Evidence-based methods in studies of biology and data analysis

When scientists use familiar data analysis methods out of comfort or convenience, disciplines can suffer in their scientific inferences if these methods are not appropriate for their ultimate goals. Older fields experience this when long-standing methods are used simply for their longevity. Newer fields experience this when scientists transfer methods from other areas without evaluating their performance in these new domains. This work represents a collection of methods and results that contribute to evidence-based analytical practice in three different domains: mass spectrometry-based metabolomics, massively parallel reporter assays, and data science training. In the first two domains, we present new methods that improve current practice for comparative (differential) analysis in those fields. Specifically these methods are shown to be statistically calibrated and powerful compared to existing alternatives. In the third domain, we present experimental results regarding the actions and perceptions in data analysis practice. These results have implications for data analysis training and education. Broadly, in these three domains, we provide tools and discuss findings that enable higher quality work in applied research

Does prior antithrombotic therapy influence recurrence and bleeding risk in stroke patients with atrial fibrillation or atrial flutter?

The authors would like to thank the patients of the NNUH Stroke Register cohort and the data team of the Norfolk and Norwich University Stroke Services. NNUH Stroke Register is maintained by the NNUH Stroke Services.Peer reviewedPostprin

Defining Plasmodium falciparum Treatment in South West Asia: A Randomized Trial Comparing Artesunate or Primaquine Combined with Chloroquine or SP

INTRODUCTION: Antimalarial resistance has led to a global policy of artemisinin-based combination therapy. Despite growing resistance chloroquine (CQ) remained until recently the official first-line treatment for falciparum malaria in Pakistan, with sulfadoxine-pyrimethamine (SP) second-line. Co-treatment with the gametocytocidal primaquine (PQ) is recommended for transmission control in South Asia. The relative effect of artesunate (AS) or primaquine, as partner drugs, on clinical outcomes and gametocyte carriage in this setting were unknown. METHODS: A single-blinded, randomized trial among Afghan refugees in Pakistan compared six treatment arms: CQ; CQ+(single-dose)PQ; CQ+(3 d)AS; SP; SP+(single-dose)PQ, and SP+(3 d)AS. The objectives were to compare treatment failure rates and effect on gametocyte carriage, of CQ or SP monotherapy against the respective combinations (PQ or AS). Outcomes included trophozoite and gametocyte clearance (read by light microscopy), and clinical and parasitological failure. FINDINGS: A total of 308 (87%) patients completed the trial. Failure rates by day 28 were: CQ 55/68 (81%); CQ+AS 19/67 (28%), SP 4/41 (9.8%), SP+AS 1/41 (2.4%). The addition of PQ to CQ or SP did not affect failure rates (CQ+PQ 49/67 (73%) failed; SP+PQ 5/33 (16%) failed). AS was superior to PQ at clearing gametocytes; gametocytes were seen on d7 in 85% of CQ, 40% of CQ+PQ, 21% of CQ+AS, 91% of SP, 76% of SP+PQ and 23% of SP+AS treated patients. PQ was more effective at clearing older gametocyte infections whereas AS was more effective at preventing emergence of mature gametocytes, except in cases that recrudesced. CONCLUSIONS: CQ is no longer appropriate by itself or in combination. These findings influenced the replacement of CQ with SP+AS for first-line treatment of uncomplicated falciparum malaria in the WHO Eastern Mediterranean Region. The threat of SP resistance remains as SP monotherapy is still common. Three day AS was superior to single-dose PQ for reducing gametocyte carriage. TRIAL REGISTRATION: ClinicalTrials.gov NCT00959517

Preoperative chemoradiation with capecitabine, irinotecan and cetuximab in rectal cancer: significance of pre-treatment and post-resection RAS mutations

Background: The influence of EGFR pathway mutations on cetuximab-containing rectal cancer preoperative chemoradiation (CRT) is uncertain. Methods: In a prospective phase II trial (EXCITE), patients with magnetic resonance imaging (MRI)-defined non-metastatic rectal adenocarinoma threatening/involving the surgical resection plane received pelvic radiotherapy with concurrent capecitabine, irinotecan and cetuximab. Resection was recommended 8 weeks later. The primary endpoint was histopathologically clear (R0) resection margin. Pre-planned retrospective DNA pyrosequencing (PS) and next generation sequencing (NGS) of KRAS, NRAS, PIK3CA and BRAF was performed on the pre-treatment biopsy and resected specimen. Results: Eighty-two patients were recruited and 76 underwent surgery, with R0 resection in 67 (82%, 90%CI: 73–88%) (four patients with clinical complete response declined surgery). Twenty–four patients (30%) had an excellent clinical or pathological response (ECPR). Using NGS 24 (46%) of 52 matched biopsies/resections were discrepant: ten patients (19%) gained 13 new resection mutations compared to biopsy (12 KRAS, one PIK3CA) and 18 (35%) lost 22 mutations (15 KRAS, 7 PIK3CA). Tumours only ever testing RAS wild-type had significantly greater ECPR than tumours with either biopsy or resection RAS mutations (14/29 [48%] vs 10/51 [20%], P=0.008), with a trend towards increased overall survival (HR 0.23, 95% CI 0.05–1.03, P=0.055). Conclusions: This regimen was feasible and the primary study endpoint was met. For the first time using pre-operative rectal CRT, emergence of clinically important new resection mutations is described, likely reflecting intratumoural heterogeneity manifesting either as treatment-driven selective clonal expansion or a geographical biopsy sampling miss

Effect of calcination time on the physicochemical properties and photocatalytic performance of carbon and nitrogen co-doped TiO2 nanoparticles

The application of highly active nano catalysts in advanced oxidation processes (AOPs) improves the production of non-selective hydroxyl radicals and co-oxidants for complete remediation of polluted water. This study focused on the synthesis and characterisation of a highly active visible light C–N-co-doped TiO2 nano catalyst that we prepared via the sol-gel method and pyrolysed at 350 ◦C for 105 min in an inert atmosphere to prevent combustion of carbon moietie

Linear models enable powerful differential activity analysis in massively parallel reporter assays

Abstract Background Massively parallel reporter assays (MPRAs) have emerged as a popular means for understanding noncoding variation in a variety of conditions. While a large number of experiments have been described in the literature, analysis typically uses ad-hoc methods. There has been little attention to comparing performance of methods across datasets. Results We present the mpralm method which we show is calibrated and powerful, by analyzing its performance on multiple MPRA datasets. We show that it outperforms existing statistical methods for analysis of this data type, in the first comprehensive evaluation of statistical methods on several datasets. We investigate theoretical and real-data properties of barcode summarization methods and show an unappreciated impact of summarization method for some datasets. Finally, we use our model to conduct a power analysis for this assay and show substantial improvements in power by performing up to 6 replicates per condition, whereas sequencing depth has smaller impact; we recommend to always use at least 4 replicates. An R package is available from the Bioconductor project. Conclusions Together, these results inform recommendations for differential analysis, general group comparisons, and power analysis and will help improve design and analysis of MPRA experiments

Joint Bounding of Peaks Across Samples Improves Differential Analysis in Mass Spectrometry-Based Metabolomics

As mass spectrometry-based metabolomics becomes more widely used in biomedical research, it is important to revisit existing data analysis paradigms. Existing data preprocessing efforts have largely focused on methods which start by extracting features separately from each sample, followed by a subsequent attempt to group features across samples to facilitate comparisons. We show that this preprocessing approach leads to unnecessary variability in peak quantifications that adversely impacts downstream analysis. We present a new method, bakedpi, for the preprocessing of both centroid and profile mode metabolomics data that relies on an intensity-weighted bivariate kernel density estimation on a pooling of all samples to detect peaks. This new method reduces this unnecessary quantification variability and increases power in downstream differential analysis

A Standardized Needs Assessment Tool to Inform the Curriculum Development Process for Pediatric Resuscitation Simulation-Based Education in Resource-Limited Settings

IntroductionUnder five mortality rates (UFMR) remain high for children in low- and middle-income countries (LMICs) in the developing world. Education for practitioners in these environments is a key factor to improve outcomes that will address United Nations Sustainable Development Goals 3 and 10 (good health and well being and reduced inequalities). In order to appropriately contextualize a curriculum using simulation, it is necessary to first conduct a needs assessment of the target learner population. The World Health Organization (WHO) has published a tool to assess capacity for emergency and surgical care in LMICs that is adaptable to this goal.Materials and methodsThe WHO Tool for Situational Analysis to Assess Emergency and Essential Surgical Care was modified to assess pediatric resuscitation capacity in clinical settings in two LMICs: Uganda and Myanmar. Modifications included assessment of self-identified learning needs, current practices, and perceived epidemiology of disease burden in each clinical setting, in addition to assessment of pediatric resuscitation capacity in regard to infrastructure, procedures, equipment, and supplies. The modified tool was administered to 94 respondents from the two settings who were target learners of a proposed simulation-based curriculum in pediatric and neonatal resuscitation.ResultsInfectious diseases (respiratory illnesses and diarrheal disease) were cited as the most common causes of pediatric deaths in both countries. Self-identified learning needs included knowledge and skill development in pediatric airway/breathing topics, as well as general resuscitation topics such as CPR and fluid resuscitation in shock. Equipment and supply availability varied substantially between settings, and critical shortages were identified in each setting. Current practices and procedures were often limited by equipment availability or infrastructural considerations.Discussion and conclusionEpidemiology of disease burden reported by respondents was relatively consistent with WHO country-specific UFMR statistics in each setting. Results of the needs assessment survey were subsequently used to refine goals and objectives for the simulation curriculum and to ensure delivery of pragmatic educational content with recommendations that were contextualized for local capacity and resource availability. Effective use of the tool in two different settings increases its potential generalizability