Analyzing the functional effects of DNA variants with gene editing.

Continual advancements in genomics have led to an ever-widening disparity between the rate of discovery of genetic variants and our current understanding of their functions and potential roles in disease. Systematic methods for phenotyping DNA variants are required to effectively translate genomics data into improved outcomes for patients with genetic diseases. To make the biggest impact, these approaches must be scalable and accurate, faithfully reflect disease biology, and define complex disease mechanisms. We compare current methods to analyze the function of variants in their endogenous DNA context using genome editing strategies, such as saturation genome editing, base editing and prime editing. We discuss how these technologies can be linked to high-content readouts to gain deep mechanistic insights into variant effects. Finally, we highlight key challenges that need to be addressed to bridge the genotype to phenotype gap, and ultimately improve the diagnosis and treatment of genetic diseases.

Evaluating the Acceptability and Feasibility of Collecting Passive Smartphone Data to Estimate Psychological Functioning in U.S. Service Members and Veterans: A Pilot Study.

INTRODUCTION: This study investigated the acceptability and feasibility of digital phenotyping in a military sample with a history of traumatic brain injury and co-occurring psychological and cognitive symptoms. The first aim was to evaluate the acceptability of digital phenotyping by (1a) quantifying the proportion of participants willing to download the app and rates of dropout and app discontinuation and (1b) reviewing the stated reasons for both refusing and discontinuing use of the app. The second aim was to investigate technical feasibility by (2a) characterizing the amount and frequency of transferred data and (2b) documenting technical challenges. Exploratory aim 3 sought to leverage data on phone and keyboard interactions to predict if a participant (a) is depressed and (b) has depression that improves over the course of the study. MATERIALS AND METHODS: A passive digital phenotyping app (Mindstrong Discovery) functioned in the background of the participants' smartphones and passively collected phone usage and typing kinematics data. RESULTS: Fifteen out of 16 participants (93.8%) consented to install the app on their personal smartphone devices. Four participants (26.7%) discontinued the use of the app partway through the study, primarily because of keyboard usability and technical issues. Fourteen out of 15 participants (93.3%) had at least one data transfer, and the median number of days with data was 40 out of a possible 57 days. The exploratory machine learning models predicting depression status and improvement in depression performed better than chance. CONCLUSIONS: The findings of this pilot study suggest that digital phenotyping is acceptable and feasible in a military sample and provides support for future larger investigations of this technology.

Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation.

Loss-of-function of DDX3X is a leading cause of neurodevelopmental disorders (NDD) in females. DDX3X is also a somatically mutated cancer driver gene proposed to have tumour promoting and suppressing effects. We perform saturation genome editing of DDX3X, testing in vitro the functional impact of 12,776 nucleotide variants. We identify 3432 functionally abnormal variants, in three distinct classes. We train a machine learning classifier to identify functionally abnormal variants of NDD-relevance. This classifier has at least 97% sensitivity and 99% specificity to detect variants pathogenic for NDD, substantially out-performing in silico predictors, and resolving up to 93% of variants of uncertain significance. Moreover, functionally-abnormal variants can account for almost all of the excess nonsynonymous DDX3X somatic mutations seen in DDX3X-driven cancers. Systematic maps of variant effects generated in experimentally tractable cell types have the potential to transform clinical interpretation of both germline and somatic disease-associated variation.

Suicidal Behaviors Among Active-Duty US Service Members: Data from the 2018 Health-Related Behaviors Survey.

Background: This study aimed to 1) determine the prevalence of past-year suicidal ideation (SI) and attempts (SA) among active-duty SMs; 2) determine whether differences exist by age, sex, and race; and 3) assess whether prevalence estimates vary by risk profiles of mental health conditions and substance use. Methods: Data were from the 2018 Health-Related Behavior Survey (HRBS), a cross-sectional survey of active-duty SMs (n = 17,166). We used the logistic model to identify the factors of SI and SA and latent class analysis (LCA) to identify the risk profiles. Results: Among active duty SMs, 8.26% had SI and 1.25% had SA in the past year. Gender and age have been shown to influence how race might contribute to suicidal behaviors. Mental health conditions were associated with higher odds of SI and SA, as were younger ages; LGB identity; being separated, divorced, or widowed; use of e-cigarettes, dual use of e-cigarettes and cigarettes, or drugs; and history of deployment of less than 12 months. Frequencies of cigarette and e-cigarette use were also associated with SI and SA, indicating the odds were increasing by 0.3% for every additional cigarette or e-cigarette used. Five risk profiles were identified: class 1 (illegal drug use), class 2 (mental health needs with tobacco and alcohol use), class 3 (mental health conditions only), class 4 ("low risk" SMs with low levels of illegal drug use, mental health visits, tobacco use, and alcohol use), and class 5 (alcohol use). Compared to class 4 ("low risk"), all other risk profiles were associated with increased odds of suicidal behaviors. Conclusion: Despite the resources and increased access provided for mental health support, the prevalence of SI among active-duty SMs is greater than in the general population of the same age, likely due to additional military exposures and stressors.

Pilot study of attentional retraining for postpartum smoking relapse.

Introduction: Tobacco smoking is a leading cause of preventable death worldwide. The perinatal period provides a unique opportunity for intervention, as many smokers quit smoking during pregnancy but relapse postpartum. Novel relapse prevention interventions that reduce the burden of treatment attendance in this population are needed. Attentional retraining (AR) has been shown to reduce attentional biases toward smoking-related stimuli, a cognitive process implicated in smoking, AR has not been applied to perinatal smokers, and the effect of AR on craving and smoking is not clear. The goal of this study was to evaluate the delivery of AR for smoking cues in perinatal smokers utilizing a mobile intervention. Methods: This pilot study utilized Ecological Momentary Assessment (EMA) methodology delivered on a mobile device to examine the relapse process and evaluate the utility of AR in former smokers attempting to remain abstinent postpartum. AR (or Control Training) was administered to abstinent smokers (N = 17) for up to 2 weeks both before and after delivery. Results: All 17 participants completed the study. There was evidence that AR reduced attentional bias in the AR group (vs. Controls). There was no evidence that AR reduced craving. An exploratory analysis revealed that there was no evidence that AR reduced smoking during the study period. Discussion: AR using EMA methodology via a mobile device is feasible in perinatal smokers. Further research using larger samples is required to evaluate the utility of mobile AR in reducing craving and smoking.

Searching for answers: expert pattern recognition and planning.

Does expertise mostly stem from pattern recognition or look-ahead search? van Opheusden et al. contribute to this important debate in cognitive psychology and artificial intelligence (AI) with a multi-method, multi-experiment study and a new model. Using a novel, relatively simple board game, they show that players increase depth of search when improving their skill.

Association between burnout and insomnia in U.S. Air Force Pararescue personnel: A cross-sectional study.

Studies have examined burnout and its impact on health, to include its influence on sleep. While many studies report a significant relationship between burnout and insomnia in civilian populations, no studies have examined this relationship in a military population. The United States Air Force (USAF) Pararescue personnel are an elite combat force who are specially trained to conduct both first-line combat and full spectrum personnel recovery and may be at high risk of burnout and insomnia. The current study investigated the association between dimensions of burnout and insomnia, and also examined potential moderators of the associations. A cross-sectional survey was administered to 203 Pararescue personnel (Mean Age = 32.1 years; 100% Male; 90.1% Caucasian) recruited from six US bases. The survey included measures of three dimensions of burnout (emotional exhaustion, depersonalization, personal achievement), insomnia, psychological flexibility, and social support. Emotional exhaustion was significantly associated with insomnia with a moderate to large effect size, when controlling for covariates. Depersonalization, but not personal achievement, was also significantly associated with insomnia. There was no evidence that associations between burnout and insomnia were moderated by psychological flexibility or social support. These findings help to identify individuals at risk of insomnia and may ultimately be useful in developing interventions for insomnia in this population.

Integrating cognitive bias modification for pain and opioid cues into medication for opioid use disorder clinical care: Feasibility, acceptability, and preliminary results.

BACKGROUND: Despite high co-occurrence, chronic pain is often unaddressed in treatment for opioid use disorder (OUD) and little is known about mechanisms that may underlie associations between pain and opioid use. Using an attentional bias (AB) task with both pain and opioid cues, we evaluated a cognitive bias modification (CBM) task administered during regularly scheduled medications for OUD (mOUD) dosing visits. The current study evaluated the feasibility, acceptability, and preliminary efficacy of the CBM task. Outcomes for AB tasks used traditional mean-based score and trial-level bias scores (TLBS). METHODS: In a double-blind, randomized controlled trial, 28 individuals with OUD and chronic pain engaged in mOUD were randomized to either CBM or an AB control condition and completed up to three tasks per week for four weeks. Standard AB task was completed at baseline and post-treatment. Participants completed feasibility and acceptability measures, and preliminary efficacy (i.e., change in AB) was assessed using ANOVA models. RESULTS: Participants attended 83.3% of scheduled sessions and generally reported the task was enjoyable, credible, and easy to complete. Preliminary results demonstrated a condition by time interaction highlighting a reduction in AB in the CBM group but not the control group in opioid TLBS variability (F[1,26]=5.01, p = .034) and pain TLBS towards (F[1,26]=6.42, p = .018) and pain TLBS variability (F[1,26]=5.24, p = .03). CONCLUSIONS: The current study supports integrating brief, computer-based tasks designed to reduce AB into mOUD clinical care. The preliminary results suggest that TLBS outcomes may be more sensitive to capture changes in AB; however, larger studies are required.

The impact of racially-targeted food marketing and attentional biases on consumption in Black adolescent females with and without obesity: Pilot data from the Black Adolescent & Entertainment (BAE) study.

Unhealthy food advertisements ("advertisements" hereafter referred to as "ads") are linked to poor diet and obesity, and food companies disproportionally target Black youth. Little is known about the mechanisms whereby food ads influence diet. One possibility may be racially-targeted ads that appeal to Black youth. Those with food-related attentional biases may be especially vulnerable. The objective of this project was to assess the feasibility and initial effects of a pilot study testing the influence of racially-targeted food ads and food-related attentional biases on eating behaviors among a sample of Black adolescent females. Feasibility of recruitment, retention, and procedures were examined. Participants (N = 41, 12-17y) were randomized to view a television episode clip of the Big Bang Theory embedded with either four 30-second racially-targeted food ads or neutral ads. A computer dot probe task assessed food-related attentional biases. The primary outcome was caloric consumption from a laboratory test meal. Interactions based on weight and ethnic identity were also examined. Analyses of variance and regressions were used to assess main and interaction effects. Exposure to racially-targeted food ads (versus neutral ads) did not affect energy consumption (p > .99). Although not statistically significant, adolescents with obesity consumed nearly 240 kcal more than non-overweight adolescents (p = 0.10). There were no significant preliminary effects related to food-related attentional biases or ethnic identity (ps = 0.22-0.79). Despite a non-significant interaction, these data provide preliminary support that adolescents with obesity may be particularly vulnerable to racially-targeted food ads. An adequately powered trial is necessary to further elucidate the associations among racially-targeted food ads among Black adolescent girls with obesity.

Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments.

MOTIVATION: CRISPR/Cas9-based technology allows for the functional analysis of genetic variants at single nucleotide resolution whilst maintaining genomic context. This approach, known as saturation genome editing (SGE), a form of deep mutational scanning, systematically alters each position in a target region to explore its function. SGE experiments require the design and synthesis of oligonucleotide variant libraries which are introduced into the genome. This technology is applicable to diverse fields such as disease variant identification, drug development, structure-function studies, synthetic biology, evolutionary genetics and host-pathogen interactions. Here, we present the Variant Library Annotation Tool (VaLiAnT) which can be used to generate variant libraries from user-defined genomic coordinates and standard input files. The software can accommodate user-specified species, reference sequences and transcript annotations. RESULTS: Coordinates for a genomic range are provided by the user to retrieve a corresponding oligonucleotide reference sequence. A user-specified range within this sequence is then subject to systematic, nucleotide and/or amino acid saturating mutator functions. VaLiAnT provides a novel way to retrieve, mutate and annotate genomic sequences for oligonucleotide library generation. Specific features for SGE library generation can be employed. In addition, VaLiAnT is configurable, allowing for cDNA and prime editing saturation library generation, with other diverse applications possible. AVAILABILITY AND IMPLEMENTATION: VaLiAnT is a command line tool written in Python. Source code, testing data, example input and output files and executables are available (https://github.com/cancerit/VaLiAnT) in addition to a detailed user manual (https://github.com/cancerit/VaLiAnT/wiki). VaLiAnT is licensed under AGPLv3. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Use of electronic cigarettes in the United States service member and Veteran populations: A narrative review (2019).

Electronic Nicotine Delivery Systems (ENDS) are an increasingly popular form of a nicotine delivery device, particularly among young adults and adolescents. The health consequences of long-term ENDS use are not known. Two populations that warrant special consideration are members of the United States Military (service members) and US Veterans. In this narrative review of literature before December 2019, research on ENDS use in these two populations is described in relation to four themes relevant to ENDS use: Prevalence of ENDS use; perceptions of ENDS; correlates of ENDS use; and use of ENDS for smoking cessation. This narrative review summarized research findings in each of these four areas and identified areas for future research.

Naturalistic measurement of dual cue attentional bias in moderate to heavy-drinking smokers: A preliminary investigation.

INTRODUCTION: Although cigarettes and alcohol are frequently used together, few studies have evaluated evidence of attentional bias to both smoking and alcohol cues. Attentional bias (AB) is defined as preferential attention to drug-specific cues and is most often studied in a laboratory with one cue type. AB may be an important mechanism associated with cigarette and alcohol co-use. In this study, we evaluated AB to both smoking and alcohol cues in daily life using ambulatory assessment. METHODS: Daily smokers (N = 21) who consume moderate to heavy amounts of alcohol completed surveys and a dot probe task four times per day using a personal digital assistant over a period of 1 week. RESULTS: Aggregated over subjects, there was evidence of AB to smoking and AB to alcohol cues. When smoking AB was higher than the person-specific average, alcohol AB was elevated, and when alcohol AB was higher than the person-specific average, smoking AB was elevated. AB was not significantly associated with craving for cigarettes or alcohol. CONCLUSIONS: It is feasible to assess AB for cigarette and alcohol cues using ambulatory assessment. To the best of our knowledge, this is the first study to report a within-subject association between AB for two drug cues. The relationship between cigarette and alcohol use is likely dynamic and depends on context and exposure to substance-specific cues. Additionally, a larger sample may be needed to evaluate relationships between AB and craving. Further research on possible cognitive mechanisms that increase the likelihood of co-use can inform targeted interventions.

Cigarette Smoking in South Korea: A Narrative Review.

Although the prevalence of cigarette smoking has declined in Western countries over the past few decades, a comparable decline among males has not been observed in Asian countries, especially in South Korea, where approximately 40%-50% of men and 4%-8% of women have been identified as smokers, and there is a pressing need to understand the background of cigarette smoking in these populations. The present study is a narrative review of the research literature on cigarette smoking in South Korea. First, we describe the social, economic, and cultural factors that impact cigarette smoking in South Korea. The paper also reviews the available peer-reviewed literature comprising observational studies and interventional studies, including randomized controlled trials. The extant literature on smoking in Korean Americans is also reviewed. Cigarette smoking in South Korea has been relatively understudied, and this review identifies priority areas for future research, including the use of mobile interventions.

Affect, motivation, temptation, and drinking among alcohol-dependent outpatients trying to maintain abstinence: An Ecological Momentary Assessment study.

OBJECTIVES: Using Ecological Momentary Assessment we aimed to describe the time course of temptation episodes in alcohol-dependent outpatients in a real-life setting. We also examined whether affective and motivational variables were cross-sectionally and prospectively associated with temptation episodes. Additionally, we tested whether outpatients who drank against treatment goals (i.e., "lapsers") differed in craving, affect, and motivation from abstainers. METHODS: Participants were 43 alcohol-dependent outpatients (13 female). Using personal digital assistants (PDAs), patients were signaled to complete three random assessments per day for 4 weeks. They were also instructed to complete a temptation assessment whenever they experienced the temptation to drink alcohol. RESULTS: The number of temptation assessments declined over time and did not differ between lapsers and abstainers. Overall, craving was generally higher in lapsers (n = 14) than abstainers (n = 27). In lapsers, but not abstainers, abstinence motivation was lower at temptation assessments vs. random assessments. Across all patients, negative affect was prospectively associated with entry of temptation assessments later the same day. There were no significant effects for positive affect. CONCLUSIONS: In alcohol-dependent outpatients attempting to remain abstinent, negative affect is cross-sectionally associated with entry of temptation assessments. There is more evidence that negative affect precipitates temptations than vice versa. Professionals should be watchful of outpatients who report generally high levels of craving, and who report more negative affect and lower abstinence motivation, when tempted.

The impact of nicotine dose and instructed dose on smokers' implicit attitudes to smoking cues: An ERP study.

It is unclear whether nicotine and perceived nicotine exposure can influence automatic evaluations of cigarette stimuli. In the present study, we investigated the effects of nicotine dose and instructed dose on motivational responses to smoking cues. Forty overnight nicotine-deprived smokers completed an Implicit Association Test (IAT) at each of the four laboratory sessions in a balanced-placebo design that crossed nicotine dose (Given-NIC [given nicotine] vs. Given-DENIC [given denicotinized]) with instructed dose expectancy (Told-NIC [told-nicotine] vs. Told-DENIC. [told-denicotinized]). We measured participants' behavioral performance, including reaction time (RT) and accuracy rate, and the early posterior negativity (EPN) component using the event-related potential (ERP) technique to the target pictures. During congruent trials when the categorization condition was smoking or unpleasant, smokers had greater classification accuracy, shorter RT latency, and greater EPN amplitudes compared to the incongruent trials when the categorization condition was smoking or pleasant. The Given-NIC condition was associated with increased classification accuracy, longer RT latency, and decreased EPN amplitudes compared to the Given-DENIC condition. Similarly, the Told-NIC condition was associated with increased accuracy and decreased EPN amplitudes compared to the Told-DENIC condition, but with shorter RT latency. Cigarette-related pictures produced greater EPN amplitudes than neutral pictures. Both behavioral and ERP results suggest that smokers have negative implicit attitudes toward smoking. While both nicotine dose and expected dose facilitated stimulus categorization, there was no evidence that either factor altered smokers' negative attitudes toward smoking cues. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Enhancing Smoking Risk Communications: The Influence of Need for Cognition.

Objectives: One way to enhance the impact of smoking health risk messages may be to tailor their content to individual difference factors such as need for cognition (NFC). In this study, we examined how NFC influenced responses to different smoking risk messages. Outcomes included knowledge, risk perceptions, and behavioral expectations related to quitting smoking. Methods: We randomized 402 participants to one of 4 different risk message sets that were manipulated in terms of emotionality and framing in a 2x2 design: (1) factual gain-framed, (2) factual loss-framed, (3) emotional gain-framed, and (4) emotional loss-framed. Results: Statistically significant main effects emerged for NFC and emotionality. For certain risk perceptions, those with lower NFC reported greater perceived risk in response to emotional messages and lower risk in response to factual messages; those with higher NFC showed an opposite pattern. Similarly, those with lower NFC reported greater risk in response to gain-framed messages and lower risk in response to loss-framed messages; the opposite pattern emerged for those lower in NFC. Conclusions: Findings highlight the importance of an individual difference variable in influencing the impact of different types of smoking risk messages.

Associations between dispositional mindfulness, craving, and drinking in alcohol-dependent patients: An ecological momentary assessment study.

Hazardous alcohol use remains a significant global public health problem. A better understanding of relapse may assist the development of new interventions. Low levels of dispositional mindfulness may be a risk factor for craving and alcohol use, but few studies have examined these associations prospectively in an alcohol-dependent sample. In an ecological momentary assessment (EMA) study, Dutch alcohol dependent patients (N = 43) carried around a personal digital assistant for 4 weeks while trying to maintain abstinence. Participants completed assessments at random times 3 times per day, and when they felt a strong urge to drink or came to the brink of drinking without doing so. At each assessment, stress, negative affect, craving, recent drinking, and attentional or approach bias were assessed. Dispositional mindfulness was assessed at baseline with the Mindful Attention Awareness Scale (MAAS). More mindful individuals (higher MAAS scores) reported lower craving than less mindful individuals. There was no evidence that stress, negative affect, attentional bias, or approach bias mediated the association between MAAS and craving. However, there was evidence for an indirect path from MAAS to drinking such that higher mindfulness was associated with lower craving ratings that in turn were associated with less drinking. There was no evidence that MAAS significantly moderated associations between stress/negative affect/cognitive biases and craving, or between craving and drinking. In sum, more mindful recovering alcohol dependent patients reported lower craving ratings than less mindful patients, and this association appeared to be independent of stress/negative affect and cognitive biases. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Associations of perceived stress and state anger with symptom burden and functional status in patients with heart failure.

Background: Psychosocial stress and anger trigger cardiovascular events, but their relationship to heart failure (HF) exacerbations is unclear. We investigated perceived stress and anger associations with HF functional status and symptoms. Methods and Results: In a prospective cohort study (BETRHEART), 144 patients with HF (77% male; 57.5 ± 11.5 years) were evaluated for perceived stress (Perceived Stress Scale; PSS) and state anger (STAXI) at baseline and every 2 weeks for 3 months. Objective functional status (6-min walk test; 6MWT) and health status (Kansas City Cardiomyopathy Questionnaire; KCCQ) were also measured biweekly. Linear mixed model analyses indicated that average PSS and greater than usual increases in PSS were associated with worsened KCCQ scores. Greater than usual increases in PSS were associated with worsened 6MWT. Average anger levels were associated with worsened KCCQ, and increases in anger were associated with worsened 6MWT. Adjusting for PSS, anger associations were no longer statistically significant. Adjusting for anger, PSS associations with KCCQ and 6MWT remained significant. Conclusion: In patients with HF, both perceived stress and anger are associated with poorer functional and health status, but perceived stress is a stronger predictor. Negative effects of anger on HF functional status and health status may partly operate through psychological stress.

Minocycline does not affect experimental pain or addiction-related outcomes in opioid maintained patients.

RATIONALE: Minocycline, a tetracycline antibiotic, inhibits activation of microglia. In preclinical studies, minocycline prevented development of opioid tolerance and opioid-induced hyperalgesia (OIH). The goal of this study was to determine if minocycline changes pain threshold and tolerance in individuals with opioid use disorder who are maintained on agonist treatment. METHODS: In this double-blind, randomized human laboratory study, 20 participants were randomized to either minocycline (200 mg/day) or placebo treatment for 15 days. The study had three test sessions (days 1, 8, and 15 of treatment) and one follow-up visit 1 week after the end of treatment. In each test session, participants were assessed on several subjective and cognitive measures, followed by assessment of pain sensitivity using the Cold Pressor Test (CPT). Daily surveys and cognitive measures using Ecological Momentary Assessment (EMA) were also collected four times a day on days 8 through 14 of treatment, and proinflammatory serum cytokines were assessed before and on the last day of treatment. RESULTS: Minocycline treatment did not change pain threshold or tolerance on the CPT. Similarly, minocycline did not change severity of pain, opioid craving, withdrawal, or serum cytokines. Minocycline treatment increased accuracy on a Go/No-Go task. CONCLUSIONS: While these findings do not support minocycline's effects on OIH, minocycline may have a potential use as a cognitive enhancer for individuals with opioid use disorder, a finding that warrants further systematic studies.