Tag: statistics

PLoS Negl Trop Dis. 2024 Jun 6;18(6):e0012232. doi: 10.1371/journal.pntd.0012232. eCollection 2024 Jun.

ABSTRACT

BACKGROUND: Ocular toxoplasmosis (OT) is the most common cause of infectious uveitis worldwide, including Thailand. This study describes the clinical presentation, visual acuity (VA) outcomes, and factors associated with VA loss in patients with active OT following antiparasitic treatment.

METHODOLOGY/PRINCIPAL FINDINGS: A retrospective chart review of patients with active OT treated with antiparasitic drugs between 2010 and 2020 was performed. Outcome measures included clinical characteristics, interval VA, and predictive factors associated with loss of VA ≤ 20/50 at 6 months post-treatment. Ninety-two patients (95 eyes) were enrolled. The median follow-up time was 10.9 months (IQR 4.9-31.8 months). The median age at presentation was 35.9 years, 51% were male, and 92.4% had unilateral OT. Eleven patients (12%) were immunocompromised (HIV infection, eight patients; receiving immunosuppressive agents, three patients). Patients mainly presented with primary retinitis without previous scar (62%), posterior pole lesion (56%), and lesion size of ≤ 2-disc area (75%). Immunocompromised patients showed a significantly larger size of retinitis than immunocompetent patients. Oral trimethoprim/sulfamethoxazole monotherapy was the primary short-term antiparasitic drug prescribed (85%). At the final visit, 21% of all affected eyes suffered VA ≤ 20/200. The cumulative incidence of recurrent OT at three years was 33.9% (95% CI, 19.7%-54.2%). Immunocompromised patients [adjusted odds ratio (aOR) 4.9, p = 0.041], macular lesion (aOR 5.4, p = 0.032), and initial VA ≤ 20/200 (aOR 9.1, p = 0.014) were predictive of having VA ≤ 20/50 at 6 months post-treatment.

CONCLUSIONS: Ocular toxoplasmosis mainly presents as unilateral primary retinitis within the posterior pole. Severe VA loss was observed in one-fifth of eyes following treatment with lesion resolution. Immunocompromised patients, eyes with macular lesions, and poor initial VA were associated with poor VA outcomes.

PMID:38843299 | DOI:10.1371/journal.pntd.0012232

PLoS One. 2024 Jun 6;19(6):e0303065. doi: 10.1371/journal.pone.0303065. eCollection 2024.

ABSTRACT

The detoxification efflux carriers (DTX) are a significant group of multidrug efflux transporter family members that play diverse functions in all kingdoms of living organisms. However, genome-wide identification and characterization of DTX family transporters have not yet been performed in banana, despite its importance as an economic fruit plant. Therefore, a detailed genome-wide analysis of DTX family transporters in banana (Musa acuminata) was conducted using integrated bioinformatics and systems biology approaches. In this study, a total of 37 DTX transporters were identified in the banana genome and divided into four groups (I, II, III, and IV) based on phylogenetic analysis. The gene structures, as well as their proteins’ domains and motifs, were found to be significantly conserved. Gene ontology (GO) annotation revealed that the predicted DTX genes might play a vital role in protecting cells and membrane-bound organelles through detoxification mechanisms and the removal of drug molecules from banana cells. Gene regulatory analyses identified key transcription factors (TFs), cis-acting elements, and post-transcriptional regulators (miRNAs) of DTX genes, suggesting their potential roles in banana. Furthermore, the changes in gene expression levels due to pathogenic infections and non-living factor indicate that banana DTX genes play a role in responses to both biotic and abiotic stresses. The results of this study could serve as valuable tools to improve banana quality by protecting them from a range of environmental stresses.

PMID:38843276 | DOI:10.1371/journal.pone.0303065

PLoS One. 2024 Jun 6;19(6):e0303354. doi: 10.1371/journal.pone.0303354. eCollection 2024.

ABSTRACT

BACKGROUND: Vietnam is experiencing an increasing prevalence of hypertension in its adult population. In addition to medical therapy, modifying adverse lifestyle practices is important for effective blood pressure control. There are limited data on unhealthy lifestyle practices in patients with chronic diseases, however, particularly among hypertensive patients living in rural Vietnam. Our study objectives were to examine the prevalence of unhealthy lifestyle practices and associated factors among rural Vietnamese adults with uncontrolled hypertension.

METHODS: Data from the baseline survey of a cluster randomized trial among hypertensive Vietnamese adults (2017-2022) were utilized. Information on unhealthy lifestyle practices including smoking, excessive alcohol consumption, physical inactivity, and inadequate fruit and vegetable intake was collected from study participants. The primary study outcome was having ≥2 unhealthy lifestyle practices. A multivariable logistic regression model was used to examine factors associated with the primary study outcome.

RESULTS: The mean age of the 671 patients was 67 years and 45.0% were men. Nearly three out of every four participants had one or fewer unhealthy practices, 24.0% had two, and 3.3% had three or all four unhealthy lifestyle practices. Men, individuals who did unpaid work or were unemployed, and individuals with hypertension level III were more likely to have ≥2 unhealthy lifestyle practices, whereas individuals with higher education were less likely to have ≥2 unhealthy lifestyle practices compared with respective comparison groups.

CONCLUSIONS: We observed a high prevalence of unhealthy lifestyle practices among rural Vietnamese patients with uncontrolled hypertension. Several demographic factors were associated with a greater number of unhealthy lifestyle practices. Newer interventions and educational programs encouraging lifestyle modification practices are needed to control hypertension among adults living in rural settings of Vietnam.

PMID:38843274 | DOI:10.1371/journal.pone.0303354

PLoS One. 2024 Jun 6;19(6):e0304162. doi: 10.1371/journal.pone.0304162. eCollection 2024.

ABSTRACT

BACKGROUND: Pulmonary tuberculosis (PTB) is the most common type of tuberculosis (TB). Rapid diagnosis of PTB can help in TB control. Although the use of molecular tests (such as the GeneXpert MTB/RIF) has improved the ability to rapidly diagnose PTB, there is still room for improvement. Nanopore sequencing is a novel means of rapid TB detection. The purpose of this study was to establish a systematic review and meta-analysis protocol for evaluating the accuracy of nanopore sequencing for the rapid diagnosis of PTB.

METHODS: We completed this protocol according to the Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) statement and registered on the PROSPERO platform. We will screen studies related to nanopore sequencing for diagnosis of PTB by searching through PubMed, EMBASE, the Cochrane Library using English, and Wanfang database, CNKI (China National Knowledge Infrastructure) using Chinese. Eligible studies will be screened according to the inclusion and exclusion criteria established in the study protocol. We will evaluate the methodological quality of the individual included studies using Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2). We will use Stata (version 15.0) with the midas command and RevMan (version 5.3) for meta-analysis and forest plots and SROC curves generation. A p < 0.05 was treated as a statistically significant difference. When significant heterogeneity exists between studies, we will explore sources of heterogeneity through meta-regression analysis and subgroup analysis.

CONCLUSION: To the best of our knowledge, this will be the first systematic review and meta-analysis of nanopore sequencing for the diagnosis of PTB. We hope that this study will find a new and effective tool for the early diagnosis of PTB.

PROSPERO REGISTRATION NUMBER: CRD42023495593.

PMID:38843269 | DOI:10.1371/journal.pone.0304162

PLoS One. 2024 Jun 6;19(6):e0301425. doi: 10.1371/journal.pone.0301425. eCollection 2024.

ABSTRACT

BACKGROUND: The influence of center volume on kidney transplant outcomes is a topic of ongoing debate. In this study, we employed competing risk analyses to accurately estimate the marginal probability of graft failure in the presence of competing events, such as mortality from other causes with long-term outcomes. The incorporation of immunosuppression protocols and extended follow-up offers additional insights. Our emphasis on long-term follow-up aligns with biological considerations where competing risks play a significant role.

METHODS: We examined data from 219,878 adult kidney-only transplantations across 256 U.S. transplant centers (January 2001-December 2015) sourced from the Organ Procurement and Transplantation Network registry. Centers were classified into quartiles by annual volume: low (Q1 = 28), medium (Q2 = 75), medium-high (Q3 = 121), and high (Q4 = 195). Our study investigated the relationship between center volume and 5-year outcomes, focusing on graft failure and mortality. Sub-population analyses included deceased donors, living donors, diabetic recipients, those with kidney donor profile index >85%, and re-transplants from deceased donors.

RESULTS: Adjusted cause-specific hazard ratios (aCHR) for Five-Year Graft Failure and Patient Death were examined by center volume, with low-volume centers as the reference standard (aCHR: 1.0). In deceased donors, medium-high and high-volume centers showed significantly lower cause-specific hazard ratios for graft failure (medium-high aCHR = 0.892, p<0.001; high aCHR = 0.953, p = 0.149) and patient death (medium-high aCHR = 0.828, p<0.001; high aCHR = 0.898, p = 0.003). Among living donors, no significant differences were found for graft failure, while a trend towards lower cause-specific hazard ratios for patient death was observed in medium-high (aCHR = 0.895, p = 0.107) and high-volume centers (aCHR = 0.88, p = 0.061).

CONCLUSION: Higher center volume is associated with significantly lower cause-specific hazard ratios for graft failure and patient death in deceased donors, while a trend towards reduced cause-specific hazard ratios for patient death is observed in living donors.

PMID:38843258 | DOI:10.1371/journal.pone.0301425

JMIR Res Protoc. 2024 Jun 6;13:e56271. doi: 10.2196/56271.

ABSTRACT

BACKGROUND: Globally, there are marked inconsistencies in how immunosuppression is characterized and subdivided into clinical risk groups. This is detrimental to the precision and comparability of disease surveillance efforts-which has negative implications for the care of those who are immunosuppressed and their health outcomes. This was particularly apparent during the COVID-19 pandemic; despite collective motivation to protect these patients, conflicting clinical definitions created international rifts in how those who were immunosuppressed were monitored and managed during this period. We propose that international clinical consensus be built around the conditions that lead to immunosuppression and their gradations of severity concerning COVID-19. Such information can then be formalized into a digital phenotype to enhance disease surveillance and provide much-needed intelligence on risk-prioritizing these patients.

OBJECTIVE: We aim to demonstrate how electronic Delphi objectives, methodology, and statistical approaches will help address this lack of consensus internationally and deliver a COVID-19 risk-stratified phenotype for “adult immunosuppression.”

METHODS: Leveraging existing evidence for heterogeneous COVID-19 outcomes in adults who are immunosuppressed, this work will recruit over 50 world-leading clinical, research, or policy experts in the area of immunology or clinical risk prioritization. After 2 rounds of clinical consensus building and 1 round of concluding debate, these panelists will confirm the medical conditions that should be classed as immunosuppressed and their differential vulnerability to COVID-19. Consensus statements on the time and dose dependencies of these risks will also be presented. This work will be conducted iteratively, with opportunities for panelists to ask clarifying questions between rounds and provide ongoing feedback to improve questionnaire items. Statistical analysis will focus on levels of agreement between responses.

RESULTS: This protocol outlines a robust method for improving consensus on the definition and meaningful subdivision of adult immunosuppression concerning COVID-19. Panelist recruitment took place between April and May of 2024; the target set for over 50 panelists was achieved. The study launched at the end of May and data collection is projected to end in July 2024.

CONCLUSIONS: This protocol, if fully implemented, will deliver a universally acceptable, clinically relevant, and electronic health record-compatible phenotype for adult immunosuppression. As well as having immediate value for COVID-19 resource prioritization, this exercise and its output hold prospective value for clinical decision-making across all diseases that disproportionately affect those who are immunosuppressed.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/56271.

PMID:38842925 | DOI:10.2196/56271

Am J Orthopsychiatry. 2024 Jun 6. doi: 10.1037/ort0000753. Online ahead of print.

ABSTRACT

Despite the importance of the school environment for mental health outcomes, there is little research on how the school context during adolescence may impact depressive symptoms among Asian Americans (AAs) over time. The purpose of this study was to investigate (a) the long-term effects of perceived prejudice from peers and teachers on school belonging and depressive symptoms in adolescence, early young adulthood, and young adulthood among AAs and (b) the mediating effects of school belonging and two early depressive symptoms on the associations between perceived prejudice from peers and teachers and young adulthood depressive symptoms. The data came from the National Longitudinal Study on Adolescent Health. The present study used a subsample of 689 AAs who completed interviews during adolescence, young adulthood, and adulthood. The major data analysis strategy was structural equation modeling. The structural equation modeling results indicated that the major path coefficients from school context to depressive symptoms at the three time points for AAs were statistically significant, except for the path from adolescent depressive symptoms to young adulthood depressive symptoms. There were three significant mediating effects of school belonging and two early depressive symptoms on the association between perceived prejudice from teachers and young adulthood depressive symptoms in AAs. The results emphasize the importance of identifying school contextual risk factors leading to mental health disparities and developing culturally appropriate intervention strategies for AAs. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

PMID:38842898 | DOI:10.1037/ort0000753

Psychol Rev. 2024 Jun 6. doi: 10.1037/rev0000463. Online ahead of print.

ABSTRACT

A central goal of research into language acquisition is explaining how, when learners generalize to new cases, they appropriately restrict their generalizations (e.g., to avoid producing ungrammatical utterances such as *the clown laughed the man; “*” indicates an ungrammatical form). The past 30 years have seen an unresolved debate between statistical preemption and entrenchment as explanations. Under preemption, the use of a verb in a particular construction (e.g., *the clown laughed the man) is probabilistically blocked by hearing that other verb constructions with similar meanings only (e.g., the clown made the man laugh). Under entrenchment, such errors (e.g., *the clown laughed the man) are probabilistically blocked by hearing any utterance that includes the relevant verb (e.g., by the clown made the man laugh and the man laughed). Across five artificial-language-learning studies, we designed a training regime such that learners received evidence for the (by the relevant hypothesis) ungrammaticality of a particular unattested verb/noun + particle combination (e.g., *chila + kem; *squeako + kem) via either preemption only or entrenchment only. Across all five studies, participants in the preemption condition (as per our preregistered prediction) rated unattested verb/noun + particle combinations as less acceptable for restricted verbs/nouns, which appeared during training, than for unrestricted, novel-at-test verbs/nouns, which did not appear during training, that is, strong evidence for preemption. Participants in the entrenchment condition showed no evidence for such an effect (and in 3/5 experiments, positive evidence for the null). We conclude that a successful model of learning linguistic restrictions must instantiate competition between different forms only where they express the same (or similar) meanings. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

PMID:38842892 | DOI:10.1037/rev0000463

Psychol Addict Behav. 2024 Jun 6. doi: 10.1037/adb0001015. Online ahead of print.

ABSTRACT

OBJECTIVE: A propensity for aggression or alcohol use may be associated with alcohol-related aggression. Previous research has shown genetic overlap between alcohol use and aggression but has not looked at how alcohol-related aggression may be uniquely influenced by genetic risk for aggression or alcohol use. The present study examined the associations of genetic risk for trait aggression, alcohol use, and alcohol use disorder (AUD) with alcohol-related aggression using a polygenic risk score (PRS) approach.

METHOD: Using genome-wide association study summary statistics, PRSs were created for trait aggression, alcohol consumption, and AUD. These PRSs were used to predict the phenotype of alcohol-related aggression among drinkers in two independent samples: the University of California at San Francisco (UCSF) Family Alcoholism Study (n = 1,162) and the National Longitudinal Study of Adolescent to Adult Health (Add Health; n = 4,291).

RESULTS: There were significant associations between the AUD PRS and lifetime alcohol-related aggression in the UCSF study sample. Additionally, the trait aggression PRS was associated with three or more experiences of hitting anyone else and getting into physical fights while under the influence of alcohol, along with a composite score of three or more experiences of alcohol-related aggression, in the UCSF study sample. No significant associations were observed in the Add Health sample. Limited sex-specific genetic effects were observed.

CONCLUSIONS: These results provide preliminary evidence that genetic influences underlying alcohol use and aggression are uniquely associated with alcohol-related aggression and suggest that these associations may differ by type and frequency of alcohol-related aggression incidents. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

PMID:38842867 | DOI:10.1037/adb0001015

J Vis. 2024 Jun 3;24(6):5. doi: 10.1167/jov.24.6.5.

ABSTRACT

Ensemble processing allows the visual system to condense visual information into useful summary statistics (e.g., average size), thereby overcoming capacity limitations to visual working memory and attention. To examine the role of attention in ensemble processing, we conducted three experiments using a novel paradigm that merged the action effect (a manipulation of attention) and ensemble processing. Participants were instructed to make a simple action if the feature of a cue word corresponded to a subsequent shape. Immediately after, they were shown an ensemble display of eight ovals of varying sizes and were asked to report either the average size of all ovals or the size of a single oval from the set. In Experiments 1 and 2, participants were cued with a task-relevant feature, and in Experiment 3, participants were cued with a task-irrelevant feature. Overall, the task-relevant cues that elicited an action influenced reports of average size in the ensemble phase more than the cues that were passively viewed, whereas task-irrelevant cues did not bias the reports of average size. The results of this study suggest that attention influences ensemble processing only when it is directed toward a task-relevant feature.

PMID:38842835 | DOI:10.1167/jov.24.6.5