An exploratory decision tree analysis to predict physical activity compliance rates in breast cancer survivors.

Background: The study of physical activity in cancer survivors has been limited to one cause, one effect relationships. In this exploratory study, we used recursive partitioning to examine multiple correlates that influence physical activity compliance rates in cancer survivors. Methods: African American breast cancer survivors (N = 267, Mean age = 54 years) participated in an online survey that examined correlates of physical activity. Recursive partitioning (RP) was used to examine complex and nonlinear associations between sociodemographic, medical, cancer-related, theoretical, and quality of life indicators. Results: Recursive partitioning revealed five distinct groups. Compliance with physical activity guidelines was highest (82% met guidelines) among survivors who reported higher mean action planning scores (P < 0.001) and lower mean barriers to physical activity (P = 0.035). Compliance with physical activity guidelines was lowest (9% met guidelines) among survivors who reported lower mean action and coping (P = 0.002) planning scores. Similarly, lower mean action planning scores and poor advanced lower functioning (P = 0.034), even in the context of higher coping planning scores, resulted in low physical activity compliance rates (13% met guidelines). Subsequent analyses revealed that body mass index (P = 0.019) and number of comorbidities (P = 0.003) were lowest in those with the highest compliance rates. Conclusion: Our findings support the notion that multiple factors determine physical activity compliance rates in African American breast cancer survivors. Interventions that encourage action and coping planning and reduce barriers in the context of addressing function limitations may increase physical activity compliance rates.

A novel method for imaging the pharmacological effects of antibiotic treatment on Clostridium difficile.

Clostridium difficile is a significant cause of nosocomial-acquired infection that results in severe diarrhea and can lead to mortality. Treatment options for C. difficile infection (CDI) are limited, however, new antibiotics are being developed. Current methods for determining efficacy of experimental antibiotics on C. difficile involve antibiotic killing rates and do not give insight into the drug's pharmacologic effects. Considering this, we hypothesized that by using scanning electron microscopy (SEM) in tandem to drug killing curves, we would be able to determine efficacy and visualize the phenotypic response to drug treatment. To test this hypothesis, supraMIC kill curves were conducted using vancomycin, metronidazole, fidaxomicin, and ridinilazole. Following collection, cells were either plated or imaged using a scanning electron microscope (SEM). Consistent with previous reports, we found that the tested antibiotics had significant bactericidal activity at supraMIC concentrations. By SEM imaging and using a semi-automatic pipeline for image analysis, we were able to determine that vancomycin and to a lesser extent fidaxomicin and ridinilazole significantly affected the cell wall, whereas metronidazole, fidaxomicin, and ridinilazole had significant effects on cell length suggesting a metabolic effect. While the phenotypic response to drug treatment has not been documented previously in this manner, the results observed are consistent with the drug's mechanism of action. These techniques demonstrate the versatility and reliability of imaging and measurements that could be applied to other experimental compounds. We believe the strategies laid out here are vital for characterizing new antibiotics in development for treating CDI.

What Complexity Science Predicts About the Potential of Artificial Intelligence/Machine Learning to Improve Primary Care.

Primary care physicians are likely both excited and apprehensive at the prospects for artificial intelligence (AI) and machine learning (ML). Complexity science may provide insight into which AI/ML applications will most likely affect primary care in the future. AI/ML has successfully diagnosed some diseases from digital images, helped with administrative tasks such as writing notes in the electronic record by converting voice to text, and organized information from multiple sources within a health care system. AI/ML has less successfully recommended treatments for patients with complicated single diseases such as cancer; or improved diagnosing, patient shared decision making, and treating patients with multiple comorbidities and social determinant challenges. AI/ML has magnified disparities in health equity, and almost nothing is known of the effect of AI/ML on primary care physician-patient relationships. An intervention in Victoria, Australia showed promise where an AI/ML tool was used only as an adjunct to complex medical decision making. Putting these findings in a complex adaptive system framework, AI/ML tools will likely work when its tasks are limited in scope, have clean data that are mostly linear and deterministic, and fit well into existing workflows. AI/ML has rarely improved comprehensive care, especially in primary care settings, where data have a significant number of errors and inconsistencies. Primary care should be intimately involved in AI/ML development, and its tools carefully tested before implementation; and unlike electronic health records, not just assumed that AI/ML tools will improve primary care work life, quality, safety, and person-centered clinical decision making.

Artificial intelligence research strategy of the United States: critical assessment and policy recommendations.

The foundations of Artificial Intelligence (AI), a field whose applications are of great use and concern for society, can be traced back to the early years of the second half of the 20th century. Since then, the field has seen increased research output and funding cycles followed by setbacks. The new millennium has seen unprecedented interest in AI progress and expectations with significant financial investments from the public and private sectors. However, the continual acceleration of AI capabilities and real-world applications is not guaranteed. Mainly, accountability of AI systems in the context of the interplay between AI and the broader society is essential for adopting AI systems via the trust placed in them. Continual progress in AI research and development (R&D) can help tackle humanity's most significant challenges to improve social good. The authors of this paper suggest that the careful design of forward-looking research policies serves a crucial function in avoiding potential future setbacks in AI research, development, and use. The United States (US) has kept its leading role in R&D, mainly shaping the global trends in the field. Accordingly, this paper presents a critical assessment of the US National AI R&D Strategic Plan and prescribes six recommendations to improve future research strategies in the US and around the globe.

Factors Contributing to SARS-CoV-2 Vaccine Hesitancy of Hispanic Population in Rio Grande Valley.

Hispanic communities have been disproportionately affected by economic disparities. These inequalities have put Hispanics at an increased risk for preventable health conditions. In addition, the CDC reports Hispanics to have 1.5× COVID-19 infection rates and low vaccination rates. This study aims to identify the driving factors for COVID-19 vaccine hesitancy of Hispanic survey participants in the Rio Grande Valley. Our analysis used machine learning methods to identify significant associations between medical, economic, and social factors impacting the uptake and willingness to receive the COVID-19 vaccine. A combination of three classification methods (i.e., logistic regression, decision trees, and support vector machines) was used to classify observations based on the value of the targeted responses received and extract a robust subset of factors. Our analysis revealed different medical, economic, and social associations that correlate to other target population groups (i.e., males and females). According to the analysis performed on males, the Matthews correlation coefficient (MCC) value was 0.972. An MCC score of 0.805 was achieved by analyzing females, while the analysis of males and females achieved 0.797. Specifically, several medical, economic factors, and sociodemographic characteristics are more prevalent in vaccine-hesitant groups, such as asthma, hypertension, mental health problems, financial strain due to COVID-19, gender, lack of health insurance plans, and limited test availability.

Advancing primary care with Artificial Intelligence and Machine Learning.

Primary care is the largest healthcare delivery platform in the US. Facing the Artificial Intelligence and Machine Learning technology (AI/ML) revolution, the primary care community would benefit from a roadmap revealing priority areas and opportunities for developing and integrating AI/ML-driven clinical tools. This article presents a framework that identifies five domains for AI/ML integration in primary care to support care delivery transformation and achieve the Quintuple Aims of the healthcare system. We concluded that primary care plays a critical role in developing, introducing, implementing, and monitoring AI/ML tools in healthcare and must not be overlooked as AI/ML transforms healthcare.

Automated pipeline for atlas-based annotation of gene expression patterns: application to postnatal day 7 mouse brain.

Massive amounts of image data have been collected and continue to be generated for representing cellular gene expression throughout the mouse brain. Critical to exploiting this key effort of the post-genomic era is the ability to place these data into a common spatial reference that enables rapid interactive queries, analysis, data sharing, and visualization. In this paper, we present a set of automated protocols for generating and annotating gene expression patterns suitable for the establishment of a database. The steps include imaging tissue slices, detecting cellular gene expression levels, spatial registration with an atlas, and textual annotation. Using high-throughput in situ hybridization to generate serial sets of tissues displaying gene expression, this process was applied toward the establishment of a database representing over 200 genes in the postnatal day 7 mouse brain. These data using this protocol are now well-suited for interactive comparisons, analysis, queries, and visualization.

EDGE20: A Cross Spectral Evaluation Dataset for Multiple Surveillance Problems.

Surveillance-related datasets that have been released in recent years focus only on one specific problem at a time (e.g., pedestrian detection, face detection, or face recognition), while most of them were collected using visible spectrum (VIS) cameras. Even though some cross-spectral datasets were presented in the past, they were acquired in a constrained setup, which limited the performance of methods for the aforementioned problems under a cross-spectral setting. This work introduces a new dataset, named EDGE19, that can be used in addressing the problems of pedestrian detection, face detection, and face recognition in images captured using trail cameras under the VIS and NIR spectra. Data acquisition was performed in an outdoor environment, during both day and night, under unconstrained acquisition conditions. The collection of images is accompanied by a rich set of annotations, consisting of person and facial bounding boxes, unique subject identifiers, and labels that characterize facial images as frontal, profile, or back faces. Moreover, the performance of several state-of-the-art methods was evaluated for each of the scenarios covered by our dataset. The baseline results we obtained highlight the difficulty of current methods in the tasks of cross-spectral pedestrian detection, face detection, and face recognition due to unconstrained conditions, including low resolution, pose variation, illumination variation, occlusions, and motion blur.

Denoising for 3-d photon-limited imaging data using nonseparable filterbanks.

In this paper, we present a novel frame-based denoising algorithm for photon-limited 3-D images. We first construct a new 3-D nonseparable filterbank by adding elements to an existing frame in a structurally stable way. In contrast with the traditional 3-D separable wavelet system, the new filterbank is capable of using edge information in multiple directions. We then propose a data-adaptive hysteresis thresholding algorithm based on this new 3-D nonseparable filterbank. In addition, we develop a new validation strategy for denoising of photon-limited images containing sparse structures, such as neurons (the structure of interest is less than 5% of total volume). The validation method, based on tubular neighborhoods around the structure, is used to determine the optimal threshold of the proposed denoising algorithm. We compare our method with other state-of-the-art methods and report very encouraging results on applications utilizing both synthetic and real data.

Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies.

A method for flexible fitting of molecular models into three-dimensional electron microscopy (3D-EM) reconstructions at a resolution range of 8-12 A is proposed. The approach uses the evolutionarily related structural variability existing among the protein domains of a given superfamily, according to structural databases such as CATH. A structural alignment of domains belonging to the superfamily, followed by a principal components analysis, is performed, and the first three principal components of the decomposition are explored. Using rigid body transformations for the secondary structure elements (SSEs) plus the cyclic coordinate descent algorithm to close the loops, stereochemically correct models are built for the structure to fit. All of the models are fitted into the 3D-EM map, and the best one is selected based on crosscorrelation measures. This work applies the method to both simulated and experimental data and shows that the flexible fitting was able to produce better results than rigid body fitting.

Image-based gating of intravascular ultrasound pullback sequences.

Intravascularultrasound (IVUS) sequences recorded in vivo are subject to a wide array of motion artifacts as the majority of these studies are performed within the coronary arteries of a beating heart. To eliminate these artifacts, an electrocardiogram (ECG) signal is typically used to gate (collect) those frames recorded at the points in time associated with a particular fraction of the cardiac cycle. However, this technique may be suboptimal for a number of reasons, among which is the difficulty of determining the optimal fraction at which to gate. This value is generally nonobvious. To circumvent this problem, we introduce a frame-gating method for IVUS pullbacks that mimics ECG (i.e., in the sense that it selects only one frame per cardiac cycle), but will automatically choose the fraction of the cycle that renders the most stable gated frame set. Stability here is gauged by measuring interframe similarity. Our method operates exclusively on the imagery data and does not require ECG or any form of image segmentation or other high-level image analysis. To validate our algorithm, we compare its behavior versus true ECG gating.

Machine Learning Outperforms ACC / AHA CVD Risk Calculator in MESA.

Background Studies have demonstrated that the current US guidelines based on American College of Cardiology/American Heart Association (ACC/AHA) Pooled Cohort Equations Risk Calculator may underestimate risk of atherosclerotic cardiovascular disease ( CVD ) in certain high-risk individuals, therefore missing opportunities for intensive therapy and preventing CVD events. Similarly, the guidelines may overestimate risk in low risk populations resulting in unnecessary statin therapy. We used Machine Learning ( ML ) to tackle this problem. Methods and Results We developed a ML Risk Calculator based on Support Vector Machines ( SVM s) using a 13-year follow up data set from MESA (the Multi-Ethnic Study of Atherosclerosis) of 6459 participants who were atherosclerotic CVD-free at baseline. We provided identical input to both risk calculators and compared their performance. We then used the FLEMENGHO study (the Flemish Study of Environment, Genes and Health Outcomes) to validate the model in an external cohort. ACC / AHA Risk Calculator, based on 7.5% 10-year risk threshold, recommended statin to 46.0%. Despite this high proportion, 23.8% of the 480 "Hard CVD " events occurred in those not recommended statin, resulting in sensitivity 0.76, specificity 0.56, and AUC 0.71. In contrast, ML Risk Calculator recommended only 11.4% to take statin, and only 14.4% of "Hard CVD " events occurred in those not recommended statin, resulting in sensitivity 0.86, specificity 0.95, and AUC 0.92. Similar results were found for prediction of "All CVD " events. Conclusions The ML Risk Calculator outperformed the ACC/AHA Risk Calculator by recommending less drug therapy, yet missing fewer events. Additional studies are underway to validate the ML model in other cohorts and to explore its ability in short-term CVD risk prediction.

Learning-based segmentation framework for tissue images containing gene expression data.

Associating specific gene activity with functional locations in the brain results in a greater understanding of the role of the gene. To perform such an association for the more than 20 000 genes in the mammalian genome, reliable automated methods that characterize the distribution of gene expression in relation to a standard anatomical model are required. In this paper, we propose a new automatic method that results in the segmentation of gene expression images into distinct anatomical regions in which the expression can be quantified and compared with other images. Our contribution is a novel hybrid atlas that utilizes a statistical shape model based on a subdivision mesh, texture differentiation at region boundaries, and features of anatomical landmarks to delineate boundaries of anatomical regions in gene expression images. This atlas, which provides a common coordinate system for internal brain data, is being used to create a searchable database of gene expression patterns in the adult mouse brain. Our framework annotates the images about four times faster and has achieved a median spatial overlap of up to 0.92 compared with expert segmentation in 64 images tested. This tool is intended to help scientists interpret large-scale gene expression patterns more efficiently.

Intraclass retrieval of nonrigid 3D objects: application to face recognition.

As the size of the available collections of 3D objects grows, database transactions become essential for their management with the key operation being retrieval (query). Large collections are also precategorized into classes so that a single class contains objects of the same type (e.g., human faces, cars, four-legged animals). It is shown that general object retrieval methods are inadequate for intraclass retrieval tasks. We advocate that such intraclass problems require a specialized method that can exploit the basic class characteristics in order to achieve higher accuracy. A novel 3D object retrieval method is presented which uses a parameterized annotated model of the shape of the class objects, incorporating its main characteristics. The annotated subdivision-based model is fitted onto objects of the class using a deformable model framework, converted to a geometry image and transformed into the wavelet domain. Object retrieval takes place in the wavelet domain. The method does not require user interaction, achieves high accuracy, is efficient for use with large databases, and is suitable for nonrigid object classes. We apply our method to the face recognition domain, one of the most challenging intraclass retrieval tasks. We used the Face Recognition Grand Challenge v2 database, yielding an average verification rate of 95.2 percent at 10-3 false accept rate. The latest results of our work can be found at http://www.cbl.uh.edu/UR8D/.

Three-dimensional face recognition in the presence of facial expressions: an annotated deformable model approach.

In this paper, we present the computational tools and a hardware prototype for 3D face recognition. Full automation is provided through the use of advanced multistage alignment algorithms, resilience to facial expressions by employing a deformable model framework, and invariance to 3D capture devices through suitable preprocessing steps. In addition, scalability in both time and space is achieved by converting 3D facial scans into compact metadata. We present our results on the largest known, and now publicly available, Face Recognition Grand Challenge 3D facial database consisting of several thousand scans. To the best of our knowledge, this is the highest performance reported on the FRGC v2 database for the 3D modality.

An Overview and Empirical Comparison of Distance Metric Learning Methods.

In this paper, we first offer an overview of advances in the field of distance metric learning. Then, we empirically compare selected methods using a common experimental protocol. The number of distance metric learning algorithms proposed keeps growing due to their effectiveness and wide application. However, existing surveys are either outdated or they focus only on a few methods. As a result, there is an increasing need to summarize the obtained knowledge in a concise, yet informative manner. Moreover, existing surveys do not conduct comprehensive experimental comparisons. On the other hand, individual distance metric learning papers compare the performance of the proposed approach with only a few related methods and under different settings. This highlights the need for an experimental evaluation using a common and challenging protocol. To this end, we conduct face verification experiments, as this task poses significant challenges due to varying conditions during data acquisition. In addition, face verification is a natural application for distance metric learning because the encountered challenge is to define a distance function that: 1) accurately expresses the notion of similarity for verification; 2) is robust to noisy data; 3) generalizes well to unseen subjects; and 4) scales well with the dimensionality and number of training samples. In particular, we utilize well-tested features to assess the performance of selected methods following the experimental protocol of the state-of-the-art database labeled faces in the wild. A summary of the results is presented along with a discussion of the insights obtained and lessons learned by employing the corresponding algorithms.

Automated left ventricular segmentation in cardiac MRI.

We present an automated left ventricular (LV) myocardial boundary extraction method. Automatic localization of the LV is achieved using a motion map and an expectation maximization algorithm. The myocardial region is then segmented using an intensity-based fuzzy affinity map and the myocardial contours are extracted by cost minimization through a dynamic programming approach. The results from the automated algorithm compared against the experienced radiologists using Bland and Altman analysis were found to have consistent mean bias of 7% and limits of agreement comparable to the inter-observer variability inherent in the manual method.

Image segmentation based on fuzzy connectedness using dynamic weights.

Traditional segmentation techniques do not quite meet the challenges posed by inherently fuzzy medical images. Image segmentation based on fuzzy connectedness addresses this problem by attempting to capture both closeness, based on characteristic intensity, and "hanging togetherness," based on intensity homogeneity, of image elements to the target object. This paper presents a modification and extension of previously published image segmentation algorithms based on fuzzy connectedness, which is computed as a linear combination of an object-feature-based and a homogeneity-based component using fixed weights. We provide a method, called fuzzy connectedness using dynamic weights (DyW), to introduce directional sensitivity to the homogeneity-based component and to dynamically adjust the linear weights in the functional form of fuzzy connectedness. Dynamic computation of the weights relieves the user of the exhaustive search process to find the best combination of weights suited to a particular application. This is critical in applications such as analysis of cardiac cine magnetic resonance (MR) images, where the optimal combination of affinity component weights can vary for each slice, each phase, and each subject, in spite of data being acquired from the same MR scanner with identical protocols. We present selected results of applying DyW to segment phantom images and actual MR, computed tomography, and infrared data. The accuracy of DyW is assessed by comparing it to two different formulations of fuzzy connectedness. Our method consistently achieves accuracy of more than 99.15% for a range of image complexities: contrast 5%-65%, noise-to-contrast ratio of 6%-18%, and bias field of four types with maximum gain factor of up to 10%.