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IntroductionThis study aimed to develop and validate a nomogram for predicting cancer-specific survival (CSS) in patients with non-keratinized large cell squamous cell carcinoma (NKLCSCC) at 3, 5, and 8 years after diagnosis.MethodsData on SCC patients were collected from the Surveillance, Epidemiology, and End Results database. Training (70%) and validation (30%) cohorts were generated using random selection of patients. Independent prognostic factors were selected using the backward stepwise Cox regression model. To predict the CSS rates in patients with NKLCSCC at 3, 5, and 8 years after diagnosis, all of the factors were incorporated into the nomogram. Indicators such as the concordance index (C-index), area under the time-dependent receiver operating characteristic curve (AUC), net reclassification index (NRI), integrated discrimination improvement (IDI), calibration curve, and decision-curve analysis (DCA) were then used to validate the performance of the nomogram.ResultsThis study included 9,811 patients with NKLCSCC. Twelve prognostic factors were identified by Cox regression analysis in the training cohort, which were age, number of regional nodes examined, number of positive regional nodes, sex, race, marital status, American Joint Committee on Cancer (AJCC) stage, surgery status, chemotherapy status, radiotherapy status, summary stage, and income. The constructed nomogram was validated both internally and externally. The nomogram had good discrimination ability, as indicated by the comparatively high C-indices and AUC values. The nomogram was properly calibrated, as indicated by the calibration curves. Our nomogram was superior to the AJCC model, as illustrated by its superior NRI and IDI values. DCA curves indicated the clinical usability of the nomogram.ConclusionThe first nomogram for prognosis predictions of patients with NKLCSCC has been developed and verified. Its performance and usability demonstrated that the nomogram could be utilized in clinical settings. However, additional external verification is still required.

In the second half of 2021, a highly pathogenic case occurred in a mixed chicken and duck family farm in Guangdong, China. After the duck flocks were immunized with live attenuated duck enteritis virus vaccine (live attenuated DEV vaccine), the chickens of the same farm showed clinical symptoms similar to duck enteritis, such as pericardial effusion, hepatic hemorrhagic spots, kidney enlargement, and intestinal bleeding, with mass mortality. The infection model of target animal tested, as well as the non-target species, was established according to the risk of live attenuated DEV vaccine and transmission in chickens. Live attenuated DEV vaccine was initially replicated in host animals, released the virus, and effectively colonized in the common environment, according to birds challenged experiments. There was evidence to suggest the mode of transmission of duck enteritis virus, and horizontal transmission is the main route of DEV transmission. In addition, high levels of virus titer were detected in chicken embryos and different tissues of SPF chickens. Different degrees of pathological damage occurred in the tissue of chickens. After the SPF chickens were inoculated with live attenuated DEV vaccine, different degrees of virulence were exhibited, pointing to a potential risk to other domestic bird species.

Avian Leukosis Virus Subgroup J (ALV-J) is a tumorigenic virus with high morbidity and rapid transmission. N6-methyladenosine (m6A) is a common epigenetic modification that may be closely related to the pathogenicity of ALV-J. Currently, there are no reports on whether m6A modification is related to ALV-J induced tumor formation. In this study, we used methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to examine the differences in m6A methylation and gene expression in normal livers and ALV-J-induced tumor livers systematically, with functional enrichment and co-expression analysis. The results identified 6,541 m6A methylated peaks, mainly enriched in CDS, and more than 83% of the transcripts contained 1-2 m6A peaks. For RNA-seq, 1,896 and 1,757 differentially expressed mRNAs and lncRNAs were identified, respectively. Gene enrichment analysis indicated that they may be involved in biological processes and pathways such as immunology-related and apoptosis. Moreover, we identified 17 lncRNAs, commonly existing in differently expressed methylome and transcriptome. Through co-expression analysis, 126 differentially expressed lncRNAs, and 18 potentially m6A-related methyltransferases were finally identified and connected, suggesting that m6A modifications might affect gene expression of lncRNAs and play a role in ALV-J induced tumor formation. This study provides the first comprehensive description of the m6A expression profile in tumor livers induced by ALV-J infection in chickens, which provides a basis for studying the role of m6A modification in ALV-J induced tumorigenesis. This study provides clues for studying the epigenetic etiology and pathogenesis of ALV-J.

Beijing Black pig is an excellent cultivated black pig breed in China, with desirable body shape, tender meat quality and robust disease resistance. To explore the level of admixture and selection signatures of Beijing Black pigs, a total number of 90 individuals covering nine pig breeds were used in our study, including Beijing Black pig, Large White, Landrace, Duroc, Lantang pig, Luchuan pig, Mashen pig, Huainan pig and Min pig. These animals were resequenced with 18.19 folds mapped read depth on average. Generally, we found that Beijing Black pig was genetically closer to commercial pig breeds by population genetic structure and genetic diversity analysis, and was also affected by Chinese domestic breeds Huainan pig and Min pig. These results are consistent with the cross-breeding history of Beijing Black pig. Selection signal detections were performed on three pig breeds, Beijing Black pig, Duroc and Large White, using three complementary methods (FST, θπ, and XP-EHH). In total, 1,167 significant selected regions and 392 candidate genes were identified. Functional annotations were enriched to pathways related to immune processes and meat and lipid metabolism. Finally, potential candidate genes, influencing meat quality (GPHA2, EHD1, HNF1A, C12orf43, GLTP, TRPV4, MVK, and MMAB), reproduction (PPP2R5B and MAP9), and disease resistance (OASL, ANKRD13A, and GIT2), were further detected by gene annotation analysis. Our results advanced the understanding of the genetic mechanism behind artificial selection of Beijing Black pigs, and provided theoretical basis for the subsequent breeding and genetic research of this breed.

Alfalfa (Medicago sativa L.) is an important forage crop, and salt stress is a major limiting factor in its yield. Melatonin (MT) is a multi-regulatory molecule in plants. We showed that basal MT content was positively correlated with the salt tolerance degree of different alfalfa varieties. MT and its precursor 5-HT fully recovered seed germination while partially ameliorated seedling growth of salt-stressed alfalfa. The 5-HT showed some divergent effects from MT with regards to growth amelioration under salinity. Salt stress caused stunted plant growth in soil culture, while MT ameliorated it by elevating plant height, fresh weight, branching number, and chlorophyll content. Silencing of a putative MT receptor, MsPMTR1, which was shown to be membrane-localized, abolished the ameliorative effects of MT on salt-stressed alfalfa seedling growth, while overexpression of MsPMTR1 improved plant growth under salt stress. The RNA sequencing analysis showed that nine pathway genes were specifically induced by MT treatment compared with salt stress. These MT-responsive differentially expressed genes include basal metabolic pathway genes, such as “ribosome, elongation factor,” “sugar and lipid metabolism,” and “photosynthesis” and stress-related genes encoding “membrane integrity” related proteins, heat shock protein, peroxidase/oxidoreductase, and protease. Several abiotic stress response-related genes, such as DRE, ARF, HD-ZF, MYB, and REM were repressed by NaCl treatment while induced by MT treatment. In summary, we demonstrated the importance of MsPMTR1 in MT-mediated salt tolerance in alfalfa, and we also analyzed the regulatory mechanism of MT during alfalfa seed germination under salt stress.

The goal of the study was to test the effects of an antibiotic substitute, plectasin, on the growth performance, immune function, intestinal morphology and structure, intestinal microflora, ileal mucosal layer construction and tight junctions, ileal immune-related cytokines, and blood biochemical indices of yellow-feathered chickens. A total of 1,500 one-day-old yellow-feathered chicks were randomly divided into four dietary treatment groups with five replicates in each group and 75 yellow-feathered chicks in each replication, as follows: basal diet (group A); basal diet supplemented with 10 mg enramycin/kg of diet (group B), basal diet supplemented with 100 mg plectasin/kg of diet (group C), and basal diet supplemented with 200 mg plectasin/kg of diet (group D). It was found that the dietary antimicrobial peptide plectasin could improve the ADG and had better F/G for the overall period of 1–63 days. Dietary plectasin can enhance H9N2 avian influenza virus (AIV) and Newcastle disease virus (NDV) antibody levels of yellow-feathered chickens at 21, and 35 days of age. Dietary plectasin can enhance the intestine structure, inhibit Escherichia coli and proinflammatory cytokines in the ileum, and ameliorate the blood biochemical indices of yellow-feathered chickens at 21 days of age. This study indicates that the antimicrobial peptide plectasin has beneficial effects on the growth performance, intestinal health and immune function of yellow-feathered chickens.

Structural variants (SVs) represent essential forms of genetic variation, and they are associated with various phenotypic traits in a wide range of important livestock species. However, the distribution of SVs in the pig genome has not been fully characterized, and the function of SVs in the economic traits of pig has rarely been studied, especially for most domestic pig breeds. Meishan pig is one of the most famous Chinese domestic pig breeds, with excellent reproductive performance. Here, to explore the genome characters of Meishan pig, we construct an SV map of porcine using whole-genome sequencing data and report 33,698 SVs in 305 individuals of 55 globally distributed pig breeds. We perform selective signature analysis using these SVs, and a number of candidate variants are successfully identified. Especially for the Meishan pig, 64 novel significant selection regions are detected in its genome. A 140-bp deletion in the Indoleamine 2,3-Dioxygenase 2 (IDO2) gene, is shown to be associated with reproduction traits in Meishan pig. In addition, we detect two duplications only existing in Meishan pig. Moreover, the two duplications are separately located in cytochrome P450 family 2 subfamily J member 2 (CYP2J2) gene and phospholipase A2 group IVA (PLA2G4A) gene, which are related to the reproduction trait. Our study provides new insights into the role of selection in SVs' evolution and how SVs contribute to phenotypic variation in pigs.

H9N2 avian influenza virus (AIV) infection in chickens is often accompanied by secondary bacterial infection, but the mechanism is unclear. The aim of the present study was to reveal that mechanism and explore non-antibiotic treatment. 16s rRNA sequencing and metabonomics were performed in the intestinal contents of chickens infected with H9N2 AIV or H9N2 AIV and fed with ageratum-liquid (AL) to reveal the metabolite that promote intestinal Escherichia coli (E. coli) proliferation caused by H9N2 AIV, as well as to determine the regulatory effect of AL. It was found that H9N2 AIV infection led E. coli to become the dominant gut microbe and promoted E. coli translocation from the intestinal tract to the visceral tissue through the damaged intestinal barrier. H9N2 AIV infection induces inflammation in the intestinal mucosa and promotes the secretion and release of nitrate from the host intestinal epithelium. In addition, nitrate promoted E. coli proliferation in the inflamed intestinal tract following H9N2 AIV infection. Furthermore, Chinese herbal medicine AL can restore intestinal homeostasis, inhibit the production of nitrate in the intestinal epithelium and effectively prevent the proliferation and translocation of E. coli in the intestines. This is the first report on the mechanism of E. coli secondary infection induced by H9N2 AIV, where herbal medicine AL was shown to have a good preventive effect on the secondary infection.

The lion head goose is one of the most important agricultural resources in China; however, its breeding process is relatively slow. In the present study, a genome-wide association study was performed for the genetic selection of egg production characters in lion head geese. We detected 30 single-nucleotide polymorphisms located in or near 30 genes that might be associated with egg production character, and quantitative real-time polymerase chain reaction was used to verify their expression level in lion head geese. The results showed that the expression levels of CRTC1 (encoding CREB-regulated transcription coactivator 1), FAAH2 (encoding fatty acid amide hydrolase 2), GPC3 (encoding glypican 3), and SERPINC1 (encoding serpin family C member 1) in high egg production population were significantly lower than those in the low egg production populations (*P < 0.05). The expression levels of CLPB (encoding caseinolytic peptidase B protein homolog), GNA12 (encoding guanine nucleotide-binding protein subunit alpha-12), and ZMAT5 (encoding zinc finger, matrin type 5) in the high egg production population were significantly higher than those in the low egg production populations (*P < 0.05). The expression of BMP4 (encoding bone morphogenetic protein 4), FRMPD3 (encoding FERM and PDZ domain containing 3), LIF (encoding leukemia inhibitory factor), and NFYC (encoding nuclear transcription factor Y subunit gamma) in the high egg production population were very significantly lower than those in the low egg production population (**P < 0.01). Our findings provide an insight into the economic traits of lion head goose. These candidate genes might be valuable for future breeding improvement.

Binocular depth perception (BDP) is one of the most demanding visual function that involves both dorsal and ventral visual information streams. Substantial research has been conducted on the disruption of BDP in patients with schizophrenia. However, research on first-episode and drug-naive patients with schizophrenia (FEDN) is limited. To assess the BDP of schizophrenia patients while controlling for the effects of antipsychotics and the duration of illness. We investigated BDP in patients with schizophrenia via the Titmus Stereopsis Test in this study, by matching the patients into three groups: FEDN (n = 17), long duration of illness and medicine treatment (LDMT) (n = 31) and the healthy control group (n = 40). Results showed that both the FEDN (mean = 1.71, 95% confidence interval [CI]: [1.57, 1.84]) and LDMT (1.73, 95% CI: [1.66, 1.81]) patients displayed a significant decline (p = 0.01, Cohen’s d = 0.67, p = 0.001, Cohen’s d = 0.92, respectively) in depth perception compared to the healthy control (1.55, 95% CI: [1.48, 1.61]) group. Additionally, there were no significant differences (p = 0.68, Cohen’s d = 0.11) between the FEDN and LDMT groups, and no correlation (Pearson r = -0.16, p = 0.38, R2 = 0.03) was observed between the duration of illness and impaired BDP in the LDMT group. The proportion of individuals with stereopsis detection in either FEDN (12/17) or LDMT (26/31) groups under stereo threshold 63 arc seconds (″), were significantly lower (Pearson χ2 = 6.29, p = 0.043, φc = 0.27) compared to the healthy control group (38/40). Significant difference in stereopsis detection also occurred at 50″ (Pearson χ2 = 12.31, p = 0.001, φc = 0.37), 40″ (Pearson χ2 = 12.38, p = 0.002, φc = 0.38), 32″ (Pearson χ2 = 6.69, p = 0.035, φc = 0.28), 25″ (Pearson χ2 = 14.82, p = 0.001, φc = 0.41) and 20″ (Pearson χ2 = 6.73, p = 0.034, φc = 0.28) between the three groups. These findings showed a moderately strong association between schizophrenia and defective stereopsis.