Brainstem Cavernous Malformations Management: Microsurgery vs. Radiosurgery, a Meta-Analysis

Given the rareness of available data, we performed a systematic review and meta-analysis on therapeutic strategy microsurgical resection and stereotactic radiosurgery (SRS) for brainstem cavernous malformations (BSCMs) and assessed mortality, permanent neurological deficits (PNDs), rebleeding rate, and patients who require reintervention to elucidate the benefits of each treatment modality. Preferred reporting items for systematic reviews and meta-analyses (PRISMA) were used for protocol development and manuscript preparation. After applying all inclusion and exclusion criteria, six remaining articles were included in the final manuscript pool. In total, this meta-analysis included 396 patients, among them 168 patients underwent microsurgical treatment and 228 underwent SRS. Findings of the present meta-analysis suggest that regarding the total group of patients, in terms of mortality, late rebleeding rate, and PNDs, there was no superiority of the one method over the other. Applying the leave-one-out method to our study suggests that with low robust of the results for the bleeding rate and patients who require reintervention outcome factor, there was no statistical difference among the surgical and SRS treatment. Microsurgical treatment of BSCMs immediately eliminates the risk of rehemorrhage; however, it requires complete excision of the lesion and it is associated with a similar rate of PNDs compared with SRS management. Apparently, SRS of BSCMs causes a marked reduction in the risk of rebleeding 2 years after treatment, but when compared with the surgical treatment, there was not any remarkable difference.

Development and Pilot Implementation of a Patient Oriented Discharge Summary for Critically Ill Patients (PODS-ICU)

Background - Patients leaving the intensive care unit (ICU) often experience gaps in care due to deficiencies in discharge communication. This study aimed to develop an ICU specific patient-oriented discharge summary tool (PODS-ICU) and pilot test the tool for acceptability and feasibility.Methods - Patient-partners, ICU clinicians, and researchers met to discuss ICU patients’ specific informational needs and design the PODS-ICU through several cycles of iterative revisions. Research team nurses piloted the PODS-ICU with patient and family-caregiver participants in two ICUs in Calgary, Canada. Follow-up surveys on the PODS-ICU and its impact on discharge were administered to participants and ICU nurses.Results – Fifteen patient and family-caregiver participants were administered the PODS-ICU. Most participants felt that their discharge from the ICU was good or better (n=13), and some (n=9) participants reported a good understanding of why the patient was in ICU. Most participants (n=12) reported that they understood ICU events and impacts on the patient’s health. ICU nurses reported that the PODS-ICU was “not reasonable” in their daily clinical workflow due to “time constraint”. Conclusions - PODS-ICU improves patients and family-caregivers’ understanding of ICU events and health-implications but requires better integration with existing care processes to be feasible. Patient or Public Contribution – This work involved patient partners (i.e., individuals with lived experience as patients or family-caregivers) in tool development, study design, participant recruitment, and manuscript preparation.

Plotgardener: Cultivating precise multi-panel figures in R

The R programming language is one of the most widely used programming languages for transforming raw genomic data sets into meaningful biological conclusions through analysis and visualization, which has been largely facilitated by infrastructure and tools developed by the Bioconductor project. However, existing plotting packages rely on relative positioning and sizing of plots, which is often sufficient for exploratory analysis but is poorly suited for the creation of publication-quality multi-panel images inherent to scientific manuscript preparation. We present plotgardener, a coordinate-based genomic data visualization package that offers a new paradigm for multi-plot figure generation in R. Plotgardener allows precise, programmatic control over the placement, aesthetics, and arrangements of plots while maximizing user experience through fast and memory-efficient data access, support for a wide variety of data and file types, and tight integration with the Bioconductor environment. Plotgardener also allows precise placement and sizing of ggplot2 plots, making it an invaluable tool for R users and data scientists from virtually any discipline.AvailabilityPackage: https://bioconductor.org/packages/plotgardenerCode: https://github.com/PhanstielLab/plotgardenerDocumentation: https://phanstiellab.github.io/plotgardener/

Development and validation of a clinical risk score to predict SARS-CoV-2 infection in emergency department patients: The CCEDRRN COVID-19 Infection Score (CCIS)

Background Clinicians face decisions around the need for severe acute respiratory coronavirus 2 (SARS-CoV-2) testing, patient isolation, and empiric therapy when patients arrive in acute care hospitals. Our objective was to develop a risk score that can accurately quantify a patient's probability of SARS-CoV-2 infection. Methods This observational study enrolled consecutive adults who presented to the emergency departments of 32 hospitals participating in Canadian COVID-19 Emergency Department Rapid Response Network (CCEDRRN) and were tested for SARS-CoV-2. We divided our study population by randomly assigning study sites into derivation (75%) and validation (25%) cohorts. We pre-specified predictors and used multiple imputation for variables with incomplete data. In the derivation cohort, we fit models using logistic regression, with spline functions for continuous variables, to predict the primary outcome of a positive SARS-CoV-2 nucleic acid test. We used a fast step-down procedure to select a concise model. The final reduced model had points allocated to each variable based on their predictive strength. We then validated the model in the geographically distinct validation cohort. Findings We derived a ten-item CCEDRRN COVID-19 Infection Score using data from 21,743 patients. This score included variables from history and physical examination, and an indicator of local disease incidence. The score had a C-statistic of 0.838 with excellent calibration. We externally validated the rule in 5,295 patients. The score maintained excellent discrimination and calibration, and had superior performance compared to another previously published risk score. Interpretation The CCEDRRN COVID-19 Infection Score uses clinical characteristics and publicly available indicators of disease incidence to quantify a patient's probability of SARS-CoV-2 infection. The score can identify patients at sufficiently high risk of SARS-CoV-2 infection to warrant isolation and empiric therapy prior to test confirmation, while also identifying patients at sufficiently low risk of infection that they may not need testing. Funding The network is funded by the Canadian Institutes of Health Research (447679), BC Academic Health Science Network Society, BioTalent Canada, Genome BC (COV024; VAC007), Ontario Ministry of Colleges and Universities (C-655-2129), the Saskatchewan Health Research Foundation (5357) and the Fondation CHU de Quebec (Octroi #4007). These organizations are not-for-profit, and had no role in study conduct, analysis, or manuscript preparation.

Clear, transparent, and timely communication for fair authorship decisions: A practical guide

Authorship conflicts are a common occurrence in academic publishing, and they can have serious implications on the careers and well-being of the involved researchers, as well as the collective success of research organizations. In addition to not inviting relevant contributors to co-author a manuscript, the order of authors, as well as honorary, gift, and ghost authors are all widely recognized problems related to authorship. Unfair authorship practices disproportionately affect those lower in the power hierarchies – early career researchers, women, researchers from the Global South, and other minoritized groups. Here we propose an approach to preparing author lists based on clear, transparent, and timely communication. This approach is aimed to minimize the potential for late-stage authorship conflicts during manuscript preparation by facilitating timely and transparent decisions on potential co-authors and their responsibilities. Furthermore, our approach can help avoid imbalances between contributions and credits in published manuscripts by recording planned and executed responsibilities. We present authorship guidelines which also include a novel authorship form, along with the documentation of the formulation process for a multidisciplinary and interdisciplinary center with more than 250 researchers. Other research groups, departments, and centers can use or build on this template to design their own authorship guidelines as a practical way to promote fair authorship practices.

The Advantage of Automatic Peer-Reviewing of 13C-NMR Reference Data Using the CSEARCH-Protocol

A systematic investigation of the experimental 13C-NMR spectra published in Molecules during the period of 1996 to 2015 with respect to their quality using CSEARCH-technology is described. It is shown that the systematic application of the CSEARCH-Robot-Referee during the peer-reviewing process prohibits at least the most trivial assignment errors and wrong structure proposals. In many cases, the correction of the assignments/chemical shift values is possible by manual inspection of the published tables; in certain cases, reprocessing of the original experimental data might help to clarify the situation, showing the urgent need for a public domain repository. A comparison of the significant key numbers derived for Molecules against those of other important journals in the field of natural product chemistry shows a quite similar level of quality for all publishers responsible for the six journals under investigation. From the results of this study, general rules for data handling, data storage, and manuscript preparation can be derived, helping to increase the quality of published NMR-data and making these data available as validated reference material.

Circulating Plasma Omega-7 Monounsaturated Fatty Acids (Cis-Vaccenic Acid and Palmitoleic Acid) Are Related to All-Cause Mortality: The Lifelines Fatty Acids Cohort Study

Objectives Determine whether plasma omega-7 cis-vaccenic acid and palmitoleic acid levels are related to all-cause mortality in a general population. Methods Plasma phospholipids (PL) and triglycerides (TG) fatty acids were measured by gas chromatography with polar column and detected with a flame ionization detector in the Lifelines fatty acids cohort study participants (n = 864). Associations with all-cause mortality were analyzed by Cox proportional hazards regression with adjustment for conventional risk factors. Results During a median follow-up of 9.3 years, 33 (3.9%) participants died. Adjusting for typical risk factors, high levels of plasma PL and TG cis-vaccenic acid, and TG palmitoleic acid were found to be associated with all-cause mortality. A 1-SD increase in PL cis-vaccenic acid, TG cis-vaccenic acid, and TG palmitoleic acid was associated with increased risk of all-cause mortality with HRs (95% CI) of 1.69 (1.17–2.46), 1.54 (1.03–1.15), and 1.44 (1.08–1.92), respectively. Compared to the lowest tertile, the HRs (95% CI, p-trend) for the highest tertile of PL cis-vaccenic acid, TG cis-vaccenic acid, and TG palmitoleic acid were 3.0 (1.05–8.56, 0.03), 2.25 (0.87–5.85), and 3.39 (1.24–9.28, 0.02), respectively. Conclusions Elevated levels of plasma cis-vaccenic acid and palmitoleic acid are risk factors for all-cause mortality. Funding Sources The data analyses from the Lifelines Cohort that were carried out in this paper were funded by Friesl and Campina. The funders had no role in study design, data collection and analysis, manuscript preparation and decision to publish.