Clinical and Health Research Clinic

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Current Notes (2022)

2022 July 14

Amy Guidera (Morgan Johnson), VAQS Fellowship

We conducted retrospective chart reviews on all Veterans who tested positive for at least one STI from 12/06/2020-12/06/2021. Outcomes sexual health history taking and STI testing. 1. Understanding health equity within STI testing and sexual health history taking 2. Exposures age, gender, race, STI location 3. Understanding the relationship between the type of provider (MD/NP/DO) and sexual health history taken 4. Examining if Veterans who had symptomatic (reactionary) testing versus preventative testing had any correlation with the amount of sexual health history taken. Mentor confirmed.

2022 June 9

Steven Allon, Medicine/General Internal Medicine

This is a replication of a previous study that had biostats clinic helped us with (data analysis). It is a multicenter study examining the effects of a gamified format for an internal medicine residency journal club curriculum on resident engagement. Residents are surveyed pre/post using a survey measure that captures multiple dimensions of engagement with Likert-type responses. Questions to address: Review the survey instrument to determine its psychometric properties, or what additional information is needed to do so. The survey was developed by our group, and we have a dataset of pre/post responses from the initial study. We will collect data during this replication.

Clinic Notes:
  • Pre/post design. Need to have everyone (100%) get pre & post surveys, no room for error. For next study, looking at multiple formats of journal club. Wanting to see engagement levels of each format.
  • Recommendations:
    • Suggest having a negative control (Questions that are completely unrelated to what you're studying - something that would not change).
    • Not a lot of people go for extreme values on likert scale, might be better to have slider (0-100) instead of "much". To combine data points from asking the survey 2 different ways (likert/slider) collect data points both ways to calibrate slider. Matrix format.
    • Psychometric properties are difficult - need test/retest to determine. Could take small random sample to ask for retest with almost 100% agree. This provides more confidence in survey, something to refer to when submitting to journal.
    • Consider randomization for types of format. Try to get response as soon as possible (before leaving room if possible).

2022 May 19

Patrick Reardon, Orthopedic Surgery, Sports

I am doing a project on the innervation of the hip labrum and knee meniscus. We are getting 10 cadavers and trying to figure out how many samples of tissue we need to take to be appropriately powered with our comparison between the two. I was hoping you would be able to assist us with this. The unfortunate part is that this is a fairly novel study and there isn't much data out there to give any baseline numbers to help with the power analysis. Measure is quant measure of density. Could take replicate samples, in effort to increase precision. Would suggest do all samples twice, if possible. The more the better. May also consider not doing stat testing. Do estimation study instead, with CIs. Not a setting for power, setting for precision. No power analysis needed.

Suggest randomizing order of cadaver analysis and blinding the people analyzing the results (reduce bias).

2022 May 5

Douglas Bryant (W. Evan Rivers), Physical Medicine and Rehabilitation

This systematic review will examine the effect of endoscopic facet joint denervation on pain and pain-related disability among adults with low back pain. It will also examine screening criteria for offering the procedure, reported complications, time to perform procedure, duration of effect, success rate (based on pain scores, disability scores, or global scales such as MacNab criteria), and patient satisfaction. Mentor confirmed.

VICTR voucher request. Kim and Frank lack experience with this type of analysis--may need to seek someone else in the VICTR group.

Systematic review and meta analysis. Team has met with librarian to help will article identification. Excel proposed to collect data, strongly suggest Redcap. Team can return to clinic at any time to discuss redcap design and what an be reliably coded.

Limitation of such a review can be considerable. In this case, we are probably looking at between 4 and 10 studies. Long term, development of a registry would be useful for this topic.

Discussion of modeling, random effects model, bayesian random effects may be the way to go.

2022 April 28

Emily Mason, Pathology/Division of Hematopathology

Small project looking at immunohistochemical stains in marginal zone lymphoma. Our VICTR protocol has already been reviewed by Frank Harrell, who recommended we attend a Thursday clinic.

Pilot study looking at stomach lymphoma, which can be difficult to differentiate. Stains are "scored", but this is not terribly exact as I understand it. But this is preferred over a binary score (pos/neg). These samples are from patients with known lymphoma, confirmed no lymphoma (gold standard). Suggestion: consider the degree to which lymphoma patients had a higher score (Wilcoxen test). Suggest 40 samples, may be too small, but reasonable. Voucher requested for staining only.

Courtney Tomblinson, Radiology

Statistical analysis of learner attitudes toward a curriculum they've participated in. Challenge is low response in baseline control group, non response rate is very high (95% would be preferred). We don't have the ability to examine those who did not respond. This is a problem in many surveys. In this case we don't have a random sample, this is conditional on response. This is a "pilot" study, although not what we would typically call a pilot study. Education methods are challenging. Sidebar: adaptive testing may be useful as we study education methods.

2022 April 21

Kristina Niehoff, Vanderbilt Home Care Services

There is an increased risk of venous thromboembolism (VTE) associated with SARS-CoV-2 infection. As a result, patients enrolled in Vanderbiltís COVID to Home program (high intensity) receive anticoagulation. To qualify for the high intensity the patient may have: 1) a hypoxia requirement new or increased home oxygen; 2) required ICU level care while admitted; or 3) have significant comorbidities (particularly age 65 or older, severe obesity, underlying heart or lung disease, is within one year of organ transplantation or is severely immunocompromised). The preferred anticoagulant was chosen as apixaban since it can be taken orally and given its lower bleeding profile compared to other oral agents. However, literature does not exist to know if low dose apixaban is safe and effective for VTE prophylaxis. We seek to understand the safety outcomes of low dose apixaban 2.5mg twice daily for 7 days in a post-hospitalization population of individuals diagnosed with SARS-CoV-2 and understand the risk for VTE event post discharge.

Clinic Notes:
  • Vanderbilt home health (covid to home program). Patients who are deemed high risk were enrolled. NP would go out to home day after discharge, implemented home health services to determine future admission. Covid makes you clot easier, so patients were given blood thinners. 400 patients. No control group. Still collecting data until end of June. Patients monitored for 4 weeks post discharged. Hypotheses: was it tolerated? was is safe? did anyone have heart attack/stroke/clot while taking blood thinners? Want to look at frequencies/descriptives.
  • Recommendations

Andrew Yi, Quality Safety & Risk Prevention (QSRP)

I have a project on children overweight/obesity study and draft of results had been accomplished. I would like to ask a few questions on data analysis and review our results for comments.

Clinic Notes:
  • Finished data analysis, wrote results section and requesting feedback on design/interpretation. Cross sectional study of children - epidemiology of obesity and their influential factors. Aims - prevalence of obesity and identifying/quantifying associations with obesity. N=16,640.
  • Recommendations
    • Not valid to dichotomize BMI. Also, don't want to analysis BMI as outcome, best way is to analyze weight as outcome with height (and age, sex) as adjustment. Next best would be to analyze log-transformed BMI as outcome.
    • Anytime you have a criterion that is based on a continuous trusted outcome (ex. weight, height), then you need to use height and weight not that calculated variable (bmi). Analyzing continuous variables gives you more statistical power.
    • Analyze data as close to raw form as you can. Do not analyze raw data as dichotomized, you will lose too much information from the raw data. Analyzing raw data (continuous) allows you to to find mean, median, etc. as well as making statements about cut points later. Want to convert to dichotomous after analysis is finished. Can use the regression model to estimate the chance of being obese for a certain threshold.
    • For continuous variable, you can use ordinary/linear regression.

2022 April 7

Hannah Fish-Trotter (Jeffrey Dendy), Cardiology

We will be investigating both the safety and image quality of MRI in post-cardiac transplant patients who still have abandoned cardiac device leads in situ. We plan to conduct a controlled prospective MRI study of post-transplant patients with abandoned leads versus controls (post-transplant patients with no devices or leads). We have discussed with the cardiac transplant team, who estimate about 25-30% of their transplant patients having abandoned leads. We would like to discuss numbers needed for power and other study design questions prior to applying for a VICTR voucher. Mentor confirmed.

Hypothesis: MRI will not cause AEs or image interpretation. The team does 6-8 transplant studies per week, ~200+ controls.20-30% of transplants have abandoned leads.

Suggest not matching, but controlling for age, sex, time from transplant in a regression model. Propose goal as an estimation study. Estimate difference in adverse events, adjusted for confounders. Or could flip the equation, predict abandoned leads with number of adverse events. For ordinal outcome scale, suggest at least three categories that are well populated.

Re: Sample size. Consider margin of error. Minimum would be 96, with relatively similar distribution of abandoned leads.

This will fit in the framework of a voucher.

2022 March 31

Amanda Peltier, Neurology

We have collected data on neuropathy phenotype, nerve conduction study results, and cardiac evaluations. we would like to verify the correct analysis and ask regarding skewed data/ graphs for publication. There are 37 patients, with ~ 28 with nerve connection studies.

2022 March 17

Milner Staub, Infectious Diseases

Practical study comparing respiratory tract infection clinical decision algorithm implementations: AgileMD vs ExpressLane. Would like input on design/analysis and ability to evaluate differences in performance as regards primary outcome of reducing antibiotic prescriptions for upper respiratory tract infections and secondary outcomes of adoption and usability.

Agile MD available to all, but Express Lane an be restricted. Providers can use either or none of these similar decision tools. Agile MD may be memorized and used without accessing the tool. Need to build in decay possibility. Time trends will be important. These are not live until April. Providers cross all clinics.

One outcome is the decision to use tool, then was the antibiotic prescribed or not prescribed.

Can we capture patient level data, especially complicated cases? Can capture allergies, diagnoses. We must capture instrument use data wherever possible. How many patients, minutes per use. Provider and patient factors are important.

2022 March 03

Alex Foy (Stacy Killen), Pediatric Cardiology

Prior Notes:

Retrospective chart review to identify mitral valve or dimensional differences apparent by fetal echocardiography in those fetuses with postnatally confirmed coarctation of the aorta who undergo biventricular repair compared to those who ultimately require univentricular palliative surgery. VICTR Biostatistics voucher. Mentor confirmed.

10 Years of data, about 100 with coarc and fetal echo, see if measures during echo can predict bi vs uni repair. Patient may have between 1-5 fetal echos. Also have multiple echos before interventions. Actual repair decision is made during surgery. Measure of mitral valve (Z score) to predict outcome. Gold standard may be the measure before surgery. Repeated measures issues-coud think of these as updated baselines. This may fit that issue, rather that a true repeated measures. A landmark analysis. This would fit in the scope of a voucher.

Return after first attending the clinic on January 6 2022. Need to discuss the statistics section for the VICTR voucher application.

New Notes: Goals: Do differences in mitral valves predict surgical outcome? Outcome: single ventrical repair or bi-ventricular repair. All patients will proceed to surgery. We have multiple baselines, and are modeling type of surgery. About 100 surgeries, unsure of outcome breakdown. Rule of thumb, 15:1 rule, based on smallest outcome group. Binary logistic regression model can be framework. Need to identify co-variates, and how they will be measured. Perhaps include the shape of the relationship in the model. Could create two (or more) models. VICTR application should capture the spirit of the project, details will be fleshed out after award.

2022 February 17

Candace Grisham (Marjan Rafat), Biomedical Engineering

We are investigating immune cell markers and the predictive power of these markers on recurrence of laryngeal head and neck cancer after radiation therapy. VICTR Biostatistics voucher. Mentor confirmed.

WBC are the marker of interest. Possible + HPV as well. Prior work: Systemic inflammation on cancer return, in breast cancer that used Cox model.

Outcomes: Death, distal met.

Could use longitudinal analysis with a a scaled outcome (death, loss of remission, etc). Define "worst thing that happened in a given week". How to handle CBC (with diff) data? Timing is not the same, and treatments may change over time. Data structure (ideal) string of dates and events on each date (long format). Also, include treatment plans, biometric data, etc. Monitor drop outs. Have drop outs, but also people who enter "late state" after diagnosis elsewhere. Establishing full timeline for everyone is important.VUMC also has expected/observed predicted mortality,

Big picture: How does immune inflammation impact cancer return.

Tomas Bermudez (Maria Hadjifrangiskou), Microbe-Host Interactions

I have measured the appearance of antibiotic resistant subpopulations within clinical urinary isolates banked by microVU. The individual isolates are paired with de-identified patient data that I would like to be able to use and see if there are any trends that could be observed in terms of particular aspects of the patient info correlating with increased counts of resistant subpopulations.Mentor confirmed.

Best method for this type of correlative study? Spearman's Rho is an option, Somer D. Somers' D = Wilcoxon-Mann-Whitney two-sample rank sum test comparing two groups

What is a more appropriate way to display this type of data, and a more appropriate way to display the distributions of subpopulation counts with my current set of screened isolates (ex. low, avg, and high producers of a subpopulation). Use rawest form of data, do not categorize. Histogram, 100 bin bar graph, rug plot, spike histogram

2022 February 10

Mryia Hubert (Kate Mittendorf, Gillian Hooker), Genetic Counseling

We report on the early phases of the Family History and Cancer Risk Study (FOREST) which was initiated to improve identification of high-risk patients and access to hereditary cancer services for the general adult patient population at Vanderbilt University Medical Center (VUMC). We are asking: what variables predict high engagement and whether engagement mediates the predictive effect of the variables on our outcome measures. Mentor confirmed.

Baseline Survey

Start health history tool

Finish health history tool

Engagement is how often one thinks about cancer (dichotomized). Suggest treating as ordinal.

Aim1: Suggest proportional odds model. Small cells sizes are an issue in these data, but ordinal will still be a better path.

Aim2: Binary

Could make initiation and completion an ordinal variable, and do a single model. Don't really have a solid measure of proportion completed.

For an intro to ordinal modeling with R go to the nonparametrics chapter of

2022 January 20

Christopher Kalmar (Galen Perdikis), Plastic Surgery

Frank Harrell requested to discuss the biostatistics during pre-review of VICTR resource request VR56032 titled ĎViscoelastic Hemostatic Assays for Microsurgical Proceduresí. VICTR voucher not including biostatistics. Mentor confirmed.

Using viscoelastic parameters for a measure of flap healing/potential low perfusion. Hypercoag is the cause of issue. Multiple measures over time, pre surgery, post surgery, and daily. Using four markers from TEG.

Advise against sensitivity/specificity. Trying to find inflection point is problematic. Risk model may be better. Flap failure is fairly rare (2-3%), and it is a yes/no, typically.

Goals for this study could be; estimate of failure. Would need about 15 failures per variable. Sample size is problematic here. Could reframe as proof of concept/proof of information. Can this study demonstrate value in using the TEG device--will the device measure correlate with flap failure. Look at correlations. Can also look at relationship with existing clinical variables, demonstate that TEG can contribute (redundancy). Suggest understanding precision of TEG device.

Dr. Perdikis could not attend.

2022 January 13

Garrett Booth, Pathology/Laboratory Medicine

We have created a database of US medical boards and their composition, including board member title (eg CEO) and gender. We have annual data related to individuals within 24 US medical boards. Our primary hypothesis is that women physicians are underrepresented in US medical boards. Question for biostats clinic? The gender composition for each medical board appears to be non-parametric (lacks a normal distribution) and I would like to compare the percent of women physicians in US medical boards between two separate years. Can I compare percentages using the Mann-Whitney test?

Are women represented at parity? Absolute parity. This is all boards combined.

Are women represented in the same proportion as included in the specialty? Relative parity by specialty. Board size has changed, some increased, some decreased.

Has there been an improvement since 2016? Defined as increase in women (usually).

We have all data (population), so no inference issue here

Suggest multi panel dot chart, aka Cleveland dot charts. Suggest Google. Also:

Sort in descending order, proportion of females.

2022 January 06

Alex Foy (Stacy Killen), Pediatric Cardiology

Retrospective chart review to identify mitral valve or dimensional differences apparent by fetal echocardiography in those fetuses with postnatally confirmed coarctation of the aorta who undergo biventricular repair compared to those who ultimately require univentricular palliative surgery. VICTR Biostatistics voucher. Mentor confirmed.

10 Years of data, about 100 with coarc and fetal echo, see if measures during echo can predict bi vs uni repair. Patient may have between 1-5 fetal echos. Also have multiple echos before interventions. Actual repair decision is made during surgery. Measure of mitral valve (Z score) to predict outcome. Gold standard may be the measure before surgery. Repeated measures issues-coud think of these as updated baselines. This may fit that issue, rather that a true repeated measures. A landmark analysis. This would fit in the scope of a voucher.

Zachary Bressman (Heather Pua), Pathology, Microbiology, and Immunology

The project is a collaboration between the Heather Pua lab and Dr. Katherine Cahill and aims to examine changes in extracellular vesicle (EV) abundance in biofluids collected from patients with aspirin exacerbated respiratory disease (AERD) during different timepoints in controlled aspirin challenges that cause them inflammation. We hope to identify potential EV biomarkers in the context of AERD progression. Currently, we track the abundance of different EV populations in AERD patient biofluids with bead-based flow cytometry. As part of the project, we want to figure out how semi-quantitative bead flow cytometry is. To help answer this question, Iíve collected a series of cell-derived EV serial dilution bead flow cytometry measurements. I collected flow cytometry data for 1/2 diluted EVs, 1/4, 1/8, 1/16, and 1/32, and because the changes between subsequent dilutions were consistent and linear, I wanted to see how linear the changes in flow cytometry measurements were. It has become increasingly clear that there are upper and lower bounds outside which bead flow cytometry measurements is unreliable and changes between different dilution measurements is nonlinear. I would like the biostatistics clinicís help with finding a statistical test to pinpoint the upper and lower limits of linearity for the data sets Iíve collected, so I can better filter out unreliable measurements. Mentor confirmed.

We can see on a scatter plot that some values do not correlate well. But is there a way to quantify this poor match. Trying to establish the true lower limit of the assay. Consider geometric median, rather than mean
Topic attachments
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Aims-10-21-15.docxdocx Aims-10-21-15.docx manage 12.5 K 29 Oct 2015 - 10:00 LiWang  
BotScoringSheet.pdfpdf BotScoringSheet.pdf manage 337.6 K 18 Nov 2016 - 13:51 AmyPerkins  
Gregory_Health_Sciences_Protocol_for__iSLEEP.docdoc Gregory_Health_Sciences_Protocol_for__iSLEEP.doc manage 33.5 K 27 Oct 2016 - 10:08 AmyPerkins  
J_Durlacher_Tables_for_Biostats_Clinic.docxdocx J_Durlacher_Tables_for_Biostats_Clinic.docx manage 61.5 K 03 Nov 2016 - 09:28 AmyPerkins  
Pilot_Full_Protocol_4.7.16.docxdocx Pilot_Full_Protocol_4.7.16.docx manage 236.2 K 13 Apr 2016 - 08:38 JonKropski Kropski - Phase Ib Trial protocol
Preterm_babies_with_CHD_database.pdfpdf Preterm_babies_with_CHD_database.pdf manage 55.3 K 07 Apr 2015 - 11:54 MeridithBlevins For April 9 Consultation
SplinesWithInteraction.dodo manage 6.3 K 13 Mar 2015 - 16:19 WilliamDupont  
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VPA_poster_AES_2008_v5_12-3-08.pdfpdf VPA_poster_AES_2008_v5_12-3-08.pdf manage 201.5 K 27 Jan 2017 - 12:07 AmyPerkins  
VR22383_Pre-review_questions_for_PI.docxdocx VR22383_Pre-review_questions_for_PI.docx manage 78.3 K 31 Oct 2016 - 14:08 AmyPerkins  
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Topic revision: r909 - 01 Jul 2022, YueGao

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