IntelligentPooling: Practical Thompson Sampling for mHealth.
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ABSTRACT:
SUBMITTER: Tomkins S
PROVIDER: S-EPMC8494236 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Over the last five years, virtual screening of ultralarge synthesis on-demand libraries has emerged as a powerful tool for hit identification in drug discovery programs. As these libraries have grown to tens of billions of molecules, we have reached a point where it is no longer cost-effective to screen every molecule virtually. To address these challenges, several groups have developed heuristic search methods to rapidly identify the best molecules on a virtual screen. This article describes the application of Thompson sampling (TS), an active learning approach that streamlines the virtual screening of large combinatorial libraries by performing a probabilistic search in the reagent space, thereby never requiring the full enumeration of the library. TS is a general technique that can be applied to various virtual screening modalities, including 2D and 3D similarity search, docking, and application of machine-learning models. In an illustrative example, we show that TS can identify more than half of the top 100 molecules from a docking-based virtual screen of 335 million molecules by evaluating 1% of the data set.
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Project description:Population pharmacokinetic (PK) data collected from routine clinical practice offers a rich source of valuable information. However, in observational population PK data, accurate time information for blood samples is often missing, resulting in measurement errors (ME) in the sampling time variable. The goal of this study was to investigate the effects on model parameters when a scheduled time is used instead of the actual blood sampling time, and to propose ME correction methods.Simulation studies were conducted based on two major factors: the curvature in PK profiles and the size of ME. As ME correction methods, transform both sides (TBS) models were developed with application of Box-Cox power transformation and Taylor expansion. The TBS models were compared to a conventional population PK model using simulations.The most important determinant of bias due to time ME was the degree of curvature (nonlinearity) in PK profiles; the smaller the curvature around sampling times, the smaller the associated bias. The second important determinant was the magnitude of ME; the larger the ME, the larger the bias. The proposed TBS models performed better than a conventional population PK modeling when curvature and ME were substantial.Time ME in sampling time can lead to bias on the parameter estimators. The following practical recommendations are provided: 1) when the curvature of PK profiles is small, conventional population PK modeling is robust to even large ME; and 2) when the curvature is moderate or large, the proposed methodology reduces bias in parameter estimates.
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Project description:Epilepsy is a chronic disorder characterized by recurring seizures, and results from excessive, synchronized discharge in populations of cells. Epilepsy affects 1% of the population and results from a variety of CNS insults. Traumatic physical brain injury causes 4% of cases. Posttraumatic epilepsy (PTE) is characterized by a delay of weeks to years between the trauma and the first seizures. Proper prophylactic intervention during this incubation time might prevent PTE. Many PTE patients are resistant to anticonvulsant medications and suffer from negative side effects. Better knowledge of the cell biology underlying injury-induced epileptogenesis should lead to better therapeutic strategies for interrupting the events occurring between the injury and the development of epilepsy. The aim of my experiments is to identify cellular factors underlying PTE using an in vitro model system to study two key aspects of brain injury in isolation: deafferentation and axonal transection. My aim is to perform a non-biased comparison of the expression of genes in area CA1, and separately in area CA3, in unlesioned cultures and in cultures lesioned 1, 3 and 7 days earlier. Changes in gene expression due to neuronal denervation will be apparent in area CA1, whereas changes in expression due to axonal transection will be apparent in area CA3. In performing these experiments, I hope to gain insight into the molecular underpinnings of the electrophysiological and immunocytochemical effects that we have already detected, as well as to generate new hypotheses that we can test further using our own expertise and techniques. We use cultured slices of rat hippocampus to study the effects of brain injury. Our model is to lesion the Schaffer collateral projection pathway between areas CA1 and CA3, producing a selective injury of the axons of CA3 cells and selective denervation of CA1 cells. Our preliminary electrophysiological and immunocytochemical data indicate that axonal sprouting is triggered in area CA3 and that the dendritic excitability is increased in CA1 pyramidal cells. Both effects occur only after about 7 days, suggesting they are mediated by changes in gene expression. My hypothesis is that the expression of numerous genes changes after Schaffer collateral transection. I predict that neurotrophins and their receptors change in area CA3 to trigger axonal sprouting, along with genes for proteins mediated axonal extension, and that changes in the expression of genes for glutamate receptors and voltage-dependent ion channels occur in area CA1 to account for their increased excitability. Hippocampal slice cultures prepared from male Sprague-Dawley rats at PN day 6. Slices will be maintained in vitro for 14 days in serum-containing medium. Cultures will then be examined and unhealthy cultures discarded. Remaining sister cultures will be divided into two groups: cultures to be lesioned and cultures remaining unlesioned. Lesioned cultures will have a sterile transection of the Schaffer collateral pathway using a razor blade shard. All cultures then returned to the incubator. At various times , cultures will be removed from the incubator. Individual cultures will be soaked in RNAlater buffer(Ambion), and a razor blade shard will be used to subdissect the CA3 and CA1 segments. Segments are sucked up with a sterile pipette-tip containing RNAlater buffer and transferred into a sterile tube. Total RNA will be prepared by homogenization in TRIzol reagent (GibcoBRL) and precipitation in isopropyl alcohol. Rneasy Kit (Qiagen) will further isolate RNA. Spectrographic analysis of RNA prepared indicates 260nm:280nm ratios above 1.6, and insignificant amounts of either degraded RNA or DNA contaminants detected on a 2% denaturing gel. We have found that it is necessary to pool 15 CA3 or CA1 segments to obtain 5+ ug of total RNA. Total RNA samples will be sent to the consortium for additional quality control, labeling, hybridizations using the Affymetrix Neuro U34 chip, scanning, and preliminary analyses. The gene array data will then be compared in several pairwise manners (lesion vs. age matched control and region vs. region, for each time point), as well as time sequence comparisons for gene expression in each region. Keywords: time-course
2006-06-09 | GSE5034 | GEO
Project description:BackgroundThe COVID-19 pandemic has become a global public health event, which has raised concerns regarding individuals' health. Individuals need to cope with the COVID-19 pandemic with guidelines on symptom recognition, home isolation, and maintain mental health. Besides routine use of mobile health (mHealth) such as accessing information to keep healthy, individuals can use mHealth services in situations requiring urgent medical care, which is defined as mHealth emergency use. It is not known whether individuals have increased their daily mHealth services emergency use as a result of disruptions caused by the COVID-19 pandemic.ObjectiveThe purpose of this diary analysis study is to assess the influences of daily disruptions related to the COVID-19 pandemic on individuals' mHealth emergency use. The secondary purpose of this study is to explore the mediating role of COVID-19-induced strain and the moderating role of promotion regulatory focus in the relationship between daily disruptions of COVID-19 and mHealth emergency use. Drawing from the cognitive activation theory of stress, we investigated the underlying mechanism and boundary condition of the influence of COVID-19-related disruptions on daily mHealth emergency use.MethodsTo test the proposed model, this study adopts the experience sampling method to collect daily data. The experience sampling method helps researchers to capture participants' fluctuations in emotions, mental engagement in an activity, and experienced stress. This study collected 550 cases nested in 110 samples in mainland China to test the conceptual model. In addition, we employed hierarchical linear modeling analysis to test the effect of COVID-19-related disruptions on mHealth emergency use.ResultsWe found that COVID-19-related disruptions increased COVID-19-induced strain (γ=0.24, P<.001) and mHealth emergency use on a daily basis (γ=0.28, P<.001). COVID-19-induced daily strain mediated this relationship (effect=0.09, 95% CI 0.05-0.14). Promotion regulatory focus moderated the relationship between COVID-19-induced strain and mHealth emergency use (γ=0.35, P=.02). In addition, the indirect relationship between disruptions and mHealth emergency use intentions through COVID-19-induced strain is contingent upon promotion regulatory focus: this relationship was stronger in those with high promotion regulatory focus (effect=0.12, 95% CI 0.06-0.19) than in those with low promotion regulatory focus (effect=0.06, 95% CI 0.02-0.11).ConclusionsEvent disruption of the COVID-19 pandemic induced mHealth emergency use intention through increased psychological strain. Furthermore, individuals' promotion regulatory focus amplified this indirect relationship. Our findings extend our understanding of the factors underlying mHealth emergency use intention and illustrate the potential contingent role of promotion regulatory focus in the cognitive activation theory of stress. This study also opens avenues for future research on mHealth emergency use intention in other countries and cultural settings.
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Project description:The choice of the best sampling strategy to capture mean values of functional traits for a species/population, while maintaining information about traits' variability and minimizing the sampling size and effort, is an open issue in functional trait ecology. Intraspecific variability (ITV) of functional traits strongly influences sampling size and effort. However, while adequate information is available about intraspecific variability between individuals (ITVBI) and among populations (ITVPOP), relatively few studies have analyzed intraspecific variability within individuals (ITVWI). Here, we provide an analysis of ITVWI of two foliar traits, namely specific leaf area (SLA) and osmotic potential (?), in a population of Quercus ilex L. We assessed the baseline ITVWI level of variation between the two traits and provided the minimum and optimal sampling size in order to take into account ITVWI, comparing sampling optimization outputs with those previously proposed in the literature. Different factors accounted for different amount of variance of the two traits. SLA variance was mostly spread within individuals (43.4% of the total variance), while ? variance was mainly spread between individuals (43.2%). Strategies that did not account for all the canopy strata produced mean values not representative of the sampled population. The minimum size to adequately capture the studied functional traits corresponded to 5 leaves taken randomly from 5 individuals, while the most accurate and feasible sampling size was 4 leaves taken randomly from 10 individuals. We demonstrate that the spatial structure of the canopy could significantly affect traits variability. Moreover, different strategies for different traits could be implemented during sampling surveys. We partially confirm sampling sizes previously proposed in the recent literature and encourage future analysis involving different traits.
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Project description:BackgroundRoutine Outcome Monitoring (ROM) should provide a dynamic, within-treatment forward feedback loop to guide individual treatment decisions across diagnostic categories. It has been suggested that the Experience Sampling Method (ESM), capturing the film of daily life adaptive processes, offers a flexible, personalised and transdiagnostic feedback system for monitoring and adapting treatment strategies. This is the first study that uses an ESM application (the PsyMate™) as a routine mobile-ROM (mROM) tool in an ambulatory mental health setting.ObjectiveTo demonstrate adequate psychometric properties of the PsyMate™ app assessing both symptom severity levels as well as daily life functioning.MethodIn a transdiagnostic sample of 64 outpatients, an mROM protocol (ESM for 6 days, at 10 semi-random moments a day) and a standard ROM instrument (HADS) were administered at baseline and at three-month follow-up. We measured positive affect (PA), negative affect (NA), quality of sleep, positive social interaction, activity-related stress, tiredness, and feeling unwell.ResultsSubjects completed 53% of the measurements at baseline (N = 64) and 48% at follow-up (N = 29). Factor analysis and subsequent reliability analysis of PA and NA confirmed the two constructs. Significant and meaningful correlations were found between PA, NA and HADS scores (ranging from r = .4 to r = .7). Multilevel analyses yielded significant change scores for all measures.ConclusionThe ESM-based, transdiagnostic mROM tool can be used reliably in clinical settings: it shows adequate psychometric properties, as well as concurrent validity and sensitivity to change over time with respect to relevant ROM constructs. Person-tailored items can be added. In addition, mROM offers added value over standard symptom-based ROM, as it provides information on adaptive functioning in the daily environment of patients.
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