Category: Statistics

Aust Endod J. 2021 Apr 26. doi: 10.1111/aej.12517. Online ahead of print.

ABSTRACT

This study evaluated the influence of ultrasonic activation (US) on the antimicrobial activity of a new final irrigant containing glycolic acid (GA). Extracted teeth were used, being 70 to counting of colony-forming units (CFUs) and 35 to confocal laser scanning microscopy. Samples were inoculated with Enterococcus faecalis and divided into 7 groups: distilled water + US; 17% EDTA; Qmix; 17% GA; 17% EDTA + US; QMix + US; and 17% GA + US and kept in contact with test solution for 1 min in the groups with or no US. In the CFUs, the highest bacterial reduction was observed in QMix + US group, followed by QMix and GA + US. In the confocal evaluation, the lowest number of viable cells was observed in EDTA + US, with no statistical difference from QMix, QMix + US and GA + US (P > 0.05). The use of US improves the antimicrobial activity of EDTA and GA, being statistically different from the isolated use of these final irrigants in both evaluation tests.

PMID:33901338 | DOI:10.1111/aej.12517

Bioinformatics. 2021 Apr 26:btab255. doi: 10.1093/bioinformatics/btab255. Online ahead of print.

ABSTRACT

SUMMARY: We developed Quickomics, a feature-rich R Shiny-powered tool to enable biologists to fully explore complex omics statistical analysis results and perform advanced analysis in an easy-to-use interactive interface. It covers a broad range of secondary and tertiary analytical tasks after primary analysis of omics data is completed. Each functional module is equipped with customizable options and generates both interactive and publication-ready plots to uncover biological insights from data. The modular design makes the tool extensible with ease.

AVAILABILITY: Researchers can experience the functionalities with their own data or demo RNA-Seq and proteomics datasets by using the app hosted at http://quickomics.bxgenomics.com and following the tutorial, https://bit.ly/3rXIyhL. The source code under GPLv3 license is provided at https://github.com/interactivereport/Quickomics for local installation.

SUPPLEMENTARY INFORMATION: Supplementary materials are available at https://bit.ly/37HP17g.

PMID:33901288 | DOI:10.1093/bioinformatics/btab255

Am J Bot. 2021 Apr;108(4):571-579. doi: 10.1002/ajb2.1639.

ABSTRACT

PREMISE: As a leaf expands, its shape dynamically changes. Previously, we documented an allometric relationship between vein and blade area in grapevine leaves. Larger leaves have a smaller ratio of primary and secondary vein area relative to blade area compared to smaller leaves. We sought to use allometry as an indicator of leaf size and plasticity.

METHODS: We measured the ratio of vein-to-blade area from the same 208 vines across four growing seasons (2013, 2015, 2016, and 2017). Matching leaves by vine and node, we analyzed the correlation between the size and shape of grapevine leaves as repeated measures with climate variables across years.

RESULTS: The proportion of leaf area occupied by vein and blade exponentially decreased and increased, respectively, during leaf expansion making their ratio a stronger indicator of leaf size than area itself. Total precipitation and leaf wetness hours of the previous year but not the current showed strong negative correlations with vein-to-blade ratio, whereas maximum air temperature from the previous year was positively correlated.

CONCLUSIONS: Our results demonstrate that vein-to-blade ratio is a strong allometric indicator of leaf size and plasticity in grapevines measured across years. Grapevine leaf primordia are initiated in buds the year before they emerge, and we found that total precipitation and maximum air temperature of the previous growing season exerted the largest statistically significant effects on leaf morphology. Vein-to-blade ratio is a promising allometric indicator of relationships between leaf morphology and climate, the robustness of which should be explored further.

PMID:33901305 | DOI:10.1002/ajb2.1639

Eur J Neurosci. 2021 Apr 26. doi: 10.1111/ejn.15247. Online ahead of print.

ABSTRACT

The blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI) signal arises as a consequence of changes in cerebral blood flow (CBF) and cerebral metabolic rate of oxygen (CMR_O2 ) that in turn are modulated by changes in neural activity. Recent advances in imaging have achieved sub-millimeter resolution and allowed investigation of the BOLD response as a function of cortical depth. Here, we adapt our previous theory relating the BOLD signal to neural activity to produce a quantitative model that incorporates venous blood draining between cortical layers. The adjustable inputs to the model are the neural activity and a parameter governing this blood draining. A three-layer version for transient neural inputs and a multi-layer version for constant or tonic neural inputs are able to account for a variety of experimental results, including negative BOLD signals.

PMID:33901325 | DOI:10.1111/ejn.15247

Bioinformatics. 2021 Apr 26:btab254. doi: 10.1093/bioinformatics/btab254. Online ahead of print.

ABSTRACT

MOTIVATION: The crucial role of protein interactions and the difficulty in characterising them experimentally strongly motivates the development of computational approaches for structural prediction. Even when protein-protein docking samples correct models, current scoring functions struggle to discriminate them from incorrect decoys. The previous incorporation of conservation and coevolution information has shown promise for improving protein-protein scoring. Here, we present a novel strategy to integrate atomic-level evolutionary information into different types of scoring functions to improve their docking discrimination.

RESULTS: : We applied this general strategy to our residue-level statistical potential from InterEvScore and to two atomic-level scores, SOAP-PP and Rosetta interface score (ISC). Including evolutionary information from as few as ten homologous sequences improves the top 10 success rates of individual atomic-level scores SOAP-PP and Rosetta ISC by respectively 6 and 13.5 percentage points, on a large benchmark of 752 docking cases. The best individual homology-enriched score reaches a top 10 success rate of 34.4%. A consensus approach based on the complementarity between different homology-enriched scores further increases the top 10 success rate to 40%.

AVAILABILITY: All data used for benchmarking and scoring results, as well as a Singularity container of the pipeline, are available at http://biodev.cea.fr/interevol/interevdata/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:33901284 | DOI:10.1093/bioinformatics/btab254

PLoS One. 2021 Apr 26;16(4):e0250633. doi: 10.1371/journal.pone.0250633. eCollection 2021.

ABSTRACT

BACKGROUND: Globally, approximately 9 million neonates develop perinatal asphyxia annually of which about 1.2 million die. Majority of the morbidity and mortality occur in Low and middle-income countries. However, little is known about the current trend in incidence, and the factors affecting mortality from hypoxic ischaemic encephalopathy (HIE), in Nigeria.

OBJECTIVE: We assessed the trends in incidence and fatality rates and evaluated the predictors of mortality among babies admitted with HIE over five years at the Lagos University Teaching Hospital.

METHODS: A temporal trend analysis and retrospective cohort study of HIE affected babies admitted to the neonatal unit of a Nigerian Teaching Hospital was conducted. The socio-demographic and clinical characteristics of the babies and their mothers were extracted from the neonatal unit records. Kaplan-Meir plots and Multivariable Cox proportional hazard ratio was used to evaluate the survival experienced using Stata version 16 (StataCorp USA) statistical software.

RESULTS: The median age of the newborns at admission was 26.5 (10-53.5) hours and the male to female ratio was 2.1:1. About one-fifth (20.8%) and nearly half (47.8%) were admitted within 6 hours and 24 hours of life respectively, while majority (84%) of the infants were out-born. The prevalence and fatality rate of HIE in our study was 7.1% and 25.3% respectively. The annual incidence of HIE among the hospital admissions declined by 1.4% per annum while the annual fatality rate increased by 10.3% per annum from 2015 to 2019. About 15.7% died within 24 hours of admission. The hazard of death was related to the severity of HIE (p = 0.001), antenatal booking status of the mother (p = 0.01) and place of delivery (p = 0.03).

CONCLUSION: The case fatality rate of HIE is high and increasing at our centre and mainly driven by the pattern of admission of HIE cases among outborn babies. Thus, community level interventions including skilled birth attendants at delivery, newborn resuscitation trainings for healthcare personnel and capacity building for specialized care should be intensified to reduce the burden of HIE.

PMID:33901237 | DOI:10.1371/journal.pone.0250633

PLoS One. 2021 Apr 26;16(4):e0250466. doi: 10.1371/journal.pone.0250466. eCollection 2021.

ABSTRACT

Sand management is essential for enhancing the production in oil and gas reservoirs. The critical total drawdown (CTD) is used as a reliable indicator of the onset of sand production; hence, its accurate prediction is very important. There are many published CTD prediction correlations in literature. However, the accuracy of most of these models is questionable. Therefore, further improvement in CTD prediction is needed for more effective and successful sand control. This article presents a robust and accurate fuzzy logic (FL) model for predicting the CTD. Literature on 23 wells of the North Adriatic Sea was used to develop the model. The used data were split into 70% training sets and 30% testing sets. Trend analysis was conducted to verify that the developed model follows the correct physical behavior trends of the input parameters. Some statistical analyses were performed to check the model’s reliability and accuracy as compared to the published correlations. The results demonstrated that the proposed FL model substantially outperforms the current published correlations and shows higher prediction accuracy. These results were verified using the highest correlation coefficient, the lowest average absolute percent relative error (AAPRE), the lowest maximum error (max. AAPRE), the lowest standard deviation (SD), and the lowest root mean square error (RMSE). Results showed that the lowest AAPRE is 8.6%, whereas the highest correlation coefficient is 0.9947. These values of AAPRE (<10%) indicate that the FL model could predicts the CTD more accurately than other published models (>20% AAPRE). Moreover, further analysis indicated the robustness of the FL model, because it follows the trends of all physical parameters affecting the CTD.

PMID:33901240 | DOI:10.1371/journal.pone.0250466

PLoS One. 2021 Apr 26;16(4):e0250426. doi: 10.1371/journal.pone.0250426. eCollection 2021.

ABSTRACT

BACKGROUND & AIM: Women with HIV/HPV coinfection and cervical lesions are at increased risk of developing HPV related anal cancer. Self-collection of anal swabs may facilitate HPV molecular testing in anal cancer screening, especially in high-risk groups, and yet it is not adequately studied. We evaluated level of agreement between self-collected anal swabs (SCAS) and clinician-collected anal swabs (CCAS) when used for HPV genotyping. We also described the anal HPV genotype distribution and HIV/HPV coinfection.

METHODS: We performed a cross sectional study with participants from a visual-inspection-with-acetic-acid and cervicography (VIAC) clinic, in Harare, Zimbabwe. In a clinic setting, the women aged ≥18 years provided anal swabs in duplicate; first CCAS and then SCAS immediately after. HPV detection and genotyping were performed using next generation amplicon sequencing of a 450bp region of the HPV L1 gene. Level of agreement of HPV genotypes between CCAS and SCAS was calculated using the kappa statistic. McNemar tests were used to evaluate agreement in the proportion of genotypes detected by either method.

RESULTS: Three-hundred women provided 600 samples for HPV genotyping. HPV genotypes were detected in 25% of SCAS and in 22% of CCAS. The most common genotypes with CCAS were HPV52, HPV62 and HPV70 and with SCAS were HPV62, HPV44, HPV52, HPV53 and HPV68. Total HPV genotypes detected in CCAS were more than those detected in SCAS, 32 versus 27. The agreement of HPV genotypes between the two methods was 0.55 in kappa value (k). The test of proportions using McNemar gave a Chi-square value of 0.75 (p = 0.39). Multiple HPV infections were detected in 28/75 and 29/67 women for CCAS and SCAS respectively.

CONCLUSIONS: SCAS and CCAS anal swabs showed moderate agreement, with no statistically significant difference in the proportion of genotypes detected by either methods. Although the differences between the two methods were not statistically significant, CCAS detected more HPV genotypes than SCAS and more HPV infections were detected in SCAS than in CCAS. Our data suggest that self-collected anal swabs can be used as an alternative to clinician-collected anal swabs for HPV genotyping.

PMID:33901223 | DOI:10.1371/journal.pone.0250426

PLoS One. 2021 Apr 26;16(4):e0250204. doi: 10.1371/journal.pone.0250204. eCollection 2021.

ABSTRACT

Understanding the dynamics by which urban areas attract visitors is important in today’s cities that are continuously increasing in population towards higher densities. Identifying services that relate to highly attractive districts is useful to make policies regarding the placement of such places. Thus, we present a framework for classifying districts in cities by their attractiveness to daily commuters and relating Points of Interests (POIs) types to districts’ attraction patterns. We used Origin-Destination matrices (ODs) mined from cell phone data that capture the flow of trips between each pair of places in Riyadh, Saudi Arabia. We define the attraction profile for a place based on three main statistical features: The number of visitors a place received, the distribution of distance traveled by visitors on the road network, and the spatial spread of locations from where trips started. We used a hierarchical clustering algorithm to classify all places in the city by their features of attraction. We discovered three main types of Urban Attractors in Riyadh during the morning period: Global, which are significant places in the city, Downtown, which contains the central business district, and Residential attractors. In addition, we uncovered what makes districts possess certain attraction patterns. We used a statistical significance testing approach to quantify the relationship between Points of Interests (POIs) types (services) and the patterns of Urban Attractors detected.

PMID:33901224 | DOI:10.1371/journal.pone.0250204

PLoS One. 2021 Apr 26;16(4):e0250504. doi: 10.1371/journal.pone.0250504. eCollection 2021.

ABSTRACT

Laminar fMRI at ultra-high magnetic field strength is typically carried out using the Blood Oxygenation Level-Dependent (BOLD) contrast. Despite its unrivalled sensitivity to detecting activation, the BOLD contrast is limited in its spatial specificity due to signals stemming from intra-cortical ascending and pial veins. Alternatively, regional changes in perfusion (i.e., cerebral blood flow through tissue) are colocalised to neuronal activation, which can be non-invasively measured using Arterial Spin Labelling (ASL) MRI. In addition, ASL provides a quantitative marker of neuronal activation in terms of perfusion signal, which is simultaneously acquired along with the BOLD signal. However, ASL for laminar imaging is challenging due to the lower SNR of the perfusion signal and higher RF power deposition i.e., specific absorption rate (SAR) of ASL sequences. In the present study, we present for the first time in humans, isotropic sub-millimetre spatial resolution functional perfusion images using Flow-sensitive Alternating Inversion Recovery (FAIR) ASL with a 3D-EPI readout at 7 T. We show that robust statistical activation maps can be obtained with perfusion-weighting in a single session. We observed the characteristic BOLD amplitude increase towards the superficial laminae, and, in apparent discrepancy, the relative perfusion profile shows a decrease of the amplitude and the absolute perfusion profile a much smaller increase towards the cortical surface. Considering the draining vein effect on the BOLD signal using model-based spatial “convolution”, we show that the empirically measured perfusion and BOLD profiles are, in fact, consistent with each other. This study demonstrates that laminar perfusion fMRI in humans is feasible at 7 T and that caution must be exercised when interpreting BOLD signal laminar profiles as direct representation of the cortical distribution of neuronal activity.

PMID:33901230 | DOI:10.1371/journal.pone.0250504