Long-term outcomes and associated factors of Crohn's disease patients achieving transmural healing based on magnetic resonance enterography: a Chinese retrospective cohort study.

Background: Transmural healing (TH) has emerged as a potential treatment goal for Crohn's disease (CD). However, further research is needed to confirm its benefits and risk factors associated with TH remain unclear. Objectives: We aimed to assess the value of TH based on magnetic resonance enterography (MRE) in Chinese CD patients regarding the long-term outcomes and its associated factors. Design: Retrospective, observational cohort study. Methods: Patients with CD diagnosed by colonoscopy and MRE examination between 2015 and 2022 were included. All patients were evaluated with endoscopy together with MRE within 6-12 months after baseline and followed up for at least 6 months after evaluation. The primary endpoint was the occurrence of major outcomes during the follow-up, including drug escalation, hospitalization, and surgery. The cumulative probabilities of major outcomes were calculated using Kaplan-Meier survival curves. Logistic regression analyses were used to predict TH within 6-12 months after baseline. Results: A total of 175 patients were included in the study. Of these, 69 (39.4%) patients achieved mucosal healing (MH), but only 34 (19.4%) of them achieved TH. The median follow-up duration was 17.4 months (interquartile range, 11.6-25.5), and major outcomes occurred in 58.3% of patients. A lower occurrence rate of major outcomes was noted in patients who achieved TH than in those who achieved MH only (p = 0.012). The baseline lymphocyte/C-reactive protein ratio (LCR) [odds ratio (OR), 1.60; 95% confidence interval (CI), 1.02-2.50; p = 0.039] and bowel wall thickness (BWT) (OR, 0.72; 95% CI, 0.59-0.90; p = 0.003) were independent predictors associated with TH. According to multivariate Cox regression analysis, low LCR [hazard ratio (HR), 2.34; 95% CI, 1.51-3.64; p < 0.001], and no healing (HR, 5.45; 95% CI, 2.28-13.00; p < 0.001) were associated with an increased risk of major outcomes. Conclusion: Patients with CD who achieved TH showed improved prognosis compared to those who achieved MH only. Baseline LCR and BWT might predict TH.

Research on the enhancement material and culture method of soil aggregates composed of feldspathic sandstone and sand.

The Mu Us Sandy Land is a region characterized by wind-blown sand and soil erosion in northern China. To enhance the soil quality of this area, various organic materials were incorporated into the mixed soil at a volume ratio of 1:2 for feldspathic sandstone to sand. Culture was conducted in the field and under constant temperature conditions in laboratory culture chambers. Four treatments were established in the experiment, each calculated based on weight ratio and controlled (with no organic material added, CK); single application of straw (5% straw, P1); single application of biochar (5% biochar, P2); combined application of biochar and straw (5% biochar + 5% straw, P3). After 90 days of culture, soil samples were collected for analysis of various indicators such as soil aggregate particle size distribution, water stability of soil aggregates, mean weight diameter, mean geometric diameter, and fractal dimension using dry sieving and wet sieving methods. The objective is to establish a scientific basis and provide technical support for addressing the challenges associated with compound soil and implementing rational fertilization measures. The research results indicate that: (1) The quantity of aggregates > 0.25 mm under different treatments follows the order CK < P1 < P2 < P3, and the differences between treatments are significant (P < 0.05); (2) Soil water stability, mean weight diameter (MWD), mean geometric diameter (GMD), and fractal dimension of soil aggregates in compound soil with different organic material additions are superior to the control, and the effect of biochar on improving soil aggregates is better than that of corn straw. The combined application of both significantly improves the effect compared to single applications. In both culture modes, under wet sieving, the P3 treatment shows the highest MWD and GMD of soil aggregates, with an increase ranging from 3.45% to 85% and 4.55% to 38.46%, respectively, compared to other treatments. (3) The trend of fractal dimension among treatments is consistent: P3 < P2 < P1 < CK, and the differences between treatments are significant (P < 0.05). Moreover, there is a good negative correlation linear equation relationship between the fractal dimension (y) and WR > 0.25 (x) of compound soil, with a correlation coefficient of up to 0.9851. In conclusion, the incorporation of organic materials can effectively enhance the proportion of macroaggregates in compound soil consisting of Feldspathic sandstone and sand, thereby improving soil stability and erosion resistance. The optimal outcome is achieved through the combined application of biochar and straw. Indoor culture proves to be more effective than field culture, while wet sieving accurately reflects the structural characteristics of compound soil under both dry and wet sieving treatments.

[Clinical observation of virtual reality technology combined with isokinetic strength training for patients after anterior cruciate ligament reconstruction].

OBJECTIVE: To explore application value and effectiveness of virtual reality technology combined with isokinetic muscle strength training in the rehabilitation of patients after anterior cruciate ligament (ACL) reconstruction surgery. METHODS: Forty patients who underwent ACL reconstruction surgery from December 2021 to January 2023 were selected and divided into control group and observation group according to treatment methods, 20 patients in each group. Control group was received routine rehabilitation training combined with isokinetic muscle strength training, including 15 males and 5 females, aged from 17 to 44 years old, with an average of (29.10±8.60) years old. Observation group was performed virtual reality technology combined with isokinetic muscle strength training, including 16 males and 4 females, aged from 17 to 45 years old with an average of (30.95±9.11) years old. Lysholm knee joint score, knee extension peak torque, and knee flexion peak torque between two groups at 12 (before training) and 16 weeks (after training) after surgery were compared. RESULTS: All patients were followed up for 1 to 6 months with an average of (3.30±1.42) months. There were no statistically significant difference in Lysholm knee joint score, peak knee extension peak torque, and peak knee flexion peak torque between two groups (P>0.05) before training. After training, Lysholm knee joint score, knee extension peak torque, and knee flexion peak torque of both groups were improved compared to before training (P<0.05);there were significant difference in Lysholm knee joint score, knee extension peak torque, and knee flexion peak torque between two groups(P<0.05). CONCLUSION: The application of virtual reality technology combined with isokinetic muscle strength training could promote recovery of knee joint function and enhance muscle strength in patients after ACL reconstruction surgery in further.

Insertion of Transposable Elements in AVR-Pib of Magnaporthe oryzae Leading to LOSS of the Avirulent Function.

Rice blast is a very serious disease caused by Magnaporthe oryzae, which threatens rice production and food supply throughout the world. The avirulence (AVR) genes of rice blast are perceived by the corresponding rice blast resistance (R) genes and prompt specific resistance. A mutation in AVR is a major force for new virulence. Exploring mutations in AVR among M. oryzae isolates from rice production fields could aid assessment of the efficacy and durability of R genes. We studied the probable molecular-evolutionary patterns of AVR-Pib alleles by assaying their DNA-sequence diversification and examining their avirulence to the corresponding Pib resistance gene under natural conditions in the extremely genetically diverse of rice resources of Yunnan, China. PCRs detected results from M. oryzae genomic DNA and revealed that 162 out of 366 isolates collected from Yunnan Province contained AVR-Pib alleles. Among them, 36.1-73.3% isolates from six different rice production areas of Yunnan contained AVR-Pib alleles. Furthermore, 36 (28.6%) out of 126 isolates had a transposable element (TE) insertion in AVR-Pib, which resulted in altered virulence. The TE insertion was identified in isolates from rice rather than from Musa nana Lour. Twelve AVR-Pib haplotypes encoding three novel AVR-Pib variants were identified among the remaining 90 isolates. AVR-Pib alleles evolved to virulent forms from avirulent forms by base substitution and TE insertion of Pot2 and Pot3 in the 5' untranslated region of AVR-Pib. These findings support the hypothesis that functional AVR-Pib possesses varied sequence structures and can escape surveillance by hosts via multiple variation manners.

Establishment of Functional PCR-Based Markers against Bacterial Leaf Blight Disease in Rice Landraces of Yunnan Province of China.

Bacterial leaf blight is a devastating disease of rice worldwide. The resistant genes are routinely transferred from landraces to cultivated varieties through backcross breeding along with marker-assisted selection. In the present study, we use the gene-specific markers to screen the rice landraces in Yunnan Province of China. We collected 404 representative samples of 24 different rice landraces from Yunnan Province of China. The initial PCR-based screening suggested that the leaf blight resistance was not evenly distributed in Yunnan Province. Our results indicate that there is a complete loss of resistance for landraces based on xa5 and xa13 genes. On the other hand, landraces harboring Xa7 and Xa21 showed a high level of resistance. Using gene-specific PCR-based data, we were able to identify the resistant, susceptible and heterozygous populations across Yunnan Province. The widely used Xa21 gene alone showed a remarkable level of resistance throughout the province, indicating its potential to develop broad-spectrum resistance in rice germplasm. The key aspects of bacterial blight spread according to local sites in Yunnan Province and the resistance conferred by different landraces due to the presence of different resistance genes are discussed.

Emergence of Rice Blast AVR-Pi9 Resistance Breaking Haplotypes in Yunnan Province, China.

The rice blast disease (caused by Magnaporthe oryzae) is a devastating disease in China. Understanding the molecular mechanisms of interaction for the cognate avirulence (AVR) gene with host resistance (R) genes, as well as their genetic evolution is essential for sustainable rice production. In the present study, we conducted a high-throughput nucleotide sequence polymorphism analysis of the AVR-Pi9 gene that was amplified from the rice-growing regions of the Yunnan Province in China. We detected the presence of seven novel haplotypes from 326 rice samples. In addition, the sequences of AVR-Pi9 were also obtained from two non-rice hosts, Eleusine coracana and Eleusine indica. The sequence analysis revealed the insertions and deletions in the coding and non-coding regions of the gene. The pathogenicity experiments of these haplotypes on previously characterized monogenic lines showed that the newly identified haplotypes are virulent in nature. The breakdown of resistance was attributed to the development of new haplotypes. Our results suggest that the mutation in the AVR-Pi9 gene is an alarming situation in the Yunnan province and thus needs attention.

A multi-scale pooling convolutional neural network for accurate steel surface defects classification.

Surface defect detection is an important technique to realize product quality inspection. In this study, we develop an innovative multi-scale pooling convolutional neural network to accomplish high-accuracy steel surface defect classification. The model was built based on SqueezeNet, and experiments were carried out on the NEU noise-free and noisy testing set. Class activation map visualization proves that the multi-scale pooling model can accurately capture the defect location at multiple scales, and the defect feature information at different scales can complement and reinforce each other to obtain more robust results. Through T-SNE visualization analysis, it is found that the classification results of this model have large inter-class distance and small intra-class distance, indicating that this model has high reliability and strong generalization ability. In addition, the model is small in size (3MB) and runs at up to 130FPS on an NVIDIA 1080Ti GPU, making it suitable for applications with high real-time requirements.

Downregulation of desmoglein 2 promotes EMT progression in gallbladder cancer.

OBJECTIVE: To explore the correlation between the expression level of Desmoglein 2 (DSG2) and the epithelial-mesenchymal transition (EMT) progression in gallbladder cancer (GBC). METHOD: 106 GBC tissue specimens and corresponding clinical information were collected to make a tissue microarray. Immunohistochemical method was used to test the expression level of DSG2 in GBC tissues. DSG2 was knocked down in the GBC cell line GBC-SD to detect the change of its invasion and metastasis ability. Then RT-qPCR and Western Blot were applied on the DSG2-knocked down GBC-SD cells to detect the expression level change of genes associated with EMT. RESULT: The high expression rate of DSG2 was significantly correlated with the N, M and TNM staging of patients (P<0.05). Survival analysis identified that GBC patients with high DSG2 expression level had significantly better survival (P<0.05). To further investigate the potential mechanism of DSG2 on regulating GBC tumor progression, we used knockdown DSG2 on GBC-SD cell lines. The results showed that GBC-SD cell lines with DSG2 knockdown showed a promotion of cell invasion and metastatic ability. The mRNA levels of EMT-related genes E-Cadherin, Snail, Twist, ZEB1, and ß-catenin, which is a key protein in the Wnt signaling pathway, were also significantly altered. Besides, protein levels of E-cadherin and Snail showed consistent results. CONCLUSION: The downregulation of DSG2 in gallbladder cancer is hypothesized to be associated with the invasion and metastasis progression of gallbladder cancer cells by regulating EMT-related pathways. Its expression level can be a novel biomarker for gallbladder cancer, providing new perspectives for diagnosis and treatment strategies.

Genome Re-Sequencing Reveals the Host-Specific Origin of Genetic Variation in Magnaporthe Species.

Rice blast is caused by Magnaporthe oryzae (M. oryzae), which is considered one of the most serious pathogens of rice around the globe. It causes severe losses owing to its proven capability to disrupt the host resistance. Recently, its invasion of new hosts like the Musa species or banana plants has been noticed. To understand the possible level of genetic variation, we sequenced the genomes of eight different isolates of the Magnaporthe species infecting rice, Digitaria (a weed), finger millet, Elusine indica, and banana plants. Comparative genomic analysis of these eight isolates with the previously well-characterized laboratory strain M. oryzae 70-15 was made. The infectivity of the newly isolated strain from Musa species suggested that there is no resistance level in the host plants. The sequence analysis revealed that despite genome similarities, both the banana and Digitaria isolates have relatively larger genome sizes (∼38.2 and 51.1 Mb, respectively) compared to those of the laboratory reference strain M. oryzae 70-15 (∼37 Mb). The gene contraction, expansion, and InDel analysis revealed that during evolution, a higher number of gene insertions and deletions occurred in the blast fungus infecting Digitaria and banana. Furthermore, each genome shared thousands of genes, which suggest their common evolution. Overall, our analysis indicates that higher levels of genes insertion or deletions and gain in the total genome size are important factors in disrupting the host immunity and change in host selection.

Effect of Molecular Architecture and Symmetry on Self-Assembly: A Quantitative Revisit Using Discrete ABA Triblock Copolymers.

The inherent statistical heterogeneities associated with chain length, composition, and architecture of synthetic block copolymers compromise the quantitative interpretation of their self-assembly process. This study scrutinizes the contribution of molecular architecture on phase behaviors using discrete ABA triblock copolymers with precise chemical structure and uniform chain length. A group of discrete triblock copolymers with varying composition and symmetry were modularly synthesized through a combination of iterative growth methods and efficient coupling reactions. The symmetric ABA triblock copolymers self-assemble into long-range ordered structures with expanded domain spacings and enhanced phase stability, compared with the diblock counterparts snipped at the middle point. By tuning the relative chain length of two end blocks, the molecular asymmetry reduces the packing frustration, and thus increases the order-to-disorder transition temperature and enlarges the domain sizes. This study would serve as a quantitative model system to correlate the experimental observations with the theoretical assessments and to provide quantitative understandings for the relationship between molecular architecture and self-assembly.

Part-Aware Mask-Guided Attention for Thorax Disease Classification.

Thorax disease classification is a challenging task due to complex pathologies and subtle texture changes, etc. It has been extensively studied for years largely because of its wide application in computer-aided diagnosis. Most existing methods directly learn global feature representations from whole Chest X-ray (CXR) images, without considering in depth the richer visual cues lying around informative local regions. Thus, these methods often produce sub-optimal thorax disease classification performance because they ignore the very informative pathological changes around organs. In this paper, we propose a novel Part-Aware Mask-Guided Attention Network (PMGAN) that learns complementary global and local feature representations from all-organ region and multiple single-organ regions simultaneously for thorax disease classification. Specifically, multiple innovative soft attention modules are designed to progressively guide feature learning toward the global informative regions of whole CXR image. A mask-guided attention module is designed to further search for informative regions and visual cues within the all-organ or single-organ images, where attention is elegantly regularized by automatically generated organ masks and without introducing computation during the inference stage. In addition, a multi-task learning strategy is designed, which effectively maximizes the learning of complementary local and global representations. The proposed PMGAN has been evaluated on the ChestX-ray14 dataset and the experimental results demonstrate its superior thorax disease classification performance against the state-of-the-art methods.

Novel Variation and Evolution of AvrPiz-t of Magnaporthe oryzae in Field Isolates.

The product of the avirulence (Avr) gene of Magnaporthe oryzae can be detected by the product of the corresponding resistance (R) gene of rice and activates immunity to rice mediated by the R gene. The high degree of variability of M. oryzae isolates in pathogenicity makes the control of rice blast difficult. That resistance of the R gene in rice has been lost has been ascribed to the instability of the Avr gene in M. oryzae. Further study on the variation of the Avr genes in M. oryze field isolates may yield valuable information on the durable and effective deployment of R genes in rice production areas. AvrPiz-t and Piz-t are a pair of valuable genes in the Rice-Magnaporthe pathosystem. AvrPiz-t is detectable by Piz-t and determines the effectiveness of Piz-t. To effectively deploy the R gene Piz-t, the distribution, variation, and evolution of the corresponding Avr gene AvrPiz-t were found among 312 M. oryzae isolates collected from Yunnan rice production areas of China. PCR amplification and pathogenicity assays of AvrPiz-t showed that 202 isolates (64.7%) held AvrPiz-t alleles and were avirulent to IRBLzt-T (holding Piz-t). There were 42.3-83.3% avirulent isolates containing AvrPiz-t among seven regions in Yunnan Province. Meanwhile, 11 haplotypes of AvrPiz-t encoding three novel AvrPiz-t variants were identified among 100 isolates. A 198 bps insertion homologous to solo-LTR of the retrotransposon inago2 in the promoter region of AvrPiz-t in one isolate and a frameshift mutation of CDS in another isolate were identified among 100 isolates, and those two isolates had evolved to virulent from avirulent. Synonymous mutation and non-AUG-initiated N-terminal extensions keeps the AvrPiz-t gene avirulence function in M. oryzae field isolates in Yunnan. A haplotype network showed that H3 was an ancestral haplotype. Structure variance for absence (28.2%) or partial fragment loss (71.8%) of AvrPiz-t was found among 39 virulent isolates and may cause the AvrPiz-t avirulence function to be lost. Overall, AvrPiz-t evolved to virulent from avirulent forms via point mutation, retrotransposon, shift mutation, and structure variance under field conditions.

Microarray Analysis for Differentially Expressed Genes Between Stromal and Epithelial Cells in Development and Metastasis of Invasive Breast Cancer.

Both epithelium and stroma are involved in breast cancer invasion and metastasis. This study aimed at identifying the roles of the stroma in breast cancer tumorigenesis and metastasis. Gene expression profiling GSE10797 was downloaded from the Gene Expression Omnibus database, and it included 28-paired stroma and epithelium breast tissue samples from invasive breast cancer patients and 10 paired normal breast tissue samples. Differentially expressed genes (DEGs) between breast cancer and normal breast tissue samples were identified by using the limma package followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses to seek the potential functions of DEGs. Moreover, a protein-protein interaction network was constructed based on the String database, and modules were selected through the BioNet tool. Further, functional annotations of DEGs were carried out by using tumor suppressor gene and tumor associated gene databases. Ultimately, KEGG pathway enrichment analysis for DEGs in modules was performed. A total of 38 and 156 DEGs were identified from normal invasive stromal cells and epithelial cells, respectively. DEGs in stromal and epithelial cells were significantly enriched in extracellular matrix (ECM)- and cell proliferation-related functions. COL1A2, a hub node in the stromal module, was mainly enriched in ECM-receptor interaction and focal adhesion pathways. JUN, a hub node in the epithelium module, was significantly enriched in cancer and ErbB signaling pathways. COL1A2, COL1A1, COL3A1, JUN, and FN1 might be vital for tumorigenesis and metastasis of invasive breast cancer. These genes might be potential therapeutic targets for breast cancer treatment.

Effects of Conservation Tillage on Soil Physicochemical Properties and Crop Yield in an Arid Loess Plateau, China.

Conservation tillage can improve soil physical structure and water storage, protect moisture, and increase crop yield. However, the long-term adoption of a single tillage method may have some adverse effects on soil and ecological environment, although crop yields have increased. Through informed allocation of soil tillage techniques, the combination and configuration of soil tillage measures, such as rotary tillage, subsoiling, and no tillage may reduce the shortcomings of traditional long-term farming. To explore the long-term production mode suitable for production of maize in the loess dryland area, a long-term experiment was conducted in Fuping County, Shaanxi Province, from 2013 to 2018. Six farming modes were used in the experiment: no tillage/subsoiling (N ↔ S), subsoiling/rotary tillage (S ↔ R), rotary tillage/no tillage (R ↔ N), continuous no tillage (N ↔ N), continuous subsoiling (S ↔ S), and continuous rotary tillage (R ↔ R). The changes in soil physical and chemical properties, soil water use patterns, soil water storage, conservation effects during the fallow and growth period, and the effects on farmland yield increase were analyzed. The results showed that rotary tillage can effectively improved soil structure and reduced soil bulk density, where N ↔ S treatment soil bulk density is low and in 0-60 cm soil layer averaged 1.31 g/cm3. Different tillage treatments could be used during the fallow period to store additional soil moisture: the N ↔ S treatment showed good water storage effect. Compared to traditional tillage, different tillage methods provided better soil moisture conditions for crops during the growth period, where N ↔ S treatment showed good soil moisture status during the growth period of spring maize. Among all the treatments, N ↔ S treatment effectively increased the organic carbon storage in the 0-60 cm soil layer, which was 54.3 t/hm2. Compared with traditional tillage, different tillage treatments effectively increased plant height and dry matter accumulation of spring maize, where N ↔ S treatment was found to be the best. Compared with the traditional rotary tillage model, the N ↔ S treatment significantly increased crop yield and water use efficiency (WUE) in continuous cropping fields of corn, the average yield of spring corn was 9340.2 kg/hm2, and the average WUE was 22.9 kg/(hm2·mm). In summary, for long-term sustainable development, the N ↔ S model is the best rotational tillage mode for continuous maize cropping in loess soil.

Complete mitochondrial genome of banana new pest Basilepta fulvipes (Coleoptera: Eumolpinae) and phylogenetic analysis.

Basilepta fulvipes (Motschulsky, 1860) is a banana new pest and mainly distributed in Eastern Asia. The complete mitogenome of B. fulvipes (GenBank accession number MT627597) is 15,762 bp in size, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a noncoding D-loop region. The D-loop region is located between 12S rRNA and tRNAIle . The base composition of the whole B. fulvipes mitogenome is 41.66% for A, 8.89% for G, 34.32% for T and 15.12% for C, with a high AT bias of 75.98%. The present data could contribute to further detailed phylogeographic analysis and comprehensive control of this banaba new pest.

Novel haplotypes and networks of AVR-Pik alleles in Magnaporthe oryzae.

BACKGROUND: Rice blast disease is one of the most destructive fungal disease of rice worldwide. The avirulence (AVR) genes of Magnaporthe oryzae are recognized by the cognate resistance (R) genes of rice and trigger race-specific resistance. The variation in AVR is one of the major drivers of new races. Detecting the variation in the AVR gene in isolates from a population of Magnaporthe oryzae collected from rice production fields will aid in evaluating the effectiveness of R genes in rice production areas. The Pik gene contains 5 R alleles (Pik, Pikh, Pikp, Pikm and Piks) corresponding to the AVR alleles (AVR-Pik/kh/kp/km/ks) of M. oryzae. The Pik gene specifically recognizes and prevents infections by isolates of M. oryzae that contain AVR-Pik. The molecular variation in AVR-Pik alleles of M. oryzae and Pik alleles of rice remains unclear. RESULTS: We studied the possible evolutionary pathways of AVR-Pik alleles by analyzing their DNA sequence variation and assaying their avirulence to the cognate Pik alleles of resistance genes under field conditions in China. The results of PCR products from genomic DNA showed that 278 of the 366 isolates of M. oryzae collected from Yunnan Province, China, carried AVR-Pik alleles. Among the isolates from six regions of Yunnan, 66.7-90.3% carried AVR-Pik alleles. Moreover, 10 AVR-Pik haplotypes encoding five novel AVR-Pik variants were identified among 201 isolates. The AVR-Pik alleles evolved to virulent from avirulent forms via stepwise base substitution. These findings demonstrate that AVR-Pik alleles are under positive selection and that mutations are responsible for defeating race-specific resistant Pik alleles in nature. CONCLUSIONS: We demonstrated the polymorphism and distribution of AVR-Pik alleles in Yunnan Province, China. By pathogenicity assays used to detect the function of the different haplotypes of AVR-Pik, for the first time, we showed the avoidance and stepwise evolution of AVR-Pik alleles in rice production areas of Yunnan. The functional AVR-Pik possesses diversified sequence structures and is under positive selection in nature.

Role of ß-Estradiol in MCF-7 Breast Cancer Cell Line Based on the Bioinformatics Analysis.

BACKGROUND: This study aimed to investigate the action mechanism of ß-estradiol in MCF-7 breast cancer (BC) cells. METHODS: The cell samples were sequenced using Hiseq 2000, including 2 MCF-7 controls and 2 samples treated with ß-estradiol. Differentially expressed genes (DEGs) were screened using the NOISeq package in R, followed by the functions and pathways analyses using Database for Annotation, Visualization and Integrated Discovery. DEGs associated with ß-estradiol were selected using the WbeGestalt software, and the corresponding target miRNAs of these genes were analyzed from different miRNA databases. Additionally, protein-protein interaction network of the drug-associated genes was constructed using Cytoscape. RESULTS: A total of 1,835 DEGs in BC samples were screened. Thereinto, DEGs associated with BC (17 upregulated and 28 downregulated DEGs) were involved in the regulation of cell proliferation, response to endogenous stimulus, and response to hormone stimulus, while the genes participated in several significant pathways. Cyclin D1, estrogen receptor 1, catechol-O-methyltransferase, and cathepsin D (CTSD; hub genes) were the predicted new genes associated with ß-estradiol. Besides, hsa-miR-140-3p was the only target miRNA of CTSD. CONCLUSION: ß-Estradiol may play a key role in contributing to BC progression and metastasis by regulating the expression of the selected genes.

Identification of differentially expressed genes and typical fusion genes associated with three subtypes of breast cancer.

BACKGROUND: This study aimed to identify the differentially expressed genes (DEGs) and the typical fusion genes in different types of breast cancers using RNA-seq. METHODS: GSE52643 was downloaded from Gene Expression Omnibus, which included 1 normal sample (MCF10A) and 7 breast cancer samples (BT-474, BT-20, MCF7, MDA-MB-231, MDA-MB-468, T47D, and ZR-75-1). The transcript abundance and the DEGs screening were performed by Cufflinks. The functional and pathway enrichment was analyzed by Gostats. SnowShoes-FTD was applied to identify the fusion genes. RESULTS: We screened 430, 445, 397, 417, 369, 557, and 375 DEGs in BT-474, BT-20, MCF7, DA-MB-231, MDA-MB-468, T47D, and ZR-75-1, respectively, compared with MCF10A. DEGs in each comparison group (such as CD40 and CDH1) were significantly enriched in the functions of cell adhesion and extracellular matrix organization and pathways of CAMs and ECM receptor interaction. UCP2 was a common DEG in the 7 comparison groups. SFRP1 and MMP7 were significantly enriched in wnt/-catenin signaling pathway in MDA-MB-231. FAS was significantly enriched in autoimmune thyroid disease pathway in BT-474. Besides, we screened 96 fusion genes, such as ESR1-C6orf97 in ZR-75-1, COBRA1-C9orf167 in BT-20, and VAPB-IKZF3 and ACACA-STAC2 in BT-474. CONCLUSIONS: The DEGs such as SFRP1, MMP7, CDH1, FAS, and UCP2 might be the potential biomarkers in breast cancer. Furthermore, some pivotal fusion genes like ESR1-C6orf97 with COBRA1-C9orf167 and VAPB-IKZF3 with ACACA-STAC2 were found in Luminal A and Luminal B breast cancer, respectively.

A redshift mechanism of high-order harmonics: Change of ionization energy.

We theoretically study the high-order harmonic generation of H2+ and its isotopes beyond the Born-Oppenheimer dynamics. It is surprising that the spectral redshift can still be observed in high harmonic spectra of H2+ driven by a sinusoidal laser pulse in which the trailing (leading) edge of the laser pulse is nonexistent. The results confirm that this spectral redshift originates from the reduction in ionization energy between recombination time and ionization time, which is obviously different from the nonadiabatic spectral redshift induced by the falling edge of the laser pulse. Additionally, the improved instantaneous frequency of harmonics by considering the changeable ionization energy can deeply verify our results. Therefore, this new mechanism must be taken into account when one uses the nonadiabatic spectral redshift to retrieve the nuclear motion.

Investigating the therapeutic potential and mechanism of curcumin in breast cancer based on RNA sequencing and bioinformatics analysis.

BACKGROUND: Breast cancer is a prevalent cancer in female. This study aims to investigate the therapeutic potential and mechanism of curcumin in breast cancer. METHODS: After cultivation, human breast cancer cells (MCF-7 cells) were treated with 0.1% (v/v) 15 µmol/ml curcumin-dimethylsulfoxide solution and 0.1% (v/v) dimethylsulfoxide, respectively, at 37 °C and 5% CO2 for 48 h. Total RNA was extracted, cDNA library was constructed, and cDNAs were amplified and sequenced. After data preprocessing, the Cufflinks software was utilized to identify differentially expressed genes (DEGs, |log2 fold change| > 0.5 and p value < 0.05). Then, functional and pathway enrichment analyses were performed through DAVID (p value < 0.05) and WebGestalt [false discovery rate (FDR) < 0.05], respectively. Furthermore, drug and disease association analyses (FDR < 0.05) were conducted through WebGestalt and DAVID, respectively. STRING was employed to construct protein-protein interaction (PPI) network (combined score > 0.4). RESULTS: After DEGs screening, 347 DEGs were identified. Up-regulated DEGs were enriched in 14 functions and 3 pathways, and associated with 12 drugs. Down-regulated DEGs were enriched in 14 functions and 9 pathways, and associated with 14 drugs. Moreover, 5 DEGs were associated with breast cancer, including PGAP3, MAP3K1, SERPINE1, PON2, and GSTO2. PPI network was constructed, and the top DEGs were FOS, VIM, FGF2, MAPK1, SPARC, TOMM7, PSMB10, TCEB2, SOCS1, COL4A1, UQCR11, SERPINE1, and ISG15. CONCLUSION: Curcumin might have therapeutic potential in breast cancer through regulating breast cancer-related genes, including SERPINE1, PGAP3, MAP3K1, MAPK1, GSTO2, VIM, SPARC, and FGF2. However, validations are required.