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Spatial transcriptome (ST) technology provides both the spatial location and transcriptional profile of spots, as well as tissue images. ST data can be utilized to construct gene regulatory networks, which can help identify gene modules that facilitate the understanding of biological processes such as cell communication. Correlation measurement is the core basis for constructing a gene regulatory network. However, due to the high noise and sparsity in ST data, common correlation measurement methods such as the Pearson correlation coefficient (PCC) and Spearman correlation coefficient (SPCC) are not suitable. In this work, a new gene correlation measurement method called STgcor is proposed. STgcor defines vertexes as spots in a two-dimensional coordinate plane consisting of axes X and Y from the gene pair (X and Y). The joint probability density of Gaussian distribution of the gene pair (X and Y) is calculated to identify and eliminate outliers. To overcome sparsity, the degree, trend, and location of the distribution of vertexes are used to measure the correlation between gene pairs (X, Y). To validate the performance of the STgcor method, it is compared with the PCC and SPCC in a weighted coexpression network analysis method using two ST datasets of breast cancer and prostate cancer. The gene modules identified by these methods are then compared and analyzed. The results show that the STgcor method detects some special gene modules and cancer-related pathways that cannot be detected by the other two methods. [ABSTRACT FROM AUTHOR]

Background: With increasing multidisciplinary care strategies, palliative medicine practitioner perceptions toward acupuncture integration are significant. Objective: To evaluate acupuncture availability and acceptability in Australian palliative care. Outcomes: (1) Domains of the survey included participant characteristics, (2) workplace availability, (3) personal attitudes, and (4) recommendation likelihood. Design: An online REDCap survey of Australian palliative medicine practitioners was administered. Results: Acupuncture was mostly not available/permitted at workplaces (45.2%) due to cost/funding (57.1%) and limited evidence (57.1%). When available by workplace (24.2%) or affiliated service (4.8%), doctors mostly administered acupuncture (66.7%). Respondents were not up to date with current research (71.4%). Referral likelihood increased with confidence in provider (80.0%), workplace availability (77.1%), and patient prior/current use (77.1%). Patient acupuncture discussions were rare (62.9%) with barriers of effectiveness uncertainty (71.4%) and limited knowledge of availability (57.1%). Conclusion: Despite available integrative services and acceptability by Australian palliative medicine practitioners, utilization is low. Further research into acupuncture effectiveness for palliative symptoms, feasibility, and patient acceptability is required. [ABSTRACT FROM AUTHOR]

Single-cell RNA sequencing (scRNA-seq) can present cellular heterogeneity at higher resolution when measuring the gene expression in an individual cell. However, there are still some computational problems in scRNA-seq data, including high dimensionality, high sparseness, and high noise. To solve them, dimensionality reduction is essential as it reduces dimensions and also removes most of the zeros and noise. Therefore, we propose a hybrid dimensionality reduction algorithm for scRNA-seq data by integrating binning-based entropy and a denoising autoencoder, named ScEDA. In ScEDA, a novel binning-based entropy estimation method is performed to select efficient genes, while removing noise. For each gene, binning-based entropy is designed to describe the differences in its expression across all cells, that is, the distribution of expression of each gene in all cells. Genes are regarded as inefficient and removed when they achieve low binning-based entropy. Moreover, by combining Kullback–Leibler (KL) divergence with the autoencoder, the objective function is reconstructed to maximize the similarity in distribution between input data and reconstructed data. Furthermore, by adding Poisson-distributed noise to the original input data, the denoising autoencoder is used to improve robustness. Compared with three other clustering methods, ScEDA provides superior average performance on 16 real scRNA-seq datasets, with obvious enhancement in large-scale datasets. [ABSTRACT FROM AUTHOR]

Objective: To determine the acceptability and feasibility of acupuncture for the treatment of endometriosis-related chronic pelvic pain. Design: A prospective, randomized controlled feasibility study. Setting: Outpatient setting in Sydney, Australia. Subjects: Participants who were aged 18–45 years, had a confirmed laparoscopic diagnosis of endometriosis in the past 5 years, and had regular menstrual periods and mean pelvic pain scores ≥4/10. Interventions: Sixteen acupuncture treatments delivered by registered acupuncturists using a standardized point protocol over 8 weeks, twice per week plus usual care compared with usual care alone. Outcome measures: Primary outcome measures were feasibility, safety, and acceptability of the acupuncture intervention. Secondary outcomes were changes in self-reported pelvic pain scores, changes in quality of life as measured by the Endometriosis Health Profile (EHP-30), changes in descending pain modulation, and changes in systemic inflammation (plasma interleukin [IL-6] concentrations). Results: Twenty-nine participants were eligible to participate, with 19 participants completing the trial. There was unequal withdrawals between groups; the acupuncture group had a withdrawal rate of 14% compared with 53% in usual care. Adverse events were uncommon (6.7%) and generally mild. A 1.9 point decrease in median nonmenstrual pain scores and a 2.0 decrease in median menstrual pain scores between baseline and end of trial were observed in the acupuncture group only. Improvements in all domains of the EHP-30 were seen in the acupuncture group, with no changes seen in usual care. There was no difference between baseline and end of treatment in IL-6 concentrations for either group. Conclusions: Acupuncture was an acceptable, well-tolerated treatment and it may reduce pelvic pain and improve quality of life; however, usual care was not an acceptable control group. Trial Registration: anzctr.org.au: ACTRN12617000053325. Prospectively registered January 11, 2017. [ABSTRACT FROM AUTHOR]