Psychometric evaluation of the computerized battery for neuropsychological evaluation of children (BENCI) among school aged children in the context of HIV in an urban Kenyan setting

IntroductionCulturally validated neurocognitive measures for children in Low- and Middle-Income Countries are important in the timely and correct identifcation of neurocognitive impairments. Such measures can inform development of interventions for children exposed to additional vulnerabilities like HIV infection. The Battery for Neuropsychological Evaluation of Children (BENCI) is an openly available, computerized neuropsychological battery specifcally developed to evaluate neurocognitive impairment. This study adapted the BENCI and evaluated its reliability and validity in Kenya.Methodology The BENCI was adapted using translation and back-translation from Spanish to English. The psy‑chometric properties were evaluated in a case–control study of 328 children (aged 6 – 14 years) living with HIV and 260 children not living with HIV in Kenya. We assessed reliability, factor structure, and measurement invariance withrespect to HIV. Additionally, we examined convergent validity of the BENCI using tests from the Kilif Toolkit. ResultsInternal consistencies (0.49<α<0.97) and test–retest reliabilities (-.34 to .81) were sufcient-to-good for most of the subtests. Convergent validity was supported by signifcant correlations between the BENCI’s Verbal memoryand Kilif’s Verbal List Learning (r=.41), the BENCI’s Visual memory and Kilif’s Verbal List Learning (r=.32) and the BENCI’s Planning total time test and Kilif’s Tower Test (r= -.21) and the BENCI’s Abstract Reasoning test and Kilif’s Raven’sProgressive Matrix (r=.21). The BENCI subtests highlighted meaningful diferences between children living with HIV and those not living with HIV. After some minor adaptions, a confrmatory four-factor model consisting of fexibility,fuency, reasoning and working memory ftted well (χ2=135.57, DF=51, N=604, p<.001, RMSEA=.052, CFI=.944, TLI=.914) and was partially scalar invariant between HIV positive and negative groups.ConclusionThe English version of the BENCI formally translated for use in Kenya can be further adapted and inte‑grated in clinical and research settings as a valid and reliable cognitive test battery

Peer review quality and transparency of the peer-review process in open access and subscription journals

BACKGROUND:Recent controversies highlighting substandard peer review in Open Access (OA) and traditional (subscription) journals have increased the need for authors, funders, publishers, and institutions to assure quality of peer-review in academic journals. I propose that transparency of the peer-review process may be seen as an indicator of the quality of peer-review, and develop and validate a tool enabling different stakeholders to assess transparency of the peer-review process. METHODS AND FINDINGS:Based on editorial guidelines and best practices, I developed a 14-item tool to rate transparency of the peer-review process on the basis of journals' websites. In Study 1, a random sample of 231 authors of papers in 92 subscription journals in different fields rated transparency of the journals that published their work. Authors' ratings of the transparency were positively associated with quality of the peer-review process but unrelated to journal's impact factors. In Study 2, 20 experts on OA publishing assessed the transparency of established (non-OA) journals, OA journals categorized as being published by potential predatory publishers, and journals from the Directory of Open Access Journals (DOAJ). Results show high reliability across items (α = .91) and sufficient reliability across raters. Ratings differentiated the three types of journals well. In Study 3, academic librarians rated a random sample of 140 DOAJ journals and another 54 journals that had received a hoax paper written by Bohannon to test peer-review quality. Journals with higher transparency ratings were less likely to accept the flawed paper and showed higher impact as measured by the h5 index from Google Scholar. CONCLUSIONS:The tool to assess transparency of the peer-review process at academic journals shows promising reliability and validity. The transparency of the peer-review process can be seen as an indicator of peer-review quality allowing the tool to be used to predict academic quality in new journals

Challenges in Data Intensive Analysis at Scientific Experimental User Facilities

Today's scientific challenges such as routes to a sustainable energy future, materials by design or biological and chemical environmental remediation methods, are complex problems that require the integration of a wide range of complementary expertise to be addressed successfully. Experimental and computational science research methods can hereby offer fundamental insights for their solution. Experimental facilities in particular can contribute through a large variety of investigative methods, which can span length scales from millions of kilometers (radar) to the sub-nucleus (LHC). These methods are used to probe structure, properties, and function of objects from single elements to whole communities. Hereby direct imaging techniques are a powerful means to develop an atomistic understanding of scientific issues. For example, the identification ofmechanisms associated with chemical, material, and biological transformations requires the direct observation of the reactions to build up an understanding of the atom-by-atom structural and chemical changes. Computational science can aid the planning of such experiments, correlate results, explain or predict the phenomena as they would be observed and thus aid their interpretation. Furthermore computational science can be essential for the investigation of phenomena that are difficult to observe due to their scale, reaction time or extreme conditions. Combining experimental and computational techniques provides scientists with the ability to research structures and processes at various levels of theory, e.g. providing molecular 'movies' of complex reactions that show bond breaking and reforming in natural time scales, along with the intermediate states to understand the mechanisms that govern the chemical transformations. This chapter will discuss the critical data intensive analysis challenges faced by the experimental science community at large scale and laboratory based facilities. The chapter will highlight current solutions and lay out perspectives for the future, such as methods to achieve real time analysis capabilities and the challenges and opportunities of data integration across experimental scales, levels of theory, and varying techniques

The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs

Replication is more than hitting the lottery twice

The main goal of our target article was to provide concrete recommendations for improving the replicability of research findings. Most of the comments focus on this point. In addition, a few comments were concerned with the distinction between replicability and generalizability and the role of theory in replication. We address all comments within the conceptual structure of the target article, and hope to convince readers that replication in psychological science amounts to much more than hitting the lottery twice

The influence of journal submission guidelines on authors' reporting of statistics and use of open research practices.

From January 2014, Psychological Science introduced new submission guidelines that encouraged the use of effect sizes, estimation, and meta-analysis (the "new statistics"), required extra detail of methods, and offered badges for use of open science practices. We investigated the use of these practices in empirical articles published by Psychological Science and, for comparison, by the Journal of Experimental Psychology: General, during the period of January 2013 to December 2015. The use of null hypothesis significance testing (NHST) was extremely high at all times and in both journals. In Psychological Science, the use of confidence intervals increased markedly overall, from 28% of articles in 2013 to 70% in 2015, as did the availability of open data (3 to 39%) and open materials (7 to 31%). The other journal showed smaller or much smaller changes. Our findings suggest that journal-specific submission guidelines may encourage desirable changes in authors' practices

Peak expiratory flow rate shows a gender-specific association with vitamin D deficiency

Context: To our knowledge, no previous studies examined the longitudinal relationship between vitamin D status and pulmonary function in a population-based sample of older persons. Objective: Our objective was to examine the cross-sectional as well as the longitudinal relationship between vitamin D status and peak expiratory flow rate (PEFR) in a representative sample of the Dutch older population. Design, Setting, and Participants: Participants included men and women in the Longitudinal Aging Study Amsterdam, an ongoing cohort study in older people. Main Outcome Measure: PEFR was measured using the mini-Wright peak flow meter. Results: Men with serum 25-hydroxyvitamin D (25-OHD) levels below 10 ng/ml (25 nmol/liter) had a significantly lower PEFR in the cross-sectional analyses, and men with serum 25-OHD levels below 20 ng/ml (50 nmol/liter) had a significantly lower PEFR in the longitudinal analyses as compared with men with serum 25-OHD levels above 30 ng/ml (75 nmol/liter) (cross-sectional: β = -47.0, P = 0.01 for serum 25-OHD<10 ng/ml; longitudinal: β = -45.0, P<0.01 for serum 25-OHD<10 ng/ml; and β = -20.2, P = 0.03 for serum 25-OHD = 10-20 ng/ml in the fully adjusted models). Physical performance (β = -32.5, P = 0.08 for serum 25-OHD<10 ng/ml) and grip strength (β = -40.0, P = 0.03 for serum 25-OHD <10 ng/ml) partly mediated the cross-sectional associations but not the longitudinal associations. In women, statistically significant associations between 25-OHD and PEFR were observed in the cross-sectional analyses after adjustment for age and season of blood collection but not in the fully adjusted models or in the longitudinal analyses. Conclusions: A strong relationship between serum 25-OHD and PEFR was observed in older men, both in the cross-sectional as well as longitudinal analyses, but not in older women. The association in men could partly be explained by physical performance and muscle strength. Copyright © 2012 by The Endocrine Society

Sunlight exposure or vitamin D supplementation for vitamin D-deficient non-western immigrants: a randomized clinical trial

Summary: Vitamin D deficiency is very common in non-western immigrants. In this randomized clinical trial, vitamin D 800 IU/day or 100,000 IU/3 months were compared with advised sunlight exposure. Vitamin D supplementation was more effective than advised sunlight exposure in improving vitamin D status and lowering parathyroid hormone levels. Introduction: Vitamin D deficiency (25-hydroxyvitamin D [25(OH)D]<25 nmol/l) is common among non-western immigrants. It can be treated with vitamin D supplementation or sunlight exposure. Methods: To determine whether the effect of vitamin

Clinical added value of MRI to CT in patients scheduled for local therapy of colorectal liver metastases (CAMINO):study protocol for an international multicentre prospective diagnostic accuracy study

Abstract Background Abdominal computed tomography (CT) is the standard imaging method for patients with suspected colorectal liver metastases (CRLM) in the diagnostic workup for surgery or thermal ablation. Diffusion-weighted and gadoxetic-acid-enhanced magnetic resonance imaging (MRI) of the liver is increasingly used to improve the detection rate and characterization of liver lesions. MRI is superior in detection and characterization of CRLM as compared to CT. However, it is unknown how MRI actually impacts patient management. The primary aim of the CAMINO study is to evaluate whether MRI has sufficient clinical added value to be routinely added to CT in the staging of CRLM. The secondary objective is to identify subgroups who benefit the most from additional MRI. Methods In this international multicentre prospective incremental diagnostic accuracy study, 298 patients with primary or recurrent CRLM scheduled for curative liver resection or thermal ablation based on CT staging will be enrolled from 17 centres across the Netherlands, Belgium, Norway, and Italy. All study participants will undergo CT and diffusion-weighted and gadoxetic-acid enhanced MRI prior to local therapy. The local multidisciplinary team will provide two local therapy plans: first, based on CT-staging and second, based on both CT and MRI. The primary outcome measure is the proportion of clinically significant CRLM (CS-CRLM) detected by MRI not visible on CT. CS-CRLM are defined as liver lesions leading to a change in local therapeutical management. If MRI detects new CRLM in segments which would have been resected in the original operative plan, these are not considered CS-CRLM. It is hypothesized that MRI will lead to the detection of CS-CRLM in ≥10% of patients which is considered the minimal clinically important difference. Furthermore, a prediction model will be developed using multivariable logistic regression modelling to evaluate the predictive value of patient, tumor and procedural variables on finding CS-CRLM on MRI. Discussion The CAMINO study will clarify the clinical added value of MRI to CT in patients with CRLM scheduled for local therapy. This study will provide the evidence required for the implementation of additional MRI in the routine work-up of patients with primary and recurrent CRLM for local therapy. Trial registration The CAMINO study was registered in the Netherlands National Trial Register under number NL8039 on September 20th 2019