Evaluating diagnostic significance: The utilization of elastography and contrast-enhanced ultrasound for differential diagnosis in breast lesions.

OBJECTIVE: The primary aim of this study is to assess the diagnostic efficacy of elastography and contrast-enhanced ultrasound (CEUS) in the identification of breast lesions subsequent to the optimization and correction of the BI-RADS category 4 classification obtained through conventional ultrasound. The objective is to augment both the specificity and accuracy of breast lesion diagnosis, thereby establishing a reliable framework for reducing unnecessary biopsies in clinical settings. METHODS: A cohort comprising 50 cases of breast lesions classified under BI-RADS category 4 was collected during the period from November 2022 and November 2023. These cases were examined utilizing strain elastography (SE), shear wave elastography (SWE), and CEUS. Novel scoring methodologies for ultrasonic elastography (UE) and CEUS were formulated for this investigation. Subsequently, the developed UE and CEUS scoring systems were used to refine and optimize the conventional BI-RADS classification, either in isolation or in conjunction. Based on the revised classification, the benign group was classified as category 3 and the suspected malignant group was classified as category 4a and above, with pathological results serving as the definitive reference standard. The diagnostic efficacy of the optimized UE and CEUS, both independently and in combination, was meticulously scrutinized and compared using receiver operating characteristic (ROC) curve analysis, with pathological findings as the reference standard. RESULTS: Within the study group, malignancy manifested in 11 cases. Prior to the implementation of the optimization criteria, 78% (39 out of 50) of patients underwent biopsies deemed unnecessary. Following the application of optimization criteria, specifically a threshold of≥8.5 points for the UE scoring method and≥6.5 points for the CEUS scoring method, the incidence of unnecessary biopsies diminished significantly. Reduction rates were observed at 53.8% (21 out of 39) with the UE protocol, 56.4% (22 out of 39) with the CEUS protocol, and 89.7% (35 out of 39) with the combined UE and CEUS optimization protocols. CONCLUSION: The diagnostic efficacy of conventional ultrasound BI-RADS category 4 classification for breast lesions is enhanced following optimized correction using UE and CEUS, either independently or in conjunction. The application of the combined protocol demonstrates a notable reduction in the incidence of unnecessary biopsies.

Classification of peanut pod rot based on improved YOLOv5s.

Peanut pod rot is one of the major plant diseases affecting peanut production and quality over China, which causes large productivity losses and is challenging to control. To improve the disease resistance of peanuts, breeding is one significant strategy. Crucial preventative and management measures include grading peanut pod rot and screening high-contributed genes that are highly resistant to pod rot should be carried out. A machine vision-based grading approach for individual cases of peanut pod rot was proposed in this study, which avoids time-consuming, labor-intensive, and inaccurate manual categorization and provides dependable technical assistance for breeding studies and peanut pod rot resistance. The Shuffle Attention module has been added to the YOLOv5s (You Only Look Once version 5 small) feature extraction backbone network to overcome occlusion, overlap, and adhesions in complex backgrounds. Additionally, to reduce missing and false identification of peanut pods, the loss function CIoU (Complete Intersection over Union) was replaced with EIoU (Enhanced Intersection over Union). The recognition results can be further improved by introducing grade classification module, which can read the information from the identified RGB images and output data like numbers of non-rotted and rotten peanut pods, the rotten pod rate, and the pod rot grade. The Precision value of the improved YOLOv5s reached 93.8%, which was 7.8%, 8.4%, and 7.3% higher than YOLOv5s, YOLOv8n, and YOLOv8s, respectively; the mAP (mean Average Precision) value was 92.4%, which increased by 6.7%, 7.7%, and 6.5%, respectively. Improved YOLOv5s has an average improvement of 6.26% over YOLOv5s in terms of recognition accuracy: that was 95.7% for non-rotted peanut pods and 90.8% for rotten peanut pods. This article presented a machine vision- based grade classification method for peanut pod rot, which offered technological guidance for selecting high-quality cultivars with high resistance to pod rot in peanut.

Transcriptome and Co-expression Network Analyses Reveal Differential Gene Expression and Pathways in Response to Severe Drought Stress in Peanut (Arachis hypogaea L.).

Drought is one of the major abiotic stress factors limiting peanut production. It causes the loss of pod yield during the pod formation stage. Here, one previously identified drought-tolerant cultivar, "L422" of peanut, was stressed by drought (35 ± 5%) at pod formation stage for 5, 7, and 9 days. To analyze the drought effects on peanut, we conducted physiological and transcriptome analysis in leaves under well-watered (CK1, CK2, and CK3) and drought-stress conditions (T1, T2, and T3). By transcriptome analysis, 3,586, 6,730, and 8,054 differentially expressed genes (DEGs) were identified in "L422" at 5 days (CK1 vs T1), 7 days (CK2 vs T2), and 9 days (CK3 vs T3) of drought stress, respectively, and 2,846 genes were common DEGs among the three-time points. Furthermore, the result of weighted gene co-expression network analysis (WGCNA) revealed one significant module that was closely correlated between drought stress and physiological data. A total of 1,313 significantly up-/down-regulated genes, including 61 transcription factors, were identified in the module at three-time points throughout the drought stress stage. Additionally, six vital metabolic pathways, namely, "MAPK signaling pathway-plant," "flavonoid biosynthesis," "starch and sucrose metabolism," "phenylpropanoid biosynthesis," "glutathione metabolism," and "plant hormone signal transduction" were enriched in "L422" under severe drought stress. Nine genes responding to drought tolerance were selected for quantitative real-time PCR (qRT-PCR) verification and the results agreed with transcriptional profile data, which reveals the reliability and accuracy of transcriptome data. Taken together, these findings could lead to a better understanding of drought tolerance and facilitate the breeding of drought-resistant peanut cultivars.

Effects of Genetic Background and Environmental Conditions on Amylopectin Chain-Length Distribution in a Recombinant Inbred Line of an Inter-subspecies Rice Cross.

Amylopectin is an essential starch property, and the chain-length distribution of amylopectin (APCLD) is closely associated with the eating and cooking quality of rice. In this study, a series of recombinant inbred lines derived from an indica/japonica cross were planted in four areas with distinct ecological conditions (LN, SC, JS, and GD), and the relationship among APCLD, environmental factors, and genetic background was analyzed. The results showed that APCLD was strongly influenced by environmental factors, which dynamically changed from heading to the mature stage. The solar radiation, luminous flux, and light hours were positively correlated with Fa but negatively correlated with Fb1 and Fb2. The temperature was negatively correlated with Fa and Fb1 but positively correlated with Fb2 and Fb3. The temperature was the primary factor affecting APCLD, followed by humidity and light. There was no significant correlation between the indica pedigree percentage and APCLD. Furthermore, we detected six quantitative trait loci related to Fa, Fb1, Fb2, and Fb3 chains, several of which shared a similar region to previously reported loci, including DENSE AND ERECT PANICLE 1 (DEP1). The truncated dep1 allele increased Fa, Fb2, and Fb3 but decreased Fb1 in LN, whereas Fa was decreased but Fb1 and Fb2 were increased in JS. Elucidating the effects of climate factors and genetic background on APCLD could provide a theoretical basis and technical guidance for high-quality rice breeding.

Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci.

BACKGROUND: Two of the most widely cultivated rice strains are Oryza sativa indica and O. sativa japonica, and understanding the genetic basis of their agronomic traits is of importance for crop production. These two species are highly distinct in terms of geographical distribution and morphological traits. However, the relationship among genetic background, ecological conditions, and agronomic traits is unclear. RESULTS: In this study, we performed the de novo assembly of a high-quality genome of SN265, a cultivar that is extensively cultivated as a backbone japonica parent in northern China, using single-molecule sequencing. Recombinant inbred lines (RILs) derived from a cross between SN265 and R99 (indica) were re-sequenced and cultivated in three distinct ecological conditions. We identify 79 QTLs related to 15 agronomic traits. We found that several genes underwent functional alterations when the ecological conditions were changed, and some alleles exhibited contracted responses to different genetic backgrounds. We validated the involvement of one candidate gene, DEP1, in determining panicle length, using CRISPR/Cas9 gene editing. CONCLUSIONS: This study provides information on the suitable environmental conditions, and genetic background, for functional genes in rice breeding. Moreover, the public availability of the reference genome of northern japonica SN265 provides a valuable resource for plant biologists and the genetic improvement of crops.

Molecular Characterization of Magnesium Chelatase in Soybean [Glycine max (L.) Merr.].

Soybean (Glycine max) seed yields rely on the efficiency of photosynthesis, which is poorly understood in soybean. Chlorophyll, the major light harvesting pigment, is crucial for chloroplast biogenesis and photosynthesis. Magnesium chelatase catalyzes the insertion of Mg2+ into protoporphyrin IX in the first committed and key regulatory step of chlorophyll biosynthesis. It consists of three types of subunits, ChlI, ChlD, and ChlH. To gain a better knowledge of chlorophyll biosynthesis in soybean, we analyzed soybean Mg-chelatase subunits and their encoding genes. Soybean genome harbors 4 GmChlI genes, 2 GmChlD genes, and 3 GmChlH genes, likely evolved from two rounds of gene duplication events. The qRT-PCR analysis revealed that GmChlI, GmChlD, and GmChlH genes predominantly expressed in photosynthetic tissues, but the expression levels among paralogs are different. In silicon promoter analyses revealed these genes harbor different cis-regulatory elements in their promoter regions, suggesting they could differentially respond to various environmental and developmental signals. Subcellular localization analyses illustrated that GmChlI, GmChlD, and GmChlH isoforms are all localized in chloroplast, consistent with their functions. Yeast two hybrid and bimolecular fluorescence complementation (BiFC) assays showed each isoform has a potential to be assembled into the Mg-chelatase holocomplex. We expressed each GmChlI, GmChlD, and GmChlH isoform in Arabidopsis corresponding mutants, and results showed that 4 GmChlI and 2 GmChlD isoforms and GmChlH1 could rescue the severe phenotype of Arabidopsis mutants, indicating that they maintain normal biochemical functions in vivo. However, GmChlH2 and GmChlH3 could not completely rescue the chlorotic phenotype of Arabidopsis gun5-2 mutant, suggesting that the functions of these two proteins could be different from GmChlH1. Considering the differences shown on primary sequences, biochemical functions, and gene expression profiles, we conclude that the paralogs of each soybean Mg-chelatase subunit have diverged more or less during evolution. Soybean could have developed a complex regulatory mechanism to control chlorophyll content to adapt to different developmental and environmental situations.

Deciphering the Environmental Impacts on Rice Quality for Different Rice Cultivated Areas.

BACKGROUND: Rice (Oryza sativa L.) is cultivated in a wide range of climatic conditions, and is one of mankind's major staple foods. The interaction of environmental factors with genotype effects major agronomic traits such as yield, quality, and resistance in rice. However, studies on the environmental factors affecting agronomic traits are often difficult to conduct because most environmental factors are dynamic and constantly changing. RESULTS: A series of recombinant inbred lines (RILs) derived from an indica/japonica cross were planted into four typical rice cultivated areas arranging from latitude N22° to N42°. The environmental data from the heading to mature (45 days) stages were recorded for each RIL in the four areas. We determined that light, temperature, and humidity significantly affected the milling quality and cooking quality overall the four areas. Within each area, these environmental factors mainly affected the head rice ratio, grain length, alkali consumption, and amylose and protein content. Moreover, the effect of these environmental factors dynamically changed from heading to mature stage. Compared to light and humidity, temperature was more stable and predictable, and night temperature showed a stronger correlation efficiency to cooking quality than day temperature, and the daily temperature range had contrary effects compared to day and night temperature on grain quality. CONCLUSIONS: The present study evaluated the critical phase during the grain filling stage by calculating the dynamic changes of correlation efficiency between the quality traits and climate parameters. Our findings suggest that the sowing date could be adjusted to improve rice quality so as to adjust for environmental changes.

Sparse estimation of backscattered echoes from underwater object using integrated dictionaries.

The problem of time-delays estimation of backscattered echoes from underwater targets is presented using a sparse reconstruction framework employing an integrated dictionary. To achieve high resolution, the used dictionary is usually defined over a finely spaced grid over the region of interest. Such a procedure may result in problems of being computational cumbersome or suffering from basis mismatch. In addition, the shape of the backscattered echoes may differ significantly from the expected waveforms used to form the dictionary, causing further mismatch problems. To alleviate such problems, the use of an integrated dictionary framework is introduced. Unlike traditional dictionaries that are defined over a set of grid points, the elements in an integrated dictionary are formed by integrating the expected waveform over bands of the parameter space. The resulting dictionary may be used to find initial regions of the parameters of interest using a smaller dictionary than otherwise required, without suffering a loss of performance. The elements can also better match with the backscattered echoes, even if these differ from their expected shape. Simulated results of the backscattered echoes from a cylindrical shell, as well as results from experimental measurements, illustrate the performance of the proposed method.

Rigid and elastic acoustic scattering signal separation for underwater target.

Underwater target elastic acoustic scattering and other acoustic scattering components are aliasing together in the time and frequency domains, and the existing signal processing methods cannot recognize the elastic scattering features under the aliasing condition because of the resolution limitation. To address this problem, this study, which is based on the target echo highlight model, analyzes the characteristics of target acoustic scattering components when the transmitted signal is a linear frequency modulation pulse. The target acoustic scattering structure in the fractional Fourier transform (FRFT) domain is deduced theoretically. Then, filtering is used in the FRFT domain to separate the target elastic acoustic scattering components. In addition, noise suppression performance and filter resolution are discussed. The target rigid and elastic acoustic scattering components are separated. Experimental results show that filtering in the FRFT domain can separate the elastic scattering components from the target echoes. Moreover, separated elastic acoustic scattering components have consistent theoretical features, which lay the foundation for studying the elastic scattering characteristics further.

Coexisting and possible primary extra-gastrointestinal stromal tumors of the pancreas and liver: A single case report.

Gastrointestinal stromal tumors (GIST) are mesenchymal neoplasms of the gastrointestinal tract (GI) that are defined, in part, by the expression of CD117, a c-Kit proto-oncogene protein. GISTs emerge outside of the GI at a very low frequency, typically in a single organ or location. GISTs that occasionally emerge outside of the GI are classified as extra-gastrointestinal stromal tumors (EGIST). The present study reports an extremely rare case of EGIST detected in the pancreas and the liver. The pancreatic and liver tumors were 4.5×2.5 cm and 2.0×1.5 cm in size, respectively. Both tumors consisted of CD117-positive spindle cells with a similar mitotic rate of 1-2 per 50 high power fields. The pancreatic and the hepatic EGISTs were at a low risk of malignancy, and both tumors were proposed to be primary stromal tumors. To the best of our knowledge, this is the first report of likely primary EGIST identified in the pancreas and liver of the same patient.

Protective effects of a bacterially expressed NIF-KGF fusion protein against bleomycin-induced acute lung injury in mice.

Current evidence suggests that the keratinocyte growth factor (KGF) and the polymorphonuclear leukocyte may play key roles in the development of lung fibrosis. Here we describe the construction, expression, purification, and identification of a novel NIF (neutrophil inhibitory factor)-KGF mutant fusion protein (NKM). The fusion gene was ligated via a flexible octapeptide hinge and expressed as an insoluble protein in Escherichia coli BL21 (DE3). The fusion protein retained the activities of KGF and NIF, as it inhibited both fibroblast proliferation and leukocyte adhesion. Next, the effects of NKM on bleomycin-induced lung fibrosis in mice were examined. The mice were divided into the following four groups: (i) saline group; (ii) bleomycin group (instilled with 5 mg/kg bleomycin intratracheally); (iii) bleomycin plus dexamethasone (Dex) group (Dex was given intraperitoneally (i.p.) at 1 mg/kg/day 2 days prior to bleomycin instillation and daily after bleomycin instillation until the end of the treatment); and (iv) bleomycin plus NKM group (NKM was given i.p. at 2 mg/kg/day using the same protocol as the Dex group). NKM significantly improved the survival rates of mice exposed to bleomycin. The marked morphological changes and increased hydroxyproline levels resulted from the instillation of bleomycin (on Day 17) in the lungs were significantly inhibited by NKM. These results revealed that NKM can attenuate bleomycin-induced lung fibrosis, suggesting that NKM could be used to prevent bleomycin-induced lung damage or other interstitial pulmonary fibrosis.