Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations

Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein-DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.

Safe Fall Recovery Education for Older Adults

High fall rates among older adults in combination with prolonged time on the floor after a fall have created an urgent need to preventatively address fall recovery strategies. The purpose of this study is to describe the outcomes of a novel safe fall recovery (SFR) educational module provided by physical therapists to older adults in their homes. A pre- and post-test descriptive study used a convenience sample to recruit 30 adults (≥65 years). A baseline assessment and SFR in-home education were provided. Pre- and post-education measures included the Steps for Safe Fall Recovery (Steps for SFR) tool, the Activity Specific Balance Confidence (ABC) scale, and a fall confidence survey. The Wilcoxon matched-pairs signed-rank test determined significance (P < .05). Participants were age 77.2 (6.8) years and 20 females. Eight reported a fall during the prior year. Statistically significant improvements were identified in the Steps to SFR tool (P = .001), the ABC scale (P = .004), and the fall recovery confidence survey (P = .001). Integration of an SFR educational intervention delivered to an older adult population in their home demonstrated improved safety and confidence to recover from a fall.

Localisation of vibrational modes in high-entropy oxides

The recently-discovered high-entropy oxides (HEO's) offer a paradoxical combination of crystalline arrangement and high disorder. They differ qualitatively from established paradigms for disordered solids such as glasses and alloys. In these latter systems, it is well known that disorder induces localised vibrational excitations. In this article, we explore the possibility of disorder-induced localisation in Mg0.2Co0.2Ni0.2Cu0.2Zn0.2O, the prototypical HEO with rock-salt structure. To describe phononic excitations, we model the interatomic potentials for the cation-oxygen interactions by fitting to the physical properties of the parent binary oxides. We validate our model against the experimentally determined crystal structure and optical conductivity. The resulting phonon spectrum shows wave-like propagating modes at low energies and localised modes at high energies. Localisation is reflected in signatures such as participation ratio and correlation amplitude. Finally, we argue that mass disorder can be increased to enhance localisation. We consider a hypothetical material, high-entropy telluride-oxide, where tellurium atoms are admixed into the anion sublattice. This shows a larger localised fraction, with additional localised modes appearing in the middle of the spectrum. Our results demonstrate that HEO's are a promising platform to study Anderson localisation of phonons.

Quantum simulation of the bosonic Kitaev chain

Superconducting quantum circuits are a natural platform for quantum simulations of a wide variety of important lattice models describing topological phenomena, spanning condensed matter and high-energy physics. One such model is the bosonic analog of the well-known fermionic Kitaev chain, a 1D tight-binding model with both nearest-neighbor hopping and pairing terms. Despite being fully Hermitian, the bosonic Kitaev chain exhibits a number of striking features associated with non-Hermitian systems, including chiral transport and a dramatic sensitivity to boundary conditions known as the non-Hermitian skin effect. Here, using a multimode superconducting parametric cavity, we implement the bosonic Kitaev chain in synthetic dimensions. The lattice sites are mapped to frequency modes of the cavity, and the in situ tunable complex hopping and pairing terms are created by parametric pumping at the mode-difference and mode-sum frequencies, respectively. We experimentally demonstrate important precursors of nontrivial topology and the non-Hermitian skin effect in the bosonic Kitaev chain, including chiral transport, quadrature wavefunction localization, and sensitivity to boundary conditions. Our experiment is an important first step towards exploring genuine many-body non-Hermitian quantum dynamics.

Neurological Effects of Repeated Blast Exposure in Special Operations Personnel

Exposure to blast overpressure has been a pervasive feature of combat-related injuries. Studies exploring the neurological correlates of repeated low-level blast exposure in career "breachers" demonstrated higher levels of tumor necrosis factor alpha (TNFα) and interleukin (IL)-6 and decreases in IL-10 within brain-derived extracellular vesicles (BDEVs). The current pilot study was initiated in partnership with the U.S. Special Operations Command (USSOCOM) to explore whether neuroinflammation is seen within special operators with prior blast exposure. Data were analyzed from 18 service members (SMs), inclusive of 9 blast-exposed special operators with an extensive career history of repeated blast exposures and 9 controls matched by age and duration of service. Neuroinflammation was assessed utilizing positron emission tomography (PET) imaging with [18F]DPA-714. Serum was acquired to assess inflammatory biomarkers within whole serum and BDEVs. The Blast Exposure Threshold Survey (BETS) was acquired to determine blast history. Both self-report and neurocognitive measures were acquired to assess cognition. Similarity-driven Multi-view Linear Reconstruction (SiMLR) was used for joint analysis of acquired data. Analysis of BDEVs indicated significant positive associations with a generalized blast exposure value (GBEV) derived from the BETS. SiMLR-based analyses of neuroimaging demonstrated exposure-related relationships between GBEV, PET-neuroinflammation, cortical thickness, and volume loss within special operators. Affected brain networks included regions associated with memory retrieval and executive functioning, as well as visual and heteromodal processing. Post hoc assessments of cognitive measures failed to demonstrate significant associations with GBEV. This emerging evidence suggests neuroinflammation may be a key feature of the brain response to blast exposure over a career in operational personnel. The common thread of neuroinflammation observed in blast-exposed populations requires further study.

Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics

Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting 1-3 genomic sites per cell. To develop a tool for higher-order ( > 3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered an Acidaminococcus Cas12a variant -- referred to as mul tiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering.

Evaluation of a Physical Therapist-Delivered Technology Literacy Algorithm and Protocol for Older Adults: A Pilot Study

Introduction Technology literacy is the ability to comfortably understand, use, and navigate digital devices. It is considered a "super social determinant of health", and yet 39% of adults aged 65+ report not using a smartphone, and 25% of seniors still lack internet access. The purpose of this study was to examine the applicability of a physical therapist-delivered clinical assessment tool related to technological literacy and to identify relationships between technology utilization and perceptions related to sociodemographic factors in community-dwelling older adults. Methods A prospective mixed-methods observational-descriptive study where physical therapists (PTs) administered a newly designed technology literacy algorithm to older adults and evaluated the results of the algorithm. A convenience sample of 30 participants aged 65 and older was evaluated for their technology literacy. The exclusion criteria were if the person had a vision deficit, lived in a nursing home or extended care facility, was unable to fluently read and understand the English language, or was not willing to have an in-home visit by a licensed PT. After informed consent was obtained, the participant completed a Past Experience with Technology Questionnaire assessing participant confidence with technology usage and a demographic questionnaire. A PT data collector visited participants' homes and administered a novel technology literacy algorithm. The PTs also provided subjective feedback after patient visits as to their perceptions of the algorithm. Inferential statistics were performed for key variables, including a Kruskal-Wallis test being utilized for variables with three or more levels and a two-sample Wilcoxon test being utilized for variables with two levels. The binary results were evaluated with chi-squared tests. Trends in distribution and measures of central tendency were analyzed for demographic data. Statistical significance was set at P<0.05 with a confidence interval of 95%. Results Participants (n=30) were evenly distributed with regard to age, and 66% of people had a college degree. Most were female, of the white race, and retired. There were statistically significant relationships between older age and decreased comfort level with using the internet (P=0.30) and sending messages (P=0.31), with individuals 80+ years old having a mean confidence of 6.78 out of 10. A statistically significant relationship was also found between higher income and increased confidence in browsing the internet (P = 0.07). Most qualitative data from physical therapist experiences included positive trends such as ease of use, efficiency, and confidence instilled. Constructive feedback included a lack of resources to assist with more advanced technology-related needs and recommendations to refine the algorithm when advanced needs were identified. Conclusion Technology literacy is a vital component of accessing health and medical care and maximizing the quality of that care, especially in the older adult population. The tools created may assist clinicians with identifying and addressing issues related to technology in older adults. This may help a patient navigate health issues that require the use of technology in their home. This study provided evidence that a PT-administered algorithm may be feasible to address technology literacy issues in the homes of older adults.

Effect of Robotic Delivery of Physical Activity and Fall Prevention Exercise in Older Adults: A Pilot Cohort Study

Introduction The high prevalence of falls, lack of stability and balance, and general physical deconditioning are concerning issues for longevity and quality of life for adults aged 65 years and older. Although supervised delivery of the Otago Exercise Program (OEP) has demonstrated evidence of effectiveness in reducing fall risk of older adults, opportunities for ongoing unsupervised exercise performance are warranted. An option to facilitate exercise and performance of health behaviors may be via a social robot. The purpose of this study was to examine feasibility and initial outcomes of a robot-delivered fall prevention exercise program for community-dwelling older adults. Methods Five participants aged 65 years and older were recruited to receive robot-delivered modified OEP and walking program three times per week for four weeks. Outcomes of demographics, self-reported performance measures (Modified Falls Self-Efficacy Scale, Activities-specific Balance Confidence, and Almere Model assessing various constructs of acceptance of use of robotic technology), and physical performance measures (Timed Up and Go Test, Short Physical Performance Battery, Balance Tracking System [BTrackS] center of pressure sway) were collected. Data were analyzed descriptively and examined for trends in change. Measures of central tendency and distribution were used according to the distribution of the data. Results The mean age of the participants was 75 years (range: 66-83 years; four females and one male). The range of participant exercise session completion was 7-12 (mode=11, n=3). Constructs on the Almere Model that started and remained positive were Attitudes Toward Technology and Perceived Enjoyment with the robot. Anxiety improved from 3.80 to 4.68, while Social Presence of the robot improved from 2.80 to 3.56. The construct of Trust was somewhat negative among participants upon commencing the program and did not substantially change over time. Two participants improved their confidence on the Activities-specific Balance Confidence scale by more than 10%, while all participants showed some improvement in confidence in their balance. Mixed results were found with the Modified Falls Self-Efficacy Scale. Mean gait speed for the participants improved by 0.76 seconds over 3 meters. Improvement was also demonstrated for the Short Physical Performance Battery, with two participants improving scores by 2-3 points out of 12. No appreciable changes were found with the Timed Up and Go test and the BTrackS assessment. Conclusion Using a robot-led exercise program is an accessible and feasible way to deliver exercise to community-dwelling older adults in the home, but some technical constraints remain. Outcomes suggest that a four-week program is sufficient to elicit some positive trends in health outcomes and has the potential to reduce fall risk.

Looking back: a review of policy implications for exercise oncology

The evidence to support the benefits of exercise for people living with and beyond cancer is robust. Still, exercise oncology interventions in the United States are only eligible for coverage by third-party payers within the restrictions of cancer rehabilitation settings. Without expanded coverage, access will remain highly inequitable, tending toward the most well-resourced. This article describes the pathway to third-party coverage for 3 programs that address a chronic disease and utilize exercise professionals: the Diabetes Prevention Program, Supervised Exercise Training for Peripheral Artery Disease, and Cancer Rehabilitation. Lessons learned will be applied toward expanding third-party coverage for exercise oncology programming.

Medical Clearance of Older Adults Participating in Preventative Direct Access Physical Therapy

Background The purpose of this study was to determine if the use of evidence-based cognitive and cardiovascular screening prior to initiating a prevention-focused exercise program that utilizes a physical therapist (PT) direct consumer access referral model is safe. Methods A retrospective descriptive analysis of data from a prior randomized controlled trial (RCT) was performed. Two data sets emerged: Group S was screened for study inclusion but not enrolled, and Group E was enrolled and participated in preventative exercise. Participant outcomes of cognitive screenings (Mini-Cog, Trail Making Test-Part B) and cardiovascular screening (American College of Sports Medicine Exercise Pre-participation Health Screening) were extracted. Descriptive statistics were generated for demographic and outcome variables and inferential statistics were analyzed (p < 0.05). Results Records from 70 individuals (Group S) and 144 individuals (Group E) were available for analysis. Overall, 18.6% (n = 13) in Group S were not enrolled due to medical instability or potential safety considerations. The need for medical clearance prior to initiating an exercise program was identified and then clearance was obtained for 40% (n = 58) of the participants in Group E. No adverse events related to program participation were reported. Conclusions A PT-led program utilizing direct access referrals from senior centers offers a safe option for older adults to participate in individualized preventative exercise programming.

Statistics and Machine Learning in Mass Spectrometry-Based Metabolomics Analysis

In this chapter, we review the cutting-edge statistical and machine learning methods for missing value imputation, normalization, and downstream analyses in mass spectrometry metabolomics studies, with illustration by example datasets. The missing peak recovery includes simple imputation by zero or limit of detection, regression-based or distribution-based imputation, and prediction by random forest. The batch effect can be removed by data-driven methods, internal standard-based, and quality control sample-based normalization. We also summarize different types of statistical analysis for metabolomics and clinical outcomes, such as inference on metabolic biomarkers, clustering of metabolomic profiles, metabolite module building, and integrative analysis with transcriptome.

Perceptions of Physical Therapists of Online Introduction and Training in the Home-based Older Persons Upstreaming Prevention Physical Therapy (HOP-UP-PT) Program: A Qualitative Study

Introduction

Traditionally, physical therapy has adopted a tertiary approach to preventative care. However, recent trends in fall-related injuries and deaths among older individuals suggest a dire need for earlier intervention. The Home-based Older Persons Upstreaming Prevention Physical Therapy (HOP-UP-PT) program has been developed to improve the health and overall function of community-dwelling older adults at risk of functional decline. As demand continually rises for HOP-UP-PT services, online training modules have been developed to safely and efficiently provide HOP-UP-PT competency to physical therapists. The purpose of this study was to examine self-reported experiences and perceptions of physical therapists after completing an asynchronous training program to deliver HOP-UP-PT.

Methods

After securing Oakland University IRB approval, a qualitative study using a sample of convenience used two structured focus group interviews. Inclusion criteria required participants to be licensed physical therapists (PTs) in the state of Michigan providing at least 20 hours of direct patient care per week. Participants completed eight 30-minute training modules, each with a corresponding quiz. Upon completion, PTs attended one of two video conference focus groups. Data was analyzed using the constant comparative method to develop themes and concepts based on responses about the training modules and the overall HOP-UP-PT program.

Results

Twelve PTs with a median age of 31-40 years participated. Analysis of two focus group sessions identified three concepts (Novel Approach to Physical Therapy Care, Integration of a Preventative Approach into Clinical Practice, and Knowledge Translation) and ten themes (Addressing an Unmet Need, Establishing a Working Relationship with Community Centers, Applicability to Various Settings, Shifting the Mindset to a Prevention-focused Paradigm, Applicability to Physical Therapists that Care for Older Adults, Patient Engagement and Prevention, Value for the Professional, Importance of Availability of Options in a Learning Platform, Ongoing Availability of Program Resources and Tools, and Clinical Application Practice).

Conclusion

PTs identified the HOP-UP-PT program as a novel, clinically applicable, and adding value to the profession. Furthermore, its upstream focus aligns with the growing role of preventative care by PTs; however, as HOP-UP-PT is not a traditional approach, additional training and clinical support materials may facilitate adoption and clinical application. HOP-UP-PT uses a preventative approach to clinical practice, but efforts to translate knowledge to PT are an important consideration. Additionally, the study identified a need for refinement and modifications to the existing HOP-UP-PT training modules.

State of the Art Physiotherapist-Led Approaches to Safe Aging in Place

Introduction

Safe aging in place (SAIP) is when an older adult can successfully and comfortably remain in their home despite increasing barriers, including falls. Various physical, medical, psychological, and psychosocial factors may individually or cumulatively impact an older adult’s ability to safely age in place. Physiotherapists should assess not only items traditionally considered within their scope of practice but should select efficient and effective outcome measures to quantify other domains of health. A comprehensive geriatric assessment (CGA) is an evidence-based clinical assessment which identifies medical, psychosocial, and functional limitations of an older person. The CGA is useful to dictate individualized exercise/intervention prescription to address identified areas of increased risk.

Purpose and importance to practice

The purpose of this Masterclass is to describe key screening, assessments, and interventions to facilitate SAIP and to provide overviews of currently available programming and care delivery models applicable to physiotherapist practice.

There are a wide variety of outcome measures and interventions that vary in depth, validity, and reliability. Measures selected for inclusion in this Masterclass were chosen based upon their clinical utility with respect to time and resource constraints and ease of administration during a comprehensive assessment for SAIP in community-dwelling older adults. Measures recommended for assessing physical function were the Short Physical Performance Battery, the Timed-Up-and-Go, the 30 second chair rise test, and the Four Test Balance Scale. Additionally, measures from the heath domain (e.g., Functional Comorbidity Index) and the environmental domain (e.g., Home FAST) are recommended. Relative to interventions, the Otago Exercise Program, motivational interviewing, home modifications, and leveraging technology are recommended. Partnerships with community-facing organizations facilitate utilization of resources for sustainable SAIP. The Home-based Older Person Upstreaming Prevention Physical Therapy (HOP-UP-PT) program is one approach led by physiotherapists framed in the screening, assessments, and interventions discussed in this Masterclass with strong scientific grounding.

Conclusion

Programs integrating both community and healthcare approaches have the strongest evidence for their utility; however, implementation for these preventative approaches are lagging behind the increased need due to the substantial population growth of those over 65 years.

Abstract 2541: Immune cell clustering in ovarian cancer tumors and its association with survival

New technologies, such as multiplex immunofluorescence microscopy (mIF), are being developed and used for the assessment and visualization of the tumor immune microenvironment (TIME). These assays produce not only an estimate of the abundance of immune cells in the TIME, but also their spatial locations; however, there are currently few approaches to analyze the spatial context of the TIME. Thus, we have developed a framework for the spatial analysis of the TIME using Ripley’s K, coupled with a permutation-based framework to estimate and measure the departure from complete spatial randomness as a measure of the interactions between immune cells. This approach was applied to mIF data collected on tissue microarrays (TMA) and intratumoral regions of interest (ROIs), defined as &gt;90% tumor cells based on pancytokeratin expression and morphology, selected from whole tissue sections from high-grade serous ovarian carcinoma patients (HGSOC) in the African American Cancer Epidemiology Study (94 subjects on TMAs resulting in 263 tissue cores; 93 subjects with 260 ROIs; 27 subjects included in both TMA and ROIs). Cox proportional hazard models, adjusting for stage and age of diagnosis, were constructed to determine the association of abundance and spatial clustering of tumor-infiltrating lymphocytes (TILs; CD3+), cytotoxic T-cells (CD3+ CD8+), and regulatory T-cells (CD3+ FoxP3+) with overall survival. For all models, the referent group was women with no positive cells for the marker of interest. In the analysis of ROIs, HGSOC patients with high abundance and low spatial clustering of TILs (hazard ratio [HR] = 0.069, 95% confidence interval [CI] = 0.01-0.35) and cytotoxic T-cells (HR and CI not estimable as no deaths observed) had the best survival. This finding of better survival in patients with high abundance and low clustering of TILs and cytotoxic T-cells was replicated in the analysis of TMAs (HR = 0.51, 95% CI = 0.31-0.85 for TILs and HR = 0.11, 95% CI = 0.02-0.53 for cytotoxic T-cells). We also demonstrated the models with both abundance and spatial information was more informative than abundance alone (p &lt; 0.01 for CD3+ and CD3+CD8+ in both ROIs and TMAs). High co-localization of regulatory T-cells and cytotoxic T-cells showed best overall survival on both ROI and TMAs (HR=0.49, 95% CI = 0.28-0.88 and HR = 0.42, 95% CI = 0.25-0.71, respectively). The model with spatial co-occurrence information was significantly better than the model with only abundance (p &lt; 0.05). These findings underscore the prognostic importance of evaluating not only immune cell abundance but also the spatial contexture of the immune cells in the ovarian TIME. The use of our framework for spatial analysis of the TIME and immune cell clustering may be applicable in other cancers and provide a novel approach to identification of biomarkers for predicting patient outcomes.

Citation Format: Alex C. Soupir, Christopher M. Wilson, Joellen M. Schildkraut, Lauren C. Peres, Brooke L. Fridley. Immune cell clustering in ovarian cancer tumors and its association with survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2541.

Racial Differences in the Tumor Immune Landscape and Survival of Women with High-Grade Serous Ovarian Carcinoma

BACKGROUND

Tumor-infiltrating lymphocytes (TIL) confer a survival benefit among patients with ovarian cancer; however, little work has been conducted in racially diverse cohorts.

METHODS

The current study investigated racial differences in the tumor immune landscape and survival of age- and stage-matched non-Hispanic Black and non-Hispanic White women with high-grade serous ovarian carcinoma (HGSOC) enrolled in two population-based studies (n = 121 in each racial group). We measured TILs (CD3+), cytotoxic T cells (CD3+CD8+), regulatory T cells (CD3+FoxP3+), myeloid cells (CD11b+), and neutrophils (CD11b+CD15+) via multiplex immunofluorescence. Multivariable Cox proportional hazard regression was used to estimate the association between immune cell abundance and survival overall and by race.

RESULTS

Overall, higher levels of TILs, cytotoxic T cells, myeloid cells, and neutrophils were associated with better survival in the intratumoral and peritumoral region, irrespective of tissue compartment (tumor, stroma). Improved survival was noted for T-regulatory cells in the peritumoral region and in the stroma of the intratumoral region, but no association for intratumoral T-regulatory cells. Despite similar abundance of immune cells across racial groups, associations with survival among non-Hispanic White women were consistent with the overall findings, but among non-Hispanic Black women, most associations were attenuated and not statistically significant.

CONCLUSIONS

Our results add to the existing evidence that a robust immune infiltrate confers a survival advantage among women with HGSOC; however, non-Hispanic Black women may not experience the same survival benefit as non-Hispanic White women with HGSOC.

IMPACT

This study contributes to our understanding of the immunoepidemiology of HGSOC in diverse populations.

The Effect of Individualized Fall Prevention Programs on Community-Dwelling Older Adults: A Scoping Review

An alarming rate of injurious falls among older adults warrants proactive measures to reduce falls and fall risk. The purpose of this article was to examine and synthesize the literature as it relates to programmatic components and clinical outcomes of individualized fall prevention programs on community-dwelling older adults. A literature search of four databases was performed using search strategies and terms unique to each database. Title, abstract, and full article reviews were performed to assure inclusion and exclusion criteria were met. Data were analyzed for type of study, program providers, interventions and strategies used to deliver the program, assessments used, and statistically significant outcomes. Queries resulted in 410 articles and 32 met all inclusion criteria (19 controlled trials and 13 quasi-experimental). Physical therapists were part of the provider team in 23 (72%) studies and the only provider in 10 (31%). There was substantial heterogeneity in procedures and outcome measures. Most common procedures were balance assessments (n=30), individualized balance exercises (n=29), cognition (n=21), home and vision assessments (n=16), specific educational modules (n=15), referrals to other providers/community programs (n=8), and motivational interviewing (n=7). Frequency of falls improved for eight of 13 (61.5%) controlled trials and four of five (80%) quasi-experimental studies. Balance and function improved in six of 11 (54.5%) controlled trials and in each of the six (100%) quasi-experimental studies. Strength improved in three of seven (43%) controlled trials and four of five (75%) quasi-experimental studies. While many programs improved falls and balance of older adults, there was no conclusive evidence as to which assessments and interventions were optimal to deliver as individualized fall prevention programming. The skill of a physical therapist and measures of fall frequency, balance, and function were common among the majority of studies reviewed. Despite the variability among programs, there is emerging evidence that individualized, multimodal fall prevention programs may improve fall risk of community-dwelling older adults and convenient access to these programs should be emphasized.

spatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics

SUMMARY

Spatially resolved transcriptomics promises to increase our understanding of the tumor microenvironment and improve cancer prognosis and therapies. Nonetheless, analytical methods to explore associations between the spatial heterogeneity of the tumor and clinical data are not available. Hence, we have developed spatialGE, a software that provides visualizations and quantification of the tumor microenvironment heterogeneity through gene expression surfaces, spatial heterogeneity statistics that can be compared against clinical information, spot-level cell deconvolution and spatially informed clustering, all using a new data object to store data and resulting analyses simultaneously.

AVAILABILITY AND IMPLEMENTATION

The R package and tutorial/vignette are available at https://github.com/FridleyLab/spatialGE. A script to reproduce the analyses in this manuscript is available in Supplementary information. The Thrane study data included in spatialGE was made available from the public available from the website https://www.spatialresearch.org/resources-published-datasets/doi-10-1158-0008-5472-can-18-0747/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Efficient gradient boosting for prognostic biomarker discovery

MOTIVATION

A gradient boosting decision tree (GBDT) is a powerful ensemble machine-learning method that has the potential to accelerate biomarker discovery from high-dimensional molecular data. Recent algorithmic advances, such as extreme gradient boosting (XGB) and light gradient boosting (LGB), have rendered the GBDT training more efficient, scalable and accurate. However, these modern techniques have not yet been widely adopted in discovering biomarkers for censored survival outcomes, which are key clinical outcomes or endpoints in cancer studies.

RESULTS

In this paper, we present a new R package 'Xsurv' as an integrated solution that applies two modern GBDT training frameworks namely, XGB and LGB, for the modeling of right-censored survival outcomes. Based on our simulations, we benchmark the new approaches against traditional methods including the stepwise Cox regression model and the original gradient boosting function implemented in the package 'gbm'. We also demonstrate the application of Xsurv in analyzing a melanoma methylation dataset. Together, these results suggest that Xsurv is a useful and computationally viable tool for screening a large number of prognostic candidate biomarkers, which may facilitate future translational and clinical research.

AVAILABILITY AND IMPLEMENTATION

'Xsurv' is freely available as an R package at: https://github.com/topycyao/Xsurv.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Implementing Home-based Prevention Physical Therapy: A Scoping Review and Path to Launch of HOP-UP-PT

The purpose of this study was to conduct a scoping review of the available service delivery models related to home-based fall prevention programs led by rehabilitation professionals and to describe the path to launching one such program entitled Home-based Older Persons Upstreaming Prevention Physical Therapy (HOP-UP-PT). Topics of review included: Medicare and private billing structures available for current prevention programs and traditional rehabilitation, the Affordable Care Act and its application to reimbursement of preventive services and direct access care models, and a comparative review of CMS' Patient Driven Group Model (PDGM) home health benefit and Medicare Part B billing and reimbursement. Additionally, a path to launch one prevention-focused program, HOP-UP-PT, is described. There is emerging evidence that upstreaming fall prevention programs can help reduce falls and have money-saving downstream effects. A reimbursement model for this type of programming must be established in order ensure long-term sustainability. Although there is evidence that home-based prevention programs such as HOP-UP-PT can reduce falls and fall-risk metrics among an older adult population, there is not a clear and sustainable payment pathway, which limits proliferation of similar programs. Therefore, this preventative care model which has emerging evidence of cost savings will require reimbursement restructuring beyond what is available with existing payment models.

spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data

Summary

Multiplex immunofluorescence (mIF) staining combined with quantitative digital image analysis is a novel and increasingly used technique that allows for the characterization of the tumor immune microenvironment (TIME). Generally, mIF data is used to examine the abundance of immune cells in the TIME; however, this does not capture spatial patterns of immune cells throughout the TIME, a metric increasingly recognized as important for prognosis. To address this gap, we developed an R package spatialTIME that enables spatial analysis of mIF data, as well as the iTIME web application that provides a robust but simplified user interface for describing both abundance and spatial architecture of the TIME. The spatialTIME package calculates univariate and bivariate spatial statistics (e.g. Ripley’s K, Besag’s L, Macron’s M and G or nearest neighbor distance) and creates publication quality plots for spatial organization of the cells in each tissue sample. The iTIME web application allows users to statistically compare the abundance measures with patient clinical features along with visualization of the TIME for one tissue sample at a time.

Availability and implementation

spatialTIME is implemented in R and can be downloaded from GitHub (https://github.com/FridleyLab/spatialTIME) or CRAN. An extensive vignette for using spatialTIME can also be found at https://cran.r-project.org/web/packages/spatialTIME/index.html. iTIME is implemented within a R Shiny application and can be accessed online (http://itime.moffitt.org/), with code available on GitHub (https://github.com/FridleyLab/iTIME).

Supplementary information

Supplementary data are available at Bioinformatics online.

Acute Palliative Physical Therapy Services for a Patient With Metastatic Rectal Cancer and Subsequent Spinal Cord Compression

Colorectal cancer is the third most common cause of cancer-related deaths with approximately 40%-50% of people diagnosed experiencing subsequent metastases. Surgery is the only curative treatment for colorectal cancer, although chemotherapy and radiation are often used neoadjuvantly or adjuvantly to decrease recurrence rates and improve survival. Many individuals experience adverse effects and physical impairments secondary to extensive medical treatment. Therefore, the purpose of this case is to signify the important role of physical therapy in the continuum of care of a patient diagnosed with metastatic rectal cancer and subsequent spinal cord compression. The patient was a 70-year-old male admitted to the hospital for lower extremity (LE) numbness and weakness secondary to metastatic rectal cancer. Seventeen months prior to hospitalization, he was diagnosed with rectal cancer and underwent neoadjuvant chemotherapy and radiation followed by laparoscopic abdominoperineal resection with posterior prostatectomy en bloc with a colostomy. Adjuvant chemotherapy included FOLFIRI. While hospitalized, the patient experienced spinal cord compression secondary to metastasis and elected decompressive laminectomy with discectomy for palliation. Due to the poor prognosis of metastatic rectal cancer, the patient’s functional mobility and independence declined throughout hospitalization. The patient was able to achieve one of two personal goals; he was able to tolerate sitting in an upright position for his daughter’s wedding but unfortunately did not return home prior to expiration. Although the patient suffered eventual mortality, consistent physical therapy allowed him to achieve a major life goal, serving as an important motivator and improved quality of life (QoL) even in end-of-life conditions. Unfortunately, physical therapy services are often overlooked and under-utilized in patients with terminal conditions receiving palliative care, despite the growing body of literature supporting the benefits. By utilizing rehabilitation in reverse as well as skilled maintenance, physical therapy assists in maintaining mobility and achieving personal goals of individuals with terminal cancer, thus improving QoL even with a poor prognosis.

Impact of the HOP-UP-PT program on older adults at risk to fall: a randomized controlled trial

Background

Reduced falls and fall risks have been observed among older adults referred to the HOP-UP-PT (Home-based Older Persons Upstreaming Prevention-Physical Therapy) program. The purpose of this study was to describe outcomes of HOP-UP-PT program participants and then to compare these outcomes to non-participants.

Methods

Six Michigan senior centers referred adults ≥65 years who were at-risk for functional decline or falls. 144 participants (n = 72 per group) were randomized to either the experimental group (EG) or the control group (CG). Physical therapists (PTs) delivered physical, environmental, and health interventions to the EG over nine encounters (six in-person, three telerehabilitation) spanning seven months. The CG participants were told to continue their usual physical activity routines during the same time frame. Baseline and re-assessments were conducted at 0-, 3-, and 7-months in both groups. Descriptions and comparisons from each assessment encounter were analyzed.

Results

Participants ages were: EG = 76.6 (7.0) years and CG = 77.2 (8.2). Baseline measures were not significantly different apart from the Short Physical Performance Battery (SPPB) which favored the EG (P = 0.02). While no significant differences were identified in the survey outcomes or home environment assessments, significant differences in favor of the EG were identified in common fall risk indicators including the Timed Up and Go (P = 0.04), Four Test Balance Scale (P = 0.01), and the modified SPPB (P = 0.02) at the 3-month assessment visit. However, these differences were not sustained at the 7-month assessment as, notably, both groups demonstrated positive improvements in the Four Test Balance Score and SPPB. For individuals at a moderate/high fall risk at baseline, 47.8% of CG reported falling at seven months; whereas, only 6.3% of EG participants meeting the same criteria reported a fall after HOP-UP-PT participation.

Conclusions

A prevention-focused multimodal program provided by PTs in older adults’ homes proved beneficial and those with the highest fall risk demonstrated a significant decrease in falls. A collaboration between PTs and community senior centers resulted in upstreaming care delivery that may reduce both the financial and personal burdens associated with falls in an older adult population.

Trial registration

This study was retrospective registered at Clinical Trials.gov, TRN: NCT04814459 on 24/03/2021.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12877-021-02450-0.

Quantum Simulation of the Bosonic Creutz Ladder with a Parametric Cavity

There has been a growing interest in realizing quantum simulators for physical systems where perturbative methods are ineffective. The scalability and flexibility of circuit quantum electrodynamics make it a promising platform for implementing various types of simulators, including lattice models of strongly coupled field theories. Here, we use a multimode superconducting parametric cavity as a hardware-efficient analog quantum simulator, realizing a lattice in synthetic dimensions with complex hopping interactions. The coupling graph, i.e., the realized model, can be programmed in situ. The complex-valued hopping interaction further allows us to simulate, for instance, gauge potentials and topological models. As a demonstration, we simulate a plaquette of the bosonic Creutz ladder. We characterize the lattice with scattering measurements, reconstructing the experimental Hamiltonian and observing important precursors of topological features including nonreciprocal transport and Aharonov-Bohm caging. This platform can be easily extended to larger lattices and different models involving other interactions.

Fenchel duality of Cox partial likelihood with an application in survival kernel learning

The Cox proportional hazard model is one of the most widely used methods in modeling time-to-event data in the health sciences. Due to the simplicity of the Cox partial likelihood function, many machine learning algorithms use it for survival data. However, due to the nature of censored data, the optimization problem becomes intractable when more complicated regularization is employed, which is necessary when dealing with high dimensional omic data. In this paper, we show that a convex conjugate function of the Cox loss function based on Fenchel duality exists, and provide an alternative framework to optimization based on the primal form. Furthermore, the dual form suggests an efficient algorithm for solving the kernel learning problem with censored survival outcomes. We illustrate performance and properties of the derived duality form of Cox partial likelihood loss in multiple kernel learning problems with simulated and the Skin Cutaneous Melanoma TCGA datasets.

Perceptions of Rehabilitation Managers on Implementation of the Home-Based Older Person Upstreaming Prevention (HOP-UP) Program: A Retrospective Qualitative Analysis

Introduction

The purpose of this study was to identify themes and concepts derived from responses of physical therapy clinical leaders related to implementing a prevention-focused, home-based older-adult program known as HOP-UP-PT (Home-Based Older Person Upstreaming Prevention Physical Therapy) into their clinical operations.

Methods

Following Institutional Review Board approval, a retrospective qualitative analysis of transcribed interviews obtained by six undergraduate students participating in the Oakland University Ideas to Business Program (I2B) was conducted. Students interviewed nine local physical therapy clinical managers throughout Michigan using 12 questions developed by content experts. Questions aimed to ascertain the perceived opportunities and barriers to implementing HOP-UP-PT into each respondent's practice setting, clinic demographics, and suggested price point of a prevention-focused continuing education. Interview data was analyzed using the constant comparative method to identify themes and concepts.

Results

Sixty-seven percent of respondents (n=6) reported practicing in an outpatient setting; 56% of respondents (n=5) indicated 50% or more of their clients were 65 years and older; and 67% of respondents (n=6) suggested a price point of $200-$500 for an eight-hour HOP-UP-PT training course. Three concepts (community involvement and partnership, administrative barriers to an innovative delivery model, and foundational physical therapy [PT] skills utilized in a novel approach) and eight themes (community altruism, referral source expansion, integrated community relationships, current payment methodology challenges, favorability of clinic setting and type, minimal additional training required, willingness to pay for certification training, and prevention-focused or upstream mindset) were identified.

Conclusion

Physical therapy clinical managers identified a willingness to expand current rehabilitation models and incorporate prevention-focused care delivery into the existing care delivery approach. However, barriers and opportunities must be addressed in advance of a program roll-out to achieve optimal outcomes and cost savings within the healthcare system.

Wide and deep learning for automatic cell type identification

Cell type classification is an important problem in cancer research, especially with the advent of single cell technologies. Correctly identifying cells within the tumor microenvironment can provide oncologists with a snapshot of how a patient’s immune system reacts to the tumor. Wide and deep learning (WDL) is an approach to construct a cell-classification prediction model that can learn patterns within high-dimensional data (deep) and ensure that biologically relevant features (wide) remain in the final model. In this paper, we demonstrate that regularization can prevent overfitting and adding a wide component to a neural network can result in a model with better predictive performance. In particular, we observed that a combination of dropout and ℓ2 regularization can lead to a validation loss function that does not depend on the number of training iterations and does not experience a significant decrease in prediction accuracy compared to models with ℓ1, dropout, or no regularization. Additionally, we show WDL can have superior classification accuracy when the training and testing of a model are completed data on that arise from the same cancer type but different platforms. More specifically, WDL compared to traditional deep learning models can substantially increase the overall cell type prediction accuracy (36.5 to 86.9%) and T cell subtypes (CD4: 2.4 to 59.1%, and CD8: 19.5 to 96.1%) when the models were trained using melanoma data obtained from the 10X platform and tested on basal cell carcinoma data obtained using SMART-seq. WDL obtains higher accuracy when compared to state-of-the-art cell classification algorithms CHETAH (70.36%) and SingleR (70.59%).

Ontogeny Related Changes in the Pediatric Liver Metabolome

Background: A major challenge in implementing personalized medicine in pediatrics is identifying appropriate drug dosages for children. The majority of drug dosing studies have been based on adult populations, often with modification of the dosing for children based on size and weight. However, the growth and development experienced by children between birth and adulthood represents a dynamically changing biological system, with implications for effective drug dosing, efficacy as well as potential drug toxicity. The purpose of this study was to apply a metabolomics approach to gain preliminary insights into the ontogeny of liver function from newborn to adolescent. Methods: Metabolites were measured in 98 post-mortem pediatric liver samples in two experiments 3 batches of samples, allowing for both technical and biological validation. After extensive quality control, imputation and normalization, non-parametric tests were used to determine which metabolite levels differ between the four age groups (AG) ranging in age from newborn to adolescent (AG1-children <1 year; AG2-children with age between 1 and 6 years; AG3-children with age between 6 and 12 years; AG4-children with age between 12 and 18 years). To identify which metabolites had different concentration levels among the age groups, Kruskal-Wallis and Spearman correlation tests were conducted. Pathway analysis utilized the Gamma Method. Correction for multiple testing was completed using Bonferroni correction. Results: We found 41 metabolites (out of 884) that were biologically validated, and of those 25 were technically replicated, of which 24 were known metabolites. For the majority of these 24 metabolites, concentration levels were significantly lower in newborns than in the other age groups, many of which were long chain fatty acids or involved in pyrimidine or purine metabolism. Additionally, we found two KEGG pathways enriched for association with age: betaine metabolism and alpha linolenic acid and linoleic acid metabolism. Conclusions: Understanding the role that ontogeny of childhood liver plays may aid in determining better drug dosing algorithms for children.

Development and Feasibility of a Prehabilitation Protocol for Patients Diagnosed with Head and Neck Cancer

Background: Head and neck (H&N) cancers account for 4% of total cancers diagnosed. However, quality of life (QoL) implications are more severe for this patient population due to the complexity, extent, and deformities resulting from treatment interventions. Principally debilitating complications include diminished functional walking capacity, reduced cervical range of motion (ROM), and scapular strength. An extensive literature search revealed a paucity of evidence utilizing physical therapy assessment and intervention for this population. The purpose of this study was to describe the development and clinical feasibility of a prehabilitation program aimed to thwart these complications for patients diagnosed with H&N cancer. 

Methods: Inclusion criteria: male or female, 18+ years, speak and read the English language, ambulate independently, diagnosed with H&N cancer, and scheduled for surgical intervention. Institutional Review Board approval was obtained. Pre- and post-surgical measurements included the six-minute walk test (6MWT), cervical ROM, manual muscle testing for scapular strength, and three questionnaires: physical activity history, health behaviors questionnaire, and the Functional Assessment Cancer Therapy H&N QoL survey. 

Results: Three participants were enrolled (two males and one female) all identifying as Caucasian and between 60-90 years of age. Pre- to post-cervical ROM demonstrated decline in extension/bilateral rotation for two of three participants. Two participants demonstrated decreased 6MWT distance while one increased. No participants experienced any adverse effects of the prehabilitation program. 

Conclusion: This is the first study protocol to describe a physical therapist-administered H&N cancer prehabilitation program. Professionally administered education and exercise has potential to prevent, manage, and mitigate the adverse effects of cancer treatment. Additional research is needed to define the importance of prehabilitation relative to improved clinical outcomes and improved QoL. Patients with a cancer diagnosis are susceptible to impairments and functional limitations as a result of treatments and this prehabilitation program demonstrates potential to positively impact outcomes across the survivorship continuum. Due to their education and integration within the medical system, physical therapists are well-positioned to lead the effort to unify theory and clearly define parameters for oncology prehabilitation.

Tripartite Genuine Non-Gaussian Entanglement in Three-Mode Spontaneous Parametric Down-Conversion

We show that the states generated by a three-mode spontaneous parametric down-conversion (SPDC) interaction Hamiltonian possess tripartite entanglement of a different nature to other paradigmatic three-mode entangled states generated by the combination of two-mode SPDC interactions. While two-mode SPDC generates Gaussian states whose entanglement can be characterized by standard criteria based on two-mode quantum correlations, these criteria fail to capture the entanglement generated by three-mode SPDC. We use criteria built from three-mode correlation functions to show that the class of states recently generated in a superconducting-circuit implementation of three-mode SPDC ideally have tripartite entanglement, contrary to recent claims in the literature. These criteria are suitable for triple SPDC but we show that they fail to detect tripartite entanglement in other states which are known to possess it, which illustrates the existence of two fundamentally different notions of tripartite entanglement in three-mode continuous-variable systems.

Rehabilitation for Rhabdomyolysis Associated With Breast Cancer Treatment

Rhabdomyolysis can result in pain, physical limitations and may require hospitalization for medical management; however, little evidence has been reported on the efficacy of physical therapy (PT) interventions for this condition. Additionally, a review of literature on occurrences of rhabdomyolysis associated with cancer treatments yielded limited results. The purpose of this case report was to describe the acute and inpatient rehabilitation (IPR) examination, interventions, and outcomes for a patient with breast cancer and rhabdomyolysis. The patient was a 57-year-old female with a history of recurrent breast cancer who presented to the hospital with a chief complaint of bilateral thigh pain and weakness after the second cycle of chemotherapy and was diagnosed with rhabdomyolysis. After initially declining PT treatment during her first hospitalization, the patient was readmitted after a fall at home. She was hospitalized for 14 days with a transfer to IPR. The patient received a total of 12 days of PT (two acute care visits and 10 IPR visits) that included patient education, neuromuscular re-education, therapeutic exercise, and gait training. The patient was discharged home at a modified independent level with improvements in pain from 8/10 to 0/10 on the Numeric Pain Rating Scale. Functionally, she improved from ambulating 20 feet (6.1 m) to 600 feet (183 m); her Timed Up and Go score improved from 62 seconds to 10 seconds. Finally, her Berg Balance Scale improved from 31/56 to 55/56. Data from this case study suggest that PT management appears to improve functional outcomes for individuals diagnosed with rhabdomyolysis while undergoing chemotherapy, however, a holistic approach was necessary for progress to educate her on the importance of participation in PT with this condition. Further research is required to explore factors that influence rhabdomyolysis in the presence of chemotherapy as well as the recommended rehabilitation program for rhabdomyolysis.

Physical therapists in integrated palliative care: a qualitative study

OBJECTIVES

The purpose of this study was to explore the perceptions and experiences of physical therapists (PTs) regarding their role in palliative care (PC) when practising in nations with advanced integration of PC into mainstream healthcare.

METHODS

This qualitative study included an electronic demographic survey and semistructured interview. Data analysis included descriptive statistics for demographics and the constant comparative method for interview results.

RESULTS

Thirteen PTs from eight nations identified four categories of roles and responsibilities: (1) working with patients and families, (2) being an interdisciplinary team (IDT) member, (3) professional responsibilities beyond direct patient care and (4) factors influencing the role of PTs in PC. Concepts identified were shifting priorities (increased family involvement, emphasis on psychosocial aspects and differences in care philosophy), care across the continuum (accommodating changes in patient status, increasing awareness of PTs' role in varying disease states and working with the IDT) and changing perceptions about PT in PC (perceptions of PTs/others regarding PTs' role in PC and professional responsibilities of the PT in PC).

CONCLUSIONS

Based on participant responses, a previously published conceptual framework by Wilson et al in 2017 was updated and included an increased emphasis on patient wishes and dignity, treating breathlessness, patient advocacy within their family and use of technology and networking. Within PC, PTs play a key role on the IDT and can improve quality of life; however, multiple barriers exist to providing PT care within PC. Further advocacy is needed from PTs and professional organisations to integrate these services.

Rehabilitation Decision-making for Lower Extremity Sarcoma with Undiagnosed Metastases: A Case Report

This case report describes the physical therapy management and clinical decision-making for a 67-year-old female patient with an initial left-hip sarcoma which subsequently metastasized. The patient had significant physical pain and emotional distress after her surgery and radiation. The patient presented to physical therapy (PT) with left hip pain and pain in the left flank and left shoulder. These issues were significantly affecting her quality of life and activities of daily living. She had undergone a previous bout of outpatient PT that did not resolve her pain. A thorough PT evaluation was completed and conservative management of the patient’s pain was initiated but she did not experience sustainable pain relief. Later it was discovered that the patient had developed spinal metastatic lesions and the pain was likely caused by a pathological fracture that was not identified upon physical examination or previous imaging. Based on this, the physical therapist chose to conduct physical therapy due to the increasing pain, and then referred her back to the physician for further evaluation of imaging results and reevaluation of the patient’s symptoms. The initial diagnosis and metastatic spread of the sarcoma had a significant negative influence on the patient’s quality of life and participation in her activities of daily living. When working with any patient with a history of cancer, metastatic disease should remain high on the differential diagnosis list and should be a focus of any new unexplained pain.

Multiple-kernel learning for genomic data mining and prediction

BACKGROUND

Advances in medical technology have allowed for customized prognosis, diagnosis, and treatment regimens that utilize multiple heterogeneous data sources. Multiple kernel learning (MKL) is well suited for the integration of multiple high throughput data sources. MKL remains to be under-utilized by genomic researchers partly due to the lack of unified guidelines for its use, and benchmark genomic datasets.

RESULTS

We provide three implementations of MKL in R. These methods are applied to simulated data to illustrate that MKL can select appropriate models. We also apply MKL to combine clinical information with miRNA gene expression data of ovarian cancer study into a single analysis. Lastly, we show that MKL can identify gene sets that are known to play a role in the prognostic prediction of 15 cancer types using gene expression data from The Cancer Genome Atlas, as well as, identify new gene sets for the future research.

CONCLUSION

Multiple kernel learning coupled with modern optimization techniques provides a promising learning tool for building predictive models based on multi-source genomic data. MKL also provides an automated scheme for kernel prioritization and parameter tuning. The methods used in the paper are implemented as an R package called RMKL package, which is freely available for download through CRAN at https://CRAN.R-project.org/package=RMKL .

Managing Palliative Patients in Inpatient Rehabilitation Through a Short Stay Family Training Program

STUDY DESIGN

Retrospective Analysis of a Quality Improvement Program.

PURPOSE

To describe the development, implementation, and outcomes of an inpatient rehabilitation-based Short Stay Family Training (SSFT) program for patients with life-limiting conditions.

BACKGROUND

Patients with terminal illnesses often have functional limitations that prohibit discharge home after hospitalization, but their condition limits their ability to participate in rehabilitation in an inpatient setting.

METHODS AND MEASURES

After a needs assessment, an interdisciplinary team developed an SSFT program to empower patients, caregivers, and family members by giving them the tools to be independent in caring for a patient with a life-limiting condition. Patients qualifying for the program were tracked in terms of acute care physical therapy and occupational therapy discharge recommendations, diagnosis, inpatient rehabilitation unit length of stay (LoS), caregiver involvement, and discharge location. Data were retrospectively analyzed from patients over the first 16 months.

RESULTS

Since program implementation, 30 patients and their family members participated in the program. Overall, these patients experienced decreased LoS, increased discharge to home, and increased palliative care involvement in the plan of care.

CONCLUSION

Short Stay Family Training is a viable alternative to traditional inpatient rehabilitation to allow patients with life-limiting conditions to discharge home safely with caregiver support.

Prospective Surveillance Screenings to Identify Physical Therapy Needs During Breast Cancer Diagnosis and Surviviorship: A Case Report

Breast cancer and its treatments can cause detrimental effects to function and quality of life (QoL). These patients do not conventionally receive physical therapy services until impairments and functional limitations have become extensive. Emerging treatment models advocate for early rehabilitation screenings and proactive interventions, which are termed prospective surveillance. The purpose of this case report was to describe two prospective surveillance screenings at initial diagnosis and survivorship and subsequent physical therapy episodes of care for a patient with breast cancer. A 39-year-old female was diagnosed with invasive ductal carcinoma of the right breast. Approximately three months after the initial diagnosis, the patient had a right nipple-sparing mastectomy and immediate reconstruction with an expander. In addition, one lymph node was removed and underwent a biopsy, which was negative for metastases. The patient was screened by a physical therapist after her initial cancer diagnosis at the breast multidisciplinary clinic. This was after her mastectomy with an expander; the therapist recommended an episode of outpatient physical therapy due to impairments in pain, fatigue, loss of range of motion, weakness, and limitations in performance of her activities of daily living. The patient was seen initially for five visits. She underwent her final reconstructive surgery one month after discharge from physical therapy. Six months after her final reconstructive surgery, she was screened by the same physical therapist in the cancer survivorship clinic. Once again, therapy was recommended due to pain as well as deficits to her range of motion, strength, and functional status. The second episode of care lasted 14 visits and the patient showed improvements in pain, range of motion, shoulder strength and gains in the patient-specific functional scale and upper extremity functional index. This case reflects the importance of prospective surveillance screenings to overall patient outcomes. This patient may not have otherwise received physical therapy and its associated benefits without the prospective screenings by the physical therapist.

Clinical Outcomes After Physical Therapy Treatment for Secondary Lymphedema After Breast Cancer

Breast cancer is the most commonly diagnosed cancer in women and approximately 33% of survivors will develop lymphedema. Untreated lymphedema may be limb threatening or cause substantial functional limitations. The purpose of this case report is to detail the physical therapy (PT) management and outcomes for a patient with right upper extremity and breast lymphedema. The goal of this case report is to provide rehabilitation clinicians with an example of effective treatment management and the underlying treatment rationale. A 64-year-old female with stage 2A breast cancer underwent neoadjuvant chemotherapy, a lumpectomy with 18 lymph nodes removed, and radiation therapy. She subsequently developed secondary lymphedema of the right breast and upper extremity. Physical therapy interventions included instruction on a complete decongestive therapy program, which consists of manual lymphatic drainage and compression bandaging and exercises to improve shoulder range of motion (ROM), posture, and strength. As a result of PT, her right shoulder ROM and anthropometric measurements improved and the patient achieved independence with self-lymphatic massage and compression bandaging techniques to maintain these gains. This case report is unique as it details the clinical decision making required during a complex course of cancer care that necessitated adjustments to the PT plan of care for sustainable outcomes.

Probing the strongly driven spin-boson model in a superconducting quantum circuit

Quantum two-level systems interacting with the surroundings are ubiquitous in nature. The interaction suppresses quantum coherence and forces the system towards a steady state. Such dissipative processes are captured by the paradigmatic spin-boson model, describing a two-state particle, the “spin”, interacting with an environment formed by harmonic oscillators. A fundamental question to date is to what extent intense coherent driving impacts a strongly dissipative system. Here we investigate experimentally and theoretically a superconducting qubit strongly coupled to an electromagnetic environment and subjected to a coherent drive. This setup realizes the driven Ohmic spin-boson model. We show that the drive reinforces environmental suppression of quantum coherence, and that a coherent-to-incoherent transition can be achieved by tuning the drive amplitude. An out-of-equilibrium detailed balance relation is demonstrated. These results advance fundamental understanding of open quantum systems and bear potential for the design of entangled light-matter states.

Two-level systems interacting with a bosonic environment appear everywhere in physics. Here, the authors use a superconducting device to study this spin-boson model in the presence of coherent driving, showing that the drive enhances dissipation into the environment and can localize or delocalize the system.

Implementation and Preliminary Analysis of FACT-G Quality of Life Questionnaire within an Oncology Survivorship Clinic

Purpose: To conduct a descriptive analysis of the results from the Functional Assessment of Cancer Therapy-General (FACT-G) quality of life (QOL) questionnaire, describe the outcomes from the FACT-G to drive treatment recommendations within the breast survivorship clinic and to quantify the severity of QOL issues experienced.

Methods: A retrospective analysis utilizing medical records of participants in a breast cancer survivorship clinic. Measurement data included demographics and FACT-G results. Descriptive analysis of demographics and trends in referral recommendations and FACT-G scores was completed.

Results: All 30 participants were females diagnosed with breast cancer of various stages, ages 28 to 81 years. Approximately 1.5 years elapsed between cancer diagnosis and completion of the FACT-G. Participants received surgery (100%), radiation (76%), and chemotherapy and/or hormonal therapy (43%). Results demonstrated that participants reported having a lack of energy (24%) and were bothered by side effects of their treatment (20%). The greatest impact on functional well-being was difficulty sleeping (50%).

Limitations: Decreased ability to generalize the data to breast cancer survivors due to small sample size from one institution and potential referral bias.

Conclusions: Cancer survivors experience QOL issues throughout the continuum of their care, which can result in long-term effects on their physical, functional, social and emotional well-being. QOL is a major focus for cancer survivors and many times determines a survivor’s healthcare decisions. QOL measurements can be utilized at multiple points during survivorship to identify the need for referrals and to guide interventions.

Quantum heat engine with coupled superconducting resonators

We propose a quantum heat engine composed of two superconducting transmission line resonators interacting with each other via an optomechanical-like coupling. One resonator is periodically excited by a thermal pump. The incoherently driven resonator induces coherent oscillations in the other one due to the coupling. A limit cycle, indicating finite power output, emerges in the thermodynamical phase space. The system implements an all-electrical analog of a photonic piston. Instead of mechanical motion, the power output is obtained as a coherent electrical charging in our case. We explore the differences between the quantum and classical descriptions of our system by solving the quantum master equation and classical Langevin equations. Specifically, we calculate the mean number of excitations, second-order coherence, as well as the entropy, temperature, power, and mean energy to reveal the signatures of quantum behavior in the statistical and thermodynamic properties of the system. We find evidence of a quantum enhancement in the power output of the engine at low temperatures.

Cerebellar Stroke Occupational Therapy and Physical Therapy Management from Intensive Care Unit to Outpatient: A Case Report

Cerebellar stroke increases the risk of extensive physical disability and long-term institutionalization. The purpose of this case report is to describe the 14-month longitudinal rehabilitation management and outcomes from the intensive care unit, inpatient rehabilitation unit and outpatient care of a patient after cerebellar stroke. A goal of this case report is to provide rehabilitation clinicians with a long-term perspective and understanding of the course of recovery for a patient after cerebellar cerebrovascular accident or related injury. A 51-year-old healthy athletic female experienced acute bilateral cerebellar infarcts with subsequent craniotomy to remove infarcted areas. The patient had postoperative hemorrhages and hydrocephalus and was deemed to have a poor prognosis. Multimodal sensory stimulation and early mobility was performed until conventional neuromuscular reeducation interventions could be tolerated. Primary deficits included decreased proximal strength, whole body ataxia, vertical diplopia, dysphagia, difficulty communicating, and emotional lability. Fourteen months after the initial infarcts, the patient was able to reside in her own home with her husband, ambulate, and stand with assistance and perform most activities of daily living with standby or set-up assistance. This patient made significant progress toward safety and mobility and was able to return home despite the early discussion about a poor prognosis and a palliative care consultation. The complex, intensive course of rehabilitation elicited slow, steady, consistent gains. The patient’s motivation and family involvement likely facilitated optimum outcomes.

Introducing a novel mechanism to control heart rate in the ancestral Pacific hagfish

Although neural modulation of heart rate is well established among chordate animals, the Pacific hagfish (Eptatretus stoutii) lacks any cardiac innervation, yet it can increase its heart rate from the steady, depressed heart rate seen in prolonged anoxia to almost double its normal normoxic heart rate, an almost fourfold overall change during the 1-h recovery from anoxia. The present study sought mechanistic explanations for these regulatory changes in heart rate. We provide evidence for a bicarbonate-activated, soluble adenylyl cyclase (sAC)-dependent mechanism to control heart rate, a mechanism never previously implicated in chordate cardiac control.

The Role of Physical Therapists Within Hospice and Palliative Care in the United States and Canada

Purpose:

Little is known regarding the extent to which physical therapy is integrated into Hospice and Palliative Care (HPC). The purpose of this study was to describe perceptions of physical therapists (PTs) regarding their role within HPC or working with patients having life-threatening illnesses and to develop a conceptual framework depicting a PTs role within HPC and factors affecting it.

Participants:

Ten PTs, 5 from the United States and 5 from Canada, with at least 5 years of physical therapy experience and 5 years working experience with patients having life-threatening illnesses or in HPC.

Methods:

Demographic data were collected by electronic questionnaire. A semistructured interview was conducted with each participant to investigate their perceptions about the role of PTs in HPC.

Data Analysis:

Interview results were analyzed for trends between participants, practice settings, regions, and other sociocultural aspects. The constant comparative method of qualitative data analysis was used to identify similarities and differences and to develop themes and concepts relative to the role of PT in HPC.

Results:

Participants identified their 3 primary roles in HPC: providing patient/family care, serving as an interdisciplinary team member, and fulfilling professional responsibilities outside of direct patient care. They described factors within and outside direct patient care which influenced their roles. Concepts included shifting priorities, care across the continuum, and changing perceptions of PTs within HPC.

Clinical Relevance:

This study described perceptions of the role of PTs within HPC that may be utilized when coordinating future strategies to appropriately promote and expand the role.

Quantum nondemolition detection of a propagating microwave photon

The ability to nondestructively detect the presence of a single, traveling photon has been a long-standing goal in optics, with applications in quantum information and measurement. Realizing such a detector is complicated by the fact that photon-photon interactions are typically very weak. At microwave frequencies, very strong effective photon-photon interactions in a waveguide have recently been demonstrated. Here we show how this type of interaction can be used to realize a quantum nondemolition measurement of a single propagating microwave photon. The scheme we propose uses a chain of solid-state three-level systems (transmons) cascaded through circulators which suppress photon backscattering. Our theoretical analysis shows that microwave-photon detection with fidelity around 90% can be realized with existing technologies.

Utilization of a 5-Meter Walk Test in Evaluating Self-selected Gait Speed during Preoperative Screening of Patients Scheduled for Cardiac Surgery

PURPOSE

The 5-Meter Walk Test (5MWT) has been recommended for use by the Society of Thoracic Surgeons as an outcome measure in the Adult Cardiac Surgery Database to predict frailty in individuals who are candidates for cardiac surgery. However, there are no published reports of performance on this test in the literature. Therefore, the purpose of this study was to provide descriptive analysis of the 5MWT for individuals who were candidates for cardiac surgery.

METHODS

Retrospective analysis of 113 preoperative cardiac surgery candidates who underwent a 5MWT. Gait speed calculated from the test was completed as part of preoperative testing administered by physical therapists. Three trials were performed with up to a one minute rest between trials. Differences by trial, gender, use of assistive device, and gait or postural deviations were determined using t-tests.

RESULTS

Mean gait speed was 1.05 (SD 0.26) m/s for the subjects. There was a statistically significant increase in gait speed from trial 1 to trial 3 by 0.05 (0.08) m/s (p < 0.0001). There were no significant differences in gait speed between males and females. Participants using assistive devices displayed a significantly slower mean gait speed of 0.70 (0.27) than those who walked unaided, with a mean gait speed of 1.08 (0.24) m/s (p < 0.0001). Participants with noted gait or postural deviations also walked significantly slower (mean 0.84, SD 0.22) than those without deviations (mean 1.15, SD 0.21) (p < 0.0001).

CONCLUSIONS

Subjects displayed a slight increase in speed from trial 1 to trial 3, reinforcing a cited benefit of the shorter distance of the 5MWT that may limit fatigue. Although statistically significant, the increase in speed from trial 1 to 3 may not be clinically significant in relation to the intent of the test. Significantly slower gait speeds were noted when a subject had an observable gait or postural deviation or used an assistive device.

Phylogeny and effects of anoxia on hyperpolarization-activated cyclic nucleotide-gated channel gene expression in the heart of a primitive chordate, the Pacific hagfish (Eptatretus stoutii)

The aneural heart of the Pacific hagfish, Eptatretus stoutii, varies heart rate fourfold during recovery from anoxia. Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, which play an important role in establishing the pacemaker rate of vertebrate hearts, were postulated to be present in this ancestral vertebrate heart, and it was also theorized that changes in hagfish heart rate with oxygen availability involved altered HCN expression. Partial gene cloning revealed six HCN isoforms in the hagfish heart. Hagfish representatives of HCN2, HCN3 and HCN4 were discovered, with HCN2 and HCN3 existing as isoforms designated as HCN2a, HCN2b, HCN3a, two paralogs of HCN3b, and HCN3c. Phylogenetic analysis revealed HCN3b and HCN3c to be ancestral, followed by HCN3a, HCN4 and HCN2. Moreover, HCN3a expression was dominant in both the atrial and ventricular chambers, suggesting that the HCN4 dominance in adult mammalian hearts appeared after hagfish divergence. HCN expression was higher in the atrium than in the ventricle, as might be expected given that atrial beating rate is known to be faster than the ventricular rate. In addition, mRNA expression under normoxic conditions was compared with that following 24 h of anoxia, and either a 2-h or 36-h recovery in normoxic water. In the ventricle, anoxia decreased HCN3a but not HCN4 expression. In contrast, atrial HCN3a expression significantly increased following 2 h of recovery, before returning to control levels following 36 h of recovery, possibly contributing to heart rate changes previously observed under these conditions.