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"Reproducibility of Results"
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Unreliable : bias, fraud, and the reproducibility crisis in biomedical research
\"Scientists specializing in the in-depth analysis of the published scientific literature have to the conclusion that a large part of the scientific literature covers results that cannot be replicated in other independent laboratories. Scientists take this to mean that the results are unreliable or untrue. In this book, biomedical researcher Csaba Szabo summarizes the causes and consequences of this so-called \"reproducibility crisis\" in biomedical research. The range of causes is wide, from the specificities of the methods used, through various pitfalls in the design of experiments and analysis of experimental data (e.g., confirmation bias), plagiarism and deliberate data falsification, to the systematic publication of fictitious experiments that have never been performed. Through a few blatant examples - e.g. Anil Potti (Duke University); Piero Anversa (Harvard University) - Szabo describes the damaging impact that blatant fraud can have on the development of an entire field of science, and introduces some of the maverick \"science investigators\" - often working in anonymity - who devote their lives to tracking down and exposing scientific fraudsters. The book also answers the questions (a) what individual and systemic factors are involved in allowing these phenomena to occur, (b) why the appropriate steps have not been taken to control them, and (c) what the implications of the crisis are for the future of medicine and, within it, for the development of new drugs\"-- Provided by publisher.
BOOK
Diagnostic validity of early proximal caries detection using near-infrared imaging technology on 3D range data of posterior teeth
ObjectivesThis in vitro study analysed potential of early proximal caries detection using 3D range data of teeth consisting of near-infrared reflection images at 850 nm (NIRR).Materials and methodsTwo hundred fifty healthy and carious permanent human teeth were arranged pairwise, examined with bitewing radiography (BWR) and NIRR and validated with micro-computed tomography. NIRR findings were evaluated from buccal, lingual and occlusal (trilateral) views according to yes/no decisions about presence of caries. Reliability assessments included kappa statistics and revealed high agreement for both methods. Statistical analysis included cross tabulation and calculation of sensitivity, specificity and AUC.ResultsUnderestimation of caries was 24.8% for NIRR and 26.4% for BWR. Overestimation was 10.4% for occlusal NIRR and 0% for BWR. Trilateral NIRR had overall accuracy of 64.8%, overestimation of 15.6% and underestimation of 19.6%. NIRR and BWR showed high specificity and low sensitivity for proximal caries detection.ConclusionsNIRR achieved diagnostic results comparable to BWR. Trilateral NIRR assessments overestimated presence of proximal caries, revealing stronger sensitivity for initial caries detection than BWR.Clinical relevanceNIRR provided valid complement to BWR as diagnostic instrument. Investigation from multiple angles did not substantially improve proximal caries detection with NIRR.
Journal Article
Validating psychological constructs : historical, philosophical, and practical dimensions
\"This book critically examines the historical and philosophical foundations of construct validity theory (CVT), and how these have and continue to inform and constrain the conceptualization of validity and its application in research. CVT has had an immense impact on how researchers in the behavioural sciences conceptualize and approach their subject matter. Yet, there is equivocation regarding the foundations of the CVT framework as well as ambiguities concerning the nature of the 'constructs' that are its raison d'etre. The book is organized in terms of three major parts that speak, respectively, to the historical, philosophical, and pragmatic dimensions of CVT. The primary objective is to provide researchers and students with a critical lens through which a deeper understanding may be gained of both the utility and limitations of CVT and the validation practices to which it has given rise.\"-- Back cover.
Book
Immune signature drives leukemia escape and relapse after hematopoietic cell transplantation
Transplantation of hematopoietic cells from a healthy individual (allogeneic hematopoietic cell transplantation (allo-HCT)) demonstrates that adoptive immunotherapy can cure blood cancers: still, post-transplantation relapses remain frequent. To explain their drivers, we analyzed the genomic and gene expression profiles of acute myeloid leukemia (AML) blasts purified from patients at serial time-points during their disease history. We identified a transcriptional signature specific for post-transplantation relapses and highly enriched in immune-related processes, including T cell costimulation and antigen presentation. In two independent patient cohorts we confirmed the deregulation of multiple costimulatory ligands on AML blasts at post-transplantation relapse (PD-L1, B7-H3, CD80, PVRL2), mirrored by concomitant changes in circulating donor T cells. Likewise, we documented the frequent loss of surface expression of HLA-DR, -DQ and -DP on leukemia cells, due to downregulation of the HLA class II regulator CIITA. We show that loss of HLA class II expression and upregulation of inhibitory checkpoint molecules represent alternative modalities to abolish AML recognition from donor-derived T cells, and can be counteracted by interferon-γ or checkpoint blockade, respectively. Our results demonstrate that the deregulation of pathways involved in T cell-mediated allorecognition is a distinctive feature and driver of AML relapses after allo-HCT, which can be rapidly translated into personalized therapies.Post-transplantation relapse in acute myeloid leukemia patients without genomic loss of HLA is driven by transcriptional alterations in antigen presentation and T cell costimulation genes.
Journal Article
How short or long should be a questionnaire for any research? Researchers dilemma in deciding the appropriate questionnaire length
A questionnaire plays a pivotal role in various surveys. Within the realm of biomedical research, questionnaires serve a role in epidemiological surveys and mental health surveys and to obtain information about knowledge, attitude, and practice (KAP) on various topics of interest. Questionnaire in border perspective can be of different types like self-administered or professionally administered and according to the mode of delivery paper-based or electronic media-based. Various studies have been conducted to assess the appropriateness of a questionnaire in a particular field and methods to translate and validate them. But very little is known regarding the appropriate length and number of questions in a questionnaire and what role it has in data quality, reliability, and response rates. Hence, this narrative review is to explore the critical issue of appropriate length and number of questions in a questionnaire while questionnaire designing.
Journal Article
Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease
A meta-analysis of previous genome-wide association studies of Crohn’s disease and ulcerative colitis, the two most common forms of inflammatory bowel disease, with a combined total of more than 75,000 cases and controls, finds that most loci contribute to both phenotypes and other immune-mediated disorders.
Pathogenesis of inflammatory bowel disease
Genetic studies have implicated unsuspected mechanisms in the pathogenesis of Crohn's disease and ulcerative colitis, two of the most common forms of inflammatory bowel disease. This paper presents a meta-analysis of published genome-wide association studies, together with validation in more than 75,000 cases and controls. In addition to several new associations, the authors find that most loci contribute to both phenotypes, but also to other immune-mediated disorders. The data reveal an overlap between susceptibility loci for inflammatory bowel disease and mycobacterial infection, and between the pathways that govern host responses to mycobacteria and those predisposing to inflammatory bowel disease.
Crohn’s disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations
1
. Genome-wide association studies and subsequent meta-analyses of these two diseases
2
,
3
as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy
4
, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases
5
. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn’s disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.
Journal Article
Accuracy of CAD/CAM-fabricated bite splints: milling vs 3D printing
ObjectivesThe aim of this study was to investigate the accuracy of CAD/CAM-fabricated bite splints in dependence of fabrication method (milling vs 3D printing), positioning (horizontal vs vertical), selection of material, and method of deviation measurement.Materials and methodsBite splints were 3D-printed in either horizontal or vertical position (n = 10) using four different resins (Dental LT, Ortho Clear, Freeprint Splint, V-Splint). As control, ten bite splints were fabricated by CNC milling (ProArt CAD Splint). The splints were scanned and deviations between the CAD-file (trueness) and between each other within one group (precision) were measured by two different software applications and methods (cloud-to-cloud vs cloud-to-mesh). Data were analyzed using univariate analysis, Kolmogorov-Smirnov, Kruskal-Wallis, and Mann-Whitney U tests.ResultsThe highest impact on accuracy was exerted by the selection of the material (trueness: ηP2 = 0.871, P < 0.001; precision: ηP2 = 0.715, P < 0.001). Milled splints showed the highest trueness (P < 0.01) but not the highest precision at the same time. Horizontally positioned 3D-printed bite splints showed the least deviations in terms of trueness while vertical positioning resulted in the highest precision. The cloud-to-cloud method showed higher measured deviations than the other methods (P < 0.001–P = 0.002).ConclusionMilled splints show higher trueness than 3D-printed ones, while the latter reveal higher reproducibility. The calculated deviations vary according to the measurement method used.Clinical relevanceIn terms of accuracy, milled and 3D-printed bite splints seem to be of equal quality.
Journal Article
Diffusion-weighted imaging of breast lesions: Region-of-interest placement and different ADC parameters influence apparent diffusion coefficient values
Objectives
To investigate the influence of region-of-interest (ROI) placement and different apparent diffusion coefficient (ADC) parameters on ADC values, diagnostic performance, reproducibility and measurement time in breast tumours.
Methods
In this IRB-approved, retrospective study, 149 histopathologically proven breast tumours (109 malignant, 40 benign) in 147 women (mean age 53.2) were investigated. Three radiologists independently measured minimum, mean and maximum ADC, each using three ROI placement approaches:1 – small 2D-ROI, 2 – large 2D-ROI and 3 – 3D-ROI covering the whole lesion. One reader performed all measurements twice. Median ADC values, diagnostic performance, reproducibility, and measurement time were calculated and compared between all combinations of ROI placement approaches and ADC parameters.
Results
Median ADC values differed significantly between the ROI placement approaches (
p
< .001). Minimum ADC showed the best diagnostic performance (AUC .928–.956), followed by mean ADC obtained from 2D ROIs (.926–.94). Minimum and mean ADC showed high intra- (ICC .85–.94) and inter-reader reproducibility (ICC .74–.94). Median measurement time was significantly shorter for the 2D ROIs (
p
< .001).
Conclusions
ROI placement significantly influences ADC values measured in breast tumours. Minimum and mean ADC acquired from 2D-ROIs are useful for the differentiation of benign and malignant breast lesions, and are highly reproducible, with rapid measurement.
Key Points
• Region of interest placement significantly influences apparent diffusion coefficient of breast tumours.
• Minimum and mean apparent diffusion coefficient perform best and are reproducible.
• 2D regions of interest perform best and provide rapid measurement times.
Journal Article
The effect of low-abundance OTU filtering methods on the reliability and variability of microbial composition assessed by 16S rRNA amplicon sequencing
PCR amplicon sequencing may lead to detection of spurious operational taxonomic units (OTUs), inflating estimates of gut microbial diversity. There is no consensus in the analytical approach as to what filtering methods should be applied to remove low-abundance OTUs; moreover, few studies have investigated the reliability of OTU detection within replicates. Here, we investigated the reliability of OTU detection (% agreement in detecting OTU in triplicates) and accuracy of their quantification (assessed by coefficient of variation (CV)) in human stool specimens. Stool samples were collected from 12 participants 22–55 years old. We applied several methods for filtering low-abundance OTUs and determined their impact on alpha-diversity and beta-diversity metrics. The reliability of OTU detection without any filtering was only 44.1% (SE=0.9) but increased after filtering low-abundance OTUs. After filtering OTUs with <0.1% abundance in the dataset, the reliability increased to 87.7% (SE=0.6) but at the expense of removing 6.97% reads from the dataset. When filtering was based on individual sample, the reliability increased to 73.1% after filtering OTUs with <10 copies while removing only 1.12% of reads. High abundance OTUs (>10 copies in sample) had lower CV, indicating better accuracy of quantification than low-abundance OTUs. Excluding very low-abundance OTUs had a significant impact on alpha-diversity metrics sensitive to the presence of rare species (observed OTUs, Chao1) but had little impact on relative abundance of major phyla and families and alpha-diversity metrics accounting for both richness and evenness (Shannon, Inverse Simpson). To increase the reliability of microbial composition, we advise removing OTUs with <10 copies in individual samples, particularly in studies where only one subsample per specimen is available for analysis.
Journal Article
Methods to Foster Transparency and Reproducibility of Federal Statistics
In 2014 the National Science Foundation (NSF) provided support to the National Academies of Sciences, Engineering, and Medicine for a series of Forums on Open Science in response to a government-wide directive to support increased public access to the results of research funded by the federal government. However, the breadth of the work resulting from the series precluded a focus on any specific topic or discussion about how to improve public access. Thus, the main goal of the Workshop on Transparency and Reproducibility in Federal Statistics was to develop some understanding of what principles and practices are, or would be, supportive of making federal statistics more understandable and reviewable, both by agency staff and the public. This publication summarizes the presentations and discussions from the workshop.
eBook