DeepCancerMap: A versatile deep learning platform for target- and cell-based anticancer drug discovery.

Discovering new anticancer drugs has been widely concerned and remains an open challenge. Target- and phenotypic-based experimental screening represent two mainstream anticancer drug discovery methods, which suffer from time-consuming, labor-intensive, and high experimental costs. In this study, we collected 485,900 compounds involving in 3,919,974 bioactivity records against 426 anticancer targets and 346 cancer cell lines from academic literature, as well as 60 tumor cell lines from NCI-60 panel. A total of 832 classification models (426 target- and 406 cell-based predictive models) were then constructed to predict the inhibitory activity of compounds against targets and tumor cell lines using FP-GNN deep learning method. Compared to the classical machine learning and deep learning methods, the FP-GNN models achieve considerable overall predictive performance, with the highest AUC values of 0.91, 0.88, 0.91 for the test sets of targets, academia-sourced and NCI-60 cancer cell lines, respectively. A user-friendly webserver called DeepCancerMap and its local version were developed based on these high-quality models, enabling users to perform anticancer drug discovery-related tasks including large-scale virtual screening, profiling prediction of anticancer agents, target fishing, and drug repositioning. We anticipate this platform to accelerate the discovery of anticancer drugs in the field. DeepCancerMap is freely available at https://deepcancermap.idruglab.cn.

Correlation analysis of Blood TM, TG and D-dimer with deep venous Thrombosis formation in patients after Total Hip Arthroplasty.

Objective: To explore the correlation of blood thrombomodulin (TM), triglyceride (TG) and D-Dimer (D-D) with the formation of deep vein thrombosis (DVT) in patients after total hip arthroplasty (THA). Methods: A retrospective analysis was carried out focusing on the clinical data of 150 patients with THA who were admitted to Sichuan Provincial Orthopedic Hospital from May 2019 to May 2022 (the study group). These patients were then subdivided into Group-A (46 cases with DVT) and Group-B (104 cases without DVT) according to whether DVT occurred after an operation. Meanwhile, another 70 patients who received physical examination in this hospital in the same period were selected as the control group. Furthermore, the levels of TM, TG, D-D, fibrinogen (Fb) and C-reactive protein (CRP) were compared between the groups. Pearson correlation was used to analyze the relationship between the levels of TM, TG, D-D, Fb, CRP and the formation of DVT. Result: The levels of TM, TG, D-D, Fb and CRP in the study group were significantly higher than those in the control group (p<0.05). The above indicators in Group-A were higher than those in Group-B one day after the operation (p<0.05). Pearson correlation analysis showed that the levels of TM, TG, D-D, Fb and CRP were significantly positively correlated with the formation of DVT. Conclusion: Patients with DVT after THA show an increase in the levels of TM, TG, D-D, Fb and CRP, indicating their diagnostic value for the formation of DVT. Findings in our study suggest that clinical tests of these indicators can be carried out according to the actual situation of patients.

Intrathyroidal Thymic Carcinoma: A Retrospective Case Series Study.

OBJECTIVE: Intrathyroidal thymic carcinoma (ITC) is a rare low-grade malignant thyroid tumor. There is neither sufficient understanding of this tumor nor its clinical treatment. This study is to explore the clinicopathological features, treatment, and prognosis of ITC and thereby provide a reference for the diagnosis and treatment of the disease. METHODS: The clinical, pathological, therapeutic, and prognostic data of 13 patients with ITC were retrospectively analyzed. RESULTS: The case series comprised 7 males and 6 females, with an average age of 51.9 ± 10.1 years. After surgical resection, all patients received post-operative neck radiotherapy at dosages of 60-66 Gy. Five patients with level VI lymph node metastasis additionally received 6 courses of cisplatin chemotherapy. All patients were followed-up for 21-132 months (median = 66 months), and all of them survived without recurrence or metastasis. CONCLUSIONS: The diagnosis of ITC depends mainly on pathological and immunohistochemical results, particularly CD5 positive staining. Surgical resection is the preferred primary treatment modality which can be supplemented with radiotherapy and chemotherapy to reduce the risk of recurrence and metastasis.

High-throughput sequencing reveals omnivorous and preferential diets of the rotifer Polyarthra in situ.

Knowledge of in situ diet of widespread rotifers is crucial for accurately understanding the trophic position, ecological function, and adaptability to environmental changes in aquatic ecosystems. However, it is challenging to achieve the in situ diet information due to the lack of efficient and comprehensive methods. Here, we investigated the diet composition of Polyarthra in a subtropical lake using high-throughput sequencing (HTS) of a rRNA metabarcode for Polyarthra and ambient water samples. After eliminating Polyarthra sequences, a total of 159 operational taxonomic units (OTUs) from taxa in 15 phyla were detected from Polyarthra gut content samples. Most of the OTUs belong to Chlorophyta, followed by unclassified Fungi, Chrysophyta, Dinoflagellata, Ciliophora, Bacillariophyta, Cryptophyta, Arthropoda, Cercozoa, Mollusca, Apicomplexa, Haptophyta, Amoebozoa, Chordata and other eukaryotes. Our results showed that Polyarthra mainly grazed on Chlorophyta, which may result from the high relative abundance of Chlorophyta in ambient waters. In contrast, Chrysophyceae and Synurophyceae were enriched in Polyarthra's gut, indicating that this rotifer prefers these taxa as food. Moreover, correlation analysis showed that total nitrogen, transparency, depth, Chlorophyll-a and total phosphorus were key factors for the variation of the eukaryotic community in the Polyarthra gut contents. When the concentration of nutrients in the water environment decreased, Polyarthra shifted from herbivorous feeding to more carnivorous feeding. Thus, Polyarthra is generally omnivorous but preference for Chrysophytes and Synurophytes, and it responds to the environmental changes by adopting a flexible feeding strategy. This could partly explain why the widespread rotifers have apparently wide tolerance toward spatial and environmental changes.

The complete chloroplast genome of Tripsacum laxum (Gramineae).

Tripsacum laxum (Guatemalan grass) is a perennial fodder grasses, which is commonly growing in large parts of Africa for a source of livestock feed. It has a high economic value as a forage. In this study, we obtained a complete chloroplast genome of T. laxum by Illumina sequencing. The results showed a circular genome of 140,556 bp, including the large single copy region (LSC, 82,939 bp), the small single-copy region (SSC, 12,573 bp), and a pair of 22,522 bp inverted repeat regions (IRs). The circular genome contained 120 genes, including 74 protein-coding genes, eight ribosomal RNA genes and 38 tRNA genes. Evolutionary relationship analysis indicates that T. laxum is more closely related to previously reported T. dactyloides.

Linking microbial community and biological functions to redox potential during black-odor river sediment remediation.

The black-odor phenomenon in polluted urban rivers is a serious environmental problem that has received increasing attention in the recent years. The low redox potential (less than - 100 mV) in the sediment is considered to be the key factor causing the occurrence of black-odor phenomenon. Here, we studied the structure and function of the microbial community during the remediation of urban rivers. Results showed a clear improvement in water quality after undergoing river remediation processes. The on-site treatments showed a succession in the microbial composition and their predicted functions. The primary iron- and sulfur-reducing bacteria (Thiobacillus, Sulfuricurvum, and Sulfursoma) and the related reactions rapidly decreased after the dredging treatment but reappeared after a year. The structure and abundance of nitrogen and methane participants were also affected by river remediation process. These results indicated that although the water quality temporarily improved shortly after a dredging process, a recurrence of the black-odor phenomenon may occur as a result of the rebound in the microbial communities.

Ceramsite Facilitated Microbial Degradation of Pollutants in Domestic Wastewater.

Although constructed wetlands (CWs) are widely used around the world with various substrates, the mechanisms of how these modified substrates affect wastewater treatment are still unknown. In this study, CW microcosms were established with and without ceramsite as a substrate, and the wastewater treatment efficiencies were evaluated during 71 days of incubation. Using the 16S rRNA high-through sequencing, the mechanisms of how CW substrate changed the microbial community was quantified. The results showed that compared to soil as substrate, the use of ceramsite as substrate material enhanced the removal of pollutants from CW systems, particularly under a short retention time (1.5-day) condition. There were more beneficial microorganism groups (nitrogen, sulfur, phosphate) in the ceramsite CW system than the non-ceramsite CW system, particularly in the bottom layers. Moreover, the CW with ceramsite substrate had more nitrification function. All of these results suggested that the ceramsite CW system enhanced the removal of pollutants because it increased the concentration of key microbes that are necessarily for nutrient cycles.

Complete genome sequence of the dissimilatory azo reducing thermophilic bacterium Novibacillus thermophiles SG-1.

With the isolation and identification of efficient azo-dye degradation bacteria, bioaugmentation with specific microbial strains has now become an effective strategy to promote the bioremediation of azo dye. However, Azo dye wastewater discharged at high temperature restricted the extensive application of the known mesophilic azoreducing microorganisms. Here we present the complete genome sequence of a bacterium capable of reducing azo dye under thermophilic condition, Novibacillus thermophiles SG-1 (=KCTC 33118T =CGMCC 1.12363T). The complete genome of strain SG-1 contains a circular chromosome of 3,629,225 bp with a G + C content of 50.44%. Genome analysis revealed that strain SG-1 possessed genes encoding riboflavin biosynthesis protein that would secrete riboflavin, which could act as electron shuttles to transport the electrons to extracellular azo dye in decolorization process. HPLC analysis showed that the concentration of riboflavin increased from 0.01 µM to 0.255 µM with the growth of strain SG-1 under azo dye reduction. Quantitative real-time PCR analysis further demonstrated that the gene encoding riboflavin biosynthesis protein would be involved in the azo dye decolorization. The results from this study would be beneficial to research the mechanism of anaerobic reduction of azo dye under thermophilic conditions.

[Spectroscopic Characterization of DOM During Hyperthermophilic Composting of Sewage Sludge].

Spectroscopy methods such as three-dimensional excitation-emission (3D-EEM) fluorescence spectroscopy were applied to analyze the structures and changes of DOM in hyperthermophilic composting of sewage sludge to fully understand the advantages of hyperthermophilic composting in promoting sludge maturity. The results showed that the temperature reached its peak value at 90℃ and remained over 80℃ for 5 d. The thermophilic period more than 50℃ lasted for 22 d. This indicated that the microorganisms were metabolically active during the composting. The parameters of UV-visible (UV-Vis), including E253/E203, SUVA280, and S275-295, significantly changed from days 0 to 23, showing that the aromaticity degree of DOM and the humification degree of the compost gradually strengthened. Combined with the fluorescence regional integration (FRI), the 3D-EEM analysis results illuminated that the protein-like materials in DOM were completely degraded during days 0 to 6 of the hyperthermophilic composting and a large amount of humic acid-like and fulvic-like materials formed from days 0 to 23, indicating the compost was mature at the hyperthermophilic stage. This was consistent with the germination index (GI) on day 23 (GI=98.5%) as well. Based on the correlation analysis between spectroscopic parameters, PⅤ,n/PⅢ,n showed close relationship with others (r ≥ 0.68), showing their potential as indicators for maturity of hyperthermophilic composting. The results above confirmed that fermentation time could be greatly shortened to about 20 d by using the hyperthermophilic composting, which has great potential for application in organic solid waste management.

Enhanced electrosynthesis performance of Moorella thermoautotrophica by improving cell permeability.

Microbial electrosynthesis systems (MES) are promising devices in which microbes obtain electrons from electrodes to produce extracellular multicarbon compounds. This study investigates whether improvement in cell permeability can enhance electrosynthesis performance of Gram-positive Moorella thermoautotrophica in MES. Results showed that when ≤30mg/L penicillin was added, the cell permeability was doubled, and the electron uptake per biomass (including both cathode-associated biomass and suspended biomass) was 1.84 times that of the control, while formate and acetate production rates per biomass were 1.96 and 2.23 times those of the control, respectively. Enhanced cell permeability caused higher redox activities of outmost cytochrome C and increased release of redox electron shuttles, both of which were beneficial to extracellular electron uptake. Coulombic efficiencies increased from 73%±3% to 88%±3% with better cell permeability, demonstrating that higher proportion of electrical energy recovered in the chemical-production reaction. This research demonstrates that making a moderate decrease in peptidoglycan of cell walls to improve cell permeability can enhance electron uptakes and chemical production rates of Gram-positive microbes in MES, which would serve as a base for the future genetic modification study of superior electrosynthesis strains.

[Analysis of 33 children with deep neck infection].

OBJECTIVE: To analyze the effective treatment of deep neck infection in children. METHODS: Thirty-three cases of deep neck infection treated from September 2005 to May 2015 were retrospectively reviewed. To observe the effect of antibiotics and surgical drainage. RESULTS: All cases were cured, including one case who was complicated with carotid artery rupture and was timely cured by vascular interventional therapy, and the cure rate was 100%. CONCLUSION: Combined application of broad-spectrum antibiotics and effective surgical drainage are key to treat deep neck infection in children. The emergence of repeated small amount of bleeding in the nose and throat in children is an indicator for big neck vessel rupture and interventional vascular therapy may be considered.

[The clinical analysis of thyriod carcinoma showing thymus-like differentiation].

OBJECTIVE: To investigate the clinical diagnosis, treatment and prognosis of carcinoma showing thymus-like differentiation (CASTLE) of thyroid, and to improve the understanding of CASTLE. METHOD: In 6 patients with CASTLE, we performed region VI lymph node dissection, the lesion resection of thyroid lobe and isthmus. After the operation, except one case of 68 years old patient, the rest patients were treated with radiotherapy 60 Gy in anterior cervical region after third week of operation and 5 courses of chemotherapy with cisplatin, each interval of 2 weeks. Insist on the oral Euthyrox. RESULT: All patients were alive without recurrence and metastasis. CONCLUSION: The diagnosis of CASTLE depends on the histology and immunohistochemistry. Operation was the main treatment. CASTLE is a rare type of thyroid carcinoma with slow progress and good prognosis.

Highly efficient graphene-based Cu(In, Ga)Se2 solar cells with large active area.

Two-dimensional graphene has tremendous potential to be used as a transparent conducting electrode (TCE), owing to its high transparency and conductivity. To date graphene films have been applied to several kinds of solar cells except the Cu(In, Ga)Se2 (CIGS) solar cell. In this work, we present a novel TCE structure consisting of a doped graphene film and a thin layer of poly(methyl methacrylate) (PMMA) to replace the ZnO:Al (AZO) electrode for CIGS. By optimizing the contact between graphene and intrinsic ZnO (i-ZnO), a high power conversion efficiency (PCE) of 13.5% has been achieved, which is among the highest efficiencies of graphene-based solar cells ever reported and approaching those of AZO-based solar cells. Besides, the active area of our solar cells reaches 45 mm(2), much larger than other highly efficient graphene-based solar cells (>10%) reported so far. Moreover, compared with AZO-based CIGS solar cells, the total reflectance of the graphene-based CIGS solar cells is decreased and the quantum efficiency of the graphene-based CIGS is enhanced in the near infrared region (NIR), which strongly support graphene as a competitive candidate material for the TCE in the CIGS solar cell. Furthermore, the graphene/PMMA film can protect the solar cell from moisture, making the graphene-based solar cells much more stable than the AZO-based solar cells.

[Expression of Survivin and Bcl-2 in sinonasal inverted papilloma].

OBJECTIVE: To investigate the expression of Survivin and its relationship with the expression of Bcl-2 in sinonasal inverted papilloma (SNIP). METHOD: Immunohistochemical method was used to determine the expression of Survivin and Bcl-2 in 30 cases of SNIP, 10 cases of sinonasal squamous cell carcinoma (SCC) and 10 cases of normal inferior concha tissues. RESULT: Survivin was expressed in 22 of 30 (73.3%) cases of SNIP, 8 of 10 (80.0%) cases of SCC and not expressed in 10 (0%) cases of normal inferior concha tissues. Expression of Survivin was significantly higher in SNIP and SCC than in normal tissues. Bcl-2 was expressed in 9 of 10 (90.0%) cases of SCC and 2 of 10 (20.0%) cases of normal inferior concha tissues. Expression of Bcl-2 was significantly higher in SCC than in normal tissues. Bcl-2 was expressed in 14 of 30 (46.7%) cases of SNIP, higher than normal tissues. Expression of Bcl-2 was positively related to expression of Survivin. CONCLUSION: Survivin may play an important role in the pathway of progression of SNIP and SCC. It may be identified as a new therapeutic target. Bcl-2 may play a synergic role with Survivin in progression of SNIP.