A survey on causal inference for recommendation.

Causal inference has recently garnered significant interest among recommender system (RS) researchers due to its ability to dissect cause-and-effect relationships and its broad applicability across multiple fields. It offers a framework to model the causality in RSs such as confounding effects and deal with counterfactual problems such as offline policy evaluation and data augmentation. Although there are already some valuable surveys on causal recommendations, they typically classify approaches based on the practical issues faced in RS, a classification that may disperse and fragment the unified causal theories. Considering RS researchers' unfamiliarity with causality, it is necessary yet challenging to comprehensively review relevant studies from a coherent causal theoretical perspective, thereby facilitating a deeper integration of causal inference in RS. This survey provides a systematic review of up-to-date papers in this area from a causal theory standpoint and traces the evolutionary development of RS methods within the same causal strategy. First, we introduce the fundamental concepts of causal inference as the basis of the following review. Subsequently, we propose a novel theory-driven taxonomy, categorizing existing methods based on the causal theory employed, namely those based on the potential outcome framework, the structural causal model, and general counterfactuals. The review then delves into the technical details of how existing methods apply causal inference to address particular recommender issues. Finally, we highlight some promising directions for future research in this field. Representative papers and open-source resources will be progressively available at https://github.com/Chrissie-Law/Causal-Inference-for-Recommendation.

UV-stimulated riboflavin exerts immunosuppressive effects in BALB/c mice and human PBMCs.

Riboflavin (RF) as a photosensitizer has been used in corneal surgery and the inactivation of blood products. However, the effect of RF on immune cells after ultraviolet (UV) light stimulation has not been investigated. This study pioneered a novel application method of RF. Firstly, UV-stimulated RF was co-cultured with human peripheral blood mononuclear cells in vitro, and the apoptosis rate of lymphocyte subsets, cell proliferation inhibition rate and concentrations of IL-1ß, IL-6, IL-10, TNF-α were assessed. UV-stimulated RF was then administered intravenously to mice via the tail vein for a consecutive period of 5 days. The levels of immunoglobulin (IgG, IgM, IgA), complement (C3, C4) and cytokines (IFN-γ, IL-4, IL17, TGF-ß) were detected by ELISA. Flow cytometry was employed to analyze the populations of CD3+T, CD4+T, CD8+T and CD4+T/CD8+T cells in spleen lymphocytes of mice. The data showed that UV-stimulated RF can effectively induce apoptosis in lymphocytes, and different lymphocyte subtypes exhibited varying degrees of treatment tolerance. Additionally, the proliferative capacity of lymphocytes was suppressed, while their cytokine secretion capability was augmented. The animal experiments demonstrated that UV-stimulated RF led to a significant reduction observed in serum immunoglobulin and complement levels, accompanied by an elevation in IFN-γ, IL-17 and TGF-ß levels, as well as a decline in IL-4 level. In summary, the results of both in vitro and in vivo experiments have demonstrated that UV-stimulated RF, exhibits the ability to partially inhibit immune function. This novel approach utilizing RF may offer innovative perspectives for diseases requiring immunosuppressive treatment.

Effect of early hemostasis strategy on secondary post-traumatic sepsis in trauma hemorrhagic patients.

INTRODUCTION: Fibrinogen and platelet, as the two main components of hemostatic resuscitation, are frequently administered in traumatic massive hemorrhage patients. It is reasonable to infer that they may have an impact on post-traumatic sepsis as more and more recognition of their roles in inflammation and immunity. This study aims to determine the association between the fibrinogen/platelet transfusion ratio during the first 24 h after trauma and the risk of the post- traumatic sepsis. METHODS: We analyzed the data from the National Trauma Data Bank (NTDB). Subjects included the critically injured adult patients admitted to Level I/II trauma center from 2013 to 2017 who received fibrinogen and platelet supplementation and more than 10 units (about 4000 ml) packed red blood cells (pRBCs) during the first 24 h after trauma. Two parts of analyses were performed: (1) multivariable stepwise regression was used to determine the variables that influence the risk of post-traumatic sepsis; (2) propensity score matching (PSM), to compare the influences of different transfusion ratio between fibrinogen and platelet on the risk of sepsis and other outcomes after trauma. RESULTS: 8 features were screened out by bi-directional multivariable stepwise logistic regression to predict the post-traumatic sepsis. They are age, sex, BMI, ISSabdomen, current smoker, COPD, Fib4h/24h and Fib/PLT24h. Fib/PLT24h was negatively related to sepsis (p < 0.05). A total of 1601 patients were included in the PSM cohort and grouped by Fib/PLT24h = 0.025 according to the fitting generalized additive model (GAM) model curve. The incidence of sepsis was significantly decreased in the high Fib/PLT group [3.3 % vs 9.4 %, OR = 0.33, 95 %CI (0.17-0.60)]; the length of stay in ICU and mechanical ventilation were both shortened as well [8 (IQR 2.00,17.00) vs 9 (IQR 3.00,19.25), p = 0.006 and 4 (IQR 2.00,10.00) vs 5 (IQR 2.00,14.00), p = 0.003, respectively. CONCLUSIONS: Early and sufficient supplementation of fibrinogen was a convenient way contribute to reduce the risk of sepsis after trauma.

Platelet membrane-derived microparticles may be biomarkers in patients with hepatocellular carcinoma and can promote the invasion and metastasis of hepatoma carcinoma cells.

BACKGROUND: Platelet membrane-derived microparticles (PMPs) released by apheresis platelets (APs) during storage are involved in immunomodulatory and tumor processes. However, few studies have emphasized the relationship between PMPs and hepatocellular carcinoma (HCC). METHODS: Enzyme-linked immunosorbent assay (ELISA) was used to detect PMPs in the plasma of HCC patients and healthy individuals. ELISA and flow cytometry were separately applied to analyze the variation in PMPs from APs prepared after 0, 3, 5, and 7 days of storage. Transwell was used to demonstrate the effects of PMPs on the invasion and migration of HCC cells. HCC-related indicators and invasion and migration-related markers were detected in vivo. RESULTS: We found the amount of PMPs was significantly increased in HCC patients. There was also a significant difference in the amount of PMPs in APs with prolonged storage time. Further, the PMPs in D5 promoted the invasion and migration of HepG2 and Huh7 cells. Transcriptomics revealed striking differences in the expression of many tumor metastasis associated genes with PMPs treatment. PMPs promoted tumor growth and weight loss in HCC-bearing mice, and Western blot results showed that invasion and migration-related indicators also increase. CONCLUSION: The content of PMPs in the plasma of HCC patients increases, and it can also promote the invasion and migration of HCC.

[Effects of Platelet-Rich Plasma on Macrophage Phenotype and Its Influencing Factors].

OBJECTIVE: To evaluate the effects of platelet-rich plasma (PRP) supernatants with different activation methods and storage time on human monocyte-derived macrophages phenotype and explore the possible mechanism. METHODS: Human monocyte-derived macrophages were cultured in vitro with PRP or activated PRP supernatants activated with different activators. The expression of marker molecules on the surface of macrophages was detected by flow cytometry, and the concentration of growth factors in PRP supernatants was detected by ELISA. RESULTS: After 24 h of coculture, the expression level of CD86 in macrophages stimulated by PRP supernatant (thrombin and Cacl2 activated) was significantly higher than that by PRP group (P<0.05), and the expression of CD163 in macrophages was increased by Cacl2 activated PRP supernatant. Compared with different activator groups, the expression of CD163 in macrophages of Cacl2 activated group was significantly higher than that of thrombin and ADP groups (P<0.05). ELISA results showed that the concentrations of FGF (P<0.001) and EGF (P<0.05) in the supernatant of PRP stored at -80 ℃ for more than 20 months and 10-20 months were significantly higher than those in the group stored at less than 10 months after Cacl2 activation, and the expressions of CD86 (P<0.01), CD163 (P<0.001) and CD206 (P<0.001) in macrophages cocultured with the supernatant of the two groups were significantly increased. CONCLUSION: PRP activated by different activators has different effects on the phenotype of macrophages. Meanwhile, the storage time will also affect the growth factor concentration and effect of PRP.

[Platelet Transfusion Strategies for MASPAT-Matched Platelet Transfusion Failed Patient with Allogeneic Hematopoietic Stem Cell Transplantation].

OBJECTIVE: To investigate the causes of ineffectiveness of platelet transfusion with monoclonal antibody solid phase platelet antibody test (MASPAT) matching in patients with allogeneic hematopoietic stem cell transplantation and explore the strategies of platelet transfusion. METHODS: A case of donor-specific HLA antibodies (DSA) induced by transfusion which ultimately resulted in transplantation failure and ineffective platelet transfusion with MASPAT matching was selected, and the causes of ineffective platelet transfusion and platelet transfusion strategy were retrospectively analyzed. RESULTS: The 32-year-old female patient was diagnosed as acute myeloid leukemia (high risk) in another hospital with the main symptoms of fever and leukopenia, who should be admitted for hematopoietic stem cell transplantation after remission by chemotherapy. In the course of chemotherapy, DSA was generated due to platelet transfusion, and had HLA gene loci incompatible with the donor of the first transplant, leading to the failure of the first transplant. The patient received platelet transfusion for several times before and after transplantation, and the results showed that the effective rate of MASPAT matched platelet transfusion was only 35.3%. Further analysis showed that the reason for the ineffective platelet transfusion was due to the missed detection of antibodies by MASPAT method. During the second hematopoietic stem cell transplantation, the DSA-negative donor was selected, and the matching platelets but ineffective transfusion during the primary transplantation were avoided. Finally, the patient was successfully transplanted and discharged from hospital. CONCLUSIONS: DSA can cause graft failure or render the graft ineffective. For the platelet transfusion of patients with DSA, the platelet transfusion strategy with matching type only using MASPAT method will miss the detection of antibodies, resulting in invalid platelet transfusion.

[Correlation Analysis of Hemolytic Transfusion Reaction Induced by Low Titer Antibody].

OBJECTIVE: To establish the diagnostic process of low titer blood group antibody in the occurrence of adverse reactions of hemolytic transfusion. METHODS: Acid elusion test, enzyme method and PEG method were used for antibody identification. Combined with the patient's clinical symptoms and relevant inspection indexes, the irregular antibodies leading to hemolysis were detected. RESULTS: The patient's irregular antibody screening was positive, and it was determined that there was anti-Lea antibody in the serum. After the transfusion reaction, the low titer anti-E antibody was detected by enhanced test. The patient's Rh typing was Ccee, while the transfused red blood cells were ccEE. The new and old samples of the patient were matched with the transfused red blood cells by PEG method, and the major were incompatible. The evidence of hemolytic transfusion reaction was found. CONCLUSION: Antibodies with low titer in serum are not easy to be detected, which often lead to severe hemolytic transfusion reaction.

Prediction of red blood cell transfusion after orthopedic surgery using an interpretable machine learning framework.

Objective: Postoperative red blood cell (RBC) transfusion is widely used during the perioperative period but is often associated with a high risk of infection and complications. However, prediction models for RBC transfusion in patients with orthopedic surgery have not yet been developed. We aimed to identify predictors and constructed prediction models for RBC transfusion after orthopedic surgery using interpretable machine learning algorithms. Methods: This retrospective cohort study reviewed a total of 59,605 patients undergoing orthopedic surgery from June 2013 to January 2019 across 7 tertiary hospitals in China. Patients were randomly split into training (80%) and test subsets (20%). The feature selection method of recursive feature elimination (RFE) was used to identify an optimal feature subset from thirty preoperative variables, and six machine learning algorithms were applied to develop prediction models. The Shapley Additive exPlanations (SHAP) value was employed to evaluate the contribution of each predictor towards the prediction of postoperative RBC transfusion. For simplicity of the clinical utility, a risk score system was further established using the top risk factors identified by machine learning models. Results: Of the 59,605 patients with orthopedic surgery, 19,921 (33.40%) underwent postoperative RBC transfusion. The CatBoost model exhibited an AUC of 0.831 (95% CI: 0.824-0.836) on the test subset, which significantly outperformed five other prediction models. The risk of RBC transfusion was associated with old age (>60 years) and low RBC count (<4.0 × 1012/L) with clear threshold effects. Extremes of BMI, low albumin, prolonged activated partial thromboplastin time, repair and plastic operations on joint structures were additional top predictors for RBC transfusion. The risk score system derived from six risk factors performed well with an AUC of 0.801 (95% CI: 0.794-0.807) on the test subset. Conclusion: By applying an interpretable machine learning framework in a large-scale multicenter retrospective cohort, we identified novel modifiable risk factors and developed prediction models with good performance for postoperative RBC transfusion in patients undergoing orthopedic surgery. Our findings may allow more precise identification of high-risk patients for optimal control of risk factors and achieve personalized RBC transfusion for orthopedic patients.

Arginine attenuates chronic mountain sickness in rats via microRNA-144-5p.

Hypobaric hypoxia is an environmental stress leading to high-altitude pulmonary hypertension. While high-altitude pulmonary hypertension has been linked to high hematocrit findings (chronic mountain sickness; CMS). The present study is designed to investigate the effect of arginine (ARG) on hypobaric hypoxia-induced CMS of rats. Hypobaric hypoxia resulted in lower body weight, decreased appetite, increased pulmonary artery pressure, and deteriorated lung tissue damage in rats. Red blood cells (RBC), hemoglobin, hematocrit, mean corpuscular volume, and mean corpuscular hemoglobin values and blood viscosity were increased in rats, which were alleviated by ARG. microRNA (miRNA) microarray analysis was used to filter differentially expressed miRNAs after ARG in rats. miR-144-5p was reduced under hypobaric hypoxia and upregulated by ARG. miR-144-5p silencing aggravated the erythrocytosis and hyperviscosity in rats, and also accentuated tissue damage and excessive accumulation of RBC. The role of miR-144-5p in rats with CMS was achieved by blocking erythropoietin (EPO)/erythropoietin receptor (EPOR). In conclusion, ARG alleviated CMS symptoms in rodents exposed to hypobaric hypoxia by decreasing EPO/EPOR via miR-144-5p.

Proteome expression profiling of red blood cells during the tumorigenesis of hepatocellular carcinoma.

The early diagnosis of hepatocellular carcinoma (HCC) has not been clinically elucidated, leading to an increased mortality rate in patients with HCC. HCC is a systemic disease related to disorders of blood homeostasis, and the association between red blood cells (RBCs) and HCC tumorigenesis remains elusive. We performed data-independent acquisition proteomic analyses of 72 clinical RBC samples, including HCC (n = 30), liver cirrhosis (LC, n = 17), and healthy controls (n = 25), and characterized the clinical relevance of RBCs and tumorigenesis in HCC. We observed dynamic changes in RBCs during HCC tumorigenesis, and our findings indicate that, based on the protein expression profiles of RBCs, LC is a developmental stage closely approaching HCC. The expression of hemoglobin (HbA and HbF) in peripheral blood dynamically changed during HCC tumorigenesis, suggesting that immature erythroid cells exist in peripheral blood of HCC patients and that erythropoiesis is influenced by the onset of LC. We also identified the disrupted autophagy pathway in RBCs at the onset of LC, which persisted during HCC tumorigenesis. The oxytocin and GnRH pathways were disrupted and first identified during the development of LC into HCC. Significantly differentially expressed SMIM1, ANXA7, HBA1, and HBE1 during tumorigenesis were verified as promising biomarkers for the early diagnosis of HCC using parallel reaction monitoring technology. This study may enhance the understanding of HCC tumorigenesis from a different point of view and aid the early diagnosis of HCC.

Mechanism of selective induction of apoptosis of HCT116 tumor cells in circulating blood by riboflavin photochemistry.

The removal or inactivation of circulating tumor cells (CTCs) can prevent distant metastasis by hematogenous route, but there is still a lack of mature and effective technical means. In the previous research, our team has initially established a method of riboflavin photosensitized treatment (RPT) for continuous treatment of peripheral blood in vitro for the inactivation of CTCs. The core of this technology is that it can selectively induce apoptosis of CTCs (HCT116 cells) without damaging immunocyte (mainly Peripheral Blood Mononuclear Cells，PBMCs) under specific parameters. To clarify the specific mechanism, firstly, the enrichment of riboflavin in HCT116 cells and PBMCs was observed under fluorescence microscope. Secondly, the apoptotic signaling pathways in HCT116 cells and PBMCs in response to RPT treatment were analyzed by transcriptomics. Finally, the mitochondrial damage in HCT116 cells and PBMCs before and after RPT treatment was observed under electron microscope. The results showed that under the same treatment conditions, HCT116 cells were significantly enriched in riboflavin compared with PBMCs. Besides, RPT treatment reduced the expression of long non﹣coding RNA (lncRNA) NEAT1, an effector gene of HCT116 cells, which further down-regulated the expression of target gene PAX2 and promoted the expression of Bax, leading to mitochondrial outer membrane permeabilization (MOMP), and consequently increased the release of pro-apoptotic factors such as cytochrome c(Cyt C), high-temperature requirement protein A2(HTRA2), apoptosis-inducing factor (AIF), endonuclease G(ENDOG), finally leading to apoptosis of HCT116 cells. In contrast, lncRNA NEAT1 remained unchanged in PBMCs before and after RPT treatment, and was unable to stimulate the PBMCs apoptotic signaling pathway. The results of the study indicated that under the specific treatment conditions, RPT technology could selectively induce apoptosis of HCT116 cells by activating the mitochondrial apoptosis pathway, which would further provide a theoretical and technical support for the effective inactivation of CTCs by RPT technology, thereby reducing the risk of recurrence of malignant tumors and improving the cure rate of malignant tumors.

Role of methylation-related genes CRYAB and SLC39A11 in the occurrence and development of lung adenocarcinoma.

Background: Previous studies have shown that human crystallin alpha B (CRYAB) is highly expressed in human cancers and associated with poor survival in cancer patients. Here we investigated whether SLC39A11 and CRYAB genes were related to the proliferation and development of lung adenocarcinoma (LUAD) to explore their potential as therapeutic targets and prognostic markers for LUAD. Methods: CRYAB and SLC39A11 genes were identified from The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database. The human lung cancer cell lines A549 and H1975 were cultured, transfected, and subjected to RNA extraction. After genomic DNA removal, the RNA was reverse-transcribed. Differences between 2 groups were compared using t-test. Results: Knockdown of SLC39A11 inhibited the proliferation of LUAD cells in A549 and H1975. Knockdown of CRYAB promoted the increase of LUAD cell clones, while knockdown of SLC39A11 suppressed LUAD cell clones. In both A549 and H1975 cell lines, knockout of CRYAB inhibited the apoptosis of LUAD cells, whereas knockout of SLC39A11 promoted the apoptosis of LUAD cells. In the H1975 cell line, knockout of CRYAB also lowered the proportion of cells in interphase and increased the proportion of mitotic cells, while knockout of SLC39A11 also slowed down the division cycle of tumor cells. Knockdown of CRYAB promoted the migration of LUAD cells in both the A549 cell line and H1975 cell line. In the H1975 cell line, knockout of SLC39A11 also reduced the invasive ability of LUAD cells. Conclusions: CRYAB and SLC39A11 could be used as prognostic indicators and therapeutic targets for LUAD.

Clinical efficacy and psychological improvement in elderly patients with knee arthritis after comprehensive traditional Chinese medicine care.

OBJECTIVE: To analyze the effect of comprehensive traditional Chinese medicine (TCM) care on the clinical efficacy and psychological improvement of elderly patients with knee arthritis. METHODS: Retrospective analysis was conducted on 114 patients with knee osteoarthritis who underwent arthroscopic minimally invasive surgery in our hospital from January 2018 to January 2022. Among them, 55 patients received routine nursing served as the control group (CG), and the remaining 59 patients received comprehensive TCM care as the observation group (OG). Patients were re-examined two weeks after discharge from the hospital, and the knee joint function recovery effect, pain score, nursing satisfaction, as well as the changes in adverse mood, hospitalization expenses and length of hospitalization during the treatment were compared between two groups. Logistic regression analysis was used to identify factors affecting the curative effect of patients. RESULTS: Compared with the CG, the OG held a significantly better clinical efficacy and lower knee joint score and visual analogue scale (VAS) score (P<0.05). After intervention, the OG showed markedly higher SF-36 score as well as notably declined scores of anxiety and depression than the CG (P<0.05). Quadriceps peak torque ratio (H/Q), as well as satisfaction of patients on nursing in the OG was comparatively better than those of the CG (P<0.05). For hospitalization costs and length of stay, the OG has proven to be more economical and effective with lower cost in both two indexes (P<0.05). Age, course of disease, and nursing program were risk factors affecting the efficacy of treatment in patients (P<0.05). CONCLUSION: Comprehensive TCM care markedly improved the clinical efficacy of the elderly with knee arthritis, relieved patients' pain, and improved knee function and quality of life, as well as reduced patients' anxiety and economic pressure.

Identification of molecular subtypes in lung adenocarcinoma based on DNA methylation and gene expression profiling-a bioinformatic analysis.

Background: Molecular typing based on deoxyribonucleic acid (DNA) methylation and gene expression can extend understandings of the molecular mechanisms involved in lung adenocarcinoma (LUAD) and enhance current diagnostic, treatment, and prognosis prediction approaches. Methods: Gene expression and DNA methylation data sets of LUAD were obtained from The Cancer Genome Atlas (TCGA), and the differential gene and methylation expression levels were analyzed. Results: We successfully divided the LUAD samples into 2 clinically relevant subtypes with significantly different survival times and tumor stages according to the transcriptome and methylation data. We found significant differences in the survival status, age, gender, tumor stage, node stage, and clinical stage between the 2 subtypes. The hub genes identified in the subnetworks, including NCAPG, CCNB1, DLGAP5, HLA-DQA1, HLA-DPA1, HLA-DPB1, SFTP, SCGBA1A, and SFTPD, were correlated with the cell cycle and immune system. The Gene Ontology annotation of the hub genes showed that the biological processes included organelle fission mitotic nuclear division, and sister chromatid segregation. The cellular components included chromosomal region, spindle, and kinetochore. The molecular functions included tubulin-binding, microtubule-binding, and DNA replication origin binding. The Kyoto Encyclopedia of Genes and Genomes signaling pathways related to the hub genes mainly included the cell cycle, human T-cell leukemia virus (type 1) infection, inflammatory bowel disease, and the intestinal immune network for immunoglobulin A production. The clinical stage difference was also confirmed in the validation group using the GSE32863 data set. Conclusions: Our findings extend understandings of the pathogenesis of LUAD and can be used to improve current diagnosis, treatment, and prognosis prediction strategies.

[A Novel Lyophilized PRP-Loaded Gel Based on Chitosan and PEG with Hemostatic and Antibacterial Properties].

OBJECTIVE: A dynamic gel loaded with lyophilized platelet-rich plasma-chitosan/difunctionalized polyethylene glycol (LPRP-CP) was prepared to investigate its hemostatic antibacterial and promoting wound healing of scald wounds through in vitro and in vivo experiments. METHODS: In this study, normal gauze/blank tablet (Ctrl), LPRP-CP, Chitosan HUCHUANG Powder(Chito P)and ChitoGauze XP PRO group (Chito G group) were set. The hemostatic effect and promoting healing effect of the four groups of materials were evaluated by establishing rabbit ear artery hemorrhage model and superficial Ⅱ° scalded model of skin on the back. The hemostatic time and bleeding amount were calculated and the gross and histological results of scald healing were observed. The antibacterial effect of the four groups of materials was evaluated by antibacterial test in vitro. RESULTS: In the rabbit ear arterial hemorrhage model, the hemostasis of all materials was successful. The hemostatic time of Ctrl, Chito P, LPRP-CP and Chito G groups was 213.33±38.30, 118.33±24.01, 115.00±8.37 and 111.67±11.69 s, respectively. The blood loss was 1233.83±992.27, 346.67±176.00, 193.33±121.47 and 147.50±80.66 mg, respectively. Compared with Ctrl, the hemostasis time of LPRP-CP, Chito P and Chito G group was significantly shorter (P<0.001), and the amount of blood loss of LPRP-CP and Chito G group was decreased (P<0.05). Compared with LPRP-CP, there were no significant differences in hemostatic time and blood loss between Chito P and Chito G group (P>0.05). In the model of superficial Ⅱ° scalded on the back of rabbit, the wound healing rate of LPRP-CP was faster than that of the other three groups at the same time, and the healing effect was perfect. In the antibacterial test in vitro, only LPRP-CP had better anti-S. aureus effect, and all groups had no anti-E. coli effect. CONCLUSION: LPRP-CP is an excellent hemostatic material for superficial wounds, and has certain antibacterial and wound healing effects, which has a wide academic value and research prospects.

[Preliminary Study on Screening and Identification of Lewis a Antigen Mimic Epitope in Alpaca Phage Display Nanobody Library].

OBJECTIVE: To establish a new method for synthesizing Lewis blood group antigens, that is, the mimotopes of Lewis blood group antigens were screened by using an alpaca phage display nanobody library. METHODS: We selected mimotopes of the Lewis a (lea) antigen by affinity panning of an alpaca phage display nanobody library using a monoclonal anti-lea antibody. Enzyme-linked immunosorbent assay (ELISA) was used to test the affinity of the positive clones for the monoclonal anti-lea antibody, and the high-affinity positive clones were selected for sequencing and synthesis. Finally, the sensitivity, specificity and reactivity of the synthesized lea mimotope in clinical samples were verified by ELISA. RESULTS: A total of 96 phage clones were randomly selected, and 24 were positive. Fourteen positive clones with the highest affinity were selected for sequencing. The result showed that there were 5 different sequences, among which 3 sequences with the highest frequency, largest difference and highest affinity were selected for expression and synthesis. The sensitivity and specificity of lea mimic antigen by ELISA showed that, the minimum detection limit of gel microcolumn assay (GMA) and ELISA method were 25 times different, and the lea mimic antigen had no cross reacted with the other five unrelated monoclonal antibodies(P<0.001). Finally, 30 clinical plasma samples were analyzed. The mean absorbance of the 15 positive plasma samples was significantly higher than that of the 15 negative plasma samples (P=0.02). However, the positive signal values of the clinical samples were much lower than those of the monoclonal antibodies. CONCLUSION: A new method of screening lea mimic antigen by using alpaca phage nanoantibody library has been established, which is expected to realize the screening of lea mimotopes, thus realizing the application of high-sensitivity detection methods such as ELISA and chemiluminescence in blood group antibody identification.

Improving biomedical named entity recognition by dynamic caching inter-sentence information.

MOTIVATION: Biomedical Named Entity Recognition (BioNER) aims to identify biomedical domain-specific entities (e.g. gene, chemical and disease) from unstructured texts. Despite deep learning-based methods for BioNER achieving satisfactory results, there is still much room for improvement. Firstly, most existing methods use independent sentences as training units and ignore inter-sentence context, which usually leads to the labeling inconsistency problem. Secondly, previous document-level BioNER works have approved that the inter-sentence information is essential, but what information should be regarded as context remains ambiguous. Moreover, there are still few pre-training-based BioNER models that have introduced inter-sentence information. Hence, we propose a cache-based inter-sentence model called BioNER-Cache to alleviate the aforementioned problems. RESULTS: We propose a simple but effective dynamic caching module to capture inter-sentence information for BioNER. Specifically, the cache stores recent hidden representations constrained by predefined caching rules. And the model uses a query-and-read mechanism to retrieve similar historical records from the cache as the local context. Then, an attention-based gated network is adopted to generate context-related features with BioBERT. To dynamically update the cache, we design a scoring function and implement a multi-task approach to jointly train our model. We build a comprehensive benchmark on four biomedical datasets to evaluate the model performance fairly. Finally, extensive experiments clearly validate the superiority of our proposed BioNER-Cache compared with various state-of-the-art intra-sentence and inter-sentence baselines. AVAILABILITYAND IMPLEMENTATION: Code will be available at https://github.com/zgzjdx/BioNER-Cache. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

[Sequencing and Proteomic Analysis of Exosomes from Apheresis Platelets in Different Storage Periods].

OBJECTIVE: To investigate the changes of gene sequencing and proteomics of apheresis platelet (AP) exosomes in different storage periods and predict the function of AP exosomes in different storage periods. METHODS: Platelets at different storage periods of 0 day (D0), 3 day (D3) and 5 day (D5) were collected, exosomes were extracted with Gradient centrifugation; gene sequencing and proteomic analysis were used to analyze the exosomes, and biological functions of platelet exosomes were analyzed and predicted by bioinformatics. Liquid mass spectrometry (LMS) was used to detect the changes and function prediction of exosomes proteins. The small RNA sequencing library was prepared, and the constructed library was sequenced and bioinformatics technology was used for data analysis. RESULTS: AP exosome iTRAQ protein analysis showed that AP exosomes stored in D3 with 55 up-regulated proteins and 94 down-regulated proteins (P<0.05, FC<0.83 or FC>1.2), while AP exosomes stored in D5 with 292 up-regulated proteins and 53 down-regulated proteins (P<0.05, FC<0.83 or FC>1.2) as compared with D0. KEGG pathway analysis showed that the proteins were mainly involved in transport and metabolism, immune system, cancer, membrane transport and other processes. There were statistically significant differences between AP exosome miRNAs in different storage days (P<0.01). The number of miRNA up-regulated and down-regulated was 374 and 255 as compared with the number of platelet exosomes miRNA stored in D3 and D0, while that was 297 and 242 in D5 and D0, and 252 and 327 in D5 and D3, respectively. The target genes of differential platelet exosome miRNAs were analyzed by GO enrichment. Target genes of differential miRNA were mainly involved in membrane composition, mainly played molecular functions binding to proteins, and participated in biological processes of transcriptional regulation. CONCLUSION: The exosome differential proteins and miRNAs in D5 are significantly different from those in the D0 of APs, and they are involved in various biological processes.

Machine learning-based screening of the diagnostic genes and their relationship with immune-cell infiltration in patients with lung adenocarcinoma.

Background: Lung adenocarcinoma (LUAD) is the most common type of lung cancer, and has a dismal mortality rate of 80%, mainly due to diagnosis at an advanced stage. Biomarkers with high specificity and sensitivity for the early diagnosis of LUAD are sparse. This study aimed to identify markers for the early diagnosis of LUAD. Methods: The GSE32863 and GSE75037 data sets were standardized and merged to screen for differentially expressed genes (DEGs). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted. The intersected DEGs from the least absolute shrinkage and selection operator (LASSO) and support vector machine (SVM) regression analyses were considered the hub genes. Then the diagnostic ability and expression of hub genes was tested in GSE63459 data set, Finally, CIBERSORT was used to analyze the correlation between the immune-infiltrating cells and hub genes. Results: The following 7 DEGs were intersected by the LASSO and SVM regression analyses: Locus 401286 (LOC401286), flavin-containing monooxygenase 2 (FMO2), XLKD1, Ras homolog family member J (RHOJ), scavenger receptor Class A member 5 (SCARA5), heat shock protein beta-2 (HSPB2), and serine incorporator 2 (SERINC2). The area under the receiver operating characteristic curve (AUC) of LOC401286, FMO2, XLKD1, RHOJ, SCARA5, HSPB2, and SERINC2 was 0.99, 1.00, 0.99, 1.00, 0.99, 0.99, and 0.98, respectively in the training groups. The AUC of LOC401286, FMO2, XLKD1, RHOJ, SCARA5, HSPB2, and SERINC2 was 0.97, 0.96, 0.94, 0.88, 0.85, 0.94 and 0.89, respectively in the validation group. The immune-cell infiltrations of naive B cells, memory B cells, plasma cells, naive cluster of differentiation (CD) 4 T cells, T follicular helper cells, regulatory T cells, gamma delta T cells, monocytes, M0 macrophages, M1 macrophages, resting mast cells, activated mast cells, and neutrophils were different between the normal and tumor tissues. Notably, these immune cells were correlated with the above-mentioned 7 diagnostic genes. Conclusions: We identified 7 DEGs in LUAD tissue that can be considered diagnostic genes based on 2 machine-learning regression methods, which could be very helpful for the early diagnosis of LUAD in clinical practice.

Cross-Lingual Knowledge Transferring by Structural Correspondence and Space Transfer.

The cross-lingual sentiment analysis (CLSA) aims to leverage label-rich resources in the source language to improve the models of a resource-scarce domain in the target language, where monolingual approaches based on machine learning usually suffer from the unavailability of sentiment knowledge. Recently, the transfer learning paradigm that can transfer sentiment knowledge from resource-rich languages, for example, English, to resource-poor languages, for example, Chinese, has gained particular interest. Along this line, in this article, we propose semisupervised learning with SCL and space transfer (ssSCL-ST), a semisupervised transfer learning approach that makes use of structural correspondence learning as well as space transfer for cross-lingual sentiment analysis. The key idea behind ssSCL-ST, at a high level, is to explore the intrinsic sentiment knowledge in the target-lingual domain and to reduce the loss of valuable knowledge due to the knowledge transfer via semisupervised learning. ssSCL-ST also features in pivot set extension and space transfer, which helps to enhance the efficiency of knowledge transfer and improve the classification accuracy in the target language domain. Extensive experimental results demonstrate the superiority of ssSCL-ST to the state-of-the-art approaches without using any parallel corpora.