Tag: statistics

Bioinformatics. 2023 Jun 30;39(Supplement_1):i131-i139. doi: 10.1093/bioinformatics/btad242.

ABSTRACT

MOTIVATION: Recent advances in spatial proteomics technologies have enabled the profiling of dozens of proteins in thousands of single cells in situ. This has created the opportunity to move beyond quantifying the composition of cell types in tissue, and instead probe the spatial relationships between cells. However, most current methods for clustering data from these assays only consider the expression values of cells and ignore the spatial context. Furthermore, existing approaches do not account for prior information about the expected cell populations in a sample.

RESULTS: To address these shortcomings, we developed SpatialSort, a spatially aware Bayesian clustering approach that allows for the incorporation of prior biological knowledge. Our method is able to account for the affinities of cells of different types to neighbour in space, and by incorporating prior information about expected cell populations, it is able to simultaneously improve clustering accuracy and perform automated annotation of clusters. Using synthetic and real data, we show that by using spatial and prior information SpatialSort improves clustering accuracy. We also demonstrate how SpatialSort can perform label transfer between spatial and nonspatial modalities through the analysis of a real world diffuse large B-cell lymphoma dataset.

AVAILABILITY AND IMPLEMENTATION: Source code is available on Github at: https://github.com/Roth-Lab/SpatialSort.

PMID:37387130 | DOI:10.1093/bioinformatics/btad242

Bioinformatics. 2023 Jun 30;39(Supplement_1):i194-i203. doi: 10.1093/bioinformatics/btad265.

ABSTRACT

MOTIVATION: Recent methods for selective sweep detection cast the problem as a classification task and use summary statistics as features to capture region characteristics that are indicative of a selective sweep, thereby being sensitive to confounding factors. Furthermore, they are not designed to perform whole-genome scans or to estimate the extent of the genomic region that was affected by positive selection; both are required for identifying candidate genes and the time and strength of selection.

RESULTS: We present ASDEC (https://github.com/pephco/ASDEC), a neural-network-based framework that can scan whole genomes for selective sweeps. ASDEC achieves similar classification performance to other convolutional neural network-based classifiers that rely on summary statistics, but it is trained 10× faster and classifies genomic regions 5× faster by inferring region characteristics from the raw sequence data directly. Deploying ASDEC for genomic scans achieved up to 15.2× higher sensitivity, 19.4× higher success rates, and 4× higher detection accuracy than state-of-the-art methods. We used ASDEC to scan human chromosome 1 of the Yoruba population (1000Genomes project), identifying nine known candidate genes.

PMID:37387128 | DOI:10.1093/bioinformatics/btad265

Stud Health Technol Inform. 2023 Jun 29;305:588-591. doi: 10.3233/SHTI230565.

ABSTRACT

Our pilot study aimed at exploratory radiogenomic data analysis in patients with NF2-associated schwannomatosis (formerly neurofibromatosis type II) to assume the potential of image biomarkers in this pathology. Fifty-three unrelated patients (37 (69.8%) women, avg. age 30.2 ± 11.2 y.o.) were enrolled in the study. First-order, gray-level co-occurrence matrix (GLCM), gray-level run length matrix (GLRLM), and geometry-based statistics were calculated (3718 features per region of interest). We demonstrated imaging patterns and statistically significant differences in radiomic features potentially related to the genotype and clinical phenotype of the disease. However, the clinical utility of these patterns should be further evaluated. The study was supported by the Russian Science Foundation grant 21-15-00262.

PMID:37387099 | DOI:10.3233/SHTI230565

Stud Health Technol Inform. 2023 Jun 29;305:487-490. doi: 10.3233/SHTI230539.

ABSTRACT

The aim of this study was to investigate whether exposure to the pandemic was associated with increased in-hospital mortality for health failure. We collected data from patients hospitalized between 2019 and 2020 and we assessed the likelihood of in-hospital death. Although the positive association of exposure to the COVID period with an increased in-hospital mortality is not statistically significant, this may underscore other factors that may influence mortality. Our study was designed to contribute to a better understanding of the impact of the pandemic on in-hospital mortality and to identify potential areas for intervention in patient care.

PMID:37387073 | DOI:10.3233/SHTI230539

Stud Health Technol Inform. 2023 Jun 29;305:479-482. doi: 10.3233/SHTI230537.

ABSTRACT

Coronavirus epidemic has quickly become a global health threat. The ophthalmology department, like all other departments, have adopted resource management and personnel adjustment maneuvers. The aim of this work was to describe the impact of covid on the Ophthalmology Department of University Hospital “Federico II” of Naples. In the study logistical regression was used for a comparison between the pandemic and the previous period, analyzing patient features. The analysis showed a decrease in the number of accesses; reduction of the length of stay; and the statistically dependent variables are as follows: LOS, discharge procedures and admission procedure.

PMID:37387071 | DOI:10.3233/SHTI230537

Stud Health Technol Inform. 2023 Jun 29;305:475-476. doi: 10.3233/SHTI230535.

ABSTRACT

This cross-sectional study aimed to explore the Mental Health Status and the relationship between socioeconomic background and mean scores of mental health variables among Caregivers (CG) in Maha Sarakham province, Northeast of Thailand. A total of 402 CGs were recruited from 32 sub-districts in 13 districts to participate with interviewing form. Data analysing used descriptive statistics and Chi-square test for the relationship of the socioeconomic and the level of mental health status of caregivers. The results shown that; 99.77% were female, age average 49.89+8.14 (range 23-75), spent time look after the elderly for average 3 days per week, worked experience for 1-4 years (mean=3.27+1.66 years). Over 59 % have lower income than 150 USD. The gender of CG was a mainly statistically significant with the mental health status (MHS) (p=0.003). Although, the other variables were not significantly statistics test, however, it found that all variables indicated in the poor level of mental health status. Therefore, the stakeholders who involves with CG should have concern to reduce their burnout, regardless of compensation as well as set up the potential of family caregivers or young carers to help the elderly in the community.

PMID:37387069 | DOI:10.3233/SHTI230535

Stud Health Technol Inform. 2023 Jun 29;305:464-468. doi: 10.3233/SHTI230532.

ABSTRACT

Covid-19 pandemic has influenced stroke care in different ways. Recent reports demonstrated a sharp decline in acute stroke admissions worldwide. Even for patients presented to dedicated healthcare services, management at the acute phase may be sub-optimal. On the other hand, Greece has been praised for the early initiation of restriction measures which were associated with a ‘milder’ surge of SARS-CoV-2 infection. Methods Data derived from a prospective cohort multicenter registry. The study population consisted of first-ever acute stroke patients, hemorrhagic or ischemic, admitted within 48 hours of symptom onset in seven national healthcare system (NHS) and University hospitals in Greece. Two different time periods have been considered, defined as “before Covid-19” (15/12/2019-15/02/2020) and “during Covid-19” (16/02/2020-15/04-2020) era. Statistical comparisons on acute stroke admission characteristics between the two different time periods have been performed. Results This exploratory analysis of 112 consecutive patients showed a reduction of acute stroke admissions by 40during Covid-19 period. No significant differences were observed regarding stroke severity, risk factor profile and baseline characteristics for patients admitted before and during Covid-19 pandemic period. There is a significant delay between symptom onset to CT scan during Covid-19 era compared to the period before pandemic reached Greece (p=0.03). Conclusions The rate of acute stroke admissions has been reduced by 40% during Covid-19 pandemic. Further research is needed to clarify whether the reduction in stroke volume is actual or not and identifying the reasons underlying the paradox.

PMID:37387066 | DOI:10.3233/SHTI230532

Disaster Med Public Health Prep. 2023 Jun 30;17:e421. doi: 10.1017/dmp.2023.89.

ABSTRACT

OBJECTIVE: Concerns about the side effects of available coronavirus disease (COVID-19) vaccines have posed a significant barrier to vaccination in several countries. Accordingly, the current study aimed to assess the acceptability of COVID-19 vaccination and its predictors among the Lebanese population.

METHODS: A cross-sectional study was conducted in February 2021 among Lebanese adults from the 5 main Lebanese districts. The questionnaire included demographic data, questions about COVID-19 experience, COVID-19 anxiety syndrome scale, and attitudes regarding the COVID-19 vaccine. Data were analyzed on SPSS, version 23. Statistical significance was considered at a P value ≤ 0.05 with a 95% CI.

RESULTS: Of 811 participants, 45.4% (95% CI: 41.9-48.9) accepted taking the COVID-19 vaccine. Choices were negatively affected by concerns about the side effects of the vaccine and positively affected by anxiety and seeking COVID-19 news very closely. Moreover, if the COVID-19 vaccination was a requirement for traveling, participants would be more willing to get the vaccine.

CONCLUSIONS: Since 54.7% of the studied Lebanese adults were either unwilling or undecided to get the vaccine and COVID-19 news was retrieved mainly from the Ministry of Public Health online site and the local news, the existing targeted campaign should be enforced toward encouraging vaccination to reach herd immunity against COVID-19 and revealing the safety of the vaccines.

PMID:37385751 | DOI:10.1017/dmp.2023.89

Open Heart. 2023 Jun;10(1):e002206. doi: 10.1136/openhrt-2022-002206.

ABSTRACT

BACKGROUND: Patients who experience acute myocardial infarction (AMI) are at risk of recurrent AMI. Contemporary data on recurrent AMI and its association with return emergency department (ED) visits for chest pain are needed.

METHODS: This Swedish retrospective cohort study linked patient-level data from six participating hospitals to four national registers to construct the Stockholm Area Chest Pain Cohort (SACPC). The AMI cohort included SACPC participants visiting the ED for chest pain diagnosed with AMI and discharged alive (first primary diagnosis of AMI during the study period not necessarily the patient’s first AMI). The rate and timing of recurrent AMI events, return ED visits for chest pain and all-cause mortality were determined during the year following index AMI discharge.

RESULTS: Among 1 37 706 patients presenting to the ED with chest pain as principal complaint from 2011 to 2016, 5.5% (7579/137 706) were hospitalised with AMI. In total, 98.5% (7467/7579) of patients were discharged alive. In the year following index AMI discharge, 5.8% (432/7467) of AMI patients experienced ≥1 recurrent AMI event. Return ED visits for chest pain occurred in 27.0% (2017/7467) of index AMI survivors. During a return ED visit, recurrent AMI was diagnosed in 13.6% (274/2017) of patients. One-year all-cause mortality was 3.1% in the AMI cohort and 11.6% in the recurrent AMI cohort.

CONCLUSIONS: In this AMI population, 3 in 10 AMI survivors returned to the ED for chest pain in the year following AMI discharge. Furthermore, over 10% of patients with return ED visits were diagnosed with recurrent AMI during that visit. This study confirms the high residual ischaemic risk and associated mortality among AMI survivors.

PMID:37385732 | DOI:10.1136/openhrt-2022-002206

Cardiol Young. 2023 Jun 30:1-6. doi: 10.1017/S1047951123001622. Online ahead of print.

ABSTRACT

BACKGROUND: Metabolic syndrome leading to type 2 diabetes mellitus and cardiovascular diseases is a chronic multifactorial syndrome, associated with low-grade inflammation status. In our study, we aimed at assessing the serum levels of follistatin (FST), pregnancy-associated plasma protein-A (PAPP-A), and platelet/endothelial cell adhesion molecule-1 (PECAM-1) in adolescent patients with metabolic syndrome.

METHODS: This study was performed in 43 (19 males, 24 females) metabolic syndrome adolescents and 37 lean controls matched for age and sex. The serum levels of FST, PECAM-1, and PAPP-A were measured by using ELISA method.

RESULTS: Serum FST and PAPP-A levels in metabolic syndrome were significantly higher than those of controls (p < 0.005 and p < 0.05). However, there was no difference in serum PECAM-1 levels between metabolic syndrome and control groups (p = 0.927). There was a significant positive correlation between serum FST and triglyceride (r = 0.252; p < 0.05), and PAPP-A and weight, (r = 0.252; p < 0.05) in metabolic syndrome groups. Follistatin was determined statistically significant in both univariate (p = 0,008) and multivariate (p = 0,011) logistic regression analysis.

CONCLUSIONS: Our findings indicated a significant relationship between FST and PAPP-A levels and metabolic syndrome. These findings offer the possibility of using these markers in diagnosis of metabolic syndrome in adolescents as the prevention of the future complications.

PMID:37385726 | DOI:10.1017/S1047951123001622