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Pseudonatural Products Occur Frequently in Biologically Relevant Compounds.

J Chem Inf Model 2021 Oct 20. Epub 2021 Oct 20.

Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany.

A new methodology for classifying fragment combinations and characterizing pseudonatural products (PNPs) is described. The source code is based on open-source tools and is organized as a Python package. Tasks can be executed individually or within the context of scalable, robust workflows. Read More

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October 2021

Constructing Japanese MeSH term dictionaries related to the COVID-19 literature.

Genomics Inform 2021 Sep 30;19(3):e25. Epub 2021 Sep 30.

Computer Science Department, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK.

The coronavirus disease 2019 (COVID-19) pandemic has led to a flood of research papers and the information has been updated with considerable frequency. For society to derive benefits from this research, it is necessary to promote sharing up-to-date knowledge from these papers. However, because most research papers are written in English, it is difficult for people who are not familiar with English medical terms to obtain knowledge from them. Read More

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September 2021

Direct-Optimization-Based DC Dictionary Learning With the MCP Regularizer.

IEEE Trans Neural Netw Learn Syst 2021 Oct 11;PP. Epub 2021 Oct 11.

Direct-optimization-based dictionary learning has attracted increasing attention for improving computational efficiency. However, the existing direct optimization scheme can only be applied to limited dictionary learning problems, and it remains an open problem to prove that the whole sequence obtained by the algorithm converges to a critical point of the objective function. In this article, we propose a novel direct-optimization-based dictionary learning algorithm using the minimax concave penalty (MCP) as a sparsity regularizer that can enforce strong sparsity and obtain accurate estimation. Read More

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October 2021

Compression for population genetic data through finite-state entropy.

J Bioinform Comput Biol 2021 Sep 30:2150026. Epub 2021 Sep 30.

Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, V5A 1S6, Canada.

We improve the efficiency of population genetic file formats and GWAS computation by leveraging the distribution of samples in population-level genetic data. We identify conditional exchangeability of these data, recommending finite state entropy algorithms as an arithmetic code naturally suited for compression of population genetic data. We show between [Formula: see text] and [Formula: see text] speed and size improvements over modern dictionary compression methods that are often used for population genetic data such as and in computation and decompression tasks. Read More

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September 2021

DDLVis: Real-time Visual Query of Spatiotemporal Data Distribution via Density Dictionary Learning.

IEEE Trans Vis Comput Graph 2021 Sep 29;PP. Epub 2021 Sep 29.

Visual query of spatiotemporal data is becoming an increasingly important function in visual analytics applications. Various works have been presented for querying large spatiotemporal data in real time. However, the real-time query of spatiotemporal data distribution is still an open challenge. Read More

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September 2021

Modeling combined ultrasound and photoacoustic imaging: Simulations aiding device development and artificial intelligence.

Photoacoustics 2021 Dec 15;24:100304. Epub 2021 Sep 15.

Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, 16802, USA.

Combined ultrasound and photoacoustic (USPA) imaging has attracted several pre-clinical and clinical applications due to its ability to simultaneously display structural, functional, and molecular information of deep biological tissue in real time. However, the depth and wavelength dependent optical attenuation and the unknown optical and acoustic heterogeneities limit the USPA imaging performance in deep tissue regions. Novel instrumentation, image reconstruction, and artificial intelligence (AI) methods are currently being investigated to overcome these limitations and improve the USPA image quality. Read More

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December 2021

Enabling qualitative research data sharing using a natural language processing pipeline for deidentification: moving beyond HIPAA Safe Harbor identifiers.

JAMIA Open 2021 Jul 23;4(3):ooab069. Epub 2021 Aug 23.

Bioethics Research Center, Division of General Medical Sciences, Washington University, St. Louis, Missouri, USA.

Objective: Sharing health research data is essential for accelerating the translation of research into actionable knowledge that can impact health care services and outcomes. Qualitative health research data are rarely shared due to the challenge of deidentifying text and the potential risks of participant reidentification. Here, we establish and evaluate a framework for deidentifying qualitative research data using automated computational techniques including removal of identifiers that are not considered HIPAA Safe Harbor (HSH) identifiers but are likely to be found in unstructured qualitative data. Read More

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Predicting Brain Amyloid Using Multivariate Morphometry Statistics, Sparse Coding, and Correntropy: Validation in 1,101 Individuals From the ADNI and OASIS Databases.

Front Neurosci 2021 6;15:669595. Epub 2021 Aug 6.

School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, United States.

Biomarker assisted preclinical/early detection and intervention in Alzheimer's disease (AD) may be the key to therapeutic breakthroughs. One of the presymptomatic hallmarks of AD is the accumulation of beta-amyloid (Aβ) plaques in the human brain. However, current methods to detect Aβ pathology are either invasive (lumbar puncture) or quite costly and not widely available (amyloid PET). Read More

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Drowning and aquatic injuries dictionary.

Resusc Plus 2021 Mar 20;5:100072. Epub 2021 Jan 20.

IDRA - International Drowning Researchers' Alliance, Kuna, Idaho, USA.

Background: Drowning is a significant public health issue with more than 320,000 deaths globally every year. These numbers are greatly underestimated, however, due to factors such as inadequate data collection, inconsistent categorization and failure to report in certain regions and cultures.The objective of this study was to develop a standardised drowning dictionary using a consensus-based approach. Read More

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Using administrative health data for palliative and end of life care research in Ireland: potential and challenges.

HRB Open Res 2021 26;4:17. Epub 2021 May 26.

School of Medicine, University of Limerick, Limerick, V94 T9PX, Ireland.

: This study aims to examine the potential of currently available administrative health and social care data for palliative and end-of-life care (PEoLC) research in Ireland. Objectives include to i) identify data sources for PEoLC research ii) describe the challenges and opportunities of using these and iii) evaluate the impact of recent health system reforms and changes to data protection laws. : The 2017 Health Information and Quality Authority catalogue of health and social care datasets was cross-referenced with a recognised list of diseases with associated palliative care needs. Read More

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Twitter, time and emotions.

R Soc Open Sci 2021 May 26;8(5):201900. Epub 2021 May 26.

Department of Psychology, Norwegian University of Science and Technology, Dragvoll Campus, Trondheim 7491, Norway.

The study of temporal trajectories of emotions shared in tweets has shown that both positive and negative emotions follow nonlinear circadian (24 h) and circaseptan (7-day) patterns. But to this point, such findings could be instrument-dependent as they rely exclusively on coding using the Linguistic Inquiry Word Count. Further, research has shown that self-referential content has higher relevance and meaning for individuals, compared with other types of content. Read More

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Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies.

Database (Oxford) 2021 05;2021

Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia.

Crop phenotypic data underpin many pre-breeding efforts to characterize variation within germplasm collections. Although there has been an increase in the global capacity for accumulating and comparing such data, a lack of consistency in the systematic description of metadata often limits integration and sharing. We therefore aimed to understand some of the challenges facing findable, accesible, interoperable and reusable (FAIR) curation and annotation of phenotypic data from minor and underutilized crops. Read More

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Validation of the Crystallography Open Database using the Crystallographic Information Framework.

J Appl Crystallogr 2021 Apr 14;54(Pt 2):661-672. Epub 2021 Feb 14.

Department of Protein-DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania.

Data curation practices of the Crystallography Open Database (COD) are described with additional focus being placed on the formal validation using the Crystallographic Information Framework (CIF). The program, capable of validating CIF files against both the DDL1 and the DDLm dictionaries, is presented and used to process the entirety of the COD. Validation results collected from over 450 000 CIF files are demonstrated to be a useful resource in the data maintenance process as well as the development of the underlying ontologies. Read More

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Fast and accurate modeling of transient-state, gradient-spoiled sequences by recurrent neural networks.

NMR Biomed 2021 07 5;34(7):e4527. Epub 2021 May 5.

Center for Image Sciences, University Medical Center Utrecht, Utrecht, the Netherlands.

Fast and accurate modeling of MR signal responses are typically required for various quantitative MRI applications, such as MR fingerprinting. This work uses a new extended phase graph (EPG)-Bloch model for accurate simulation of transient-state, gradient-spoiled MR sequences, and proposes a recurrent neural network (RNN) as a fast surrogate of the EPG-Bloch model for computing large-scale MR signals and derivatives. The computational efficiency of the RNN model is demonstrated by comparisons with other existing models, showing one to three orders of acceleration compared with the latest GPU-accelerated, open-source EPG package. Read More

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Low-Velocity Impact Localization on a Honeycomb Sandwich Panel Using a Balanced Projective Dictionary Pair Learning Classifier.

Sensors (Basel) 2021 Apr 7;21(8). Epub 2021 Apr 7.

State Key Laboratory of Mechanics and Control of Mechanical Structures, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China.

Carbon-fiber aluminum honeycomb sandwich panels are vulnerable to low-velocity impacts, which can cause structural damage and failures that reduce the bearing performance and reliability of the structure. Therefore, a method for locating such impacts through a sensor network is very important for structural health monitoring. Unlike composite laminates, the stress wave generated by an impact is damped rapidly in a sandwich panel, meaning that the signal qualities measured by different sensors vary greatly, thereby making it difficult to locate the impact. Read More

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Efficacy and correlative analyses of avelumab plus axitinib versus sunitinib in sarcomatoid renal cell carcinoma: post hoc analysis of a randomized clinical trial.

ESMO Open 2021 Jun 23;6(3):100101. Epub 2021 Apr 23.

Department of Medical Oncology, Institut Gustave Roussy, Villejuif, France.

Background: Among patients with advanced renal cell carcinoma (RCC), those with sarcomatoid histology (sRCC) have the poorest prognosis. This analysis assessed the efficacy of avelumab plus axitinib versus sunitinib in patients with treatment-naive advanced sRCC.

Methods: The randomized, open-label, multicenter, phase III JAVELIN Renal 101 trial (NCT02684006) enrolled patients with treatment-naive advanced RCC. Read More

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ATLAS trial of adjuvant axitinib in patients with renal cell carcinoma: subgroup analyses with focus on axitinib dosing and racial groups.

ESMO Open 2021 Jun 24;6(3):100105. Epub 2021 Apr 24.

Department of Medical Oncology, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France.

Background: The ATLAS trial, investigating adjuvant axitinib versus placebo in renal cell carcinoma (RCC), was stopped for futility at a preplanned interim analysis. We report subgroup outcome analyses by ethnicity, time on treatment, dose modification and toxicity.

Patients And Methods: Patient demographics, baseline characteristics, treatment duration and exposure and safety were analysed for Asian versus non-Asian patients treated with axitinib versus placebo. Read More

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Level of Vocabulary Development and Selected Elements Regarding Sensory Integration and Balance in 5-Year-Old Girls and Boys.

Children (Basel) 2021 Mar 7;8(3). Epub 2021 Mar 7.

Municipal Psychological and Pedagogical Clinic Complex, Kielce, 75-215 Koszalin, Poland.

The aim of this research was to assess relationships between the level of vocabulary and selected elements of sensory integration and balance in 5-year-old girls and boys, showing the differences between them. The study group consisted of 290 5-year-old children (172 boys and 118 girls) with different levels of vocabulary development and selected disturbances in sensory integration and balance processes. To evaluate the developmental deficits of speech with regard to vocabulary, the Children's Dictionary Test was used. Read More

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Fast Open-Source Toolkit for Water T2 Mapping in the Presence of Fat From Multi-Echo Spin-Echo Acquisitions for Muscle MRI.

Front Neurol 2021 26;12:630387. Epub 2021 Feb 26.

Department of Neurology, Buffalo Neuroimaging Analysis Center, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, United States.

Imaging has become a valuable tool in the assessment of neuromuscular diseases, and, specifically, quantitative MR imaging provides robust biomarkers for the monitoring of disease progression. Quantitative evaluation of fat infiltration and quantification of the T2 values of the muscular tissue's water component (wT2) are two of the most essential indicators currently used. As each voxel of the image can contain both water and fat, a two-component model for the estimation of wT2 must be used. Read More

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February 2021

Global Harmonization of Morphological Definitions in Hidradenitis Suppurativa for a Proposed Glossary.

JAMA Dermatol 2021 04;157(4):449-455

Department of Dermatology, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania.

Importance: Standard morphological terminology and definitions are vital for identification of lesion types in the clinical trial setting and communication about the condition. For hidradenitis suppurativa (HS), morphological definitions have been proposed by different groups, representing various regions of the world, but no international consensus has been reached regarding such definitions. A lack of globally harmonized terminology and definitions may contribute to poor-quality data collection in clinical trials as well as poor communication among clinicians, investigators, and patients. Read More

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Three-dimensional spatially resolved phase graph framework.

Magn Reson Med 2021 07 19;86(1):551-560. Epub 2021 Feb 19.

Department of Radiology, Medical Physics, Medical Center University of Freiburg, University of Freiburg, Freiburg, Germany.

Purpose: An open-source spatially resolved phase graph framework is proposed for simulating arbitrary pulse sequences in the presence of piece-wise constant gradients with arbitrary orientations in three dimensions. It generalizes the extended phase graph algorithm for analysis of nonperiodic sequences while preserving its efficiency, and is able to estimate the signal modulation in the 3D spatial domain.

Methods: The framework extends the recursive magnetization-evolution algorithm to account for anisotropic diffusion and exploits a novel 3D k-space grid-merging method to balance the computational effort and memory requirements against acceptable simulation errors. Read More

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The conect4children (c4c) Consortium: Potential for Improving European Clinical Research into Medicines for Children.

Pharmaceut Med 2021 03 4;35(2):71-79. Epub 2021 Feb 4.

Division of Pediatric Infectious Diseases, Department of Woman's and Child's Health, University of Padua, Padua, Italy.

The need for information about new and existing drugs used in children was recognized in the European Union (EU) with the implementation of the Paediatric Regulation in 2007. In 2017, the 10-year review of the Paediatric Regulation identified barriers to the conduct of clinical trials, including delays in setting up and completing paediatric trials. Across Europe, the difficulties with clinical research are compounded by variation within countries and between countries. Read More

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Dictionary-based protoacoustic dose map imaging for proton range verification.

Photoacoustics 2021 Mar 16;21:100240. Epub 2021 Jan 16.

Nuclear Physics Group, EMFTEL and IPARCOS, Faculty of Physical Sciences, University Complutense of Madrid, CEI Moncloa, 28040 Madrid, Spain.

Proton radiotherapy has the potential to provide state-of-the-art dose conformality in the tumor area, reducing possible adverse effects on surrounding organs at risk. However, uncertainties in the exact location of the proton Bragg peak inside the patient prevent this technique from achieving full clinical potential. In this context, verification of the range of protons in patients is key to reduce uncertainty margins. Read More

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Co-developing a common glossary with stakeholders for engagement on new genetic approaches for malaria control in a local African setting.

Malar J 2021 Jan 21;20(1):53. Epub 2021 Jan 21.

Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.

Stakeholder engagement is an essential pillar for the development of innovative public health interventions, including genetic approaches for malaria vector control. Scientific terminologies are mainly lacking in local languages, yet when research activities involve international partnership, the question of technical jargon and its translation is crucial for effective and meaningful communication with stakeholders. Target Malaria, a not-for-profit research consortium developing innovative genetic approaches to malaria vector control, carried out a linguistic exercise in Mali, Burkina Faso and Uganda to establish the appropriate translation of its key terminology to local languages of sites where the teams operate. Read More

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January 2021

A framework to identify structured behavioral patterns within rodent spatial trajectories.

Sci Rep 2021 01 11;11(1):468. Epub 2021 Jan 11.

Institute of Cognitive Sciences and Technologies (ISTC), National Research Council (CNR), Via San Martino della Battaglia 44, 00185, Rome, Italy.

Animal behavior is highly structured. Yet, structured behavioral patterns-or "statistical ethograms"-are not immediately apparent from the full spatiotemporal data that behavioral scientists usually collect. Here, we introduce a framework to quantitatively characterize rodent behavior during spatial (e. Read More

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January 2021

Social Media Insights Into US Mental Health During the COVID-19 Pandemic: Longitudinal Analysis of Twitter Data.

J Med Internet Res 2020 12 14;22(12):e21418. Epub 2020 Dec 14.

Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, United States.

Background: The COVID-19 pandemic led to unprecedented mitigation efforts that disrupted the daily lives of millions. Beyond the general health repercussions of the pandemic itself, these measures also present a challenge to the world's mental health and health care systems. Considering that traditional survey methods are time-consuming and expensive, we need timely and proactive data sources to respond to the rapidly evolving effects of health policy on our population's mental health. Read More

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December 2020

Implementation of a learning healthcare system for sickle cell disease.

JAMIA Open 2020 Oct 23;3(3):349-359. Epub 2020 Oct 23.

Nemours Sickle Cell Center of Biomedical Research Excellence (COBRE), Nemours Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA.

Objective: Using sickle cell disease (SCD) as a model, the objective of this study was to create a comprehensive learning healthcare system to support disease management and research. A multidisciplinary team developed a SCD clinical data dictionary to standardize bedside data entry and inform a scalable environment capable of converting complex electronic healthcare records (EHRs) into knowledge accessible in real time.

Materials And Methods: Clinicians expert in SCD care developed a data dictionary to describe important SCD-associated health maintenance and adverse events. Read More

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October 2020

Predictive article recommendation using natural language processing and machine learning to support evidence updates in domain-specific knowledge graphs.

JAMIA Open 2020 Oct 29;3(3):332-337. Epub 2020 Sep 29.

IBM Watson Health, Cambridge, Massachusetts, USA.

Objectives: Describe an augmented intelligence approach to facilitate the update of evidence for associations in knowledge graphs.

Methods: New publications are filtered through multiple machine learning study classifiers, and filtered publications are combined with articles already included as evidence in the knowledge graph. The corpus is then subjected to named entity recognition, semantic dictionary mapping, term vector space modeling, pairwise similarity, and focal entity match to identify highly related publications. Read More

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October 2020

Systematic classification of maternal and fetal intervention-related complications following open fetal myelomeningocele repair - results from a large prospective cohort.

BJOG 2021 06 30;128(7):1184-1191. Epub 2020 Nov 30.

Division of Obstetrics, University Hospital of Zurich, Zurich, Switzerland.

Objective: To systematically categorise all maternal and fetal intervention-related complications after open fetal myelomeningocele (fMMC) repair of the first 124 cases operated at the Zurich Centre for Fetal Diagnosis and Therapy.

Design: A prospective cohort study.

Setting: Single centre. Read More

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