Tag: statistics

Sci Rep. 2021 Jun 25;11(1):13323. doi: 10.1038/s41598-021-92725-8.

ABSTRACT

Lung cancer is one of the deadliest cancers in the world. Two of the most common subtypes, lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), have drastically different biological signatures, yet they are often treated similarly and classified together as non-small cell lung cancer (NSCLC). LUAD and LUSC biomarkers are scarce, and their distinct biological mechanisms have yet to be elucidated. To detect biologically relevant markers, many studies have attempted to improve traditional machine learning algorithms or develop novel algorithms for biomarker discovery. However, few have used overlapping machine learning or feature selection methods for cancer classification, biomarker identification, or gene expression analysis. This study proposes to use overlapping traditional feature selection or feature reduction techniques for cancer classification and biomarker discovery. The genes selected by the overlapping method were then verified using random forest. The classification statistics of the overlapping method were compared to those of the traditional feature selection methods. The identified biomarkers were validated in an external dataset using AUC and ROC analysis. Gene expression analysis was then performed to further investigate biological differences between LUAD and LUSC. Overall, our method achieved classification results comparable to, if not better than, the traditional algorithms. It also identified multiple known biomarkers, and five potentially novel biomarkers with high discriminating values between LUAD and LUSC. Many of the biomarkers also exhibit significant prognostic potential, particularly in LUAD. Our study also unraveled distinct biological pathways between LUAD and LUSC.

PMID:34172784 | DOI:10.1038/s41598-021-92725-8

Sci Rep. 2021 Jun 25;11(1):13348. doi: 10.1038/s41598-021-92587-0.

ABSTRACT

Silicosis is a diffuse interstitial lung disease caused by sustained inhalation of silica and silicates. Several cytokines are activated by their inhalation and can mediate the process of pulmonary fibrosis. The identification of biomarkers could allow an early diagnosis before the development of radiological alterations and help monitor the evolution of patients. The objetive of this study was to determine the clinical significance of specific biomarkers, to estimate their association with the development, severity and/or progression of silicosis, and identify determinants of this evolution. We conducted a prospective observational study in patients attending the pulmonology clinic from 2009 to 2018. Serum levels of the following inflammatory mediators were assessed: interleukin-6 (IL-6), interleukin 2 receptor subunit alpha (IL2R) interleukin 1 beta (IL1B), interleukin-8 (IL-8), tumour necrosis factor-alpha (TNF-α), transforming growth factor-beta1 (TGF-β1), alpha-1 antitrypsin (AAT), C-reactive protein (CRP), lactate dehydrogenase (LDH) and ferritin in subjects exposed to silica, with and without silicosis. Association between those inflammatory mediators with lung function measurements and radiological severity of disease and their impact on prognosis were analysed. 337 exposed to silica (278 with silicosis) and 30 subjects in the control group were included. IL-8, α1AT, ferritin, CRP and LDH levels were higher in silicosis than in those exposed to silica without silicosis. IL-8, LDH and AAT levels were associated with progression of silicosis and IL-6, IL-8, LDH, AAT, ferritin, and CRP with vital status. The results of the ROC analysis indicated the potential of IL-8 as a biomarker in the presence of silicosis and for the prediction of mortality.

PMID:34172787 | DOI:10.1038/s41598-021-92587-0

Nat Commun. 2021 Jun 25;12(1):3978. doi: 10.1038/s41467-021-24154-0.

ABSTRACT

Social transmission of information is taxonomically widespread and could have profound effects on the ecological and evolutionary dynamics of animal communities. Demonstrating this in the wild, however, has been challenging. Here we show by field experiment that social transmission among predators can shape how selection acts on prey defences. Using artificial prey and a novel approach in statistical analyses of social networks, we find that blue tit (Cyanistes caeruleus) and great tit (Parus major) predators learn about prey defences by watching others. This shifts population preferences rapidly to match changes in prey profitability, and reduces predation pressure from naïve predators. Our results may help resolve how costly prey defences are maintained despite influxes of naïve juvenile predators, and suggest that accounting for social transmission is essential if we are to understand coevolutionary processes.

PMID:34172738 | DOI:10.1038/s41467-021-24154-0

Sci Rep. 2021 Jun 25;11(1):13336. doi: 10.1038/s41598-021-92638-6.

ABSTRACT

Dodonaea viscosa L.Jacq. is an evergreen shrub and native to Asia, Africa, and Australia. It has been used as traditional medicine in different countries. The foremost objective of the current study was to discover the protective potential of D. viscosa flowers Methanol (DVM) and Chloroform (DVC) extracts against CCL₄ induced toxicity in mice. This study was intended to identify phytochemicals through HPLC, GCMS, and FT-IR, as well as in vitro antioxidant and in vitro anti-tuberculosis activity. Our comprehensive findings indicate that Dodonaea viscosa is valuable and widespread herbal medicine through therapeutic potentials for curing various ailments. Dodonaeaviscosa flowersare found to have a protective effect against oxidative stress produced by CCL₄ in the liver, kidney, and spleen. The intake of DV extracts restored the level of hepatic enzymes (ALP, AST ALT, and Direct bilirubin), hematological parameters (RBCs, WBCs, and Platelets), total protein, and liver antioxidant enzymes (SOD, GPx, and CAT) after a decline in levels by CCL₄. Histopathological results discovered the defensive effect of 300 mg/kg of DVM extract against CCL₄ induced damage, thus having an improved protective effect compared to DVC and control. As a result of metabolite screening, the total flavonoids and total phenolics were present in abundance. A phytochemical investigation by HPLC identified gallic acid, epicatechin, cumeric acid, flavonoids, while GCMS estimated oleic acid (Octadecenoic acid) (C₁₈H₃₄O₂), Stearic acid (C₁₈H₃₆O₂), Ricinoleic acid (C₁₈H₃₄O₃), and Cedrol (C₁₅H₂₆O). DVM extract exhibited resistance against in vitro Mycobacterium tuberculosis strains. So this study proposed that the protective effect of DV against oxidative damage induced in the liver, kidney, and spleen can be correlated to the antioxidant compounds.

PMID:34172756 | DOI:10.1038/s41598-021-92638-6

Sci Rep. 2021 Jun 25;11(1):13363. doi: 10.1038/s41598-021-92253-5.

ABSTRACT

Despite the global efforts to mitigate the ongoing COVID-19 pandemic, the disease transmission and the effective controls still remain uncertain as the outcome of the epidemic varies from place to place. In this regard, the province-wise data from Nepal provides a unique opportunity to study the effective control strategies. This is because (a) some provinces of Nepal share an open-border with India, resulting in a significantly high inflow of COVID-19 cases from India; (b) despite the inflow of a considerable number of cases, the local spread was quite controlled until mid-June of 2020, presumably due to control policies implemented; and (c) the relaxation of policies caused a rapid surge of the COVID-19 cases, providing a multi-phasic trend of disease dynamics. In this study, we used this unique data set to explore the inter-provincial disparities of the important indicators, such as epidemic trend, epidemic growth rate, and reproduction numbers. Furthermore, we extended our analysis to identify prevention and control policies that are effective in altering these indicators. Our analysis identified a noticeable inter-province variation in the epidemic trend (3 per day to 104 per day linear increase during third surge period), the median daily growth rate (1 to 4% per day exponential growth), the basic reproduction number (0.71 to 1.21), and the effective reproduction number (maximum values ranging from 1.20 to 2.86). Importantly, results from our modeling show that the type and number of control strategies that are effective in altering the indicators vary among provinces, underscoring the need for province-focused strategies along with the national-level strategy in order to ensure the control of a local spread.

PMID:34172764 | DOI:10.1038/s41598-021-92253-5

J Craniofac Surg. 2021 Jun 23. doi: 10.1097/SCS.0000000000007709. Online ahead of print.

ABSTRACT

OBJECTIVES: Mandible fractures can be treated with different plate systems, that is, miniplates or three-dimensional (3D) plates. This systematic review describes the effectiveness and clinical outcomes of 3D plates used in fractures of the mandible and aims to critically evaluate its risks and benefits.

MATERIALS AND METHODS: A comprehensive electronic search was conducted without date but with restriction to articles written in English. Studies in humans, including randomized or quasi-randomized controlled trials and retrospective studies, were included. The outcome parameters measured were number of patients, fracture classification, results, follow-up period, postoperative complications, and mean age of patients. Major complications were defined as those needing additional surgical intervention, for example, malocclusion, infection or plate fracture. Accordingly, complications not needing additional surgical intervention were defined as minor (ie, dehiscence, trismus).

RESULTS: Guided by the PRISMA statement and the Cochrane Handbook for Systematic Reviews of Interventions, the authors identified 44 publications with a total of 1790 patients. Among the articles selected for the final review, there were 32 reported prospective studies, 12 reported retrospective studies. Regarding the evaluation of quality, 8 studies showed a low value of the risk of bias, 17 a moderate risk, and 19 a high risk. There were statistically significant advantages for 3D plates in mandibular fractures in terms of postoperative complications, for example, wound dehiscences or plate fracture.

CONCLUSIONS: The 3D plate is an effective treatment modality for mandibular fractures, with low incidence of major complications, decreased length of operation time, and increased stability of osteosynthesis.

PMID:34172684 | DOI:10.1097/SCS.0000000000007709

Epidemiology. 2021 Jun 7. doi: 10.1097/EDE.0000000000001390. Online ahead of print.

ABSTRACT

BACKGROUND: The speed with which a pathogen circulates in a sexual network is a function of network connectivity. Cross-sectional connectivity is a function of network features like momentary degree and assortative mixing. Temporal connectivity is driven by partner acquisition rates. The forward-reachable path has been proposed as a summary measure of these two aspects of transmission potential. We use empirical data from San Francisco and Atlanta to estimate the generative parameters of the forward-reachable path and compare results to the HIV/sexually-transmitted infection (STI) epidemics in each city.

METHODS: We used temporal exponential random graph models to estimate the generative parameters for each city’s dynamic sexual network from survey data. We then simulated stochastic dynamic networks from the fitted models and calculated the forward-reachable path for each realization, overall and stratified by partnership type and demographics.

RESULTS: The overall mean and median paths were higher in San Francisco than in Atlanta. The overall paths for each city were greater than the sum of the paths in each individual partnership network. In the casual partnership network, the mean path was highest in the youngest age group and lowest in the oldest age group, despite the fact that the youngest group had the lowest mean momentary degree and past-year partner counts.

CONCLUSIONS: The forward-reachable path by age group revealed additional utility of the measure beyond the temporal and cross-sectional network connectivity measures. Other non-network factors are still necessary to infer total epidemic potential for any specific pathogen.

PMID:34172692 | DOI:10.1097/EDE.0000000000001390

Med Sci Monit. 2021 Jun 26;27:e931327. doi: 10.12659/MSM.931327.

ABSTRACT

BACKGROUND The aim of this study was to evaluate the effectiveness of grayscale ultrasound (GSUS), power Doppler imaging (PDI), and contrast-enhanced ultrasonography (CEUS) in early rheumatoid arthritis (RA) diagnosis through animal experiments. MATERIAL AND METHODS A rabbit RA model was constructed. The animals were randomly divided into 2 groups, namely, the RA model group and the control group. GSUS, PDI, and CEUS were performed in the model group during early RA and were compared with pathology of synovial biopsies. The consistency of 3 types of ultrasonography was evaluated in tandem with pathological grading. RESULTS 23 rabbits in the RA model group completed the experiment. GSUS showed that the synovial thickening of grades 1, 2 and 3 occurred in 12, 19, and 15 joints, respectively. The sensitivity, specificity, and accuracy of PDI in the diagnosis of knee joint synovitis in RA grades 1, 2, and 3 were 80.56% (29/36), 60.00% (6/10), and 76.09% (35/46), respectively, while those with CEUS were 94.44% (34/36), 90.00% (9/10), and 93.47% (43/46), respectively. The differences in diagnostic sensitivity, specificity, and accuracy of the 2 methods were statistically significant. Additionally, the thickness of the synovium measured with GSUS precontrast was greater than that of postcontrast. CONCLUSIONS RA evaluated with GSUS is often more hypertrophied than when evaluated with CEUS, while evaluation by PDI is less hypertrophied than that by CEUS. However, from a practical view point, GSUS and PDI are of sufficient practical value, except for in a few special cases.

PMID:34172694 | DOI:10.12659/MSM.931327

J Craniofac Surg. 2021 Jun 23. doi: 10.1097/SCS.0000000000007712. Online ahead of print.

ABSTRACT

The purpose of this study was to investigate three-dimensional facial soft tissue changes after bimaxillary orthognathic surgery (BOGS) in patients with cleft lip and palate. The samples consisted of 34 Korean young adult patients with skeletal class III malocclusion who underwent BOGS for maxillary advancement/posterior impaction and mandibular setback. They were divided into cleft-class III (C-CIII) group (n = 18) and noncleft-class III (NC-CIII) group (n = 16). Three-dimensional computed tomography images were taken 1 month before (T1) and 3 months after (T2) surgery. After 34 hard/soft tissue landmarks were automatically identified using software, the amount and direction of change in landmarks and the amount of change in 16 soft tissue variables during T1-T2 were calculated. Then, statistical analysis was performed. Compared to NC-CIII group, C-CIII group showed more posteriorly-positioned hard/soft tissue landmarks, larger alar width, alar base width and philtrum width, and more obtuse nasal tip angle at both T1 and T2 stages. C-CIII group exhibited higher soft-to-hard tissue movement ratios at the bottom of the nose (ΔSn/ΔANS, 1.08 versus 0.81) and the upper part of the upper lip (ΔPoint A’/ΔPoint A, 1.08 versus 0.91), but a lower ratio at the lower part of the upper lip (ΔLs’/ΔIs, 0.72 versus 1.01) than NC-CIII group. The number of hard-soft tissue landmarks with high correlation (>0.90) was smaller in C-CIII group than in NC-CIII group (2 versus 6). Scar tissues and abnormal muscles in the nose and upper lip might elicit different responses in the nasolabial soft tissues to BOGS between C-CIII and NC-CIII patients.

PMID:34172680 | DOI:10.1097/SCS.0000000000007712

J Craniofac Surg. 2021 Jun 23. doi: 10.1097/SCS.0000000000007716. Online ahead of print.

ABSTRACT

OBJECTIVE: To evaluate the effect of orthognathic surgery on the long-term quality of life of patients with presurgical skeletal Class III and to identify its strongest effect-whether esthetic, social, or functional.

MATERIALS AND METHODS: In this retrospective cohort study, the subjects were patients after orthognathic surgery for repairing skeletal Class III. Fifty-five patients who had undergone orthognathic surgery from 2013 to 2018 in the oral and maxillofacial surgery department participated in this study. Each participant completed a modified questionnaire used to assess the patient’s esthetic, social, and functional abilities after orthognathic surgery.

RESULTS: The rate of esthetic improvement in orthognathic surgery patients was 88%. More than four-fifths (81.8%) of the patients reported improvement in their personal and social self-esteem and confidence. Finally, 40.7% of the patients reported functional improvement. No significant differences between male and female patients were found. All but one of the patients recommended orthognathic surgery for patients with similar problems. One in six (17.3%) patients was dissatisfied with the nasal appearance after the surgical procedure, while almost a quarter (21.8%) reported worsening of their mouth opening, and 25.4% reported worsening of TMJ (Temporo-Mandibular Joint) symptoms. Analysis of the results revealed no statistically significant pattern connecting preoperative overjet or overbite measures with satisfaction rates.

CONCLUSIONS: In this study, patient satisfaction with the orthognathic surgical procedure was mostly a result of improvements in facial esthetics, followed by psychological well-being and functional abilities. Most dissatisfaction after the orthognathic surgical procedure was related to nasal appearance, mouth opening, and TMJ complaints.

PMID:34172683 | DOI:10.1097/SCS.0000000000007716