Mass Spectrometry-Based Label-Free Quantitative Proteomics

In order to study the differential protein expression in complex biological samples, strategies for rapid, highly reproducible and accurate quantification are necessary. Isotope labeling and fluorescent labeling techniques have been widely used in quantitative proteomics research. However, researchers are increasingly turning to label-free shotgun proteomics techniques for faster, cleaner, and simpler results. Mass spectrometry-based label-free quantitative proteomics falls into two general categories. In the first are the measurements of changes in chromatographic ion intensity such as peptide peak areas or peak heights. The second is based on the spectral counting of identified proteins. In this paper, we will discuss the technologies of these label-free quantitative methods, statistics, available computational software, and their applications in complex proteomics studies

Capital social, brechas digitales y transmisión intergeneracional del capital cultural en comunidades urbanas estadounidenses desfavorecidas: un estudio exploratorio

Advancing the classic network model of cultural capital, this study draws on social capital theories and digital divide and inclusion literature to examine the implications of social capital and digital connections for parents’ cultural capital in marginalized urban communities in two aspects: parents’ cultural knowledge and intergenerational cultural participation. Drawing on a household survey of an extremely disadvantaged population living in public housing communities in a major American city, results show that parents with greater social capital command greater cultural knowledge, which in turn can increase their intergenerational cultural participation. Parents’ social capital, however, has no direct impacts on intergenerational cultural participation. By contrast, the findings suggested that internet access alone is not enough for digital inclusion to increase cultural capital.Este estudio busca contribuir al modelo de red clásico del capital cultural, basándose en las teorías del capital social y la literatura sobre brecha digital e inclusión. Pretende examinar la influencia del capital social y las conexiones digitales en el capital cultural de los padres de comunidades urbanas marginadas en dos aspectos: el conocimiento cultural de estos y la participación cultural intergeneracional. A partir de una encuesta a hogares de una población de extremadamente desfavorecida, que vive en comunidades de viviendas públicas de una gran ciudad estadounidense, los resultados muestran que los padres con mayor capital social poseen mayor conocimiento cultural, que puede aumentar su participación cultural intergeneracional. Sin embargo, el capital social de estos no tiene efectos directos en la participación cultural intergeneracional. En cambio, los resultados sugieren que el acceso a Internet por sí solo no es suficiente para que la inclusión digital en las comunidades desfavorecidas aumente el capital cultural

Oriented Three-Dimensional Magnetic Biskyrmion in MnNiGa Bulk Crystals

A biskyrmion consists of two bound, topologically stable skyrmion spin textures. These coffee-bean-shaped objects have been observed in real-space in thin plates using Lorentz transmission electron microscopy (LTEM). From LTEM imaging alone, it is not clear whether biskyrmions are surface-confined objects, or, analogously to skyrmions in non-centrosymmetric helimagnets, three-dimensional tube-like structures in bulk sample. Here, we investigate the biskyrmion form factor in single- and polycrystalline MnNiGa samples using small angle neutron scattering (SANS). We find that biskyrmions are not long-range ordered, not even in single-crystals. Surprisingly all of the disordered biskyrmions have their in-plane symmetry axis aligned along certain directions, governed by the magnetocrystalline anisotropy. This anisotropic nature of biskyrmions may be further exploited to encode information

High-sensitive and rapid detection of Mycobacterium tuberculosis infection by IFN-γ release assay among HIV-infected individuals in BCG-vaccinated area

<p>Abstract</p> <p>Background</p> <p>An accurate test for <it>Mycobacterium tuberculosis </it>infection is urgently needed in immunosuppressed populations. The aim of this study was to investigate the diagnostic power of enzyme-linked immunospot (ELISPOT)-based IFN-γ release assay in detecting active and latent tuberculosis in HIV-infected population in <it>bacillus Calmette-Guerin </it>(BCG)-vaccinated area. A total of 100 HIV-infected individuals including 32 active tuberculosis patients were recruited. An ELISPOT-based IFN-γ release assay, T-SPOT.TB, was used to evaluate the <it>M. tuberculosis </it>ESAT-6 and CFP-10 specific IFN-γ response. Tuberculin skin test (TST) was performed for all recruited subjects.</p> <p>Results</p> <p>The subjects were divided into group HIV+ATB (HIV-infected individuals with active tuberculosis, n = 32), group HIV+LTB (HIV-infected individuals with positive results of T-SPOT.TB assay, n = 46) and group HIV only (HIV-infected individuals with negative results of T-SPOT.TB assay and without evidence of tuberculosis infection, n = 22). In group HIV+ATB and HIV+LTB, T-SPOT.TB positive rate in subjects with TST <5 mm were 50% (16/32) and 41.3% (19/46), respectively. Individuals in group HIV+ATB and HIV+LTB with CD4+ T cells <500/μl, T-SPOT.TB showed a higher sensitivity than TST (64.5% vs. 22.6% and 62.2% vs. 29.7%, respectively, both <it>P </it>< 0.0001). In addition, the sensitivity of T-SPOT.TB assay in group HIV+ATB increased to >85% in patients with TB treatment for less than 1 month and CD4+ T cells ≥200/μl, while for patients treated for more than 3 months and CD4+ T cells <200/μl, the sensitivity was decreased to only 33.3%. Furthermore, the results could be generated by T-SPOT.TB assay within 24 hours, which was more rapid than TST with 48–72 hours.</p> <p>Conclusion</p> <p>ELISPOT-based IFN-γ release assay is more sensitive and rapid for the diagnosis of TB infection in Chinese HIV-infected individuals with history of BCG vaccination, and could be an effective tool for guiding preventive treatment with isoniazid in latently infected people and for TB control in China.</p

Identification and analysis of chemokine-related and NETosis-related genes in acute pancreatitis to develop a predictive model

Background: Chemokines and NETosis are significant contributors to the inflammatory response, yet there still needs to be a more comprehensive understanding regarding the specific molecular characteristics and interactions of NETosis and chemokines in the context of acute pancreatitis (AP) and severe AP (SAP).Methods: To address this gap, the mRNA expression profile dataset GSE194331 was utilized for analysis, comprising 87 AP samples (77 non-SAP and 10 SAP) and 32 healthy control samples. Enrichment analyses were conducted for differentially expressed chemokine-related genes (DECRGs) and NETosis-related genes (DENRGs). Three machine-learning algorithms were used for the identification of signature genes, which were subsequently utilized in the development and validation of nomogram diagnostic models for the prediction of AP and SAP. Furthermore, single-gene Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were performed. Lastly, an interaction network for the identified signature genes was constructed.Results: We identified 12 DECRGs and 7 DENRGs, and enrichment analyses indicated they were primarily enriched in cytokine-cytokine receptor interaction, chemokine signaling pathway, TNF signaling pathway, and T cell receptor signaling pathway. Moreover, these machine learning algorithms finally recognized three signature genes (S100A8, AIF1, and IL18). Utilizing the identified signature genes, we developed nomogram models with high predictive accuracy for AP and differentiation of SAP from non-SAP, as demonstrated by area under the curve (AUC) values of 0.968 (95% CI 0.937–0.990) and 0.862 (95% CI 0.742–0.955), respectively, in receiver operating characteristic (ROC) curve analysis. Subsequent single-gene GESA and GSVA indicated a significant positive correlation between these signature genes and the proteasome complex. At the same time, a negative association was observed with the Th1 and Th2 cell differentiation signaling pathways.Conclusion: We have identified three genes (S100A8, AIF1, and IL18) related to chemokines and NETosis, and have developed accurate diagnostic models that might provide a novel method for diagnosing AP and differentiating between severe and non-severe cases