scholarly journals Data detectives, self-love, and humility: a research parasite's perspective

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Claire Duvallet
Keyword(s):  
Best Practices ◽  
Scientific Knowledge ◽  
Secondary Analysis ◽  
Junior Research ◽  
Secondary Analyses ◽  
Community Of Researchers

Abstract Secondary analysis solidifies and expands upon scientific knowledge through the re-analysis of existing datasets. However, researchers performing secondary analyses must develop specific skills to be successful and can benefit from adopting some computational best practices. Recognizing this work is also key to building and supporting a community of researchers who contribute to the scientific ecosystem through secondary analyses. The Research Parasite Awards are one such avenue, celebrating outstanding contributions to the rigorous secondary analysis of data. As the recipient of a 2019 Junior Research Parasite Award, I was asked to provide some perspectives on life as a research parasite, which I share in this commentary.

Abstract P533: Incidence and Outcomes of Thrombectomy Rescue Therapies in Acute Basilar Artery Occlusions

Stroke ◽  
2021 ◽  
Vol 52 (Suppl_1) ◽  
Author(s):  
Ronda Lun ◽  
Greg B Walker ◽  
David Weisenburger-Lile ◽  
Bertrand Lapergue ◽  
Adrien Guenego ◽  
...  
Keyword(s):  
Primary Outcome ◽  
Secondary Analysis ◽  
Hematoma Expansion ◽  
Primary Analysis ◽  
Predictive Values ◽  
Previous Definition ◽  
Secondary Analyses ◽  
Revised Definitions ◽  
Definition Of ◽  
Sensitivity Specificity

Background: Hematoma expansion (HE) is an important therapeutic target in intracerebral hemorrhage. Recently proposed HE definitions have not been validated, and no previous definition has accounted for withdrawal of care (WOC). Objective: To compare conventional and revised definitions of hematoma expansion (HE), while accounting for WOC. Methods: We analyzed data from the ATACH-2 trial, comparing revised definitions of HE incorporating intraventricular hemorrhage (IVH) expansion to the conventional definition of “≥6 mL or ≥33%”. The primary outcome was modified Rankin Scale of 4-6 at 90-days. We calculated the incidence, sensitivity, specificity, positive and negative predictive values, and c- statistic for all definitions of HE. Definitions were compared using non-parametric methods. Secondary analyses were performed after removing patients who experienced WOC. Results: Primary analysis included 948 patients. Using the conventional definition, the sensitivity was 37.1% and specificity was 83.2% for the primary outcome. Sensitivity improved with all three revised definitions (53.3%, 48.7%, and 45.3%, respectively), with minimal change to specificity (78.4%, 80.5%, and 81.0%, respectively). The greatest improvement was seen with the definition “≥6 mL or ≥33% or any IVH”, with increased c -statistic from 60.2% to 65.9% (p < 0.001). Secondary analysis excluded 46 participants who experienced WOC. The revised definitions outperformed the conventional definition in this population as well, with the greatest improvement in c -statistic using “≥6 mL or ≥33% or any IVH” (58.1% vs 64.1%, p < 0.001). Conclusions: HE definitions incorporating intraventricular expansion outperformed conventional definitions for predicting poor outcome, even after accounting for care limitations.

scholarly journals Best (but oft-forgotten) practices: identifying and accounting for regression to the mean in nutrition and obesity research

2019 ◽  
Vol 111 (2) ◽  
pp. 256-265 ◽  
Author(s):  
Diana M Thomas ◽  
Nicholas Clark ◽  
Dusty Turner ◽  
Cynthia Siu ◽  
Tanya M Halliday ◽  
...  
Keyword(s):  
Best Practices ◽  
Repeated Measurements ◽  
Regression To The Mean ◽  
Intervention Effects ◽  
Measured Variable ◽  
Web Based ◽  
Obesity Research ◽  
Secondary Analyses ◽  
The Mean ◽  
Study Designs

ABSTRACT Background Regression to the mean (RTM) is a statistical phenomenon where initial measurements of a variable in a nonrandom sample at the extreme ends of a distribution tend to be closer to the mean upon a second measurement. Unfortunately, failing to account for the effects of RTM can lead to incorrect conclusions on the observed mean difference between the 2 repeated measurements in a nonrandom sample that is preferentially selected for deviating from the population mean of the measured variable in a particular direction. Study designs that are susceptible to misattributing RTM as intervention effects have been prevalent in nutrition and obesity research. This field often conducts secondary analyses of existing intervention data or evaluates intervention effects in those most at risk (i.e., those with observations at the extreme ends of a distribution). Objectives To provide best practices to avoid unsubstantiated conclusions as a result of ignoring RTM in nutrition and obesity research. Methods We outlined best practices for identifying whether RTM is likely to be leading to biased inferences, using a flowchart that is available as a web-based app at https://dustyturner.shinyapps.io/DecisionTreeMeanRegression/. We also provided multiple methods to quantify the degree of RTM. Results Investigators can adjust analyses to include the RTM effect, thereby plausibly removing its biasing influence on estimating the true intervention effect. Conclusions The identification of RTM and implementation of proper statistical practices will help advance the field by improving scientific rigor and the accuracy of conclusions. This trial was registered at clinicaltrials.gov as NCT00427193.

What Has EMDR Taught Us About the Psychological Characteristics of Tinnitus Patients?

2020 ◽  
Vol 14 (4) ◽  
pp. 229-240
Author(s):  
Tal Moore ◽  
John S. Phillips ◽  
Sally E. Erskine ◽  
Ian Nunney
Keyword(s):  
Stress Disorder ◽  
Outcome Measure ◽  
Secondary Analysis ◽  
Psychological Characteristics ◽  
Evidence Based ◽  
Depression And Anxiety ◽  
Post Discharge ◽  
The United Kingdom ◽  
Secondary Analyses ◽  
Emdr Therapy

Tinnitus is a common and distressing symptom affecting at least 10% of the population. It is poorly understood. There are many proposed therapies but a significant lack of well-controlled trials. This study is a secondary analysis from our recent study to determine the effectiveness of eye movement desensitization and reprocessing (EMDR) therapy as a treatment for tinnitus. It was designed as a single-site prospective interventional clinical trial and took place at a teaching hospital in the United Kingdom. Participants received a maximum of 10 sessions of EMDR. The EMDR used was a bespoke protocol: EMDR-for-tinnitus protocol (tEMDR). Outcome measures included evidence-based tinnitus and mood questionnaires recorded at baseline, discharge, and at 6 months post-discharge. The main outcome measure was the Tinnitus Handicap Inventory, and scores demonstrated a statistically significant improvement. Secondary analyses conducted indicate statistically significant improvement for tinnitus patients with and without probable posttraumatic stress disorder (PTSD) diagnoses. There was no significant decrease in depression and anxiety measures, however these were at the minimal range at the start. The purpose of this article is to describe the rationale behind the use of EMDR in tinnitus, the process of administrating a bespoke EMDR protocol, and the differences between tinnitus sufferers with differing experiences of trauma. To date our study is one of only two published studies investigating the use of EMDR for tinnitus; we therefore introduce an evolving and exciting application for EMDR therapy.

scholarly journals Conducting secondary analysis of qualitative data: Should we, can we, and how?

2017 ◽  
Vol 18 (1) ◽  
pp. 81-97 ◽  
Author(s):  
Nicole Ruggiano ◽  
Tam E Perry
Keyword(s):  
Data Analysis ◽  
Best Practices ◽  
Qualitative Data ◽  
Secondary Analysis ◽  
Secondary Data ◽  
Secondary Data Analysis ◽  
Ethical Problems ◽  
Current State ◽  
Critical Interpretive Synthesis ◽  
Recommended Guidelines

While secondary data analysis of quantitative data has become commonplace and encouraged across disciplines, the practice of secondary data analysis with qualitative data has met more criticism and concerns regarding potential methodological and ethical problems. Though commentary about qualitative secondary data analysis has increased, little is known about the current state of qualitative secondary data analysis or how researchers are conducting secondary data analysis with qualitative data. This critical interpretive synthesis examined research articles (n = 71) published between 2006 and 2016 that involved qualitative secondary data analysis and assessed the context, purpose, and methodologies that were reported. Implications of findings are discussed, with particular focus on recommended guidelines and best practices of conducting qualitative secondary data analysis.

scholarly journals Psychological Distress during Ovarian Cancer Treatment: Improving Quality by Examining Patient Problems and Advanced Practice Nursing Interventions

2011 ◽  
Vol 2011 ◽  
pp. 1-14 ◽  
Author(s):  
Cynthia Kline O'Sullivan ◽  
Kathryn H. Bowles ◽  
Sangchoon Jeon ◽  
Elizabeth Ercolano ◽  
Ruth McCorkle
Keyword(s):  
Mental Health ◽  
Ovarian Cancer ◽  
Psychological Distress ◽  
Best Practices ◽  
Secondary Analysis ◽  
Health Intervention ◽  
The Other ◽  
Advanced Practice ◽  
Mental Health Intervention ◽  
High Distress

Background/Significance. Ovarian cancer patients are prone to psychological distress. The clinical significance and best practices for distress among this population are poorly understood.Method. Secondary analysis of research records from a six month randomized control trial included 32 women with primary ovarian cancer. All received 18 advanced practice nurse (APN) visits over six months. Three sub-samples were determined by distress level (high/low) and mental health service consent for high distress. Demographic, clinical factors, patient problems and APN interventions obtained through content analysis and categorized via the Omaha System were compared.Results. Clinically-significant psychiatric conditions were identified in 8/18 (44%) high distress subjects consenting to mental health intervention. High distress subjects who refused mental health intervention had more income and housing problems than the other subjects, received the fewest interventions at baseline, and progressively more throughout the study, exceeding the other sub-samples by study completion.Conclusions. Highly-distressed women not psychologically ready to work through emotional consequences of cancer at treatment onset may obtain support from APNs to manage cancer problems as they arise. Additional studies may identify best practices for all highly-distressed women with cancer, particularly those who do not accept mental health services for distress, but suffer from its effects.

Validation in Inquiry-Guided Research: The Role of Exemplars in Narrative Studies

1990 ◽  
Vol 60 (4) ◽  
pp. 415-443 ◽  
Author(s):  
Elliot Mishler
Keyword(s):  
Scientific Knowledge ◽  
Research Practice ◽  
Socially Constructed ◽  
Narrative Studies ◽  
Validity Claims ◽  
Community Of Researchers ◽  
Field Of Inquiry ◽  
Formal Rules

In this article Elliot Mishler reformulates validation as a process through which a community of researchers evaluates the "trustworthiness" of a particular study as the basis for their own work. Rather than relying for their assessments on an investigator's adherence to formal rules or standardized procedures, skilled researchers, Mishler argues, depend on their tacit understanding of actual, situated practices in a field of inquiry. Validity claims are tested through the ongoing discourse among researchers and, in this sense, scientific knowledge is socially constructed. Within this perspective, Mishler proposes an approach to the problem of validation in inquiry-guided studies that relies on Kuhn's concept of exemplars— concrete models of research practice. He then examines three studies of narrative, suggesting them as candidate exemplars for this area of research since they provide reasonable grounds for evaluating their trustworthiness.

scholarly journals Secondary Data Analysis: Lessons and perspective of a research parasite

2021 ◽  
Author(s):  
Ayush Raman
Keyword(s):  
Data Analysis ◽  
Signal To Noise Ratio ◽  
Secondary Analysis ◽  
Scientific Progress ◽  
Secondary Data ◽  
Secondary Data Analysis ◽  
Research Directions ◽  
Award Recipient ◽  
Junior Research ◽  
New Research

Secondary data analysis refers to re-analyzing publicly available datasets to investigate the questions that original scientists had not posited. This helps in scientific progress by paving the path to more reliable and robust analyses and new research directions without any considerable expense. However, these datasets are anything but perfect, and researchers must investigate and assess the signal to noise ratio robustly to extract meaningful information. These efforts of rigorous secondary analysis are further recognized and supported by the Research Parasite Awards. As the 2020 Junior Research Parasite Award recipient, I share my journey and perspective of a research parasite in this commentary article.

Effectiveness of bevacizumab (BV) beyond disease progression in metastatic colorectal cancer (mCRC): Analyses by sex in the ARIES observational cohort study (OCS).

2013 ◽  
Vol 31 (4_suppl) ◽  
pp. 514-514
Author(s):  
Allen Lee Cohn ◽  
Herbert Hurwitz ◽  
Tanios S. Bekaii-Saab ◽  
Johanna C. Bendell ◽  
Mark Kozloff ◽  
...  
Keyword(s):  
Disease Progression ◽  
Cox Regression ◽  
Secondary Analysis ◽  
Average Risk ◽  
Primary Analysis ◽  
Men And Women ◽  
Hazard Ratios ◽  
Secondary Analyses ◽  
Observational Cohort ◽  
Clinical Trial Information

514 Background: Randomized trials and OCSs have demonstrated that BV treatment in 1st-line (1L), in 2L, and across multiple lines is associated with longer survival in patients (pts) with mCRC. This analysis was aimed at comparing the effectiveness of BV after 1st disease progression (PD) between male and female mCRC pts who received 1L BV-containing therapy in a real-world setting. Methods: ARIES is a large, prospective OCS that enrolled pts who received BV and chemotherapy (CT) for 1L mCRC. Post-PD effectiveness was assessed for men and women characterizing BV use by cumulative and dichotomous approaches. The primary analysis treated BV exposure as cumulative BV doses after 1st PD and post-progression overall survival (ppOS) as the time from 1st PD to death. A time-dependent Cox regression model was fitted to assess the effect of cumulative BV exposure on ppOS, while controlling for potential confounders. A dichotomous secondary analysis characterized BV exposure as receipt of CT + BV (BBP) or CT alone (No BBP) within 2 months after PD and ppOS as time from 1st PD + 2 months to death. Results: Among the 1,550 1L mCRC pts enrolled, 1,199 (532 women) had PD. In the primary analysis, hazard ratios (HRs) for ppOS decreased, on average, by 1.2% with each additional BV dose. When stratified by sex, the average risk reduction per BV dose over 15 doses was 1.8% in women and 0.7% in men. In the secondary analysis that included 331 women (BBP, 180; No BBP, 151) and 417 men (BBP, 245, No BBP, 172) who received BV ± CT within 2 months post-PD, the HRs for ppOS with BBP treatment were 0.46 (95% CI, 0.35–0.59) in women and 0.52 (95% CI, 0.41–0.67) in men. Statistical interaction tests for differences in the effectiveness of BV between men and women were negative for primary and secondary analyses (P of 0.58 and 0.77). Protocol-specified adverse events occurred in 17.8% of women and 10.2% of men in the BBP population; this difference was largely related to rates of hypertension (8.3% vs 2.4%, respectively). Conclusions: In ARIES, the effectiveness of BV after first PD was not statistically different between women and men with mCRC. Clinical trial information: NCT00388206.

Is Group B Streptococcus Colonization Associated with Maternal Peripartum Infection in an Era of Routine Prophylaxis?

2020 ◽  
Author(s):  
Kartik K. Venkatesh ◽  
Catherine J. Vladutiu ◽  
Angelica V. Glover ◽  
Robert A. Strauss ◽  
Jeffrey S.A. Stringer ◽  
...  
Keyword(s):  
Group B Streptococcus ◽  
Secondary Analysis ◽  
Lower Odds ◽  
Trial Of Labor ◽  
Prepregnancy Body Mass Index ◽  
Key Points ◽  
Routine Prophylaxis ◽  
Secondary Analyses ◽  
Multivariable Analyses ◽  
Group B

Objective This study aimed to assess whether colonization with group B streptococcus (GBS) is associated with maternal peripartum infection in an era of routine prophylaxis. Study Design This study presented a secondary analysis of women delivering ≥37 weeks who underwent a trial of labor from the U.S. Consortium on Safe Labor (CSL) study. The exposure was maternal GBS colonization and the outcome was a diagnosis of chorioamnionitis, and secondarily, analyses were restricted to deliveries not admitted in labor and measures of postpartum infection (postpartum fever, endometritis, and surgical site infection). Logistic regression with generalized estimating equations was used accounting for within-woman correlations. Models adjusted for maternal age, parity, race, prepregnancy body mass index, pregestational diabetes, insurance status, study site/region, year of delivery, number of vaginal exams from admission to delivery, and time (in hours) from admission to delivery. Results Among 170,804 assessed women, 33,877 (19.8%) were colonized with GBS and 5,172 (3.0%) were diagnosed with chorioamnionitis. While the frequency of GBS colonization did not vary by chorioamnionitis status (3.0% in both groups), in multivariable analyses, GBS colonization was associated with slightly lower odds of chorioamnionitis (adjusted odds ratio [AOR]: 0.89; 95% confidence interval [CI]: 0.83–0.96). In secondary analyses, this association held regardless of spontaneous labor on admission; and the odds of postpartum infectious outcomes were not higher with GBS colonization. Conclusion In contrast to historical data, GBS colonization was associated with lower odds of chorioamnionitis in an era of routine GBS screening and prophylaxis. Key Points

scholarly journals An Evaluation of the Performance of Sea-Bird Scientific's Autonomous SeaFET<sup>TM</sup>: Considerations for the Broader Oceanographic Community

2018 ◽  
Author(s):  
Cale A. Miller ◽  
Katie Pocock ◽  
Wiley Evans ◽  
Amanda L. Kelley
Keyword(s):  
Best Practices ◽  
Single Point ◽  
Calibration Method ◽  
South Central ◽  
Autonomous Sensor ◽  
Seawater Ph ◽  
Community Of Researchers ◽  
Robust Measurements ◽  
Broad Community

Abstract. The commercially available Sea-Bird SeaFETTM provides an accessible way for a broad community of researchers to study ocean acidification and obtain robust measurements of seawater pH via the use of an in situ autonomous sensor. There are pitfalls, however, that have been detailed in previous best practices for sensor care, deployment, and data handling. Here, we took advantage of two distinctly different coastal settings to evaluate the Sea-Bird SeaFETTM and examine the multitude of scenarios in which problems may arise confounding the accuracy of measured pH. High-resolution temporal measurements of pH were obtained during 3- to 5-month field deployments in three separate locations (two in south-central, Alaska, USA, and one British Columbia, CA) spanning a broad range of nearshore temperature and salinity conditions. Both the internal and external electrodes onboard the SeaFETTM were evaluated against robust benchtop measurements for accuracy utilizing either the factory calibration, an in situ single-point calibration, or in situ multi-point calibration. In addition, two sensors deployed in parallel in Kasitsna Bay, AK, USA, were compared for inter-sensor variability in order to quantify other factors contributing to SeaFETTM intrinsic inaccuracies. Based on our results, the multi-point calibration method provided the highest accuracy (

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