Fully automatic resolution of untargeted GC-MS data with deep learning assistance.

DeepResolution (Deep learning-assisted multivariate curve Resolution) has been proposed to solve the co-eluting problem for GC-MS data. However, DeepResolution models must be retrained when encountering unknown components, which is undoubtedly time-consuming and burdensome. In this study, a new pipeline named DeepResoution2 was proposed to overcome these limitations. DeepResolution2 utilizes deep neural networks to divide the profile into segments, estimate the number of components in each segment, and predict the elution region of each component. Subsequently, the information obtained by these deep learning models is used to assist the multivariate curve resolution procedure. Only seven models (1 + 1 + 5) are required to automate the whole analysis procedure of untargeted GC-MS data, which is an important improvement over DeepResolution. These seven models are stable and universal. Once established, they can be used to resolve most GC-MS data. Compared with MS-DIAL, ADAP-GC, and AMDIS, DeepResolution2 can obtain more reasonable mass spectra, chromatograms and peak areas to identify and quantify compounds. DeepResoution2 (0.955) outperformed AMDIS (0.939), MS-DIAL (0.948) and ADAP-GC (0.860) in terms of the linear correlation between concentrations and peak areas on overlapped peaks in fatty acid dataset. In real biological samples of human male infertility plasma, the peak areas and mass spectra of 136 untargeted GC-MS files were automatically extracted by DeepResolution2 without any prior information and manual intervention. DeepResolution2 includes all the functions for analyzing untargeted GC-MS datasets from the feature extraction of raw data files to the establishment of discriminant models.

A new torsion tester based on an electronic autocollimator for characterizing the torsional behaviors of microfibers.

Torsional properties of single fibers have considerable effects on the performance of fabrics. A new torsion tester with high resolution is developed based on the torsion-balance method and the autocollimation principle for measuring the torsional properties of single fibers. The tester can measure the torque accurately using the torsion wire of known torsional rigidity. The angular displacement of the torsion wire is measured by a non-contact electronic autocollimator. The calibration results show that the maximum torque capability is around 6 × 10-6 N m with a theoretical resolution of about 8 × 10-11 N m. The instrument's validity is verified by comparing the measurement result with that obtained by a torsion pendulum. Torsion tests on four industrially microfibers, including glass fiber, polyimide fiber, carbon fiber, and gold wire, are performed with the tester, which gives shear moduli 71.0 ± 0.4, 5.6 ± 0.1, 22.6 ± 3.1, and 34.3 ± 0.5 GPa, respectively. Young's moduli of these fibers are also provided. It is demonstrated that these fibers have a high anisotropy in mechanical properties.

Hydroxyapatite-reinforced alginate fibers with bioinspired dually aligned architectures.

Biological materials have excellent mechanical properties due to their organized structures from nano- to macro-scale. Artificial manufacture of materials with anisotropic microstructures still remains challenging. We described a stress-induced method to fabricate anisotropic alginate fibers. Organic-inorganic composite fibers were obtained by incorporating aligned hydroxyapatite (HAP) nanowires into the alginate fiber. Detailed structural characterization revealed the bone-like structure of the HAP-reinforced alginate fibers. Tensile test results showed that the maximum Young's modulus and tensile strength were 4.3 GPa and 153.8 MPa, respectively. A multiscale reinforcing mechanism is proposed after the discussion of the structure-property relationship: highly ordered and compacted nanofibrils aligned along the longitudinal direction at the microscale, and two kinds of alginate gels with different mechanical behaviors at the nanoscale coexisted (acidic alginate gel and calcium-alginate gel). This work validates the effectiveness of the bioinspired fabrication strategy, which inspires further manufacturing and optimization of materials for diverse applications.

Spider dragline silk as torsional actuator driven by humidity.

Self-powered actuation driven by ambient humidity is of practical interest for applications such as hygroscopic artificial muscles. We demonstrate that spider dragline silk exhibits a humidity-induced torsional deformation of more than 300°/mm. When the relative humidity reaches a threshold of about 70%, the dragline silk starts to generate a large twist deformation independent of spider species. The torsional actuation can be precisely controlled by regulating the relative humidity. The behavior of humidity-induced twist is related to the supercontraction behavior of spider dragline silk. Specifically, molecular simulations of MaSp1 and MaSp2 proteins in dragline silk reveal that the unique torsional property originates from the presence of proline in MaSp2. The large proline rings also contribute to steric exclusion and disruption of hydrogen bonding in the molecule. This property of dragline silk and its structural origin can inspire novel design of torsional actuators or artificial muscles and enable the development of designer biomaterials.

Long non-coding RNA DANCR promotes the progression of non-small-cell lung cancer by inhibiting p21 expression.

BACKGROUND: Long non-coding RNAs (lncRNAs) play important roles in human cancers. However, the functional roles of lncRNAs in non-small-cell lung cancer (NSCLC) and the underlying mechanisms are not well understood. METHODS: We examined the expression of lncRNA DANCR in NSCLC by qRT-PCR and explored its biological roles in NSCLC progression by cell and molecular biology studies. RESULTS: DANCR expression level was increased in human NSCLC. The knockdown of DANCR inhibited NSCLC cell proliferation by inducing cell apoptosis and cell cycle arrest. In addition, DANCR knockdown suppressed NSCLC cell migration and invasion via inhibition of epithelial-mesenchymal transition (EMT). On the contrary, DANCR overexpression had the opposite effects. DANCR knockdown inhibited EZH-2-mediated epigenetic silencing of p21 promoter and increased p21 expression. Moreover, DANCR knockdown inhibited NSCLC cell proliferation, migration, and invasion in a p21-dependent manner. CONCLUSION: DANCR plays oncogenic roles in NSCLC and may provide a novel biomarker for NSCLC diagnosis and prognosis.

Genetic polymorphisms of ERCC-1 and ERCC-2 are not prognostic markers in osteosarcoma patients with chemotherapy: A meta-analysis in Chinese population.

AIM: To make an accurate estimation of the association of ERCC1 and ERCC2 polymorphisms with osteosarcoma (OS) prognosis in Chinese population. METHODS: Total 7 qualified studies with 1404 osteosarcoma patients were included. Odds ratios (OR) with 95% CIs were pooled for the survival rate in different osteosarcoma patients with ERCC1 and ERCC2 genetic polymorphisms. The heterogeneity was assessed by I test. Potential publication bias was assessed by Begg funnel plot and Egger linear regression test. RESULTS: In rs11615, no significant association was found under dominant [TT+TC vs. CC: OR = 1.252, 95% CI:0.864-1.815, P = .235], recessive [TT vs. TC+CC: OR = 0.850, 95% CI: 0.695-1.030, P = .095] or allelic model [T vs. C Allele: OR = 1.219, 95% CI: 0.922-1.612, P = .165]. In rs13181, no significant association was found under dominant [AA+AC vs. CC: OR = 1.031, 95% CI: 0.800-1.329, P = .801], recessive [AA vs. AC+CC: OR = 1.005, 95% CI: 0.875, 1.154, P = .944] or allelic model [A vs. C Allele: OR = 1.009, 95% CI: 0.903-1.128, P = .870]. In rs1799793, no significant association was found under dominant [GG+GA vs. AA: OR = 1.134, 95% CI: 0.884-1.454, P = .322, recessive [GG vs. AG+AA: OR = 1.025, 95% CI: 0.881-1.192, P = .750], or allelic model [G vs. A Allele: OR = 1.046, 95% CI: 0.930-1.177, P = .450]. CONCLUSION: This study did not support rs11615, rs13181 or rs1799793 to be used as surrogate markers for clinical outcome of osteosarcoma with chemotherapy.

Tetrandrine suppresses ß­glucan­induced macrophage activation via inhibiting NF­κB, ERK and STAT3 signaling pathways.

Macrophages are important in inflammation through the production of various proinflammatory mediators. ß­glucan is a polymer of glucose, which is produced by numerous different organisms, including fungi, and acts as a trigger for the induction of inflammatory responses. Tetrandrine (TET), a bis­benzylisoquinoline alkaloid isolated from the Chinese herb Radix Stephania tetrandra, has been demonstrated to modulate inflammatory responses. In the present study, it was investigated whether TET affects the inflammatory reaction induced by ß­glucan in murine and human macrophages. It was demonstrated that ß­glucan induced the activation of nuclear factor (NF)­κB and markedly increased the levels of tumor necrosis factor­α (TNF­α) and interleukin 1 ß (IL­1ß) in macrophages. Treatment with TET resulted in downregulation of phosphorylated NF­κB p65 and reduction of the production of TNF­α and IL­1ß. In addition, the phosphorylation of ERK and STAT3 was decreased by TET in activated macrophages. Furthermore, it was demonstrated that the inhibitory effects of TET on ß­glucan­induced macrophage activation was not due to its cytotoxic action. Conclusively, these results indicate that TET can decrease the inflammatory responses mediated by ß­glucan in macrophages. Thus, TET may serve as an effective tool for the treatment of ß­glucan­associated inflammatory diseases.

LYN, a Key Gene From Bioinformatics Analysis, Contributes to Development and Progression of Esophageal Adenocarcinoma.

BACKGROUND Esophageal adenocarcinoma is a lethal malignancy whose incidence is rapidly growing in recent years. Previous reports suggested that Barrett's esophagus (BE), which is represented by metaplasia-dysplasia-carcinoma transition, is regarded as the premalignant lesion of esophageal neoplasm. However, our knowledge about the development of esophageal adenocarcinoma is still very limited. MATERIAL AND METHODS In order to acquire better understanding about the pathological mechanisms in this field, we obtained gene profiling data on BE, esophageal adenocarcinoma patients, and normal controls from the Gene Expression Omnibus (GEO) database. Bioinformatics analyses, including Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were conducted. RESULTS Our results revealed that several pathways, such as the wound healing, complement, and coagulation pathways, were closely correlated with cancer development and progression. The mitogen-activated protein kinase (MAPK) pathway was discovered to be responsible for the predisposition stage of cancer; while response to stress, cytokine-cytokine receptor interaction, nod-like receptor signaling pathway, and ECM-receptor interaction were chief contributors of cancer progression. More importantly, we discovered in this study that LYN was a critical gene. It was found to be the key nodule of several significant biological networks, which suggests its close correlation with cancer initiation and progression. CONCLUSIONS These results provided more information on the mechanisms of esophageal adenocarcinoma, which enlightened our way to the clinical discovery of novel therapeutic makers for conquering esophageal cancer.

Digital image frequency spectrum method for analyzing speckle displacement in frequency domain.

A technique called the digital image frequency spectrum (DIFS) method, used for analyzing digital speckle patterns with deformations in the frequency domain, is proposed. Two subimages in the same position as two digital speckle patterns before and after deformation are used to form a Young's fringe. The parallel Young's fringe pattern is automatically analyzed in the frequency domain. One finds that the displacement between the two subimages can be directly obtained, and a matching procedure used in digital image correlation (DIC) is unnecessary when DIFS is applied. Experimental results show that the relative error of this method is less than 3%, and it takes less time in computing integer-pixel displacement procedure.

Anomalous plasticity in the cyclic torsion of micron scale metallic wires.

The plasticity of micron scale Cu and Au wires under cyclic torsion is investigated for the first time by using a torsion balance technique. In addition to a size effect, a distinct Bauschinger effect and an anomalous plastic recovery, wherein reverse plasticity even occurs upon unloading, are unambiguously revealed. The Bauschinger effect and plastic recovery have been observed in molecular dynamics and discrete dislocation dynamics simulations of ideal single-crystal wires; the results here are an excellent confirmation that these effects also occur in experiment in nonideal polycrystalline wires. A physical model consistent with the simulations is described in which the geometrically necessary dislocations induced by the nonuniform deformation in torsion play the key role in these anomalous plastic behaviors.

[Detection of IgG and IgM antibodies against Chlamydia trachomatis in semen of asymptomatic infertile patients].

OBJECTIVES: To evaluate the clinical significance of the detection of IgG and IgM antibodies against Chlamydia trachomatis (CT) in semen of asymptomatic infertile patients. METHODS: One hundred and sixteen asymptomatic infertile patients and eighteen fertile males were selected randomly. The routine parameter analysis of semen was fulfilled by computer aided semen analysis(CASA). Then the seminal plasma was separated and the IgG, IgM antibodies against CT in seminal plasma were determined with ELISA method. RESULTS: IgG and IgM antibodies against CT were present in 13.8% (16/116) and 3.4% (4/116) of the semen of infertile patients, while for the fertile males the percentages were 11.1% (2/18) and 0, respectively. There were no differences between the two groups(P > 0.05). In the infertile patients, 22 patients were azoospermia. And in the rest 94 infertile patients, the percentages of IgG and IgM antibodies in abnormal sperm density group were 21.4% (6/28) and 7.1% (2/28), which were higher than those in normal group, but there were no statistical differences(P > 0.05). Similarly, the IgG, IgM antibodies were not correlated with the sperm motility(P > 0.05). The positive percentage of CT in 116 patients was 25.9% (30/116). CONCLUSIONS: The percentages of IgG and IgM antibodies against CT in semen of asymptomatic infertile patients are similar to that in fertile males, which do not correlate with the changes of semen parameters, and may not be used for indication of CT infection.