New resources for genetic studies in maize (Zea mays L.): a genome-wide Maize6H-60K single nucleotide polymorphism array and its application.

Despite the availability of numerous molecular markers in maize, effective evaluation of all types of germplasm resources, accurate identification of varieties and analysis of a large number of materials in a timely, low-cost manner is challenging. Here, we present Maize6H-60K, a genome-wide single nucleotide polymorphism (SNP) array to facilitate maize genotyping. We first identified 160 million variants by sequencing data of 388 representative inbreds and then tiled 200 000 high-quality variants on a screening array. These variants were further narrowed down to 61 282 using stringent filtering criteria. Among the 60 000 markers, 21 460 SNPs (35%) were within genic regions and 12 835 (21%) were located in coding regions. To assess their effectiveness, 329 inbreds, 221 hybrids, 34 parent-offspring sets and six breeding samples were genotyped. Overall, 48 972 SNPs (80%) were categorized into the highest quality class, that of 'poly high resolution'. A total of 54 658 (89.29%) and 53 091 (86.73%) SNPs had minor allele frequency values ≥ 0.20 in inbreds and hybrids respectively. A linkage disequilibrium (LD) analysis revealed that LD decline was in equilibrium when r2 was between 0.10 and 0.15, which corresponds to a physical distance of 400-600 kb. UPGMA clustering analysis divided the 329 inbred lines into nine groups that were consistent with known pedigrees. A background analysis of breeding materials indicated that the 60 000 markers were suitable for evaluation of breeding populations constructed by materials between or within heterotic groups. The developed Maize6H-60K array should be an important tool in maize genetic studies, variety identification and molecular breeding.

Development and psychometric properties of an informant assessment scale of theory of mind for adults with traumatic brain injury.

Impairment of theory of mind (ToM) is a common phenomenon following traumatic brain injury (TBI) that has clear effects on patients' social functioning. A growing body of research has focused on this area, and several methods have been developed to assess ToM deficiency. Although an informant assessment scale would be useful for examining individuals with TBI, very few studies have adopted this approach. The purpose of the present study was to develop an informant assessment scale of ToM for adults with traumatic brain injury (IASToM-aTBI) and to test its reliability and validity with 196 adults with TBI and 80 normal adults. A 44-item scale was developed following a literature review, interviews with patient informants, consultations with experts, item analysis, and exploratory factor analysis (EFA). The following three common factors were extracted: social interaction, understanding of beliefs, and understanding of emotions. The psychometric analyses indicate that the scale has good internal consistency reliability, split-half reliability, test-retest reliability, inter-rater reliability, structural validity, discriminate validity and criterion validity. These results provide preliminary evidence that supports the reliability and validity of the IASToM-aTBI as a ToM assessment tool for adults with TBI.

Exploring the role of innate immunity in Cholangiocarcinoma: implications for prognosis, immune infiltration, and tumor metastasis.

The innate immune system serves as the body's primary physiological defense against the intrusion of pathogenic microorganisms, playing a pivotal role in restricting viral infections. However, current research on the interplay between innate immune pathways and cancer is limited, with reported effects often inconsistent. Therefore, we aimed to elucidate the relationship between innate immune pathways and tumors through an amalgamation of bioinformatics and extensive data analysis. Conducting a pan-cancer analysis encompassing expression, genomic alterations, and clinical prognosis, we identified a close association between the innate immune pathway and cholangiocarcinoma. Subsequently, our focus shifted to unraveling the role of innate immune pathway proteins in cholangiocarcinoma. TIMER database analysis showed that the innate immune pathway predominantly influences the infiltration of macrophages and B cells in cholangiocarcinoma. Additionally, gene ontology (GO) and pathway analyses were performed for significantly differentially expressed genes correlated with the innate immune pathway in cholangiocarcinoma. Single-cell transcriptome analysis in cholangiocarcinoma demonstrated that genes in the innate immune pathway are primarily expressed in malignant cells, endothelial cells, monocytes and macrophages. To further validate the expression of proteins in the innate immune pathway in the tumor tissues of patients with cholangiocarcinoma, tumor tissue slices from patients with liver intrahepatic cholangiocarcinoma and normal tissue slices from the HPA database were analyzed. These results indicated pronounced activation of the innate immune pathway in the tumor tissues of patients with cholangiocarcinoma. Finally, proteomic data from patients with or without intrahepatic cholangiocarcinoma metastasis were analyzed. The results revealed a significant correlation between the expression and phosphorylation of IKKε and the occurrence of intrahepatic cholangiocarcinoma metastasis. These findings not only demonstrate the significance of the innate immune pathway in cholangiocarcinoma but also its potential as a prospective prognostic biomarker and therapeutic target for this malignancy.

A Scalable and Robust Chloroplast Genotyping Solution: Development and Application of SNP and InDel Markers in the Maize Chloroplast Genome.

Maize(Zea mays. L) is a globally important crop, and understanding its genetic diversity is crucial for plant breeding phylogenetic analyses and comparative genetics. While nuclear markers have been extensively used for mapping agriculturally important genes, they are limited in recognizing characteristics, such as cytoplasmic male sterility and reciprocal cross hybrids. In this study, we performed next-generation sequencing of 176samples, and the maize cultivars represented five distinct groups. A total of 89 single nucleotide polymorphisms (SNPs) and 11 insertion/deletion polymorphisms (InDels) were identified. To enable high-throughput detection, we successfully amplified and confirmed 49 SNP and InDel markers, which were defined as a Varietal Chloroplast Panel (VCP) using the Kompetitive Allele Specific PCR (KASP). The specific markers provided a valuable tool for identifying chloroplast groups. The verification experiment, focusing on the identification of reciprocal cross hybrids and cytoplasmic male sterility hybrids, demonstrated the significant advantages of VCP markers in maternal inheritance characterization. Furthermore, only a small subset of these markers is needed to provide useful information, showcasing the effectiveness of these markers in elucidating the artificial selection process of elite maize lines.

[Disability identification for cases with clinical diagnosis of diffuse axonal injury due to traffic accidents: a study of 89 cases].

OBJECTIVE: To study the disability identification for cases with clinical diagnosis of diffuse axonal injury (DAI) due to traffic accidents, and to explore the possible effects of DAI on identification results. METHODS: Five hundred and fifty-six cases of cerebral injury due to traffic accidents were collected, including 467 cases diagnosed with cerebral contusion or laceration and 89 cases diagnosed with DAI. The identification results of different groups with diagnosis of DAI diagnosis, diagnosis of DAI with cerebral contusion (laceration), and diagnosis of cerebral contusion or laceration without DAI were compared and statistically analyzed, based on the results of CT and MRI re-review. RESULTS: The disability identification levels in DAI group (20 cases), DAI group (69 cases) with cerebral contusion (laceration) and DAI group (467 cases) not complicated by cerebral contusion (laceration) were 7.72 +/- 1.09, 7.78 +/- 1.11, and 8.86 +/- 0.66, respectively. The disability levels of the two groups diagnosed with DAI were higher than those of the group without DAI diagnosis (P < 0.05). CONCLUSION: Patients with DAI diagnosis might have more severe cerebral injury. In the identification process, one should pay attention to the possible missed diagnosis and misdiagnosis, and meanwhile avoid relying on those evidences provided only by CT and MRI.

Finding the priority and cluster of inflammatory biomarkers for infectious preterm birth: a systematic review.

Infectious preterm birth (PTB) is one of the most important causes of perinatal death. It is difficult to find reliable biomarkers accurate to gestational weeks for infectious PTB prediction clinically. Infectious PTB is found usually accompanied with immune imbalance. Thus, the systematic study to find the priority of inflammatory biomarkers and innovative inflammatory clusters for infectious PTB prediction is urgently needed.This systematic study that focused on the inflammatory clusters and infectious PTB in the PubMed database was analyzed by using the criteria of the Population, Intervention, Comparison, Outcome, and Study design (PICOS) framework according to the recommendations of preferred reporting items for systematic reviews and meta-analysis (PRISMA).The network meta-analyzed results showed that the prioritization of the inflammatory factors for infectious PTB prediction is soluble tumor necrosis factor receptor 2 (sTNFR2) > tumor necrosis factor α (TNFα) > interleukin-10 (IL-10) > interleukin-6 (IL-6) > C-reactive protein (CRP) > interleukin-1ß (IL-1ß). Furthermore, the results also indicated that global consideration of multiple inflammatory factors, such as CRP/IL-1ß/IL-6 biomarker cluster in gestational 27-34 weeks, and the tumor necrosis factor/nerve growth factor (TNF/NGF) family during gestational 25-33 weeks, were potential biomarker clusters that specific for infectious PTB prediction.This study systematically pointed out prioritization of the inflammatory factors for infectious PTB prediction. The results also provided evidence that maternal inflammatory clusters can predict infectious PTB occurrence at accurate gestational week. The global consideration of multiple inflammatory factors at accurate gestational age is highlighted.

Relationship of Oropharyngeal Colonization Microorganisms to Clinical Outcomes within 100 Days after Allogeneic Hematopoietic Stem Cell Transplantation.

Little is known about oropharyngeal colonization microorganisms in patients during allogeneic hematopoietic stem cell transplantation (allo-HSCT), and updated epidemiologic investigations are advisable. This study aimed to characterize oropharyngeal colonization microorganisms in patients during allo-HSCT and confirm whether they were related to clinical outcomes. This retrospective, matched case-control study included 1267 consecutive patients undergoing allo-HSCT between January 2018 and December 2020 at our institution. Patients with oropharyngeal colonization microorganisms were those with a positive throat swab before or on the day of transplantation without the occurrence of any symptoms of infection. Propensity score matching was used. Characteristics of oropharyngeal colonization microorganisms were evaluated among patients in the transplant medicine wards and compared with clinical outcomes within 100 days in positive and negative colonization groups. A total of 127 patients had oropharyngeal colonization microorganisms before or on the day of transplantation. Using propensity score matching, we matched the 127 patients in the positive colonization group with 508 patients in the negative colonization group at a 1:4 ratio (total of 635 cases). None of the differences in clinical traits between the 2 groups remained significant. Among the 127 patients with oropharyngeal colonization microorganisms, 90 patients suffered from the documented infection subsequently, and the others were asymptomatic. A total of 82 single gram-negative bacteria were identified in 127 isolates. There were no differences between the positive and negative colonization groups in the occurrence of oral mucositis, Epstein-Barr virus, or acute graft-versus-host disease and relapse within 100 days. However, the rate of neutrophil or platelet recovery was significantly lower in the positive colonization group compared with the negative colonization group (hazard ratio [HR], .71; 95% confidence interval [CI], .59 to .84; P < .001; HR .69; 95% CI, .58 to .83; P = .003; separately). The risk of bloodstream infection was higher in the positive colonization group compared with the negative colonization group (HR, 6.09; 95% CI, 3.16 to 11.75; P < .001). The continency rate between the bacteria isolated from the blood samples and oropharyngeal colonization microorganisms among the patients with positive results was 73.3%. Patients in the positive colonization group were more vulnerable to cytomegalovirus infection compared with the negative colonization group (HR, 1.41; 95% CI, 1.00 to 1.99; P = .049). The nonrelapse mortality at day +100 was higher in the positive colonization group (HR, 3.46; 95% CI, 1.69 to 7.08; P < .001). The survival probability within 100 days was significantly lower in the positive colonization group (HR, 3.38; 95% CI, 1.78 to 6.41; P < .001). Our data show that the presence of oropharyngeal colonization microorganisms is related to clinical outcomes, and that oropharyngeal microorganism monitoring may be useful during allo-HSCT.

PIDS: A User-Friendly Plant DNA Fingerprint Database Management System.

The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in plant breeding. DNA fingerprint databases are essential and important tools for plant molecular research because they provide powerful technical and information support for crop breeding, variety quality control, variety right protection, and molecular marker-assisted breeding. Building a DNA fingerprint database involves the production of large amounts of heterogeneous data for which storage, analysis, and retrieval are time and resource consuming. To process the large amounts of data generated by laboratories and conduct quality control, a database management system is urgently needed to track samples and analyze data. We developed the plant international DNA-fingerprinting system (PIDS) using an open source web server and free software that has automatic collection, storage, and efficient management functions based on merging and comparison algorithms to handle massive microsatellite DNA fingerprint data. PIDS also can perform genetic analyses. This system can match a corresponding capillary electrophoresis image on each primer locus as fingerprint data to upload to the server. PIDS provides free customization and extension of back-end functions to meet the requirements of different laboratories. This system can be a significant tool for plant breeders and can be applied in forensic science for human fingerprint identification, as well as in virus and microorganism research.

Identification and Fine Mapping of RppM, a Southern Corn Rust Resistance Gene in Maize.

Southern corn rust (SCR) caused by Puccinia polysora Underw. is a major disease causing severe yield losses during maize production. Here, we identified and mapped the SCR resistance gene RppM from the near-isogenic line Kangxiujing2416 (Jing2416K), which harbors RppM in the genetic background of the susceptible inbred line Jing2416. In this study, the inheritance of SCR resistance was investigated in F2 and F3 populations derived from a cross between Jing2416K and Jing2416. The observed 3:1 segregation ratio of resistant to susceptible plants indicated that the SCR resistance is controlled by a single dominant gene. Using an F2 population, we performed bulked segregant analysis (BSA) sequencing and mapped RppM to a 3.69-Mb region on chromosome arm 10S. To further narrow down the region harboring RppM, we developed 13 insertion/deletion (InDel) markers based on the sequencing data. Finally, RppM was mapped to a region spanning 110-kb using susceptible individuals from a large F2 population. Two genes (Zm00001d023265 and Zm00001d023267) encoding putative CC-NBS-LRR (coiled-coiled, nucleotide-binding site, and leucine-rich repeat) proteins, a common characteristic of R genes, were located in this region (B73 RefGen_v4 reference genome). Sequencing and comparison of the two genes cloned from Jing2416K and Jing2416 revealed sequence variations in their coding regions. The relative expression levels of these two genes in Jing2416K were found to be significantly higher than those in Jing2416. Zm00001d023265 and Zm00001d023267 are thus potential RppM candidates.

Association of vitamin D receptor polymorphisms with the risk of prostate cancer in the Han population of Southern China.

BACKGROUND: Molecular epidemiological studies have shown that gene polymorphisms of vitamin D receptor (VDR) are associated with prostate cancer risks. However, previous results from many molecular studies remain inconsistent. METHODS: Blood samples were collected from 122 prostate cancer patients and 130 age-matched control subjects in the Han population of Southern China. The differences of VDR gene polymorphism between cancer cases and controls were determined by PCR-RFLP, examiming FokI (exon 2), BsmI, Tru9I, ApaI (intron 9), and TaqI (exon 9). Associations between the VDR gene polymorphism and prostate cancer risk were calculated in an unconditional logistic regression model. Linkage disequilibrium and haplotypes were analyzed with the SHEsis software. RESULTS: Of five polymorphisms, BsmI was shown to associate with prostate cancer, while FokI, Tru9I, ApaI, and TaqI did not show any significant association. After adjustment for age, the BsmI 'B' allele was associated with an almost 1/3-fold risk (OR = 0.35, 95%CI: 0.15-0.80) of the occurrence of prostate cancer, a 1/5-fold risk (OR = 0.20, 95%CI: 0.06-0.68) of poorly differentiated prostate cancer, and a 1/10-fold risk (OR = 0.10, 95%CI: 0.01-0.78) of aggressive prostate cancer compared with the 'b' allele, especially among older men (>71 years). In addition, haplotype analysis revealed that the 'F-b-U-A-T' was more frequent found in cases than in controls (3.4% vs 0.0%, P = 0.0035), while the frequency of haplotype 'F-B-U-a-T' was 0.8% in cases, significantly lower than in controls (3.9%, P = 0.019). CONCLUSION: Our experiments provide evidences that genetic polymorphisms in the VDR gene may be potential risk factors for prostate cancer in the Han population of southern China and the susceptibility to prostate cancer is associated with ethnicity and geographic location.

[Related analysis of mental disability and retardation due to traffic brain injury].

OBJECTIVE: To analyze the relevant factors of determining the degree of mental disability after brain injuries in the traffic accidents. METHODS: A total of 157 forensic psychiatry cases involving the assessment of mental disability caused by traffic accidents were collected and divided into three groups (mild, moderate and severe) according to the conclusion of the forensic identification. The demographic, clinical and forensic data were compared in the three groups and analyzed with ordinal logistic regression. RESULTS: There was no statistically significant difference in the demographic data among three groups (P > 0.05). While there was statistically significant difference in the coma duration, severity of intracranial hemorrhage, working capacity, family duties, social functions, self care capacity and intelligence quotient (P < 0.05) among the groups. Intracranial hemorrhage, family duties, social functions and self care capacity were chosen as the factors in the logistic regression equation. CONCLUSION: The degree of the brain damage influenced the mental disability. Family duties, social functions and self care capacity are the major factors for determining the degree of mental disability after injured.

The HuangZaoSi Maize Genome Provides Insights into Genomic Variation and Improvement History of Maize.

Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of six completed sequenced maize genomes show that 638 proteins fall into 264 HZS-specific gene families with the majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZS-related lines reveals the breeding history of HILs. More than 60% of identified selective sweeps were clustered in identity-by-descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. Furthermore, we demonstrated that HZS-specific family genes were not uniformly distributed in the genome but enriched in improvement/function-related genomic regions. This study provides an important and novel resource for maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize.

[Expression of cyclin D1 and p27kip1 in renal cell carcinoma and its significance].

OBJECTIVE: To investigate the role of cyclin D1 and p27(kip1) in the occurrence and development of conventional renal cell carcinoma(CRCC). METHODS: RT-PCR and Western-blot were used to detect mRNA and protein contents of cyclin D1 and p27(kip1) in 25 CRCCs and 10 normal renal tissue distant to tumor. Immunohistochemistry was used to investigate the expression of cyclin D1 and p27(kip1) in pathological tissue sections of 76 CRCCs. The relationship between those index and clinicopathological parameters was analyzed statistically. RESULT: In CRCC, the expression of cyclin D1 was higher than that of the control group. The higher cyclin D1 content was related to big tumor size (P<0.05); The expression of p27(kip1) was lower than that of the control group, and the lower p27(kip1) was related to higher nuclear grade and TNM stage (P<0.01). The 5-year cumulative survival rate of the p27(kip1) high expression group is longer than that of the low group (P<0.01). CONCLUSION: The excessive expression of cyclin D1 and lower expression of p27(kip1) play an important role in the carcinogenesis of CRCC. The lower expression of p27(kip1) may affect the progression of the tumors. The detection of p27(kip1) may be as a reference marker in the prognosis of CRCC.