Study on the initiation and propagation of mining induced fractures by underground coal mining in the loess gully region.

Mining-induced fractures resulting from shallow coal seam extraction in the loess gully region of China are complex and variable, presenting critical hazards including water and sand inrush, as well as air leakage, all of which severely endanger operational safety. This study aims to examine the spatiotemporal evolution characteristics of mining-induced fractures in shallow coal seams within China's loess gully region. Focusing on the Shenfu mining area, a combination of theoretical analysis, numerical modeling, and physical similarity simulation is employed to investigate mining processes and fracture development in shallow coal seams within loess gully.

Machine Learning-Enhanced Extraction of Protein Signatures of Renal Cell Carcinoma from Proteomics Data.

In this study, we generated label-free data-independent acquisition (DIA)-based liquid chromatography (LC)-mass spectrometry (MS) proteomics data from 261 renal cell carcinomas (RCC) and 195 normal adjacent tissues (NAT). The RCC tumors included 48 non-clear cell renal cell carcinomas (non-ccRCC) and 213 ccRCC. A total of 219,740 peptides and 11,943 protein groups were identified with 9,787 protein groups per sample on average.

Improving Glycoproteomic Analysis Workflow by Systematic Evaluation of Glycopeptide Enrichment, Quantification, Mass Spectrometry Approach, and Data Analysis Strategies.

Glycosylation is one of the most prevalent and crucial protein modifications. Quantitative site-specific characterization of glycosylation usually requires sophisticated intact glycopeptide analysis using glycoproteomics. Recent efforts have focused on the interrogation of intact glycopeptide analyses using tandem mass spectrometry.

MS-PyCloud: A Cloud Computing-Based Pipeline for Proteomic and Glycoproteomic Data Analyses.

Rapid development and wide adoption of mass spectrometry-based glycoproteomic technologies have empowered scientists to study proteins and protein glycosylation in complex samples on a large scale. This progress has also created unprecedented challenges for individual laboratories to store, manage, and analyze proteomic and glycoproteomic data, both in the cost for proprietary software and high-performance computing and in the long processing time that discourages on-the-fly changes of data processing settings required in explorative and discovery analysis. We developed an open-source, cloud computing-based pipeline, MS-PyCloud, with graphical user interface (GUI), for proteomic and glycoproteomic data analysis.

Consolidation therapy with autologous stem cell transplantation after remission of induction chemotherapy prolongs the survival of patients with peripheral T-cell lymphoma.

Background: There was little evidence of autologous stem cell transplantation (ASCT) as consolidation therapy after remission of induction for patients with Peripheral T-cell lymphoma (PTCL). In this study, we conducted a comparative analysis of real-world survival outcomes between consolidation therapy and observation in patients with PTCL.

Methods: A total of 92 patients with peripheral T-cell lymphoma (PTCL) who were admitted to the Department of Hematology, Huadong Hospital Affiliated with Fudan University from January 2013 to April 2019 were divided into two groups based on whether they were treated with high-dose therapy (HDT) followed by autologous hematopoietic stem cell transplantation (ASCT): ASCT as consolidation therapy (n=30) and observation (n=62).

Deep eutectic solvent self-assembled reverse nanomicelles for transdermal delivery of sparingly soluble drugs.

Background: Transdermal delivery of sparingly soluble drugs is challenging due to their low solubility and poor permeability. Deep eutectic solvent (DES)/or ionic liquid (IL)-mediated nanocarriers are attracting increasing attention. However, most of them require the addition of auxiliary materials (such as surfactants or organic solvents) to maintain the stability of formulations, which may cause skin irritation and potential toxicity.

Proteogenomic insights suggest druggable pathways in endometrial carcinoma.

We characterized a prospective endometrial carcinoma (EC) cohort containing 138 tumors and 20 enriched normal tissues using 10 different omics platforms. Targeted quantitation of two peptides can predict antigen processing and presentation machinery activity, and may inform patient selection for immunotherapy. Association analysis between MYC activity and metformin treatment in both patients and cell lines suggests a potential role for metformin treatment in non-diabetic patients with elevated MYC activity.

Maintenance regimen of GM-CSF with rituximab and lenalidomide improves survival in high-risk B-cell lymphoma by modulating natural killer cells.

Background: The treatment of high-risk B-cell lymphoma (BCL) remains a challenge, especially in the elderly.

Methods: A total of 83 patients (median age 65 years), who have achieved a complete response after induction therapy, were divided into two groups: R  + GM-CSF regimen (lenalidomide, rituximab, granulocyte-macrophage colony-stimulating factor [GM-CSF]) as maintenance therapy (n = 39) and observation (n = 44). The efficacy of the R  + GM-CSF regimen as maintenance in patient with high-risk BCL was analyzed and compared with observation.

Integrated glycoproteomic characterization of clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC), a common form of RCC, is responsible for the high mortality rate of kidney cancer. Dysregulations of glycoproteins have been shown to associate with ccRCC. However, the molecular mechanism has not been well characterized.

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness.

Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases.

Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma.

Background: The identification of differentially expressed tumor-associated proteins and genomic alterations driving neoplasia is critical in the development of clinical assays to detect cancers and forms the foundation for understanding cancer biology. One of the challenges in the analysis of pancreatic ductal adenocarcinoma (PDAC) is the low neoplastic cellularity and heterogeneous composition of bulk tumors. To enrich neoplastic cells from bulk tumor tissue, coring, and laser microdissection (LMD) sampling techniques have been employed.

Characterization of core fucosylation via sequential enzymatic treatments of intact glycopeptides and mass spectrometry analysis.

Core fucosylation of N-linked glycoproteins has been linked to the functions of glycoproteins in physiological and pathological processes. However, quantitative characterization of core fucosylation remains challenging due to the complexity and heterogeneity of N-linked glycosylation. Here we report a mass spectrometry-based method that employs sequential treatment of intact glycopeptides with enzymes (STAGE) to analyze site-specific core fucosylation of glycoproteins.

Improving the detection of aggressive prostate cancer using immunohistochemical staining of protein marker panels.

Prostate cancer (PCa) is a heterogeneous group of tumors, including non-aggressive (NAG) and aggressive (AG) cancer, with variable clinical outcomes. Clinically, in order to assess the aggressiveness of a PCa, a core needle biopsy of a tumor is usually obtained to evaluate the Gleason pattern and score of the tumor. However, it may be difficult to assign on a small biopsy sample using histology.

Characterization of Protein Complexes Chemical Cross-Linking and Mass Spectrometry.

Cells perform various functions by proteins protein complexes. Characterization of protein complexes is critical to understanding their biological and clinical significance and has been one of the major efforts of functional proteomics. To date, most protein complexes are characterized by the system from protein extracts after the cells or tissues are lysed, and it has been challenging to determine which of these protein complexes are formed in intact cells.

OmicsOne: associate omics data with phenotypes in one-click.

Background: The rapid advancements of high throughput "omics" technologies have brought a massive amount of data to process during and after experiments. Multi-omic analysis facilitates a deeper interrogation of a dataset and the discovery of interesting genes, proteins, lipids, glycans, metabolites, or pathways related to the corresponding phenotypes in a study. Many individual software tools have been developed for data analysis and visualization.

Data-Independent Acquisition-Based Mass Spectrometry (DIA-MS) for Quantitative Analysis of Intact N-Linked Glycopeptides.

N-linked protein glycosylation is a key regulator in various biological functions. Previous studies have shown that aberrant glycosylation is associated with many diseases. Therefore, it is essential to elucidate protein modifications of glycosylation by quantitatively profiling intact N-linked glycopeptides.

Proteomic characterization of primary and metastatic prostate cancer reveals reduced proteinase activity in aggressive tumors.

Prostate cancer (PCa) is a heterogeneous group of tumors with variable clinical courses. In order to improve patient outcomes, it is critical to clinically separate aggressive PCa (AG) from non-aggressive PCa (NAG). Although recent genomic studies have identified a spectrum of molecular abnormalities associated with aggressive PCa, it is still challenging to separate AG from NAG.

Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal pancreatic ductal tissues. Proteomic, phosphoproteomic, and glycoproteomic analyses were used to characterize proteins and their modifications.

F-fluorodeoxyglucose positron emission tomography-based prediction for splenectomy in patients with suspected splenic lymphoma.

Background: Diagnostic splenectomy is often performed on patients with suspected splenic lymphoma. However, unnecessary splenectomy entails more harm than benefit for patients. Therefore, a preliminary screening method for patients with suspected splenic lymphoma that has high sensitivity and specificity is urgently needed.

Survival Benefit and Efficiency of Low Dose Decitabine With CEG Regimen Compared to Decitabine Alone in the Elderly MDS - A Multicenter, Retrospective Study.

Background: Decitabine are used in the treatment of myelodysplastic syndrome (MDS), but none trials reported overall survival improvement.

Methods: High-risk MDS and MDS transformed AML (sAML) patients (IPSS-R > 4.5, age above 60 years) in 6 medical centers of China were treated and compared a new regimen (decitabine with CEG) consisted of low dose decitabine (15 mg/m, days 1-3), low dose etoposide (30 mg/m, days 4,6,8,10,12), cytarabine (10 mg/m per day, days 4-12) and granulocyte colony-stimulating factor (G-CSF, 5ug/kg, adjusted by patients' WBC level, 12 hours prior to decitabine administration) with decitabine alone.