Automated graptolite identification at high taxonomic resolution using residual networks.

Graptolites, fossils significant for evolutionary studies and shale gas exploration, are traditionally identified visually by taxonomists due to their intricate morphologies and preservation challenges. Artificial intelligence (AI) holds great promise for transforming such meticulous tasks. In this paper, we demonstrate that graptolites can be identified with taxonomist accuracy using a deep learning model. We construct the most sophisticated and largest professional single organisms image dataset to date, which is composed of >34,000 images of 113 graptolite species annotated at pixel-level resolution to train the model, develop, and evaluate deep learning networks to classify graptolites. The model's performance surpassed taxonomists in accuracy, time, and generalization, achieving 86% and 81% accuracy in identifying graptolite genus and species, respectively. This AI-based method, capable of recognizing minute morphological details better than taxonomists, can be integrated into web and mobile apps, extending graptolite identification beyond research institutes and enhancing shale gas exploration efficiency.

Estrogen receptor-negative/progesterone receptor-positive breast cancer has distinct characteristics and pathologic complete response rate after neoadjuvant chemotherapy.

PURPOSE: The status of hormone receptors (HR) is an independent factor affecting survival and chemotherapy sensitivity in breast cancer (BC) patients, with estrogen receptor (ER) and progesterone receptor (PR) having the most significant effects. The ER-/PR + phenotype has been controversial in BC, and experts will face many challenges in determining treatment strategies. Herein, we systematically analyzed the clinicopathological characteristics of the ER-/PR + phenotype in BC patients and the response to chemotherapy. PATIENTS AND METHODS: We included two cohorts. The first cohort counted the relationship between clinicopathologic data and survival outcomes for 72,666 female patients in the Surveillance, Epidemiology, and End Results (SEER) database. The second cohort analyzed the relationship between clinicopathological data and pathologic complete response (pCR) rate in 879 patients at the Harbin Medical University Cancer Hospital. The classification data were compared by the chi-square test and Fister's exact test of the Logistic regression model, and predictor variables with P < 0.05 in the univariate analysis were included in the multivariate regression analysis. The Kaplan-Meier method evaluated breast cancer-specific survival (BCSS) and overall survival (OS) to investigate the relationship between different HR typing and survival and pCR. RESULTS: In the two cohorts, 704 (0.9%) and 11 (1.3%) patients had the ER-/PR + phenotype, respectively. The clinicopathologic features of patients with the ER-/PR + phenotype are more similar to those of the ER-/PR- phenotype. The ER-/PR + phenotype is more common in younger and premenopausal women, and most ER-/PR + phenotypes exhibit higher histological grades. Survival analysis showed that there were significant differences in OS and BCSS among patients with different HR states (P < 0.001). The survival results of patients with the ER + /PR + phenotype were the best. The prognosis of the ER-/PR + phenotype was similar to that of the ER-/PR- phenotype. On the other hand, we found that HR status was also an independent predictor of post-NAC pCR rate in BC patients. The ER + /PR- and ER-/PR- phenotypes were more sensitive to chemotherapy than the ER + /PR + phenotypes. CONCLUSION: HR status is the main factor affecting BC's survival outcome and pCR rate. Patients with the ER-/PR + phenotype possess more aggressive biological factors and can benefit significantly from chemotherapy. We need to pay more attention to this group and achieve individualized treatment, which will help us treat BC better and provide new targets and blueprints for our clinical treatment.

Clinical characteristics and pathologic complete response (pCR) rate after neoadjuvant chemotherapy in postpartum women with breast cancer.

PURPOSE: Breast cancer (BC) is currently the leading cause of death in women worldwide. Studies have confirmed that pregnancy is an independent factor affecting the survival of BC patients. BC found during pregnancy, lactation, or shortly after delivery is what we used to think of as pregnancy-associated breast cancer (PABC). The current expert definition of this concept is not uniform; however, there is growing evidence that postpartum breast cancer (PPBC) differs from other types of BC in terms of both biological features and prognosis, with a slightly different focus on diagnosis and treatment. With the increase of female reproductive age population and changes in fertility policies in China, patients with PPBC are receiving increasing attention. Here, we systematically analyzed the clinicopathological characteristics and chemotherapeutic response of patients with PPBC. We retrospectively analyzed the clinicopathological data, molecular subtypes, chemotherapy regimens, and pathological complete remission (pCR) rates of 1343 patients with non-metastatic BC at Harbin Medical University Cancer Hospital from January 1, 2012 to May 31, 2023. The categorical data were compared by chi-square test and Fisher exact test using logistic regression model. Predictor variables with P < 0.05 in the univariate analysis were included in the multivariate regression analysis to investigate the relationship between different age groups and pCR. RESULTS: A total of 714 patients were eligible for analysis in this study, and 667 patients had a history of pregnancy, 40 (5.6%) of whom were PPBC patients. When diagnosed with BC, patients with PPBC were younger, more likely to undergo breast-conserving surgery (BCS), and more likely to achieve pCR (P < 0.05). In molecular typing, human epidermal growth factor receptor 2 (HER-2)-positive and triple-negative breast cancer (TNBC) were more frequent. In the entire cohort, HER-2 expression and delivery status were independent predictors of pCR rates in BC patients after neoadjuvant chemotherapy (NAC). CONCLUSION: Our findings suggest that postpartum status is an independent predictor of pCR attainment in BC patients. PPBC is more sensitive to chemotherapy than other patients.We need to pay more attention to this group and achieve individualized treatment, which will help us treat BC better and provide new targets and blueprints for our clinical therapy.

Investigation of a gel-based delivery method for the administration of a live, attenuated Salmonella Typhimurium vaccine.

Poultry vaccines are often administered using water as a suspension media and applied using an oral or coarse spray method. Gel-based vaccine diluents have been developed as an alternative vaccine delivery method. Gels are more viscous, and droplets adhere more effectively to feathers giving the vaccine a longer time to be ingested (through preening). Application of gel diluents with live bacterial vaccines, however, is limited. The present study tested a gel diluent prepared in various media, using a live, attenuated Salmonella Typhimurium vaccine, Vaxsafe ST. Reconstitution in gel diluent did not negatively affect vaccine viability or motility. The invasive capacity of vaccine suspended in gel diluent into cultured intestinal epithelial cells was also tested. Results demonstrated that vaccine suspended in gel diluent retained invasiveness. Day old chicks were orally administered with Vaxsafe ST suspended in gel diluent to characterize in vivo colonization capacity of the vaccine. The results revealed that the VaxSafe ST suspended in gel diluent could efficiently colonize the caeca of chicks, which is needed for the development of effective immunity.

Colorectal cancer: Metabolic interactions reshape the tumor microenvironment.

Colorectal cancer (CRC) is one of the most common cancers worldwide, which ranks third in terms of incidence and the second leading cause of cancer-related mortality. Metabolic reprogramming within the tumor microenvironment (TME) has been proved intimately involved in the initiation and malignant progression of CRC. Signal messengers, including cytokines, metabolites, and exosomes among others, derived from cancer cells can be utilized by the surrounding cells within the TME to induce metabolic alteration and cancer-associated transformation. In turn, the cargos secreted from cancer-associate cells further provide the nutrition and energy supply for cancer cells, supporting their metabolic reprogramming to promote proliferation, migration, metastasis, and radiochemoresistance. In this review, we focus on the main cellular components in the TME: CAFs, TAMs, lymphocytes and neutrophils, and enumerate and integrate how the metabolic interactions between these components and cancer cells reshape TME to foster CRC malignancy.

Coordinated development of high-quality agricultural transformation and technological innovation: a case study of main grain-producing areas, China.

The high-quality development of agriculture is closely related to technological innovation, but the evolutionary characteristics of the relationship between agricultural transformation and technological innovation have received little study. This study takes 13 main grain-producing areas of China as the research object. Data collection was from 2004 to 2019. Based on the coupling coordination and responsiveness models, we analyze the spatio-temporal agriculture comprehensive level and the associated response degree of agricultural transformation to technological innovation. The results showed that (1) the comprehensive development of technological innovation showed a growth trend, while the agricultural transformation showed a U-shaped growth trend; (2) the coordinated development of these two systems has been significantly improved, but there are differences in the development speed of each province; (3) the coordinated gravity center moved southward in the spatial pattern, eventually presenting the characteristics of "higher level in the east and lower level in the west, while the higher level in the south and lower level in the north"; (4) the influence of technological innovation on agricultural transformation gradually changed from inhibition to positive promotion. In the end, this paper puts forward suggestions on the high-quality development of agriculture from the relationship of technological innovation and agricultural transformation.

Challenges in Vaccinating Layer Hens against Salmonella Typhimurium.

Salmonella Typhimurium is among the most common causes of bacterial foodborne gastrointestinal disease in humans. Food items containing raw or undercooked eggs are frequently identified during traceback investigation as the source of the bacteria. Layer hens can become persistently infected with Salmonella Typhimurium and intermittently shed the bacteria over the course of their productive lifetime. Eggs laid in a contaminated environment are at risk of potential exposure to bacteria. Thus, mitigating the bacterial load on farms aids in the protection of the food supply chain. Layer hen producers use a multifaceted approach for reducing Salmonella on farms, including the all-in-all-out management strategy, strict biosecurity, sanitization, and vaccination. The use of live attenuated Salmonella vaccines is favored because they elicit a broader host immune response than killed or inactivated vaccines that have been demonstrated to provide cross-protection against multiple serovars. Depending on the vaccine, two to three doses of Salmonella Typhimurium vaccines are generally administered to layer hens within the first few weeks. The productive life of a layer hen, however, can exceed 70 weeks and it is unclear whether current vaccination regimens are effective for that extended period. The objective of this review is to highlight layer hen specific challenges that may affect vaccine efficacy.

Using microarray analysis to identify genes and pathways that regulate fetal hemoglobin levels.

Increased levels of fetal hemoglobin (HbF: α2γ2) can ameliorate the clinical severity of the ß-hemoglobinopathies. Microarray analysis represents a powerful approach to identify novel genetic factors regulating the γ-globin gene. Gene expression profiling was previously performed on 14 individuals with high or normal HbF levels to identify the genetic factors that control γ-globin gene expression. To obtain more accurate and reliable results, our results were combined with public microarray dataset GSE22109 deposited in the Gene Expression Omnibus database. Annotation of case versus control samples was taken directly from the microarray documentation. The differentially expressed genes (DEGs) were obtained and were deeply analyzed by bioinformatics methods. Combined with our own chip expression data, potential genes HBE1, TFRC, and CSF2 were selected out for subsequent qRT-PCR validation. A total of 184 DEGs were identified from GSE22109 and the protein-protein interaction network was constructed. Gene set enrichment analysis showed that the hematopoietic cell lineage pathway overlaps in the two datasets. HBE1, CSF2, and TFRC were confirmed by qRT-PCR. Our results suggest novel candidate genes and pathways associated with the γ-globin gene expression.

Construction and Analysis of a Long Non-Coding RNA (lncRNA)-Associated ceRNA Network in ß-Thalassemia and Hereditary Persistence of Fetal Hemoglobin.

BACKGROUND Higher fetal hemoglobin (HbF) levels can ameliorate the clinical severity of ß-thalassemia. The use of integrative strategies to combine results from gene microarray expression profiling, experimental evidence, and bioinformatics helps reveal functional long noncoding RNAs (lncRNAs) in ß-thalassemia and HbF induction. MATERIAL AND METHODS In a previous study, a microarray profiling was performed of 7 individuals with high HbF levels and 7 normal individuals. Thirteen paired samples were used for validation. lncRNA NR_001589 and uc002fcj.1 were chosen for further research. The quantitative reverse transcription-PCR was used to detect the expression levels of 2 lncRNAs. The Spearman correlation test was employed. The nuclear and cytoplasmic distribution experiment in K562 cells was used to verify the subcellular localization of 2 lncRNAs. Potential relationships among lncRNAs, predicted microRNAs (miRNAs), and target gene HBG1/2 were based on competitive endogenous RNA theory and bioinformatics analysis. RESULTS Average expression levels of NR_001589 and uc002fcj.1 were significantly higher in the high-HbF group than in the control group. A positive correlation existed between NR_001589, uc002fcj.1, and HbF. The expression of NR_001589 was in both the cytoplasm and the nucleus, mostly (77%) in the cytoplasm. The expression of uc002fcj.1 was in both the cytoplasm and the nucleus; the cytoplasmic proportion was 43% of the total amount. A triple lncRNA-miRNA-mRNA network was established. CONCLUSIONS Novel candidate genetic factors associated with the HBG1/2 expression were identified. Further functional investigation of NR_001589 and uc002fcj.1 can help deepen the understanding of molecular mechanisms in ß-thalassemia.

Identification of novel pathogenic F13A1 mutation and novel NBEAL2 gene missense mutation in a pedigree with hereditary congenital factor XIII deficiency.

The genetic defects of a 12-year-old patient with factor XIII deficiency (FXIIID) and eight pedigree members suspected with FXIIID were studied. Clinical diagnosis, pedigree investigation, phenotypic study and genetic analysis were performed. DNA sequence analysis revealed that the proband had a novel deletion mutation of F13A1 gene (NM_000129: exon 12: c.1652delC: p.Thr551LysfsTer26) which he inherited from both the parents who were heterozygous for the same 1652delC deletion. This frameshift (p.Thr551LysfsTer26) led in homozygous form to severe FXIIID. Additionally, a homozygous missense mutation of NBEAL2 gene (NM_015175: exon 13: c.1367C > T: p.Ala456Val) was identified in the proband. Again, the mutation was inherited from both the parents who were heterozygous for the same c.1367C > T novel mutation. Other members of the pedigree were also revealed to be heterozygous for the same proband's F13A1 and NBEAL2 genes mutations. We first report a pedigree with pathogenic F13A1 gene mutation and a novel mutant NBEAL2 gene.

A novel PKLR gene mutation identified using advanced molecular techniques.

This study's purposes were to diagnose intractable hemolytic anemia and to provide guiding treatment for the affected family members. We performed NGS in a panel of 600 genes for blood diseases on a patient with obscure hemolytic anemia and her parents. We confirmed the diagnosis of pyruvate kinase deficiency, identified a novel homozygous mutation of the PKLR gene (NM_000298: exon 6: c.T941C: p.I314T), and ruled out other blood diseases in the Chinese family. Furthermore, amniotic fluid was taken from the mother during the second trimester, and DNA was extracted to analyze the type of PKLR gene mutation. The proband received cord blood and bone marrow from the second child of the mother for hematopoietic stem cell transplantation and achieved normal hematopoiesis. The genetic characterization analysis and genotype-phenotype correlation study of PKLR gene suggested that NGS was an effective method to confirm the molecular diagnosis of intractable hemolytic anemia. The identification of the mutation aided in prenatal diagnosis in the second pregnancy and the effective clinical management of the affected family.

ARHGAP18 is a novel gene under positive natural selection that influences HbF levels in ß-thalassaemia.

Foetal haemoglobin (HbF) plays a dominant role in ameliorating the morbidity and mortality of ß-thalassaemia. A better understanding of the loci and genes involved in HbF expression would be beneficial for the treatment of ß-thalassaemia major. However, the genes associated with HbF expression remain largely unknown. In this study, we first explored large-scale data sets and examined the human genome for evidence of positive natural selection to screen out single nucleotide polymorphisms (SNPs). A genetic analysis of HbF levels was conducted in a Chinese cohort of patients with ß-thalassaemia to confirm the bioinformatics results. A total of 1141 subjects with ß-thalassaemia were recruited. The results showed that the SNP rs11759328 in the ARHGAP18 gene was significantly associated with HbF levels (Ρ = 5.1 × 10-4). ARHGAP18 belongs to the RhoGAP family and controls angiogenesis, cellular morphology and motility. Second, after determining that ARHGAP18 was highly expressed in the human K562 cell line, we used lentiviral-mediated small interfering RNA to knock down ARHGAP18 expression and subsequently assessed cell proliferation and apoptosis using cell proliferation assays and flow cytometry, respectively. ARHGAP18 downregulation in K562 cells significantly increased HBG1/2 expression and apoptosis, but proliferation was not significantly affected in vitro. Our data suggest that ARHGAP18, which was located by the SNP rs11759328 via positive selection, plays a potential role in regulating HbF expression in ß-thalassaemia and may be a promising therapeutic target. Knockout studies of ARHGAP18 warrant further investigation into its aetiology in HbF.

Novel mutations in patients with hereditary red blood cell membrane disorders using next-generation sequencing.

To diagnose and investigate the genotype-phenotype relationship in intractable hereditary red blood cell (RBC) membrane cases, we have utilized next-generation sequencing (NGS) to develop a high-throughput, highly sensitive assay. Three unrelated families including 15 individuals were analysed with a panel interrogating 600 genes related to haematopathy disorders. Where possible, inheritance patterns of pathogenic mutations were determined by sequencing the relatives. We identified 2 novel mutations in ANK1 (Y216X and E142X) responsible for hereditary spherocytosis (HS) that were stop-gain single nucleotide variants (SNVs). Furthermore, a novel SPTA1 mutation (H54P) was identified; it is a nonsynonymous SNV and is associated with hereditary elliptocytosis (HE). In addition, patients who also carried erythropoiesis gene mutations showed more severe disease phenotype. The NGS panel provides a fast and accurate method for molecular diagnosis in patients with intractable hereditary RBC membrane disorders. An approach integrating medical history, clinical and molecular testing, and pedigree analysis is beneficial for these patients and families.

Genome-wide analysis of aberrantly expressed lncRNAs and miRNAs with associated co-expression and ceRNA networks in ß-thalassemia and hereditary persistence of fetal hemoglobin.

The implications of lncRNAs regarding fetal hemoglobin (HbF) induction in hemoglobin disorders remain poorly understood. In this study, microarray analysis was performed to profile lncRNAs, miRNAs and mRNAs in individuals with hereditary persistence of fetal hemoglobin (HPFH), ß-thalassemia carriers with high HbF levels and healthy controls. The results show aberrant expression of 862 lncRNAs, 568 mRNAs and 63 miRNAs in the high-HbF group compared with the control group. Altered NR_001589, NR_120526, T315543, miR-486-3p, miR-19b-1-5p and miR-20a-3p expression was confirmed by quantitative reverse transcription-polymerase chain reaction, and Spearman correlation coefficients revealed significant positive correlations with HbF. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses showed the hematopoietic cell lineage and apoptosis to be most significantly dysregulated in HbF induction. We analyzed coding genes near the lncRNAs and constructed a coding-noncoding co-expression network. Based on the results, lncRNAs likely contribute to increased HbF levels by activating expression of HBE1 and hematopoietic cell lineage-inducible molecules and by inhibiting that of apoptosis-inducible molecules. Finally, through construction of a competing endogenous RNA network, we found that 6 lncRNAs could bind competitively with miR-486-3p, resulting in increased HbF levels. Taken together, our findings provide new insights into the mechanisms of HbF induction and potentially provide new targets for the treatment of ß-thalassemia major.

Blocking mPTP on Neural Stem Cells and Activating the Nicotinic Acetylcholine Receptor α7 Subunit on Microglia Attenuate Aß-Induced Neurotoxicity on Neural Stem Cells.

ß-Amyloid (Aß) can stimulate microglia to release a variety of proinflammatory cytokines and induce neurotoxicity. Nicotine has been reported to inhibit TNF-α, IL-1, and ROS production in microglia. Mitochondrial permeability transition pore (mPTP) plays an important role in neurotoxicity as well. Here, we investigated whether activating the microglial α7-nAChR has a neuroprotective role on neural stem cells (NSCs) and the function of mPTP in NSCs in this process. The expression of α7-nAChR in rat NSCs was detected by immunocytochemistry and RT-PCR. The viability of microglia and NSCs was examined by MTT assay. The mitochondrial membrane potential (ΔΨm) and morphological characteristics of NSCs was measured by JC-1 staining and transmission electron microscopy respectively. The distribution of cytochrome c in the subcellular regions of NSCs was visualized by confocal laser scanning microscopy, and the expression levels of cyclophilin D and cleaved caspase-3 were assayed by western blot. The apoptotic rate of NSCs was measured by flow cytometry. The expression of α7-nAChR was detected in microglial cells, but no expression was found in NSCs. The viability of rat microglial cells and NSCs was not affected by reagents or coculture itself. Aß1-42-mediated microglial activation impaired the morphology and the ΔΨm of mitochondria of NSCs as well as increased cell apoptosis. However, the damage was attenuated when the α7-nAChRs on microglial cells were activated or the mPTPs on NSCs were blocked. Blockade of mPTPs on NSCs and activation of α7-nAChRs on microglia exhibit neuroprotective roles in Aß-induced neurotoxicity of NSCs.

Accelerated regeneration of skin injury by co-transplantation of mesenchymal stem cells from Wharton's jelly of the human umbilical cord mixed with microparticles.

This study was set to explore a new strategy for repairing skin wounds, co-transplantation of mesenchymal stem cells from Wharton's Jelly of the human umbilical cord (hUC-Wharton's jelly-MSCs) and microparticles. A mixture of hUC-Wharton's jelly-MSCs and microparticles was co-transplanted to 10-mm diameter, full-thickness, mid-dorsal, excisional skin wounds of mice. After 7, 14, and 21 days, the tissue sections were sampled for reconstruction analysis and histological examination. Our results showed that hUC-Wharton's jelly-MSCs possess the potentials for multi-directional differentiation. After co-transplantation, there was remarkable development of newborn skin and its appendages. Newly generated layers of epidermis, sebaceous glands, hair follicle, and sweat glands were observed. This promising innovative strategy could significantly increase the quality of repair and regeneration of skin after injuries.

Continuous renal replacement therapy as a supportive treatment for acute pediatric necrotizing fasciitis.

Acute necrotizing fasciitis (NF) in children is a dangerous illness characterized by progressive necrosis of the skin and subcutaneous tissue. The present study summarizes our recent experience with the treatment of pediatric patients with severe NF. Between 2000 and 2009, eight children suffering from NF were admitted to our department. Four of the children received an active treatment strategy including continuous renal replacement therapy (CRRT), radical debridement, and broad-spectrum antibiotics. Another four children presented at a late stage of illness, and did not complete treatment. Clinical data for these two patient groups were retrospectively analyzed. The four patients that completed CRRT, radical debridement, and a course of broad-spectrum antibiotics were cured without any significant residual morbidity. The other four infants died shortly after admission. Early diagnosis, timely debridement, and aggressive use of broad-spectrum antibiotics are key factors for achieving a satisfactory outcome for cases of acute NF. Early intervention with CRRT to prevent septic shock may also improve patient outcome.

4-[4-(4-Amino-1,2,5-oxadiazol-3-yl)-1,2,5-oxadiazol-3-yl]-1,2,5-oxadiazol-3-amine.

The complete molecule of the compound, C(6)H(4)N(8)O(3), is generated by a crystallographic twofold rotation axis that runs through the central ring. The flanking ring is twisted by 20.2 (1)° with respect to the central ring. One of the amino H atoms forms an intra-molecular N-H⋯N hydrogen bond; adjacent mol-ecules are linked by N-H⋯N hydrogen bonds forming a chain running along [10-2].

[Screening of AGGF1 interacting with inhibitor of differentiation-1].

OBJECTIVE: To screen the proteins interacting with inhibitor of differentiation 1(Id1) using yeast two-hybrid analysis in adult human lung cDNA libraries. METHODS: The coding sequence of Id1 was amplified by PCR and cloned into the bait plasmid. The recombinant bait vector pHybLex/Zeo-Id1 was verified by restriction endonuclease digestion before transformation into the yeast strain EGY48/pSH18-34, which was tested subsequently for reporter genes Leu2 and LacZ activation. The pHybLex/Zeo-Id1 plasmid and the cDNA library plasmid were sequentially transformed into the yeast strains and screened to obtain Leu2(+) and Leu2(+)LacZ(+) clones, with the false positive clones excluded using positive and negative controls, and the plasmid of the true positive clone was sequenced and blasted for homological analysis. RESULTS: Successful construction of pHybLex/Zeo-Id1 was confirmed by enzyme digestion. After transformation of pHybLex/Zeo-Id1 into EGY48/pSH18-34, no specific reporter genes Leu2 and LacZ activation was found. The pHybLex/Zeo-Id1 plasmid and the cDNA library plasmid were sequentially transformed into yeast strain, and 198 Leu(+) clones and 19 Leu(+)LacZ(+) double positive clones were obtained. After elimination of the false positive clones, one true positive clone was obtained, whose plasmid analysis by sequencing and blasting indicated high homology (99.5%, 556/559) to AGGF1 (an angiogenic factor with G-patch and FHA domains 1). AGGF1 expression was confirmed in the true positive yeast cells by Western blotting. CONCLUSION: AGGF1 is confirmed to interact with Id1 by yeast two-hybrid analysis for screening adult human lung cDNA libraries.