Tag: statistics

Nicotine Tob Res. 2021 Jun 4:ntab120. doi: 10.1093/ntr/ntab120. Online ahead of print.

ABSTRACT

INTRODUCTION: Menthol has been shown to target similar brain regions and neural receptors as nicotine, yet the association between menthol cigarette use and cognitive performance remains unknown.

METHODS: This study examined differences in cognitive task performance between menthol (MS) and non-menthol (NMS) cigarette smokers after acute cigarette consumption. Sixty White and Black/African American, non-abstinent, MS (n=30) and NMS (n=30) were assessed pre- and post-smoking their preferred cigarette on four computerized tasks: Continuous Performance Task (CPT; alerting attention), N-Back Task (working memory), Finger Tapping Task (motor control), and Apple Picker Task (reinforcement enhancement). Self-reported nicotine dependence and objective smoking topography measures were also compared between groups.

RESULTS: Initial unadjusted analyses showed a significant effect of cigarette type x time on CPT speed (p=.042), where MS improved while NMS group worsened in CPT speed after smoking. After controlling for baseline cigarette craving and cigarette nicotine levels, the effect of cigarette type x time for all cognitive outcomes was statistically non-significant (ps>.05). However, there remained a significant effect of cigarette type, where MS vs. NMS had poorer CPT (p=.046) and N-Back Task accuracy (p=.006) but faster N-Back speed (p=.039). There were no statistically significant differences between groups on reinforcement enhancement, nicotine dependence, or smoking behavior outcomes (ps>.05).

CONCLUSIONS: Contrary to our hypotheses, results did not find a significant effect of cigarette type on the change in cognitive performance after acute smoking in non-abstinent smokers. Further studies are needed to clarify the specific pharmacological effects of nicotine and menthol on cognitive functioning.

PMID:34086950 | DOI:10.1093/ntr/ntab120

J Appl Lab Med. 2021 Jun 4:jfab044. doi: 10.1093/jalm/jfab044. Online ahead of print.

ABSTRACT

BACKGROUND: Serum protein electrophoresis is one of the core investigations for screening for monoclonal proteins. Among the available capillary systems, the Helena V8 system has been evaluated in a limited number of studies.

METHODS: In total, 310 sera samples were assessed on the Helena V8 system and compared with the Sebia Capillarys instrument. Abnormalities suggestive of monoclonal proteins were confirmed by immunofixation. Imprecision studies and reference intervals were determined.

RESULTS: The imprecision of the Helena V8 was inferior or equal to 5.8%. The mean bias of Helena V8 vs Sebia Capillarys was about -0.9 g/L for albumin; -0.2 g/L foralpha-1; 1.1 g/L for alpha-2; -0.2 g/L for beta; 0.3 g/L for gamma; -0.5 g/L for monoclonal protein in beta; and 0.3 g/L for monoclonal protein in gamma. Among the 56 samples with monoclonal proteins confirmed by immunofixation, all were seen on both methods, with only 1 discordant result at a cutoff of 5.0 g/L. Reference intervals were statistically different between the 2 analyzers, except for the beta fraction.

CONCLUSIONS: Our evaluation confirms the good analytical performance of the Helena V8 analyzer as a suitable alternative to the Sebia Capillarys instrument.

PMID:34086920 | DOI:10.1093/jalm/jfab044

Bioinformatics. 2021 Jun 4:btab428. doi: 10.1093/bioinformatics/btab428. Online ahead of print.

ABSTRACT

MOTIVATION: Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree-species tree discordance. Incomplete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, where weights correspond to the relative importance of quartets, and subsequently amalgamating the weighted quartets to infer a single coherent species tree can allow for a statistically consistent way of estimating species trees. However, handling weighted quartets is challenging.

RESULTS: We propose wQFM, a highly accurate method for species tree estimation from multi-locus data, by extending the quartet FM (QFM) algorithm to a weighted setting. wQFM was assessed on a collection of simulated and real biological datasets, including the avian phylogenomic dataset which is one of the largest phylogenomic datasets to date. We compared wQFM with wQMC, which is the best alternate method for weighted quartet amalgamation, and with ASTRAL, which is one of the most accurate and widely used coalescent-based species tree estimation methods. Our results suggest that wQFM matches or improves upon the accuracy of wQMC and ASTRAL.

AVAILABILITY: wQFM is available in open source form at https://github.com/Mahim1997/wQFM-2020.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:34086858 | DOI:10.1093/bioinformatics/btab428

J Exp Biol. 2021 Jun 1;224(11):jeb241059. doi: 10.1242/jeb.241059. Epub 2021 Jun 4.

ABSTRACT

The magnitude of many biological traits relates strongly and regularly to body size. Consequently, a major goal of comparative biology is to understand and apply these ‘size-scaling’ relationships, traditionally quantified by using linear regression analyses based on log-transformed data. However, recently some investigators have questioned this traditional method, arguing that linear or non-linear regression based on untransformed arithmetic data may provide better statistical fits than log-linear analyses. Furthermore, they advocate the replacement of the traditional method by alternative specific methods on a case-by-case basis, based simply on best-fit criteria. Here, I argue that the use of logarithms in scaling analyses presents multiple valuable advantages, both statistical and conceptual. Most importantly, log-transformation allows biologically meaningful, properly scaled (scale-independent) comparisons of organisms of different size, whereas non-scaled (scale-dependent) analyses based on untransformed arithmetic data do not. Additionally, log-based analyses can readily reveal biologically and theoretically relevant discontinuities in scale invariance during developmental or evolutionary increases in body size that are not shown by linear or non-linear arithmetic analyses. In this way, log-transformation advances our understanding of biological scaling conceptually, not just statistically. I hope that my Commentary helps students, non-specialists and other interested readers to understand the general benefits of using log-transformed data in size-scaling analyses, and stimulates advocates of arithmetic analyses to show how they may improve our understanding of scaling conceptually, not just statistically.

PMID:34086905 | DOI:10.1242/jeb.241059

Bioinformatics. 2021 Jun 4:btab427. doi: 10.1093/bioinformatics/btab427. Online ahead of print.

ABSTRACT

MOTIVATION: Genome wide association studies (GWAS) can reveal important genotype-phenotype associations, however, data quality and interpretability issues must be addressed. For drug discovery scientists seeking to prioritize targets based on the available evidence, these issues go beyond the single study.

METHODS: Here, we describe rational ranking, filtering and interpretation of inferred gene-trait associations and data aggregation across studies by leveraging existing curation and harmonization efforts. Each gene-trait association is evaluated for confidence, with scores derived solely from aggregated statistics, linking a protein-coding gene and phenotype. We propose a method for assessing confidence in gene-trait associations from evidence aggregated across studies, including a bibliometric assessment of scientific consensus based on the iCite Relative Citation Ratio, and meanRank scores, to aggregate multivariate evidence.

RESULTS: This method, intended for drug target hypothesis generation, scoring and ranking, has been implemented as an analytical pipeline, available as open source, with public datasets of results, and a web application designed for usability by drug discovery scientists.

AVAILABILITY: Web application, datasets, and source code via: https://unmtid-shinyapps.net/tiga/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:34086846 | DOI:10.1093/bioinformatics/btab427

Bioinformatics. 2021 Jun 4:btab426. doi: 10.1093/bioinformatics/btab426. Online ahead of print.

ABSTRACT

MOTIVATION: The advancement in technologies and the growth of available single-cell datasets motivate integrative analysis of multiple single-cell genomic datasets. Integrative analysis of multimodal single-cell datasets combines complementary information offered by single-omic datasets and can offer deeper insights on complex biological process. Clustering methods that identify the unknown cell types are among the first few steps in the analysis of single-cell datasets, and they are important for downstream analysis built upon the identified cell types.

RESULTS: We propose scAMACE for the integrative analysis and clustering of single-cell data on chromatin accessibility, gene expression and methylation. We demonstrate that cell types are better identified and characterized through analyzing the three data types jointly. We develop an efficient expectationmaximization (EM) algorithm to perform statistical inference, and evaluate our methods on both simulation study and real data applications. We also provide the GPU implementation of scAMACE, making it scalable to large datasets.

AVAILABILITY: The software and datasets are available at https://github.com/cuhklinlab/scAMACE_py (python implementation) and https://github.com/cuhklinlab/scAMACE (R implementation).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:34086847 | DOI:10.1093/bioinformatics/btab426

PLoS One. 2021 Jun 4;16(6):e0252829. doi: 10.1371/journal.pone.0252829. eCollection 2021.

ABSTRACT

BACKGROUND: Esophageal cancer is a highly malignant cancer with a very poor prognosis. For resectable esophageal cancer, neoadjuvant treatment could improve the prognosis of esophageal cancer. However, current clinical neoadjuvant treatment options for esophageal cancer are still limited. The application of immunotherapy is a potentially beneficial new neoadjuvant treatment option for esophageal cancer. The objective of this meta-analysis is to evaluate the efficacy and safety of immunotherapy for the neoadjuvant treatment of esophageal cancer.

METHODS: We will search Wanfang Database, SinoMed, China National Knowledge Infrastructure, Embase, Web of Science, Pubmed, and Cochrane Library for relevant articles published before July, 2021. We will also search the unpublished clinical trials of neoadjuvant immunotherapy in esophageal cancer in preprint website (such as bioRXiv and medRxiv) up to July, 2021. We will perform a meta-analysis to evaluate the efficacy and safety of neoadjuvant immunotherapy for resectable esophageal cancer. Randomized controlled trials (RCTs) will be included in this study. The risk of bias will be evaluated for each included study using the Cochrane Handbook for Systematic Reviews of Interventions. We will use RevMan 5.3 software for statistical analysis of the data.

RESULTS: The results of this study will provide evidence of immunotherapy using as neoadjuvant treatment for esophageal cancer. This meta-analysis will be submitted to a peer-reviewed journal seeking for publication.

CONCLUSION: The results of this study will provide a reliable basis for clinicians and patients to formulate the best pre-surgical treatment plan for resectable esophageal cancer.

SYSTEMATIC REVIEW REGISTRATION: INPLASY202120026.

PMID:34086821 | DOI:10.1371/journal.pone.0252829

PLoS One. 2021 Jun 4;16(6):e0252722. doi: 10.1371/journal.pone.0252722. eCollection 2021.

ABSTRACT

BACKGROUND: Despite huge changes in demographic behaviors, the family continues to be the major source of psychosocial support for older adults in India. The loss of household headship can be a cause of disregard for the aged and is associated in a very fundamental way with other status losses. Our study used the two rounds of the India Human Development Survey to understand the association of family structure on the gain or loss status of household headship among 10,527 older adults.

METHOD: Bivariate analysis was done using the chi-square test for association. Equivalently, the multivariate analysis involved estimating multivariable logistic regression models. Multicollinearity did not affect the estimates from the regression models. For examining headship transition, we performed two complete sets of analysis, by taking gain in headship and loss in headship as the outcome variable respectively.

RESULTS: Across two rounds, a major shift in family structure was noticed as 6.8% of households moved from extended to a single generation. Results indicate that family structure was significantly associated with gaining and losing headship among older adults. Headship loss was more common among nuclear [OR: 2.16; CI: 1.28, 3.65] and extended [OR: 2.76; CI: 1.64, 4.66] family structures. Moreover, gaining headship was found to be significantly associated with married, educated, and working older adults.

CONCLUSION: Since living in single generation household may preferably be encouraged among older adults than their living in a complex household without headship and value they deserve, the public intervention may support the independent living within the older population through housing policies that create additional choices presented to older adults making residential decisions.

PMID:34086833 | DOI:10.1371/journal.pone.0252722

PLoS One. 2021 Jun 4;16(6):e0252716. doi: 10.1371/journal.pone.0252716. eCollection 2021.

ABSTRACT

BACKGROUND: Regional analgesia is worth performing in the multimodal postoperative management of hip fracture (HF) because it reduces hospital morbidity and mortality. The aim of this study is to compare the efficacy and side effects of the recently described “Pericapsular Nerve Group (PENG) Block” with those of the femoral block, which is considered the standard of care for postoperative pain control after femoral neck fracture.

MATERIALS AND METHODS: We conducted a comparative observational study at a university hospital (Saint Antoine Hospital, Sorbonne University, Paris, France), where the PENG block was introduced in August 2019. We include all patients from June to October 2019, who were coming for femoral neck fractures and who had an analgesic femoral block or PENG block before their surgery. The primary outcome was the comparison of cumulative postoperative morphine consumption 48 hours after surgery.

RESULTS: Demographics, medical charts, and perioperative data of 42 patients were reviewed: 21 patients before (Femoral group) and 21 patients after the introduction of PENG block (PENG group) in clinical practice. Thirteen total hip arthroplasties (THA) and eight hemi arthroplasties (HA) were included in each group. Demographics were also comparable. The median, postoperative, morphine equivalent consumption at 48 hours was 10 [0-20] mg and 20 [0-50] mg in Femoral and PENG groups respectively (p = 0.458). No statistically significant differences were found in postoperative pain intensity, time to ambulation, incidence of morphine-related side effects, or length of hospital stay. The postoperative muscle strength of the quadriceps was greater in the PENG group than in the Femoral group (5/5 vs. 2/5, p = 0.001).

CONCLUSION: In the management of hip fractures, PENG block is not associated in our study with a significant change in postoperative morphine consumption, compared to femoral block. However, it does significantly improve the immediate mobility of the operated limb, making it appropriate for inclusion in enhanced recovery programs after surgery.

PMID:34086782 | DOI:10.1371/journal.pone.0252716

PLoS One. 2021 Jun 4;16(6):e0252640. doi: 10.1371/journal.pone.0252640. eCollection 2021.

ABSTRACT

BACKGROUND: Transparent and complete publications of randomised controlled trials (RCT) ought to comply with the guidelines of the CONSORT Statement, which stipulates sample size calculation as an important aspect of trial planning. The objective of this study was to analyse and compare the reporting of statistical sample size calculations in RCT papers on the treatment of age-related macular degeneration (AMD), glaucoma and cataract published in 2018.

MATERIAL AND METHODS: This study comprises a total of 113 RCT papers (RCT-P) published in 2018 (AMD: 14, glaucoma: 28, cataract: 71), in English or German, and identified through an internet-based literature search in PubMed and EMBASE. The primary outcome measure of the study was the number of trials providing a complete description of the underlying sample case calculation on the basis of the variables required (significance level, expected outcomes, power, and resulting sample size).

RESULTS: Of the RCTs reviewed, 64% (AMD), 61% (glaucoma) and 31% (cataract) provided a justification of the number of patients included. A complete description of the described studies’ sample size calculation including all the necessary values (primary outcome measure of this study) was described by 21% of the AMD, 29% of the cataract and 18% of the glaucoma RCT publications (in total: 24 of 113 (21%) at a confidence interval of 95%: [13%; 29%]).

CONCLUSION: All three treatment areas analysed lacked reporting quality regarding the justification of the number of patients included in a clinical trial based on a sample size calculation required for ethical reasons. More than half of all RCT publications reviewed did not provide all of the required information on statistical sample size calculation, and thus lacked transparency and completeness. It is therefore urgently required to involve methodologists in a study’s planning and publishing processes to ensure that methodology descriptions are transparent and of high quality.

PMID:34086796 | DOI:10.1371/journal.pone.0252640