Category: Statistics

Brief Bioinform. 2024 Jul 25;25(5):bbae419. doi: 10.1093/bib/bbae419.

ABSTRACT

The human gut microbiota produces diverse, extensive metabolites that have the potential to affect host physiology. Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut microbiota is still lacking. Here, we present Enteropathway, a metabolic pathway database that integrates 3269 compounds, 3677 reactions, and 876 modules that were obtained from 1012 manually curated scientific literature. Notably, 698 modules of these modules are new entries and cannot be found in any other databases. The database is accessible from a web application (https://enteropathway.org) that offers a metabolic diagram for graphical visualization of metabolic pathways, a customization interface, and an enrichment analysis feature for highlighting enriched modules on the metabolic diagram. Overall, Enteropathway is a comprehensive reference database that can complement widely used databases, and a tool for visual and statistical analysis in human gut microbiota studies and was designed to help researchers pinpoint new insights into the complex interplay between microbiota and host metabolism.

PMID:39222063 | DOI:10.1093/bib/bbae419

Br J Dev Psychol. 2024 Sep 2. doi: 10.1111/bjdp.12520. Online ahead of print.

ABSTRACT

Examining mechanisms underlying sex differences in children’s play styles, we studied girls with congenital adrenal hyperplasia (CAH) who provide a test of the relative effects of prenatal androgens versus rearing, and of behavioural similarity versus gender identity and cognitions. In this exploratory study, 40 focal children (girls and boys with and without CAH), aged 3-8 years, played for 14 min with a same-sex peer in a task designed to elicit rough-and-tumble play. Time-indexed ratings of positive affect and vigour of activity were evaluated via network mapping for sex-related differences in both levels and play dynamics (temporal relations among behaviours). Results suggest influences of both gender identity-aligned social cognitions and prenatal androgens: there was greater dyadic synchrony between positive affect for girls (regardless of CAH status) than boys, but girls with CAH displayed positive affect levels and directed vigorous peer play dynamics similar to boys.

PMID:39222059 | DOI:10.1111/bjdp.12520

Immun Inflamm Dis. 2024 Sep;12(9):e1371. doi: 10.1002/iid3.1371.

ABSTRACT

OBJECTIVE: To examine the relationship between C-reactive protein (CRP) and knee pain, and further explore whether this association is mediated by obesity.

METHODS: The population was derived from 1999 to 2004 National Health and Nutrition Examination Survey. Logistic regression was used to analyze the relationship between CRP and knee pain in three different models, and the linear trend was analyzed. A restricted cubic spline model to assess the nonlinear dose-response relationship between CRP and knee pain. Mediation analyses were used to assess the potential mediating role of obesity. Subgroup analyses and sensitivity analyses were performed to ensure robustness.

RESULTS: Compared with adults with lower CRP (first quartile), those with higher CRP had higher risks of knee pain (odds ratio 1.39, 95% confidence interval 1.12-1.72 in third quartile; 1.56, 1.25-1.95 in fourth quartile) after adjusting for covariates (except body mass index [BMI]), and the proportion mediated by BMI was 76.10% (p < .001). BMI and CRP were linear dose-response correlated with knee pain. The odds ratio for those with obesity compared with normal to knee pain was 2.27 (1.42-3.65) in the first quartile of CRP, 1.99 (1.38-2.86) in the second, 2.15 (1.38-3.33) in the third, and 2.92 (1.72-4.97) in the fourth.

CONCLUSION: Obesity mediated the systemic inflammation results in knee pain in US adults. Moreover, higher BMI was associated with higher knee pain risk in different degree CRP subgroups, supporting an important role of weight loss in reducing knee pain caused by systemic inflammation.

PMID:39222043 | DOI:10.1002/iid3.1371

Appl Neuropsychol Child. 2024 Sep 2:1-7. doi: 10.1080/21622965.2024.2394178. Online ahead of print.

ABSTRACT

OBJECTIVES: Mental chronometry is the scientific study of cognitive processing speed measured by reaction time (RT), which is the elapsed time between the onset of a stimulus and an individual’s response. This study aims at measuring the RT among young children with autism spectrum disorders (ASD) and comparing it with normal (typically developing) children.

METHODS: 60 ASD children were selected from different ASD centers, and 60 normal children were selected from different kindergartens for participation in this study. Participants were aged 3-6 years old. The RT was measured using the Fitlight trainer device. The findings were statistically evaluated using independent t-tests and ANOVA tests.

RESULT: Significant differences (p < 0.0001) were found between both groups in all tasks, and ASD children demonstrated slower RT compared to the normal group. The RT measured through three senses (visual, auditory, and touch) for ASD and normal were 3.64 ± 2.16, 13.19 ± 2.41(trial), 1835.23 ± 757.95, 697.12 ± 87.83 (second), and 1550.89 ± 499.76, 752.67 ± 124.02 (second) respectively.

CONCLUSION: The evaluated RT showed significant impairment in RT among ASD in comparison to normal children and this was true for the three senses. The Fitlight trainer could be used to assess RT and stimulus-response among ASD children in various cognitive tasks. Similar studies, involving larger samples from different areas and involving other sense organs, are indicated to confirm the results.

PMID:39222037 | DOI:10.1080/21622965.2024.2394178

Biometrics. 2024 Jul 1;80(3):ujae082. doi: 10.1093/biomtc/ujae082.

ABSTRACT

Testing multiple hypotheses of conditional independence with provable error rate control is a fundamental problem with various applications. To infer conditional independence with family-wise error rate (FWER) control when only summary statistics of marginal dependence are accessible, we adopt GhostKnockoff to directly generate knockoff copies of summary statistics and propose a new filter to select features conditionally dependent on the response. In addition, we develop a computationally efficient algorithm to greatly reduce the computational cost of knockoff copies generation without sacrificing power and FWER control. Experiments on simulated data and a real dataset of Alzheimer’s disease genetics demonstrate the advantage of the proposed method over existing alternatives in both statistical power and computational efficiency.

PMID:39222026 | DOI:10.1093/biomtc/ujae082

Clinics (Sao Paulo). 2024 Aug 31;79:100477. doi: 10.1016/j.clinsp.2024.100477. Online ahead of print.

ABSTRACT

OBJECTIVES: To determine the prevalence and association of HPV and Herpesviruses in saliva and tissue samples of patients with orofacial tumors.

METHODS: Biopsies of tumors were done, and saliva samples were collected from patients with orofacial tumors for the determination of viruses using nested multiplex PCR. Independent variables were sex, age, comorbidities, tumor stage, and length of stay. Outcome variables were the presence or absence of herpesviruses and HPV. Descriptive summaries and inferential statistics were done.

RESULTS: A hundred patients were included in the study. Prevalence of herpesviruses and HPV were 17.6 % and 57.0 % in tumors, and 48.3 % and 60.0 % in the saliva of patients respectively. Herpesviruses detected included EBV (21.3 %), HHV-7 (11.2 %), CMV (6.7 %), HSV-1 (5.1 %), HSV-2 (1.1 %), VZV (1.1 %), and Kaposi sarcoma virus (0.6 %). The most prevalent HPV genotypes were HPV-42 (29 %), HPV-43 (22.7 %), HPV-52 (22.2 %), HPV-39 (18.8 %), and HPV-18 (9.1 %). The odds of EBV being detected in malignant orofacial tumors were 2 times that of benign orofacial tumors. HPV DNA in the saliva of patients with orofacial tumors was 69.7 %, compared to 18.2 % of the control sample (p < 0.001). The median length of stay for all participants was 6.5 days, those associated with viruses stayed longer.

CONCLUSION: There was a high prevalence of Herpesviruses and HPV in saliva and tumor samples of patients with orofacial tumors, signalling some potential for more work to be done in this area.

PMID:39217675 | DOI:10.1016/j.clinsp.2024.100477

Psychiatry Res Neuroimaging. 2024 Aug 24;344:111880. doi: 10.1016/j.pscychresns.2024.111880. Online ahead of print.

ABSTRACT

BACKGROUND: Major Depressive Disorder (MDD), as a chronic mental disorder, causes changes in mood, thoughts, and behavior. The pathophysiology of the disorder and its treatment are still unknown. One of the most notable changes observed in patients with MDD through fMRI is abnormal functional brain connectivity.

METHODS: Preprocessed data from 60 MDD patients and 60 normal controls (NCs) were selected, which has been performed using the DPARSF toolbox. The whole-brain functional networks and topologies were extracted using graph theory-based methods. A two-sample, two-tailed t-test was used to compare the topological features of functional brain networks between the MDD and NCs groups using the DPABI-Net/Statistical Analysis toolbox.

RESULTS: The obtained results showed a decrease in both global and local efficiency in MDD patients compared to NCs, and specifically, MDD patients showed significantly higher path length values. Acceptable p-values were obtained with a small sample size and less computational volume compared to the other studies on large datasets. At the node level, MDD patients showed decreased and relatively decreased node degrees in the sensorimotor network (SMN) and the dorsal attention network (DAN), respectively, as well as decreased node efficiency in the SMN, default mode network (DMN), and DAN. Also, MDD patients showed slightly decreased node efficiency in the visual networks (VN) and the ventral attention network (VAN), which were reported after FDR correction with Q < 0.05.

LIMITATIONS: All participants were Chinese.

CONCLUSIONS: Collectively, increased path length, decreased global and local efficiency, and also decreased nodal degree and efficiency in the SMN, DAN, DAN, VN, and VAN were found in patients compared to NCs.

PMID:39217670 | DOI:10.1016/j.pscychresns.2024.111880

Poult Sci. 2024 Aug 22;103(11):104237. doi: 10.1016/j.psj.2024.104237. Online ahead of print.

ABSTRACT

Organic acids and botanicals have shown protective effects on gut barrier and against inflammation in broilers. However, their effects on intestinal digestive enzymes and nutrients transporters expression and functions have not been fully studied. The objective of this study was to understand how a microencapsulated blend of botanicals and organic acids affected intestinal enzyme activities and nutrient transporters expression and functions in broilers. A total of 288 birds were assigned to a commercial control diet or diet supplemented with 500 g/MT (metric ton) of the microencapsulated additive. Growth performance was recorded weekly. At d 21 and d 42, jejunum and ileum were isolated for enzyme (maltase, sucrase, and aminopeptidase) and transporter (SGLT1, GLUT2, GLUT1, EAAT3, B⁰AT1, and PepT1) analyses. Jejunum specific nutrients (glucose, alanine, and glutamate) transport activities were evaluated by Ussing chamber. Protein expression of nutrient transporters in small intestine were measured in mucosa and brush-border membrane (BBM) samples by western blot. Intestinal gene expression of the transporters was determined by RT-PCR. Statistical analysis was performed using Student’s t-test comparing the supplemented diet to the control. The feed efficiency was significantly improved through the study period in the supplemented group (P ≤ 0.05). Significant changes of intestinal histology were shown in both jejunum (P ≤ 0.10) and ileum (P ≤ 0.05) after 21 d of treatment. At d21, jejunal maltase activity was upregulated (P ≤ 0.10). The Ussing chamber transport of glucose and alanine was increased, which was in line with increased gene expression (GLUT2, GLUT1, EAAT3, and B⁰AT1) (P ≤ 0.10 and P ≤ 0.05, respectively) and BBMV protein levels (B⁰AT1, P < 0.10). At d21, ileal sucrase and maltase activities were upregulated (P ≤ 0.05). Increased expressions of GLUT1, EAAT3, and B⁰AT1 were observed in both mRNA and protein levels (P ≤ 0.05). Similar pattern of changes was also shown at d42 of age. Our results suggest that feeding microencapsulated additives improves intestinal nutrient digestion and transporter expression and function in broilers, thereby enhancing feed efficiency.

PMID:39217663 | DOI:10.1016/j.psj.2024.104237

Clin Chem Lab Med. 2024 Sep 2. doi: 10.1515/cclm-2024-0647. Online ahead of print.

NO ABSTRACT

PMID:39217629 | DOI:10.1515/cclm-2024-0647

Eur Heart J Acute Cardiovasc Care. 2024 Sep 1:zuae093. doi: 10.1093/ehjacc/zuae093. Online ahead of print.

ABSTRACT

AIMS: In a recent meta-analysis of randomized controlled trials, routine use of veno-arterial ECMO (VA-ECMO) did not improve outcomes in patients with acute myocardial infarction-related cardiogenic shock (AMI-CS), while a microaxial flow pump reduced mortality in a selected group of patients with AMI-CS in the DanGer-Shock trial.

METHODS AND RESULTS: Individual patient data of patients included in four randomized clinical trials investigating the routine use of VA-ECMO in AMI-CS were centrally analysed. For the purpose of this sub-analysis, DanGer-Shock-like patients were analysed (STEMI only, presumed low likelihood of brain injury). The primary endpoint was 180-day all-cause mortality. A total of 202 patients (106 randomized to VA-ECMO and 96 to control) were included. There were no differences in baseline characteristics, angiographic and interventional features between the two groups. Mortality after 6 months was numerically lower with VA-ECMO between the groups [45% in VA-ECMO group vs. 51% in control group; hazard ratio, 0.84; 95% confidence interval (CI), 0.56-1.26], while major bleeding (OR, 2.24; 95% CI, 1.08-4.64) and peripheral vascular complications (OR, 3.65; 95% CI, 1.15-11.56) were increased with the use of VA-ECMO.

CONCLUSION: In this exploratory subgroup analysis in patients with CS, STEMI, and a low likelihood of brain injury, there was no mortality benefit with the routine use of VA-ECMO. However, as indicated by the large confidence intervals, the statistical power was limited to draw definite conclusions.

PMID:39217624 | DOI:10.1093/ehjacc/zuae093