The Estimation of Item Response Models with the lmer Function from the lme4 Package in R

In this paper we elaborate on the potential of the lmer function from the lme4 package in R for item response (IRT) modeling. In line with the package, an IRT framework is described based on generalized linear mixed modeling. The aspects of the framework refer to (a) the kind of covariates -- their mode (person, item, person-by-item), and their being external vs. internal to responses, and (b) the kind of effects the covariates have -- fixed vs. random, and if random, the mode across which the effects are random (persons, items). Based on this framework, three broad categories of models are described: Item covariate models, person covariate models, and person-by-item covariate models, and within each category three types of more specific models are discussed. The models in question are explained and the associated lmer code is given. Examples of models are the linear logistic test model with an error term, differential item functioning models, and local item dependency models. Because the lme4 package is for univariate generalized linear mixed models, neither the two-parameter, and three-parameter models, nor the item response models for polytomous response data, can be estimated with the lmer function.

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees

PANDIT is a database of homologous sequence alignments accompanied by estimates of their corresponding phylogenetic trees. It provides a valuable resource to those studying phylogenetic methodology and the evolution of coding-DNA and protein sequences. Currently in version 17.0, PANDIT comprises 7738 families of homologous protein domains; for each family, DNA and corresponding amino acid sequence multiple alignments are available together with high quality phylogenetic tree estimates. Recent improvements include expanded methods for phylogenetic tree inference, assessment of alignment quality and a redesigned web interface, available at the URL

Towards a Molecular Systems Model of Coronary Artery Disease

Peer reviewe

The effect of a multidisciplinary outpatient team approach on outcomes in diabetic foot care:a single center study

BACKGROUND: Recent studies showed no reduction in major amputation rates after introduction of a multidisciplinary team (MDT) approach for the treatment of diabetic foot ulcer. The efficacy of MDTs in the current standard of care is being questioned. This retrospective single-center study evaluated the efficacy of an outpatient MDT approach on limb salvage and ulcer healing in treating diabetic foot ulcers.METHODS: Patients with a diabetic foot ulcer treated before (2015) and after (2017) implementation of an MDT in a single center were compared. The MDT met weekly and consisted of a vascular surgeon, physiatrist, internist, shoe technician, wound care nurse, nurse practitioner, cast technician, and podiatrist. The primary outcome was limb salvage at 1 year. Secondary outcomes were ulcer healing, amputation-free survival, freedom from any amputation, and overall survival. Multivariable Cox regression models were used to assess predictors for major amputation.RESULTS: A vascular surgeon treated 104 patients with 148 ulcers in 2015, and the multidisciplinary team treated 133 patients with 188 ulcers in 2017. Limb salvage (90.9% vs. 95.5%, P = 0.050), freedom from any amputation (56.5% vs. 78.0%, P &lt; 0.001), and ulcer healing (48.3% vs. 69.2%, P &lt; 0.001) were significantly lower in the non-MDT group than in the MDT group. Amputation-free survival and overall survival did not differ significantly between the groups. Predictors for major amputation were University of Texas Wound Classification 3D (hazard ratio, 2.8; 95% confidence interval, 1.17-6.45) and being treated in the non-MDT group (hazard ratio, 3.7; 95% confidence interval, 1.25-11.08).CONCLUSIONS: This retrospective study found an MDT dedicated to diabetic foot care was highly effective in increasing limb salvage and ulcer healing. We advise that such an MDT is an integrated part of the patient's chain-based care.</p

Довідкові регіональні видання з геральдики

Одним з джерел інформації про наявність історичних гербів міст України та новотворів 60-х–80-х рр. ХХ ст. виступає «Алфавитный каталог городов, поселков, сел, губерний и областей России, СНГ, бывших союзных республик СССР, имеющих старые и современные гербы». Автор рецензії проаналізував принципи укладання подібних джерел інформації, зробив свої зауваження та висловив побажання щодо їх вдосконалення.«Alphabetical catalogue of towns, settlements, villages, provinces and regions of Russia, Commonwealth of Independent States, former Soviet Republics of the USSR, which have old and present-day coat of arms» is one of the sources that gives information about historical coat of arms and newly formed emblems of Ukraine during 60th – 80th of XX century. The author of the review analysed the structure of similar sources and made her remarks and suggestion regarding to its improvement

Urinary Albumin Excretion and Its Relation With C-Reactive Protein and the Metabolic Syndrome in the Prediction of Type 2 Diabetes

OBJECTIVE—To investigate urinary albumin excretion (UAE) and its relation with C-reactive protein (CRP) and the metabolic syndrome in the prediction of the development of type 2 diabetes. RESEARCH DESIGN AND METHODS—We used data from the Prevention of Renal and Vascular End Stage Disease (PREVEND) study, an ongoing, community-based, prospective cohort study initiated in 1997 in the Netherlands. The initial cohort consisted of 8,592 subjects. After 4 years, 6,894 subjects participated in a follow-up survey. Subjects with diabetes at baseline or missing data on fasting glucose were excluded, leaving 5,654 subjects for analysis. The development of type 2 diabetes, defined as a fasting glucose ≥7.0 mmol/l and/or the use of antidiabetic medication, was used as the outcome measure. UAE was calculated as the mean UAE from two consecutive 24-h urine collections. Logistic regression models were used, with the development of type 2 diabetes as the dependent variable. RESULTS—Of the 5,654 subjects for whom data were analyzed, 185 (3.3%) developed type 2 diabetes during a mean follow-up period of 4.2 years. UAE, CRP, and the presence of the metabolic syndrome at baseline were significantly associated with the incidence of type 2 diabetes (P &lt; 0.001 for all variables). In a univariate model, the odds ratio (OR) for UAE was 1.59 (95% CI 1.42–1.79). In our full model, adjusted for age, sex, number of criteria of metabolic syndrome, and other known risk factors for the development of type 2 diabetes (including fasting insulin), the association between UAE and type 2 diabetes remained significant (OR 1.53, 95% CI 1.25–1.88, P &lt; 0.001). There was a significant interaction between UAE and CRP (P = 0.002). After CRP was stratified into tertiles, the ORs for the association between baseline UAE and the development of type 2 diabetes were 2.2 (1.47–3.3), 1.33 (0.96–1.84), and 1.04 (0.83–1.31) for the lowest to highest tertiles, respectively. CONCLUSIONS—UAE predicts type 2 diabetes independent of the metabolic syndrome and other known risk markers of development of type 2 diabetes. The predictive value of UAE was modified by the level of CRP

IL28B Alleles Exert an Additive Dose Effect When Applied to HCV-HIV Coinfected Persons Undergoing Peginterferon and Ribavirin Therapy

BACKGROUND: Genetic studies have demonstrated a strong association between single nucleotide polymorphisms (SNPs) at IL28B and response to treatment with peginterferon (PEG) and ribavirin (RBV) in HCV monoinfected persons. We sought to test these associations in a prospective PEG / weight based ribavirin (WBR) treatment trial (ACTG A5178) (National Institution of Health registration number NCT00078403) in persons with HCV-HIV coinfection, and to develop a prediction score. METHODS: We selected subjects enrolled in A5178 who completed at least the first 12 weeks of the trial and had DNA available, and genotyped three SNPs at IL28B (rs12979860, rs12980275, rs8099917). We used multivariate logistic regression analysis to evaluate the association between IL28B SNPs and HCV treatment outcomes and to develop the prediction score. RESULTS: 231 HCV/HIV coinfected subjects were included. We observed a strong association between IL28B genotype and response to therapy among those with genotypes 1 or 4 (odds ratio for complete early virologic responses (cEVR) and sustained virologic response (SVR) was 2.98 [1.7-5.3] and 3.4 [1.7-6.9], respectively, for each additional copy of the C allele of rs12979860). Differences in frequency of the responder allele explained some of the discrepancy in HCV treatment outcomes between blacks and whites. A simple pretreatment prediction score that incorporates the IL28B genotype and baseline HCV viral load has a 93% negative predictive value (NPV) for SVR. CONCLUSIONS: IL28B SNPs have an additive allele dose effect in predicting HCV treatment outcomes in HCV/HIV coinfected persons and can be incorporated into a simple pretreatment prediction score that could minimize the risk of exposure to PEG/RBV therapy for persons with unfavorable scores