Repurposing an integrated national influenza platform for genomic surveillance of SARS-CoV-2 in Ghana: a molecular epidemiological analysis.

BACKGROUND: Genomic surveillance of SARS-CoV-2 is crucial for monitoring the spread of COVID-19 and guiding public health decisions, but the capacity for SARS-CoV-2 testing and sequencing in Africa is low. We integrated SARS-CoV-2 surveillance into an existing influenza surveillance network with the aim of providing insights into SARS-CoV-2 transmission and genomics in Ghana. METHODS: In this molecular epidemiological analysis, which is part of a wider multifaceted prospective observational study, we collected national SARS-CoV-2 test data from 35 sites across 16 regions in Ghana from Sept 1, 2020, to Nov 30, 2021, via the Ghanaian integrated influenza and SARS-CoV-2 surveillance network. SARS-CoV-2-positive samples collected through this integrated national influenza surveillance network and from international travellers arriving in Accra were sequenced with Oxford Nanopore Technology sequencing and the ARTIC tiled amplicon method. The sequence lineages were typed with pangolin and the phylogenetic analysis was conducted with IQ-Tree2 and TreeTime. FINDINGS: During the study period, 5495 samples were submitted for diagnostic testing through the national influenza surveillance network (2121 [46·1%] of 4021 samples with complete demographic data were from female individuals and 2479 [53·9%] of 4021 samples were from male individuals). We also obtained 2289 samples from travellers who arrived in Accra and had a positive lateral flow test, of whom 1626 (71·0%, 95% CI 69·1-72·9) were confirmed to be SARS-CoV-2 positive. Co-circulation of influenza and SARS-CoV-2 in Ghana was detected, with increased cases of influenza in November, 2020, November, 2021, and January and June, 2021. In 4124 samples from individuals with influenza-like illness, SARS-CoV-2 was identified in 583 (14·1%, 95% CI 13·1-15·2) samples and influenza in 356 (8·6%, 7·8-9·5). Conversely, in 476 samples from individuals with of severe acute respiratory illness, SARS-CoV-2 was detected in 58 (12·2%, 9·5-15·5) samples and influenza in 95 (19·9%, 16·5-23·9). We detected four waves of SARS-CoV-2 infections in Ghana; each wave was driven by a different variant: B.1 and B.1.1 were the most prevalent lineages in wave 1, alpha (B.1.1.7) was responsible for wave 2, delta (B.1.617.2) and its sublineages (closely related to delta genomes from India) were responsible for wave 3, and omicron variants were responsible for wave 4. We detected omicron variants among 47 (32%) of 145 samples from travellers during the start of the omicron spread in Ghana (wave 4). INTERPRETATION: This study shows the value of repurposing existing influenza surveillance platforms to monitor SARS-CoV-2. Influenza continued to circulate in Ghana in 2020 and 2021, and remained a major cause of severe acute respiratory illness. We detected importations of SARS-CoV-2 variants into Ghana, including those that did or did not lead to onward community transmission. Investment in strengthening national influenza surveillance platforms in low-income and middle-income countries has potential for ongoing monitoring of SARS-CoV-2 and future pandemics. FUNDING: The EDCTP2 programme supported by the EU.

Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections.

B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA is significantly increased in B.1.1.7 (alpha) infections (n = 879). This increase is seen over the previous dominant lineage in the UK, B.1.177 (n = 943), which is independent of genomic reads, E cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median sgRNA abundance. We demonstrate that ORF9b protein levels are increased 6-fold in B.1.1.7 compared to a B lineage virus in vitro. We hypothesise that increased ORF9b in B.1.1.7 is a direct consequence of a triple nucleotide mutation in nucleocapsid (28280:GAT > CAT, D3L) creating a transcription regulatory-like sequence complementary to a region 3' of the genomic leader. These findings provide a unique insight into the biology of B.1.1.7 and support monitoring of sgRNA profiles to evaluate emerging potential variants of concern.

Demographic Covariates, Vocational Rehabilitation Services, and Employment Outcomes of Working-Age Adults with Anxiety Disorders: A Multivariate Logistic Regression Analysis.

PURPOSE: This study aimed to investigate the relationships between demographic covariates, vocational rehabilitation (VR) services, and employment outcomes of individuals with anxiety disorders. The specific research question for the current study investigate demographic variables and vocational rehabilitation services as predictors of competitive employment outcomes. METHODS: Data for the present study were extracted from the most recent United States Rehabilitation Service Administration 2018 Case Service Report (RSA-911) data. A purposeful selection, multivariate logistic regression analysis was conducted to examine the case service report data of 9266 individuals with anxiety disorders who received vocational rehabilitation services based on their demographic variables and receipt of VR services. RESULTS: The results indicated that African Americans and Latinx, people who have completed high school or more, people who do not receive disability-related benefits, and those who received more vocational rehabilitation services were more likely to be gainfully employed. In addition, receipt of financial support for life crises and occupational credentials (i.e., other services and maintenance services) and vocational rehabilitation counseling and guidance services were significant predictors of employment outcomes. Conversely, receipt of supported employment and transition services were negatively associated with employment outcome. CONCLUSIONS: In the present study, we identified VR services that can improve and risk factors that can impede employment outcomes of people with anxiety disorders. We also identified medical, psychosocial, and vocational interventions that can lessen the effect of anxiety disorders on physical and mental health functioning.

Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves.

Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th J'uly 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onward transmission, earlier identification of nosocomial cases will be required to break hospital transmission chains.

Revealing nuclear receptor hub modules from Basal-like breast cancer expression networks.

Nuclear receptors are a class of transcriptional factors. Together with their co-regulators, they regulate development, homeostasis, and metabolism in a ligand-dependent manner. Their ability to respond to environmental stimuli rapidly makes them versatile cellular components. Their coordinated activities regulate essential pathways in normal physiology and in disease. Due to their complexity, the challenge remains in understanding their direct associations in cancer development. Basal-like breast cancer is an aggressive form of breast cancer that often lacks ER, PR and Her2. The absence of these receptors limits the treatment for patients to the non-selective cytotoxic and cytostatic drugs. To identify potential drug targets it is essential to identify the most important nuclear receptor association network motifs in Basal-like subtype progression. This research aimed to reveal the transcriptional network patterns, in the hope to capture the underlying molecular state driving Basal-like oncogenesis. In this work, we illustrate a multidisciplinary approach of integrating an unsupervised machine learning clustering method with network modelling to reveal unique transcriptional patterns (network motifs) underlying Basal-like breast cancer. The unsupervised clustering method provides a natural stratification of breast cancer patients, revealing the underlying heterogeneity in Basal-like. Identification of gene correlation networks (GCNs) from Basal-like patients in both the TCGA and METABRIC databases revealed three critical transcriptional regulatory constellations that are enriched in Basal-like. These represent critical NR components implicated in Basal-like breast cancer transcription. This approach is easily adaptable and applicable to reveal critical signalling relationships in other diseases.

Understanding differences in alcohol consumption and depressed mood between U.S.- and foreign-born Asian and Caucasian college students.

The number and proportion of foreign-born individuals in the U.S. population has increased in recent decades. From 1970 to 2007, the foreign-born population more than tripled to approximately 37 million (U.S. Census Bureau, 1997 , 2008 ). Foreign-born students are a key subpopulation of college students. About 23% of U.S. undergraduate college students in 2007-2008 were either born outside of the United States (10%) or were children of at least one first-generation immigrant parent (13%; National Center for Education Statistics, U.S. Department of Education [NCES], 2012 ). Asian students constitute the majority (30%) of foreign-born undergraduates. Although foreign-born Asian students compose nearly one-quarter of the college population, limited research has examined how rates of alcohol use and depression differ between foreign-born and U.S.-born Asian college students (Gonzalez, Reynolds, & Skewes, 2011 ; Ralston & Palfai, 2012 ). The limited research is worrisome given their increasing rates of college enrollment (U.S. Census Bureau, 2011 ), alcohol consumption (Aud, Fox, & KewalRamani, 2010 ), alcohol abuse and dependence (Grant et al., 2004 ), and underutilization of mental health services (U.S. Department of Health and Human Services, 2001 ). Collectively, these factors point to the need for further research tailored to Asian college drinkers.

Relative efficacy of mindfulness-based relapse prevention, standard relapse prevention, and treatment as usual for substance use disorders: a randomized clinical trial.

IMPORTANCE: Relapse is highly prevalent following substance abuse treatments, highlighting the need for improved aftercare interventions. Mindfulness-based relapse prevention (MBRP), a group-based psychosocial aftercare, integrates evidence-based practices from mindfulness-based interventions and cognitive-behavioral relapse prevention (RP) approaches. OBJECTIVE: To evaluate the long-term efficacy of MBRP in reducing relapse compared with RP and treatment as usual (TAU [12-step programming and psychoeducation]) during a 12-month follow-up period. DESIGN, SETTING, AND PARTICIPANTS: Between October 2009 and July 2012, a total of 286 eligible individuals who successfully completed initial treatment for substance use disorders at a private, nonprofit treatment facility were randomized to MBRP, RP, or TAU aftercare and monitored for 12 months. Participants medically cleared for continuing care were aged 18 to 70 years; 71.5% were male and 42.1% were of ethnic/racial minority. INTERVENTIONS: Participants were randomly assigned to 8 weekly group sessions of MBRP, cognitive-behavioral RP, or TAU. MAIN OUTCOMES AND MEASURES: Primary outcomes included relapse to drug use and heavy drinking as well as frequency of substance use in the past 90 days. Variables were assessed at baseline and at 3-, 6-, and 12-month follow-up points. Measures used included self-report of relapse and urinalysis drug and alcohol screenings. RESULTS: Compared with TAU, participants assigned to MBRP and RP reported significantly lower risk of relapse to substance use and heavy drinking and, among those who used substances, significantly fewer days of substance use and heavy drinking at the 6-month follow-up. Cognitive-behavioral RP showed an advantage over MBRP in time to first drug use. At the 12-month follow-up, MBRP participants reported significantly fewer days of substance use and significantly decreased heavy drinking compared with RP and TAU. CONCLUSIONS AND RELEVANCE: For individuals in aftercare following initial treatment for substance use disorders, RP and MBRP, compared with TAU, produced significantly reduced relapse risk to drug use and heavy drinking. Relapse prevention delayed time to first drug use at 6-month follow-up, with MBRP and RP participants who used alcohol also reporting significantly fewer heavy drinking days compared with TAU participants. At 12-month follow-up, MBRP offered added benefit over RP and TAU in reducing drug use and heavy drinking. Targeted mindfulness practices may support long-term outcomes by strengthening the ability to monitor and skillfully cope with discomfort associated with craving or negative affect, thus supporting long-term outcomes. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT01159535

Exploring relationships between facets of self-esteem and drinking behavior among diverse groups of young adults.

Theory and empirical evidence suggest that North American-based measures of self-esteem, which measure individualistic positive self-regard, may be less applicable to Eastern cultures. In the present exploratory study, we examined how different conceptualizations of self-esteem, as measured by the Rosenberg Self-esteem Scale and the Collective Self-esteem (CSE) Scale, predicted drinking behavior among three groups of American college students (N=326) with varying ethnicities: White, Korean, and Chinese/Taiwanese. Hierarchical negative binomial regression was employed to evaluate these relations. Ethnic identity was controlled for in all analyses. Findings indicated that while global self-esteem was positively associated with drinking for the whole sample, ethnicity moderated this relationship such that global self-esteem was related to drinking for White participants but not for their Chinese/Taiwanese counterparts. In addition, while CSE did not associate with drinking for the whole sample, effects emerged for specific ethnicities. Specifically, private CSE was associated with less drinking for Korean and Chinese/Taiwanese participants. Depending on specific Asian ethnicity, public CSE served as a risk (Korean participants) or a protective factor (Chinese/Taiwanese participants) for drinking. Findings suggest that above and beyond ethnic identity, differential relationships between facets of self-esteem and drinking behavior may exist among White, Korean, and Chinese/Taiwanese young adults. Intervention and prevention programs should develop strategies to help Chinese/Taiwanese and Korean American young adults cultivate protective factors within domains of CSE.

The relationship between collective self-esteem, acculturation, and alcohol-related consequences among Asian American young adults.

We examined the relationship between collective self-esteem (i.e., the value one places on being part of a collective group), acculturation, and alcohol-related consequences in a sample of 442 Asian American young adults. We found that membership self-esteem and public collective self-esteem interacted with acculturation such that low levels of both predicted greater rates of consequences. Participants with lower acculturation and greater private collective self-esteem experienced more alcohol consequences. This study suggests that differential aspects of collective self-esteem may serve as protective or risk factors for Asian American young adults depending on degree of acculturation.

Examining psychometric properties of distress tolerance and its moderation of mindfulness-based relapse prevention effects on alcohol and other drug use outcomes.

Distress tolerance refers to the degree to which an individual is able to withstand negative psychological and/or physical states. Empirical literature has indicated that lower distress tolerance is associated with a number of negative alcohol and other drug (AOD) use outcomes and psychopathology. Mindfulness meditation focuses on enhancing affect regulation, and may be particularly beneficial for individuals with lower distress tolerance. This secondary analysis evaluated the basic psychometric properties of the Distress Tolerance Scale (DTS) in a clinical sample of individuals with AOD-use disorders and tested whether distress tolerance for negative psychological states moderated treatment effects on AOD outcomes in an initial efficacy trial of mindfulness-based relapse prevention (MBRP). It was hypothesized that participants with lower distress tolerance would report fewer AOD use days over the 4-month follow-up if they received MBRP versus treatment as usual (TAU). Participants (N=168) in the parent RCT were recruited from a private, nonprofit agency providing inpatient and outpatient care for individuals with AOD-use disorders. Assessments of 60-day frequency of AOD use, as measured by the Timeline Followback, were conducted at baseline, immediately postintervention, and 2months and 4months following the intervention. Distress tolerance, as measured by the DTS, was assessed at baseline. Results indicated a one-factor solution, which is consistent with how the DTS has been implemented in other studies. As predicted, DTS was positively associated with all mindfulness subscales, suggesting its convergent validity in this clinical sample. Findings showed the hypothesized time×treatment×distress tolerance interaction, and thereby indicated that participants with lower distress tolerance who received MBRP treatment experienced a greater curvilinear decrease in AOD use days over time than those with lower distress tolerance who received TAU. However, the observed plateau effect suggests that these effects were not maintained at the 4-month follow-up. Findings suggest that distress tolerance is a clinically relevant client characteristic to consider in matching participants to aftercare treatment and that MBRP may be particularly helpful for individuals with lower distress tolerance.

Mindfulness-based relapse prevention for substance craving.

Craving, defined as the subjective experience of an urge or desire to use substances, has been identified in clinical, laboratory, and preclinical studies as a significant predictor of substance use, substance use disorder, and relapse following treatment for a substance use disorder. Various models of craving have been proposed from biological, cognitive, and/or affective perspectives, and, collectively, these models of craving have informed the research and treatment of addictive behaviors. In this article we discuss craving from a mindfulness perspective, and specifically how mindfulness-based relapse prevention (MBRP) may be effective in reducing substance craving. We present secondary analyses of data from a randomized controlled trial that examined MBRP as an aftercare treatment for substance use disorders. In the primary analyses of the data from this trial, Bowen and colleagues (2009) found that individuals who received MBRP reported significantly lower levels of craving following treatment, in comparison to a treatment-as-usual control group, which mediated subsequent substance use outcomes. In the current study, we extend these findings to examine potential mechanisms by which MBRP might be associated with lower levels of craving. Results indicated that a latent factor representing scores on measures of acceptance, awareness, and nonjudgment significantly mediated the relation between receiving MBRP and self-reported levels of craving immediately following treatment. The mediation findings are consistent with the goals of MBRP and highlight the importance of interventions that increase acceptance and awareness, and help clients foster a nonjudgmental attitude toward their experience. Attending to these processes may target both the experience of and response to craving.

The effect of progressive resistance training on leg strength, aerobic capacity and functional tasks of daily living in persons with Down syndrome.

PURPOSE: The purpose of this study was to examine the effect of progressive resistance training on leg strength, aerobic capacity and physical function in persons with Down syndrome (DS). METHOD: Thirty persons with DS (age 28 SD 8 years) were assigned to an intervention or control group. The intervention group performed resistance training 2 days per week for 10 weeks. Participants performed tests to measure isometric and isokinetic knee extensor and flexor peak torque, peak aerobic capacity and timed performance on chair rise, walking and stair ascent and descent. RESULT: Persons with DS receiving the intervention significantly increased their isokinetic knee extensor and flexor peak torque [Absolute change (post minus pre-value) was 17.0 SD 29.6 and 12.6 SD 18.9 N m, respectively] and isometric knee extensor peak torque at angles of 45° (2.9 SD 23.2 N m), 60° (3.0 SD 22.9 N m) and 75° (14.2 SD 30.0 N m). These changes were significantly greater than in the control group. In addition, the time to ascend (-0.3 SD 0.8 s) and descend (-0.6 SD 0.9 s) stairs significantly decreased in the intervention group compared to the control group. CONCLUSION: These findings show that progressive resistance training is an effective intervention for persons with DS to improve leg strength and stair-climbing ability.

Psychosocial factors of stages of change among adults with intellectual disabilities.

Relationships among full constructs of the transtheoretical model using a sample of 121 adults with mild intellectual disabilities in Taiwan were examined. Self-reports of stages of change and transtheoretical model psychosocial measures were gathered through interviews. Although MANCOVA revealed that behavioral processes of change, cognitive processes of change, self-efficacy, and perceived pros increased across stages, we did not find a clear linear pattern of association. Direct discriminant function analysis indicated that the most important predictors of stages of change were behavioral processes, cognitive processes, and self-efficacy. The overall stage of change classification accuracy using transtheoretical model psychosocial constructs was 56.2%. Psychosocial measures specifically developed for this population should be further explored.

The mindfulness-based relapse prevention adherence and competence scale: development, interrater reliability, and validity.

The present study describes the development of the Mindfulness-Based Relapse Prevention Adherence and Competence Scale (MBRP-AC), a measure of treatment integrity for mindfulness-based relapse prevention (MBRP). MBRP is a newly developed treatment integrating core aspects of relapse prevention with mindfulness practices. The MBRP-AC was developed in the context of a randomized controlled trial (RCT) of MBRP efficacy and consists of two sections: Adherence (adherence to individual components of MBRP and discussion of key concepts) and Competence (ratings of therapist style/approach and performance). Audio recordings from 44 randomly selected group treatment sessions (50%) were rated by independent raters for therapist adherence and competence in the RCT. Findings evinced high interrater reliability for all treatment adherence and competence ratings, and adequate internal consistency for Therapist Style/Approach and Therapist Performance summary scales. Ratings on the MBRP-AC suggested that therapists in the recent RCT adhered to protocol, discussed key concepts in each session, and demonstrated the intended style and competence in treatment delivery. Finally, overall ratings on the Adherence section were positively related to changes in mindfulness over the course of the treatment.

Physical fitness predicts functional tasks in individuals with Down syndrome.

UNLABELLED: Individuals with Down syndrome (DS) exhibit reduced strength and aerobic capacity, which may limit their ability to perform functional tasks of daily living. PURPOSE: This study was conducted to examine the relationship between timed performance on functional tasks of daily living and age, knee isometric strength, and peak aerobic capacity in a group of individuals with DS. METHODS: This was a cross-sectional study involving 35 individuals (27 +/- 7.5 yr) with DS. Participants completed an isometric test of knee extensor and flexor strength, an individualized exercise test to measure peak aerobic capacity, and three timed functional tasks of daily living, which included chair rise, gait speed, and stair ascent and descent. Multiple regression analyses were performed to examine the relationship between timed task performance and age, knee isometric strength, and peak aerobic capacity. RESULTS: The multiple regression models explained 11-29% of the variance in timed task performance. Knee extensor strength was the most influential variable in predicting timed task performance (squared semipartial correlation coefficient [sr2] = 0.11-0.20), followed by aerobic capacity (sr2 = 0.10-0.14). Age was not a significant predictor of timed task performance. CONCLUSION: These findings suggest that physical fitness (defined here as aerobic capacity and knee extensor strength) limits the ability of adults with DS to perform functional tasks of daily living. Randomized controlled trials should be performed to test the probable causal relationship between exercises designed to improve physical fitness and functional tasks of daily living.

Language-based measures of mindfulness: initial validity and clinical utility.

This study examined relationships among language use, mindfulness, and substance-use treatment outcomes in the context of an efficacy trial of mindfulness-based relapse prevention (MBRP) for adults with alcohol and other drug use (AOD) disorders. An expert panel generated two categories of mindfulness language (ML) describing the mindfulness state and the more encompassing "mindfulness journey," which included words describing challenges of developing a mindfulness practice. MBRP participants (n = 48) completed baseline sociodemographic and AOD measures, and participated in the 8-week MBRP program. AOD data were collected during the 4-month follow-up. A word count program assessed the frequency of ML and other linguistic markers in participants' responses to open-ended questions about their postintervention impressions of mindfulness practice and MBRP. Findings supported concurrent validity of ML categories: ML words appeared more frequently in the MBRP manual compared to the 12-step Big Book. Further, ML categories correlated with other linguistic variables related to the mindfulness construct. Finally, predictive validity was supported: greater use of ML predicted fewer AOD use days during the 4-month follow-up. This study provided initial support for ML as a valid, clinically useful mindfulness measure. If future studies replicate these findings, ML could be used in conjunction with self-report to provide a more complete picture of the mindfulness experience.

Mindfulness-based relapse prevention for substance use disorders: a pilot efficacy trial.

The current study is the first randomized-controlled trial evaluating the feasibility and initial efficacy of an 8-week outpatient Mindfulness-Based Relapse Prevention (MBRP) program as compared to treatment as usual (TAU). Participants were 168 adults with substance use disorders who had recently completed intensive inpatient or outpatient treatment. Assessments were administered pre-intervention, post-intervention, and 2 and 4 months post-intervention. Feasibility of MBRP was demonstrated by consistent homework compliance, attendance, and participant satisfaction. Initial efficacy was supported by significantly lower rates of substance use in those who received MBRP as compared to those in TAU over the 4-month post-intervention period. Additionally, MBRP participants demonstrated greater decreases in craving, and increases in acceptance and acting with awareness as compared to TAU. Results from this initial trial support the feasibility and initial efficacy of MBRP as an aftercare approach for individuals who have recently completed an intensive treatment for substance use disorders.