Skip to main content
eScholarship
Open Access Publications from the University of California

Open Access Policy Deposits

This series is automatically populated with publications deposited by UCSF Department of Epidemiology and Biostatistics researchers in accordance with the University of California’s open access policies. For more information see Open Access Policy Deposits and the UC Publication Management System.

Examining the Impact of the Golden Compass Clinical Care Program for Older People with HIV: A Qualitative Study.

(2022)

The combined burden of geriatric conditions, comorbidities, and HIV requires a model of HIV care that offers a comprehensive clinical approach with people 50 years or older with HIV. Golden Compass is an outpatient, multidisciplinary HIV-geriatrics program with an onsite HIV geriatrician, cardiologist, pharmacist, and social worker, offering specialist referrals, care navigation, and classes on improving functional status and cognition. Participants (13 patients and 11 primary care providers) were recruited using a non-probability sampling method to participate in semi-structured interviews on the perceived impact of Golden Compass on care delivered to older people with HIV. Interviews were transcribed verbatim and framework analysis used to analyze the transcripts. The perceived impacts of Golden Compass by patients and providers were organized by the Compass points (Northern: Heart and Mind, Eastern: Bones and Strength, Southern: Navigation and Network, Western: Dental, Hearing, and Vision). Overall, patients valued the focus on functional health and whole-person care, leading to greater trust in the ability of providers. Providers gained new skills through the geriatrics, cardiology and/or pharmacist consultations. The HIV-geriatrics specialty approach of Golden Compass improved functional ability and quality of life for older adults with HIV. Few integrated care programs for older people with HIV have been evaluated. This study adds to the limited literature demonstrating high patient and provider satisfaction with a HIV-care model that incorporated principles of geriatric medicine emphasizing a comprehensive approach to sustaining functional ability and improving quality of life.

Cover page of Clinical Outcomes and Qualitative Perceptions of In-person, Hybrid, and Virtual Cardiac Rehabilitation.

Clinical Outcomes and Qualitative Perceptions of In-person, Hybrid, and Virtual Cardiac Rehabilitation.

(2022)

Cardiac rehabilitation (CR) is evolving to include both in-person and virtual delivery. Our objective was to compare, in CR patients, the association of in-person, hybrid, and virtual CR with change in performance on the 6-min walk test (6MWT) between enrollment and completion. Patients enrolled in CR between October 22, 2019, and May 10, 2021, were categorized into in-person, hybrid, or virtual groups by number of in-person and virtual visits. All patients received individualized exercise training and health behavior counseling. Cardiac rehabilitation was delivered to patients in the hybrid and virtual cohorts using synchronous video exercise and/or asynchronous telephone visits. Measurements at CR enrollment and completion included the 6MWT, blood pressure (BP), depression, anxiety, waist-to-hip ratio, and cardiac self-efficacy. Of 187 CR patients, 37/97 (38.1%) were in-person patients and 58/90 (64.4%) were hybrid/virtual patients (P = .001). Compared to in-person (51.5 ± 59.4 m) improvement in the 6MWT was similar in hybrid (63.4 ± 55.6; P = .46) and virtual (63.2 ± 59.6; P = .55) compared with in-person (51.5 ± 59.4). Hybrid and virtual patients experienced similar improvements in BP control and anxiety. Virtual patients experienced less improvement in depression symptoms. There were no statistically significant changes in waist-to-hip ratio or cardiac self-efficacy. Qualitative themes included the adaptability of virtual CR, importance of relationships between patients and CR staff, and need for training and organizational adjustments to adopt virtual CR. Hybrid and virtual CR were associated with similar improvements in functional capacity to in-person. Virtual and hybrid CR have the potential to expand availability without compromising outcomes.

Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis.

(2022)

Fecal microbiota transplant is a promising therapy for ulcerative colitis. Parameters maximizing effectiveness and tolerability are not yet clear, and it is not known how import the transmission of donor microbes to patients is. Here (clinicaltrails.gov: NCT03006809) we have tested the effects of antibiotic pretreatment and compared two modes of maintenance dose delivery, capsules versus enema, in a randomized, pilot, open-label, 2 × 2 factorial design with 22 patients analyzed with mild to moderate UC. Clinically, the treatment was well-tolerated with favorable safety profile. Of patients who received antibiotic pretreatment, 6 of 11 experienced remission after 6 weeks of treatment, versus 2 of 11 non-pretreated patients (log odds ratio: 1.69, 95% confidence interval: -0.25 to 3.62). No significant differences were found between maintenance dosing via capsules versus enema. In exploratory analyses, microbiome turnover at both the species and strain levels was extensive and significantly more pronounced in the pretreated patients. Associations were also revealed between taxonomic turnover and changes in the composition of primary and secondary bile acids. Together these findings suggest that antibiotic pretreatment contributes to microbiome engraftment and possibly clinical effectiveness, and validate longitudinal strain tracking as a powerful way to monitor the dynamics and impact of microbiota transfer.

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro.

(2022)

Single nucleotide polymorphisms (SNPs) in metagenomics are used to quantify population structure, track strains and identify genetic determinants of microbial phenotypes. However, existing alignment-based approaches for metagenomic SNP detection require high-performance computing and enough read coverage to distinguish SNPs from sequencing errors. To address these issues, we developed the GenoTyper for Prokaryotes (GT-Pro), a suite of methods to catalog SNPs from genomes and use unique k-mers to rapidly genotype these SNPs from metagenomes. Compared to methods that use read alignment, GT-Pro is more accurate and two orders of magnitude faster. Using high-quality genomes, we constructed a catalog of 104 million SNPs in 909 human gut species and used unique k-mers targeting this catalog to characterize the global population structure of gut microbes from 7,459 samples. GT-Pro enables fast and memory-efficient metagenotyping of millions of SNPs on a personal computer.

Cover page of Identifying falls remotely in people with multiple sclerosis.

Identifying falls remotely in people with multiple sclerosis.

(2022)

Background

Falling is common in people with multiple sclerosis (MS) but tends to be under-ascertained and under-treated.

Objective

To evaluate fall risk in people with MS.

Methods

Ninety-four people with MS, able to walk > 2 min with or without an assistive device (Expanded Disability Status Scale (EDSS ≤ 6.5) were recruited. Clinic-based measures were recorded at baseline and 1 year. Patient-reported outcomes (PROs), including a fall survey and the MS Walking Scale (MSWS-12), were completed at baseline, 1.5, 3, 6, 9, and 12 months. Average daily step counts (STEPS) were recorded using a wrist-worn accelerometer.

Results

50/94 participants (53.2%) reported falling at least once. Only 56% of participants who reported a fall on research questionnaires had medical-record documented falls. Fallers had greater disability [median EDSS 5.5 (IQR 4.0-6.0) versus 2.5 (IQR 1.5-4.0), p < 0.001], were more likely to have progressive MS (p = 0.003), and took fewer STEPS (mean difference - 1,979, p = 0.007) than Non-Fallers. Stepwise regression revealed MSWS-12 as a major predictor of future falls.

Conclusions

Falling is common in people with MS, under-reported, and under-ascertained by neurologists in clinic. Multimodal fall screening in clinic and remotely may help improve patient care by identifying those at greatest risk, allowing for timely intervention and referral to specialized physical rehabilitation.

Cover page of Validation of Anticorrelated TGFβ Signaling and Alternative End-Joining DNA Repair Signatures that Predict Response to Genotoxic Cancer Therapy.

Validation of Anticorrelated TGFβ Signaling and Alternative End-Joining DNA Repair Signatures that Predict Response to Genotoxic Cancer Therapy.

(2022)

Purpose

Loss of TGFβ signaling increases error-prone alternative end-joining (alt-EJ) DNA repair. We previously translated this mechanistic relationship as TGFβ and alt-EJ gene expression signatures, which we showed are anticorrelated across cancer types. A score representing anticorrelation, βAlt, predicts patient outcome in response to genotoxic therapy. Here we sought to verify this biology in live specimens and additional datasets.

Experimental design

Human head and neck squamous carcinoma (HNSC) explants were treated in vitro to test whether the signatures report TGFβ signaling, indicated by SMAD2 phosphorylation, and unrepaired DNA damage, indicated by persistent 53BP1 foci after irradiation or olaparib. A custom NanoString assay was implemented to analyze the signatures' expression in explants. Each signature gene was then weighted by its association with functional responses to define a modified score, βAltw, that was retested for association with response to genotoxic therapies in independent datasets.

Results

Most genes in each signature were positively correlated with the expected biological response in tumor explants. Anticorrelation of TGFβ and alt-EJ signatures measured by NanoString was confirmed in explants. βAltw was significantly (P < 0.001) better than βAlt in predicting overall survival in response to genotoxic therapy in The Cancer Genome Atlas (TCGA) pancancer patients and in independent HNSC and ovarian cancer patient datasets.

Conclusions

Association of the TGFβ and alt-EJ signatures with their biological response validates TGFβ competency as a key mediator of DNA repair that can be readily assayed by gene expression. The predictive value of βAltw supports its development to assist in clinical decision making.

  • 1 supplemental PDF

SARS COV-2 anti-nucleocapsid and anti-spike antibodies in an emergency department healthcare worker cohort: September 2020 - April 2021.

(2022)

Background

Emergency department (ED) workers have an increased seroprevalence of SARS-CoV-2 antibodies. However, breakthrough infections in ED workers have led to a reduced workforce within a strained healthcare system. By measuring levels of IgG antibodies to the SARS-CoV-2 nucleocapsid and spike antigens in ED workers, we determined the incidence of infection and described the course of antibody levels. We also measured the antibody response to vaccination and examined factors associated with immunogenicity.

Methods

We conducted a prospective cohort study of ED workers conducted at a single ED from September 2020-April 2021. IgG antibodies to the SARS-CoV-2 nucleocapsid antigen were measured at baseline, 3, and 6 months, and IgG antibodies to the SARS-CoV-2 spike antigen were measured at 6 months.

Results

At baseline, we found 5 out of 139 (3.6%) participants with prior infection. At 6 months, 4 of the 5 had antibody results below the test manufacturer's positivity threshold. We identified one incident case of SARS-COV-2 infection out of 130 seronegative participants (0.8%, 95% CI 0.02-4.2%). In 131 vaccinated participants (125 BNT162b2, 6 mRNA-1273), 131 tested positive for anti-spike antibodies. We identified predictors of anti-spike antibody levels: time since vaccination, prior COVID-19 infection, age, and vaccine type. Each additional week since vaccination was associated with an 11.1% decrease in anti-spike antibody levels. (95% CI 6.2-15.8%).

Conclusion

ED workers experienced a low incidence of SARS-CoV-2 infection and developed antibodies in response to vaccines and prior infection. Antibody levels decreased markedly with time since infection or vaccination.