract
Recent outbreaks of highly pathogenic avian influenza in Europe have raised questions regarding the epidemiological role of commensal wild birds on free-range poultry farms. This study aimed to assess the prevalence of avian influenza viruses (AIV), avulaviruses, coronaviruses and Chlamydia sp. in commensal wild birds on a free-range duck farm in southwestern France and to evaluate possible transmission events at the wild‒domestic interface. From 2019 through 2021, a longitudinal study was conducted on wild birds, domestic ducks and their shared environment on farms. Commensal wild birds were captured and sampled for blood and swabs, and fresh feces from cattle egrets visiting the farm were collected. In parallel, domestic ducks were sampled, and environmental samples were collected. The presence of the four pathogens was tested by q(RT-)PCR, and the immunity of wild birds to AIV and Newcastle disease virus (NDV) was tested by ELISA. Wild birds were found to shed AIV and Chlamydia only, with a low prevalence (< 3%). The seroprevalence rates were less than 10% for AIV and less than 4.5% for NDV. No significant temporal trend was identified. Ducks and their environment frequently test simultaneously positive for the same pathogens (19 to 44% of flocks), mostly during fall‒winter. In addition to unrelated temporal patterns, the identification of pathogens in wild birds seemed unrelated to that in domestic ducks. These results suggest a low transmissibility of the avian pathogens tested in our study at the wild‒domestic interface and highlight the limited contribution of commensal wild birds in comparison with free-range poultry to the global microbiological pressure on the environment.
A novel high-throughput screen identifies phenazine-1-carboxylic acid as an inhibitor of African swine fever virus replication in primary porcine alveolar macrophages
Authors: Lan Jing , Luo Rui , Liu Di , Qi Changxing , Song Xin , Lu Zhanhao , Huang Ruojia , Yang Yuying , Sun Yuan , Zhang Yonghui , Wang Tao , Qiu Hua-Ji 
Published: February 2025

Abstract
African swine fever (ASF), caused by African swine fever virus (ASFV), has resulted in significant economic impacts on the global swine industry. Currently, there is no safe and effective commercial vaccine available for ASFV. Thus, the development of effective and readily available therapeutics for ASF is urgently needed. To conduct high-throughput screening (HTS) for anti-ASFV drugs, we initially developed a recombinant dual-reporter virus (rASFV-Gluc/EGFP) using the virulent strain ASFV HLJ/18 (ASFV-WT). The enhanced green fluorescent protein (EGFP)- and Gaussia luciferase (Gluc)-encoding genes were incorporated downstream of the ASFV MGF300-4L gene without disrupting viral genes. The growth kinetics, hemadsorption, and transmission electron microscopy analysis of rASFV-Gluc/EGFP in primary porcine alveolar macrophages (PAMs) revealed that rASFV-Gluc/EGFP exhibits similar biological characteristics to ASFV-WT. Furthermore, analysis of Gluc activities, fluorescence, and next-generation sequencing indicated that rASFV-Gluc/EGFP maintains good genetic stability after 20 consecutive passages in PAMs. Using the HTS platform established with rASFV-Gluc/EGFP, we screened and identified phenazine-1-carboxylic acid (PCA) as an effective inhibitor of ASFV replication from 246 small molecule compounds in PAMs. Importantly, PCA was found to reduce ASFV replication by as much as 100-fold at a concentration of 25 μM. Overall, this study suggests that rASFV-Gluc/EGFP is suitable for rapid screening of anti-ASFV drugs. Importantly, we showed that PCA has significant anti-ASFV activity in PAMs.
Site-selective dimethylation of flavonoids using fusion flavonoid O-methyltransferases
Authors: Lee Kyungha , Bhoo Seong Hee , Lee Sang-Won , Cho Man-Ho 
Published: February 2025

Abstract
Flavonoids are often decorated with methyl groups, which are catalyzed by flavonoid O-methyltransferases (FOMTs). Most FOMTs methylate flavonoids in a regiospecific manner. Because of the regiospecific nature of FOMTs, the synthesis of polymethoxyflavonoids is accomplished by multiple O-methylation steps. The multistep synthesis of dimethoxyflavonoids can be efficiently performed by a one-pot procedure using a multienzyme biocatalyst. For the one-pot production of dimethoxyflavonoids, fusion FOMTs were generated by the combination of two different regiospecific FOMTs. RdOMT10 (flavonoid 3-OMT), OsNOMT (flavonoid 7-OMT), and ObFOMT5 (flavonoid 4'-OMT) were used in the FOMT fusion. The fusion FOMTs (OsNOMT/ObFOMT5, OsNOMT/RdOMT10, and ObFOMT5/RdOMT10) were heterologously expressed in Escherichia coli. Activity assays of the recombinant fusion FOMTs demonstrated that OsNOMT/ObFOMT5, OsNOMT/RdOMT10, and ObFOMT5/RdOMT10 catalyze 7/4'-O-methylations, 7/3-O-methylations, and 4'/3-O-methylations of flavonoids, respectively. OsNOMT/ObFOMT5 and OsNOMT/RdOMT10 showed strong dimethylation activity towards diverse flavonoids and were therefore used in the site-selective bioconversion of flavonoids into dimethoxyflavonoids. The E. coli cells bearing OsNOMT/ObFOMT5 successfully converted flavonoids into 7,4'-dimethoxyflavonoids. The engineered E. coli expressing OsNOMT/RdOMT10 converted flavonoids into 3,7-dimethoxyflavonoids. This result indicates that the fusion FOMTs are useful multienzyme biocatalysts for the site-selective production of dimethoxyflavonoids by one-pot bioconversion.
Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencing
Authors: Xu Naiyi , Zhang Linyun , Chen Feifan , Feng Zhengfu , Zheng Jiangtao , Li DongHua , Zhao Yongju , Kang Xiangtao 
Published: February 2025

Abstract

Background
As an important genetic resource of chickens, gamecock has unique morphological and behavioral characteristics such as large size, muscular development and strong aggression, making it a good model for studying muscle development and behavior patterns, as well as an excellent breeding material. Gamecocks are distributed worldwide, forming different breeds and strains. However, the single or multiple origin of global gamecocks has not been fully established and much remains unknown about genetic introgression events between gamecocks and other chickens. Therefore, in this study, based on whole genome data of gamecocks, Chinese indigenous chickens, commercial chickens and wild jungle fowls, we performed population structure analysis, selection signal analysis, and genomic introgression analysis of gamecocks.

Results
The population structure analysis revealed that gamecocks have multiple origins. In addition, we used Fst, π-Ratio and XP-EHH methods to explore the candidate signatures of positive selection in gamecocks. A total number of fifteen shared candidate genes were identified using the three different detection strategies. Among these candidate genes, ETV1, DGKB, AGMO, MEOX2, ISPD and PLCB4 are related to the growth and muscle development, fighting performance and neurodevelopment of gamecocks. Furthermore, we detected the introgression event at the MYBPHL region from the Gallus sonneratii into Euramerican gamecocks and at the CPZ gene region from the Gallus gallus gallus into multiple gamecock populations, respectively, indicating the introgression from the wild junglefowl may impact the skeletal and muscle development as well as aggressive behavior of gamecocks.

Conclusions
In summary, we conducted a genome-wide exploration of gamecocks from multiple regions worldwide. Our analysis confirmed multiple origins of gamecocks and detected several candidate genes that are possibly related to important traits and characteristics in gamecocks. More importantly, this is the first study that has detected introgression events and genes from wild jungle fowls to gamecocks, which provides evidence of the wild jungle fowls contributing to the genetic diversity of gamecocks. Our findings offer new perspectives on the impact of introgression on gamecocks, and provide a basis for further resource conservation and utilization of gamecock, as well as provide excellent material for the genetic improvement of domestic chickens.
Preoperative prediction of IDH genotypes and prognosis in adult-type diffuse gliomas: intratumor heterogeneity habitat analysis using dynamic contrast-enhanced MRI and diffusion-weighted imaging
Authors: Wang Xingrui , Xie Zhenhui , Wang Xiaoqing , Song Yang , Suo Shiteng , Ren Yan , Hu Wentao , Zhu Yi , Cao Mengqiu , Zhou Yan 
Published: February 2025

Abstract

Background
Intratumor heterogeneity (ITH) is a key biological characteristic of gliomas. This study aimed to characterize ITH in adult-type diffuse gliomas and assess the feasibility of using habitat imaging based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and diffusion-weighted imaging (DWI) to preoperatively predict isocitrate dehydrogenase (IDH) genotypes and prognosis.

Methods
Sixty-three adult-type diffuse gliomas with known IDH genotypes were enrolled. Volume transfer constant (Ktrans) and apparent diffusion coefficient (ADC) maps were acquired from DCE-MRI and DWI, respectively. After tumor segmentation, the k-means algorithm clustered Ktrans and ADC image voxels to generate spatial habitats and extract quantitative image features. Receiver operating characteristic (ROC) curves and area under the curve (AUC) were used to evaluate IDH predictive performance. Multivariable logistic regression models were constructed and validated using leave-one-out cross-validation, and the contrast-enhanced subgroup was analyzed independently. Kaplan-Meier and Cox proportional hazards regression analyses were used to investigate the relationship between tumor habitats and progression-free survival (PFS) in the two IDH groups.

Results
Three habitats were identified: Habitat 1 (hypo-vasopermeability and hyper-cellularity), Habitat 2 (hypo-vasopermeability and hypo-cellularity), and Habitat 3 (hyper-vasopermeability). Compared to the IDH wild-type group, the IDH mutant group exhibited lower mean Ktrans values in Habitats 1 and 2 (both P < 0.001), higher volume (P < 0.05) and volume percentage (pVol, P < 0.01) of Habitat 2, and lower volume and pVol of Habitat 3 (both P < 0.001). The optimal logistic regression model for IDH prediction yielded an AUC of 0.940 (95% confidence interval [CI]: 0.880–1.000), which improved to 0.948 (95% CI: 0.890–1.000) after cross-validation. Habitat 2 contributed the most to the model, consistent with the findings in the contrast-enhanced subgroup. In IDH wild-type group, pVol of Habitat 2 was identified as a significant risk factor for PFS (high- vs. low-pVol subgroup, hazard ratio = 2.204, 95% CI: 1.061–4.580, P = 0.034), with a value below 0.26 indicating a 5-month median survival benefit.

Conclusions
Habitat imaging employing DCE-MRI and DWI may facilitate the characterization of ITH in adult-type diffuse gliomas and serve as a valuable adjunct in the preoperative prediction of IDH genotypes and prognosis.

Clinical trial number
Not applicable.
Medial sural artery perforator free flap for small- to medium-sized defects in head and neck reconstruction: a suitable replacement for radial forearm free flap
Authors: Zhang Yulian , Pan Keran , Wu Jian , Tang Xi 
Published: February 2025

Abstract

Background and objectives
To compare clinical outcomes and donor site morbidity between medial sural artery perforator (MSAP) flap and radial forearm free (RFF) flap for soft tissue reconstruction of head and neck.

Methods
Forty-six patients who underwent free flap reconstruction at the head and neck cancer center from February 2019 to March 2021 were included, of which 25 RFF flaps and 21 MSAP flaps. The patient and flap characteristics (age, sex, flap size, harvest time, etc.) and outcomes (success rate, donor site complications including infection, hematoma, and fistula, donor site morbidity including abnormal sensation, weakness, range of motion, postoperative oral function) were recorded and compared. Patients were followed up for at least 12 months after surgery. The patients were assessed subjective donor-site morbidity and satisfaction with overall functional results using a self-reported questionnaire.

Results
The success rates of RFF flaps and MSAP flaps were 96% and 95.2%. There were no significant differences in age, sex, flap size, pedicle length, postoperative treatment, and postoperative oral function. MSAP flap showed less donor site morbidity and better subjective satisfaction at the donor site than RFF flap did after a 12-month follow-up. A dominant perforator of the medial sural artery emerges constantly near the point which is approximately 15 cm from the popliteal fossa center vertically, and 3 cm from the postor midline of the leg horizontally.

Conclusion
Due to less donor site morbidity and higher patient satisfaction, MSAP flap can be used as a replacement for RFF flap for small to medium-sized defects in head and neck reconstruction.
Radiation-induced meningiomas following childhood cranial radiotherapy—report of four cases
Authors: Ay Larisa Andrada , Ozgiray Erkin , Akintürk Nevhis , Kamer Emine Serra , Ertan Yeşim 
Published: February 2025

Abstract

Background
Radiation-induced meningiomas represent a late side effect of cranial radiation therapy. The most widely used diagnostic criteria, despite the lack of a standard description, is a meningioma that develops in a previously irradiated area following a predetermined time interval.

Case presentation
We present four cases of late-onset cranial atypical meningiomas following childhood cranial radiotherapy. Four patients (two females and two males) between 4 and 13 years of age at the time of cranial irradiation developed secondary intracranial meningioma after a latency period of 8–34 years. Surgical resection of the tumors was performed, and histopathological examination revealed a diagnosis of atypical meningioma in all four patients.

Conclusion
Radiation-induced tumors continue to be a significant side effect of radiotherapy and radiosurgery, and they are frequently identified as recurrent, numerous, and more aggressive. Prolonged follow-up should definitely not be ignored in patients with antecedents of radiotherapy for a primary cerebral tumor or cranial irradiation for an early age malignancy.
Metabolomics profiling reveals p-aminobenzoic acid enhances resistance to Fusarium head blight in wheat
Authors: Tan Yiluo , Wang Kangjun , Guo Mingming , Zhang Guangxu , Li Xiaofeng , Shi Yijun , He Maosheng , Xu Dayong , Chen Feng , Fan Jiwei 
Published: February 2025

Abstract

Fusarium head blight (FHB) not only causes severe yield losses but also mycotoxin contamination in wheat, posing a serious threat to food security and public health. The mechanisms of resistance to FHB in wheat are critical for effective prevention and control of the pathogen. In this research, we investigated and analyzed the metabolite changes induced by FHB colonization in the FHB-resistant cultivar Lianmai12 through Fusarium graminearum inoculation and mock inoculation. A total of 1001 metabolites were detected, 109 of which were significantly changed due to FHB infection. The majority of these 109 metabolites belonged to alkaloids, flavonoids, phenolic acids, lipids and organic acids. The most enriched KEGG pathways were plant hormone signal transduction and phenylpropanoid biosynthesis, which may constitute the major defence responses to FHB challenge. The metabolite p-aminobenzoic acid (PABA) significantly suppressed the growth of mycelia and the production of conidia in vitro. Further studies revealed that spraying PABA at early anthesis on wheat spikes reduced the development of FHB disease. These results provide preliminary insights into the metabolic basis of resistance in Lianmai12 and will be beneficial in the development of potential biocontrol agents against FHB.

Graphical Abstract
Unraveling relationship between the genetic polymorphism CYP2A13 and nicotine metabolism of male smokers in Medan, Indonesia
Authors: Soeroso Noni Novisari , Zain-Hamid Rozaimah , Bihar Syamsul , Soliha Chaliza , Ananda Fannie Rizki , Aida  
Published: February 2025

Abstract

Background
Nicotine metabolism significantly influences the levels of harmful nicotine metabolites in smokers. CYP2A13, a key enzyme in nicotine and xenobiotic metabolism, is implicated in tobacco smoke-related lung cancer.

Aim
This study investigated the association between CYP2A13 genetic polymorphism and nicotine metabolism in male smokers in Medan, Indonesia.

Materials and methods
This cross-sectional study included 66 male smokers (aged 20–65 years) who met pre-defined inclusion and exclusion criteria. Nicotine metabolite levels were quantified in urine samples using high-performance liquid chromatography (HPLC). CYP2A13 polymorphism was determined using polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) analysis of venous blood samples. Logistic regression analysis (Epi Info-7) assessed the association between CYP2A13 genotype and nicotine metabolism.

Results
No significant association (p > 0.05) was found between CYP2A13 genotype and nicotine metabolism. The CC genotype was most prevalent. The majority of participants exhibited rapid nicotine metabolism.

Conclusion
Further research with larger sample sizes and diverse populations is needed to elucidate the relationship between CYP2A13 genetic polymorphism and nicotine metabolism.
Spatial analysis of speculation in the US housing market
Authors: Manochehri Salaheddin , Amani Ramin , Mamkhezri Jamal 
Published: February 2025

Abstract
This study examines the spatial impact of speculation on the US housing market from 1990 to 2021, highlighting regional variations and economic implications. Employing advanced analytical techniques, including nonlinear least squares and time-varying parameter ordinary least squares, we delve into the spatial patterns of speculation within the housing market. This study aims to illuminate the role of speculation in influencing housing market dynamics, which has significant implications for economic stability and housing policy. Our investigation reveals that speculation is primarily driven by price expectations and historical price trend analysis, exerting a significant influence on housing market dynamics. Given the inherent constraints in housing supply, effectively managing these fluctuations necessitates a multifaceted strategy. This approach involves measures such as accelerating production, streamlining supply chains, and facilitating affordable land access and tax incentives for low-income households, all designed to stimulate investment in construction and housing. Our empirical findings indicate variations in speculation prevalence across different regions of the USA, with a higher incidence in the western and midwestern regions compared to the eastern counterparts. In light of these insights, policymakers are urged to consider tailored regulatory interventions to mitigate excessive speculation in the US housing market. These measures could encompass stricter lending standards and enhanced transparency requirements in real estate transactions. This study contributes to a deeper understanding of the dynamics of speculation within the US housing market, offering valuable insights for policymakers and researchers seeking to address its implications for economic stability. Moreover, Our findings not only highlight regional variations but also validate theories of speculative behavior, particularly the role of price expectations and feedback loops, as established by Shiller (2005) and Glaeser (2013). These insights contribute to a deeper understanding of the dynamics driving speculation in the housing market.
Tumor microbiome: roles in tumor initiation, progression, and therapy
Authors: Zhang Shengxin , Huang Jing , Jiang Zedong , Tong Huan , Ma Xuelei , Liu Yang 
Published: February 2025

Abstract
Over the past few years, the tumor microbiome is increasingly recognized for its multifaceted involvement in cancer initiation, progression, and metastasis. With the application of 16S ribosomal ribonucleic acid (16S rRNA) sequencing, the intratumoral microbiome, also referred to as tumor-intrinsic or tumor-resident microbiome, has also been found to play a significant role in the tumor microenvironment (TME). Understanding their complex functions is critical for identifying new therapeutic avenues and improving treatment outcomes. This review first summarizes the origins and composition of these microbial communities, emphasizing their adapted diversity across a diverse range of tumor types and stages. Moreover, we outline the general mechanisms by which specific microbes induce tumor initiation, including the activation of carcinogenic pathways, deoxyribonucleic acid (DNA) damage, epigenetic modifications, and chronic inflammation. We further propose the tumor microbiome may evade immunity and promote angiogenesis to support tumor progression, while uncovering specific microbial influences on each step of the metastatic cascade, such as invasion, circulation, and seeding in secondary sites. Additionally, tumor microbiome is closely associated with drug resistance and influences therapeutic efficacy by modulating immune responses, drug metabolism, and apoptotic pathways. Furthermore, we explore innovative microbe-based therapeutic strategies, such as engineered bacteria, oncolytic virotherapy, and other modalities aimed at enhancing immunotherapeutic efficacy, paving the way for microbiome-centered cancer treatment frameworks.