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Introduction and Objectives: Relevant, meaningful, and achievable data points are critical in objectively assessing quality, utility, and outcomes in female stress urinary incontinence (SUI) surgery. A minimum data set female SUI surgery studies was proposed by the first American Urological Association guidelines on the surgical management of female SUI in 1997, but recommendation adherence has been suboptimal. The Female Stress Urinary Incontinence Surgical Publication Working Group (WG) was created from members of several prominent organizations to formulate a recommended standard of study structure, description, and minimum outcome data set to be utilized in designing and publishing future SUI studies. The goal of this WG was to create a body of evidence better able to assess the outcomes of female SUI surgery., Methods: The WG reviewed the minimum data set proposed in the 1997 AUA SUI Guideline document, and other relevant literature. The body of literature was examined in the context of the profound changes in the field over the past 25 years. Through a DELPHI process, a standard study structure and minimum data set were generated. Care was taken to balance the value of several meaningful and relevant data points against the burden of creating an excessively difficult or restrictive standard that would disincentivize widespread adoption and negatively impact manuscript production and acceptance., Results: The WG outlined standardization in four major areas: (1) study design, (2) pretreatment demographics and characterization of the study population, (3) intraoperative events, and (4) posttreatment evaluation, and complications. Forty-two items were evaluated and graded as: STANDARD-must be included; ADDITIONAL-may be included for a specific study and is inclusive of the Standard items; OPTIMAL-may be included for a comprehensive study and is inclusive of the Standard and Additional items; UNNECESSARY/LEGACY-not relevant., Conclusions: A reasonable, achievable, and clinically meaningful minimum data set has been constructed. A structured framework will allow future surgical interventions for female SUI to be objectively scrutinized and compared in a clinically significant manner. Ultimately, such a data set, if adopted by the academic community, will enhance the quality of the scientific literature, and ultimately improve short and long-term outcomes for female patients undergoing surgery to correct SUI., (© 2024 The Authors. Published by Wiley Periodicals LLC, by Elsevier B.V on behalf of International Continence Society, and by Wolters Kluwer Health, Inc. on behalf of American Urogynecologic Society.)

Background and Objectives: Current national or regional guidelines for the pathology reporting on invasive breast cancer differ in certain aspects, resulting in divergent reporting practice and a lack of comparability of data. Here we report on a new international dataset for the pathology reporting of resection specimens with invasive cancer of the breast. The dataset was produced under the auspices of the International Collaboration on Cancer Reporting (ICCR), a global alliance of major (inter-)national pathology and cancer organizations., Methods and Results: The established ICCR process for dataset development was followed. An international expert panel consisting of breast pathologists, a surgeon, and an oncologist prepared a draft set of core and noncore data items based on a critical review and discussion of current evidence. Commentary was provided for each data item to explain the rationale for selecting it as a core or noncore element, its clinical relevance, and to highlight potential areas of disagreement or lack of evidence, in which case a consensus position was formulated. Following international public consultation, the document was finalized and ratified, and the dataset, which includes a synoptic reporting guide, was published on the ICCR website., Conclusions: This first international dataset for invasive cancer of the breast is intended to promote high-quality, standardized pathology reporting. Its widespread adoption will improve consistency of reporting, facilitate multidisciplinary communication, and enhance comparability of data, all of which will help to improve the management of invasive breast cancer patients., (© 2024 The Authors. Histopathology published by John Wiley & Sons Ltd.)

Background: A targeted structure for recording, monitoring, and follow-up of patients with neuromyelitis optica spectrum disorders (NMOSD) is in demand. To obtain the correct and uniform standardized information registry system, it is necessary to use a data set that has good validity to help policy-makers systematically plan for improvements in the quality of care. The main goal of the present study was to develop a NMOSD data set for the national registry system in Iran (NMORI) and to evaluate the validity of the presented data set., Methods: The NMORI data set consisted of baseline characteristics, disease and exposure history, background and past medical history, diagnosis and treatment, clinical features, imaging, and para-clinical findings. The content validity was evaluated by 18 experts from Iran, Japan, and Denmark by scoring each of the questionnaire items in term of transparency, simplicity, and relevance. According to the points given, the content validity index (CVI) and content validity ratio (CVR) scores were calculated and compared with the critical limit., Results: The current study was designed as a 125-items data set which was considered valid. In terms of relevance 110 out of 125 items, simplicity 113 out of 125 items, and transparency 123 out of 125 items had Item-CVI>0.79. All Scale-level-CVI values were greater than 0.9, showing noticeable content validity. In this data set, 112 items had CVR > 0.49, which was considered an acceptable level of significance., Conclusion: The implementing of NMORI is important in a developing country such as Iran with significant increasing prevalence of this disease. This registry facilitates a uniform and valid diagnosis and is considered valid for clinical investigation and epidemiological research on NMOSD. Scientists and healthcare policymakers can rely on a validated data set in order to have access to accurate data., Competing Interests: Declaration of competing interest None., (Copyright © 2024 Elsevier B.V. All rights reserved.)

This paper presents a standardised dataset versioning framework for improved reusability, recognition and data version tracking, facilitating comparisons and informed decision-making for data usability and workflow integration. The framework adopts a software engineering-like data versioning nomenclature ("major.minor.patch") and incorporates data schema principles to promote reproducibility and collaboration. To quantify changes in statistical properties over time, the concept of data drift metrics (d) is introduced. Three metrics (d P , d E , PCA , and d E,AE ) based on unsupervised Machine Learning techniques (Principal Component Analysis and Autoencoders) are evaluated for dataset creation, update, and deletion. The optimal choice is the d E , PCA metric, combining PCA models with splines. It exhibits efficient computational time, with values below 50 for new dataset batches and values consistent with seasonal or trend variations. Major updates (i.e., values of 100) occur when scaling transformations are applied to over 30% of variables while efficiently handling information loss, yielding values close to 0. This metric achieved a favourable trade-off between interpretability, robustness against information loss, and computation time., (© 2024. The Author(s).)

Previous work on clinical relation extraction from free-text sentences leveraged information about semantic types from clinical knowledge bases as a part of entity representations. In this paper, we exploit additional evidence by also making use of domain-specific semantic type dependencies . We encode the relation between a span of tokens matching a Unified Medical Language System (UMLS) concept and other tokens in the sentence. We implement our method and compare against different named entity recognition (NER) architectures (i.e., BiLSTM-CRF and BiLSTM-GCN-CRF) using different pre-trained clinical embeddings (i.e., BERT, BioBERT, UMLSBert). Our experimental results on clinical datasets show that in some cases NER effectiveness can be significantly improved by making use of domain-specific semantic type dependencies. Our work is also the first study generating a matrix encoding to make use of more than three dependencies in one pass for the NER task., (©2022 AMIA - All rights reserved.)

Micro-expression (ME) is a significant non-verbal communication clue that reveals one person's genuine emotional state. The development of micro-expression analysis (MEA) has just gained attention in the last decade. However, the small sample size problem constrains the use of deep learning on MEA. Besides, ME samples distribute in six different databases, leading to database bias. Moreover, the ME database development is complicated. In this article, we introduce a large-scale spontaneous ME database: CAS(ME) 3 . The contribution of this article is summarized as follows: (1) CAS(ME) 3 offers around 80 hours of videos with over 8,000,000 frames, including manually labeled 1,109 MEs and 3,490 macro-expressions. Such a large sample size allows effective MEA method validation while avoiding database bias. (2) Inspired by psychological experiments, CAS(ME) 3 provides the depth information as an additional modality unprecedentedly, contributing to multi-modal MEA. (3) For the first time, CAS(ME) 3 elicits ME with high ecological validity using the mock crime paradigm, along with physiological and voice signals, contributing to practical MEA. (4) Besides, CAS(ME) 3 provides 1,508 unlabeled videos with more than 4,000,000 frames, i.e., a data platform for unsupervised MEA methods. (5) Finally, we demonstrate the effectiveness of depth information by the proposed depth flow algorithm and RGB-D information.

Biomedical datasets are increasing in size, stored in many repositories, and face challenges in FAIRness (findability, accessibility, interoperability, reusability). As a Consortium of infectious disease researchers from 15 Centers, we aim to adopt open science practices to promote transparency, encourage reproducibility, and accelerate research advances through data reuse. To improve FAIRness of our datasets and computational tools, we evaluated metadata standards across established biomedical data repositories. The vast majority do not adhere to a single standard, such as Schema.org, which is widely-adopted by generalist repositories. Consequently, datasets in these repositories are not findable in aggregation projects like Google Dataset Search. We alleviated this gap by creating a reusable metadata schema based on Schema.org and catalogued nearly 400 datasets and computational tools we collected. The approach is easily reusable to create schemas interoperable with community standards, but customized to a particular context. Our approach enabled data discovery, increased the reusability of datasets from a large research consortium, and accelerated research. Lastly, we discuss ongoing challenges with FAIRness beyond discoverability., (© 2023. The Author(s).)

A practical problem in supervised deep learning for medical image segmentation is the lack of labeled data which is expensive and time-consuming to acquire. In contrast, there is a considerable amount of unlabeled data available in the clinic. To make better use of the unlabeled data and improve the generalization on limited labeled data, in this paper, a novel semi-supervised segmentation method via multi-task curriculum learning is presented. Here, curriculum learning means that when training the network, simpler knowledge is preferentially learned to assist the learning of more difficult knowledge. Concretely, our framework consists of a main segmentation task and two auxiliary tasks, i.e. the feature regression task and target detection task. The two auxiliary tasks predict some relatively simpler image-level attributes and bounding boxes as the pseudo labels for the main segmentation task, enforcing the pixel-level segmentation result to match the distribution of these pseudo labels. In addition, to solve the problem of class imbalance in the images, a bounding-box-based attention (BBA) module is embedded, enabling the segmentation network to concern more about the target region rather than the background. Furthermore, to alleviate the adverse effects caused by the possible deviation of pseudo labels, error tolerance mechanisms are also adopted in the auxiliary tasks, including inequality constraint and bounding-box amplification. Our method is validated on ACDC2017 and PROMISE12 datasets. Experimental results demonstrate that compared with the full supervision method and state-of-the-art semi-supervised methods, our method yields a much better segmentation performance on a small labeled dataset. Code is available at https://github.com/DeepMedLab/MTCL.

Polyp segmentation has accomplished massive triumph over the years in the field of supervised learning. However, obtaining a vast number of labeled datasets is commonly challenging in the medical domain. To solve this problem, we employ semi-supervised methods and suitably take advantage of unlabeled data to improve the performance of polyp image segmentation. First, we propose an encoder-decoder-based method well suited for the polyp with varying shape, size, and scales. Second, we utilize the teacher-student concept of training the model, where the teacher model is the student model's exponential average. Third, to leverage the unlabeled dataset, we enforce a consistency technique and force the teacher model to generate a similar output on the different perturbed versions of the given input. Finally, we propose a method that upgrades the traditional pseudo-label method by learning the model with continuous update of pseudo-label. We show the efficacy of our proposed method on different polyp datasets, and hence attaining better results in semi-supervised settings. Extensive experiments demonstrate that our proposed method can propagate the unlabeled dataset's essential information to improve performance., (© 2022. The Author(s).)

Objective: The aim of this study to describe a new international dataset for pathology reporting of colorectal cancer surgical specimens, produced under the auspices of the International Collaboration on Cancer Reporting (ICCR)., Background: Quality of pathology reporting and mutual understanding between colorectal surgeon, pathologist and oncologist are vital to patient management. Some pathology parameters are prone to variable interpretation, resulting in differing positions adopted by existing national datasets., Methods: The ICCR, a global alliance of major pathology institutions with links to international cancer organizations, has developed and ratified a rigorous and efficient process for the development of evidence-based, structured datasets for pathology reporting of common cancers. Here we describe the production of a dataset for colorectal cancer resection specimens by a multidisciplinary panel of internationally recognized experts., Results: The agreed dataset comprises eighteen core (essential) and seven non-core (recommended) elements identified from a review of current evidence. Areas of contention are addressed, some highly relevant to surgical practice, with the aim of standardizing multidisciplinary discussion. The summation of all core elements is considered to be the minimum reporting standard for individual cases. Commentary is provided, explaining each element's clinical relevance, definitions to be applied where appropriate for the agreed list of value options and the rationale for considering the element as core or non-core., Conclusions: This first internationally agreed dataset for colorectal cancer pathology reporting promotes standardization of pathology reporting and enhanced clinicopathological communication. Widespread adoption will facilitate international comparisons, multinational clinical trials and help to improve the management of colorectal cancer globally., Competing Interests: The authors report no conflicts of interest., (Copyright © 2021 The Author(s). Published by Wolters Kluwer Health, Inc.)

Introduction: Harmonized neuropsychological assessment for neurocognitive disorders, an international priority for valid and reliable diagnostic procedures, has been achieved only in specific countries or research contexts., Methods: To harmonize the assessment of mild cognitive impairment in Europe, a workshop (Geneva, May 2018) convened stakeholders, methodologists, academic, and non-academic clinicians and experts from European, US, and Australian harmonization initiatives., Results: With formal presentations and thematic working-groups we defined a standard battery consistent with the U.S. Uniform DataSet, version 3, and homogeneous methodology to obtain consistent normative data across tests and languages. Adaptations consist of including two tests specific to typical Alzheimer's disease and behavioral variant frontotemporal dementia. The methodology for harmonized normative data includes consensus definition of cognitively normal controls, classification of confounding factors (age, sex, and education), and calculation of minimum sample sizes., Discussion: This expert consensus allows harmonizing the diagnosis of neurocognitive disorders across European countries and possibly beyond., (© 2021 The Authors. Alzheimer's & Dementia published by Wiley Periodicals LLC on behalf of Alzheimer's Association.)

Large single-cell atlases are now routinely generated to serve as references for analysis of smaller-scale studies. Yet learning from reference data is complicated by batch effects between datasets, limited availability of computational resources and sharing restrictions on raw data. Here we introduce a deep learning strategy for mapping query datasets on top of a reference called single-cell architectural surgery (scArches). scArches uses transfer learning and parameter optimization to enable efficient, decentralized, iterative reference building and contextualization of new datasets with existing references without sharing raw data. Using examples from mouse brain, pancreas, immune and whole-organism atlases, we show that scArches preserves biological state information while removing batch effects, despite using four orders of magnitude fewer parameters than de novo integration. scArches generalizes to multimodal reference mapping, allowing imputation of missing modalities. Finally, scArches retains coronavirus disease 2019 (COVID-19) disease variation when mapping to a healthy reference, enabling the discovery of disease-specific cell states. scArches will facilitate collaborative projects by enabling iterative construction, updating, sharing and efficient use of reference atlases., (© 2021. The Author(s).)

Surveys are a crucial tool for understanding public opinion and behaviour, and their accuracy depends on maintaining statistical representativeness of their target populations by minimizing biases from all sources. Increasing data size shrinks confidence intervals but magnifies the effect of survey bias: an instance of the Big Data Paradox 1 . Here we demonstrate this paradox in estimates of first-dose COVID-19 vaccine uptake in US adults from 9 January to 19 May 2021 from two large surveys: Delphi-Facebook 2,3 (about 250,000 responses per week) and Census Household Pulse 4 (about 75,000 every two weeks). In May 2021, Delphi-Facebook overestimated uptake by 17 percentage points (14-20 percentage points with 5% benchmark imprecision) and Census Household Pulse by 14 (11-17 percentage points with 5% benchmark imprecision), compared to a retroactively updated benchmark the Centers for Disease Control and Prevention published on 26 May 2021. Moreover, their large sample sizes led to miniscule margins of error on the incorrect estimates. By contrast, an Axios-Ipsos online panel 5 with about 1,000 responses per week following survey research best practices 6 provided reliable estimates and uncertainty quantification. We decompose observed error using a recent analytic framework 1 to explain the inaccuracy in the three surveys. We then analyse the implications for vaccine hesitancy and willingness. We show how a survey of 250,000 respondents can produce an estimate of the population mean that is no more accurate than an estimate from a simple random sample of size 10. Our central message is that data quality matters more than data quantity, and that compensating the former with the latter is a mathematically provable losing proposition., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

As neuroimagery datasets continue to grow in size, the complexity of data analyses can require a detailed understanding and implementation of systems computer science for storage, access, processing, and sharing. Currently, several general data standards (e.g., Zarr, HDF5, precomputed) and purpose-built ecosystems (e.g., BossDB, CloudVolume, DVID, and Knossos) exist. Each of these systems has advantages and limitations and is most appropriate for different use cases. Using datasets that don't fit into RAM in this heterogeneous environment is challenging, and significant barriers exist to leverage underlying research investments. In this manuscript, we outline our perspective for how to approach this challenge through the use of community provided, standardized interfaces that unify various computational backends and abstract computer science challenges from the scientist. We introduce desirable design patterns and share our reference implementation called intern.

Gene set analysis has been widely used to gain insight from high-throughput expression studies. Although various tools and methods have been developed for gene set analysis, there is no consensus among researchers regarding best practice(s). Most often, evaluation studies have reported contradictory recommendations of which methods are superior. Therefore, an unbiased quantitative framework for evaluations of gene set analysis methods will be valuable. Such a framework requires gene expression datasets where enrichment status of gene sets is known a priori . In the absence of such gold standard datasets, artificial datasets are commonly used for evaluations of gene set analysis methods; however, they often rely on oversimplifying assumptions that make them biased in favor of or against a given method. In this paper, we propose a quantitative framework for evaluation of gene set analysis methods by synthesizing expression datasets using real data, without relying on oversimplifying or unrealistic assumptions, while preserving complex gene-gene correlations and retaining the distribution of expression values. The utility of the quantitative approach is shown by evaluating ten widely used gene set analysis methods. An implementation of the proposed method is publicly available. We suggest using Silver to evaluate existing and new gene set analysis methods. Evaluation using Silver provides a better understanding of current methods and can aid in the development of gene set analysis methods to achieve higher specificity without sacrificing sensitivity.

Given multiple source datasets with labels, how can we train a target model with no labeled data? Multi-source domain adaptation (MSDA) aims to train a model using multiple source datasets different from a target dataset in the absence of target data labels. MSDA is a crucial problem applicable to many practical cases where labels for the target data are unavailable due to privacy issues. Existing MSDA frameworks are limited since they align data without considering labels of the features of each domain. They also do not fully utilize the target data without labels and rely on limited feature extraction with a single extractor. In this paper, we propose Multi-EPL, a novel method for MSDA. Multi-EPL exploits label-wise moment matching to align the conditional distributions of the features for the labels, uses pseudolabels for the unavailable target labels, and introduces an ensemble of multiple feature extractors for accurate domain adaptation. Extensive experiments show that Multi-EPL provides the state-of-the-art performance for MSDA tasks in both image domains and text domains, improving the accuracy by up to 13.20%., Competing Interests: The authors have declared that no competing interests exist.

Background: Probabilistic linkage can link patients from different clinical databases without the need for personal information. If accurate linkage can be achieved, it would accelerate the use of linked datasets to address important clinical and public health questions., Objective: We developed a step-by-step process for probabilistic linkage of national clinical and administrative datasets without personal information, and validated it against deterministic linkage using patient identifiers., Study Design and Setting: We used electronic health records from the National Bowel Cancer Audit and Hospital Episode Statistics databases for 10,566 bowel cancer patients undergoing emergency surgery in the English National Health Service., Results: Probabilistic linkage linked 81.4% of National Bowel Cancer Audit records to Hospital Episode Statistics, vs. 82.8% using deterministic linkage. No systematic differences were seen between patients that were and were not linked, and regression models for mortality and length of hospital stay according to patient and tumour characteristics were not sensitive to the linkage approach., Conclusion: Probabilistic linkage was successful in linking national clinical and administrative datasets for patients undergoing a major surgical procedure. It allows analysts outside highly secure data environments to undertake linkage while minimizing costs and delays, protecting data security, and maintaining linkage quality., (Copyright © 2021. Published by Elsevier Inc.)

Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis. After decades of effort, 17% of the total residues in human protein sequences are covered by an experimentally determined structure 1 . Here we markedly expand the structural coverage of the proteome by applying the state-of-the-art machine learning method, AlphaFold 2 , at a scale that covers almost the entire human proteome (98.5% of human proteins). The resulting dataset covers 58% of residues with a confident prediction, of which a subset (36% of all residues) have very high confidence. We introduce several metrics developed by building on the AlphaFold model and use them to interpret the dataset, identifying strong multi-domain predictions as well as regions that are likely to be disordered. Finally, we provide some case studies to illustrate how high-quality predictions could be used to generate biological hypotheses. We are making our predictions freely available to the community and anticipate that routine large-scale and high-accuracy structure prediction will become an important tool that will allow new questions to be addressed from a structural perspective., (© 2021. The Author(s).)

Background and Objectives: A standardized data set for esophageal carcinoma pathology reporting was developed based on the approach of the International Collaboration on Cancer Reporting (ICCR) for the purpose of improving cancer patient outcomes and international benchmarking in cancer management., Materials and Methods: The ICCR convened a multidisciplinary international expert panel to identify the best evidence-based clinical and pathological parameters for inclusion in the data set for esophageal carcinoma. The data set incorporated the current edition of the World Health Organization Classification of Tumours of the Digestive System, and Tumour-Node-Metastasis staging systems., Results: The scope of the data set encompassed resection specimens of the esophagus and esophagogastric junction with tumor epicenter ≤20 mm into the proximal stomach. Core reporting elements included information on neoadjuvant therapy, operative procedure used, tumor focality, tumor site, tumor dimensions, distance of tumor to resection margins, histological tumor type, presence and type of dysplasia, tumor grade, extent of invasion in the esophagus, lymphovascular invasion, response to neoadjuvant therapy, status of resection margin, ancillary studies, lymph node status, distant metastases, and pathological staging. Additional non-core elements considered useful to report included clinical information, specimen dimensions, macroscopic appearance of tumor, and coexistent pathology., Conclusions: This is the first international peer-reviewed structured reporting data set for surgically resected specimens of the esophagus. The ICCR carcinoma of the esophagus data set is recommended for routine use globally and is a valuable tool to support standardized reporting, to benefit patient care by providing diagnostic and prognostic best-practice parameters., (Copyright © 2021 Elsevier Inc. All rights reserved.)

As a major method for relation extraction, distantly supervised relation extraction (DSRE) suffered from the noisy label problem and class imbalance problem (these two problems are also common for many other NLP tasks, e.g., text classification). However, there seems no existing research in DSRE or other NLP tasks that can simultaneously solve both problems, which is a significant insufficiency in related researches. In this paper, we propose a loss function which is robust to noisy label and efficient for the imbalanced class dataset. More specific, first we quantify the negative impacts of the noisy label and class imbalance problems. And then we construct a loss function that can minimize these negative impacts through a linear programming method. As far as we know, this seems to be the first attempt to address the noisy label problem and class imbalance problem simultaneously. We evaluated the constructed loss function on the distantly labeled dataset, our artificially noised dataset, human-annotated dataset of Docred, as well as the artificially noised dataset of CoNLL 2003. Experimental results indicate that a DNN model adopting the constructed loss function can outperform other models that adopt the state-of-the-art noisy label robust or negative sample robust loss functions., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

The complexity of neoplasia and its treatment are a challenge to the formulation of general criteria that are applicable across solid cancers. Determining the number of prior lines of therapy (LoT) is critically important for optimising future treatment, conducting medication audits, and assessing eligibility for clinical trial enrolment. Currently, however, no accepted set of criteria or definitions exists to enumerate LoT. In this article, we seek to open a dialogue to address this challenge by proposing a systematic and comprehensive framework to determine LoT uniformly across solid malignancies. First, key terms, including LoT and 'clinical progression of disease' are defined. Next, we clarify which therapies should be assigned a LoT, and why. Finally, we propose reporting LoT in a novel and standardised format as LoT N (CLoT + PLoT), where CLoT is the number of systemic anti-cancer therapies (SACT) administered with curative intent and/or in the early setting, PLoT is the number of SACT given with palliative intent and/or in the advanced setting, and N is the sum of CLoT and PLoT. As a next step, the cancer research community should develop and adopt standardised guidelines for enumerating LoT in a uniform manner., (© 2021. The Author(s).)

Over the last 5 years, single cell methods have enabled the monitoring of gene and protein expression, genetic, and epigenetic changes in thousands of individual cells in a single experiment. With the improved measurement and the decreasing cost of the reactions and sequencing, the size of these datasets is increasing rapidly. The critical bottleneck remains the analysis of the wealth of information generated by single cell experiments. In this review, we give a simplified overview of the analysis pipelines, as they are typically used in the field today. We aim to enable researchers starting out in single cell analysis to gain an overview of challenges and the most commonly used analytical tools. In addition, we hope to empower others to gain an understanding of how typical readouts from single cell datasets are presented in the published literature., (Copyright © 2021 by the American Society of Nephrology.)

Retrospective observational research relies on databases that do not routinely record lines of therapy or reasons for treatment change. Standardized approaches to estimate lines of therapy were developed and evaluated in this study. A number of rules were developed, assumptions varied and macros developed to apply to large datasets. Results were investigated in an iterative process to refine line of therapy algorithms in three different cancers (lung, colorectal and gastric). Three primary factors were evaluated and included in the estimation of lines of therapy in oncology: defining a treatment regimen, addition/removal of drugs and gap periods. Algorithms and associated Statistical Analysis Software (SAS ® ) macros for line of therapy identification are provided to facilitate and standardize the use of real-world databases for oncology research.

Abstract: Visual analogue scales are widely used to measure subjective responses. Norris' 16 visual analogue scales (N_VAS) measure subjective feelings of alertness and mood. Up to now, different scientists have clustered items of N_VAS into different ways and Bond and Lader's way has been the most frequently used in clinical research. However, there are concerns about the stability of this clustering over different subject samples and different drug classes. The aim of this study was to test whether Bond and Lader's clustering was stable in terms of subject samples and drug effects. Alternative clustering of N_VAS was tested.Data from studies with 3 types of drugs: cannabinoid receptor agonist (delta-9-tetrahydrocannabinol [THC]), muscarinic antagonist (scopolamine), and benzodiazepines (midazolam and lorazepam), collected between 2005 and 2012, were used for this analysis. Exploratory factor analysis (EFA) was used to test the clustering algorithm of Bond and Lader. Consensus clustering was performed to test the stability of clustering results over samples and over different drug types. Stability analysis was performed using a three-cluster assumption, and then on other alternative assumptions.Heat maps of the consensus matrix (CM) and density plots showed instability of the three-cluster hypothesis and suggested instability over the 3 drug classes. Two- and four-cluster hypothesis were also tested. Heat maps of the CM and density plots suggested that the two-cluster assumption was superior.In summary, the two-cluster assumption leads to a provably stable outcome over samples and the 3 drug types based on the data used., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2021 the Author(s). Published by Wolters Kluwer Health, Inc.)

Data-driven digital health technologies have the power to transform health care. If these tools could be sustainably delivered at scale, they might have the potential to provide everyone, everywhere, with equitable access to expert-level care, narrowing the global health and wellbeing gap. Conversely, it is highly possible that these transformative technologies could exacerbate existing health-care inequalities instead. In this Viewpoint, we describe the problem of health data poverty: the inability for individuals, groups, or populations to benefit from a discovery or innovation due to a scarcity of data that are adequately representative. We assert that health data poverty is a threat to global health that could prevent the benefits of data-driven digital health technologies from being more widely realised and might even lead to them causing harm. We argue that the time to act is now to avoid creating a digital health divide that exacerbates existing health-care inequalities and to ensure that no one is left behind in the digital era., (Copyright © 2021 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

Objective: The lack of representative coronavirus disease 2019 (COVID-19) data is a bottleneck for reliable and generalizable machine learning. Data sharing is insufficient without data quality, in which source variability plays an important role. We showcase and discuss potential biases from data source variability for COVID-19 machine learning., Materials and Methods: We used the publicly available nCov2019 dataset, including patient-level data from several countries. We aimed to the discovery and classification of severity subgroups using symptoms and comorbidities., Results: Cases from the 2 countries with the highest prevalence were divided into separate subgroups with distinct severity manifestations. This variability can reduce the representativeness of training data with respect the model target populations and increase model complexity at risk of overfitting., Conclusions: Data source variability is a potential contributor to bias in distributed research networks. We call for systematic assessment and reporting of data source variability and data quality in COVID-19 data sharing, as key information for reliable and generalizable machine learning., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Comprehensive two-dimensional gas chromatography (GC × GC) is amongst the most powerful separation technologies currently existing. Since its advent in early 1990, it has become an established method which is readily available. However, one of its most challenging aspects, especially in hyphenation with mass spectrometry is the high amount of chemical information it provides for each measurement. The GC × GC community agrees that there, the highest demand for action is found. In response, the number of software packages allowing for in-depth data processing of GC × GC data has risen over the last couple of years. These packages provide sophisticated tools and algorithms allowing for more streamlined data evaluation. However, these tools/algorithms and their respective specific functionalities differ drastically within the available software packages and might result in various levels of findings if not appropriately implemented by the end users. This study focuses on two main objectives. First, to propose a data analysis framework and second to propose an open-source dataset for benchmarking software options and their specificities. Thus, allowing for an unanimous and comprehensive evaluation of GC × GC software. Thereby, the benchmark data includes a set of standard compound measurements and a set of chocolate aroma profiles. On this foundation, eight readily available GC × GC software packages were anonymously investigated for fundamental and advanced functionalities such as retention and detection device derived parameters, revealing differences in the determination of e.g. retention times and mass spectra., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020. Published by Elsevier B.V.)

Objectives: Pelvic floor disorders (PFDs) are important public health concerns due to their increasing prevalence. Hence, there is an increasing need for developing systematically collected quality data to assist appropriate clinical decision-making. This study aimed to develop a core data set for patients with PFDs based on the PFDs registry., Methods: A descriptive cross-sectional study was conducted in 2019. Data were retrieved from electronic databases including PubMed, Embase and Google scholar. Available documents and data systems in clinical centers were also assessed. The Delphi technique was applied to reach a consensus about the data elements using a questionnaire. A panel of experts evaluated the content validity of the questionnaire., Results: We developed a dataset for PFDs that included two classes of data (65 data items) identified from the related literature. In the Delphi survey, 74 data elements were determined by the experts and final data were divided into two demographic and clinical categories that included 12 and 62 data elements, respectively., Conclusions: This dataset has the potential for standardizing the data by providing accurate, consistent, complete and uniform data elements. Furthermore, it can provide valuable research facilities for clinicians and researchers in the healthcare system resulting in improvement of the quality of care and containment of costs., (© 2020 John Wiley & Sons Australia, Ltd.)

Background: Data quality is fundamental to the integrity of quantitative research. The role of external researchers in data quality assessment (DQA) remains ill-defined in the context of secondary use for research of large, centrally curated health datasets. In order to investigate equity of palliative care provided to Indigenous Australian patients, researchers accessed a now-historical version of a national palliative care dataset developed primarily for the purpose of continuous quality improvement., Objectives: (i) To apply a generic DQA framework to the dataset and (ii) to report the process and results of this assessment and examine the consequences for conducting the research., Method: The data were systematically examined for completeness, consistency and credibility. Data quality issues relevant to the Indigenous identifier and framing of research questions were of particular interest., Results: The dataset comprised 477,518 records of 144,951 patients (Indigenous N = 1515; missing Indigenous identifier N = 4998) collected from participating specialist palliative care services during a period (1 January 2010-30 June 2015) in which data-checking systems underwent substantial upgrades. Progressive improvement in completeness of data over the study period was evident. The data were error-free with respect to many credibility and consistency checks, with anomalies detected reported to data managers. As the proportion of missing values remained substantial for some clinical care variables, multiple imputation procedures were used in subsequent analyses., Conclusion and Implications: In secondary use of large curated datasets, DQA by external researchers may both influence proposed analytical methods and contribute to improvement of data curation processes through feedback to data managers.

Study Question: Can consensus definitions for the core outcome set for infertility be identified in order to recommend a standardized approach to reporting?, Summary Answer: Consensus definitions for individual core outcomes, contextual statements, and a standardized reporting table have been developed., What Is Known Already: Different definitions exist for individual core outcomes for infertility. This variation increases the opportunities for researchers to engage with selective outcome reporting, which undermines secondary research and compromises clinical practice guideline development., Study Design, Size, Duration: Potential definitions were identified by a systematic review of definition development initiatives and clinical practice guidelines and by reviewing Cochrane Gynaecology and Fertility Group guidelines. These definitions were discussed in a face-to-face consensus development meeting, which agreed consensus definitions. A standardized approach to reporting was also developed as part of the process., Participants/materials, Setting, Methods: Healthcare professionals, researchers, and people with fertility problems were brought together in an open and transparent process using formal consensus development methods., Main Results and the Role of Chance: Forty-four potential definitions were inventoried across four definition development initiatives, including the Harbin Consensus Conference Workshop Group and International Committee for Monitoring Assisted Reproductive Technologies, 12 clinical practice guidelines, and Cochrane Gynaecology and Fertility Group guidelines. Twenty-seven participants, from 11 countries, contributed to the consensus development meeting. Consensus definitions were successfully developed for all core outcomes. Specific recommendations were made to improve reporting., Limitations, Reasons for Caution: We used consensus development methods, which have inherent limitations. There was limited representation from low- and middle-income countries., Wider Implications of the Findings: A minimum data set should assist researchers in populating protocols, case report forms, and other data collection tools. The generic reporting table should provide clear guidance to researchers and improve the reporting of their results within journal publications and conference presentations. Research funding bodies, the Standard Protocol Items: Recommendations for Interventional Trials statement, and over 80 specialty journals have committed to implementing this core outcome set., Study Funding/competing Interest(s): This research was funded by the Catalyst Fund, Royal Society of New Zealand, Auckland Medical Research Fund, and Maurice and Phyllis Paykel Trust. Siladitya Bhattacharya reports being the Editor-in-Chief of Human Reproduction Open and an editor of the Cochrane Gynaecology and Fertility group. Hans Evers reports being the Editor Emeritus of Human Reproduction. Richard Legro reports consultancy fees from Abbvie, Bayer, Ferring, Fractyl, Insud Pharma and Kindex and research sponsorship from Guerbet and Hass Avocado Board. Ben Mol reports consultancy fees from Guerbet, iGenomix, Merck, Merck KGaA and ObsEva. Craig Niederberger reports being the Editor-in-Chief of Fertility and Sterility and Section Editor of the Journal of Urology, research sponsorship from Ferring, and a financial interest in NexHand. Ernest Ng reports research sponsorship from Merck. Annika Strandell reports consultancy fees from Guerbet. Jack Wilkinson reports being a statistical editor for the Cochrane Gynaecology and Fertility group. Andy Vail reports that he is a Statistical Editor of the Cochrane Gynaecology & Fertility Review Group and of the journal Reproduction. His employing institution has received payment from HFEA for his advice on review of research evidence to inform their 'traffic light' system for infertility treatment 'add-ons'. Lan Vuong reports consultancy and conference fees from Ferring, Merck and Merck Sharp and Dohme. The remaining authors declare no competing interests in relation to the work presented. All authors have completed the disclosure form., Trial Registration Number: Core Outcome Measures in Effectiveness Trials Initiative: 1023., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Health and healthcare disparities continue despite clinical, research, and policy efforts. Large clinical datasets may not contain data relevant to healthcare disparities and leveraging these for research may be crucial to improve health equity. The Health Disparities Collaborative Research Group was commissioned by the Patient-Centered Outcomes Research Institute to examine the data science needs for quality and complete data and provide recommendations for improving data science around health disparities. The group convened content experts, researchers, clinicians, and patients to produce these recommendations and suggestions for implementation. Our desire was to produce recommendations to improve the usability of healthcare datasets for health equity research. The recommendations are summarized in 3 primary domains: patient voice, accurate variables, and data linkage. The implementation of these recommendations in national datasets has the potential to accelerate health disparities research and promote efforts to reduce health inequities., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

The estimation of the effect of contributors to crash injury severity and the prediction of crash injury severity outcomes suffer often from biases related to missing data in crash datasets that contain incomplete records. As both estimation and prediction would greatly improve if the missing values were recovered, this study proposes a sequential approach to handle incomplete crash datasets and rank contributors to the injury severity of crashes on mountainous freeways in China. The sequential approach consists of two parts: (i) multivariate imputation by chained equations imputes the missing values of independent variables; (ii) a random forest classifier analyses the correlation between the dependent and the independent variables. The first part considers different imputation methods in light of the independent variables being either binary, categorical or continuous, whereas the second part classifies the correlations according to the random forest classifier. The proposed method was applied to the case-study about mountainous freeways in China and compared to the analysis of the raw dataset to evaluate its effectiveness, and the results illustrate that the method improves significantly the classification accuracy when compared with existing methods. Moreover, the classifier ranked the contributors to the injury severity of traffic crashes on mountainous freeways: in order of importance vehicle type, crash type, road longitudinal gradient, crash cause, curve radius, and deflection angles. Interestingly, a lower importance was found for environmental factors., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Background: ACMG/AMP and AMP/ASCO/CAP have released guidelines for variation interpretation, and ESHG for diagnostic sequencing. These guidelines contain recommendations including the use of computational prediction methods. The guidelines per se and the way they are implemented cause some problems., Methods: Logical reasoning based on domain knowledge., Results: According to the guidelines, several methods have to be used and they have to agree. This means that the methods with the poorest performance overrule the better ones. The choice of the prediction method(s) should be made by experts  based on systematic benchmarking studies reporting all the relevant performance measures. Currently variation interpretation methods have been applied mainly to amino acid substitutions and splice site variants; however, predictors for some other types of variations are available and there will be tools for new application areas in the near future. Common problems in prediction method usage are discussed. The number of features used for method training or the number of variation types predicted by a tool are not indicators of method performance. Many published gene, protein or disease-specific benchmark studies suffer from too small dataset rendering the results useless. In the case of binary predictors, equal number of positive and negative cases is beneficial for training, the imbalance has to be corrected for performance assessment. Predictors cannot be better than the data they are based on and used for training and testing. Minor allele frequency (MAF) can help to detect likely benign cases, but the recommended MAF threshold is apparently too high. The fact that many rare variants are disease-causing or -related does not mean that rare variants in general would be harmful. How large a portion of the tested variants a tool can predict (coverage) is not a quality measure., Conclusion: Methods used for variation interpretation have to be carefully selected. It should be possible to use only one predictor, with proven good performance or a limited number of complementary predictors with state-of-the-art performance. Bear in mind that diseases and pathogenicity have a continuum and variants are not dichotomic i.e. either pathogenic or benign, either., (© 2020 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc.)

Objective: Commercially available business (CAB) datasets for food environments have been investigated for error in large urban contexts and some rural areas, but there is a relative dearth of literature that reports error across regions of variable rurality. The objective of the current study was to assess the validity of a CAB dataset using a government dataset at the provincial scale., Design: A ground-truthed dataset provided by the government of Newfoundland and Labrador (NL) was used to assess a popular commercial dataset. Concordance, sensitivity, positive-predictive value (PPV) and geocoding errors were calculated. Measures were stratified by store types and rurality to investigate any association between these variables and database accuracy., Setting: NL, Canada., Participants: The current analysis used store-level (ecological) data., Results: Of 1125 stores, there were 380 stores that existed in both datasets and were considered true-positive stores. The mean positional error between a ground-truthed and test point was 17·72 km. When compared with the provincial dataset of businesses, grocery stores had the greatest agreement, sensitivity = 0·64, PPV = 0·60 and concordance = 0·45. Gas stations had the least agreement, sensitivity = 0·26, PPV = 0·32 and concordance = 0·17. Only 4 % of commercial data points in rural areas matched every criterion examined., Conclusions: The commercial dataset exhibits a low level of agreement with the ground-truthed provincial data. Particularly retailers in rural areas or belonging to the gas station category suffered from misclassification and/or geocoding errors. Taken together, the commercial dataset is differentially representative of the ground-truthed reality based on store-type and rurality/urbanity.

Background: We describe the latest improvements to the long-range phasing (LRP) and haplotype library imputation (HLI) algorithms for successful phasing of both datasets with one million individuals and datasets genotyped using different sets of single nucleotide polymorphisms (SNPs). Previous publicly available implementations of the LRP algorithm implemented in AlphaPhase could not phase large datasets due to the computational cost of defining surrogate parents by exhaustive all-against-all searches. Furthermore, the AlphaPhase implementations of LRP and HLI were not designed to deal with large amounts of missing data that are inherent when using multiple SNP arrays., Methods: We developed methods that avoid the need for all-against-all searches by performing LRP on subsets of individuals and then concatenating the results. We also extended LRP and HLI algorithms to enable the use of different sets of markers, including missing values, when determining surrogate parents and identifying haplotypes. We implemented and tested these extensions in an updated version of AlphaPhase, and compared its performance to the software package Eagle2., Results: A simulated dataset with one million individuals genotyped with the same 6711 SNPs for a single chromosome took less than a day to phase, compared to more than seven days for Eagle2. The percentage of correctly phased alleles at heterozygous loci was 90.2 and 99.9% for AlphaPhase and Eagle2, respectively. A larger dataset with one million individuals genotyped with 49,579 SNPs for a single chromosome took AlphaPhase 23 days to phase, with 89.9% of alleles at heterozygous loci phased correctly. The phasing accuracy was generally lower for datasets with different sets of markers than with one set of markers. For a simulated dataset with three sets of markers, 1.5% of alleles at heterozygous positions were phased incorrectly, compared to 0.4% with one set of markers., Conclusions: The improved LRP and HLI algorithms enable AlphaPhase to quickly and accurately phase very large and heterogeneous datasets. AlphaPhase is an order of magnitude faster than the other tested packages, although Eagle2 showed a higher level of phasing accuracy. The speed gain will make phasing achievable for very large genomic datasets in livestock, enabling more powerful breeding and genetics research and application.

Background: There is an increased interest in the analysis of large, national palliative care data sets including patient reported outcomes (PROs). No study has investigated if it was best to include or exclude data from services with low response rates in order to obtain the patient reported outcomes most representative of the national palliative care population. Thus, the aim of this study was to investigate whether services with low response rates should be excluded from analyses to prevent effects of possible selection bias., Methods: Data from the Danish Palliative Care Database from 24,589 specialized palliative care admittances of cancer patients was included. Patients reported ten aspects of quality of life using the EORTC QLQ-C15-PAL-questionnaire. Multiple linear regression was performed to test if response rate was associated with the ten aspects of quality of life., Results: The score of six quality of life aspects were significantly associated with response rate. However, in only two cases patients from specialized palliative care services with lower response rates (< 20.0%, 20.0-29.9%, 30.0-39.9%, 40.0-49.9% or 50.0-59.9) were feeling better than patients from services with high response rates (≥60%) and in both cases it was less than 2 points on a 0-100 scale., Conclusions: The study hypothesis, that patients from specialized palliative care services with lower response rates were reporting better quality of life than those from specialized palliative care services with high response rates, was not supported. This suggests that there is no reason to exclude data from specialized palliative care services with low response rates.

Artificial intelligence (AI) systems for computer-aided diagnosis and image-based screening are being adopted worldwide by medical institutions. In such a context, generating fair and unbiased classifiers becomes of paramount importance. The research community of medical image computing is making great efforts in developing more accurate algorithms to assist medical doctors in the difficult task of disease diagnosis. However, little attention is paid to the way databases are collected and how this may influence the performance of AI systems. Our study sheds light on the importance of gender balance in medical imaging datasets used to train AI systems for computer-assisted diagnosis. We provide empirical evidence supported by a large-scale study, based on three deep neural network architectures and two well-known publicly available X-ray image datasets used to diagnose various thoracic diseases under different gender imbalance conditions. We found a consistent decrease in performance for underrepresented genders when a minimum balance is not fulfilled. This raises the alarm for national agencies in charge of regulating and approving computer-assisted diagnosis systems, which should include explicit gender balance and diversity recommendations. We also establish an open problem for the academic medical image computing community which needs to be addressed by novel algorithms endowed with robustness to gender imbalance., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)

The burden of several common diseases including obesity, diabetes, hypertension, asthma, and depression is increasing in most world populations. However, the mechanisms underlying the numerous epidemiological and genetic correlations among these disorders remain largely unknown. We investigated whether common polymorphic inversions underlie the shared genetic influence of these disorders. We performed an inversion association analysis including 21 inversions and 25 obesity-related traits on a total of 408,898 Europeans and validated the results in 67,299 independent individuals. Seven inversions were associated with multiple diseases while inversions at 8p23.1, 16p11.2, and 11q13.2 were strongly associated with the co-occurrence of obesity with other common diseases. Transcriptome analysis across numerous tissues revealed strong candidate genes for obesity-related traits. Analyses in human pancreatic islets indicated the potential mechanism of inversions in the susceptibility of diabetes by disrupting the cis-regulatory effect of SNPs from their target genes. Our data underscore the role of inversions as major genetic contributors to the joint susceptibility to common complex diseases., (Copyright © 2020 American Society of Human Genetics. All rights reserved.)

Open data allows researchers to explore pre-existing datasets in new ways. However, if many researchers reuse the same dataset, multiple statistical testing may increase false positives. Here we demonstrate that sequential hypothesis testing on the same dataset by multiple researchers can inflate error rates. We go on to discuss a number of correction procedures that can reduce the number of false positives, and the challenges associated with these correction procedures., Competing Interests: WT, JW, PB, RP No competing interests declared, (© 2020, Thompson et al.)

Accurate construction of polygenic scores (PGS) can enable early diagnosis of diseases and facilitate the development of personalized medicine. Accurate PGS construction requires prediction models that are both adaptive to different genetic architectures and scalable to biobank scale datasets with millions of individuals and tens of millions of genetic variants. Here, we develop such a method called Deterministic Bayesian Sparse Linear Mixed Model (DBSLMM). DBSLMM relies on a flexible modeling assumption on the effect size distribution to achieve robust and accurate prediction performance across a range of genetic architectures. DBSLMM also relies on a simple deterministic search algorithm to yield an approximate analytic estimation solution using summary statistics only. The deterministic search algorithm, when paired with further algebraic innovations, results in substantial computational savings. With simulations, we show that DBSLMM achieves scalable and accurate prediction performance across a range of realistic genetic architectures. We then apply DBSLMM to analyze 25 traits in UK Biobank. For these traits, compared to existing approaches, DBSLMM achieves an average of 2.03%-101.09% accuracy gain in internal cross-validations. In external validations on two separate datasets, including one from BioBank Japan, DBSLMM achieves an average of 14.74%-522.74% accuracy gain. In these real data applications, DBSLMM is 1.03-28.11 times faster and uses only 7.4%-24.8% of physical memory as compared to other multiple regression-based PGS methods. Overall, DBSLMM represents an accurate and scalable method for constructing PGS in biobank scale datasets., (Copyright © 2020 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

There are currently no proven or approved treatments for coronavirus disease 2019 (COVID-19). Early anecdotal reports and limited in vitro data led to the significant uptake of hydroxychloroquine (HCQ), and to lesser extent chloroquine (CQ), for many patients with this disease. As an increasing number of patients with COVID-19 are treated with these agents and more evidence accumulates, there continues to be no high-quality clinical data showing a clear benefit of these agents for this disease. Moreover, these agents have the potential to cause harm, including a broad range of adverse events including serious cardiac side effects when combined with other agents. In addition, the known and potent immunomodulatory effects of these agents which support their use in the treatment of auto-immune conditions, and provided a component in the original rationale for their use in patients with COVID-19, may, in fact, undermine their utility in the context of the treatment of this respiratory viral infection. Specifically, the impact of HCQ on cytokine production and suppression of antigen presentation may have immunologic consequences that hamper innate and adaptive antiviral immune responses for patients with COVID-19. Similarly, the reported in vitro inhibition of viral proliferation is largely derived from the blockade of viral fusion that initiates infection rather than the direct inhibition of viral replication as seen with nucleoside/tide analogs in other viral infections. Given these facts and the growing uncertainty about these agents for the treatment of COVID-19, it is clear that at the very least thoughtful planning and data collection from randomized clinical trials are needed to understand what if any role these agents may have in this disease. In this article, we review the datasets that support or detract from the use of these agents for the treatment of COVID-19 and render a data informed opinion that they should only be used with caution and in the context of carefully thought out clinical trials, or on a case-by-case basis after rigorous consideration of the risks and benefits of this therapeutic approach., (© 2020 The Authors. The FASEB Journal published by Wiley Periodicals LLC on behalf of Federation of American Societies for Experimental Biology.)

Ligand enrichment assessment based on benchmarking data sets has become a necessity for the rational selection of the best-suited approach for prospective data mining of drug-like molecules. Up to now, a variety of benchmarking data sets had been generated and frequently used. Among them, MUBD-HDACs from our prior research efforts was regarded as one of five state-of-the-art benchmarks in 2017 by Frontiers in Pharmacology. This benchmarking set was generated by one of our unique de-biasing algorithms. It also rendered quite a few other cases of successful applications in recent years, thus is expected to have more impact in modern drug discovery. To make our algorithm amenable to more users, we developed a Python GUI application called MUBD-DecoyMaker 2.0. Moreover, it has two new additional functional modules, i. e. "Detect 2D Bias" and "Quality Control". This new GUI version had been proved to be easy to use while generate benchmarking data sets of the same quality. MUBD-DecoyMaker 2.0 is freely available at https://github.com/jwxia2014/MUBD-DecoyMaker2.0, along with its manual and testcase., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Objective: Development of systematic approaches for understanding and assessing data quality is becoming increasingly important as the volume and utilization of health data steadily increases. In this study, a taxonomy of data defects was developed and utilized when automatically detecting defects to assess Medicaid data quality maintained by one of the states in the United States., Materials and Methods: There were more than 2.23 million rows and 32 million cells in the Medicaid data examined. The taxonomy was developed through document review, descriptive data analysis, and literature review. A software program was created to automatically detect defects by using a set of constraints whose development was facilitated by the taxonomy., Results: Five major categories and seventeen subcategories of defects were identified. The major categories are missingness, incorrectness, syntax violation, semantic violation, and duplicity. More than 3 million defects were detected indicating substantial problems with data quality. Defect density exceeded 10% in five tables. The majority of the data defects belonged to format mismatch, invalid code, dependency-contract violation, and implausible value types. Such contextual knowledge can support prioritized quality improvement initiatives for the Medicaid data studied., Conclusions: This research took the initial steps to understand the types of data defects and detect defects in large healthcare datasets. The results generally suggest that healthcare organizations can potentially benefit from focusing on data quality improvement. For those purposes, the taxonomy developed and the approach followed in this study can be adopted., (© The Author(s) 2019. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

A key requirement for longitudinal studies using routinely-collected health data is to be able to measure what individuals are present in the datasets used, and over what time period. Individuals can enter and leave the covered population of administrative datasets for a variety of reasons, including both life events and characteristics of the datasets themselves. An automated, customizable method of determining individuals' presence was developed for the primary care dataset in Swansea University's SAIL Databank. The primary care dataset covers only a portion of Wales, with 76% of practices participating. The start and end date of the data varies by practice. Additionally, individuals can change practices or leave Wales. To address these issues, a two step process was developed. First, the period for which each practice had data available was calculated by measuring changes in the rate of events recorded over time. Second, the registration records for each individual were simplified. Anomalies such as short gaps and overlaps were resolved by applying a set of rules. The result of these two analyses was a cleaned set of records indicating start and end dates of available primary care data for each individual. Analysis of GP records showed that 91.0% of events occurred within periods calculated as having available data by the algorithm. 98.4% of those events were observed at the same practice of registration as that computed by the algorithm. A standardized method for solving this common problem has enabled faster development of studies using this data set. Using a rigorous, tested, standardized method of verifying presence in the study population will also positively influence the quality of research., Competing Interests: The authors have declared that no competing interests exist.