Nitrogen deprivation-induced de novo transcriptomic profiling of the oleaginous green alga Botryococcus braunii 779

AbstractTo assess the effect of nitrogen deprivation (ND), a moderately growing A-race Botryococcus braunii subisolate 779 was subjected to nitrogen deprivation for 3days. De novo transcriptome was assembled and annotated by using Trinity software and Basic Local Alignment Search Tools (BLAST), respectively. Comparative analysis indicates that transcriptomes of A-races differ from those of B-races. Furthermore, majority of the homologous ESTs in A-race but not B-race transcriptomes were unknown sequences. Upon ND, level of photosynthetic transcripts, but not photosynthetic efficiency was downregulated. Unlike hydrocarbon contents, ESTs involved in hydrocarbon biosynthesis were not upregulated. Taken together, our results imply that A- and B-races belong to different B. braunii subspecies. Upon ND, excess photosynthetic transcripts are recycled for nitrogen; and hydrocarbon accumulation is not via de novo biosynthesis. Here we describe in details the data contents and analytic methodologies associated with the data uploaded to Gene Expression Omnibus (accession number GSE71296)

Analysis of crucial molecules involved in herniated discs and degenerative disc disease

OBJECTIVES: Herniated discs and degenerative disc disease are major health problems worldwide. However, their pathogenesis remains obscure. This study aimed to explore the molecular mechanisms of these ailments and to identify underlying therapeutic targets. MATERIAL AND METHODS: Using the GSE23130 microarray datasets downloaded from the Gene Expression Omnibus database, differentially co-expressed genes and links were identified using the differentially co-expressed gene and link method with a false discovery rate ,0.25 as a significant threshold. Subsequently, the underlying molecular mechanisms of the differential co-expression of these genes were investigated using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. In addition, the transcriptional regulatory relationship was also investigated. RESULTS: Through the analysis of the gene expression profiles of different specimens from patients with these diseases, 539 differentially co-expressed genes were identified for these ailments. The ten most significant signaling pathways involving the differentially co-expressed genes were identified by enrichment analysis. Among these pathways, apoptosis and extracellular matrix-receptor interaction pathways have been reported to be related to these diseases. A total of 62 pairs of regulatory relationships between transcription factors and their target genes were identified as critical for the pathogenesis of these diseases. CONCLUSION: The results of our study will help to identify the mechanisms responsible for herniated discs and degenerative disc disease and provides a theoretical basis for further therapeutic study

Prevalence and severity of anxiety and depression in Chinese patients with breast cancer: a systematic review and meta-analysis

ContextAnxiety/depression in breast cancer (BC) is common around the world, and Chinese BC patients should not be ignored. The prevalence of anxiety and depression among BC patients are various in different regions of China, but no clear summarization has been made.PurposeThis meta-analysis aimed to evaluate the prevalence and severity of anxiety and depression among breast cancer (BC) patients in China.MethodsA literature search on PubMed, Web of Science, Embase, CINAHL, Scopus, PsycINFO, Cochrane database library, CNKI, Wanfang, and SinoMed was conducted up to 29 December 2021. The effect size (ES) or standard mean difference (SMD) and the corresponding 95% confidence intervals (CIs) for the prevalence and severity of anxiety/depression were calculated using the STATA 12.0 software.ResultsA total of 63 identified studies were included, containing a total of 53,513 Chinese women confirmed breast cancer. The results showed a high pooled prevalence of anxiety (38%, 95% CI, 27–50%, I2 = 99.4%, p < 0.001) and depression (38%, 95% CI, 33–44%, I2 = 99.2%, p < 0.001) among Chinese BC patients. Moreover, both anxiety (SMD = 0.30, 95% CI, 0.08–0.53, I2 = 91.6%, p < 0.001) and depression (SMD = 0.25, 95% CI, −0.05–0.55, I2 = 95.3%, p < 0.001) in BC patients were more serious than those in healthy controls, but not significantly different from patients with other diseases. Specifically, among the six regions included, the prevalence of anxiety and depression were both the highest in Northeast China, obviously superior than the second-highest region.ConclusionThe study showed high levels of anxiety and depression among BC patients in China, especially those in the northeast. Clinicians and researchers should pay attention to the psychological problems of patients with breast cancer and regard it as one of the important prognostic outcomes of patients.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/index.php, PROSPERO: CRD42020151752

CT synthesis from MRI with an improved multi-scale learning network

Introduction: Using MRI to synthesize CT and substitute its function in radiation therapy has drawn wide research interests. Currently, deep learning models have become the first choice for MRI—CT synthesis because of their ability to study complex non-linear relations. However, existing studies still lack the ability to learn complex local and global MRI–CT relations in the same time , which influences the intensity and structural performance of synthetic images.Methods: This study proposes a hybrid multi-scale model to explore rich local and global MRI—CT relations, relations, namely, the hybrid multi-scale synthesis network (HMSS-Net). It includes two modules modelling different resolution inputs. In the low-resolution module, the Transformer method is applied to build its bottleneck part to expand the receptive field and explore long-range MRI—CT relations to estimate the coarse distribution of widely spread tissues and large organs. In the high-resolution module, residual and dense connections are applied to explore complex local MRI—CT relations under multiple step sizes. Then, the feature spaces of two modules are combined together and utilized to provide synthetic CT. HMSS-Net also introduces the multi-scale structural similarity index measure loss to provide multi-scale supervision during training.Results: The experimental results on head and neck regions of 78 patients showed that HMSS–Net reduced the average of 7.6/3.13 HU on the mean absolute error and increased the average of 2.1/1.8% on the dice coefficient of bone compared with competing image–to–image synthesis methods.Conclusion: The results imply that HMSS–Net could effectively improve the intensity and structural performances of synthetic CT