Centralized Interactive Phenomics Resource: an integrated online phenomics knowledgebase for health data users.

OBJECTIVE: Development of clinical phenotypes from electronic health records (EHRs) can be resource intensive. Several phenotype libraries have been created to facilitate reuse of definitions. However, these platforms vary in target audience and utility. We describe the development of the Centralized Interactive Phenomics Resource (CIPHER) knowledgebase, a comprehensive public-facing phenotype library, which aims to facilitate clinical and health services research. MATERIALS AND METHODS: The platform was designed to collect and catalog EHR-based computable phenotype algorithms from any healthcare system, scale metadata management, facilitate phenotype discovery, and allow for integration of tools and user workflows. Phenomics experts were engaged in the development and testing of the site. RESULTS: The knowledgebase stores phenotype metadata using the CIPHER standard, and definitions are accessible through complex searching. Phenotypes are contributed to the knowledgebase via webform, allowing metadata validation. Data visualization tools linking to the knowledgebase enhance user interaction with content and accelerate phenotype development. DISCUSSION: The CIPHER knowledgebase was developed in the largest healthcare system in the United States and piloted with external partners. The design of the CIPHER website supports a variety of front-end tools and features to facilitate phenotype development and reuse. Health data users are encouraged to contribute their algorithms to the knowledgebase for wider dissemination to the research community, and to use the platform as a springboard for phenotyping. CONCLUSION: CIPHER is a public resource for all health data users available at https://phenomics.va.ornl.gov/ which facilitates phenotype reuse, development, and dissemination of phenotyping knowledge.

A semi-supervised approach to unobtrusively predict abnormality in breathing patterns using hydraulic bed sensor data in older adults aging in place.

Shortness of breath is often considered a repercussion of aging in older adults, as respiratory illnesses like COPD1 or respiratory illnesses due to heart-related issues are often misdiagnosed, under-diagnosed or ignored at early stages. Continuous health monitoring using ambient sensors has the potential to ameliorate this problem for older adults at aging-in-place facilities. In this paper, we leverage continuous respiratory health data collected by using ambient hydraulic bed sensors installed in the apartments of older adults in aging-in-place Americare facilities to find data-adaptive indicators related to shortness of breath. We used unlabeled data collected unobtrusively over the span of three years from a COPD-diagnosed individual and used data mining to label the data. These labeled data are then used to train a predictive model to make future predictions in older adults related to shortness of breath abnormality. To pick the continuous changes in respiratory health we make predictions for shorter time windows (60-s). Hence, to summarize each day's predictions we propose an abnormal breathing index (ABI) in this paper. To showcase the trajectory of the shortness of breath abnormality over time (in terms of days), we also propose trend analysis on the ABI quarterly and incrementally. We have evaluated six individual cases retrospectively to highlight the potential and use cases of our approach.

Cardiovascular sex-differences: insights via physiology-based modeling and potential for noninvasive sensing via ballistocardiography.

In this study, anatomical and functional differences between men and women in their cardiovascular systems and how these differences manifest in blood circulation are theoretically and experimentally investigated. A validated mathematical model of the cardiovascular system is used as a virtual laboratory to simulate and compare multiple scenarios where parameters associated with sex differences are varied. Cardiovascular model parameters related with women's faster heart rate, stronger ventricular contractility, and smaller blood vessels are used as inputs to quantify the impact (i) on the distribution of blood volume through the cardiovascular system, (ii) on the cardiovascular indexes describing the coupling between ventricles and arteries, and (iii) on the ballistocardiogram (BCG) signal. The model-predicted outputs are found to be consistent with published clinical data. Model simulations suggest that the balance between the contractile function of the left ventricle and the load opposed by the arterial circulation attains similar levels in females and males, but is achieved through different combinations of factors. Additionally, we examine the potential of using the BCG waveform, which is directly related to cardiovascular volumes, as a noninvasive method for monitoring cardiovascular function. Our findings provide valuable insights into the underlying mechanisms of cardiovascular sex differences and may help facilitate the development of effective noninvasive cardiovascular monitoring methods for early diagnosis and prevention of cardiovascular disease in both women and men.

Diversity and Scale: Genetic Architecture of 2,068 Traits in the VA Million Veteran Program.

Genome-wide association studies (GWAS) have underrepresented individuals from non-European populations, impeding progress in characterizing the genetic architecture and consequences of health and disease traits. To address this, we present a population-stratified phenome-wide GWAS followed by a multi-population meta-analysis for 2,068 traits derived from electronic health records of 635,969 participants in the Million Veteran Program (MVP), a longitudinal cohort study of diverse U.S. Veterans genetically similar to the respective African (121,177), Admixed American (59,048), East Asian (6,702), and European (449,042) superpopulations defined by the 1000 Genomes Project. We identified 38,270 independent variants associating with one or more traits at experiment-wide P<4.6×10-11 significance; fine-mapping 6,318 signals identified from 613 traits to single-variant resolution. Among these, a third (2,069) of the associations were found only among participants genetically similar to non-European reference populations, demonstrating the importance of expanding diversity in genetic studies. Our work provides a comprehensive atlas of phenome-wide genetic associations for future studies dissecting the architecture of complex traits in diverse populations.

Flight of the bumble bee: Buzzes predict pollination services.

Multiple interacting factors drive recent declines in wild and managed bees, threatening their pollination services. Widespread and intensive monitoring could lead to more effective management of wild and managed bees. However, tracking their dynamic populations is costly. We tested the effectiveness of an inexpensive, noninvasive and passive acoustic survey technique for monitoring bumble bee behavior and pollination services. First, we assessed the relationship between the first harmonic of the flight buzz (characteristic frequency) and pollinator functional traits that influence pollination success using flight cage experiments and a literature search. We analyzed passive acoustic survey data from three locations on Pennsylvania Mountain, Colorado to estimate bumble bee activity. We developed an algorithm based on Computational Auditory Scene Analysis that identified and quantified the number of buzzes recorded in each location. We then compared visual and acoustic estimates of bumble bee activity. Using pollinator exclusion experiments, we tested the power of buzz density to predict pollination services at the landscape scale for two bumble bee pollinated alpine forbs (Trifolium dasyphyllum and T. parryi). We found that the characteristic frequency was correlated with traits known to affect pollination efficacy, explaining 30-52% of variation in body size and tongue length. Buzz density was highly correlated with visual estimates of bumble bee density (r = 0.97), indicating that acoustic signals are predictive of bumble bee activity. Buzz density predicted seed set in two alpine forbs when bumble bees were permitted access to the flowers, but not when they were excluded from visiting. Our results indicate that acoustic signatures of flight can be deciphered to monitor bee activity and pollination services to bumble bee pollinated plants. We propose that applications of this technique could assist scientists and farmers in rapidly detecting and responding to bee population declines.

Affective meanings of 1,469 Bengali concepts.

This article provides semantic differential ratings of 1,469 concepts in Bengali, a language spoken by about 250 million individuals in eastern India and Bangladesh. These data were collected from 20 male and 20 female Calcutta respondents who rated stimuli on three culturally universal affective dimensions: evaluation-potency-activity (EPA). This study employs pan-respondent component analyses as a means of examining the respondents' usage of the standard EPA scales. The pan-respondent component analyses indicate that some respondents used the rating scales in unexpected ways, recording their feelings about one component of concepts' EPA with ratings on a scale intended to measure a different dimension. When scores were based only on respondents who used the scales appropriately, several interesting patterns were found. For respondents of both genders, potency scores have a curvilinear relation with evaluation, such that very good and very bad concepts are mostly seen as very potent, whereas evaluatively neutral concepts are seen as somewhat impotent or just slightly potent. A moderate linear correlation exists between activity and evaluation, and a modest positive relation exists between potency and activity. Gender correlations are high on evaluation, .93, but much lower for potency scores, with a correlation of .55, and even lower for activity, .30. In this article we examine several explanations for why scales denoting potency and activity were reinterpreted as indicating goodness by certain respondents, and consider the matter of including data collected from respondents who used scales in this way.

Heartbeat detection from a hydraulic bed sensor using a clustering approach.

Encouraged by previous performance of a hydraulic bed sensor, this work presents a new hydraulic transducer configuration which improves the system's ability to capture a heartbeat signal from four subjects with different body weight and height, gender, age and cardiac history. It also proposes a new approach for detecting the occurrence of heartbeats from ballistocardiogram (BCG) signals through the use of the k-means clustering algorithm, based on finding the location of the J-peaks. Preliminary testing showed that the new transducer arrangement was able to capture the occurrence of heartbeats for all the participants, and the clustering approach achieved correct heartbeat detection ranging from 98.6 to 100% for three of them. Some considerations are discussed regarding adjustments that can be done in order to increase the correct detection of heartbeats for the participant whose percentage of correct detection ranged from 71.0 to 92.5%.

Refinement and evaluation of a hydraulic bed sensor.

Research indicates that long-term monitoring of vital signs and activity in elderly adults may provide opportunities for maintaining quality-of-life and extending independence into later years. Such a strategy requires development of a system to collect this data while imposing minimal intrusion into the lives of those being monitored. To further this goal, we have developed a hydraulic bed sensor to non-invasively monitor heartbeat and respiration during sleep. This paper describes the refinement of our developed prototype and signal processing methods, along with an evaluation of the robustness of our algorithms and results from testing. An evaluation of our sensor on a group of five diverse subjects (ranging in age from 24 to 67, two with cardiac history), in three different positions, demonstrates accuracy within 8 beats per minute up to 97.5% of the time.

Monitoring pulse and respiration with a non-invasive hydraulic bed sensor.

A hydraulic bed sensor has been developed to non-invasively monitor pulse and respiration during sleep. This sensor is designed for in-home use, to be part of an integrated sensor network for the early detection of illness and functional decline in elderly adults. Experience with another bed sensor has motivated a desire to acquire enhanced, quantitative data related to pulse and respiration. This paper describes a working prototype, the signal processing methods used to extract data from the constructed transducer, and results from preliminary testing.