Category: Statistics

Proc Natl Acad Sci U S A. 2024 Mar 12;121(11):e2321882121. doi: 10.1073/pnas.2321882121. Epub 2024 Mar 5.

NO ABSTRACT

PMID:38442168 | DOI:10.1073/pnas.2321882121

Proc Natl Acad Sci U S A. 2024 Mar 12;121(11):e2321196121. doi: 10.1073/pnas.2321196121. Epub 2024 Mar 5.

NO ABSTRACT

PMID:38442167 | DOI:10.1073/pnas.2321196121

PLoS One. 2024 Mar 5;19(3):e0300030. doi: 10.1371/journal.pone.0300030. eCollection 2024.

ABSTRACT

Community-based tourism (CBT) in Thailand faces challenges in adapting to COVID-19 prevention measures. The purpose of the study was to evaluate levels of knowledge, practice, and compliance regarding safety and health measures of the entrepreneur in managing CBT under the Safety and Health Administration (SHA) standard in the new normal situation. A descriptive cross-sectional study was conducted on twenty-one entrepreneurs from three CBTs in three districts in Nakhon Si Thammarat, in the months of February-May 2021. Levels of knowledge and practice were evaluated by questionnaires and compliance level was evaluated by SHA standard checklist. The level of knowledge and practice were categorized sufficient and insufficient, while compliance level was categorized as high or low if scores met or exceeded 80%, based on Bloom’s cut-off point. Information on sociodemographic characteristics was also gathered. Fisher’s exact test with a 95% confidence level (α < 0.05) was used for statistical analysis. The findings revealed that 66.7% and 38.1% of the establishments in the study had sufficient knowledge (Mean ± SD: 46.9 ± 7.2, Max: 55.0, Min: 33.0) and sufficient practice (Mean ± SD: 40.4 ± 9.2, Max: 55.0, Min: 29.0), respectively. In addition, the study found that knowledge level was significantly associated with practice level at a p-value of 0.018. However, compliance level was not related to knowledge and practice. In conclusion, the low level of compliance was due to a lack of understanding and motivation to comply with the standard, and the budget of small establishments in CBT for bringing them up to the SHA standard was quite limited. Therefore, the related organizations should use a variety of strategies to encourage entrepreneurs, such as partnership building and resource support.

PMID:38442100 | DOI:10.1371/journal.pone.0300030

PLoS One. 2024 Mar 5;19(3):e0299026. doi: 10.1371/journal.pone.0299026. eCollection 2024.

ABSTRACT

BACKGROUND: The peripheral immune system is altered in Parkinson’s disease (PD), but the causal relationship between the two remains controversial. In this study, we aimed to estimate the causal relationship between peripheral immune features and PD using a two-sample Mendelian randomization (MR) approach.

METHODS: Genome-wide association study (GWAS) data of peripheral blood immune signatures from European populations were used for exposure and PD summary statistics were used as results. We conducted a two-sample MR study using the inverse-variance weighted (IVW), MR-Egger, and weighted median methods to evaluate the causal association between these factors. MR-Egger and MR-PRESSO were used for sensitivity analysis to test and correct horizontal pleiotropy.

RESULTS: A total of 731 immune traits were analyzed for association with PD using three MR methods. After adjustment for FDR, we observed four peripheral immunological features associated with PD using the IVW method, including expression of CX3CR1 on monocytes [OR: 0.85, 95% CI: (0.81, 0.91), P = 6.56E-07] and CX3CR1 on CD14+CD16+ monocytes [OR: 0.87, 95% CI: (0.82, 0.93), P = 9.95E-06].

CONCLUSIONS: Our study further revealed the important role of monocytes in PD and indicated that CX3CR1 expression on monocytes is associated with a reduced risk of PD.

PMID:38442099 | DOI:10.1371/journal.pone.0299026

PLoS One. 2024 Mar 5;19(3):e0297625. doi: 10.1371/journal.pone.0297625. eCollection 2024.

ABSTRACT

Narcolepsy type 1 (NT1) is an enigmatic sleep disorder characterized by the selective loss of neurons producing orexin (also named hypocretin) in the lateral hypothalamus. Although NT1 is believed to be an autoimmune disease, the orexinergic neuron-specific antigens targeted by the pathogenic immune response remain elusive. In this study, we evaluated the differential binding capacity of various peptides to serum immunoglobin G from patients with NT1 and other hypersomnolence complaints (OHCs). These peptides were selected using an unbiased phage display technology or based on their significant presence in the serum of NT1 patients as identified from previous studies. Although the subtractive biopanning strategy successfully enriched phage clones with high reactivity against NT1 serum IgG, the 101 randomly selected individual phage clones could not differentiate the sera from NT1 and OHC. Compared to the OHC control group, serum from several NT1 patients exhibited increased reactivity to the 12-mer peptides derived from TRBV7, BCL-6, NRXN1, RXRG, HCRT, and RTN4 proteins, although not statistically significant. Collectively, employing both unbiased and targeted methodologies, we were unable to detect the presence of specific autoantibodies in our NT1 patient cohort. This further supports the hypothesis that the autoimmune response in NT1 patients likely stems primarily from T cell-mediated immunity rather than humoral immunity.

PMID:38442093 | DOI:10.1371/journal.pone.0297625

PLoS One. 2024 Mar 5;19(3):e0299109. doi: 10.1371/journal.pone.0299109. eCollection 2024.

ABSTRACT

Population structure and genetic diversity are the key parameters to study the breeding history of animals. This research aimed to provide a characterization of the population structure and to compare the effective population size (Ne), LD decay, genetic diversity, and genomic inbreeding in Iranian native Caspian (n = 38), Turkmen (n = 24) and Kurdish (n = 29) breeds and some other exotic horses consisting of Arabian (n = 24), Fell pony (n = 21) and Akhal-Teke (n = 20). A variety of statistical population analysis techniques, such as principal component analysis (PCA), discriminant analysis of principal component (DAPC) and model-based method (STRUCTURE) were employed. The results of the population analysis clearly demonstrated a distinct separation of native and exotic horse breeds and clarified the relationships between studied breeds. The effective population size (Ne) for the last six generations was estimated 54, 49, 37, 35, 27 and 26 for the Caspian, Kurdish, Arabian, Turkmen, Akhal-Teke and Fell pony breeds, respectively. The Caspian breed showed the lowest LD with an average r2 value of 0.079, while the highest was observed in Fell pony (0.148). The highest and lowest average observed heterozygosity were found in the Kurdish breeds (0.346) and Fell pony (0.290) breeds, respectively. The lowest genomic inbreeding coefficient based on run of homozygosity (FROH) and excess of homozygosity (FHOM) was in the Caspian and Kurdish breeds, respectively, while based on genomic relationship matrix) FGRM) and correlation between uniting gametes) FUNI) the lowest genomic inbreeding coefficient was found in the Kurdish breed. The estimation of genomic inbreeding rates in the six breeds revealed that FROH yielded lower estimates compared to the other three methods. Additionally, the Iranian breeds displayed lower levels of inbreeding compared to the exotic breeds. Overall, the findings of this study provide valuable insights for the development of effective breeding management strategies aimed at preserving these horse breeds.

PMID:38442089 | DOI:10.1371/journal.pone.0299109

J Stroke Cerebrovasc Dis. 2023 Dec;32(12):107446. doi: 10.1016/j.jstrokecerebrovasdis.2023.107446. Epub 2023 Oct 31.

ABSTRACT

OBJECTIVES: This study aimed to investigate the causal relationship between Atrial Fibrillation (AF) and the risk of Stroke using a Mendelian randomization (MR) approach.

METHODS: A two-sample MR analysis was conducted using publicly available genome-wide association study (GWAS) summary statistics data. In this analysis, genetic variants associated with AF were used as instrumental variables to estimate the causal effect. The inverse-variance weighted (IVW) method, weighted median estimator, and MR-Egger regression were employed for estimation. Additionally, sensitivity analysis was performed using the leave-one-out method.

RESULTS: The analysis included 87 single nucleotide polymorphisms (SNPs) associated with AF. The results from the IVW method indicated a positive association between genetic predisposition to AF and the risk of stroke (OR 1.002, 95 % CI 1.001-1.003, P < 0.001). The weighted median and MR-Egger methods showed consistent results (weighted median: OR 1.001, 95 % CI 1.000-1.002, P = 0.034; MR-Egger: OR 1.001, 95 % CI 1.000-1.003, P = 0.086). Sensitivity analysis demonstrated that no individual SNP significantly influenced the causal inference.

CONCLUSIONS: This study provides evidence of a causal relationship between AF and an elevated risk of stroke. These findings emphasize the significance of managing AF in order to prevent and treat strokes. Additional research is required to better understand the underlying mechanisms of this causal association.

PMID:38442074 | DOI:10.1016/j.jstrokecerebrovasdis.2023.107446

IEEE J Biomed Health Inform. 2024 Mar 5;PP. doi: 10.1109/JBHI.2024.3372999. Online ahead of print.

ABSTRACT

Performance degradation due to distribution discrepancy is a longstanding challenge in intelligent imaging, particularly for chest X-rays (CXRs). Recent studies have demonstrated that CNNs are biased toward styles (e.g., uninformative textures) rather than content (e.g., shape), in stark contrast to the human vision system. Radiologists tend to learn visual cues from CXRs and thus perform well across multiple domains. Motivated by this, we employ the novel on-the-fly style randomization modules at both image (SRM-IL) and feature (SRM-FL) levels to create rich style perturbed features while keeping the content intact for robust cross-domain performance. Previous methods simulate unseen domains by constructing new styles via interpolation or swapping styles from existing data, limiting them to available source domains during training. However, SRM-IL samples the style statistics from the possible value range of a CXR image instead of the training data to achieve more diversified augmentations. Moreover, we utilize pixel-wise learnable parameters in the SRM-FL compared to pre-defined channel-wise mean and standard deviations as style embeddings for capturing more representative style features. Additionally, we leverage consistency regularizations on global semantic features and predictive distributions from with and without style-perturbed versions of the same CXR to tweak the model’s sensitivity toward content markers for accurate predictions. Our proposed method, trained on CheXpert and MIMIC-CXR datasets, achieves 77.32&±0.35, 88.38&±0.19, 82.63&±0.13 AUCs(%) on the unseen domain test datasets, i.e., BRAX, VinDr-CXR, and NIH chest X-ray14, respectively, compared to 75.56&±0.80, 87.57&±0.46, 82.07&±0.19 from state-of-the-art models on five-fold cross-validation with statistically significant results in thoracic disease classification.

PMID:38442052 | DOI:10.1109/JBHI.2024.3372999

IEEE J Biomed Health Inform. 2024 Mar 5;PP. doi: 10.1109/JBHI.2024.3372968. Online ahead of print.

ABSTRACT

OBJECTIVE: To develop a cuffless method for estimating blood pressure (BP) from fingertip strain plethysmography (SPG) recordings.

METHODS: A custom-built micro-electromechanical systems (MEMS) strain sensor is employed to record heartbeat-induced vibrations at the fingertip. An XGboost regressor is then trained to relate SPG recordings to beat-to-beat systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP) values. For this purpose, each SPG segment in this setup is represented by a feature vector consisting of cardiac time interval, amplitude features, statistical properties, and demographic information of the subjects. In addition, a novel concept, coined geometric features, are introduced and incorporated into the feature space to further encode the dynamics in SPG recordings. The performance of the regressor is assessed on 32 healthy subjects through 5-fold cross-validation (5-CV) and leave-subject-out cross validation (LSOCV).

RESULTS: Mean absolute errors (MAEs) of 3.88 mmHg and 5.45 mmHg were achieved for DBP and SBP estimations, respectively, in the 5-CV setting. LSOCV yielded MAEs of 8.16 mmHg for DBP and 16.81 mmHg for SBP. Through feature importance analysis, 3 geometric and 26 integral-related features introduced in this work were identified as primary contributors to BP estimation. The method exhibited robustness against variations in blood pressure level (normal to critical) and body mass index (underweight to obese), with MAE ranges of [1.28, 4.28] mmHg and [2.64, 7.52] mmHg, respectively.

CONCLUSION: The findings suggest high potential for SPG-based BP estimation at the fingertip.

SIGNIFICANCE: This study presents a fundamental step towards the augmentation of optical sensors that are susceptible to dark skin tones.

PMID:38442050 | DOI:10.1109/JBHI.2024.3372968