Contribution of zinc accumulation to ischemic brain injury and its mechanisms about oxidative stress, inflammation, and autophagy: an update.

Ischemic stroke is a leading cause of death and disability worldwide, and presently, there is no effective neuroprotective therapy. Zinc is an essential trace element that plays important physiological roles in the central nervous system. Free zinc concentration is tightly regulated by zinc-related proteins in the brain under normal conditions. Disruption of zinc homeostasis, however, has been found to play an important role in the mechanism of brain injury following ischemic stroke. A large of free zinc releases from storage sites after cerebral ischemia, which affects the functions and survival of nerve cells, including neurons, astrocytes, and microglia, resulting in cell death. Ischemia-triggered intracellular zinc accumulation also disrupts the function of blood-brain barrier via increasing its permeability, impairing endothelial cell function, and altering tight junction levels. Oxidative stress and neuroinflammation have been reported to be as major pathological mechanisms in cerebral ischemia/reperfusion injury. Studies have showed that the accumulation of intracellular free zinc could impair mitochondrial function to result in oxidative stress, and form a positive feedback loop between zinc accumulation and reactive oxygen species production, which leads to a series of harmful reactions. Meanwhile, elevated intracellular zinc leads to neuroinflammation. Recent studies also showed that autophagy is one of the important mechanisms of zinc toxicity after ischemic injury. Interrupting the accumulation of zinc will reduce cerebral ischemia injury and improve neurological outcomes. This review summarizes the role of zinc toxicity in cellular and tissue damage following cerebral ischemia, focusing on the mechanisms about oxidative stress, inflammation, and autophagy.

Acute renal failure after kidney transplantation due to mizoribine-induced ureteral stones.

INTRODUCTION: Mizoribine (MZR) is used to prevent rejection reactions after kidney transplantation and increase the risk of hyperuricemia. There is a lack of reports of MZR-induced ureteral stones after kidney transplantation. The surgery treatment of ureteral stones in transplanted kidney is a challenging clinical issue that should only be performed by experienced urologists at professional centers. It is very important to have a thorough understanding of the patient's medical history, analyze the causes of stone formation, and choose a reasonable treatment plan based on the characteristics of the stones. The case report is aim to emphasize the recognition of the possibility of mizoribine-induced ureteral uric acid stones in transplanted kidney and to avoid unnecessary surgery. CASE PRESENTATION: A patient after kidney transplantation was diagnosed with acute renal failure caused by ureteral stones. The medical history, CT images of the renal graft, the results of laboratory test and stone composition analysis were provided. Based on medical history and laboratory test results, it was determined that the ureteral stones of renal graft was induced by MZR. To our best knowledge, this is the first report of MZR-induced stones in transplanted kidney and ureters. It was completely cured by urinary alkalinization, avoiding surgery treatment. We summarize the characteristics, treatment and methods for preventing the formation of uric acid stones of patients with MZR. CONCLUSION: By analyze our case report, it shows that acute renal failure with ureteral stones after kidney transplantation can caused by MZR. Urinary alkalinization for MZR induced uric acid stones is simple and effective.

Pyruvate maintains and enhances the pro-inflammatory response of microglia caused by glucose deficiency in early stroke.

Pro-inflammatory microglia mainly rely on glycolysis to maintain cytokine production during ischemia, accompanied by an increase in inducible nitric oxide synthase (iNOS) and monocarboxylate transporter 1 (MCT1). The role of energy metabolism in the pro-inflammatory response of microglia is currently unclear. In this study, we tested the response of microglia in mice after cerebral ischemia and simulated an energy environment in vitro using low glucose culture medium. The research results indicate that the expression levels of iNOS and arginase 1 (ARG1) increase in the ischemic mouse brain, but the upregulation of MCT1 expression is mainly present in iNOS positive microglia. In microglia exposed to low glucose conditions, iNOS and MCT1 levels increased, while ARG1 levels decreased. Under the same conditions, knocking down MCT1 in microglia leads to a decrease in iNOS levels, while overexpression of MCT1 leads to the opposite result. The use of NF-κB inhibitors reduced the expression levels of iNOS and MCT1 in microglia. In summary, our data indicate that pyruvate maintains and enhances the NF-κB regulated pro-inflammatory response of microglia induced by low glucose.

Sex-Specific Early Retinal Dysfunction in Mutant TDP-43 Transgenic Mice.

BACKGROUND: Increasing evidence has highlighted retinal impairments in neurodegenerative diseases. Dominant mutations in TAR DNA-binding protein 43 (TDP-43) cause amyotrophic lateral sclerosis (ALS), and the accumulation of TDP-43 in the cytoplasm is a pathological hallmark of ALS, frontotemporal dementia (FTD), and many other neurodegenerative diseases. OBJECTIVE: While homozygous transgenic mice expressing the disease-causing human TDP-43 M337V mutant (TDP-43M337V mice) experience premature death, hemizygous TDP-43M337V mice do not suffer sudden death, but they exhibit age-dependent motor-coordinative and cognitive deficits. This study aims to leverage the hemizygous TDP-43M337V mice as a valuable ALS/FTD disease model for the assessment also of retinal changes during the disease progression. METHODS: We evaluated the retinal function of young TDP-43M337V mice by full field electroretinogram (ERG) recordings. RESULTS: At 3-4 months of age, well before the onset of brain dysfunction at 8 months, the ERG responses were notably impaired in the retinas of young female TDP-43M337V mice in contrast to their male counterparts and age-matched non-transgenic mice. Mitochondria have been implicated as critical targets of TDP-43. Further investigation revealed that significant changes in the key regulators of mitochondrial dynamics and bioenergetics were only observed in the retinas of young female TDP-43M337V mice, while these alterations were not present in the brains of either gender. CONCLUSIONS: Together our findings suggest a sex-specific vulnerability within the retina in the early disease stage, and highlight the importance of retinal changes and mitochondrial markers as potential early diagnostic indicators for ALS, FTD, and other TDP-43 related neurodegenerative conditions.

Comparison of adverse effects of anti-tumor therapy for breast cancer shortly after COVID-19 diagnosis vs. the control period.

Background: COVID-19 is an acute infectious disease caused by SARS-CoV-2. The best time to restart antitumor therapy in breast cancer patients after SARS-CoV-2 infection is unknown. This study aimed to evaluate treatment-related adverse events in breast cancer patients who received antitumor therapies within a short time after SARS-CoV-2 infection (observation) as well as before (control) and to provide safety data. Methods: We conducted a self-controlled cohort study using the data from the Breast Disease Center of Peking University First Hospital. We identified patients who received antitumor therapy within 28 days after COVID-19 infection between December 20, 2022, and January 20, 2023. The primary outcome was treatment-related adverse events. McNemar's test was used to compare the incidence rate of adverse reactions between periods. Results: We identified 183 patients with breast cancer, of whom 109 were infected with SARS-CoV-2 within 28 days before antitumor treatment and were included. In total, 28 patients (25.7%) received neoadjuvant therapy, 60 (55.0%) received adjuvant therapy, and 21 (19.3%) received advanced rescue therapy. None of patients required hospitalization for severe or critical COVID-19, but 15 patients (13.8%) still had sequelae of COVID-19 while receiving antitumor treatment. The most common adverse events were peripheral neuropathy (n = 32 [29.4%]), pain (n = 29 [26.6%]), fatigue (n = 28 [25.7%]), nausea (n = 23 [21.1%]), and neutropenia (n = 19 [17.4%]). There was no increased risk of overall treatment-related adverse events (n = 87 [79.8%] vs. n = 91 [83.5%]; p = 0.42) or serious adverse events (n = 13 [11.9%] vs. n = 12 [11.0%]; p = 1.00) from receiving antitumor therapy shortly after the diagnosis of COVID-19. We also found no increased risk in subgroup analyses, and no patients discontinued antitumor therapy due to adverse events. Conclusion: Restarting antitumor therapy 2-4 weeks after having mild or moderate COVID-19 is a relatively safe strategy for breast cancer patients that does not increase the risk of treatment-related adverse events.

Achieving Efficient CO2 Electrolysis to CO by Local Coordination Manipulation of Nickel Single-Atom Catalysts.

Selective electroreduction of CO2 to C1 feed gas provides an attractive avenue to store intermittent renewable energy. However, most of the CO2-to-CO catalysts are designed from the perspective of structural reconstruction, and it is challenging to precisely design a meaningful confining microenvironment for active sites on the support. Herein, we report a local sulfur doping method to precisely tune the electronic structure of an isolated asymmetric nickel-nitrogen-sulfur motif (Ni1-NSC). Our Ni1-NSC catalyst presents >99% faradaic efficiency for CO2-to-CO under a high current density of -320 mA cm-2. In situ attenuated total reflection surface-enhanced infrared absorption spectroscopy and differential electrochemical mass spectrometry indicated that the asymmetric sites show a significantly weaker binding strength of *CO and a lower kinetic overpotential for CO2-to-CO. Further theoretical analysis revealed that the enhanced CO2 reduction reaction performance of Ni1-NSC was mainly due to the effectively decreased intermediate activation energy.

Zinc accumulation aggravates cerebral ischemia/reperfusion injury by promoting inflammation.

Intracellular zinc accumulation has been shown to be associated with neuronal death after cerebral ischemia. However, the mechanism of zinc accumulation leading to neuronal death in ischemia/reperfusion (I/R) is still unclear. Intracellular zinc signals are required for the production of proinflammatory cytokines. The present study investigated whether intracellular accumulated zinc aggravates I/R injury through inflammatory response, and inflammation-mediated neuronal apoptosis. Male Sprague-Dawley rats were treated with vehicle or zinc chelator TPEN 15 mg/kg before a 90-min middle cerebral artery occlusion (MCAO). The expressions of proinflammatory cytokines TNF-α, IL-6, NF-κB p65, and NF-κB inhibitory protein IκB-α, as well as anti-inflammatory cytokine IL-10 were assessed at 6 or 24 h after reperfusion. Our results demonstrated that the expression of TNF-α, IL-6, and NF-κB p65 increased after reperfusion, while the expression of IκB-α and IL-10 decreased, suggesting that cerebral ischemia triggers inflammatory response. Furthermore, TNF-α, NF-κB p65, and IL-10 were all colocalized with the neuron-specific nuclear protein (NeuN), suggesting that the ischemia-induced inflammatory response occurs in neurons. Moreover, TNF-α was also colocalized with the zinc-specific dyes Newport Green (NG), suggesting that intracellular accumulated zinc might be associated with neuronal inflammation following cerebral I/R. Chelating zinc with TPEN reversed the expression of TNF-α, NF-κB p65, IκB-α, IL-6, and IL-10 in ischemic rats. Besides, IL-6-positive cells were colocalized with TUNEL-positive cells in the ischemic penumbra of MCAO rats at 24 h after reperfusion, indicating that zinc accumulation following I/R might induce inflammation and inflammation-associated neuronal apoptosis. Taken together, this study demonstrates that excessive zinc activates inflammation and that the brain injury caused by zinc accumulation is at least partially due to specific neuronal apoptosis induced by inflammation, which may provide an important mechanism of cerebral I/R injury.

Poorly Controlled Diabetes Mellitus Increases the Risk of Deaths and Castration-Resistance in Locally Advanced Prostate Cancer Patients.

The association between DM and prostate cancer progression remains controversial. Previous studies mainly focused on early stage prostate cancer patients. We aimed to study the association between DM and prostate cancer progression in locally advanced prostate cancer patients. 598 locally advanced prostate cancer patients in a top tertiary hospital in China between 2012 and 2021 were divided into three groups based on the postoperative average HbA1c level. The follow-up time is 46.96 ± 27.07 months. Three hundred and forty-eight (58.2%) were normal glucose, 175 (29.3%) were moderate glucose, and 75 (12.5%) were high glucose. Higher postoperative-average HbA1c was associated with poorer OS, PCSM, and PSA-RFS. We concluded that poorly controlled DM was correlated with poorer OS, PCSM, and PSA-RFS in locally advanced prostate cancer patients.

Inhibition of the JAK2/STAT3 pathway and cell cycle re-entry contribute to the protective effect of remote ischemic pre-conditioning of rat hindlimbs on cerebral ischemia/reperfusion injury.

AIMS: Remote ischemic pre-conditioning (RIPC) protects against ischemia/reperfusion (I/R) injury. However, the mechanisms underlying this protection remain unclear. In the present study, we investigated the role of Janus-activated kinase 2 (JAK2)/signal transducer and activator of transcription 3 (STAT3) pathway and cell cycle arrest, and their relationship with neuronal apoptosis following RIPC. METHODS: A rat cerebral I/R injury model was induced by middle cerebral artery occlusion (MCAO), and AG490 was used to investigate the mechanisms of RIPC. p-JAK2-, p-STAT3-, cyclin D1-, and cyclin-dependent kinase 6 (CDK6) expression was assessed by Western blotting and immunofluorescence staining. RESULTS: RIPC reduced the infarct volume, improved neurological function, and increased neuronal survival. Furthermore, p-JAK2 and p-STAT3 were detected during the initial phase of reperfusion; the expression levels were significantly increased at 3 and 24 h after reperfusion and were suppressed by RIPC. Additionally, the MCAO-induced upregulation of the cell cycle regulators cyclin D1 and CDK6 was ameliorated by RIPC. Meanwhile, cyclin D1 and CDK6 were colocalized with p-STAT3 in the ischemic brain. CONCLUSION: RIPC ameliorates the induction of the JAK2/STAT3 pathway and cell cycle regulators cyclin D1 and CDK6 by MCAO, and this net inhibition of cell cycle re-entry by RIPC is associated with downregulation of STAT3 phosphorylation.

Nitric oxide promotes cerebral ischemia/reperfusion injury through upregulating hypoxia-inducible factor1-α-associated inflammation and apoptosis in rats.

Nitric oxide (NO) was one of the key factors to sustain hypoxia-inducible factor-1- α (HIF-1α) activation during hypoxia. However, the mechanism by which NO production promotes upregulation of HIF-1α to cause cerebral ischemia/reperfusion (I/R) injury remains unclear. The present study investigated whether eliminating NO would decrease HIF-1α level, and then reduce the subsequent inflammatory actions as well as neuronal apoptotic death in middle cerebral artery occlusion (MCAO) rats. Our results revealed that HIF-1α was correlated with 3-NT, a marker for nitrosative/oxidative stress, in the brain of MCAO rats. Treatment with NOS inhibitor L-NAME suppressed HIF-1α/3-NT double-positive cells, suggesting that HIF-1α was correlated with NO overproduction during cerebral I/R. Furthermore, pro-inflammatory cytokines TNF-α, IL-1ß and NF-κB p65 were significantly increased and colocalized with HIF-1α in the brain of MCAO rats, all of which could be attenuated by NO inhibition, suggesting that eliminating NO reduced MCAO-induced HIF-1α upregulation, which in turn exerted anti-inflammatory actions. Accordingly, cleaved caspase-3, as well as HIF-1α and TUNEL double-positive cells in ischemic brain were also decreased by L-NAME treatment. These results suggest that NO accumulation after cerebral ischemia leads to HIF-1α upregulation, which may activate pro-inflammatory cytokines, resulting in neuronal apoptotic death. These findings demonstrate a novel mechanism of NO-induced cerebral I/R injury.

Repair of complex digital soft-tissue defects using a free composite ulnar artery perforator flap from the volar wrist.

Digital skin defects resulting from trauma are often associated with dysfunction of the digital nerve and the extensor and flexor tendons in the affected fingers. The repair of these complex tissue defects requires a graft containing multiple tissues that can be used to reconstruct the tendons and nerves and restore the skin. Such procedures can cause multiple injuries and significant damage to the donor site. The current study used a novel technique to repair complex dorsal and palmar digital soft-tissue defects. First, multiple tissues were cut and collected from the donor site. Then, part of the flexor carpi ulnaris tendon was transplanted to repair the tendon defect, and a medial antebrachial cutaneous nerve graft was used to repair the digital nerve defect. Finally, a skin flap was used to cover the skin defect. This paper reports on 31 cases of complex soft-tissue digital defects, with defect areas of 2-18 cm2 . One patient presented with a postoperative arterial crisis in the flap. All other patients recovered without experiencing a vascular crisis, flap necrosis, or wound infection. The postoperative flaps were similar in texture to the original digital skin. The sensation and the extension/flexion functions in the affected fingers recovered well. The effect on grip strength, wrist flexion, and forearm sensation was minor and the postoperative total active motion scores of the affected digits were good or excellent in 96.77% of the cases. The flap sensation recovery rate was also excellent in 83.87% of the cases. The present technique facilitates the repair of multiple dorsal and palmar digital soft-tissue, tendon and nerve defects, reduces the damage to the donor site, and significantly improves the success of surgical repair.

Hyperglycemia is associated with worse 3-year survival in older patients admitted to the intensive care unit after non-cardiac surgery: Post hoc analysis of a randomized trial.

Objective: Hyperglycemia is common in critically ill patients after surgery and is associated with worse perioperative outcomes. Yet, the impact of postoperative hyperglycemia on long-term outcomes remains unclear. We therefore analyzed the association between early postoperative hyperglycemia and 3-year overall survival in older patients who were admitted to the intensive care unit after surgery. Methods: This was a post hoc analysis of database obtained from a previous randomized trial and 3-year follow-up. The underlying trial enrolled 700 patients aged 65 years or older who were admitted to the intensive care unit after elective non-cardiac surgery. Early postoperative time-weighted average blood glucose was calculated and was divided into three levels, i.e., <8.0 mmol/L, from 8.0 to 10.0 mmol/L, and >10.0 mmol/L. The primary outcome was 3-year overall survival. The association between time-weighted average blood glucose level and 3-year overall survival was analyzed with Cox proportional hazard regression models. Subgroup analyses were also performed in patients with or without diabetes, and in patients following cancer or non-cancer surgery. Results: A total of 677 patients (mean age 74 years, 60% male sex) were included in the final analysis. Within 3 years after surgery, deaths occurred in 22.1% (30/136) of patients with time-weighted average blood glucose <8.0 mmol/L, compared with 35.7% (81/227) of those from 8.0 to 10.0 mmol/L (unadjusted hazard ratio 1.75, 95% CI 1.15 to 2.67, P = 0.009), and 36.9% (116/314) of those >10.0 mmol/L (unadjusted hazard ratio 1.91, 95% CI 1.28 to 2.85, P = 0.002). After adjustment for confounding factors, the risk of 3-year mortality remained higher in patients with time-weighted average blood glucose from 8.0 to 10.0 mmol/L (adjusted hazard ratio 2.28, 95% CI 1.47 to 3.54, P < 0.001) and in those >10.0 mmol/L (adjusted hazard ratio 2.00, 95% CI 1.29 to 3.10, P = 0.002). Similar results were obtained in the subgroups of patients without diabetes and patients following cancer surgery. Conclusion: For older patients admitted to the intensive care unit after elective non-cardiac surgery, high early blood glucose (time-weighted average blood glucose ≥ 8.0 mmol/L) was associated with poor 3-year overall survival. The impact of moderate glycemic control on long-term survival deserves further investigation.

Influence of Rosaceous Species and Driving Factors on Differentiation of Rhizospheric Bacteria in a Deciduous Broad-Leaved Forest.

Understanding plant-microbe interactions could provide the basis for improved phytoremediation, microbial resource utilization, and secondary metabolite production. Rhizosphere bacterial communities are strongly influenced by abiotic factors such as soil nutrient availability and the composition of such communities exhibits differentiation under different host plants. In a deciduous broad-leaved forest in Anhui Province, eastern China, the rhizospheric bacteria of three different tree species of the Rosaceae family (Sorbus alnifolia, Cerasus serrulata, and Photinia beauverdiana) were studied, with the bacteria of the bulk soil as controls. Bacterial community composition was determined using the Illumina platform for high-throughput sequencing of 16S rRNA genes. The results showed that the bacterial community composition varied between rhizospheric and bulk soils, and dominant bacterial phyla as Proteobacteria, Actinobacteria, and Acidobacteria were found in both soils. Information on predicted functional genes and pathways revealed significant differences between rhizospheric and bulk soil bacteria. It provided ample evidence for the different metabolic characteristics of the rhizosphere bacterial communities of the three tree species. Electrical conductivity (22.72%), total phosphorus concentration (21.89%), and urease activity (22%) were the main drivers for changes in the composition of the rhizosphere bacterial communities from the three tree species.

In-Person or Online? The Effect of Delivery Mode on Team-Based Learning of Clinical Reasoning in a Family Medicine Clerkship.

In health professions education, team-based learning (TBL) has been used to help learners develop clinical reasoning and decision-making skills. The COVID-19 pandemic has challenged institutions to move curriculum delivery from largely in-person to online. With the anticipated return to in-person instruction and arguments made in favor of online instruction in certain circumstances, evidence is needed to support decision making in curriculum planning. The purpose of this study was to examine the effect of delivery mode (in-person vs. online) on student learning of clinical reasoning and clinical decision-making (CR/CDM) in the family medicine clerkship. Data from three cohorts of third-year medical students were included in the study: 2018/2019 cohort, in-person; 2019/2020 cohort, half of the cohort in-person, half of the cohort online; 2020/2021 cohort, online. Students' performance data-individual readiness assurance test (IRAT) and group readiness assurance test (GRAT) scores-were used. The Generalized Estimating Equations (GEE) analysis was performed. As expected, students scored higher in GRAT than IRAT across the three cohorts. No significant IRAT-GRAT differences were observed between in-person and online delivery of TBL sessions. Student learning of CR/CDM in TBL is comparable between the two modes of delivery in the family medicine clerkship. Future research in other clerkships, years of medical education, and professional programs is needed to inform decision making regarding the TBL delivery mode.

Zinc Accumulation Aggravates Cerebral Ischemia/Reperfusion Injury Through Inducing Endoplasmic Reticulum Stress.

Zinc is highly enriched in the central nervous system. Numerous evidences suggest that high concentration of zinc acts as a critical mediator of neuronal death in the ischemic brain, however, the possible mechanisms of neurotoxicity of zinc during cerebral ischemia/reperfusion (I/R) remain elusive. Endoplasmic reticulum (ER) is a storage location of intracellular zinc. ER stress related genes were up-regulated during zinc-induced neuronal death in vascular-type senile dementia. In the present study, we investigated whether intracellular accumulated zinc aggravates I/R injury through ER stress and ER stress-associated apoptosis. Male Sprague-Dawley rats were subjected to 90 min middle cerebral artery occlusion (MCAO) and received either vehicle or zinc chelator TPEN 15 mg/kg. The expression of ER stress related factors glucose-regulated protein 78 (GRP78) and phosphorylated eukaryotic initiation factor 2α (p-eIF2α), ER stress related apoptotic proteins CCAAT-enhancer-binding protein homologous protein (CHOP) and caspase-12, as well as anti-apoptotic factor B-cell lymphoma-2 (Bcl-2) were assessed 24 h after reperfusion. Our results showed that the levels of GRP78 and p-eIF2α, as well as CHOP and caspase-12, were increased in ischemic brain, indicating that cerebral I/R triggers ER stress. Furthermore, GRP78, CHOP and caspase-12 were all colocalized with the zinc-specific dyes NG, suggesting that there is certain relationship between cytosolic labile zinc and ER stress following cerebral ischemia. Chelating zinc with TPEN reversed the expression of GRP78, p-eIF2α in ischemic rats. Moreover, CHOP and NeuN double staining positive cells, as well as caspase-12 and TUNEL double staining positive cells were also decreased after TPEN treatment, indicating that chelating zinc might inhibit ER stress and decreased ER stress associated neuronal apoptosis. In addition, TPEN treatment reversed the downregulated level of Bcl-2, which localized in the ER membrane and involved in the dysfunction of ER, confirming that the anti-apoptosis effects of chelating zinc following I/R are exerted via inhibition of the ER stress. Taken together, this study demonstrated that excessive zinc activates ER stress and zinc induced neuronal cell death is at least partially due to ER stress specific neuronal apoptosis in ischemic penumbra, which may provide an important mechanism of cerebral I/R injury.

DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions.

Predicting drug-target interactions (DTIs) is essential for both drug discovery and drug repositioning. Recently, deep learning methods have achieved relatively significant performance in predicting DTIs. Generally, it needs a large amount of approved data of DTIs to train the model, which is actually tedious to obtain. In this work, we propose DeepFusion, a deep learning based multi-scale feature fusion method for predicting DTIs. To be specific, we generate global structural similarity feature based on similarity theory, convolutional neural network and generate local chemical sub-structure semantic feature using transformer network respectively for both drug and protein. Data experiments are conducted on four sub-datasets of BIOSNAP, which are 100%, 70%, 50% and 30% of BIOSNAP dataset. Particularly, using 70% sub-dataset, DeepFusion achieves ROC-AUC and PR-AUC by 0.877 and 0.888, which is close to the performance of some baseline methods trained by the whole dataset. In case study, DeepFusion achieves promising prediction results on predicting potential DTIs in case study.

Predicting Drug-Target Affinity Based on Recurrent Neural Networks and Graph Convolutional Neural Networks.

BACKGROUND: Drug development requires a lot of money and time, and the outcome of the challenge is unknown. So, there is an urgent need for researchers to find a new approach that can reduce costs. Therefore, the identification of drug-target interactions (DTIs) has been a critical step in the early stages of drug discovery. These computational methods aim to narrow the search space for novel DTIs and to elucidate the functional background of drugs. Most of the methods developed so far use binary classification to predict the presence or absence of interactions between the drug and the target. However, it is more informative but also more challenging to predict the strength of the binding between a drug and its target. If the strength is not strong enough, such a DTI may not be useful. Hence, the development of methods to predict drug-target affinity (DTA) is of significant importance Method: We have improved the GraphDTA model from a dual-channel model to a triple-channel model. We interpreted the target/protein sequences as time series and extracted their features using the LSTM network. For the drug, we considered both the molecular structure and the local chemical background, retaining the four variant networks used in GraphDTA to extract the topological features of the drug and capturing the local chemical background of the atoms in the drug by using BiGRU. Thus, we obtained the latent features of the target and two latent features of the drug. The connection of these three feature vectors is then inputted into a 2 layer FC network, and a valuable binding affinity is the output. RESULT: We used the Davis and Kiba datasets, using 80% of the data for training and 20% of the data for validation. Our model showed better performance when compared with the experimental results of GraphDTA Conclusion: In this paper, we altered the GraphDTA model to predict drug-target affinity. It represents the drug as a graph and extracts the two-dimensional drug information using a graph convolutional neural network. Simultaneously, the drug and protein targets are represented as a word vector, and the convolutional neural network is used to extract the time-series information of the drug and the target. We demonstrate that our improved method has better performance than the original method. In particular, our model has better performance in the evaluation of benchmark databases.

DL-SMILES#: A Novel Encoding Scheme for Predicting Compound Protein Affinity Using Deep Learning.

INTRODUCTION: Drug repositioning aims to screen drugs and therapeutic goals from approved drugs and abandoned compounds that have been identified as safe. This trend is changing the landscape of drug development and creating a model of drug repositioning for new drug development. In the recent decade, machine learning methods have been applied to predict the binding affinity of compound proteins, while deep learning is recently becoming prominent and achieving significant performances. Among the models, the way of representing the compounds is usually simple, which is the molecular fingerprints, i.e., a single SMILES string. METHODS: In this study, we improve previous work by proposing a novel representing manner, named SMILES#, to recode the SMILES string. This approach takes into account the properties of compounds and achieves superior performance. After that, we propose a deep learning model that combines recurrent neural networks with a convolutional neural network with an attention mechanism, using unlabeled data and labeled data to jointly encode molecules and predict binding affinity. RESULTS: Experimental results show that SMILES# with compound properties can effectively improve the accuracy of the model and reduce the RMS error on most data sets. CONCLUSION: We used the method to verify the related and unrelated compounds with the same target, and the experimental results show the effectiveness of the method.

Network-Based Approaches for Drug Repositioning.

With deep learning creeping up into the ranks of big data, new models based on deep learning and massive data have made great leaps forward rapidly in the field of drug repositioning. However, there is no relevant review to summarize the transformations and development process of models and their data in the field of drug repositioning. Among all the computational methods, network-based methods play an extraordinary role. In view of these circumstances, understanding and comparing existing network-based computational methods applied in drug repositioning will help us recognize the cutting-edge technologies and offer valuable information for relevant researchers. Therefore, in this review, we present an interpretation of the series of important network-based methods applied in drug repositioning, together with their comparisons and development process.

[Effects of BiejiaYugan Granule on TGF-ß1/Smads pathway in rats with hepatic fibrosis caused by compound factors].

Objective: To investigate the therapeutic effects of Biejia Yugan Granule on hepatic fibrosis caused by compound factors in rats and its effect on TGF-ß1/Smads signaling pathway. Methods: SD rats were randomly divided into blank control group, model control group, colchicine group, Biejia Yugan Granule low, medium and high dose (1.85, 3.70, 7.40 g/kg) groups (n= 8 in each group). The rat model of hepatic fibrosis was established by treating with 5% alcohol 15 ml/kg (ig) everyday and injecting with 40% carbon tetrachloride (sc) twice a week for 42 days. The effects of Biejia Yugan Granule on liver function, liver index and water content, serum hepatic fibrosis related indicators, key proteins and gene expression of TGF-ß1/Smads signaling pathway in rats were observed. Results: Biejia Yugan Granule at the doses of 1.85, 3.70 and 7.40 g/kg could decrease the serum levels of ALT, AST, ALP and HA, PCⅢ, C-Ⅳ, LN significantly, reduce the water content of liver tissue leads to the decrease of liver index, regulate the liver tissue TGF-ß1, Smad3 mRNA and Smad7 mRNA expressions. Conclusion: Biejia Yugan Granule has obvious effects of reducing enzyme and protecting liver and inhibiting hepatic fibrosis, and inhibiting TGF-ß1/Smads signaling pathway is one of its mechanisms of anti-hepatic fibrosis.