CytoSVM: an advanced server for identification of cytokine-receptor interactions

The interactions between cytokines and their complementary receptors are the gateways to properly understand a large variety of cytokine-specific cellular activities such as immunological responses and cell differentiation. To discover novel cytokine-receptor interactions, an advanced support vector machines (SVMs) model, CytoSVM, was constructed in this study. This model was iteratively trained using 449 mammal (except rat) cytokine-receptor interactions and about 1 million virtually generated positive and negative vectors in an enriched way. Final independent evaluation by rat's data received sensitivity of 97.4%, specificity of 99.2% and the Matthews correlation coefficient (MCC) of 0.89. This performance is better than normal SVM-based models. Upon this well-optimized model, a web-based server was created to accept primary protein sequence and present its probabilities to interact with one or several cytokines. Moreover, this model was applied to identify putative cytokine-receptor pairs in the whole genomes of human and mouse. Excluding currently known cytokine-receptor interactions, total 1609 novel cytokine-receptor pairs were discovered from human genome with probability ∼80% after further transmembrane analysis. These cover 220 novel receptors (excluding their isoforms) for 126 human cytokines. The screening results have been deposited in a database. Both the server and the database can be freely accessed at http://bioinf.xmu.edu.cn/software/cytosvm/cytosvm.php

Prognostic value of computed tomography radiomics features in patients with gastric neuroendocrine neoplasm

PurposeThe present study aimed to investigate the clinical prognostic significance of radiomics signature (R-signature) in patients with gastric neuroendocrine neoplasm (GNEN).Methods and MaterialsA retrospective study of 182 patients with GNEN who underwent dual-phase enhanced computed tomography (CT) scanning was conducted. LASSO-Cox regression analysis was used to screen the features and establish the arterial, venous and the arteriovenous phase combined R-signature, respectively. The association between the optimal R-signature with the best prognostic performance and overall survival (OS) was assessed in the training cohort and verified in the validation cohort. Univariate and multivariate Cox regression analysis were used to identify the significant factors of clinicopathological characteristics for OS. Furthermore, the performance of a combined radiomics-clinical nomogram integrating the R-signature and independent clinicopathological risk factors was evaluated.ResultsThe arteriovenous phase combined R-signature had the best performance in predicting OS, and its C-index value was better than the independent arterial and venous phase R-signature (0.803 vs 0.784 and 0.803 vs 0.756, P<0.001, respectively). The optimal R-signature was significantly associated with OS in the training cohort and validation cohort. GNEN patients could be successfully divided into high and low prognostic risk groups with radiomics score median. The combined radiomics-clinical nomogram combining this R-signature and independent clinicopathological risk factors (sex, age, treatment methods, T stage, N stage, M stage, tumor boundary, Ki67, CD56) exhibited significant prognostic superiority over clinical nomogram, R-signature alone, and traditional TNM staging system (C-index, 0.882 vs 0.861, 882 vs 0.803, and 0.882 vs 0.870 respectively, P<0.001). All calibration curves showed remarkable consistency between predicted and actual survival, and decision curve analysis verified the usefulness of the combined radiomics-clinical nomogram for clinical practice.ConclusionsThe R-signature could be used to stratify patients with GNEN into high and low risk groups. Furthermore, the combined radiomics-clinical nomogram provided better predictive accuracy than other predictive models and might aid clinicians with therapeutic decision-making and patient counseling

Kinetic Studies on Radical Scavenging Activity of Kaempferol Decreased by Sn(II) Binding

Sn(II) binds to kaempferol (HKaem, 3,4′,5,7-tetrahydroxy-2-(4-hydroxyphenyl)-4H-1-benzopyran-4-one) at the 3,4-site forming [Sn(II)(Kaem)2] complex in ethanol. DPPH• scavenging efficiency of HKaem is dramatically decreased by SnCl2 coordination due to formation of acid inhibiting deprotonation of HKaem as ligands and thus reduces the radical scavenging activity of the complex via a sequential proton-loss electron transfer (SPLET) mechanism. Moderate decreases in the radical scavenging of HKaem are observed by Sn(CH3COO)2 coordination and by contact between Sn and HKaem, in agreement with the increase in the oxidation potential of the complex compared to HKaem, leading to a decrease in antioxidant efficiency for fruits and vegetables with Sn as package materials

Alkaline earth metal ion coordination increases the radical scavenging efficiency of kaempferol

Flavonoids are used as natural additives and antioxidants in foods, and after coordination to metal ions, as drug candidates, depending on the flavonoid structure. The rate of radical scavenging of the ubiquitous plant flavonoid kaempferol (3,5,7,4′-tetrahydroxyflavone, Kaem) was found to be significantly enhanced by coordination of Mg(ii), Ca(ii), Sr(ii), and Ba(ii) ions, whereas the radical scavenging rate of apigenin (5,7,4′-trihydroxyflavone, Api) was almost unaffected by alkaline earth metal (AEM) ions, as studied for short-lived β-carotene radical cations (β-Car˙(+)) formed by laser flash photolysis in chloroform/ethanol (7 : 3) and for the semi-stable 2,2-diphenyl-1-picrylhydrazyl radical, DPPH˙, in ethanol at 25 °C. A 1 : 1 Mg(ii)–Kaem complex was found to be in equilibrium with a 1 : 2 Mg(ii)–Kaem(2) complex, while for Ca(ii), Sr(ii) and Ba(ii), only 1 : 2 AEM(ii)–Kaem complexes were detected, where all complexes showed 3-hydroxyl and 4-carbonyl coordination and stability constants of higher than 10(9) L(2) mol(−2). The 1 : 2 Ca(ii)–Kaem(2) complex had the highest second order rate constant for both β-Car˙(+) (5 × 10(8) L mol(−1) s(−1)) and DPPH˙ radical (3 × 10(5) L mol(−1) s(−1)) scavenging, which can be attributed to the optimal combination of the stronger electron withdrawing capability of the (n − 1)d orbital in the heavier AEM ions and their spatially asymmetrical structures in 1 : 2 AEM–Kaem complexes with metal ion coordination of the least steric hindrance of two perpendicular flavone backbones as ligands in the Ca(ii) complex, as shown by density functional theory calculations

Case Report: Durable complete response of metastatic hepatocellular carcinoma with asymptomatic hyperamylasemia to combined immunotherapy of anti-cytotoxic T lymphocyte-associated antigen 4 plus anti-programmed cell death-1 antibodies

BackgroundCombined immunotherapy has shown promising results in the treatment of advanced HCC, whereas the priority population that would respond to the combined immunotherapy is still elusive. In addition, HCC with asymptomatic hyperamylasemia was not reported previously.Case presentationAn aged patient was diagnosed as HCC with BCLC stage C (bone metastasis). Notably, this patient showed asymptomatic hyperamylasemia. The patient was then enrolled in a trial evaluating combined immunotherapy of anti-PD-1 antibody sintilimab (IBI308) plus anti-CTLA-4 antibody (IBI310) in advanced HCC. After being treated with combined immunotherapy, this patient rapidly achieved complete response (CR) according to mRECIST criteria or immune partial response (iPR) according to iRECIST criteria and maintain the CR state for more than 12 months. Interestingly, serum levels of amylase and lipase in this patient were reduced after treatment.ConclusionWe reported, for the first time, a case of metastatic HCC with asymptomatic hyperamylasemia, and suggested that HCC patients with asymptomatic hyperamylasemia may benefit from combined immunotherapy of anti-CTLA-4 and PD-1 antibodies

Tailoring of spatial coherence in a multimode fiber by selectively exciting groups of eigenmodes

Control of the properties of speckle patterns produced by mutual interference of light waves is important for various applications of multimode optical fibers. It has been shown previously that a high signal-to-noise ratio in a multimode fiber can be achieved by preferential excitation of lower order spatial eigenmodes in optical fiber communication. Here we demonstrate that signal spatial coherence can be tailored by changing relative contributions of the lower and higher order multimode fiber eigenmodes for the research of speckle formation and spatial coherence. It is found that higher order spatial eigenmodes are more conducive to the final speckle formation. The minimum speckle contrast occurs in the lower order spatial eigenmodes dominated regime. This work paves the way for control and manipulation of the spatial coherence of light in a multimode fiber varying from partially coherent or totally incoherent light