Quality control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures, and highly scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a “QC-Preprocess-QC” workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA, Digital Gene Expression, and metagenomic experiments, respectively. As a workflow-like tool, SOAPnuke centralizes processing functions into 1 executable and predefines their order to avoid the necessity of reformatting different files when switching tools. Furthermore, the MapReduce framework enables large scalability to distribute all the processing works to an entire compute cluster. We conducted a benchmarking where SOAPnuke and other tools are used to preprocess a ∼30× NA12878 dataset published by GIAB. The standalone operation of SOAPnuke struck a balance between resource occupancy and performance. When accelerated on 16 working nodes with MapReduce, SOAPnuke achieved ∼5.7 times the fastest speed of other tools.

Objective: The purpose of this study was to explore the effects of music therapy on pain, anxiety and depression in patients after coronary artery bypass grafting. Methods: A retrospective study of 99 patients after coronary artery bypass from January 2017 to January 2019 was conducted in a cardiac center in China. According to the different interventions, all the participants were divided into 3 groups: group A: music therapy; group B: rest without music therapy; and group C: conventional treatment. The Numerical Rating Scale (NRS), Self-Rating Anxiety Scale (SAS) and Self-Rating Depression Scale (SDS) were used to measure the patient’s pain, anxiety and depression before and after 30 min of the intervention. Results: There were no significant differences in the NRS, SDS and SAS scores between the three groups of patients before the intervention. After 30 min of music therapy, the NRS, SDS and SAS scores of patients in group A were significantly lower than those before music therapy, and the differences were statistically significant. However, before and after the intervention in groups B and C, the NRS, SDS and SAS scores were not statistically significant. By comparison among the three groups after 30 min of intervention, the NRS, SDS and SAS scores in patients in group A were significantly lower than those in groups B and C, and the differences were statistically significant. The scores were not significantly different between groups B and C. Conclusion: Music therapy can effectively alleviate the pain, anxiety and depression of patients after coronary artery bypass grafting.

To investigate the effect of Xiaoaiping Injection (XAP) on advanced hepatocellular carcinoma (HCC) in patients. Sixty-eight patients with advanced HCC were assigned to a control group of 36 and a treatment group of 32. The control group was treated with best supportive treatment (BST) and the treatment group was given XAP plus BST. XAP was administered daily by iv and the treatment course was lasted for 30 days for both groups. The immediate therapeutic efficacy, Karnofsky performance status (KPS) scores, and the changes in immunity indicators (CD3+, CD4+ and CD8+ T cells) were measured and compared before and after treatment. The progression-free survival (PFS) rate and overall survival (OS) rate in the 2 groups were analyzed. The immediate therapeutic efficacy and KPS of the treatment group were better than those in the control group (P0.05). The PFS was 18 weeks in the treatment group and 15 weeks in control group (P<0.05). XAP enhances the quality of life (QOL) of patients with advanced HCC, improves their immunity and extends their PFS.

Hypoxia-inducible factor 1α (HIF-1α), a major mediator of tumor physiology, is activated during tumor progression, and its abundance is correlated with therapeutic resistance in a broad range of solid tumors. The accumulation of HIF-1α is mainly caused by hypoxia or through the mutated succinate dehydrogenase A (SDHA) or fumarate hydratase (FH) expression to inhibit its degradation. However, its activation under normoxic conditions, termed pseudohypoxia, in cells without mutated SDHA or FH is not well documented. Here, we show that dimethyl-2-ketoglutarate (DKG), a cell membrane-permeable precursor of a key metabolic intermediate, α-ketoglutarate (α-KG), known for its ability to rescue glutamine deficiency, transiently stabilized HIF-1α by inhibiting activity of the HIF prolyl hydroxylase domain-containing protein, PHD2. Consequently, prolonged DKG-treatment under normoxia elevated HIF-1α abundance and up-regulated the expression of its downstream target genes, thereby inducing a pseudohypoxic condition. This HIF-1α stabilization phenotype is similar to that from treatment of cells with desferrioxamine (DFO), an iron chelator, or dimethyloxalyglycine (DMOG), an established PHD inhibitor, but was not recapitulated with other α-KG analogues, such as Octyl-2KG, MPTOM001 and MPTOM002. Our study is the first example of an α-KG precursor to increase HIF-1α abundance and activity. We propose that DKG acts as a potent HIF-1α activator, highlighting the potential use of DKG to investigate the contribution of PHD2-HIF-1α pathway to tumor biology.

The goal of this work was to investigate the molecular profiles and metastasis markers in Chinese patients with gastric carcinoma (GC). In total, we performed whole exome sequencing (WES) on 74 GC patients with tumor and adjacent normal formalin-fixed, paraffin-embedded (FFPE) tissue samples. The mutation spectrum of these samples showed a high concordance with TCGA and other studies on GC. PTPRT is significantly associated with metastasis of GC, suggesting its predictive role in metastasis of GC. Patients carrying BRCA2 mutations tend not to metastasize, which may be related to their sensitivity to chemotherapy. Mutations in MACF1, CDC27, HMCN1, CDH1 and PDZD2 were moderately enriched in peritoneal metastasis (PM) samples. Furthermore, we found two genomic regions (1p36.21 and Xq26.3) were associated with PM of GC, and patients with amplification of 1p36.21 and Xq26.3 have a worse prognosis (P = 0.002, 0.01, respectively). Our analysis provides GC patients with potential markers for single and combination therapies.

Right submammary thoracotomy and right vertical infra-axillary thoracotomy are performed for ventricular septal defect (VSD) to reduce the invasiveness of the conventional surgical repair through median sternotomy approach. No comparative studies have been conducted among these three procedures. From January 2016 to December 2016, 182 patients with isolated VSD who underwent surgical repair via one of these 3 approaches were reviewed to compare these three procedures. The procedure success rates were similar in these three groups. There was no statistically significant difference in operative time, aortic cross-clamping time, the duration of CPB, blood transfusion amount and medical cost. However, postoperative mechanical ventilation time, the duration of intensive care and postoperative length of hospital stay were longer in median sternotomy group than the other two groups. (P < 0.05) The median sternotomy group required the longest incision. No significant difference was noted in major adverse events. There were different advantages and disadvantages in the three kinds of operative procedures. Regarding conventional surgical repair VSD, right submammary thoracotomy and right vertical infra-axillary thoracotomy both delivered better cosmetic results for patients with isolated VSD, while all the three procedures could obtain satisfactory clinical effect.