Category: Nevin Manimala

Proc Natl Acad Sci U S A. 2022 Oct 18;119(42):e2212930119. doi: 10.1073/pnas.2212930119. Epub 2022 Oct 10.

ABSTRACT

Bacterial secondary metabolites are a major source of antibiotics and other bioactive compounds. In microbial communities, these molecules can mediate interspecies interactions and responses to environmental change. Despite the importance of secondary metabolites in human health and microbial ecology, little is known about their roles and regulation in the context of multispecies communities. In a simplified model of the rhizosphere composed of Bacillus cereus, Flavobacterium johnsoniae, and Pseudomonas koreensis, we show that the dynamics of secondary metabolism depend on community species composition and interspecies interactions. Comparative metatranscriptomics and metametabolomics reveal that the abundance of transcripts of biosynthetic gene clusters (BGCs) and metabolomic molecular features differ between monocultures or dual cultures and a tripartite community. In both two- and three-member cocultures, P. koreensis modified expression of BGCs for zwittermicin, petrobactin, and other secondary metabolites in B. cereus and F. johnsoniae, whereas the BGC transcriptional response to the community in P. koreensis itself was minimal. Pairwise and tripartite cocultures with P. koreensis displayed unique molecular features that appear to be derivatives of lokisin, suggesting metabolic handoffs between species. Deleting the BGC for koreenceine, another P. koreensis metabolite, altered transcript and metabolite profiles across the community, including substantial up-regulation of the petrobactin and bacillibactin BGCs in B. cereus, suggesting that koreenceine represses siderophore production. Results from this model community show that bacterial BGC expression and chemical output depend on the identity and biosynthetic capacity of coculture partners, suggesting community composition and microbiome interactions may shape the regulation of secondary metabolism in nature.

PMID:36215464 | DOI:10.1073/pnas.2212930119

J Opt Soc Am A Opt Image Sci Vis. 2022 May 1;39(5):979-986. doi: 10.1364/JOSAA.453689.

ABSTRACT

Expressions for the temporal covariance function and temporal frequency spectrum for a plane wave propagation in an underwater turbulent medium are developed analytically. Temporal correlation in moving natural water is presented, which is shown to be dependent upon the moving velocity, the delay between two instants of time, propagation distance, average temperature, and average salinity concentration. Coherence time and zero crossing time also are calculated. The results show that the velocity of the moving natural water has a significant impact on the temporal correlation of irradiance fluctuations. Additionally, the propagation distance, average temperature, average salinity concentration, and temperature-salinity gradient ratio also impact the temporal correlation up to a certain level.

PMID:36215459 | DOI:10.1364/JOSAA.453689

J Opt Soc Am A Opt Image Sci Vis. 2022 May 1;39(5):820-828. doi: 10.1364/JOSAA.455823.

ABSTRACT

A model of multivariate Gaussian statistics has been applied to study the higher-order statistics of the polarization speckle at two spatial or temporal points. Based on the Gaussian assumption for the random electric field, the joint probability density functions of the Stokes parameters and the parameters characterizing the polarization ellipse for the produced random polarization fields at two points are obtained. Subsequently, the corresponding statistics of an isotropic polarization speckle at two points have been investigated to obtain the joint and conditional probability densities of these random variables.

PMID:36215443 | DOI:10.1364/JOSAA.455823

J Opt Soc Am A Opt Image Sci Vis. 2022 May 1;39(5):959-968. doi: 10.1364/JOSAA.443326.

ABSTRACT

There are two types of uncertainty in image reconstructions from list-mode data: statistical and deterministic. One source of statistical uncertainty is the finite number of attributes of the detected particles, which are sampled from a probability distribution on the attribute space. A deterministic source of uncertainty is the effect that null functions of the imaging operator have on reconstructed pixel or voxel values. Quantifying the reduction in this deterministic source of uncertainty when more attributes are measured for each detected particle is the subject of this work. Specifically, upper bounds on an error metric are derived to quantify the error introduced in the reconstruction by the presence of null functions, and these upper bounds are shown to be reduced when the number of attributes is increased. These bounds are illustrated with an example of a two-dimensional single photon emission computed tomography (SPECT) system where the depth of interaction in the scintillation crystal is added to the attribute vector.

PMID:36215457 | DOI:10.1364/JOSAA.443326

Stat Appl Genet Mol Biol. 2022 Oct 10;21(1). doi: 10.1515/sagmb-2022-0003. eCollection 2022 Jan 1.

ABSTRACT

Batch effect Reduction of mIcroarray data with Dependent samples usinGEmpirical Bayes (BRIDGE) is a recently developed statistical method to address the issue of batch effect correction in batch-confounded microarray studies with dependent samples. The key component of the BRIDGE methodology is the use of samples run as technical replicates in two or more batches, “bridging samples”, to inform batch effect correction/attenuation. While previously published results indicate a relationship between the number of bridging samples, M, and the statistical power of downstream statistical testing on the batch-corrected data, there is of yet no formal statistical framework or user-friendly software, for estimating M to achieve a specific statistical power for hypothesis tests conducted on the batch-corrected data. To fill this gap, we developed pwrBRIDGE, a simulation-based approach to estimate the bridging sample size, M, in batch-confounded longitudinal microarray studies. To illustrate the use of pwrBRIDGE, we consider a hypothetical, longitudinal batch-confounded study whose goal is to identify Alzheimer’s disease (AD) progression-associated genes from amnestic mild cognitive impairment (aMCI) to AD in human blood after a 5-year follow-up. pwrBRIDGE helps researchers design and plan batch-confounded microarray studies with dependent samples to avoid over- or under-powered studies.

PMID:36215429 | DOI:10.1515/sagmb-2022-0003

Disabil Rehabil Assist Technol. 2022 Oct 10:1-10. doi: 10.1080/17483107.2022.2129849. Online ahead of print.

ABSTRACT

PURPOSE: This study aimed to understand Bangladeshi users’ satisfaction with their assistive devices, including (a) device characteristics, e.g., size, weight, safety, ease of use, comfort, and effectiveness, and (b) availability of parts and repair services. We also described how frequently individuals with disabilities living in the community used assistive devices in their daily activities and how the use of assistive devices promoted individuals’ wellbeing.

METHOD: We conducted a cross-sectional survey with assistive device users or their guardians (if under 18) in Bangladesh about their experience and satisfaction with their assistive device 6 months after receiving it. The research team developed a survey questionnaire consisting of both closed and open-ended questions. All data were collected via telephone interviews. We employed descriptive statistics to analyse quantitative data and inductive analysis for the qualitative data.

RESULTS: We found that out of the 376 participants, nearly 95% used assistive devices on a regular basis, and their satisfaction with the devices was high. Participants reported that assistive devices improved mobility, independence, and wellbeing of persons with disabilities. A few participants (6.4%) reported that their devices were damaged. Some participants identified concerns with their assistive devices, including (i) inappropriate size of ankle-foot orthoses, manual self-propelled wheelchairs, and prostheses, (ii) back slabs (a type of brace) being too short, and (iii) walking frames being too large. Several participants noted pain and discomfort when they used their assistive device. Additionally, some participants stated that environmental factors (e.g., muddy roads) contributed to the disrepair of their assistive devices. Finally, participants recounted that repair services were limited in rural areas of Bangladesh.

CONCLUSION: These findings indicate that the provision of assistive devices requires accommodating individuals’ needs and ensuring appropriate environments in which to function. The results support the need for follow-up services after distributing assistive devices. Further research could explore the impact of assistive devices on the family quality of life of persons with disabilities.IMPLICATIONS FOR REHABILITATIONIt is essential for rehabilitation professionals to conduct follow-up services after distributing assistive devices among persons with disabilities.There is a need for the government of Bangladesh to revisit the Rights and Protection of Persons with Disability Act of 2013 and provide further clarity about their commitment to the provision of assistive devices and associated services (e.g., repair services) and its subsequent implementation.Policymakers in Bangladesh must be proactive to translate policy commitments into practice, as it relates to building an accessible environment for people using assistive devices. Further, government efforts are needed to educate policy implementers in all relevant ministries so that all responsible bodies are fully familiar with their national and international commitments regarding the rights of persons with disabilities.Future research could (i) include user’s satisfaction with the service delivery process and (ii) measure the impact of assistive devices on family quality of life of persons with disabilities.

PMID:36215415 | DOI:10.1080/17483107.2022.2129849

JAMA. 2022 Oct 10. doi: 10.1001/jama.2022.18931. Online ahead of print.

ABSTRACT

IMPORTANCE: Some individuals experience persistent symptoms after initial symptomatic SARS-CoV-2 infection (often referred to as Long COVID).

OBJECTIVE: To estimate the proportion of males and females with COVID-19, younger or older than 20 years of age, who had Long COVID symptoms in 2020 and 2021 and their Long COVID symptom duration.

DESIGN, SETTING, AND PARTICIPANTS: Bayesian meta-regression and pooling of 54 studies and 2 medical record databases with data for 1.2 million individuals (from 22 countries) who had symptomatic SARS-CoV-2 infection. Of the 54 studies, 44 were published and 10 were collaborating cohorts (conducted in Austria, the Faroe Islands, Germany, Iran, Italy, the Netherlands, Russia, Sweden, Switzerland, and the US). The participant data were derived from the 44 published studies (10 501 hospitalized individuals and 42 891 nonhospitalized individuals), the 10 collaborating cohort studies (10 526 and 1906), and the 2 US electronic medical record databases (250 928 and 846 046). Data collection spanned March 2020 to January 2022.

EXPOSURES: Symptomatic SARS-CoV-2 infection.

MAIN OUTCOMES AND MEASURES: Proportion of individuals with at least 1 of the 3 self-reported Long COVID symptom clusters (persistent fatigue with bodily pain or mood swings; cognitive problems; or ongoing respiratory problems) 3 months after SARS-CoV-2 infection in 2020 and 2021, estimated separately for hospitalized and nonhospitalized individuals aged 20 years or older by sex and for both sexes of nonhospitalized individuals younger than 20 years of age.

RESULTS: A total of 1.2 million individuals who had symptomatic SARS-CoV-2 infection were included (mean age, 4-66 years; males, 26%-88%). In the modeled estimates, 6.2% (95% uncertainty interval [UI], 2.4%-13.3%) of individuals who had symptomatic SARS-CoV-2 infection experienced at least 1 of the 3 Long COVID symptom clusters in 2020 and 2021, including 3.2% (95% UI, 0.6%-10.0%) for persistent fatigue with bodily pain or mood swings, 3.7% (95% UI, 0.9%-9.6%) for ongoing respiratory problems, and 2.2% (95% UI, 0.3%-7.6%) for cognitive problems after adjusting for health status before COVID-19, comprising an estimated 51.0% (95% UI, 16.9%-92.4%), 60.4% (95% UI, 18.9%-89.1%), and 35.4% (95% UI, 9.4%-75.1%), respectively, of Long COVID cases. The Long COVID symptom clusters were more common in women aged 20 years or older (10.6% [95% UI, 4.3%-22.2%]) 3 months after symptomatic SARS-CoV-2 infection than in men aged 20 years or older (5.4% [95% UI, 2.2%-11.7%]). Both sexes younger than 20 years of age were estimated to be affected in 2.8% (95% UI, 0.9%-7.0%) of symptomatic SARS-CoV-2 infections. The estimated mean Long COVID symptom cluster duration was 9.0 months (95% UI, 7.0-12.0 months) among hospitalized individuals and 4.0 months (95% UI, 3.6-4.6 months) among nonhospitalized individuals. Among individuals with Long COVID symptoms 3 months after symptomatic SARS-CoV-2 infection, an estimated 15.1% (95% UI, 10.3%-21.1%) continued to experience symptoms at 12 months.

CONCLUSIONS AND RELEVANCE: This study presents modeled estimates of the proportion of individuals with at least 1 of 3 self-reported Long COVID symptom clusters (persistent fatigue with bodily pain or mood swings; cognitive problems; or ongoing respiratory problems) 3 months after symptomatic SARS-CoV-2 infection.

PMID:36215063 | DOI:10.1001/jama.2022.18931

JAMA Netw Open. 2022 Oct 3;5(10):e2234445. doi: 10.1001/jamanetworkopen.2022.34445.

ABSTRACT

IMPORTANCE: Obesity rates have risen in the United States since the 1980s. Several studies have shown links between obesity and the incidence of specific cancer types, but none have systematically examined obesity prevalence at the time of cancer diagnosis, or among clinical trial participants, all of which may affect clinical outcomes.

OBJECTIVE: To examine the prevalence of obesity and, separately, overweight and obesity over 30 years among patients with cancer enrolled in clinical treatment trials for obesity-related cancers; and to compare trends with corresponding trends in the US.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study examined clinical treatment trials for obesity-related cancers conducted by the SWOG Cancer Research Network at community and academic sites. Participants included adult patients enrolled in phase 2 or phase 3 clinical treatment trials in obesity-related cancers between 1986 and 2016. Statistical analysis was performed from June 2020 to July 2022.

EXPOSURES: Year of enrollment to a clinical trial.

MAIN OUTCOMES AND MEASURES: Prevalence of obesity (body mass index [BMI] ≥ 30) and overweight or obesity (BMI > 25) at the time of clinical trial enrollment. Multivariable logistic regression analysis, adjusted for demographic and clinical factors, was used to analyze patient height and weight collected at clinical trial enrollment.

RESULTS: Among 23 926 patients (median [IQR] age, 58 [51-66] years; 17 594 [73.5%] female; 969 [4.0%] Hispanic, 2173 [9.1%] non-Hispanic Black, 19 890 [83.1%] non-Hispanic White) enrolled between 1986 and 2016, unadjusted obesity rates increased from 23.5% (in 1986 to 1990 [n = 657]) to 42.3% (in 2011 to 2016 [n = 836]). There was an increasing linear trend in obesity (odds ratio [OR], 1.23 for each 5-year increase; 95% CI, 1.21-1.26; P < .001), which persisted after covariate adjustment for demographic and clinical characteristics. Findings were consistent for the combined prevalence of overweight and obesity. The observed overall increasing trend in obesity prevalence from 1999-2000 to 2015-2016 was greater in trial patients (21.3% [SE = 0.7] to 49.1% [SE = 1.6]) than in US adults (30.5% [SE = 1.5] to 39.6% [SE = 1.6]) (P for trend = .03), but was similar to US cancer survivors (18.9% [SE = 1.9] to 42.2% [SE = 2.1]; P for trend = .31).

CONCLUSIONS AND RELEVANCE: This cohort study found that patients with cancer and obesity are currently well-represented in cancer clinical trials, increasing confidence that trial findings are generalizable to patients with obesity in clinical practice. Availability of data on height and weight at diagnosis through cancer registries will enable a more rigorous analysis of obesity prevalence among patients with cancer.

PMID:36215073 | DOI:10.1001/jamanetworkopen.2022.34445

Med Educ. 2022 Oct 10. doi: 10.1111/medu.14949. Online ahead of print.

ABSTRACT

CONTEXT: Applicant perceptions of selection methods can affect motivation, performance and withdrawal, and may therefore be of relevance in the context of widening access. However, it is unknown how applicant subgroups perceive different selection methods.

OBJECTIVES: Using organizational justice theory, the present multi-site study examined applicant perceptions of various selection methods, rationales behind perceptions, and subgroup differences.

METHODS: Applicants to five Dutch undergraduate health professions programs (N=704) completed an online survey including demographics and a questionnaire on applicant perceptions applied to 11 commonly used selection methods. Applicants rated general favorability and justice dimensions (7-point Likert scale), and could add comments for each method.

RESULTS: Descriptive statistics revealed a preference for selection methods on which applicants feel more “in control”: general favorability ratings were highest for curriculum-sampling tests (mean [M]=5.32) and skills tests (M=5.13), while weighted lottery (M=3.05) and unweighted lottery (M=2.97) were perceived least favorable. Additionally, applicants preferred to distinguish themselves on methods that assess attributes beyond cognitive abilities. Qualitative content analysis of comments revealed several conflicting preferences, including a desire for multiple selection methods versus concerns of experiencing too much stress. Results from a linear mixed model of general favorability indicated some small subgroup differences in perceptions (based on gender, migration background, prior education and parental education), but practical meaning of these differences was negligible. Nevertheless, concerns were expressed that certain selection methods can hinder equitable admission due to inequal access to resources.

CONCLUSIONS: Our findings illustrate that applicants desire to demonstrate a variety of attributes on a combination of selection tools, but also observe that this can result in multiple drawbacks. The present study can help programs in deciding which selection methods to include, which more negatively perceived methods should be better justified to applicants, and how to adapt methods to meet applicants’ needs.

PMID:36215062 | DOI:10.1111/medu.14949

JAMA Neurol. 2022 Oct 10. doi: 10.1001/jamaneurol.2022.3185. Online ahead of print.

ABSTRACT

IMPORTANCE: No lifestyle-based randomized clinical trial directly targets psychoaffective risk factors of dementia. Meditation practices recently emerged as a promising mental training exercise to foster brain health and reduce dementia risk.

OBJECTIVE: To investigate the effects of meditation training on brain integrity in older adults.

DESIGN, SETTING, AND PARTICIPANTS: Age-Well was a randomized, controlled superiority trial with blinded end point assessment. Community-dwelling cognitively unimpaired adults 65 years and older were enrolled between November 24, 2016, and March 5, 2018, in France. Participants were randomly assigned (1:1:1) to (1) an 18-month meditation-based training, (2) a structurally matched non-native language (English) training, or (3) no intervention arm. Analysis took place between December 2020 and October 2021.

INTERVENTIONS: Meditation and non-native language training included 2-hour weekly group sessions, practice of 20 minutes or longer daily at home, and 1-day intensive practices.

MAIN OUTCOMES AND MEASURES: Primary outcomes included volume and perfusion of anterior cingulate cortex (ACC) and insula. Main secondary outcomes included a global composite score capturing metacognitive, prosocial, and self-regulatory capacities and constituent subscores.

RESULTS: Among 137 participants (mean [SD] age, 69.4 [3.8] years; 83 [60.6%] female; 54 [39.4%] male) assigned to the meditation (n = 45), non-native language training (n = 46), or no intervention (n = 46) groups, all but 1 completed the trial. There were no differences in volume changes of ACC (0.01 [98.75% CI, -0.02 to 0.05]; P = .36) or insula (0.01 [98.75% CI, -0.02 to 0.03]; P = .58) between meditation and no intervention or non-native language training groups, respectively. Differences in perfusion changes did not reach statistical significance for meditation compared with no intervention in ACC (0.02 [98.75% CI, -0.01 to 0.05]; P = .06) or compared with non-native language training in insula (0.02 [98.75% CI, -0.01 to 0.05]; P = .09). Meditation was superior to non-native language training on 18-month changes in a global composite score capturing attention regulation, socioemotional, and self-knowledge capacities (Cohen d, 0.52 [95% CI, 0.19-0.85]; P = .002).

CONCLUSIONS AND RELEVANCE: The study findings confirm the feasibility of meditation and non-native language training in elderly individuals, with high adherence and very low attrition. Findings also show positive behavioral effects of meditation that were not reflected on volume, and not significantly on perfusion, of target brain areas.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02977819.

PMID:36215061 | DOI:10.1001/jamaneurol.2022.3185