Pathogenic Detection by Metagenomic next-generation Sequencing in Spinal Infections.

STUDY DESIGN: Retrospective, observational study. OBJECTIVE: To evaluate the ability and value of metagenomic next-generation sequencing (mNGS) in detecting pathogens from spinal infections. BACKGROUND: The pathogenic diagnosis of primary spinal infection is challenging. The widespread application of mNGs in clinical practice makes it particularly useful in detecting rare, emerging, and atypical complex infectious diseases. METHODS: From January 2019 to December 2023, a retrospective collection of 120 samples was obtained from patients suspected of spinal infections and undergoing treatment. Pairwise comparisons between traditional laboratory tests and mNGS were conducted for all cases. RESULTS: Among the 120 cases, 95 were diagnosed as spinal infections, while 25 were classified as non-infectious. Microbiological evidence was found in 59 cases, while 36 cases were clinically diagnosed as spinal infection without definitive microbiological evidence. Rare microorganisms such as Aspergillus fumigatus, Taifanglania major, and Coxiella burnetii were detected by mNGS. The positive rate of mNGS was significantly higher at 88.42% compared to microbiological culture (43.16%), P<0.001. At the genus level, mNGS exhibited a consistency rate of 86.44% (51/59) with confirmed microorganisms. MNGS demonstrated very good agreement with clinically confirmed microorganisms at the genus level (kappa=0.833). The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were 86.44%, 92.00%, 96.23%, and 74.19%, respectively. CONCLUSIONS: The mNGS test exhibits rapidity, efficiency, and accuracy, rendering it of immense diagnostic and therapeutic value in the realm of spinal infection diseases.

DNA methylation analysis reveals local changes in resistant and susceptible soybean lines in response to Phytophthora sansomeana.

Phytophthora sansomeana is an emerging oomycete pathogen causing root rot in many agricultural species including soybean. However, as of now, only one potential resistance gene has been identified in soybean, and our understanding of how genetic and epigenetic regulation in soybean contributes to responses against this pathogen remains largely unknown. In this study, we performed whole genome bisulfite sequencing (WGBS) on two soybean lines, Colfax (resistant) and Williams 82 (susceptible) in response to P. sansomeana at two time points: 4 and 16 hours post inoculation to compare their methylation changes. Our findings revealed that there were no significant changes in genome-wide CG, CHG (H = A, T, or C), and CHH methylation. However, we observed local methylation changes, specially an increase in CHH methylation around genes and transposable elements (TEs) after inoculation, which occurred earlier in the susceptible line and later in the resistant line. After inoculation, we identified differentially methylated regions (DMRs) in both Colfax and Williams 82, with a predominant presence in TEs. Notably, our data also indicated that more TEs exhibited changes in their methylomes in the susceptible line compared to the resistant line. Furthermore, we discovered 837 DMRs within or flanking 772 differentially expressed genes (DEGs) in Colfax and 166 DMRs within or flanking 138 DEGs in Williams 82. These DEGs had diverse functions, with Colfax primarily showing involvement in metabolic process, defense response, plant and pathogen interaction, anion and nucleotide binding, and catalytic activity, while Williams 82 exhibited a significant association with photosynthesis. These findings suggest distinct molecular responses to P. sansomeana infection in the resistant and susceptible soybean lines.

Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana.

Phytophthora root rot, caused by oomycete pathogens in the Phytophthora genus, poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied in soybean, the molecular basis underlying immune responses to Phytophthora sansomeana remains unclear. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 h post inoculation [hpi]) after P. sansomeana inoculation. Comparative transcriptomic analyses revealed a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in resistant lines, particularly at 8 and 16 hpi. These DEGs were predominantly associated with defense response, ethylene, and reactive oxygen species-mediated defense pathways. Moreover, DE transposons were predominantly upregulated after inoculation, and more of them were enriched near genes in Colfax than other soybean lines. Notably, we identified a long non-coding RNA (lncRNA) within the mapped region of the resistance gene that exhibited exclusive upregulation in the resistant lines after inoculation, potentially regulating two flanking LURP-one-related genes. Furthermore, DNA methylation analysis revealed increased CHH (where H = A, T, or C) methylation levels in lncRNAs after inoculation, with delayed responses in Colfax compared to Williams 82. Overall, our results provide comprehensive insights into soybean responses to P. sansomeana, highlighting potential roles of lncRNAs and epigenetic regulation in plant defense.

Development and implementation of nested single-nucleotide polymorphism (SNP) assays for breeding and genetic research applications.

SoySNP50K and SoySNP6K are commonly used for soybean (Glycine max) genotyping. The SoySNP50K assay has been used to genetically analyze the entire USDA Soybean Germplasm Collection, while the SoySNP6K assay, containing a subset of 6000 single-nucleotide polymorphisms (SNPs) from SoySNP50K, has been used for quantitative trait loci mapping of different traits. To meet the needs for genomic selection, selection of parents for crosses, and characterization of breeding populations, especially early selection of ideal offspring from thousands of lines, we developed two assays, SoySNP3K and SoySNP1K, containing 3072 and 1252 SNPs, respectively, based on SoySNP50K and SoySNP6K mark sets. These two assays also contained the trait markers reported or contributed by soybean breeders. The SNPs in the SoySNP3K are a subset from SoySNP6K, while the SNPs in the SoySNP1K are a subset from SoySNP3K. These SNPs were chosen to reduce the SNP number in the large linkage blocks while capturing as much of the haplotype diversity as possible. They are highly polymorphic and of high quality. The mean minor allele frequencies of the SNPs in the southern and northern US elites were 0.25 and 0.27 for SoySNP3K, respectively, and 0.29 and 0.33 for SoySNP1K. The selected SNPs are a valuable source for developing targeted amplicon sequencing assay or beadchip assay in soybean. SoySNP3K and SoySNP1K assays are commercialized by Illumina Inc. and AgriPlex Genomics, respectively. Together with SoySNP50K and SoySNP6K, a series of nested assays with different marker densities will serve as additional low-cost genomic tools for genetic, genomic, and breeding research.

Important role and underlying mechanism of non­SMC condensin I complex subunit G in tumours (Review).

At present, the incidence of tumours is increasing on a yearly basis, and tumourigenesis is usually associated with chromosomal instability and cell cycle dysregulation. Moreover, abnormalities in the chromosomal structure often lead to DNA damage, further exacerbating gene mutations and chromosomal rearrangements. However, the non­SMC condensin I complex subunit G (NCAPG) of the structural maintenance of chromosomes family is known to exert a key role in tumour development. It has been shown that high expression of NCAPG is closely associated with tumour development and progression. Overexpression of NCAPG variously affects chromosome condensation and segregation during cell mitosis, influences cell cycle regulation, promotes tumour cell proliferation and invasion, and inhibits apoptosis. In addition, NCAPG has been associated with tumour cell stemness, tumour resistance and recurrence. The aim of the present review was to explore the underlying mechanisms of NCAPG during tumour development, with a view towards providing novel targets and strategies for tumour therapy, and through the elucidation of the mechanisms involved, to lay the foundation for future developments in health.

Identification and molecular mapping of a major gene conferring resistance to Phytophthora sansomeana in soybean 'Colfax'.

KEY MESSAGE: The first single dominant resistance gene contributing major resistance to the oomycete pathogen Phytophthora sansomeana was identified and mapped from soybean 'Colfax'. Phytophthora root rot (PRR) is one of the most important diseases in soybean (Glycine max). PRR is well known to be caused by Phytophthora sojae, but recent studies showed that P. sansomeana also causes extensive root rot of soybean. Depending upon the isolate, it might produce aggressive symptoms, especially in seeds and seedlings. Unlike P. sojae which can be effectively managed by Rps genes, no known major resistance genes have yet been reported for P. sansomeana. Our previous study screened 470 soybean germplasm lines for resistance to P. sansomeana and found that soybean 'Colfax' (PI 573008) carries major resistance to the pathogen. In this study, we crossed 'Colfax' with a susceptible parent, 'Senaki', and developed three mapping populations with a total of 234 F2:3 families. Inheritance pattern analysis indicated a 1:2:1 ratio for resistant: segregating: susceptible lines among all the three populations, indicating a single dominant gene conferring the resistance in 'Colfax' (designated as Rpsan1). Linkage analysis using extreme phenotypes anchored Rpsan1 to a 30 Mb region on chromosome 3. By selecting nine polymorphic SNP markers within the region, Rpsan1 was genetically delimited into a 21.3 cM region between Gm03_4487138_A_C and Gm03_5451606_A_C, which corresponds to a 1.06 Mb genomic region containing nine NBS-LRR genes based on Gmax2.0 assembly. The mapping results were then validated using two breeding populations derived from 'E12076T-03' × 'Colfax' and 'E16099' × 'Colfax'. Marker-assisted resistance spectrum analyses with 9 additional isolates of P. sansomeana indicated that Rpsan1 may be effective towards a broader range of P. sansomeana isolates and has strong merit in protecting soybean to this pathogen in the future.

Accuracy of the Cage Placement in Oblique Lumbar Interbody Fusion and its Effects on the Radiological Outcome in Lumbar Degenerative Disease.

STUDY DESIGN: A retrospective study. OBJECTIVES: This study aimed to check how accurately cages were inserted and how they affected the radiological results in oblique lumbar interbody fusion (OLIF) at L2-L5. METHODS: A total of 137 patients diagnosed with lumbar degenerative disease, 184 intervertebral discs were included. We used a new cage deviation classification system on magnetic resonance imaging (MRI) to determine cage insertion accuracy. Cage deviation angles (CDA) were classified into four groups based on the angle formed by the long axis of the cage and the horizontal axis of the vertebral body. Other radiological parameters on plain radiographs and MRI were compared based on this classification. RESULTS: Among 183 cages, 19 were in zone Ⅰ-Ⅱ (10.32%), 163 were in zone II-III (88.59%), and two were in zone III-IV (1.09%). The median cage deviation was 4.97°. No significant differences (H = 2.479, P = .290 > .05) of CDA were found among different segments. Posterior cage deviation accounted 94.57%. The minimal, mild, moderate, and severe cage deviation was 89 (48.4%), 51 (27.7%), 30 (16.3%), and 14 (7.6%) respectively. No differences in radiological parameter changes were noted among different cage obliquity categories. CONCLUSIONS: Approximately 98.91% of cages were placed in zones I-II and II-III. Most cages deviated posteriorly with CDA ranging minimal to moderate. Minimal to moderate cage deviation did not impact radiological outcomes significantly in OLIF at L2-L5. However, avoiding severe cage deviation is crucial to prevent contralateral traversing nerve root injuries.

Genome-wide association study on resistance of cultivated soybean to Fusarium oxysporum root rot in Northeast China.

BACKGROUND: Fusarium oxysporum is a prevalent fungal pathogen that diminishes soybean yield through seedling disease and root rot. Preventing Fusarium oxysporum root rot (FORR) damage entails on the identification of resistance genes and developing resistant cultivars. Therefore, conducting fine mapping and marker development for FORR resistance genes is of great significance for fostering the cultivation of resistant varieties. In this study, 350 soybean germplasm accessions, mainly from Northeast China, underwent genotyping using the SoySNP50K Illumina BeadChip, which includes 52,041 single nucleotide polymorphisms (SNPs). Their resistance to FORR was assessed in a greenhouse. Genome-wide association studies utilizing the general linear model, mixed linear model, compressed mixed linear model, and settlement of MLM under progressively exclusive relationship models were conducted to identify marker-trait associations while effectively controlling for population structure. RESULTS: The results demonstrated that these models effectively managed population structure. Eight SNP loci significantly associated with FORR resistance in soybean were detected, primarily located on Chromosome 6. Notably, there was a strong linkage disequilibrium between the large-effect SNPs ss715595462 and ss715595463, contributing substantially to phenotypic variation. Within the genetic interval encompassing these loci, 28 genes were present, with one gene Glyma.06G088400 encoding a protein kinase family protein containing a leucine-rich repeat domain identified as a potential candidate gene in the reference genome of Williams82. Additionally, quantitative real-time reverse transcription polymerase chain reaction analysis evaluated the gene expression levels between highly resistant and susceptible accessions, focusing on primary root tissues collected at different time points after F. oxysporum inoculation. Among the examined genes, only this gene emerged as the strongest candidate associated with FORR resistance. CONCLUSIONS: The identification of this candidate gene Glyma.06G088400 improves our understanding of soybean resistance to FORR and the markers strongly linked to resistance can be beneficial for molecular marker-assisted selection in breeding resistant soybean accessions against F. oxysporum.

Estimation of heart rate and respiratory rate by monitoring cardiopulmonary signals with flexible sensor.

Monitoring of cardiopulmonary signals plays an important role in many clinical applications. A portable magnetic induction cardiopulmonary signal monitoring system with the flexible sensor of double micro-coils is presented in this paper. The detection of cardiopulmonary signals is realized with double micro-coils. The proposed system is safe, non-invasive, simple, and portable compared with traditional direct contact methods. The Hilbert-Huang transform (HHT) based on complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) is applied to cardiopulmonary signal processing, decomposing cardiopulmonary signal effectively. The sensor to monitor respiration rate and heart rate is validated and demonstrated with healthy volunteers. The root mean squared errors (RMSE) of heart rate, respiration rate under deep breathing and normal breathing are 3.8 beats/min, 0.61 times/min, and 0.98 times/min respectively. The flexible sensor of double micro-coils has little influence on the measurement results at the bending curvature of 33.9 m-1. Therefore, a suggested solution for monitoring and decomposition of cardiopulmonary signals is easy-to-use, and quick, which can be applied as a respected analytical device on mobile occasions in this study.

Genome-wide association study of powdery mildew resistance in cultivated soybean from Northeast China.

Powdery mildew (PMD), caused by the pathogen Microsphaera diffusa, leads to substantial yield decreases in susceptible soybean under favorable environmental conditions. Effective prevention of soybean PMD damage can be achieved by identifying resistance genes and developing resistant cultivars. In this study, we genotyped 331 soybean germplasm accessions, primarily from Northeast China, using the SoySNP50K BeadChip, and evaluated their resistance to PMD in a greenhouse setting. To identify marker-trait associations while effectively controlling for population structure, we conducted genome-wide association studies utilizing factored spectrally transformed linear mixed models, mixed linear models, efficient mixed-model association eXpedited, and compressed mixed linear models. The results revealed seven single nucleotide polymorphism (SNP) loci strongly associated with PMD resistance in soybean. Among these, one SNP was localized on chromosome (Chr) 14, and six SNPs with low linkage disequilibrium were localized near or in the region of previously mapped genes on Chr 16. In the reference genome of Williams82, we discovered 96 genes within the candidate region, including 17 resistance (R)-like genes, which were identified as potential candidate genes for PMD resistance. In addition, we performed quantitative real-time reverse transcription polymerase chain reaction analysis to evaluate the gene expression levels in highly resistant and susceptible genotypes, focusing on leaf tissues collected at different times after M. diffusa inoculation. Among the examined genes, three R-like genes, including Glyma.16G210800, Glyma.16G212300, and Glyma.16G213900, were identified as strong candidates associated with PMD resistance. This discovery can significantly enhance our understanding of soybean resistance to PMD. Furthermore, the significant SNPs strongly associated with resistance can serve as valuable markers for genetic improvement in breeding M. diffusa-resistant soybean cultivars.

Comparison between OLIF and MISTLIF in degenerative lumbar stenosis: an age-, sex-, and segment-matched cohort study.

To compare outcomes after oblique lateral interbody fusion (OLIF) versus minimally invasive transforaminal lumbar interbody fusion (MISTLIF) with bilateral decompression via unilateral approach for treating mild to moderate symptomatic degenerative lumbar spinal stenosis (DLSS). We retrospectively compared patients who underwent single-level (L4/5) OLIF with an age-, sex-, and segment-matched MISTLIF with bilateral decompression via unilateral approach cohort. Perioperative data were collected for the operative time, intraoperative blood loss, drainage in the first postoperative day, postoperative hospital stay, cost, intraoperative fluoroscopy, and complications. Lumbar radiographs were measured for changes in posterior intervertebral space height (PISH), intervertebral space foramen height (IFH), intervertebral foramen area (IFA), and area of the spinal canal (ASC). Clinical and psychological outcomes included the visual analog scale (VAS), Oswestry Disability Index (ODI), and hospital anxiety and depression scale (HADS). 35 OLIF patients were compared with 35 MISTLIF patients in L4/5 DLSS. The OLIF group had shorter bedtime, postoperative hospital stays, less intraoperative and postoperative blood loss (all P < 0.05), but had more times of intraoperative fluoroscopy, longer operative time, and higher cost (all P < 0.05). The complication rates were equivalent (OLIF vs MISTLIF: 22.86% vs 17.14%). PISH (11.94 ± 1.78 mm vs 9.42 ± 1.94 mm, P < 0.05), IFH (23.87 ± 3.05 mm vs 21.41 ± 2.95 mm, P < 0.05), and IFA (212.14 ± 51.82 mm2 vs 177.07 ± 51.73 mm2, P < 0.05) after surgery were significantly increased in the OLIF group. The ASC was increased significantly after the operation in both groups, but the ASC in the MISTLIF group was increased significantly more than that in the OLIF group (450.04 ± 66.66 mm2 vs 171.41 ± 58.55 mm2, P < 0.05). The lumbar VAS scores at 1 month (1.89 ± 0.87 vs 2.34 ± 0.84, P = 0.028) and 6 months (1.23 ± 0.97 vs 1.80 ± 0.99, P = 0.018) after operation in the OLIF group were significantly lower. There were no significant differences in lower extremity VAS and ODI scores between the two groups. Compared with MISTLIF group, HADS scores on postoperative day 3 (2.91 ± 1.46 vs 4.89 ± 1.78, P < 0.05) and prior to hospital discharge (PTD) (2.54 ± 1.38 vs 3.80 ± 1.78, P = 0.002) in the OLIF group were decreased significantly. OLIF showed more advantages of less surgical invasion, lower incidence of postoperative low back pain, faster postoperative recovery, and less anxiety compared with MISTLIF. Regardless of cost, OLIF seems to be a better option to treat mild to moderate symptomatic DLSS.

Andrographolide Inhibits Static Mechanical Pressure-Induced Intervertebral Disc Degeneration via the MAPK/Nrf2/HO-1 Pathway.

Purpose: To explore the molecular mechanism by which andrographolide (ADR) inhibits static mechanical pressure-induced apoptosis in nucleus pulposus cells (NPCs) and to assess the role of ADR in inhibiting IDD. Methods: Hematoxylin-eosin (HE), toluidine blue, and immunofluorescence staining were used to identify NPCs. An NPC apoptosis model was constructed using a homemade cell pressurization device. The proliferation activity, reactive oxygen species (ROS) content, and apoptosis rate were detected using kits. The expression of related proteins was detected using Western blot. A rat tailbone IDD model was constructed using a homemade tailbone stress device. HE staining and safranine O-fast green FCF cartilage staining were used to observe the degeneration degree of the intervertebral disk. Results: ADR inhibits static mechanical pressure-induced apoptosis and ROS accumulation in NPCs and improves cell viability. ADR can promote the expression of Heme oxygenase-1 (HO-1), p-Nrf2, p-p38, p-Erk1/2, p-JNK, and other proteins, and its effects can be blocked by inhibitors of the above proteins. Conclusion: ADR can inhibit IDD by activating the MAPK/Nrf2/HO-1 signaling pathway and suppressing static mechanical pressure-induced ROS accumulation in the NPCs.

Haplotype and Genetic Analysis of 41 Y-STR Loci in the Wuwei Han Population from Gansu Province, China.

OBJECTIVE: Y-Chromosomal short tandem repeat polymorphism (Y-STR) analysis plays an indispensable role in the identification of male individuals, population genetics, and biogeographic research. While profiles of many populations based on Y-STR markers in human genomes are ample, haplotype data for the Wuwei Han are still scarce. METHODS: In this study, 2180 unrelated Wuwei Han male individuals residing in Gansu Province, China were collected and genotyped using the novel Microreader™ 40Y Plus ID system. Phylogenetic relationship reconstructions, multidimensional scaling (MDS), and heatmap analysis were performed based on the genetic distance (Rst) values between our studied population and other populations of the Ymax module in the Y-STR Haplotype Reference Database (YHRD). RESULTS: A total of 2129 unique haplotypes were obtained, and the haplotype diversity (HD) and discrimination capacity (DC) for the Wuwei Han were 0.9999 and 0.9931, respectively. CONCLUSION: Our results demonstrate that the Wuwei Han population had intimate genetic relationships with East Asians, especially the geographically close Han populations. Overall, this Y-Chromosomal assay gives valuable information about paternal lineages in male individual tracking and genealogical database construction.

Identification and characterization of pleiotropic and epistatic QDRL conferring partial resistance to Pythium irregulare and P. sylvaticum in soybean.

KEY MESSAGE: Pleiotropic and epistatic quantitative disease resistance loci (QDRL) were identified for soybean partial resistance to different isolates of Pythium irregulare and Pythium sylvaticum. Pythium root rot is an important seedling disease of soybean [Glycine max (L.) Merr.], a crop grown worldwide for protein and oil content. Pythium irregulare and P. sylvaticum are two of the most prevalent and aggressive Pythium species in soybean producing regions in the North Central U.S. Few studies have been conducted to identify soybean resistance for management against these two pathogens. In this study, a mapping population (derived from E13390 x E13901) with 228 F4:5 recombinant inbred lines were screened against P. irregulare isolate MISO 11-6 and P. sylvaticum isolate C-MISO2-2-30 for QDRL mapping. Correlation analysis indicated significant positive correlations between soybean responses to the two pathogens, and a pleiotropic QDRL (qPirr16.1) was identified. Further investigation found that the qPirr16.1 imparts dominant resistance against P. irregulare, but recessive resistance against P. sylvaticum. In addition, two QDRL, qPsyl15.1, and qPsyl18.1 were identified for partial resistance to P. sylvaticum. Further analysis revealed epistatic interactions between qPirr16.1 and qPsyl15.1 for RRW and DRX, whereas qPsyl18.1 contributed resistance to RSE. Marker-assisted resistance spectrum analysis using F6:7 progeny lines verified the resistance of qPirr16.1 against four additional P. irregulare isolates. Intriguingly, although the epistatic interaction of qPirr16.1 and qPsyl15.1 can be confirmed using two additional isolates of P. sylvaticum, the interaction appears to be suppressed for the other two P. sylvaticum isolates. An 'epistatic gene-for-gene' model was proposed to explain the isolate-specific epistatic interactions. The integration of the QDRL into elite soybean lines containing all the desirable alleles has been initiated.

Breeding for disease resistance in soybean: a global perspective.

KEY MESSAGE: This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world. Breeding disease-resistant soybean [Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.

A Machine Learning-Based System for Real-Time Polyp Detection (DeFrame): A Retrospective Study.

Background and Aims: Recent studies have shown that artificial intelligence-based computer-aided detection systems possess great potential in reducing the heterogeneous performance of doctors during endoscopy. However, most existing studies are based on high-quality static images available in open-source databases with relatively small data volumes, and, hence, are not applicable for routine clinical practice. This research aims to integrate multiple deep learning algorithms and develop a system (DeFrame) that can be used to accurately detect intestinal polyps in real time during clinical endoscopy. Methods: A total of 681 colonoscopy videos were collected for retrospective analysis at Xiangya Hospital of Central South University from June 2019 to June 2020. To train the machine learning (ML)-based system, 6,833 images were extracted from 48 collected videos, and 1,544 images were collected from public datasets. The DeFrame system was further validated with two datasets, consisting of 24,486 images extracted from 176 collected videos and 12,283 images extracted from 259 collected videos. The remaining 198 collected full-length videos were used for the final test of the system. The measurement metrics were sensitivity and specificity in validation dataset 1, precision, recall and F1 score in validation dataset 2, and the overall performance when tested in the complete video perspective. Results: A sensitivity and specificity of 79.54 and 95.83%, respectively, was obtained for the DeFrame system for detecting intestinal polyps. The recall and precision of the system for polyp detection were determined to be 95.43 and 92.12%, respectively. When tested using full colonoscopy videos, the system achieved a recall of 100% and precision of 80.80%. Conclusion: We have developed a fast, accurate, and reliable DeFrame system for detecting polyps, which, to some extent, is feasible for use in routine clinical practice.

Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent Latitude Distribution.

Adaptation of soybean cultivars to the photoperiod in which they are grown is critical for optimizing plant yield. However, despite its importance, only the major loci conferring variation in flowering time and maturity of US soybean have been isolated. By contrast, over 200 genes contributing to floral induction in the model organism Arabidopsis thaliana have been described. In this work, putative alleles of a library of soybean orthologs of these Arabidopsis flowering genes were tested for their latitudinal distribution among elite US soybean lines developed in the United States. Furthermore, variants comprising the alleles of genes with significant differences in latitudinal distribution were assessed for amino acid conservation across disparate genera to infer their impact on gene function. From these efforts, several candidate genes from various biological pathways were identified that are likely being exploited toward adaptation of US soybean to various maturity groups.