Tag: statistics

Sci Rep. 2022 May 4;12(1):7299. doi: 10.1038/s41598-022-10711-0.

ABSTRACT

Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.

PMID:35508560 | DOI:10.1038/s41598-022-10711-0

Sci Rep. 2022 May 4;12(1):7308. doi: 10.1038/s41598-022-11184-x.

ABSTRACT

Children born very preterm are at significant risk of neurodevelopmental impairment. This study sought to identify differences in cognitive function in children born very preterm compared to term-born controls and investigate alteration in white matter microstructure and functional connectivity (FC) based on tract-based spatial statistics (TBSS) and resting-state functional MRI, respectively. At 6 years of age, 36 children born very preterm (< 32 weeks’ gestation) without major neurological disabilities and 26 term-born controls were tested using the Wechsler Intelligence Scale for Children, 4th edition, and Child Behavior Checklist. Whole-brain deterministic tractography and FC measurements were performed in both groups. The very preterm group had significantly lower intelligence scores than the term-born controls. The TBSS revealed no significant differences between the two groups, whereas FC was significantly increased between the frontoparietal network and the language network and was significantly decreased between the right salience network nodes in the very preterm group. The altered FC patterns between specific regions of the higher-order networks may reflect underlying deficits in the functional network architecture associated with cognitive function. Further studies are needed to demonstrate a direct connection between FC in these regions and cognitive function.

PMID:35508563 | DOI:10.1038/s41598-022-11184-x

Heredity (Edinb). 2022 May 4. doi: 10.1038/s41437-022-00539-9. Online ahead of print.

ABSTRACT

We evaluated the performances of three BLUP and five Bayesian methods for genomic prediction by using nine actual and 54 simulated datasets. The genomic prediction accuracy was measured using Pearson’s correlation coefficient between the genomic estimated breeding value (GEBV) and the observed phenotypic data using a fivefold cross-validation approach with 100 replications. The Bayesian alphabets performed better for the traits governed by a few genes/QTLs with relatively larger effects. On the contrary, the BLUP alphabets (GBLUP and CBLUP) exhibited higher genomic prediction accuracy for the traits controlled by several small-effect QTLs. Additionally, Bayesian methods performed better for the highly heritable traits and, for other traits, performed at par with the BLUP methods. Further, genomic BLUP (GBLUP) was identified as the least biased method for the GEBV estimation. Among the Bayesian methods, the Bayesian ridge regression and Bayesian LASSO were less biased than other Bayesian alphabets. Nonetheless, genomic prediction accuracy increased with an increase in trait heritability, irrespective of the sample size, marker density, and the QTL type (major/minor effect). In sum, this study provides valuable information regarding the choice of the selection method for genomic prediction in different breeding programs.

PMID:35508540 | DOI:10.1038/s41437-022-00539-9

Sci Rep. 2022 May 4;12(1):7247. doi: 10.1038/s41598-022-10923-4.

ABSTRACT

The pandemic burden caused by the SARS-CoV-2 coronavirus constitutes a global public health emergency. Increasing understanding about predisposing factors to infection and severity is now a priority. Genetic, metabolic, and environmental factors can play a crucial role in the course and clinical outcome of COVID-19. We aimed to investigate the putative relationship between genetic factors associated to obesity, metabolism and lifestyle, and the presence and severity of SARS-CoV-2 infection. A total of 249 volunteers (178 women and 71 men, with mean and ± SD age of 49 ± 11 years) characterized for dietary, lifestyle habits and anthropometry, were studied for presence and severity of COVID-19 infection, and genotyped for 26 genetic variants related to obesity, lipid profile, inflammation, and biorhythm patterns. A statistically significant association was found concerning a protective effect of APOE rs7412 against SARS-CoV-2 infection (p = 0.039; OR 0.216; CI 0.084, 0.557) after correction for multiple comparisons. This protective effect was also ascribed to the APOɛ2 allele (p = 0.001; OR 0.207; CI 0.0796, 0.538). The genetic variant rs7412 resulting in ApoE2, genetic determinant of lipid and lipoprotein levels, could play a significant role protecting against SARS-CoV-2 infection.

PMID:35508522 | DOI:10.1038/s41598-022-10923-4

Sci Rep. 2022 May 4;12(1):7211. doi: 10.1038/s41598-022-10945-y.

ABSTRACT

With the COVID-19 pandemic, documenting whether health care workers (HCWs) are at increased risk of SARS-CoV-2 contamination and identifying risk factors is of major concern. In this multicenter prospective cohort study, HCWs from frontline departments were included in March and April 2020 and followed for 3 months. SARS-CoV-2 serology was performed at month 0 (M0), M1, and M3 and RT-PCR in case of symptoms. The primary outcome was laboratory-confirmed SARS-CoV-2 infection at M3. Risk factors of laboratory-confirmed SARS-CoV-2 infection at M3 were identified by multivariate logistic regression. Among 1062 HCWs (median [interquartile range] age, 33 [28-42] years; 758 [71.4%] women; 321 [30.2%] physicians), the cumulative incidence of SARS-CoV-2 infection at M3 was 14.6% (95% confidence interval [CI] [12.5; 16.9]). Risk factors were the working department specialty, with increased risk for intensive care units (odds ratio 1.80, 95% CI [0.38; 8.58]), emergency departments (3.91 [0.83; 18.43]) and infectious diseases departments (4.22 [0.92; 18.28]); current smoking was associated with reduced risk (0.36 [0.21; 0.63]). Age, sex, professional category, number of years of experience in the job or department, and public transportation use were not significantly associated with laboratory-confirmed SARS-CoV-2 infection at M3. The rate of SARS-CoV-2 infection in frontline HCWs was 14.6% at the end of the first COVID-19 wave in Paris and occurred mainly early. The study argues for an origin of professional in addition to private life contamination and therefore including HCWs in the first-line vaccination target population. It also highlights that smokers were at lower risk.Trial registration The study has been registered on ClinicalTrials.gov: NCT04304690 first registered on 11/03/2020.

PMID:35508515 | DOI:10.1038/s41598-022-10945-y

J Chem Inf Model. 2022 May 4. doi: 10.1021/acs.jcim.2c00255. Online ahead of print.

ABSTRACT

Optimization of binding affinities for ligands to their target protein is a primary objective in rational drug discovery. Herein, we report on a collaborative study that evaluates various compounds designed to bind to the SET and MYND domain-containing protein 3 (SMYD3). SMYD3 is a histone methyltransferase and plays an important role in transcriptional regulation in cell proliferation, cell cycle, and human carcinogenesis. Experimental measurements using the scintillation proximity assay show that the distributions of binding free energies from a large number of independent measurements exhibit non-normal properties. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to predict the binding free energies and to provide a detailed chemical insight into the nature of ligand-protein binding. Our results show that the 1-trajectory ESMACS protocol works well for the set of ligands studied here. Although one unexplained outlier exists, we obtain excellent statistical ranking across the set of compounds from the ESMACS protocol and good agreement between calculations and experiments for the relative binding free energies from the TIES protocol. ESMACS and TIES are again found to be powerful protocols for the accurate comparison of the binding free energies.

PMID:35508076 | DOI:10.1021/acs.jcim.2c00255

Arq Bras Cardiol. 2022 Apr;118(4):756-765. doi: 10.36660/abc.20200651.

ABSTRACT

BACKGROUND: It has recently been demonstrated that the application of high-energy ultrasound and microbubbles, in a technique known as sonothrombolysis, dissolves intravascular thrombi and increases the angiographic recanalization rate in patients with ST-segment-elevation myocardial infarction (STEMI).

OBJECTIVE: To evaluate the effects of sonothrombolysis on left ventricular wall motion and myocardial perfusion in patients with STEMI, using real-time myocardial perfusion echocardiography (RTMPE).

METHODS: One hundred patients with STEMI were randomized into the following 2 groups: therapy (50 patients treated with sonothrombolysis and primary coronary angioplasty) and control (50 patients treated with primary coronary angioplasty). The patients underwent RTMPE for analysis of left ventricular ejection fraction (LVEF), wall motion score index (WMSI), and number of segments with myocardial perfusion defects 72 hours after STEMI and at 6 months of follow-up. P < 0.05 was considered statistically significant.

RESULTS: Patients treated with sonothrombolysis had higher LVEF than the control group at 72 hours (50% ± 10% versus 44% ± 10%; p = 0.006), and this difference was maintained at 6 months of follow-up (53% ± 10% versus 48% ± 12%; p = 0.008). The WMSI was similar in the therapy and control groups at 72 hours (1.62 ± 0.39 versus 1.75 ± 0.40; p = 0.09), but it was lower in the therapy group at 6 months (1.46 ± 0.36 versus 1.64 ± 0.44; p = 0.02). The number of segments with perfusion defects on RTMPE was similar in therapy and control group at 72 hours (5.92 ± 3.47 versus 6.94 ± 3.39; p = 0.15), but it was lower in the therapy group at 6 months (4.64 ± 3.31 versus 6.57 ± 4.29; p = 0.01).

CONCLUSION: Sonothrombolysis in patients with STEMI resulted in improved wall motion and ventricular perfusion scores over time.

PMID:35508053 | DOI:10.36660/abc.20200651

Braz Dent J. 2022 Mar-Apr;33(2):61-67. doi: 10.1590/0103-6440202204929.

ABSTRACT

To assess the impact of oral conditions on oral health-related quality of life (OHRQoL) in infants in ten Latin America countries (LAC). A cross-sectional study was conducted with 930 pairs of 1-to-3-year-old children/parents from 10 LAC, as a complementary study of the Research Observatory for Dental Caries of the Latin American Region. The scale ECOHIS, previously tested and valid in ten countries, was applied to parents/caregivers of children to measure OHRQoL. Statistical analysis included descriptive data analysis and one-way analysis of variance (ANOVA-One-Way) were performed to compare age groups with OHRQoL. Bootstrapping procedures (1000 re-samplings; 95%CI Bca) were performed. The mean scores of the ‘Child Impact’ section in the LAC was 4.0(±8.3), in the ‘Family Impact’ section was 2.0(±4.0), and in overall ECOHIS score was 6.0(±12.0). In the ‘Child Impact’ section, Argentina 10.0(+2.4) and Venezuela 17.8(±17.5) demonstrated mean scores higher than the LAC total data. In the ‘Family Impact’ section, the countries with higher mean scores were Argentina 4.9(±2.0), Ecuador 2.1(±3.1) and Venezuela 7.9(±7.8). In the overall ECOHIS score, Argentina 15.1 (±4.1) and Venezuela 25.7(±25.2) has higher mean scores than the values of LAC. There is an association between children’s age and parents’ report of impact on the OHRQoL (p<0.001). Three-year-olds had a higher mean when compared to one- and two-year-olds, both in the Impact on the Child and Impact on the Family (p<0.001) sections, as well as in the overall ECOHIS (p<0.001). In conclusion, there are differences in OHRQoL among Latin American countries, impacting older children more significantly.

PMID:35508037 | DOI:10.1590/0103-6440202204929

Arq Bras Cardiol. 2022 Apr;118(4):694-700. doi: 10.36660/abc.20210050.

ABSTRACT

BACKGROUND: The prognostic importance of the classification ‘heart failure (HF) with mid-range ejection fraction (EF)’ remains uncertain.

OBJECTIVE: To analyze the clinical characteristics, comorbidities, complications, and in-hospital and late mortality of patients classified as having HF with mid-range EF (HFmrEF – EF: 40%-49%), and to compare them to those of patients with HF with preserved EF (HFpEF – EF > 50%) and with HF with reduced EF (HFrEF – EF < 40%) on admission for decompensated HF.

METHODS: Ambispective cohort of patients admitted to the cardiac intensive care unit due to decompensated HF. Clinical characteristics, comorbidities, complications, and in-hospital and late mortality were assessed. The software R was used, with a 5% significance, for the tests chi-square, analysis of variance, Cox multivariate, and Kaplan-Meier survival curve, in addition to machine-learning techniques (Elastic Net and survival tree).

RESULTS: 519 individuals were included between September 2011 and June 2019 (mean age, 74.87 ± 13.56 years; 57.6% were men). The frequencies of HFpEF, HFmrEF and HFrEF were 25.4%, 27% and 47.6%, respectively. Previous infarction was more frequent in HFmrEF. The mean follow-up time was 2.94 ± 2.55 years, with no statistical difference in mortality between the groups (53.8%, 52.1%, 57.9%). In the survival curve, there was difference between neither the HFpEF and HFmrEF groups, nor the HFpEF and HFrEF groups, but between the HFmrEF and HFrEF groups. Age over 77 years, previous HF, history of readmission, dementia and need for vasopressors were associated with higher late mortality in the survival tree.

CONCLUSION: The EF was not selected as a variable associated with mortality in patients with decompensated HF.

PMID:35508046 | DOI:10.36660/abc.20210050

Braz Dent J. 2022 Mar-Apr;33(2):12-21. doi: 10.1590/0103-6440202204772.

ABSTRACT

The purpose of this in vitro study was to evaluate the shaping ability of reciprocating and continuous rotary systems after root canal retreatment. After preparation and root canal filling, mesial canals of 54 mandibular molars were distributed into 3 groups (n=18), according to the filling material removal and re-instrumentation protocols: WOG group – WaveOne Gold system; PTN group – ProTaper Next system; and PTU group – ProTaper Universal system. Cone-beam computed tomographic (CBCT) images acquisition of the mesial root canals was performed at different moments: (1) before instrumentation (unprepared root canals), (2) after preparation and filling, (3) after filling material removal and (4) re-instrumentation. The apical transportation (AT), centering ability (CA) and change in root canal diameter were assessed by CBCT analysis. The remaining filling material quantification was performed by radiographic examination. The statistical analyses were performed using the 3-way ANOVA, Tukey-Kramer, Kruskal-Wallis and Dunn multiple Comparison tests (p<0.05). The tested instruments did not show full CA (=1.0). PTN group had greater AT at the 5th mm in comparison with the WOG group (p<0.05). After re-instrumentation, WOG group had greater root canal diameter change at the 1st and 5th mm than PTN and PTU groups (p<0.05). There was no significant difference among groups when comparing the amount of remaining filling material after re-instrumentation (p>0.05). The tested systems provided minimal alteration in root canal morphology at the apical portion after root canal retreatment. However, WOG promoted greater change in root canal diameter.

PMID:35508032 | DOI:10.1590/0103-6440202204772