Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR

Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typically combine results from a variety of bioinformatics resources in an attempt to portray and understand cancer relevance. As a means to simplify and strengthen the support for this endeavor, we have developed oncoEnrichR, a flexible bioinformatics tool that allows cancer researchers to comprehensively interrogate a given gene list along multiple facets of cancer relevance. oncoEnrichR differs from general gene set analysis frameworks through the integration of an extensive set of prior knowledge specifically relevant for cancer, including ranked gene-tumor type associations, literature-supported proto-oncogene and tumor suppressor gene annotations, target druggability data, regulatory interactions, synthetic lethality predictions, as well as prognostic associations, gene aberrations and co-expression patterns across tumor types. The software produces a structured and user-friendly analysis report as its main output, where versions of all underlying data resources are explicitly logged, the latter being a critical component for reproducible science. We demonstrate the usefulness of oncoEnrichR through interrogation of two candidate lists from proteomic and CRISPR screens. oncoEnrichR is freely available as a web-based service hosted by the Galaxy platform ( https://oncotools.elixir.no ), and can also be accessed as a stand-alone R package ( https://github.com/sigven/oncoEnrichR ).     

Visual fixations and visually induced dizziness: An exploratory study

BackgroundVisually induced dizziness can develop as a sequala of a vestibular disorder and is characterized by symptoms of nausea, dizziness, and imbalance in rich visual environments such as supermarkets and shopping malls. To date the mechanisms underlying visually induced dizziness are poorly understood.Research questionWhat are the characteristics of visual fixations and postural sway in adults with visually induced dizziness compared to healthy adults when exposed to increasingly complex visual environments?MethodsWe recruited 20 adults with visually induced dizziness and 20 healthy adults to this cross-sectional exploratory study. Participants were instructed to maintain gaze on letters projected on a large screen with backgrounds of differing visual complexity. The number of visual refixations, movement of the centre of pressure, and movement of the head and body centres of mass were recorded.ResultsAdults with visually induced dizziness showed a significantly higher number of visual refixations (F= 10.592, p < 0.01), and increased mean velocity of head and body centres of mass movement (F= 14.034, p < 0.01 and F= 6.553, p < 0.05 respectively) compared to healthy adults.SignificanceAdults with visually induced dizziness exhibited visual fixational instability and increased postural and head sway compared to healthy adults. This was mainly observed in conditions with complex and moving backgrounds. This may account for reports from adults with visually induced dizziness of worsening symptoms in busy environments. The results from the study may assist in guiding intervention development to reduce symptoms of visually induced dizziness.     

Anatomic vs. reverse shoulder arthroplasty for glenohumeral osteoarthritis with intact rotator cuff: a retrospective comparison of patient-reported outcomes using the systems outcomes database with up to 5-year follow-up

BackgroundThe growing enthusiasm for the use of reverse shoulder arthroplasty (RSA) in the treatment of primary glenohumeral osteoarthritis (GHOA) with an intact rotator cuff is based on data derived from single-center studies with limited generalizability and follow-up. This study compared patient-reported outcomes (PROs) between RSA and total shoulder arthroplasty (TSA) for the treatment of primary GHOA with up to 5-year follow-up and examined temporal trends in the treatment of GHOA between 2012 and 2021.MethodsA retrospective review was performed on patients with primary GHOA undergoing primary arthroplasty surgery from the Surgical Outcomes System global registry between 2012 and 2021. PROs including the American Shoulder and Elbow Surgeons (ASES) score, Single Assessment Numeric Evaluation (SANE) score, and visual analog scale (VAS) for pain were compared between RSA and TSA at 1, 2, and 5 years postoperatively.ResultsA total of 4451 patients were included, with 2693 (60.5%) undergoing TSA and 1758 (39.5%) undergoing RSA. Both RSA and TSA provided clinically excellent outcomes at 1 year postoperatively (ASES: 80.8 ± 17.9 vs. 85.9 ± 15.2, respectively; SANE: 74.8 ± 24.7 vs. 79.5 ± 22.9; VAS pain: 1.3 ± 2.0 vs. 1.1 ± 1.7; all P < .05) that were maintained at 2 years (ASES: 81.3 ± 19.3 vs. 87.3 ± 14.9; SANE: 74.8 ± 26.2 vs. 79.7 ± 24.7; VAS pain: 1.3 ± 2.1 vs. 1.0 ± 1.6; all P < .05) and 5 years (ASES: 81.7 ± 16.5 vs. 86.9 ± 15.3; SANE: 71.6 ± 28.5 vs. 78.2 ± 25.9; VAS pain: 1.0 ± 1.7 vs. 1.0 ± 1.7; all P < .05), with statistical significance favoring TSA. After controlling for age and sex, there was an adjusted difference of 4.5 units in the ASES score favoring TSA (P = .005) at 5 years postoperatively but no differences in adjusted SANE (P = .745) and VAS pain (P = .332) scores. The use of RSA for GHOA grew considerably over time, from representing only 17% of all replacements performed for GHOA in 2012 to nearly half (47%) in 2021 (P < .001).ConclusionRSA as a treatment for GHOA with an intact rotator cuff seems to yield PROs that are largely clinically equivalent to TSA extending to 5 years postoperatively. The observed statistical significance favoring TSA appears to be of marginal clinical benefit based on established minimal clinically important differences and may be a result of the large sample size. Further research using more granular clinical data and examining differences in range of motion and complications is warranted as it may change the value analysis.     

基于CiteSpace可视化分析代谢组学在中医药领域的研究现状及趋势＊

目的 应用可视化方法分析代谢组学在中医药领域的现状及趋势。方法 检索中国知网数据库（CNKI）和Web of Science 核心合集数据库2021年3月15日之前收录的中医药领域代谢组学研究的相关文献，应用CiteSpace软件对纳入的文献进行关键词、作者、研究机构等内容进行可视化分析。结果 共纳入中文文献247篇，英文文献350篇。文献数量在波动中迅速上升。中、英文文献作者合作网络显示，张爱华是中医药领域代谢组学研究发文量最多的作者，并形成了核心研究团队。发文机构显示，中国医学科学院是该领域的重要研究机构，机构间合作紧密。中、英文文献关键词分析显示，研究内容主要集中在核磁共振、代谢标记物、冠心病、质谱技术、代谢通路等相关领域。结论 中医药领域代谢组学研究的热点主要为中医药治疗代谢性疾病的机制研究。研究趋势为卵泡代谢组学研究及中药有效成分的研究。     

Evaluation of Eye Movement Desensitization and Reprocessing in the management of tinnitus. An observational study

ObjectivesTinnitus can induce disabling psychological suffering, requiring an integrative multimodal approach, combining neuromodulation and psychotherapeutic methods. We sought to evaluate the therapeutic efficacy and acceptability of Eye Movement Desensitization and Reprocessing (EMDR) in tinnitus.Materials and methodsThis was a single-center prospective non-comparative study. Inclusion criteria comprised: adult patient, with chronic tinnitus, Tinnitus Handicap Inventory (THI) score > 17, causing psychological distress motivating active treatment after ineffective “classic” treatment (combining advice, sound therapy and first-line drug treatment), and agreement to EMDR therapy. Therapeutic efficacy was defined by a decrease in THI or Visual Analog Scale (VAS) scores. Treatment acceptability was defined by the rate of included patients who completed therapy.ResultsThirty-eight patients were included. There was a significant reduction of 53.5% in THI score in 78.9% of patients (P < 0.0001; 64.8 ± 20.8 before versus 31.8 ± 24.7 after treatment), and of 51% in VAS score in 76.3% of patients (P < 0.0001; 7.24 ± 2.12 before versus 3.58 ± 2.03 after treatment). The treatment acceptability was 86.8%.ConclusionEMDR appeared to be an effective alternative that was acceptable to the majority of patients, after failure of “classic” first-line treatment, improving quality of life in tinnitus patients and thus relieving disability.     

基于CiteSpace的结直肠癌患者生命质量研究

目的：通过中英文文献了解结直肠癌患者生命质量研究现状及发展趋势。方法：运用CiteSpace对中国知网（CNKI）、万方数据知识服务平台、中国生物医学文献数据库、Web of Science核心数据集、PubMed、Cochrane Library中收录的关于结直肠癌患者生命质量研究的中英文文献进行可视化分析。结果：检索得到中文文献1 285篇，英文文献871篇，中英文文献发文量均呈上升趋势，相关研究关注的重点主要是结直肠癌患者造口、抑郁、免疫、肠道功能、化疗及化疗药物，但机构之间、学者之间合作程度及研究类型等方面存在一定差异。结论：中文文献相关研究起步晚、发展快，但在研究质量与研究深度等方面与英文文献相比还有一定差距；国内学者之间、机构之间应加强合作，关心患者肠道功能、心理状况，提高患者体力活动水平，开展更多高质量研究。     

Enhancing adherence and management in patients with hypertension: Impact of form and frequency of knowledge intervention

BackgroundThe alarming rise in prevalence of hypertension warrants psychosocial methods supplementing pharmacotherapy for better management and prevention of cardiac emergencies. The objective of the study was to assess the differential impact of the form and frequency of knowledge intervention on management of primary hypertension.Materials and methodThe study was conducted on 256 hypertensive patients recruited through purposive sampling at health centers in Hyderabad, India. Pretest post-test control group quasi-experimental design was adopted for the study. There were two forms of the knowledge intervention, namely ‘Direct Interaction’ and ‘Audio-Visual’. Each form was presented in two frequencies namely ‘single exposure’ and ‘double exposure’. The four groups were labelled as Direct Intervention Single (DIS), Direct Intervention Double (DID), Audio-Visual Single (AVS) and Audio-Visual Double (AVD). Adherence and management of hypertension were assessed at baseline and six weeks post experiment. Analysis of Covariance (ANCOVA) was applied using IBM SPSS Statistics version 20.ResultsANCOVA followed by Bonferroni Multiple Group Comparison Test revealed significant differences between the four intervention groups and control group on adherence (p< .001). In case of hypertension management significant differences were observed between Control group and DIS, DID (p < .001), Control and AVS (p < .01). Control group did not differ from AVD.ConclusionThere was a positive impact of Knowledge Intervention on adherence and management of hypertension. Double exposure in audio visual form was counterproductive in hypertension management.