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Nevin Manimala Statistics

Statistical method accounts for microscopic electric field distortions around neurons when simulating activation thresholds

bioRxiv [Preprint]. 2024 Oct 26:2024.10.25.619982. doi: 10.1101/2024.10.25.619982.

ABSTRACT

Notwithstanding advances in computational models of neuromodulation, there are mismatches between simulated and experimental activation thresholds. Transcranial Magnetic Stimulation (TMS) of the primary motor cortex generates motor evoked potentials (MEPs). At the threshold of MEP generation, whole-head models predict macroscopic (at millimeter scale) electric fields (50-70 V/m) which are considerably below conventionally simulated cortical neuron thresholds (200-300 V/m). We hypothesize that this apparent contradiction is in part a consequence of electrical field warping by brain microstructure. Classical neuronal models ignore the physical presence of neighboring neurons and microstructure and assume that the macroscopic field directly acts on the neurons. In previous work, we performed advanced numerical calculations considering realistic microscopic compartments (e.g., cells, blood vessels), resulting in locally inhomogeneous (micrometer scale) electric field and altered neuronal activation thresholds. Here we combine detailed neural threshold simulations under homogeneous field assumptions with microscopic field calculations, leveraging a novel statistical approach. We show that, provided brain-region specific microstructure metrics, a single statistically derived scaling factor between microscopic and macroscopic electric fields can be applied in predicting neuronal thresholds. For the cortical sample considered, the statistical methods match TMS experimental thresholds. Our approach can be broadly applied to neuromodulation models, where fully coupled microstructure scale simulations may not be practical.

PMID:39484517 | PMC:PMC11527135 | DOI:10.1101/2024.10.25.619982

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Nevin Manimala Statistics

Quality assessment and control of unprocessed anatomical, functional, and diffusion MRI of the human brain using MRIQC

bioRxiv [Preprint]. 2024 Oct 22:2024.10.21.619532. doi: 10.1101/2024.10.21.619532.

ABSTRACT

Quality control of MRI data prior to preprocessing is fundamental, as substandard data are known to increase variability spuriously. Currently, no automated or manual method reliably identifies subpar images, given pre-specified exclusion criteria. In this work, we propose a protocol describing how to carry out the visual assessment of T1-weighted, T2-weighted, functional, and diffusion MRI scans of the human brain with the visual reports generated by MRIQC. The protocol describes how to execute the software on all the images of the input dataset using typical research settings (i.e., a high-performance computing cluster). We then describe how to screen the visual reports generated with MRIQC to identify artifacts and potential quality issues and annotate the latter with the “rating widget” – a utility that enables rapid annotation and minimizes bookkeeping errors. Integrating proper quality control checks on the unprocessed data is fundamental to producing reliable statistical results and crucial to identifying faults in the scanning settings, preempting the acquisition of large datasets with persistent artifacts that should have been addressed as they emerged.

PMID:39484445 | PMC:PMC11526949 | DOI:10.1101/2024.10.21.619532

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Nevin Manimala Statistics

The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity

bioRxiv [Preprint]. 2024 Oct 23:2024.10.23.619767. doi: 10.1101/2024.10.23.619767.

ABSTRACT

The NHGRI-EBI GWAS Catalog serves as a vital resource for the genetic research community, providing access to the most comprehensive database of human GWAS results. Currently, it contains close to 7,000 publications for more than 15,000 traits, from which more than 625,000 lead associations have been curated. Additionally, 85,000 full genome-wide summary statistics datasets – containing association data for all variants in the analysis – are available for downstream analyses such as meta-analysis, fine-mapping, Mendelian randomisation or development of polygenic risk scores. As a centralised repository for GWAS results, the GWAS Catalog sets and implements standards for data submission and harmonisation, and encourages the use of consistent descriptors for traits, samples and methodologies. We share processes and vocabulary with the PGS Catalog, improving interoperability for a growing user group. Here, we describe the latest changes in data content, improvements in our user interface, and the implementation of the GWAS-SSF standard format for summary statistics. We address the challenges of handling the rapid increase in large-scale molecular quantitative trait GWAS and the need for sensitivity in the use of population and cohort descriptors while maintaining data interoperability and reusability.

PMID:39484403 | PMC:PMC11526975 | DOI:10.1101/2024.10.23.619767

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Nevin Manimala Statistics

Fiber Microstructure Quantile (FMQ) Regression: A Novel Statistical Approach for Analyzing White Matter Bundles from Periphery to Core

bioRxiv [Preprint]. 2024 Oct 22:2024.10.19.619237. doi: 10.1101/2024.10.19.619237.

ABSTRACT

The structural connections of the brain’s white matter are critical for brain function. Diffusion MRI tractography enables the in-vivo reconstruction of white matter fiber bundles and the study of their relationship to covariates of interest, such as neurobehavioral or clinical factors. In this work, we introduce Fiber Microstructure Quantile (FMQ) Regression, a new statistical approach for studying the association between white matter fiber bundles and scalar factors (e.g., cognitive scores). Our approach analyzes tissue microstructure measures based on quantile-specific bundle regions . These regions are defined according to the quantiles of fractional anisotropy (FA) from the periphery to the core of a population fiber bundle, which pools all individuals’ bundles. To investigate how fiber bundle tissue microstructure relates to covariates of interest, we employ the statistical technique of quantile regression. Unlike ordinary regression, which only models a conditional mean, quantile regression models the conditional quantiles of a response variable. This enables the proposed analysis, where a quantile regression is fitted for each quantile-specific bundle region. To demonstrate FMQ Regression, we perform an illustrative study in a large healthy young adult tractography dataset derived from the Human Connectome Project-Young Adult (HCP-YA), focusing on particular bundles expected to relate to particular aspects of cognition and motor function. Importantly, our analysis considers sex-specific effects in brain-behavior associations. In comparison with a traditional method, Automated Fiber Quantification (AFQ), which enables FA analysis in regions defined along the trajectory of a bundle, our results suggest that FMQ Regression is much more powerful for detecting brain-behavior associations. Importantly, FMQ Regression finds significant brain-behavior associations in multiple bundles, including findings unique to males or to females. In both males and females, language performance is significantly associated with FA in the left arcuate fasciculus, with stronger associations in the bundle’s periphery. In males only, memory performance is significantly associated with FA in the left uncinate fasciculus, particularly in intermediate regions of the bundle. In females only, motor performance is significantly associated with FA in the left and right corticospinal tracts, with a slightly lower relationship at the bundle periphery and a slightly higher relationship toward the bundle core. No significant relationships are found between executive function and cingulum bundle FA. Our study demonstrates that FMQ Regression is a powerful statistical approach that can provide insight into associations from bundle periphery to bundle core. Our results also identify several brain-behavior relationships unique to males or to females, highlighting the importance of considering sex differences in future research.

PMID:39484397 | PMC:PMC11526951 | DOI:10.1101/2024.10.19.619237

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Nevin Manimala Statistics

Deletions Rate-Limit Breast and Ovarian Cancer Initiation

bioRxiv [Preprint]. 2024 Oct 21:2024.10.17.618945. doi: 10.1101/2024.10.17.618945.

ABSTRACT

Optimizing prevention and early detection of cancer requires understanding the number, types and timing of driver mutations. To quantify this, we exploited the elevated cancer incidence and mutation rates in germline BRCA1 and BRCA2 (gBRCA1/2) carriers. Using novel statistical models, we identify genomic deletions as the likely rate-limiting mutational processes, with 1-3 deletions required to initiate breast and ovarian tumors. gBRCA1/2 -driven hereditary and sporadic tumors undergo convergent evolution to develop a similar set of driver deletions, and deletions explain the elevated cancer risk of gBRCA1/2 -carriers. Orthogonal mutation timing analysis identifies deletions of chromosome 17 and 13q as early, recurrent events. Single-cell analyses confirmed deletion rate differences in gBRCA1/2 vs. non-carrier tumors as well as cells engineered to harbor gBRCA1/2 . The centrality of deletion-associated chromosomal instability to tumorigenesis shapes interpretation of the somatic evolution of non-malignant tissue and guides strategies for precision prevention and early detection.

PMID:39484366 | PMC:PMC11526986 | DOI:10.1101/2024.10.17.618945

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Nevin Manimala Statistics

Systematic review and meta-analysis of the association between ABCA7 common variants and Alzheimer’s disease in non-Hispanic White and Asian cohorts

Front Aging Neurosci. 2024 Oct 17;16:1406573. doi: 10.3389/fnagi.2024.1406573. eCollection 2024.

ABSTRACT

BACKGROUND AND AIMS: The relationship between the ABCA7 gene and Alzheimer’s disease (AD) has been widely studied across various populations. However, the results have been inconsistent. This meta-analysis aimed to evaluate the association of ABCA7 polymorphisms with AD risk, including specific subtypes such as late-onset Alzheimer’s disease (LOAD).

METHODS: Relevant studies were identified through comprehensive database searches, and the quality of each study was assessed using the Newcastle-Ottawa Scale (NOS). Allele and genotype frequencies were extracted from the included studies. The pooled odds ratios (OR) with corresponding 95% confidence intervals (CI) were calculated using random-effects or fixed-effects models. Multiple testing corrections were conducted using the false discovery rate (FDR) method. The Cochran Q statistic and I2 metric were used to evaluate heterogeneity between studies, while Egger’s test and funnel plots were employed to assess publication bias.

RESULTS: A total of 36 studies, covering 21 polymorphisms and involving 31,809 AD cases and 44,994 controls, were included in this meta-analysis. NOS scores ranged from 7 to 9, indicating high-quality studies. A total of 11 SNPs (rs3764650, rs3752246, rs4147929, rs3752232, rs3752243, rs3764645, rs4147934, rs200538373, rs4147914, rs4147915, and rs115550680) in ABCA7 were significantly associated with AD risk. Among these SNPs, two (rs3764650 and rs3752246) were also found to be related to the late-onset AD (LOAD) subtype. In addition, two SNPs (rs4147929 and rs4147934) were associated with the susceptibility to AD only in non-Hispanic White populations. A total of 10 SNPs (rs3764647, rs3752229, rs3752237, rs4147932, rs113809142, rs3745842, rs3752239, rs4147918, rs74176364, and rs117187003) showed no significant relationship with AD risk. Sensitivity analyses confirmed the reliability of the original results, and heterogeneity was largely attributed to deviations from Hardy-Weinberg equilibrium, ethnicity, and variations between individual studies.

CONCLUSION: The available evidence suggests that specific ABCA7 SNPs may be associated with AD risk. Future studies with larger sample sizes will be necessary to confirm these results.

SYSTEMATIC REVIEW REGISTRATION: https://www.crd.york.ac.uk/prospero/, identifier: CRD42024540539.

PMID:39484364 | PMC:PMC11524920 | DOI:10.3389/fnagi.2024.1406573

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Nevin Manimala Statistics

Connectivity changes in two-channel prefrontal ERP associated with early cognitive decline in the elderly population: beta band responses to the auditory oddball stimuli

Front Aging Neurosci. 2024 Oct 17;16:1456169. doi: 10.3389/fnagi.2024.1456169. eCollection 2024.

ABSTRACT

BACKGROUND: This study utilized recent advancements in electroencephalography (EEG) technology that enable the measurement of prefrontal event-related potentials (ERPs) to facilitate the early detection of mild cognitive impairment (MCI). We investigated two-channel prefrontal ERP signals obtained from a large cohort of elderly participants and compare among cognitively normal (CN), subjective cognitive decline (SCD), amnestic MCI (aMCI), and nonamnestic MCI (naMCI) groups.

METHODS: Signal processing and ERP component analyses, specifically adapted for two-channel prefrontal ERP signals evoked by the auditory oddball task, were performed on a total of 1,754 elderly participants. Connectivity analyses were conducted to assess brain synchronization, especially in the beta band involving the phase locking value (PLV) and coherence (COH). Time-frequency, time-trial, grand average, and further statistical analyses of the standard and target epochs were also conducted to explore differences among the cognition groups.

RESULTS: The MCI group’s response to target stimuli was characterized by greater response time variability (p < 0.001) and greater variability in the P300 latency (p < 0.05), leading to less consistent responses than those of the healthy control (HC) group (CN+SCD subgroups). In the connectivity analyses of PLV and COH waveforms, significant differences were observed, indicating a loss of synchronization in the beta band in response to standard stimuli in the MCI group. In addition, the absence of event-related desynchronization (ERD) indicated that information processing related to readiness and task performance in the beta band was not efficient in the MCI group. Furthermore, the observed decline in the P200 amplitude as the standard trials progressed suggests the impaired attention and inhibitory processes in the MCI group compared to the HC group. The aMCI subgroup showed high variability in COH values, while the naMCI subgroup showed impairments in their overall behavioral performance.

CONCLUSION: These findings highlight the variability and connectivity measures can be used as markers of early cognitive decline; such measures can be assessed with simple and fast two-channel prefrontal ERP signals evoked by both standard and target stimuli. Our study provides deeper insight of cognitive impairment and the potential use of the prefrontal ERP connectivity measures to assess early cognitive decline.

PMID:39484363 | PMC:PMC11524914 | DOI:10.3389/fnagi.2024.1456169

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Nevin Manimala Statistics

Evaluation of a training course for general practitioners within the melanoma multimedia education programme of the Italian Melanoma Intergroup: a study protocol

Dermatol Reports. 2024 Feb 9;16(3):9919. doi: 10.4081/dr.2024.9919. eCollection 2024 Sep 2.

ABSTRACT

The text discusses the role of general practitioners (GPs) in the prevention and early diagnosis of melanoma, a type of skin cancer. It highlights the need for GPs to be able to recognize suspicious skin lesions and refer patients to specialist dermatology centers. However, many GPs lack comprehensive training in diagnosing melanoma. The text mentions that various training courses have been conducted for GPs, but their impact on clinical practice has been limited. The MelaMEd Programme is an e-learning course developed by the Italian Melanoma Intergroup (IMI). The programme aims to provide GPs with comprehensive knowledge of melanoma prevention, diagnosis, and treatment. It includes an e-learning section, and a dedicated platform called MelaMEd platform, which offers a multimedia atlas of melanoma. The objective of the study is to evaluate the impact of the MelaMEd programme on GPs’ diagnostic accuracy, knowledge of melanoma, and management of suspicious lesions. The methodology involves administering pre-training and post-training questionnaires to participants, assessing their diagnostic skills and evaluating the training course’s effectiveness. The study aims to demonstrate the effectiveness of the MelaMEd programme in improving GPs’ ability to recognize and manage melanoma. It also seeks to identify areas for improvement and recommend interventions to enhance diagnostic accuracy. The results will be analyzed statistically using descriptive, univariate, and multivariate analysed methods.

PMID:39484362 | PMC:PMC11526653 | DOI:10.4081/dr.2024.9919

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Nevin Manimala Statistics

Patterns of referral to interprofessional services among frail older adults presenting to emergency departments in Canada

J Am Geriatr Soc. 2024 Oct 31. doi: 10.1111/jgs.19253. Online ahead of print.

ABSTRACT

BACKGROUND: Geriatric Emergency Department (ED) Guidelines recommend optimizing transitions of care for older patients with complex needs. In this study, we investigated referral patterns to interprofessional services, including occupational therapy, physiotherapy, dietician, social work, home care, and specialized geriatric services, among older adults presenting to the ED with high-risk characteristics.

METHODS: We recruited community-dwelling older adults presenting to 10 EDs across Ontario, Quebec, and Newfoundland, Canada, from April 2017 to July 2018. To observe processes of care in the ED, we deployed a two-stage high-risk case-finding and focused comprehensive assessment process based on the interRAI ED-Screener and ED Contact Assessment to identify and characterize older adults at high risk. We analyzed the secondary data using descriptive statistics and logistic regression.

RESULTS: We screened 5265 individuals with the ED Screener, further assessed 1479 with the ED Contact Assessment, and analyzed data from a subset of 1055 community-dwelling older adults assessed with the ED Contact Assessment. Participants in our study sample had a mean age of 83 years, 58% were female, and many had a complex burden of cognitive and functional impairment and social needs. Over half of this high-needs sample were referred to general home care services (62.7%), occupational therapy (59.3%), and physiotherapy services (55.2%), while 16% were referred to specialized geriatric services. We also found a significant positive association between interprofessional referrals and the Assessment Urgency Algorithm and Institutional Risk Scale. The most important determinants of referral to interprofessional services were hospital province, functional, clinical, and social burden and support measures.

CONCLUSIONS: The referral patterns identified suggest that patient needs and risk intensity did not always guide referral patterns in the Canadian EDs investigated. We suggest that EDs critically examine the appropriateness of their documentation and referral systems for supporting person-centered care provision.

PMID:39482258 | DOI:10.1111/jgs.19253

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Nevin Manimala Statistics

Pulsed dye laser in jellyfish-induced keloids

J Cosmet Laser Ther. 2024 Oct 31:1-5. doi: 10.1080/14764172.2024.2420990. Online ahead of print.

ABSTRACT

Jellyfish stings can cause acute inflammatory skin lesions that may hesitate in keloids. Pulsed dye laser (PDL) represents one of the most effective treatments for newly developed keloids. Aim of this study was to evaluate the efficacy of PDL on newly developed keloids specifically induced by jellyfish stings in pediatric patients.We conducted a retrospective observational study on pediatric patients with newly developed keloids from jellyfish stings, treated in the last two years with 595 nm wavelength PDL with a duration of 0.45-1.5 msec, spot-size 7 mm and fluence 8.5-9.5 J/cm2. PDL therapy was administered for a mean of 7.4 treatment sessions, every 1-3 months. Two expert dermatologists evaluated the vascularity, pigmentation, height, and pliability of keloids, according to the Vancouver Scar Scale (VSS), pre-and-post treatment. A total of 17 patients (7 males, 10 females) were included in the study, mean age of 11 years. Overall, mean pre-treatment global VSS was 11.0 ± 1.50. After treatment, global VSS was 3.88 ± 1.87. At paired t-test, the difference between pre-treatment and post-treatment was highly statistically significant (p < .0001). Commonly, manipulation and therapeutic intervention on jellyfish scars and keloids is feared. The present study supports the use of PDL in keloids secondary to jellyfish stings, though conducted on a limited number of patients.

PMID:39482257 | DOI:10.1080/14764172.2024.2420990