Journal articles on the topic 'Reproducibility and Representativeness'
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Samar, Thaer, Alejandro Bellogín, and Arjen P. de Vries. "The strange case of reproducibility versus representativeness in contextual suggestion test collections." Information Retrieval Journal 19, no. 3 (December 28, 2015): 230–55. http://dx.doi.org/10.1007/s10791-015-9276-9.
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Bozkurt, Selen, Eli M. Cahan, Martin G. Seneviratne, Ran Sun, Juan A. Lossio-Ventura, John P. A. Ioannidis, and Tina Hernandez-Boussard. "Reporting of demographic data and representativeness in machine learning models using electronic health records." Journal of the American Medical Informatics Association 27, no. 12 (September 16, 2020): 1878–84. http://dx.doi.org/10.1093/jamia/ocaa164.
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Abstract Objective The development of machine learning (ML) algorithms to address a variety of issues faced in clinical practice has increased rapidly. However, questions have arisen regarding biases in their development that can affect their applicability in specific populations. We sought to evaluate whether studies developing ML models from electronic health record (EHR) data report sufficient demographic data on the study populations to demonstrate representativeness and reproducibility. Materials and Methods We searched PubMed for articles applying ML models to improve clinical decision-making using EHR data. We limited our search to papers published between 2015 and 2019. Results Across the 164 studies reviewed, demographic variables were inconsistently reported and/or included as model inputs. Race/ethnicity was not reported in 64%; gender and age were not reported in 24% and 21% of studies, respectively. Socioeconomic status of the population was not reported in 92% of studies. Studies that mentioned these variables often did not report if they were included as model inputs. Few models (12%) were validated using external populations. Few studies (17%) open-sourced their code. Populations in the ML studies include higher proportions of White and Black yet fewer Hispanic subjects compared to the general US population. Discussion The demographic characteristics of study populations are poorly reported in the ML literature based on EHR data. Demographic representativeness in training data and model transparency is necessary to ensure that ML models are deployed in an equitable and reproducible manner. Wider adoption of reporting guidelines is warranted to improve representativeness and reproducibility.
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Araújo dos Santos, Ana Carolina, Gabriel Antônio Batista Nascimento, Natália Barbosa da Silva, Victor Laurent Sampaio Ferreira, Yan Valdez Santos Rodrigues, Ana Lúcia Barbosa, Ewerton Emmanuel Da Silva Calixto, and Fernando Luiz Pellegrini Pessoa. "Mathematical Modeling of the Extraction Process Essential Oils Schinus terebinthifolius Raddi Using Supercritical Fluids." JOURNAL OF BIOENGINEERING AND TECHNOLOGY APPLIED TO HEALTH 2, no. 4 (February 4, 2020): 130–35. http://dx.doi.org/10.34178/jbth.v2i4.91.
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Schinus terebinthifolius Raddi is a plant rich in nutrients and is used medicinally and industrially. Supercritical oil extraction from S. terebinthifolius can result in higher value-added products. Mathematical models (Sovová and Esquível) are used to describe the behavior of supercritical extractions. This study aims to compare both models in terms of yields in conditions of 223 bar and 50°C. We observed that the model proposed by Sovová provided good reproducibility and representativeness.
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Makowski, Dominique, An Shu Te, Tam Pham, Zen Juen Lau, and S. H. Annabel Chen. "The Structure of Chaos: An Empirical Comparison of Fractal Physiology Complexity Indices Using NeuroKit2." Entropy 24, no. 8 (July 27, 2022): 1036. http://dx.doi.org/10.3390/e24081036.
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Complexity quantification, through entropy, information theory and fractal dimension indices, is gaining a renewed traction in psychophsyiology, as new measures with promising qualities emerge from the computational and mathematical advances. Unfortunately, few studies compare the relationship and objective performance of the plethora of existing metrics, in turn hindering reproducibility, replicability, consistency, and clarity in the field. Using the NeuroKit2 Python software, we computed a list of 112 (predominantly used) complexity indices on signals varying in their characteristics (noise, length and frequency spectrum). We then systematically compared the indices by their computational weight, their representativeness of a multidimensional space of latent dimensions, and empirical proximity with other indices. Based on these considerations, we propose that a selection of 12 indices, together representing 85.97% of the total variance of all indices, might offer a parsimonious and complimentary choice in regards to the quantification of the complexity of time series. Our selection includes CWPEn, Line Length (LL), BubbEn, MSWPEn, MFDFA (Max), Hjorth Complexity, SVDEn, MFDFA (Width), MFDFA (Mean), MFDFA (Peak), MFDFA (Fluctuation), AttEn. Elements of consideration for alternative subsets are discussed, and data, analysis scripts and code for the figures are open-source.
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Kibugu, James, Raymond Mdachi, Leonard Munga, David Mburu, Thomas Whitaker, Thu P. Huynh, Delia Grace, and Johanna F. Lindahl. "Improved Sample Selection and Preparation Methods for Sampling Plans Used to Facilitate Rapid and Reliable Estimation of Aflatoxin in Chicken Feed." Toxins 13, no. 3 (March 16, 2021): 216. http://dx.doi.org/10.3390/toxins13030216.
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Aflatoxin B1 (AFB1), a toxic fungal metabolite associated with human and animal diseases, is a natural contaminant encountered in agricultural commodities, food and feed. Heterogeneity of AFB1 makes risk estimation a challenge. To overcome this, novel sample selection, preparation and extraction steps were designed for representative sampling of chicken feed. Accuracy, precision, limits of detection and quantification, linearity, robustness and ruggedness were used as performance criteria to validate this modification and Horwitz function for evaluating precision. A modified sampling protocol that ensured representativeness is documented, including sample selection, sampling tools, random procedures, minimum size of field-collected aggregate samples (primary sampling), procedures for mass reduction to 2 kg laboratory (secondary sampling), 25 g test portion (tertiary sampling) and 1.3 g analytical samples (quaternary sampling). The improved coning and quartering procedure described herein (for secondary and tertiary sampling) has acceptable precision, with a Horwitz ratio (HorRat = 0.3) suitable for splitting of 25 g feed aliquots from laboratory samples (tertiary sampling). The water slurring innovation (quaternary sampling) increased aflatoxin extraction efficiency to 95.1% through reduction of both bias (−4.95) and variability of recovery (1.2–1.4) and improved both intra-laboratory precision (HorRat = 1.2–1.5) and within-laboratory reproducibility (HorRat = 0.9–1.3). Optimal extraction conditions are documented. The improved procedure showed satisfactory performance, good field applicability and reduced sample analysis turnaround time.
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Didona, Diego, Nikolas Ioannou, Radu Stoica, and Kornilios Kourtis. "Toward a better understanding and evaluation of tree structures on flash SSDs." Proceedings of the VLDB Endowment 14, no. 3 (November 2020): 364–77. http://dx.doi.org/10.14778/3430915.3430926.
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Solid-state drives (SSDs) are extensively used to deploy persistent data stores, as they provide low latency random access, high write throughput, high data density, and low cost. Tree-based data structures are widely used to build persistent data stores, and indeed they lie at the backbone of many of the data management systems used in production and research today. We show that benchmarking a persistent tree-based data structure on an SSD is a complex process, which may easily incur subtle pitfalls that can lead to an inaccurate performance assessment. At a high-level, these pitfalls stem from the interaction of complex software running on complex hardware. On the one hand, tree structures implement internal operations that have non-trivial effects on performance. On the other hand, SSDs employ firmware logic to deal with the idiosyncrasies of the underlying flash memory, which are well known to also lead to complex performance dynamics. We identify seven benchmarking pitfalls using RocksDB and WiredTiger, two widespread implementations of an LSM-Tree and a B+Tree, respectively. We show that such pitfalls can lead to incorrect measurements of key performance indicators, hinder the reproducibility and the representativeness of the results, and lead to suboptimal deployments in production environments. We also provide guidelines on how to avoid these pitfalls to obtain more reliable performance measurements, and to perform more thorough and fair comparisons among different design points.
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Aboulela, Amr, Matthieu Peyre Lavigne, Amaury Buvignier, Marlène Fourré, Maud Schiettekatte, Tony Pons, Cédric Patapy, et al. "Laboratory Test to Evaluate the Resistance of Cementitious Materials to Biodeterioration in Sewer Network Conditions." Materials 14, no. 3 (February 2, 2021): 686. http://dx.doi.org/10.3390/ma14030686.
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The biodeterioration of cementitious materials in sewer networks has become a major economic, ecological, and public health issue. Establishing a suitable standardized test is essential if sustainable construction materials are to be developed and qualified for sewerage environments. Since purely chemical tests are proven to not be representative of the actual deterioration phenomena in real sewer conditions, a biological test–named the Biogenic Acid Concrete (BAC) test–was developed at the University of Toulouse to reproduce the biological reactions involved in the process of concrete biodeterioration in sewers. The test consists in trickling a solution containing a safe reduced sulfur source onto the surface of cementitious substrates previously covered with a high diversity microbial consortium. In these conditions, a sulfur-oxidizing metabolism naturally develops in the biofilm and leads to the production of biogenic sulfuric acid on the surface of the material. The representativeness of the test in terms of deterioration mechanisms has been validated in previous studies. A wide range of cementitious materials have been exposed to the biodeterioration test during half a decade. On the basis of this large database and the expertise gained, the purpose of this paper is (i) to propose a simple and robust performance criterion for the test (standardized leached calcium as a function of sulfate produced by the biofilm), and (ii) to demonstrate the repeatability, reproducibility, and discriminability of the test method. In only a 3-month period, the test was able to highlight the differences in the performances of common cement-based materials (CEM I, CEM III, and CEM V) and special calcium aluminate cement (CAC) binders with different nature of aggregates (natural silica and synthetic calcium aluminate). The proposed performance indicator (relative standardized leached calcium) allowed the materials to be classified according to their resistance to biogenic acid attack in sewer conditions. The repeatability of the test was confirmed using three different specimens of the same material within the same experiment and the reproducibility of the results was demonstrated by standardizing the results using a reference material from 5 different test campaigns. Furthermore, developing post-testing processing and calculation methods constituted a first step toward a standardized test protocol.
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Mpouam, Serge Eugene, Jean Pierre Kilekoung Mingoas, Mohamed Moctar Mouliom Mouiche, Jean Marc Kameni Feussom, and Claude Saegerman. "Critical Systematic Review of Zoonoses and Transboundary Animal Diseases’ Prioritization in Africa." Pathogens 10, no. 8 (August 3, 2021): 976. http://dx.doi.org/10.3390/pathogens10080976.
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Background: Disease prioritization aims to enhance resource use efficiency concerning human and animal health systems’ preparedness and response to the most important problems for the optimization of beneficial outcomes. In sub-Sahara Africa (SSA), several prioritizations of zoonoses and transboundary animal diseases (TADs) have been implemented at different scales to characterize potential disease impacts. Method and principal findings: In this systematic review, we analyze the methodologies used, outcomes, and their relevance by discussing criteria required to align decision-makers’ perceptions of impacts to those of other stakeholders for different prioritization in SSA. In general, the sectorial representativeness of stakeholders for processes implemented with the support of international partners showed slight differences with the absence of local stakeholders. Whatever the tool prioritized, zoonoses were similar in general because of the structured nature of those tools in assessing decision-makers’ preferences through value trade-offs between criteria while ensuring transparency and reproducibility. However, by involving field practitioners and farmers, there were different outcomes with processes concerning only decision makers and experts who were more sensitive to infectious TADs, while the former raised parasitic disease constraints. In this context, multicriteria decision analysis-based zoonoses and TADs prioritizations involving a balanced participation of stakeholders might contribute to bridging these divergences, whatever the scale. Conclusion and significance: Prioritization processes were important steps toward building and harmonizing technical laboratory and surveillance networks to coordinate projects to address priority zoonoses and TADs at the country and/or sub-regional level. Those processes should be enhanced.
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Lüning, Sebastian, and Philipp Lengsfeld. "How Reliable Are Global Temperature Reconstructions of the Common Era?" Earth 3, no. 1 (March 3, 2022): 401–8. http://dx.doi.org/10.3390/earth3010024.
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Global mean annual temperature has increased by more than 1 °C during the past 150 years, as documented by thermometer measurements. Such observational data are, unfortunately, not available for the pre-industrial period of the Common Era (CE), for which the climate development is reconstructed using various types of palaeoclimatological proxies. In this analysis, we compared seven prominent hemispheric and global temperature reconstructions for the past 2000 years (T2k) which differed from each other in some segments by more than 0.5 °C. Whilst some T2k show negligible pre-industrial climate variability (“hockey sticks”), others suggest significant temperature fluctuations. We discuss possible sources of error and highlight three criteria that need to be considered to increase the quality and stability of future T2k reconstructions. Temperature proxy series are to be thoroughly validated with regards to (1) reproducibility, (2) seasonal stability, and (3) areal representativeness. The T2k represents key calibration data for climate models. The models need to first reproduce the reconstructed pre-industrial climate history before being validated and cleared for climate projections of the future. Precise attribution of modern warming to anthropogenic and natural causes will not be possible until T2k composites stabilize and are truly representative for a well-defined region and season. The discrepancies between the different T2k reconstructions directly translate into a major challenge with regards to the political interpretation of the climate change risk profile. As a rule of thumb, the larger/smaller the pre-industrial temperature changes, the higher/lower the natural contribution to the current warm period (CWP) will likely be, thus, reducing/increasing the CO2 climate sensitivity and the expected warming until 2100.
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Ternström, Sten, and Peter Pabon. "Voice Maps as a Tool for Understanding and Dealing with Variability in the Voice." Applied Sciences 12, no. 22 (November 9, 2022): 11353. http://dx.doi.org/10.3390/app122211353.
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Individual acoustic and other physical metrics of vocal status have long struggled to prove their worth as clinical evidence. While combinations of metrics or “features” are now being intensely explored using data analytics methods, there is a risk that explainability and insight will suffer. The voice mapping paradigm discards the temporal dimension of vocal productions and uses fundamental frequency (fo) and sound pressure level (SPL) as independent control variables to implement a dense grid of measurement points over a relevant voice range. Such mapping visualizes how most physical voice metrics are greatly affected by fo and SPL, and more so individually than has been generally recognized. It is demonstrated that if fo and SPL are not controlled for during task elicitation, repeated measurements will generate “elicitation noise”, which can easily be large enough to obscure the effect of an intervention. It is observed that, although a given metric’s dependencies on fo and SPL often are complex and/or non-linear, they tend to be systematic and reproducible in any given individual. Once such personal trends are accounted for, ordinary voice metrics can be used to assess vocal status. The momentary value of any given metric needs to be interpreted in the context of the individual’s voice range, and voice mapping makes this possible. Examples are given of how voice mapping can be used to quantify voice variability, to eliminate elicitation noise, to improve the reproducibility and representativeness of already established metrics of the voice, and to assess reliably even subtle effects of interventions. Understanding variability at this level of detail will shed more light on the interdependent mechanisms of voice production, and facilitate progress toward more reliable objective assessments of voices across therapy or training.
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Michaelis, Martina, Monika A. Rieger, and Eva Rothermund. "Der deutsche Work Role Functioning Questionnaire – Zur Evaluation seiner Messeigenschaften." ASU Arbeitsmedizin Sozialmedizin Umweltmedizin 2022, no. 12 (November 29, 2022): 787–91. http://dx.doi.org/10.17147/asu-1-240599.
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The German Work Role Functioning Questionnaire – on the evaluation of its measurement properties Objectives: Measures to maintain the employability of workers should also take their functional ability into account. The Work Role Functioning Questionnaire (WRFQ), which is available in several languages, is suitable for such an assessment. A validated version in German had been missing until now. The 27-item questionnaire was culturally adapted from the Dutch version of WRFQ 2.0 and used with a heterogeneous sample of employees with the aim of psychometrically validating the overall scale and the four subscales. Methods: After adaptation, members of a commercial online access panel with a wide variety of occupations were recruited (T0: n = 653). Two follow-ups were conducted to assess further psychometric properties (T1: n = 66, T2: n = 95). We examined the 1) structural, 2) convergent and 3) discriminant validity using exploratory factor analysis, 4) floor and ceiling effects, as well as 5) the internal consistency, 6) reproducibility, and 7) responsiveness. Results: Measurement properties were found to be good, with the exception of responsiveness and structural validity. In the exploratory factor analysis, satisfactory replicability was found for three of the four subscales (mental and social demands, physical demands and flexibility demands, but not scheduling and output demands). Conclusions: The WRFQ is aimed at the fit between demands and the individual and thus at the ability to participate. With the development and validation of a German-language version, the scale can be used in practice, e.g. in interventions aimed at secondary prevention to maintain the ability to work, tertiary prevention to support a successful return to work, or the identification of employees with declining functional ability. The limitations of the study (limited representativeness of online access panels and poor replicability of the fourth subscale) require further research. Keywords: work capacity evaluation – Work Role Functioning Questionnaire – survey – psychometric measurement properties
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Russell, Lahiru, Anna Ugalde, Donna Milne, David Austin, and Patricia M. Livingston. "Digital Characteristics and Dissemination Indicators to Optimize Delivery of Internet-Supported Mindfulness-Based Interventions for People With a Chronic Condition: Systematic Review." JMIR Mental Health 5, no. 3 (August 21, 2018): e53. http://dx.doi.org/10.2196/mental.9645.
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Background Internet-supported mindfulness-based interventions (MBIs) are increasingly being used to support people with a chronic condition. Characteristics of MBIs vary greatly in their mode of delivery, communication patterns, level of facilitator involvement, intervention period, and resource intensity, making it difficult to compare how individual digital features may optimize intervention adherence and outcomes. Objective The aims of this review were to (1) provide a description of digital characteristics of internet-supported MBIs and examine how these relate to evidence for efficacy and adherence to the intervention and (2) gain insights into the type of information available to inform translation of internet-supported MBIs to applied settings. Methods MEDLINE Complete, PsycINFO, and CINAHL databases were searched for studies assessing an MBI delivered or accessed via the internet and engaging participants in daily mindfulness-based activities such as mindfulness meditations and informal mindfulness practices. Only studies using a comparison group of alternative interventions (active compactor), usual care, or wait-list were included. Given the broad definition of chronic conditions, specific conditions were not included in the original search to maximize results. The search resulted in 958 articles, from which 11 articles describing 10 interventions met the inclusion criteria. Results Internet-supported MBIs were more effective than usual care or wait-list groups, and self-guided interventions were as effective as facilitator-guided interventions. Findings were informed mainly by female participants. Adherence to interventions was inconsistently defined and prevented robust comparison between studies. Reporting of factors associated with intervention dissemination, such as population representativeness, program adoption and maintenance, and costs, was rare. Conclusions More comprehensive descriptions of digital characteristics need to be reported to further our understanding of features that may influence engagement and behavior change and to improve the reproducibility of MBIs. Gender differences in determinants and patterns of health behavior should be taken into account at the intervention design stage to accommodate male and female preferences. Future research could compare MBIs with established evidence-based therapies to identify the population groups that would benefit most from internet-supported programs. Trial Registration PROSPERO CRD42017078665; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=78665 (Archived by WebCite at http://www.webcitation.org/71ountJpu)
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Zhaivoronok, Ihor, and Yurii Kovalenko. "INCREASING THE ACCURACY OF DETERMINING THE WORKING PARAMETERS OF THE RIBBON-SHAPED ELECTRONIC FLOW IN THE ELECTRON-BEAM MICRO-PROCESSING OF DIELECTRICS." Bulletin of Kyiv Polytechnic Institute. Series Instrument Making, no. 64(2) (December 24, 2022): 33–41. http://dx.doi.org/10.20535/1970.64(2).2022.269983.
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The article shows the possibility of increasing the accuracy of determining the operating parameters of the ribbon-shaped electron flow during electron beam micromachining of dielectric materials in a vacuum (using the example of Kp0 grade polycrystalline silicon and K8 grade optical glass) as a result of the analysis and selection of the most acceptable energy modes of operation of the Pierce wire electron-beam gun. The purpose of the work is to study the influence of the volt-current characteristics of the Pierce wire electron-beam gun on the quality and repeatability of the process of processing dielectric materials with a ribbon-shaped electron flow, which allows choosing the most rational modes of determining the operating parameters of the electron flow with higher accuracy.
The paper proposes a technological experiment on electron-beam micromachining of dielectric surfaces, as well as defined and investigated the working parameters of the process of such processing, depending on the possible energy characteristics of the main working node of the electron-beam equipment, namely, the Pierce electron-beam gun.
The operating parameters of the ribbon-shaped electron flow obtained as a result of the experimental study made it possible to ensure the highest quality processing of the surfaces of dielectric materials due to the improvement of such indicators of the accuracy of determining these parameters as precision (for example, the standard deviation of the repeatability of Sr decreased from 8.33% to 4.95%, and the standard the SR reproducibility deviation decreased from 13.28% to 6.18%), which confirms the representativeness of the working parameters, as well as the correctness (the bias of the method of determining the working parameters in the electronic flow is statistically insignificant under the conditions of the confidence interval on the axis d = 0 at the significance level a = 0.05). The analysis of the obtained results regarding the electron-beam microprocessing of the surfaces of dielectric materials according to the selected operating parameters proves the improvement of quality and the increase in the reproducibility of the results of the processing of these surfaces in terms of purity, as well as the reduction of the residual nanorelief by 18-25%.
A comparison of the results of experimental electron-beam microprocessing of dielectrics with the results of their laser surface treatment made it possible to establish a reduction in residual micro-uniformities of the surface, as in electron-beam microprocessing (for optical glass K8 by 17-27 times; for silicon Kp0 - by 14-22 times) , as well as during surface laser treatment (for both types of material – 12-14 times). At the same time, surface laser treatment does not allow to eliminate surface waviness, which is related to the specifics of the interaction of the laser beam with the surface of the optical material, while when processing with an electron flow of the ribbon form, the occurrence of such waviness is not observed.
The conclusions and analyzed data obtained in the article based on the results of experimental research can be used to optimize the technological regimes of electron-beam micromachining in the production of products of microoptics, integrated optics, nanoelectronics, etc.
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Hedley, C. B., I. J. Payton, I. H. Lynn, S. T. Carrick, T. H. Webb, and S. McNeill. "Random sampling of stony and non-stony soils for testing a national soil carbon monitoring system." Soil Research 50, no. 1 (2012): 18. http://dx.doi.org/10.1071/sr11171.
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The New Zealand Soil Carbon Monitoring System (Soil CMS) was designed, and has been used, to account for soil organic carbon change under land-use change, during New Zealand’s first Commitment Period (2008–2012) to the Kyoto Protocol. The efficacy of the Soil CMS model has been tested for assessing soil organic carbon stocks in a selected climate–land-use–soil grouping (cell). The cell selected for this test represents an area of 709 683 ha and contains soils with a high-activity clay mineralogy promoting long-term stabilisation of organic matter, and is under low-producing grassland in a dry temperate New Zealand climate. These soils have been sampled at randomly selected positions to assess total soil organic carbon stocks to 0.3 m, and to compare with the modelled value. Results show no significant difference between the field estimation (67 ± 30 Mg C/ha), the mean value of the model calibration dataset (79 ± 28 Mg C/ha), and the value predicted by the model (101 ± 41 Mg C/ha), although all estimates have large uncertainties associated with them. The model predicts national soil organic carbon stocks as a function of soil texture, clay mineralogy, land use, climate class, and a slope–rainfall erosivity product. Components of uncertainty within the model include the size and distribution of the calibration dataset, and lack of representativeness of the calibration soil samples, which were sampled for other reasons, e.g. soil survey and forest mensuration. Our study has shown that major components of uncertainty in our field estimation of soil organic carbon stocks (investigated using the indices reproducibility, RP; and coefficient of variation, CV) are short-range (within-plot) and regional (between-sites) spatial variability. Soil organic carbon stocks vary within our selected climate–land-use–soil cell due to varying stoniness (stony soils RP 44%, CV 21%; non-stony soils RP 27%, CV 13%), soil depth, slope position, and climatic effects. When one outlier soil was removed from the model calibration dataset, and the three very stony sites were removed from the randomly selected field validation set, the model calibration dataset and the field dataset means agreed well (78 ± 26 and 78 ± 21 Mg C/ha, respectively). The higher modelled value, before removal of the outlier, is likely to reflect a bias in the model dataset towards conventionally selected modal profiles containing less stony soils than those encountered by the random sampling strategy of our field campaign. Therefore, our results indicate (1) that the Soil CMS provides an adequate estimation of soil organic carbon for the selected cell, and (2) ongoing refinements are required to reduce the uncertainty of prediction.
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Valtonen, L., Saku J. Mäkinen, and Johanna Kirjavainen. "Advancing Reproducibility and Accountability of Unsupervised Machine Learning in Text Mining: Importance of Transparency in Reporting Preprocessing and Algorithm Selection." Organizational Research Methods, September 21, 2022, 109442812211249. http://dx.doi.org/10.1177/10944281221124947.
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Machine learning (ML) enables the analysis of large datasets for pattern discovery. ML methods and the standards for their use have recently attracted increasing attention in organizational research; recent accounts have raised awareness of the importance of transparent ML reporting practices, especially considering the influence of preprocessing and algorithm choice on analytical results. However, efforts made thus far to advance the quality of ML research have failed to consider the special methodological requirements of unsupervised machine learning (UML) separate from the more common supervised machine learning (SML). We confronted these issues by studying a common organizational research dataset of unstructured text and discovered interpretability and representativeness trade-offs between combinations of preprocessing and UML algorithm choices that jeopardize research reproducibility, accountability, and transparency. We highlight the need for contextual justifications to address such issues and offer principles for assessing the contextual suitability of UML choices in research settings.
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Green, Kayla H., Ilse H. Van De Groep, Lysanne W. Te Brinke, Renske van der Cruijsen, Fabienne van Rossenberg, and Hanan El Marroun. "A perspective on enhancing representative samples in developmental human neuroscience: Connecting science to society." Frontiers in Integrative Neuroscience 16 (September 2, 2022). http://dx.doi.org/10.3389/fnint.2022.981657.
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Marginalized groups are often underrepresented in human developmental neuroscientific studies. This is problematic for the generalizability of findings about brain-behavior mechanisms, as well as for the validity, reliability, and reproducibility of results. In the present paper we discuss selection bias in cohort studies, which is known to contribute to the underrepresentation of marginalized groups. First, we address the issue of exclusion bias, as marginalized groups are sometimes excluded from studies because they do not fit the inclusion criteria. Second, we highlight examples of sampling bias. Recruitment strategies are not always designed to reach and attract a diverse group of youth. Third, we explain how diversity can be lost due to attrition of marginalized groups in longitudinal cohort studies. We provide experience- and evidence-based recommendations to stimulate neuroscientists to enhance study population representativeness via science communication and citizen science with youth. By connecting science to society, researchers have the opportunity to establish sustainable and equal researcher-community relationships, which can positively contribute to tackling selection biases.
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Ibrahim, Asmaa, Ayat G. Lashen, Ayaka Katayama, Raluca Mihai, Graham Ball, Michael S. Toss, and Emad A. Rakha. "Defining the area of mitoses counting in invasive breast cancer using whole slide image." Modern Pathology, December 11, 2021. http://dx.doi.org/10.1038/s41379-021-00981-w.
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AbstractAlthough counting mitoses is part of breast cancer grading, concordance studies showed low agreement. Refining the criteria for mitotic counting can improve concordance, particularly when using whole slide images (WSIs). This study aims to refine the methodology for optimal mitoses counting on WSI. Digital images of 595 hematoxylin and eosin stained sections were evaluated. Several morphological criteria were investigated and applied to define mitotic hotspots. Reproducibility, representativeness, time, and association with outcome were the criteria used to evaluate the best area size for mitoses counting. Three approaches for scoring mitoses on WSIs (single and multiple annotated rectangles and multiple digital high-power (×40) screen fields (HPSFs)) were evaluated. The relative increase in tumor cell density was the most significant and easiest parameter for identifying hotspots. Counting mitoses in 3 mm2 area was the most representative regarding saturation and concordance levels. Counting in area <2 mm2 resulted in a significant reduction in mitotic count (P = 0.02), whereas counting in area ≥4 mm2 was time-consuming and did not add a significant rise in overall mitotic count (P = 0.08). Using multiple HPSF, following calibration, provided the most reliable, timesaving, and practical method for mitoses counting on WSI. This study provides evidence-based methodology for defining the area and methodology of visual mitoses counting using WSI. Visual mitoses scoring on WSI can be performed reliably by adjusting the number of monitor screens.
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Bertamini, Luca, Giuseppe Bertuglia, and Stefania Oliva. "Beyond Clinical Trials in Patients With Multiple Myeloma: A Critical Review of Real-World Results." Frontiers in Oncology 12 (May 11, 2022). http://dx.doi.org/10.3389/fonc.2022.844779.
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The current strategies for the treatment of multiple myeloma (MM) have improved, thanks to effective drug classes and combination therapies, for both the upfront and relapsed settings. Clinical trials for newly diagnosed transplant-ineligible patients led to the approval of immunomodulatory drugs (IMiDs) and proteasome inhibitors (PIs) in combination with anti-CD38 monoclonal antibodies (mAbs), to be administered during the induction phase before transplantation and during maintenance treatment, with lenalidomide recommended until relapse. In relapsed/refractory patients, the complex treatment scenario currently includes several options, such as triplets with anti-CD38 mAbs plus IMiDs or PIs, and novel targeted molecules. Comparisons among clinical trials and real-world data showed a good degree of reproducibility of some important results, particularly in terms of overall response rate, progression-free survival, and overall survival. This may help clinicians towards a proper selection of the best treatment options, particularly in real-world settings. However, as compared with the management of real-world settings, clinical trials have some pitfalls in terms of outcome and especially in terms of safety and quality of life. In fact, trials include younger and presumably healthier patients, excluding those with worst clinical conditions due to MM features (e.g., renal insufficiency or bone disease, which can impair the performance status) and comorbidities (e.g., cardiac and pulmonary disease), thus resulting in a possible lack of representativeness of data about the patients enrolled. In this review, we analyze comparable and discrepant results from clinical trials vs. real-world settings published in the last 10 years, focusing on different drugs and combinations for the treatment of MM and providing an overview of treatment choices.
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Himmelreich, J. C. L., S. Virdone, A. J. Camm, R. E. Harskamp, K. S. Pieper, K. A. A. Fox, J. P. Bassand, et al. "Safety and efficacy of apixaban and rivaroxaban versus warfarin in real-world atrial fibrillation patients are similar to their randomized trials: insights from GARFIELD-AF registry." European Heart Journal 42, Supplement_1 (October 1, 2021). http://dx.doi.org/10.1093/eurheartj/ehab724.0559.
Full textAbstract:
Abstract Introduction Generalisability of patient selection in the landmark trials for the approval of apixaban (ARISTOTLE) and rivaroxaban (ROCKET AF) for use in non-valvular atrial fibrillation (AF) is limited. Although observational data have confirmed the safety and efficacy of these non-vitamin K oral anticoagulants (NOACs) in unselected AF populations, robust replication of randomized trials in observational studies is warranted. Purpose To investigate the proportion of real-world AF patients who would have been eligible for the landmark trials for ARISTOTLE and ROCKET AF, and to assess reproducibility of these landmark trials in the largest, worldwide, prospective registry of newly diagnosed AF patients. Methods We analysed data from the Global Anticoagulant Registry in the FIELD–Atrial Fibrillation (GARFIELD-AF) registry. We assessed the eligibility of AF patients treated with apixaban or vitamin K antagonist (VKA) for ARISTOTLE, and those treated with rivaroxaban or VKA for ROCKET AF, using the selection criteria of the original trials. We replicated the inclusion and exclusion criteria of ARISTOTLE and ROCKET AF by deriving the set of patients eligible for each trial and calculating the adjusted hazard ratios (HRs) for stroke or systemic embolism, major bleeding, and all-cause mortality within 2 years of enrolment, using a propensity score overlap weighted Cox model. We compared the results from observational data with those reported in the original ARISTOTLE and ROCKET AF publications. Results Among all patients enrolled in GARFIELD-AF, 67% were eligible for recruitment in ARISTOTLE and 37% in ROCKET AF. The corresponding proportions among anticoagulated patients were 70% and 39%, respectively. Among patients on apixaban and VKA, 2570/3615 (71%) and 8005/11718 (68%), respectively, were eligible for ARISTOTLE. Of patients using rivaroxaban and VKA, 2005/4914 (41%) and 4368/11721 (37%), respectively, were eligible for ROCKET AF. Annual eligibility rates among real-world NOAC users were stable over time (Figure 1). Registry participants on rivaroxaban or VKA eligible for ROCKET AF had a higher burden of cardiovascular co-morbidity than those on apixaban or VKA eligible for ARISTOTLE. The adjusted HRs in observational data were compatible with results of the original trials in all selected outcomes (Figure 2). Conclusion Representativeness of ARISTOTLE and ROCKET AF for real-world AF populations was limited, with ROCKET AF's criteria being more restrictive. Despite inclusion of only incident AF cases in GARFIELD-AF versus mostly prevalent AF cases in the original trials, the results were similar. Our work indicates that the results from ARISTOTLE and ROCKET AF appear robust and reproducible in real-world patients with newly diagnosed AF. Funding Acknowledgement Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): This work was supported by an unrestricted research grant from Bayer AG, Berlin, Germany, to TRI, London, UK, which sponsors the GARFIELD-AF registry. This work is supported by KANTOR CHARITABLE FOUNDATION for the Kantor-Kakkar Global Centre for Thrombosis Science.