bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation, Molecular Identification of Mycoplasma Putrefaciens Local Strains and Its Associated Pathological Lesions in Goats
Authors: Saeed Muhammad , Anwar Farhan , Khan Farhan Anwar , Rehman Faiz Ur , Khan Hayatullah , Ahmed Faisal , Ali Mehboob , Ahmed Mushtaq , Ullah Qudrat , Khan Aamir 
Published: December 2021

Abstract
Mycoplasma putrifaciens (Mp) is a dreadful pathogen that causes a severe, usually fatal disease in domestic goats known as MAKePS syndrome in small ruminants. The present lack of effective diagnostic and control measures leaves Pakistani farmers at perpetual great risk of financially disastrous MAKePS outbreaks. Thus far, very limited information is available on the detection and molecular characterization of the unique Mp strains prevalent in Pakistan. This study was proposed to apply modern molecular techniques to characterize endemic Mp isolates and their associated specific lesions in goats to devise an effective control strategies. For the collection of samples Northern areas of Pakistan were focused including Chitral, Gilgit and Swat. Samples were collected from Mycoplasma putrifaciens suspected animals (Chitral n=200, Gilgit n=200, Swat n=200). Clinical samples including nasal swab (NS) and synovial fluid (SF) from live animals (n=50), whereas pleural fluid (PF) and lungs samples from dead goats (n=50) were collected from each representative northern area of Pakistan. All samples were subjected to isolation of Mp local strain, while tissue samples were examined for pathological lesions. Culture positive PPLO broth was first confirmed for Mp by specific PCR. From Gilgit Baltistan 38.83% samples were found positive for Mp by PCR, whereas 25% and 19.38% samples from Chitral and Swat, respectively, were detected positive for Mp by generating an amplicon of 540 bp. The PCR positive PPLO broth samples were cultured on PPLO agar for isolation of Mp. A single colony with fried egg like appearance was picked and sub-cultured in PPLO broth for purification and later on confirmed with PCR. The Histopathological study of lungs showed that there was emphysema, rupture of alveoli, in bronchioles ciliated epithelium were sloughed and infiltration of leukocytes. We successfully isolated and purified Mp local strain prevalent in northern area of Pakistan. The Mp was detected prevalent in 27.76% goats of Northern regions by PCR. This study laid down a foundation to develop an effective diagnostic kit and vaccine against Mp infection in Goats.
Identification of Tumor Specific Neoantigens and Their Implications in Dendritic Cell Immunotherapy Using Liquid Biopsy Results: Findings from an Observational Cohort Study
Authors: Myint Khin Zay Yar , Shimabuku Masamori , Horio Ruriko , Kaneda Munehisa , Shimizu Yoko , Taguchi Junichi 
Published: December 2021

Abstract
Liquid biopsies can be a rapid, cost-effective and noninvasive alternative to tumor biopsies for detecting genetic mutations in somatic tumors. Genetic profiling of liquid biopsies can also be used to identify novel antigens for targeted therapy, provide updated information on disease prognosis and evaluate treatment efficacy. In this study, we aimed to examine mutations that could be identified in liquid biopsy and their potential implications for personalized dendritic cell immunotherapy using these antigens. We analyzed the genomic profiles of 99 blood samples from 85 patients with 22 different types of cancer using two commercially available liquid biopsy tests before the patients underwent standard cancer treatment and dendritic cell immunotherapy. Nonsynonymous mutations were detected in more than 90% of the samples, with an average frequency of 3.6 mutations per sample. The tumor mutations were specific to each patient, as approximately 94.7% of the mutations were so unique that there was almost no duplication among the patients. Clonal evolution was observed in two patients just before or after chemotherapy, radiotherapy and immunotherapy. These findings indicate that liquid biopsy can be a potential surrogate for tumor-specific antigen-based immunotherapy and the importance of tailoring immunotherapy in accordance with the liquid biopsy result in each treatment stage.
Imidacloprid - Induced Pathophysiological Damage in the Midgut of Locusta Migratoria (Orthoptera: Acrididae) in the Field
Authors: El-Samad Lamia M. , El-Gerbed Mohamed S. , Hussein Hanaa S. , Flaven-Pouchon Justin , Wakil Abeer El , Moussian Bernard 
Published: December 2021

Abstract
Neonicotinoids are modern insecticides widely used in agriculture worldwide. Their impact on target (nervous system) and non-target (midgut) tissues has been well studied in beneficial insects including honeybees. However, their effects on pest insects on the field are comparably rarely described. Here, we have studied the effects of the neonicotinoid imidacloprid on the midgut of the pest insect Locusta migratoria caught in the field. We found that in the midgut of imidacloprid-exposed locusts the activity of enzymes involved in reactive oxygen metabolism was perturbed. By contrast, the activity of P450 enzymes that have been shown to be activated in a detoxification response and that were also reported to produce reactive oxygen species was elevated. Probably as a consequence, markers of oxidative stress including protein carbonylation and lipid peroxidation accumulated in midgut samples of these locusts. Histological analyses revealed that their midgut epithelium is disorganized and that the brush border of the epithelial cells is markedly reduced. Indeed, microvilli are significantly shorter, misshapen and possibly non-functional in imidacloprid-treated locusts. We hypothesize that imidacloprid induces oxidative stress in the locust midgut, thereby changing the shape of midgut epithelial cells and probably in turn compromising their physiological function. Presumably, these effects reduce the survival rate of imidacloprid-treated locusts and the damage they cause in the field.
Shen-su-yin, a Traditional Herbal Medicine, Attenuates Lipopolysaccharide-induced Acute Lung Injury in Rats Through Its Anti-inflammatory and Anti-oxidative Effects
Authors: Xiao Peng , Ke Jun , Zhang Jiuyun , Zhou Haijun , Zheng Wuhong 
Published: December 2021

Abstract
Most components of Shen-su-yin (SSY), an herbal formula, have anti-inflammatory and antioxidant activities. The present study was designed to investigate potential effects and mechanisms of SSY on lipopolysaccharide (LPS)-induced acute lung injury (ALI) in rats. 48 rats were randomly divided into 4 groups: control (Ctrl) group, LPS-induced ALI group, low- (SSY-LD) and high- (SSY-HD) dose SSY-treated ALI group. SSY was administered to SSY-treated rats immediately after LPS induction. After 24 hours, blood gas analysis and lactate determination were performed; and bronchoalveolar lavage fluid was collected for detecting protein concentration and levels of cytokines. Lung tissues were obtained for Western blot analysis, histopathological analysis, wet-to-dry weight ratio calculation and measurement of oxidative stress levels. SSY improved oxygenation index and mean arterial pressure, decreased levels of lactate and heart rate, alleviated lung histopathology indexes including lung injury score, wet-to-dry weight ratio and exudation of protein as well as inflammatory cells in ALI rats. Furthermore, SSY reduced levels of pro-inflammatory and oxidative mediums, while increasing levels of anti-inflammatory cytokine and anti-oxidative activity in lung tissues. SSY also suppressed NF-κB signalling pathway and further activated Keap1-Nrf2-ARE signalling pathway activated by LPS. Moreover, all the effects caused by SSY in the SSY-HD group were more encouraging than those in the SSY-LD group. The results indicate that the preventive use of SSY can alleviate ALI through the anti-inflammatory and antioxidant effects mediated by inhibition of NF-κB signalling pathway and activation of Keap1-Nrf2-ARE signalling pathway, and the effect of high dose is better.
Intergenerational Transmission of Parental Risky Health Behaviors in Chinese Children: Are There Socioeconomic Differences?
Authors: Yu Zexuan , Li Jiajia 
Published: December 2021

Abstract
Background: Risky health behaviors in childhood, including smoking, drinking alcohol, and poor diet, are major sources of non-communicable diseases in adulthood. This study was intended to examine how parents affect children’s risky health behaviors, and whether intergenerational transmission differed by Socioeconomic Status (SES). Methods: Data were extracted from the 1991-2015 China Health and Nutrition Survey (CHNS). Smoking (n=5946), alcohol drinking (n=7821), and sugar-sweetened beverages (SSBs) drinking (n=3537) were singled out as proxies for risky health behaviors in children. A binary choice model for panel data with random effect specification was employed to examine whether the risky health behaviors can be transmitted from parents to their children. Subsequently, we conducted a seemingly unrelated test to explore the difference in parental transmission between SES groups. Results: We found strong intergenerational persistence of smoking, alcohol drinking, and SSBs drinking behaviors, except mothers’ smoking behavior. Mothers had a greater influence on children’s alcohol drinking and SSBs drinking behaviors than fathers, both in urban and rural areas, and in different SES groups. The intergenerational transmission of SSBs drinking behaviors exhibited a downward SES gradient for both urban and rural families. In urban areas, mothers’ drinking behavior has a downward gradient with their education level, occupation, and income, but in rural areas, the influence of mothers' drinking behavior is in the same direction with the upward gradient of education level and occupation type. In rural areas, the influence of fathers’ drinking and smoking behaviors appears to show a mainly positive gradient with SES, while some become a downward gradient among urban fathers. Conclusions: Parents’ behaviors and socioeconomic status could make sense in the initiation of their offspring’s risky health behaviors. To promote healthy behaviors, policymakers can introduce health education programs for parents, especially for rural areas and low SES parents.
Transarterial Chemoembolization Combined with Lenvatinib plus PD-1 Inhibitor for Advanced Hepatocellular Carcinoma: A Retrospective Cohort Study
Authors: Cai Mingyue , Huang Wensou , Huang Jingjun , Shi Wenbo , Guo Yongjian , Liang Licong , Zhou Jingwen , Lin Liteng , Cao Bihui , Chen Ye , Zhou Juan , Zhu Kangshun 
Published: December 2021

Abstract
Purpose To investigate the efficacy and safety of transarterial chemoembolization (TACE) combined with lenvatinib plus PD-1 inhibitor (TACE-L-P) versus TACE combined with lenvatinib (TACE-L) for patients with advanced hepatocellular carcinoma (HCC).Methods Data of advanced HCC patients treated with TACE-L-P or TACE-L from January 2019 to December 2020 were retrospectively analyzed. The differences in overall survival (OS), progression-free survival (PFS), tumor responses (based on modified Response Evaluation Criteria in Solid Tumors) and adverse events (AEs) were compared between the two groups. Potential factors affecting OS and PFS were determined.Results A total of 81 patients were included in this study (41 received TACE-L-P and 40 received TACE-L). The patients in TACE-L-P group had prolonged OS (median, 16.9 vs. 12.1 months, p=0.009), longer PFS (median, 7.3 vs. 4.0 months, p=0.002) and higher objective response rate (56.1% vs. 32.5%, p=0.033) and disease control rate (85.4% vs. 62.5%, p=0.019) than those in TACE-L group. Multivariate analyses revealed that the treatment option of TACE-L, main portal vein invasion and extrahepatic metastasis were the independent risk factors for OS, while TACE-L and extrahepatic metastasis were the independent risk factors for PFS. In subgroup analyses, a superior survival benefit was achieved with TACE-L-P in patients with extrahepatic metastasis or tumor number >3 but not in those with main portal vein invasion. The incidence and severity of AEs in TACE-L-P group were comparable to those in TACE-L group (any grade, 92.7% vs. 95.0%, p=1.000; grade 3, 36.6% vs. 32.5%, p=0.699).Conclusion TACE-L-P significantly improved survival over TACE-L with an acceptable safety profile in advanced HCC patients, especially those with extrahepatic metastasis or tumor number >3 but without main portal vein invasion.
Dissecting the Microbial Community Structure of Internal Organs During the Early Postmortem Period in a Murine Corpse Model
Authors: Liu Ruina , Zhang Kai , Li Huan , Sun Qinru , Wei Xin , Li Huiyu , Zhang Siruo , Fan Shuanliang , Wang Zhenyuan 
Published: December 2021

Abstract
Background
Microorganisms inhabit and proliferate throughout the body both externally and internally, which are the primary mediators of putrefaction after death. However, limited information is available about the changes in the postmortem microbiota of extraintestinal body sites in the early decomposition stage of mammalian corpses.
Results
This study applied 16S rRNA barcoding to investigate microbial composition variations among different organs and the relationship between microbial communities and time since death over 1 day of decomposition. During 1 day of decomposition, Agrobacterium, Prevotella, Bacillus, and Turicibacter were regarded as time-relevant genera in internal organs at different timepoints. Pathways associated with lipid, amino acid, carbohydrate and terpenoid and polyketide metabolism were significantly enriched at 8 hours than that at 0.5 or 4 hours. The microbiome compositions and postmortem metabolic pathways differed by time since death, and more importantly, these alterations were organ specific.
Conclusion
The dominant microbes differed by organ, while they tended toward similarity as decomposition progressed. The observed thanatomicrobiome variation by body site provides new knowledge into decomposition ecology and forensic microbiology. Additionally, the microbes detected at 0.5 hours in internal organs may inform a new direction for organ transplantation.
Distribution of Cracks in an Anchored Cavern Under Blast Load Based on Cohesive Elements
Authors: Luo Yi , Pei Chenhao , Qu Dengxing , Li Xinping , Ma Ruiqiu , Gong Hangli 
Published: December 2021

Abstract
To explore the distribution of cracks in anchored caverns under the blast load, cohesive elements with zero thickness were employed to simulate crack propagation through numerical analysis based on a similar model test. Furthermore, the crack propagation process in anchored caverns under top explosion was analysed and the distribution and mode of propagation of cracks in anchored caverns when a fracture with different dip angles was present in the vault were discussed. With the propagation of the explosive stress waves, cracks successively occur at the boundary of the anchored zone of the vault, arch foot, and floor of the anchored caverns. Tensile cracks are preliminarily found in rocks surrounding the caverns. In the case that a pre-fabricated fracture is present in the upper part of the vault, the number of cracks at the boundary of the anchored zone of the vault decreases, then increases with increasing dip angle of the pre-fabricated fracture. The fewest cracks at the boundary of the anchored zone occur if the dip angle of the pre-fabricated fracture is 45º. The wing cracks deflected to the vault are formed at the tip of the pre-fabricated fracture, around which tensile and shear cracks are synchronously present. Under top explosion, both the peak displacement and peak particle velocity in surrounding rocks of anchored caverns reach their maximum values at the vault, successively followed by the side wall and the floor. In addition, they show asymmetry with the difference of the dip angle of the pre-fabricated fracture; the vault displacement of anchored caverns is mainly attributed to the formation of tensile cracks at the boundary of the anchored zone generated due to tensile waves reflected from the free face of the vault. When a fracture is present in the vault, the peak displacement of the vault decreases while the residual displacement increases.
Identification and Validation of N6-methyladenosine-related Biomarkers for Bladder Cancer: Implications for Immunotherapy
Authors: Deng Hongyu , Tang Faqing , Zhou Ming , Shan Dongyong , Chen Xingyu , Cao Ke 
Published: December 2021

Abstract
N6-methyladenosine (m6A) has emerged as one of the most important modifications of RNA. Based on the expression of 23 kinds of m6A regulatory factors, we identified three different m6A modification patterns in bladder cancer. The effects of the three kinds of m6A modification modes on clinicopathological characteristics, immune cell infiltration level, and gene expression level of immune checkpoint genes were comprehensively analyzed. In addition, the effects of different m6A modification modes on the therapeutic efficacy of anti-PD-L1 (atezolizumab) are also discussed. Our results confirm that m6A methylation plays an important role in the immune cell recruitment process in the tumor microenvironment of bladder cancer, which is influences the efficacy of anti-PD-L1 therapy for bladder cancer. We further confirmed the important role of FTO on the biological function of bladder cancer cells by in vitro experiments, FTO functions as an oncogene in bladder cancer cells, and after FTO knockdown, the level of m6A enzyme activity in bladder cancer cells was significantly increased, apoptosis was increased, and cell proliferation and cell invasion were reduced. In addition, our study also confirmed that K216H and K216E probably are important targets for regulating FTO in the future. We provide new insights into the regulatory pathways of the immune microenvironment and the methylation function of m6A in bladder cancer, which will help to design novel diagnostic methods, prognostic tools, and therapeutic targets.
Computing MicroRNA-Gene Interaction Networks in Pan-cancer Using MiRDriver
Authors: Bose Banabithi , Moravec Matthew , Bozdag Serdar 
Published: December 2021

Abstract
DNA copy number aberrated regions in cancer are known to harbor cancer driver genes and the short non-coding RNA molecules, i.e., microRNAs. In this study, we integrated the multi-omics datasets such as copy number aberration, DNA methylation, gene and microRNA expression to identify the signature microRNA-gene associations from frequently aberrated DNA regions across pan-cancer utilizing a LASSO-based regression approach. We studied 7,294 patient samples associated with eighteen different cancer types from The Cancer Genome Atlas (TCGA) database and identified several cancer-specific microRNA-gene interactions enriched in experimentally validated microRNA-target databases. We highlighted several oncogenic and tumor suppressor microRNAs and genes that were common in several cancer types. Our method substantially outperformed the five state-of-art methods in selecting significantly known microRNA-gene interactions in multiple cancer types. Several microRNAs and genes were found to be associated with tumor survival and progression. Selected target genes were found to be significantly enriched in cancer-related pathways, cancer Hallmark and Gene Ontology (GO) terms. Furthermore, subtype-specific potential gene signatures were discovered in multiple cancer types.
Isolation, Culture and Bioactive Substances Elicitation of Sanghuangporus Baumii
Authors: Wang Shixin , Liu Zengcai , Wang Xutong , Li Yawei , Liu Ruipeng , Zou Li 
Published: December 2021

Abstract
Sanghuangporus baumii is a forest pathogenic fungus and also a medicine mushroom. In the wild, S. baumii parasitize on living host plants and there have been no reports of cultivating fruiting bodies under artificial conditions. In this study, we identified and isolated a S. baumii strain, and successfully cultivated the fruiting bodies on sawdust medium by optimizing culture conditions. The optimum medium, culture temperature and pH for mycelial growth of S. baumii were WBA and YPA, at pH 5.5–7.5 and 28℃, respectively. The contents of total flavonoids, total polysaccharides and total triterpenoids in S. baumii were compared with those in other two medicinal sanghuang, S. vaninii and S. sanghuang. The results showed that both the fruiting bodies and mycelia of S. baumii were rich in bioactive substances. The content of total flavonoids was higher in the fruiting bodies (34.91 mg/g), while the contents of total polysaccharides and total triterpenoids were higher in the mycelia (45.41 mg/g, 14.06 mg/g, respectively). In addition, the mycelia of S. baumii could be elicited to produce more bioactive substances. The use of sealing film in culture increased the polysaccharides content in mycelia by 51.8%, while the light increased the flavonoids content by 151.0%. The cultivation of fruiting bodies and the elicitation of bioactive substances from mycelia provide biological materials for the study and utilization of S. baumii.
Magnaporthe Oryzae Chloroplast-Targeting Endo-β-1,4-Xylanase I MoXYL1A Regulates Conidiation, Appressorium Maturation and Virulence of the Rice Blast Fungus
Authors: Shabbir Ammarah , Batool Wajjiha , Dan Yu , Lin Lili , Anquoli An , Chen Xiaomin , Hengyuan Guo , Shuangshuang Yuan , Sekete Malota , Zonghua Wang , Norvienyeku Justice 
Published: December 2021

Abstract
Endo-β-1,4-Xylanases are a group of extracellular enzymes that catalyze the hydrolysis of xylan, a principal constituent of the plant primary cell wall. The contribution of Endo-β-1,4-Xylanase I to both physiology and pathogenesis of the rice blast fungus M. oryzae is unknown. Here, we characterized the biological function of two endoxylanase I (MoXYL1A and MoXYL1B) genes in the development of M. oryzae using targeted gene deletion, biochemical analysis, and fluorescence microscopy. Phenotypic analysis of ∆Moxyl1A strains showed that MoXYL1A is required for the full virulence of M. oryzae but is dispensable for the vegetative growth of the rice blast fungus. MoXYL1B, in contrast, did not have a clear role in the infectious cycle but has a critical function in asexual reproduction of the fungus. The double deletion mutant was severely impaired in pathogenicity and virulence as well as asexual development. We found that MoXYL1A deletion compromised appressorium morphogenesis and function, leading to failure to penetrate host cells. Fluorescently tagged MoXYL1A and MoXYL1B displayed cytoplasmic localization in M. oryzae, while analysis of MoXYL1A-GFP and MoXYL1B-GFP in-planta revealed translocation and accumulation of these effector proteins into host cells. Meanwhile, sequence feature analysis showed that MoXYL1A possesses a transient chloroplast targeting signal peptide, and results from an Agrobacterium infiltration assay confirmed co-localization of MoXYL1A-GFP with ChCPN10C-RFP in the chloroplasts of host cells. MoXYL1B, accumulated to the cytoplasm of the host. Taken together, we conclude that MoXYL1A is a secreted effector protein that likely promotes the virulence of M. oryzae by interfering in the proper functioning of the host chloroplast, while the related xylanase MoXYL1B does not have a major role in virulence of M. oryzae.