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The Evolving Nature of Health Technology Assessment: A Critical Appraisal of NICE's New Methods Manual. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2023; 26:1503-1509. [PMID: 37268059 DOI: 10.1016/j.jval.2023.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/04/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023]
Abstract
OBJECTIVES The National Institute for Health and Care Excellence (NICE) recently completed a review of its methods for health technology assessment, involving a 2-stage public consultation. We appraise proposed methodological changes and analyze key decisions. METHODS We categorize all changes proposed in the first consultation as "critical," "moderate" or "limited" updates, considering the importance of the topic and the degree of change or the level of reinforcement. Proposals were followed through the review process, for their inclusion, exclusion, or amendment in the second consultation and the new manual. RESULTS The end-of-life value modifier was replaced with a new "disease severity" modifier and other potential modifiers were rejected. The usefulness of a comprehensive evidence base was emphasized, clarifying when nonrandomized studies can be used, with further guidance on "real-world" evidence developed separately. A greater degree of uncertainty was accepted in circumstances when evidence generation raised challenges, in particular for children, rare diseases, and innovative technologies. For some topics, such as health inequality, discounting, unrelated healthcare costs, and value of information, significant changes were possibly warranted, but NICE decided not to make any revisions at present. CONCLUSION Most of the changes to NICE's health technology assessment methods are appropriate and modest in impact. Nevertheless, some decisions were not well justified and further research is needed on several topics, including investigation of societal preferences. Ultimately, NICE's role of protecting National Health Services resources for valuable interventions that can contribute toward improving overall population health must be safeguarded, without accepting weaker evidence.
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Tortoise or Hare? The Associations between Physical Activity Volume and Intensity Distribution and the Risk of All-Cause Mortality: A Large Prospective Analysis of the UK Biobank. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6401. [PMID: 37510633 PMCID: PMC10378963 DOI: 10.3390/ijerph20146401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/23/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
Analysis methods to determine the optimal combination of volume and intensity of objectively measured physical activity (PA) with prospective outcomes are limited. Participants in UK Biobank were recruited in the UK between 2006 and 2010. We linked the questionnaire and accelerometer with all-cause mortality data from the NHS Information Centre and NHS Central Register up to April 2021. We developed a novel method, extending the penalized spline model of Augustin et al. to a smooth additive Cox model for survival data, and estimated the prospective relationship between intensity distribution and all-cause mortality, adjusting for the overall volume of PA. We followed 84,166 men and women (aged 40-69) for an average of 6.4 years (range 5.3-7.9), with an observed mortality rate of 22.2 deaths per 1000. Survival rates differed by PA volume quartile, with poorer outcomes for the lowest PA volumes. Participants with more sedentary to light intensity PA (<100 milligravities (mg)) and/or less vigorous intensity PA (>250 mg) than average for a given volume of PA, had higher mortality rates than vice versa. Approximate hazard ratios were 0.83 (95% credible interval [CI]: 0.79, 0.88) for an average-risk profile compared to a high-risk profile and 0.80 (95% CI: 0.74, 0.87) for a low-risk profile compared to an average-risk profile. A high- versus low-risk profile has the equivalent of 15 min more slow walking, but 10 min less moderate walking. At low PA volumes, increasing overall volume suggests the most benefit in reducing all-cause mortality risk. However, at higher overall volumes, substituting lighter with more vigorous intensity activity suggests greater benefit.
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Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction. J Clin Microbiol 2023; 61:e0157822. [PMID: 36815861 PMCID: PMC10035339 DOI: 10.1128/jcm.01578-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Universal access to drug susceptibility testing for newly diagnosed tuberculosis patients is recommended. Access to culture-based diagnostics remains limited, and targeted molecular assays are vulnerable to emerging resistance mutations. Improved protocols for direct-from-sputum Mycobacterium tuberculosis sequencing would accelerate access to comprehensive drug susceptibility testing and molecular typing. We assessed a thermo-protection buffer-based direct-from-sample M. tuberculosis whole-genome sequencing protocol. We prospectively analyzed 60 acid-fast bacilli smear-positive clinical sputum samples in India and Madagascar. A diversity of semiquantitative smear positivity-level samples were included. Sequencing was performed using Illumina and MinION (monoplex and multiplex) technologies. We measured the impact of bacterial inoculum and sequencing platforms on genomic read depth, drug susceptibility prediction performance, and typing accuracy. M. tuberculosis was identified by direct sputum sequencing in 45/51 samples using Illumina, 34/38 were identified using MinION-monoplex sequencing, and 20/24 were identified using MinION-multiplex sequencing. The fraction of M. tuberculosis reads from MinION sequencing was lower than from Illumina, but monoplexing grade 3+ samples on MinION produced higher read depth than Illumina (P < 0.05) and MinION multiplexing (P < 0.01). No significant differences in sensitivity and specificity of drug susceptibility predictions were seen across sequencing modalities or within each technology when stratified by smear grade. Illumina sequencing from sputum accurately identified 1/8 (rifampin) and 6/12 (isoniazid) resistant samples, compared to 2/3 (rifampin) and 3/6 (isoniazid) accurately identified with Nanopore monoplex. Lineage agreement levels between direct and culture-based sequencing were 85% (MinION-monoplex), 88% (Illumina), and 100% (MinION-multiplex). M. tuberculosis direct-from-sample whole-genome sequencing remains challenging. Improved and affordable sample treatment protocols are needed prior to clinical deployment.
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Missing Pieces in Structure Puzzles: How Hyperpolarized NMR Spectroscopy Can Complement Structural Biology and Biochemistry. Chembiochem 2023; 24:e202200703. [PMID: 36624049 DOI: 10.1002/cbic.202200703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Structure determination lies at the heart of many biochemical research programs. However, the "giants": X-ray diffraction, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, among others, leave quite a few dark spots on the structural pictures drawn of proteins, nucleic acids, membranes, and other biomacromolecules. For example, structural models under physiological conditions or of short-lived intermediates often remain out of reach of the established experimental methods. This account frames the possibility of including hyperpolarized, that is, dramatically signal-enhanced NMR in existing workflows to fill these spots with detailed depictions. We highlight how integrating methods based on dissolution dynamic nuclear polarization can provide valuable complementary information about formerly inaccessible conformational spaces for many systems. A particular focus will be on hyperpolarized buffers to facilitate the NMR structure determination of challenging systems.
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Stability of polygenic scores across discovery genome-wide association studies. HGG ADVANCES 2022; 3:100091. [PMID: 35199043 PMCID: PMC8841810 DOI: 10.1016/j.xhgg.2022.100091] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 01/18/2022] [Indexed: 01/19/2023] Open
Abstract
Polygenic scores (PGS) are commonly evaluated in terms of their predictive accuracy at the population level by the proportion of phenotypic variance they explain. To be useful for precision medicine applications, they also need to be evaluated at the individual level when phenotypes are not necessarily already known. We investigated the stability of PGS in European American (EUR) and African American (AFR)-ancestry individuals from the Philadelphia Neurodevelopmental Cohort and the Adolescent Brain Cognitive Development study using different discovery genome-wide association study (GWAS) results for post-traumatic stress disorder (PTSD), type 2 diabetes (T2D), and height. We found that pairs of EUR-ancestry GWAS for the same trait had genetic correlations >0.92. However, PGS calculated from pairs of same-ancestry and different-ancestry GWAS had correlations that ranged from <0.01 to 0.74. PGS stability was greater for height than for PTSD or T2D. A series of height GWAS in the UK Biobank suggested that correlation between PGS is strongly dependent on the extent of sample overlap between the discovery GWAS. Focusing on the upper end of the PGS distribution, different discovery GWAS do not consistently identify the same individuals in the upper quantiles, with the best case being 60% of individuals above the 80th percentile of PGS overlapping from one height GWAS to another. The degree of overlap decreases sharply as higher quantiles, less heritable traits, and different-ancestry GWAS are considered. PGS computed from different discovery GWAS have only modest correlation at the individual level, underscoring the need to proceed cautiously with integrating PGS into precision medicine applications.
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Abstract
The DIALS software for the processing of X‐ray diffraction data is presented, with an emphasis on how the suite may be used as a toolkit for data processing. The description starts with an overview of the history and intent of the toolkit, usage as an automated system, command‐line use, and ultimately how new tools can be written using the API to perform bespoke analysis. Consideration is also made to the application of DIALS to techniques outside of macromolecular X‐ray crystallography.
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Visual pursuit behavior in mice maintains the pursued prey on the retinal region with least optic flow. eLife 2021; 10:e70838. [PMID: 34698633 PMCID: PMC8547958 DOI: 10.7554/elife.70838] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/30/2021] [Indexed: 11/26/2022] Open
Abstract
Mice have a large visual field that is constantly stabilized by vestibular ocular reflex (VOR) driven eye rotations that counter head-rotations. While maintaining their extensive visual coverage is advantageous for predator detection, mice also track and capture prey using vision. However, in the freely moving animal quantifying object location in the field of view is challenging. Here, we developed a method to digitally reconstruct and quantify the visual scene of freely moving mice performing a visually based prey capture task. By isolating the visual sense and combining a mouse eye optic model with the head and eye rotations, the detailed reconstruction of the digital environment and retinal features were projected onto the corneal surface for comparison, and updated throughout the behavior. By quantifying the spatial location of objects in the visual scene and their motion throughout the behavior, we show that the prey image consistently falls within a small area of the VOR-stabilized visual field. This functional focus coincides with the region of minimal optic flow within the visual field and consequently area of minimal motion-induced image-blur, as during pursuit mice ran directly toward the prey. The functional focus lies in the upper-temporal part of the retina and coincides with the reported high density-region of Alpha-ON sustained retinal ganglion cells.
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Macromolecular crystallography using microcrystal electron diffraction. Acta Crystallogr D Struct Biol 2021; 77:313-324. [PMID: 33645535 PMCID: PMC7919406 DOI: 10.1107/s2059798320016368] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/16/2020] [Indexed: 11/10/2022] Open
Abstract
Microcrystal electron diffraction (MicroED) has recently emerged as a promising method for macromolecular structure determination in structural biology. Since the first protein structure was determined in 2013, the method has been evolving rapidly. Several protein structures have been determined and various studies indicate that MicroED is capable of (i) revealing atomic structures with charges, (ii) solving new protein structures by molecular replacement, (iii) visualizing ligand-binding interactions and (iv) determining membrane-protein structures from microcrystals embedded in lipidic mesophases. However, further development and optimization is required to make MicroED experiments more accurate and more accessible to the structural biology community. Here, we provide an overview of the current status of the field, and highlight the ongoing development, to provide an indication of where the field may be going in the coming years. We anticipate that MicroED will become a robust method for macromolecular structure determination, complementing existing methods in structural biology.
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Microbiology in the Field: Construction and Validation of a Portable Incubator for Real-Time Quantification of Coliforms and Other Bacteria. Front Public Health 2020; 8:607997. [PMID: 33324604 PMCID: PMC7723852 DOI: 10.3389/fpubh.2020.607997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/28/2020] [Indexed: 11/24/2022] Open
Abstract
Performing microbiological assays on environmental samples in field settings poses logistical challenges with respect to the availability of suitable equipment or the ability to get samples to the laboratory in a timely fashion. For example, the viability of some bacteria can decrease greatly between sampling and arrival to the laboratory for processing. We developed and constructed rugged, reliable, and cost-effective portable incubators that were used by 10 independent field teams to perform microbiological assays on surface water samples from lakes across Canada. Rigorous testing and validation of our incubators ensured that incubation conditions were consistent within and across all 10 field teams and 2 sampling years. Samples from all sites were processed in duplicate and bacterial counts were highly repeatable within and across sampling teams. Bacterial counts were also found to be statistically equivalent to counts obtained with standard laboratory techniques using a conventional incubator. Using this method, thermotolerant coliforms (TTCs) and Escherichia coli were quantified from 432 lakes, allowing comparison to both historical datasets that relied on TTCs and those following current guidelines that use E. coli counts. We found higher loads at the shoreline than the middle of lakes and different patterns between ecozones. E. coli was not frequently detected, but many lakes exceeded Canadian guideline values for activities such as swimming and some even exceeded the guideline value for secondary recreational activities such as boating. To the best of our knowledge, this is the largest bacteriological water quality assessment of freshwater lakes to date in terms of both spatial scale and the number of lakes sampled. Our incubator design can be easily adapted for a wide variety of researcher goals and represents a robust platform for field studies and other applications, including those in remote or low-resources settings.
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Detection of Metal-Doped Fluorescent PVC Microplastics in Freshwater Mussels. NANOMATERIALS 2020; 10:nano10122363. [PMID: 33261080 PMCID: PMC7759941 DOI: 10.3390/nano10122363] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022]
Abstract
The large-scale production of plastic and the resulting release of waste is leading to a huge accumulation of micro-sized particles in the environment that could have an impact on not only aquatic organisms but also on humans. Despite the extensive literature on the subject, there is still an insufficient harmonization of methodologies for the collection and analysis of microplastics (MPs) in complex matrices; especially for high density polymers; such as polyvinyl chloride (PVC), which tend to sink and accumulate in sediments, becoming available to benthonic organisms. In this article, mussels have been chosen as model for microplastic accumulation due to their extensive filtering activity and their wide distribution in both fresh and salt water basins. To facilitate the identification and quantification of microplastics taken up by mussels, novel fluorescent and metal-doped PVC microplastics (PVC-Platinum octaethylporphyrin (PtOEP) MPs in the size range of 100 µm) have been synthesized and characterized. For the analysis of the mussels following exposure, an enzymatic protocol using amylase, lipase, papain, and SDS for organic material digestion and a sucrose-ZnCl2 density gradient for the selective separation of ingested microplastics has been developed. The final identification of MPs was performed by fluorescence microscopy. This work can greatly benefit the scientific community by providing a means to study the behavior of PVC MPs, which represent an example of a very relevant yet poorly studied high density polymeric contaminant commonly found in complex environmental matrices.
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Simplified Analysis of Measurement Data from A Rapid E. coli qPCR Method (EPA Draft Method C) Using A Standardized Excel Workbook. WATER 2020; 12:1-775. [PMID: 32461809 PMCID: PMC7252523 DOI: 10.3390/w12030775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Draft method C is a standardized method for quantifying E. coli densities in recreational waters using quantitative polymerase chain reaction (qPCR). The method includes a Microsoft Excel workbook that automatically screens for poor-quality data using a set of previously proposed acceptance criteria, generates weighted linear regression (WLR) composite standard curves, and calculates E. coli target gene copies in test samples. We compared standard curve parameter values and test sample results calculated with the WLR model to those from a Bayesian master standard curve (MSC) model using data from a previous multi-lab study. The two models' mean intercept and slope estimates from twenty labs' standard curves were within each other's 95% credible or confidence intervals for all labs. E. coli gene copy estimates of six water samples analyzed by eight labs were highly overlapping among labs when quantified with the WLR and MSC models. Finally, we compared multiple labs' 2016-2018 composite curves, comprised of data from individual curves where acceptance criteria were not used, to their corresponding composite curves with passing acceptance criteria. Composite curves developed from passing individual curves had intercept and slope 95% confidence intervals that were often narrower than without screening and an analysis of covariance test was passed more often. The Excel workbook WLR calculation and acceptance criteria will help laboratories implement draft method C for recreational water analysis in an efficient, cost-effective, and reliable manner.
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Abstract
Stressor-response research on stony corals in the laboratory relies on detecting relatively small changes in the size of coral fragments throughout the course of an experiment. Coral colonies are complex, three-dimensional (3D) communities of organisms, so small changes in size are best detected by changes in 3D surface area. Traditional methods to estimate 3D coral surface area commonly require destruction of the sample, thereby eliminating repeat measurements and the ability to calculate growth rate. However, non-destructive two-dimensional (2D) photogrammetry can be used if defensible relationships with 3D surface area can be established. In this study, 165 coral skeletons representing four stony coral species (Pocillopora damicornis, Madracis mirabilis, Orbicella faveolata, Porites porites) were photographed in 2D (top and side views) and then imaged with 3D laser scanning. Significant linear relationships were found between the 3D surface areas (laser) and the sum of various combinations of top and side view surface areas captured by 2D digital photography. The relationships were very strong for simple colony shapes and more variable as coral fragments increased in size and complexity. This study demonstrates an efficient method for obtaining estimates of 3D coral surface area from non-destructive 2D photogrammetry, allowing measurement of growth rate throughout experimental exposure periods.
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Development and Comparison of Complementary Methods to Study Potential Skin and Inhalational Exposure to Pathogens During Personal Protective Equipment Doffing. Clin Infect Dis 2019; 69:S231-S240. [PMID: 31517983 PMCID: PMC6761368 DOI: 10.1093/cid/ciz616] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Fluorescent tracers are often used with ultraviolet lights to visibly identify healthcare worker self-contamination after doffing of personal protective equipment (PPE). This method has drawbacks, as it cannot detect pathogen-sized contaminants nor airborne contamination in subjects' breathing zones. METHODS A contamination detection/quantification method was developed using 2-µm polystyrene latex spheres (PSLs) to investigate skin contamination (via swabbing) and potential inhalational exposure (via breathing zone air sampler). Porcine skin coupons were used to estimate the PSL swabbing recovery efficiency and limit of detection (LOD). A pilot study with 5 participants compared skin contamination levels detected via the PSL vs fluorescent tracer methods, while the air sampler quantified potential inhalational exposure to PSLs during doffing. RESULTS Average PSL skin swab recovery efficiency was 40% ± 29% (LOD = 1 PSL/4 cm2 of skin). In the pilot study, all subjects had PSL and fluorescent tracer skin contamination. Two subjects had simultaneously located contamination of both types on a wrist and hand. However, for all other subjects, the PSL method enabled detection of skin contamination that was not detectable by the fluorescent tracer method. Hands/wrists were more commonly contaminated than areas of the head/face (57% vs 23% of swabs with PSL detection, respectively). One subject had PSLs detected by the breathing zone air sampler. CONCLUSIONS This study provides a well-characterized method that can be used to quantitate levels of skin and inhalational contact with simulant pathogen particles. The PSL method serves as a complement to the fluorescent tracer method to study PPE doffing self-contamination.
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Nano-enabled medicinal products: time for an international advanced community? Nanomedicine (Lond) 2019; 14:1787-1790. [PMID: 31274378 DOI: 10.2217/nnm-2019-0173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Methodological Issues in Assessing the Economic Value of Next-Generation Sequencing Tests: Many Challenges and Not Enough Solutions. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2018; 21:1033-1042. [PMID: 30224106 PMCID: PMC6159915 DOI: 10.1016/j.jval.2018.06.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/11/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Clinical use of next-generation sequencing (NGS) tests has been increasing, but few studies have examined their economic value. Several studies have noted that there are methodological challenges to conducting economic evaluations of NGS tests. OBJECTIVE Our objective was to examine key methodological challenges for conducting economic evaluations of NGS tests, prioritize these challenges for future research, and identify how studies have attempted solutions to address these challenges. METHODS We identified challenges for economic evaluations of NGS tests using prior literature and expert judgment of the co-authors. We used a modified Delphi assessment to prioritize challenges, based on importance and probability of resolution. Using a structured literature review and article extraction we then assessed whether published economic evaluations had addressed these challenges. RESULTS We identified 11 challenges for conducting economic evaluations of NGS tests. The experts identified three challenges as the top priorities for future research: complex model structure, timeframe, and type of analysis and comparators used. Of the 15 published studies included in our literature review, four studies described specific solutions relevant to five of the 11 identified challenges. CONCLUSIONS Major methodological challenges to economic evaluations of NGS tests remain to be addressed. Our results can be used to guide future research and inform decision-makers on how to prioritize research on the economic assessment of NGS tests.
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DIALS: implementation and evaluation of a new integration package. Acta Crystallogr D Struct Biol 2018; 74:85-97. [PMID: 29533234 PMCID: PMC5947772 DOI: 10.1107/s2059798317017235] [Citation(s) in RCA: 642] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/30/2017] [Indexed: 01/07/2023] Open
Abstract
The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.
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Signal enhancement ratio imaging of the lung parenchyma with ultra-fast steady-state free precession MRI at 1.5T. J Magn Reson Imaging 2018; 48:48-57. [PMID: 29297607 DOI: 10.1002/jmri.25928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Lung perfusion MRI after i.v. gadolinium (Gd) contrast administration is commonly based on spoiled gradient-echo acquisitions, such as volume-interpolated breath-hold examinations (VIBE), suffering from low signal-to-noise in the parenchyma. PURPOSE To investigate the lung signal enhancement ratio (SER) with ultra-fast steady-state free precession (ufSSFP) after Gd-administration. STUDY TYPE Retrospective. SUBJECTS Ten subjects with healthy lungs; nine patients with pulmonary diseases (chronic obstructive pulmonary disease [COPD], lung cancer, pulmonary fibrosis, lung contusion). FIELD STRENGTH/SEQUENCE VIBE and ufSSFP imaging of the chest was performed at 1.5T before and 3 minutes after i.v. gadobenate dimeglumine. ASSESSMENT A workflow including deformable image registration and median filtering was used to compute 3D SER maps. SER was analyzed in the lung, blood pool, liver, muscles, and fat. The artifacts were assessed by a radiologist. In the COPD patients, ufSSFP-SER was compared to 99m Tc-MAA-SPECT/CT by visual scoring of lung enhancement deficits. STATISTICAL TESTS Mean signal, standard deviation (SD), intersubject SD, and coefficient of variation (CV) were calculated for SER. Statistical significance of differences in signal and artifacts were determined using Wilcoxon signed-rank paired test. Intermodality agreement between ufSSFP-SER and SPECT/CT was calculated by Cohen's kappa (κq ). RESULTS In healthy lungs, ufSSFP-SER (99% ± 23%, mean ± pooled intrasubject SD, CV = 23%) was significantly higher (P < 10-3 ) and more homogeneous (P < 10-3 ) than VIBE (47% ± 26%, CV = 57%). UfSSFP-SER was significantly higher (P < 10-3 ) for the lungs (99% ± 9%, mean ± intersubject SD) than for the blood (81% ± 7%) and other tissues (liver 33% ± 8%, muscle 26% ± 5%, fat 2% ± 1%). In the lung ufSSFP-SER exhibits homogeneity on iso-gravitational planes, and an anterior-posterior gradient. In COPD patients, ufSSFP-SER was reduced and less homogeneous compared to the control group (73% ± 33%, mean ± pooled intrasubject SD, CV = 42%). ufSSFP-SER had moderate intermodality agreement with SPECT/CT (κq = 0.64). DATA CONCLUSION UfSSFP-SER of the lung is a rapid and simple method. Our preliminary data show plausible results in different pulmonary diseases, motivating further evaluation in larger cohorts. LEVEL OF EVIDENCE 2 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018.
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Connecting Sarcomere Protein Mutations to Pathogenesis in Cardiomyopathies: The Development of "Disease in a Dish" Models. Front Physiol 2016; 7:566. [PMID: 27920728 PMCID: PMC5118458 DOI: 10.3389/fphys.2016.00566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/07/2016] [Indexed: 12/22/2022] Open
Abstract
Recent technological and protocol developments have greatly increased the ability to utilize stem cells transformed into cardiomyocytes as models to study human heart muscle development and how this is affected by disease associated mutations in a variety of sarcomere proteins. In this perspective we provide an overview of these emerging technologies and how they are being used to create better models of “disease in a dish” for both research and screening assays. We also consider the value of these assays as models to explore the seminal processes in initiation of the disease development and the possibility of early interventions.
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Rapid evidence assessment: increasing the transparency of an emerging methodology. J Eval Clin Pract 2015; 21:1199-204. [PMID: 26123092 DOI: 10.1111/jep.12405] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/18/2015] [Indexed: 11/29/2022]
Abstract
RATIONALE, AIMS AND OBJECTIVES Within the field of evidence-based practice, policy makers, health care professionals and consumers require timely reviews to inform decisions on efficacious health care and treatments. Rapid evidence assessment (REA), also known as rapid review, has emerged in recent years as a literature review methodology that fulfils this need. It highlights what is known in a clinical area to the target audience in a relatively short time frame. METHODS This article discusses the lack of transparency and limited critical appraisal that can occur in REA, and goes on to propose general principles for conducting a REA. The approach that we describe is consistent with the principles underlying systematic review methodology, but also makes allowances for the rapid delivery of information as required while utilizing explicit and reproducible methods at each stage. RESULTS Our method for conducting REA includes: developing an explicit research question in consultation with the end-users; clear definition of the components of the research question; development of a thorough and reproducible search strategy; development of explicit evidence selection criteria; and quality assessments and transparent decisions about the level of information to be obtained from each study. In addition, the REA may also include an assessment of the quality of the total body of evidence. CONCLUSIONS Transparent reporting of REA methodologies will provide greater clarity to end-users about how the information is obtained and about the trade-offs that are made between speed and rigour.
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Spatiotemporal Discordance in Five Common Measures of Rurality for US Counties and Applications for Health Disparities Research in Older Adults. Front Public Health 2015; 3:267. [PMID: 26636064 PMCID: PMC4658471 DOI: 10.3389/fpubh.2015.00267] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 11/10/2015] [Indexed: 11/13/2022] Open
Abstract
Introduction Rural populations face numerous barriers to health, including poorer health care infrastructure, access to care, and other sociodemographic factors largely associated with rurality. Multiple measures of rurality used in the biomedical and public health literature can help assess rural–urban health disparities and may impact the observed associations between rurality and health. Furthermore, understanding what makes a place truly “rural” versus “urban” may vary from region to region in the US. Purpose The objectives of this study are to compare and contrast five common measures of rurality and determine how well-correlated these measures are at the national, regional, and divisional level, as well as to assess patterns in the correlations between the prevalence of obesity in the population aged 60+ and each of the five measures of rurality at the regional and divisional level. Methods Five measures of rurality were abstracted from the US Census and US Department of Agriculture (USDA) to characterize US counties. Obesity data in the population aged 60+ were abstracted from the Behavioral Risk Factor Surveillance System (BRFSS). Spearman’s rank correlations were used to quantify the associations among the five rurality measurements at the national, regional, and divisional level, as defined by the US Census Bureau. Geographic information systems were used to visually illustrate temporal, spatial, and regional variability. Results Overall, Spearman’s rank correlations among the five measures ranged from 0.521 (percent urban–urban influence code) to 0.917 (rural–urban continuum code–urban influence code). Notable discrepancies existed in these associations by Census region and by division. The associations between measures of rurality and obesity in the 60+ population varied by rurality measure used and by region. Conclusion This study is among the first to systematically assess the spatial, temporal, and regional differences and similarities among five commonly used measures of rurality in the US. There are important, quantifiable distinctions in defining what it means to be a rural county depending on both the geographic region and the measurement used. These findings highlight the importance of developing and selecting an appropriate rurality metric in health research.
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Lessons from comparative effectiveness research methods development projects funded under the Recovery Act. J Comp Eff Res 2015; 3:601-7. [PMID: 25494566 DOI: 10.2217/cer.14.64] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The American Recovery and Reinvestment Act of 2009 (ARRA) directed nearly US$29.2 million to comparative effectiveness research (CER) methods development. AIM To help inform future CER methods investments, we describe the ARRA CER methods projects, identify barriers to this research and discuss the alignment of topics with published methods development priorities. METHODS We used several existing resources and held discussions with ARRA CER methods investigators. RESULTS & CONCLUSION Although funded projects explored many identified priority topics, investigators noted that much work remains. For example, given the considerable investments in CER data infrastructure, the methods development field can benefit from additional efforts to educate researchers about the availability of new data sources and about how best to apply methods to match their research questions and data.
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Methodological considerations regarding cognitive interventions in dementia. Front Aging Neurosci 2014; 6:212. [PMID: 25165450 PMCID: PMC4131264 DOI: 10.3389/fnagi.2014.00212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 08/01/2014] [Indexed: 11/13/2022] Open
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Creating and validating GIS measures of urban design for health research. JOURNAL OF ENVIRONMENTAL PSYCHOLOGY 2009; 29:457-466. [PMID: 22956856 PMCID: PMC3433081 DOI: 10.1016/j.jenvp.2009.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Studies relating urban design to health have been impeded by the unfeasibility of conducting field observations across large areas and the lack of validated objective measures of urban design. This study describes measures for five dimensions of urban design - imageability, enclosure, human scale, transparency, and complexity - created using public geographic information systems (GIS) data from the US Census and city and state government. GIS measures were validated for a sample of 588 New York City block faces using a well-documented field observation protocol. Correlations between GIS and observed measures ranged from 0.28 to 0.89. Results show valid urban design measures can be constructed from digital sources.
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