Integrated transcriptome catalog of Tenualosa ilisha as a resource for gene discovery and expression profiling.

The silver pride of Bangladesh, migratory shad, Tenualosa ilisha (Hilsa), makes the highest contribution to the total fish production of Bangladesh. Despite its noteworthy contribution, a well-annotated transcriptome data is not available. Here we report a transcriptomic catalog of Hilsa, constructed by assembling RNA-Seq reads from different tissues of the fish including brain, gill, kidney, liver, and muscle. Hilsa fish were collected from different aquatic habitats (fresh, brackish, and sea water) and the sequencing was performed in the next generation sequencing (NGS) platform. De novo assembly of the sequences obtained from 46 cDNA libraries revealed 462,085 transcript isoforms that were subsequently annotated using the Universal Protein Resource Knowledgebase (UniPortKB) as a reference. Starting from the sampling to final annotation, all the steps along with the workflow are reported here. This study will provide a significant resource for ongoing and future research on Hilsa for transcriptome based expression profiling and identification of candidate genes.

Use of relevancy and complementary information for discriminatory gene selection from high-dimensional gene expression data.

With the advent of high-throughput technologies, life sciences are generating a huge amount of varied biomolecular data. Global gene expression profiles provide a snapshot of all the genes that are transcribed in a cell or in a tissue under a particular condition. The high-dimensionality of such gene expression data (i.e., very large number of features/genes analyzed with relatively much less number of samples) makes it difficult to identify the key genes (biomarkers) that are truly attributing to a particular phenotype or condition, (such as cancer), de novo. For identifying the key genes from gene expression data, among the existing literature, mutual information (MI) is one of the most successful criteria. However, the correction of MI for finite sample is not taken into account in this regard. It is also important to incorporate dynamic discretization of genes for more relevant gene selection, although this is not considered in the available methods. Besides, it is usually suggested in current studies to remove redundant genes which is particularly inappropriate for biological data, as a group of genes may connect to each other for downstreaming proteins. Thus, despite being redundant, it is needed to add the genes which provide additional useful information for the disease. Addressing these issues, we proposed Mutual information based Gene Selection method (MGS) for selecting informative genes. Moreover, to rank these selected genes, we extended MGS and propose two ranking methods on the selected genes, such as MGSf-based on frequency and MGSrf-based on Random Forest. The proposed method not only obtained better classification rates on gene expression datasets derived from different gene expression studies compared to recently reported methods but also detected the key genes relevant to pathways with a causal relationship to the disease, which indicate that it will also able to find the responsible genes for an unknown disease data.

puffMarker: A Multi-Sensor Approach for Pinpointing the Timing of First Lapse in Smoking Cessation.

Recent researches have demonstrated the feasibility of detecting smoking from wearable sensors, but their performance on real-life smoking lapse detection is unknown. In this paper, we propose a new model and evaluate its performance on 61 newly abstinent smokers for detecting a first lapse. We use two wearable sensors - breathing pattern from respiration and arm movements from 6-axis inertial sensors worn on wrists. In 10-fold cross-validation on 40 hours of training data from 6 daily smokers, our model achieves a recall rate of 96.9%, for a false positive rate of 1.1%. When our model is applied to 3 days of post-quit data from 32 lapsers, it correctly pinpoints the timing of first lapse in 28 participants. Only 2 false episodes are detected on 20 abstinent days of these participants. When tested on 84 abstinent days from 28 abstainers, the false episode per day is limited to 1/6.

Continuous in-the-field measurement of heart rate: Correlates of drug use, craving, stress, and mood in polydrug users.

BACKGROUND: Ambulatory physiological monitoring could clarify antecedents and consequences of drug use and could contribute to a sensor-triggered mobile intervention that automatically detects behaviorally risky situations. Our goal was to show that such monitoring is feasible and can produce meaningful data. METHODS: We assessed heart rate (HR) with AutoSense, a suite of biosensors that wirelessly transmits data to a smartphone, for up to 4 weeks in 40 polydrug users in opioid-agonist maintenance as they went about their daily lives. Participants also self-reported drug use, mood, and activities on electronic diaries. We compared HR with self-report using multilevel modeling (SAS Proc Mixed). RESULTS: Compliance with AutoSense was good; the data yield from the wireless electrocardiographs was 85.7%. HR was higher when participants reported cocaine use than when they reported heroin use (F(2,9)=250.3, p<.0001) and was also higher as a function of the dose of cocaine reported (F(1,8)=207.7, p<.0001). HR was higher when participants reported craving heroin (F(1,16)=230.9, p<.0001) or cocaine (F(1,14)=157.2, p<.0001) than when they reported of not craving. HR was lower (p<.05) in randomly prompted entries in which participants reported feeling relaxed, feeling happy, or watching TV, and was higher when they reported feeling stressed, being hassled, or walking. CONCLUSIONS: High-yield, high-quality heart-rate data can be obtained from drug users in their natural environment as they go about their daily lives, and the resultant data robustly reflect episodes of cocaine and heroin use and other mental and behavioral events of interest.

Identifying Drug (Cocaine) Intake Events from Acute Physiological Response in the Presence of Free-living Physical Activity.

A variety of health and behavioral states can potentially be inferred from physiological measurements that can now be collected in the natural free-living environment. The major challenge, however, is to develop computational models for automated detection of health events that can work reliably in the natural field environment. In this paper, we develop a physiologically-informed model to automatically detect drug (cocaine) use events in the free-living environment of participants from their electrocardiogram (ECG) measurements. The key to reliably detecting drug use events in the field is to incorporate the knowledge of autonomic nervous system (ANS) behavior in the model development so as to decompose the activation effect of cocaine from the natural recovery behavior of the parasympathetic nervous system (after an episode of physical activity). We collect 89 days of data from 9 active drug users in two residential lab environments and 922 days of data from 42 active drug users in the field environment, for a total of 11,283 hours. We develop a model that tracks the natural recovery by the parasympathetic nervous system and then estimates the dampening caused to the recovery by the activation of the sympathetic nervous system due to cocaine. We develop efficient methods to screen and clean the ECG time series data and extract candidate windows to assess for potential drug use. We then apply our model on the recovery segments from these windows. Our model achieves 100% true positive rate while keeping the false positive rate to 0.87/day over (9+ hours/day of) lab data and to 1.13/day over (11+ hours/day of) field data.

Are We There Yet? Feasibility of Continuous Stress Assessment via Wireless Physiological Sensors.

Stress can lead to headaches and fatigue, precipitate addictive behaviors (e.g., smoking, alcohol and drug use), and lead to cardiovascular diseases and cancer. Continuous assessment of stress from sensors can be used for timely delivery of a variety of interventions to reduce or avoid stress. We investigate the feasibility of continuous stress measurement via two field studies using wireless physiological sensors - a four-week study with illicit drug users (n = 40), and a one-week study with daily smokers and social drinkers (n = 30). We find that 11+ hours/day of usable data can be obtained in a 4-week study. Significant learning effect is observed after the first week and data yield is seen to be increasing over time even in the fourth week. We propose a framework to analyze sensor data yield and find that losses in wireless channel is negligible; the main hurdle in further improving data yield is the attachment constraint. We show the feasibility of measuring stress minutes preceding events of interest and observe the sensor-derived stress to be rising prior to self-reported stress and smoking events.

Assessing the Availability of Users to Engage in Just-in-Time Intervention in the Natural Environment.

Wearable wireless sensors for health monitoring are enabling the design and delivery of just-in-time interventions (JITI). Critical to the success of JITI is to time its delivery so that the user is available to be engaged. We take a first step in modeling users' availability by analyzing 2,064 hours of physiological sensor data and 2,717 self-reports collected from 30 participants in a week-long field study. We use delay in responding to a prompt to objectively measure availability. We compute 99 features and identify 30 as most discriminating to train a machine learning model for predicting availability. We find that location, affect, activity type, stress, time, and day of the week, play significant roles in predicting availability. We find that users are least available at work and during driving, and most available when walking outside. Our model finally achieves an accuracy of 74.7% in 10-fold cross-validation and 77.9% with leave-one-subject-out.