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Unraveling the Interplay of Image Formation, Data Representation and Learning in CT-based COPD Phenotyping Automation: The Need for a Meta-Strategy.

Med Phys 2021 Jun 15. Epub 2021 Jun 15.

Siemens Healthineers, CT R&D Image Analytics, Forchheim, Germany.

Purpose: In the literature on automated phenotyping of Chronic Obstructive Pulmonary Disease (COPD), there is a multitude of isolated classical machine learning and deep learning techniques, mostly investigating individual phenotypes, with small study cohorts and heterogeneous meta-parameters, e.g. different scan protocols or segmented regions. Read More

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Going Backwards to Fill in the Missing Processes for Training and Evaluation of Clinical Bioethicists: What Has Been Needed for Decades to Move Real Professionalism Forward.

Evan G DeRenzo

J Clin Ethics 2021 ;32(2):149-154

John J. Lynch Center for Ethics, MedStar Washington Hospital Center, Washington, District of Columbia 20020 USA.

As the field of clinical bioethics has moved from its pioneers, who turned their attention to ethics problems in clinical medicine and clinical and animal research, to today's ubiquity of university degrees and fellowships in bioethics, there has been a steady drumbeat to professionalize the field. The problem has been that the necessary next steps-to specify the skills, knowledge, and personal and professional attributes of a clinical bioethicist, and to have a method to train and evaluate mastery of these standards-are lacking. Ordinarily, the path to professionalism in medicine starts with the intellectual pioneers. Read More

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January 2021

A computational method for learning disease trajectories from partially observable EHR data.

IEEE J Biomed Health Inform 2021 Jun 15;PP. Epub 2021 Jun 15.

Diseases can show different courses of progression even when patients share the same risk factors. Recent studies have revealed that the use of trajectories, the order in which diseases manifest throughout life, can be predictive of the course of progression. In this study, we propose a novel computational method for learning disease trajectories from EHR data. Read More

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Active Subdivision Surfaces for the Semiautomatic Segmentation of Biomedical Volumes.

IEEE Trans Image Process 2021 Jun 15;PP. Epub 2021 Jun 15.

We present a new family of active surfaces for the semiautomatic segmentation of volumetric objects in 3D biomedical images. We represent our deformable model by a subdivision surface encoded by a small set of control points and generated through a geometric refinement process. The subdivision operator confers important properties to the surface such as smoothness, reproduction of desirable shapes and interpolation of the control points. Read More

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"It's Really Like Any Other Study": Rural Radiology Facilities Performing Low-Dose Computed Tomography for Lung Cancer Screening.

Ann Am Thorac Soc 2021 Jun 15. Epub 2021 Jun 15.

Oregon Health & Science University, 6684, Portland, Oregon, United States.

Rationale: The majority of eligible people have not been screened for lung cancer. There is emerging evidence that there are location-based disparities applicable to lung cancer screening.

Objective: Describe lung cancer screening radiologic services in rural Oregon and understand the barriers and facilitators to implementation of lung cancer screening using LDCT. Read More

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Semi-Automated Creation of Density Functional Tight Binding Models through Leveraging Chebyshev Polynomial-Based Force Fields.

J Chem Theory Comput 2021 Jun 15. Epub 2021 Jun 15.

Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States.

Density functional tight binding (DFTB) is an attractive method for accelerated quantum simulations of condensed matter due to its enhanced computational efficiency over standard density functional theory (DFT) approaches. However, DFTB models can be challenging to determine for individual systems of interest, especially for metallic and interfacial systems where different bonding arrangements can lead to significant changes in electronic states. In this regard, we have created a rapid-screening approach for determining systematically improvable DFTB interaction potentials that can yield transferable models for a variety of conditions. Read More

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Analysis of covariance under variance heteroscedasticity in general factorial designs.

Stat Med 2021 Jun 14. Epub 2021 Jun 14.

Team Biostatistics and Big Medical Data, IDA Lab Salzburg, Paracelsus Medical University, Salzburg, Austria.

Adjusting for baseline values and covariates is a recurrent statistical problem in medical science. In particular, variance heteroscedasticity is non-negligible in experimental designs and ignoring it might result in false conclusions. Approximate inference methods are developed to test null hypotheses formulated in terms of adjusted treatment effects and regression parameters in general analysis of covariance designs with arbitrary numbers of factors. Read More

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Factor copula models for right-censored clustered survival data.

Lifetime Data Anal 2021 Jun 14. Epub 2021 Jun 14.

Department of Statistics, Federal University of Lavras, Lavras, Minas Gerais, Brazil.

In this article we extend the factor copula model to deal with right-censored event time data grouped in clusters. The new methodology allows for clusters to have variable sizes ranging from small to large and intracluster dependence to be flexibly modeled by any parametric family of bivariate copulas, thus encompassing a wide range of dependence structures. Incorporation of covariates (possibly time dependent) in the margins is also supported. Read More

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A human isogenic iPSC-derived cell line panel identifies major regulators of aberrant astrocyte proliferation in Down syndrome.

Commun Biol 2021 Jun 14;4(1):730. Epub 2021 Jun 14.

Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.

Astrocytes exert adverse effects on the brains of individuals with Down syndrome (DS). Although a neurogenic-to-gliogenic shift in the fate-specification step has been reported, the mechanisms and key regulators underlying the accelerated proliferation of astrocyte precursor cells (APCs) in DS remain elusive. Here, we established a human isogenic cell line panel based on DS-specific induced pluripotent stem cells, the XIST-mediated transcriptional silencing system in trisomic chromosome 21, and genome/chromosome-editing technologies to eliminate phenotypic fluctuations caused by genetic variation. Read More

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Cost-effectiveness analysis with unordered decisions.

Artif Intell Med 2021 Jul 20;117:102064. Epub 2021 Apr 20.

Department of Artificial Intelligence, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain. Electronic address:

Introduction: Cost-effectiveness analysis (CEA) is used increasingly in medicine to determine whether the health benefit of an intervention is worth the economic cost. Decision trees, the standard decision modeling technique for non-temporal domains, can only perform CEAs for very small problems. Influence diagrams can model much larger problems, but only when the decisions are totally ordered. Read More

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Influence of intrauterine growth status on aortic intima-media thickness and aortic diameter in near-term fetuses: a comparative cross-sectional study.

J Dev Orig Health Dis 2021 Jun 15:1-8. Epub 2021 Jun 15.

Maternal Fetal Medicine Unit, Department of Obstetrics and Gynaecology, Aga Khan University, Pakistan.

Intrauterine undernutrition may lead to fetal vascular programming. We compared abdominal aortic intima-media thickness (aIMT) and aortic diameter (aD) between appropriate for gestational age (AGA) and growth-restricted fetuses (GRF). We recruited 136 singleton fetuses at 34-37 weeks of gestation from Fetal Medicine Unit of Aga Khan University Hospital, Karachi (January-November 2017). Read More

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A cross-country comparison of malaria policy as a premise for contextualized appropriation of foreign aid in global health.

Health Res Policy Syst 2021 Jun 14;19(1):93. Epub 2021 Jun 14.

Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City, 235, Taiwan.

Background: Foreign aid continues to play an essential role in health sector development in low-resource countries, particularly in terms of providing a vital portion of their health expenditures. However, the relationship between foreign aid allocation and malaria policy formulation and/or implementation among state aid recipients remains unknown.

Methods: Publicly available data were collected with the country as observational unit to set up the conceptual framework. Read More

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Dye-sensitized solar cells under ambient light powering machine learning: towards autonomous smart sensors for the internet of things.

Chem Sci 2020 Feb 13;11(11):2895-2906. Epub 2020 Feb 13.

Department of Chemistry, Ångström Laboratory, Uppsala University P. O. Box 523 SE-75120 Uppsala Sweden.

The field of photovoltaics gives the opportunity to make our buildings ''smart'' and our portable devices "independent", provided effective energy sources can be developed for use in ambient indoor conditions. To address this important issue, ambient light photovoltaic cells were developed to power autonomous Internet of Things (IoT) devices, capable of machine learning, allowing the on-device implementation of artificial intelligence. Through a novel co-sensitization strategy, we tailored dye-sensitized photovoltaic cells based on a copper(ii/i) electrolyte for the generation of power under ambient lighting with an unprecedented conversion efficiency (34%, 103 μW cm at 1000 lux; 32. Read More

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February 2020

Chembot: A Machine Learning Approach to Selective Configuration Interaction.

J Chem Theory Comput 2021 Jun 14. Epub 2021 Jun 14.

Lawrence Livermore National Laboratory, Livermore, California 94550, United States.

We introduce a machine learning-based approach to selective configuration interaction, dubbed Chembot, that utilizes many novel choices for its model design and training. These choices include the use of a support vector machine to select important configurations, the use of the charge density matrix and configuration energy as features, and heuristics to improve the quality of training data. We test Chembot's ability to obtain near full configuration interaction quality energies and find that it definitively outperforms its purely Stochastic cousin Monte Carlo configuration interaction by requiring fewer iterations to converge, fewer determinants in the variational space, and fewer important configurations to achieve the same energy. Read More

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Dummy Atoms in Alchemical Free Energy Calculations.

J Chem Theory Comput 2021 Jun 14. Epub 2021 Jun 14.

Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria.

In calculations of relative free energy differences, the number of atoms of the initial and final states is rarely the same. This necessitates the introduction of dummy atoms. These placeholders interact with the physical system only by bonded energy terms. Read More

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COSMO-RS predictions of logP in the SAMPL7 blind challenge.

J Comput Aided Mol Des 2021 Jun 14. Epub 2021 Jun 14.

Dassault Systemes Deutschland GmbH, Imbacher Weg 46, 51379, Leverkusen, Germany.

We applied the COSMO-RS method to predict the partition coefficient logP between water and 1-octanol for 22 small drug like molecules within the framework of the SAMPL7 blind challenge. We carefully collected a set of thermodynamically meaningful microstates, including tautomeric forms of the neutral species, and calculated the logP using the current COSMOtherm implementation on the most accurate level. With this approach, COSMO-RS was ranked as the 6st most accurate method (Measured by the mean absolute error (MAE) of 0. Read More

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Improving Docking Power for Short Peptides Using Random Forest.

J Chem Inf Model 2021 Jun 14. Epub 2021 Jun 14.

Koliber Biosciences, Inc., 12265 World Trade Drive, Suite G, San Diego, California 92128, United States.

In recent years, therapeutic peptides have gained a lot interest as demonstrated by the 60 peptides approved as drugs in major markets and 150+ peptides currently in clinical trials. However, while small molecule docking is routinely used in rational drug design efforts, docking peptides has proven challenging partly because docking scoring functions, developed and calibrated for small molecules, perform poorly for these molecules. Here, we present random forest classifiers trained to discriminate correctly docked peptides. Read More

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Estimating costs for nitrate and perchlorate treatment for small drinking water systems.

AWWA Water Sci 2021 ;3(2)

US Environmental Protection Agency (USEPA), Cincinnati, Ohio.

When choosing a treatment technology for nitrate or perchlorate removal, drinking water utilities overwhelmingly choose ion exchange. However, of late, biological treatment and point-of-use systems have received a great deal of attention. This article utilizes several new U. Read More

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January 2021

Finding key players in complex networks through deep reinforcement learning.

Nat Mach Intell 2020 Jun 25;2(6):317-324. Epub 2020 May 25.

Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.

Finding an optimal set of nodes, called key players, whose activation (or removal) would maximally enhance (or degrade) certain network functionality, is a fundamental class of problems in network science. Potential applications include network immunization, epidemic control, drug design, and viral marketing. Due to their general NP-hard nature, those problems typically cannot be solved by exact algorithms with polynomial time complexity. Read More

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The Implementation of a Collaborative Pediatric Telesimulation Intervention in Rural Critical Access Hospitals.

AEM Educ Train 2021 Jul 31;5(3):e10558. Epub 2021 Jan 31.

Department of Pediatrics Johns Hopkins University School of Medicine Baltimore MD USA.

Background: Over 5.8 million pediatric visits to rural emergency department (EDs) occur each year in the United States. Most rural EDs care for less than five pediatric patients per day and are not well prepared for pediatrics. Read More

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The validity and reliability of an open source biosensing board to quantify heart rate variability.

Heliyon 2021 Jun 27;7(6):e07148. Epub 2021 May 27.

Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada.

Background: Heart rate variability (HRV) is a popular tool to quantify autonomic function. However, this typically requires an expensive 3-12 lead electrocardiogram (ECG) and BioAmp system. This investigation sought to determine the validity and reliability of an OpenBCI cyton biosensing board (open source) for accurately quantifying HRV. Read More

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Association of Mutation With Better Clinical Outcomes in NSCLC Patients Treated With Immune Checkpoint Blockades.

Front Oncol 2021 27;11:650122. Epub 2021 May 27.

Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong, China.

The common gamma receptor-dependent cytokines and their JAK-STAT pathways play important roles in T cell immunity and have been demonstrated to be related with response to immune checkpoint blockades (ICBs). PTPRD and PTPRT are phosphatases involved in JAK-STAT pathway. However, their clinical significance for non-small cell lung cancer (NSCLC) treated with ICBs is still unclear. Read More

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Only two out of five articles by New Zealand researchers are free-to-access: a multiple API study of access, citations, cost of Article Processing Charges (APC), and the potential to increase the proportion of open access.

PeerJ 2021 26;9:e11417. Epub 2021 May 26.

Office of the Provost, Massey University, Palmerston North, New Zealand.

We studied journal articles published by researchers at all eight New Zealand universities in 2017 to determine how many were freely accessible on the web. We wrote software code to harvest data from multiple sources, code that we now share to enable others to reproduce our work on their own sample set. In May 2019, we ran our code to determine which of the 2017 articles were open at that time and by what method; where those articles would have incurred an Article Processing Charge (APC) we calculated the cost if those charges had been paid. Read More

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An experimental approach for controlling confinement effects at catalyst interfaces.

Chem Sci 2020 Sep 11;11(40):11024-11029. Epub 2020 Sep 11.

Van 't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904 Amsterdam 1098 XH The Netherlands

Catalysts are conventionally designed with a focus on enthalpic effects, manipulating the Arrhenius activation energy. This approach ignores the possibility of designing materials to control the entropic factors that determine the pre-exponential factor. Here we investigate a new method of designing supported Pt catalysts with varying degrees of molecular confinement at the active site. Read More

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September 2020

Photo-crosslink analysis in nonribosomal peptide synthetases reveals aberrant gel migration of branched crosslink isomers and spatial proximity between non-neighboring domains.

Chem Sci 2020 Aug 11;11(33):8945-8954. Epub 2020 Aug 11.

Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Muenster D-48149 Münster Germany

Nonribosomal peptide synthetases (NRPSs) are large, multi-modular enzyme templates for the biosynthesis of important peptide natural products. Modules are composed of a set of semi-autonomous domains that facilitate the individual reaction steps. Only little is known about the existence and relevance of a higher-order architecture in these mega-enzymes, for which contacts between non-neighboring domains in three-dimensional space would be characteristic. Read More

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Explore the Underlying Mechanism Between Atopic Dermatitis and Major Depressive Disorder.

Front Genet 2021 28;12:640951. Epub 2021 May 28.

Human Biochemical Genetics Section, National Institutes of Health, Bethesda, MD, United States.

Adult patients with atopic dermatitis (AD) present relatively higher rates of major depressive disorder (MDD). However, the underlying mechanism is largely unknown. Here, we first conducted a systematic literature-based data mining to identify entities linking AD and MDD, including proteins, cells, functional classes, and small molecules. Read More

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Genomics-Enabled Novel Insight Into the Pathovar-Specific Population Structure of the Bacterial Leaf Streak Pathogen in Small Grain Cereals.

Front Microbiol 2021 28;12:674952. Epub 2021 May 28.

Department of Plant Protection, University of Tehran, Karaj, Iran.

The Gram-negative bacterium infects a wide range of gramineous plants with a notable impact on small grain cereals. However, genomics-informed intra-species population structure and virulence repertories of the pathogen have rarely been investigated. In this study, the complete genome sequences of seven strains representing an entire set of genetic diversity of two pathovars pv. Read More

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The Aerobic and Anaerobic Contribution During Repeated 30-s Sprints in Elite Cyclists.

Front Physiol 2021 26;12:692622. Epub 2021 May 26.

Centre for Elite Sports Research, Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, Trondheim, Norway.

Although the ability to sprint repeatedly is crucial in road cycling races, the changes in aerobic and anaerobic power when sprinting during prolonged cycling has not been investigated in competitive elite cyclists. Here, we used the gross efficiency (GE)-method to investigate: (1) the absolute and relative aerobic and anaerobic contributions during 3 × 30-s sprints included each hour during a 3-h low-intensity training (LIT)-session by 12 cyclists, and (2) how the energetic contribution during 4 × 30-s sprints is affected by a 14-d high-volume training camp with (SPR, = 9) or without (CON, = 9) inclusion of sprints in LIT-sessions. The aerobic power was calculated based on GE determined before, after sprints, or the average of the two, while the anaerobic power was calculated by subtracting the aerobic power from the total power output. Read More

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Short-term prediction of COVID-19 spread using grey rolling model optimized by particle swarm optimization.

Zeynep Ceylan

Appl Soft Comput 2021 Jun 9:107592. Epub 2021 Jun 9.

Samsun University, Faculty of Engineering, Industrial Engineering Department, 55420, Samsun, Turkey.

The prediction of the spread of coronavirus disease 2019 (COVID-19) is vital in taking preventive and control measures to reduce human health damage. The Grey Modeling (1,1) is a popular approach used to construct a predictive model with a small-sized data set. In this study, a hybrid model based on grey prediction and rolling mechanism optimized by particle swarm optimization algorithm (PSO) was applied to create short-term estimates of the total number of confirmed COVID-19 cases for three countries, Germany, Turkey, and the USA. Read More

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Simplifying Computer Aided Ergonomics: A User-Product Interaction-Modeling Framework in CAD based on a Taxonomy of Elementary Affordances.

IISE Trans Occup Ergon Hum Factors 2021 Jun 13:1-16. Epub 2021 Jun 13.

Engineering Design (KTmfk), Friedrich-Alexander-Universität Erlangen-Nürnberg.

Occupational ApplicationsThis contribution provides a framework for modeling user-product interactions (in CAD) for in-depth ergonomic analysis of product design, using digital human models. The framework aims to be applicable to a wide range of different products while being suitable for designers - especially those who do not have specialized ergonomic expertise or training in human behavior - by providing an intuitive, standardized, and time-efficient modeling procedure. The framework contains 31 elementary affordances, which describe mechanical dependencies between product geometries and human end effectors. Read More

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