Are your covariates under control? How normalization can re-introduce covariate effects

Many statistical tests rely on the assumption that the residuals of a model are normally distributed. Rank-based inverse normal transformation (INT) of the dependent variable is one of the most popular approaches to satisfy the normality assumption. Studies regularly adjust for covariates and then normalize the residuals. This study investigated the effect of regressing covariates against the dependent variable and then applying rank-based INT to the residuals. The correlation between the dependent variable and covariates at each stage of processing was assessed. An alternative approach was tested of applying rank-based INT to the dependent variable before regressing covariates was tested. Analyses based on both simulated and real data examples demonstrated that applying rank-based INT to the dependent variable residuals after regressing out covariates re-introduces a linear correlation between the dependent variable and covariates in almost all situations. This will increase type-1 errors and reduce power. Our proposed alternative approach, where rank-based INT was applied prior to controlling for covariate effects, gave residuals that were normally distributed and linearly uncorrelated with covariates. This approach is therefore recommended

Associations of vitamin D pathway genes with circulating 25-hydroxyvitamin-D, 1,25-dihydroxyvitamin-D, and prostate cancer:a nested case-control study

Vitamin D pathway single nucleotide polymorphisms (SNPs) are potentially useful proxies for investigating whether circulating vitamin D metabolites [total 25-hydroxyvitamin-D, 25(OH)D; 1,25-dihydroxyvitamin, 1,25(OH)2D] are causally related to prostate cancer. We investigated associations of sixteen SNPs across seven genes with prostate-specific antigen-detected prostate cancer

Incontinentia pigmenti presenting as hypodontia in a 3-year-old girl: a case report

<p>Abstract</p> <p>Introduction</p> <p>Incontinentia pigmenti or Bloch-Sulzberger syndrome is a rare X-linked dominant disease that mainly affects the skin, eyes, hair, central nervous system and teeth. The disease is predominant among women. Although dermatologic manifestations are among the most important aspects for the diagnosis of the syndrome, they are less damaging to the patient and do not require treatment. However, oral involvement characterized by hypodontia of deciduous and permanent teeth is important for the diagnosis and treatment of the patient.</p> <p>Case presentation</p> <p>We report the case of a 3-year-old girl with ophthalmologic and neurologic disturbances, cutaneous manifestations and hypodontia. Since the patient did not present more damaging manifestations such as neurologic and/or ophthalmologic problems, her most severe complications were related to dental anomalies. The importance of integrated dental treatment, which combines pediatric dentistry, orthodontics and conventional prosthesis, is emphasized.</p> <p>Conclusion</p> <p>Hypodontia is a frequent finding in incontinentia pigmenti, and dentists should be aware of this condition in order to help with the diagnosis.</p

The growth in newspaper coverage of tobacco control in China, 2000-2010

<p>Abstract</p> <p>Background</p> <p>Media coverage of tobacco-related issues can potentially shape individual beliefs, attitudes and behaviors about tobacco use. This study aims to describe news coverage of tobacco control related issues in Chinese newspapers from 2000 to 2010.</p> <p>Methods</p> <p>All 1149 articles related to tobacco control were extracted from the Database of Chinese Important Newspapers and content analyzed for the period Jan 1, 2000 to Dec 31, 2010. The changing pattern of tobacco control topic, article type, viewpoint, and article origin, and their relationship were analysed.</p> <p>Results</p> <p>News coverage of tobacco control related issues increased significantly (<it>p </it>< 0.01) from 2000 to 2010, with news coverage being relatively intensive in May and June (<it>p </it>< 0.01), around World No Tobacco Day. 24.9% (n = 286) of all articles focused on secondhand smoke, 25.3% (n = 291) warned about the dangers of active smoking, and 10.0% (n = 115) focused on prevention and cessation programs and campaigns. Tobacco control topics varied significantly between national vs city/regional newspapers (<it>χ</it>²= 24.09, <it>p </it>= 0.002) and article types (<it>χ</it>²= 193.35, <it>p </it>< 0.001). Articles in national newspapers had more coverage of the dangers of tobacco and on enforcing bans on tobacco-advertising. News stories centered around monitoring tobacco use and smoke free activity, while editorials focused on enforcing bans on tobacco-advertising, youth access and programs and campaigns. Letters to editors focused on the dangers of smoking, raising tax, and smoking cessation. More articles (50.4%) took an anti-tobacco position (compared with 10.5% which were pro-smoking), with the amount of negative coverage growing significantly across the decade. National articles tended to lean toward anti-tobacco, however, local articles tended mix of pro-tobacco and neutral/balance positions. Editorials seemed to be more anti-tobacco oriented, but letters to the editor tended to show a mix of anti-tobacco and pro-tobacco positions.</p> <p>Conclusion</p> <p>Chinese newspapers are giving increasing attention to tobacco control, but coverage remains lower than in the USA and Australia. Health workers need to give higher priority to efforts to increase news coverage beyond the present concentration around World No Tobacco Day and to develop strategies for making tobacco control issues more newsworthy to both national and local news outlets.</p

Evaluation of the psychometric properties of the London Measure of Unplanned Pregnancy in Brazilian Portuguese

Background: Estimates of unplanned pregnancy worldwide are of concern, especially in low and middle-income countries, including Brazil. Although the contraceptive prevalence rate is high in Brazil, almost half of all pregnancies are reported as unintended. The only source of nationally representative data about pregnancy intention is the Demographic and Health Survey, as with many other countries. In more recent years, however, it has been realized that concept of unintended pregnancy is potentially more complex and requires more sophisticated measurement strategies, such as the London Measure of Unplanned Pregnancy (LMUP). The LMUP has been translated and validated in other languages, but not Portuguese yet. In this study, we evaluate the psychometric properties of the LMUP in the Portuguese language, Brazilian version. Methods: A Brazilian Portuguese version of the LMUP was produced via translation and back-translation. After piloting, the mode of administration was changed from self-completion to interviewer-administration. The measure was field tested with pregnant, postpartum, and postabortion women recruited at maternity and primary health care services in Sao Paulo city. Reliability (internal consistency) was assessed using Cronbach’s alpha and item-total correlations. Construct validity was assessed using principal components analysis and hypothesis testing. Scaling was assessed with Mokken analysis. Results: 759 women aged 15–44 completed the Brazilian Portuguese LMUP. There were no missing data. The measure was acceptable and well targeted. Reliability testing demonstrated good internal consistency (alpha = 0.81, all item-rest correlations >0.2). Validity testing confirmed that the measure was unidimensional and that all hypotheses were met: there were lower LMUP median scores among women in the extreme age groups (p<0.001), among non-married women (p<0.001) and those with lower educational attainment (p<0.001). The Loevinger H coefficient was 0.60, indicating a strong scale. Conclusion: The Brazilian Portuguese LMUP is a valid and reliable measure of pregnancy planning/intention that is now available for use in Brazil. It represents a useful addition to the public health research and surveillance toolkit in Brazil

Prevalence of physical frailty, including risk factors, up to 1 year after hospitalisation for COVID-19 in the UK: a multicentre, longitudinal cohort study.

BACKGROUND: The scale of COVID-19 and its well documented long-term sequelae support a need to understand long-term outcomes including frailty. METHODS: This prospective cohort study recruited adults who had survived hospitalisation with clinically diagnosed COVID-19 across 35 sites in the UK (PHOSP-COVID). The burden of frailty was objectively measured using Fried's Frailty Phenotype (FFP). The primary outcome was the prevalence of each FFP group-robust (no FFP criteria), pre-frail (one or two FFP criteria) and frail (three or more FFP criteria)-at 5 months and 1 year after discharge from hospital. For inclusion in the primary analysis, participants required complete outcome data for three of the five FFP criteria. Longitudinal changes across frailty domains are reported at 5 months and 1 year post-hospitalisation, along with risk factors for frailty status. Patient-perceived recovery and health-related quality of life (HRQoL) were retrospectively rated for pre-COVID-19 and prospectively rated at the 5 month and 1 year visits. This study is registered with ISRCTN, number ISRCTN10980107. FINDINGS: Between March 5, 2020, and March 31, 2021, 2419 participants were enrolled with FFP data. Mean age was 57.9 (SD 12.6) years, 933 (38.6%) were female, and 429 (17.7%) had received invasive mechanical ventilation. 1785 had measures at both timepoints, of which 240 (13.4%), 1138 (63.8%) and 407 (22.8%) were frail, pre-frail and robust, respectively, at 5 months compared with 123 (6.9%), 1046 (58.6%) and 616 (34.5%) at 1 year. Factors associated with pre-frailty or frailty were invasive mechanical ventilation, older age, female sex, and greater social deprivation. Frail participants had a larger reduction in HRQoL compared with before their COVID-19 illness and were less likely to describe themselves as recovered. INTERPRETATION: Physical frailty and pre-frailty are common following hospitalisation with COVID-19. Improvement in frailty was seen between 5 and 12 months although two-thirds of the population remained pre-frail or frail. This suggests comprehensive assessment and interventions targeting pre-frailty and frailty beyond the initial illness are required. FUNDING: UK Research and Innovation and National Institute for Health Research

De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference

Transcription factors are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in promoters. The de-novo discovery of transcription factor binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not been fully solved yet. Here, we present a de-novo motif discovery tool called Dispom for finding differentially abundant transcription factor binding sites that models existing positional preferences of binding sites and adjusts the length of the motif in the learning process. Evaluating Dispom, we find that its prediction performance is superior to existing tools for de-novo motif discovery for 18 benchmark data sets with planted binding sites, and for a metazoan compendium based on experimental data from micro-array, ChIP-chip, ChIP-DSL, and DamID as well as Gene Ontology data. Finally, we apply Dispom to find binding sites differentially abundant in promoters of auxin-responsive genes extracted from Arabidopsis thaliana microarray data, and we find a motif that can be interpreted as a refined auxin responsive element predominately positioned in the 250-bp region upstream of the transcription start site. Using an independent data set of auxin-responsive genes, we find in genome-wide predictions that the refined motif is more specific for auxin-responsive genes than the canonical auxin-responsive element. In general, Dispom can be used to find differentially abundant motifs in sequences of any origin. However, the positional distribution learned by Dispom is especially beneficial if all sequences are aligned to some anchor point like the transcription start site in case of promoter sequences. We demonstrate that the combination of searching for differentially abundant motifs and inferring a position distribution from the data is beneficial for de-novo motif discovery. Hence, we make the tool freely available as a component of the open-source Java framework Jstacs and as a stand-alone application at http://www.jstacs.de/index.php/Dispom

Predicting Progression of IgA Nephropathy: New Clinical Progression Risk Score

IgA nephropathy (IgAN) is a common cause of end-stage renal disease (ESRD) in Asia. In this study, based on a large cohort of Chinese patients with IgAN, we aim to identify independent predictive factors associated with disease progression to ESRD. We collected retrospective clinical data and renal outcomes on 619 biopsy-diagnosed IgAN patients with a mean follow-up time of 41.3 months. In total, 67 individuals reached the study endpoint defined by occurrence of ESRD necessitating renal replacement therapy. In the fully adjusted Cox proportional hazards model, there were four baseline variables with a significant independent effect on the risk of ESRD. These included: eGFR [HR = 0.96(0.95–0.97)], serum albumin [HR = 0.47(0.32–0.68)], hemoglobin [HR = 0.79(0.72–0.88)], and SBP [HR = 1.02(1.00–1.03)]. Based on these observations, we developed a 4-variable equation of a clinical risk score for disease progression. Our risk score explained nearly 22% of the total variance in the primary outcome. Survival ROC curves revealed that the risk score provided improved prediction of ESRD at 24th, 60th and 120th month of follow-up compared to the three previously proposed risk scores. In summary, our data indicate that IgAN patients with higher systolic blood pressure, lower eGFR, hemoglobin, and albumin levels at baseline are at a greatest risk of progression to ESRD. The new progression risk score calculated based on these four baseline variables offers a simple clinical tool for risk stratification