58,748 results match your criteria computational approach


Learning Electron Densities in the Condensed Phase.

J Chem Theory Comput 2021 Oct 20. Epub 2021 Oct 20.

Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.

We introduce a local machine-learning method for predicting the electron densities of periodic systems. The framework is based on a numerical, atom-centered auxiliary basis, which enables an accurate expansion of the all-electron density in a form suitable for learning isolated and periodic systems alike. We show that, using this formulation, the electron densities of metals, semiconductors, and molecular crystals can all be accurately predicted using symmetry-adapted Gaussian process regression models, properly adjusted for the nonorthogonal nature of the basis. Read More

View Article and Full-Text PDF
October 2021

Mobile PCR-based surveillance for SARS-CoV-2 to reduce visiting restrictions in nursing homes during the COVID-19 pandemic: a pilot study.

Infection 2021 Oct 20. Epub 2021 Oct 20.

Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, North Rhine-Westphalia, Germany.

Purpose: Residents in nursing homes for the elderly (NH) are at high risk for death from COVID-19. We investigated whether repeated non-mandatory RT-PCR SARS-CoV-2 surveillance of NH staff and visitors reduces COVID-19 incidence rates in NH residents and allows to reduce visiting restrictions.

Methods: This pilot study at the beginning of the COVID-19 pandemic compared a surveillance approach of regular, twice-weekly voluntary PCR testing of health-care workers (HCW) and visitors in interventional NH (INH) with a setting without regular testing in control NH (CNH). Read More

View Article and Full-Text PDF
October 2021

OMEX metadata specification (version 1.2).

J Integr Bioinform 2021 Oct 20. Epub 2021 Oct 20.

University of Greifswald, Greifswald, Germany.

A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models and data, and enable semantic comparisons between models. Motivated by these potential benefits and guided by consensus across the COmputational Modeling in BIology NEtwork (COMBINE) community, we have developed a specification for encoding annotations in Open Modeling and EXchange (OMEX)-formatted archives. This document details version 1. Read More

View Article and Full-Text PDF
October 2021

SOMA: Subject-, Object-, and Modality-Adapted Precision Atlas Approach for Automatic Anatomy Recognition and Delineation in Medical Images.

Med Phys 2021 Oct 19. Epub 2021 Oct 19.

Medical Image Processing Group, Department of Radiology, University of Pennsylvania, 602 Goddard building, 3710 Hamilton Walk, Philadelphia, 19104, United States.

Purpose: In the multi-atlas segmentation (MAS) method, a large enough atlas set which can cover the complete spectrum of the whole population pattern of the target object will benefit the segmentation quality. However, the difficulty in obtaining and generating such a large set of atlases and the computational burden required in the segmentation procedure make this approach impractical. In this paper, we propose a method called SOMA to select subject-, object-, and modality-adapted precision atlases for automatic anatomy recognition in medical images with pathology, following the idea that different regions of the target object in a novel image can be recognized by different atlases with regionally best similarity, so that effective atlases have no need to be globally similar to the target subject and also have no need to be overall similar to the target object. Read More

View Article and Full-Text PDF
October 2021

Mapping input noise to escape noise in integrate-and-fire neurons: a level-crossing approach.

Authors:
Tilo Schwalger

Biol Cybern 2021 Oct 19. Epub 2021 Oct 19.

Institute of Mathematics, Technical University Berlin, 10623, Berlin, Germany.

Noise in spiking neurons is commonly modeled by a noisy input current or by generating output spikes stochastically with a voltage-dependent hazard rate ("escape noise"). While input noise lends itself to modeling biophysical noise processes, the phenomenological escape noise is mathematically more tractable. Using the level-crossing theory for differentiable Gaussian processes, we derive an approximate mapping between colored input noise and escape noise in leaky integrate-and-fire neurons. Read More

View Article and Full-Text PDF
October 2021

A novel chemical biology and computational approach to expedite the discovery of new-generation polymyxins against life-threatening .

Chem Sci 2021 Sep 19;12(36):12211-12220. Epub 2021 Aug 19.

Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702.

Multidrug-resistant Gram-negative bacteria represent a major medical challenge worldwide. New antibiotics are desperately required with 'old' polymyxins often being the only available therapeutic option. Here, we systematically investigated the structure-activity relationship (SAR) of polymyxins using a quantitative lipidomics-informed outer membrane (OM) model of and a series of chemically synthesized polymyxin analogs. Read More

View Article and Full-Text PDF
September 2021

High five! Methyl probes at five ring positions of phenylalanine explore the hydrophobic core dynamics of zinc finger miniproteins.

Chem Sci 2021 Sep 24;12(34):11455-11463. Epub 2021 Jul 24.

Philipps-University Marburg 35043 Marburg Germany

The elucidation of internal dynamics in proteins is essential for the understanding of their stability and functionality. Breaking the symmetry of the degenerate rotation of the phenyl side chain provides additional structural information and allows a detailed description of the dynamics. Based on this concept, we propose a combination of synthetic and computational methods, to study the rotational mobility of the Phe ring in a sensitive zinc finger motif. Read More

View Article and Full-Text PDF
September 2021

DNA-methylation patterns imply a common cellular origin of virus- and UV-associated Merkel cell carcinoma.

Oncogene 2021 Oct 19. Epub 2021 Oct 19.

Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany.

Merkel cell carcinoma (MCC) is a neuroendocrine tumor either induced by integration of the Merkel cell polyomavirus into the cell genome or by accumulation of UV-light-associated mutations (VP-MCC and UV-MCC). Whether VP- and UV-MCC have the same or different cellular origins is unclear; with mesenchymal or epidermal origins discussed. DNA-methylation patterns have a proven utility in determining cellular origins of cancers. Read More

View Article and Full-Text PDF
October 2021

Global quantification exposes abundant low-level off-target activity by base editors.

Genome Res 2021 Oct 19. Epub 2021 Oct 19.

Tel Aviv University.

Base editors are dedicated engineered deaminases that enable directed conversion of specific bases in the genome or transcriptome in a precise and efficient manner, and hold promise for correcting pathogenic mutations. A major concern limiting application of this powerful approach is the issue of off-target edits. Several recent studies have shown substantial off-target RNA activity induced by base editors and demonstrated that off-target mutations may be suppressed by improved deaminases versions or optimized guide RNAs. Read More

View Article and Full-Text PDF
October 2021

Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry.

J Chem Theory Comput 2021 Oct 20. Epub 2021 Oct 20.

Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy.

The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical-chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of the role played by dynamical and environmental effects in tuning their overall behavior. For small semi-rigid systems in the gas phase, state-of-the-art quantum chemical computations rival the most sophisticated experimental (from, for example, high-resolution spectroscopy) results. For larger molecules, more effective computational approaches must be devised. Read More

View Article and Full-Text PDF
October 2021

Reply to the 'Comment on "Exploiting electronic strategies to stabilize a planar tetracoordinate carbon in cyclic aromatic hydrocarbons"' by V. S. Thimmakondu, , 2019, DOI: 10.1039/c9cc04639a.

Chem Commun (Camb) 2019 Oct 17;55(84):12721-12722. Epub 2019 Oct 17.

Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, Santiago, Chile.

The effectiveness of our proposed approach to stabilize a planar tetracoordinate carbon (ptC) in cyclic aromatic hydrocarbons, introduced in the title article, is unquestionable as our exhaustive searches on the singlet and triplet potential energy surfaces of the new ptC molecules identified as viable species are reproducible. Besides, the diagnostic value for the SiCH system reported in the comment seems to be the amplitudes. We recomputed the diagnostic value using different software (Gaussian and ORCA), which gave similar values to that reported in our communication. Read More

View Article and Full-Text PDF
October 2019

A Probabilistic Programming Approach to Protein Structure Superposition.

Proc IEEE Symp Comput Intell Bioinforma Comput Biol 2019 Jul 8;2019. Epub 2019 Aug 8.

Department of Computer Science. University of Copenhagen, Denmark.

Optimal superposition of protein structures or other biological molecules is crucial for understanding their structure, function, dynamics and evolution. Here, we investigate the use of probabilistic programming to superimpose protein structures guided by a Bayesian model. Our model THESEUS-PP is based on the THESEUS model, a probabilistic model of protein superposition based on rotation, translation and perturbation of an underlying, latent mean structure. Read More

View Article and Full-Text PDF

A functional approach for characterizing safety risk of signalized intersections at the movement level: An exploratory analysis.

Accid Anal Prev 2021 Oct 16;163:106446. Epub 2021 Oct 16.

Department of Civil and Urban Engineering, New York University, 6 MetroTech Center 4th Floor, Brooklyn, NY 11201, USA. Electronic address:

Safety evaluation of signalized intersections is often conducted by developing statistical and data-driven methods based on data aggregated at certain temporal and spatial levels (e.g., yearly, hourly, or per signal cycle; intersection or approach leg). Read More

View Article and Full-Text PDF
October 2021

Innovation in regulatory approaches for endocrine disrupting chemicals: The journey to risk assessment modernization in Canada.

Environ Res 2021 Oct 16:112225. Epub 2021 Oct 16.

Institut National de la Recherche Scientifique (INRS), Centre Eau Terre Environnement, Quebec City, QC, Canada.

Globally, regulatory authorities grapple with the challenge of assessing the hazards and risks to human and ecosystem health that may result from exposure to chemicals that disrupt the normal functioning of endocrine systems. Rapidly increasing number of chemicals in commerce, coupled with the reliance on traditional, costly animal experiments - often with limited sensitivity to many important mechanisms of endocrine disruption,- for hazard characterization, presents ongoing challenges for chemical regulation. The consequence is a limited number of chemicals for which there is sufficient data to assess if there is endocrine toxicity and hence few chemicals with thorough hazard characterization. Read More

View Article and Full-Text PDF
October 2021

Estimating ectopic beat probability with simplified statistical models that account for experimental uncertainty.

PLoS Comput Biol 2021 Oct 19;17(10):e1009536. Epub 2021 Oct 19.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America.

Ectopic beats (EBs) are cellular arrhythmias that can trigger lethal arrhythmias. Simulations using biophysically-detailed cardiac myocyte models can reveal how model parameters influence the probability of these cellular arrhythmias, however such analyses can pose a huge computational burden. Here, we develop a simplified approach in which logistic regression models (LRMs) are used to define a mapping between the parameters of complex cell models and the probability of EBs (P(EB)). Read More

View Article and Full-Text PDF
October 2021

A data-driven approach for constructing mutation categories for mutational signature analysis.

PLoS Comput Biol 2021 Oct 19;17(10):e1009542. Epub 2021 Oct 19.

Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America.

Mutational processes shape the genomes of cancer patients and their understanding has important applications in diagnosis and treatment. Current modeling of mutational processes by identifying their characteristic signatures views each base substitution in a limited context of a single flanking base on each side. This context definition gives rise to 96 categories of mutations that have become the standard in the field, even though wider contexts have been shown to be informative in specific cases. Read More

View Article and Full-Text PDF
October 2021

Content and Dynamics of Websites Shared over Vaccine-Related Tweets in COVID-19 Conversations: A Computational Analysis.

J Med Internet Res 2021 Oct 2. Epub 2021 Oct 2.

Translational Data Analytics Institute, The Ohio State University, Colombus, US.

Background: The onset of the Coronavirus disease 2019 (COVID-19) pandemic and the consequent "infodemic" increased concerns about Twitter's role in advancing anti-vaccination messages, even before a vaccine became available to the public. New computational methods allow for analysis of cross-platform use by tracking links to websites shared over Twitter, which in turn can uncover some of the content and dynamics of information sources and agenda setting processes. Such understanding can advance theory and efforts to reduce misinformation. Read More

View Article and Full-Text PDF
October 2021

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Mol Syst Biol 2021 Oct;17(10):e10387

Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Read More

View Article and Full-Text PDF
October 2021

Self-assembling, structure and nonlinear optical properties of fluorescent organic nanoparticles in water.

Phys Chem Chem Phys 2021 Oct 19. Epub 2021 Oct 19.

Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, F-33400 Talence, France.

Owing to their intense emission, low toxicity and solubility in aqueous medium, fluorescent organic nanoparticles (FONs) have emerged as promising alternatives to inorganic ones for the realization of exogenous probes for bioimaging applications. However, the intimate structure of FONs in solution, as well as the role played by intermolecular interactions on their optical properties, remains challenging to study. Following a recent Second-Harmonic Scattering (SHS) investigation led by two of us [Daniel , , 2015, , 1209], we report herein a computational study of the structural organization and second-order nonlinear optical (NLO) properties of FONs based on dipolar chromophores incorporating a hydrophobic triphenylamine electron-donating unit and a slightly hydrophilic aldehyde electron-withdrawing unit at their extremities. Read More

View Article and Full-Text PDF
October 2021

Comparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders.

Sci Rep 2021 Oct 18;11(1):20607. Epub 2021 Oct 18.

North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK.

The development of computational methods to assess pathogenicity of pre-messenger RNA splicing variants is critical for diagnosis of human disease. We assessed the capability of eight algorithms, and a consensus approach, to prioritize 249 variants of uncertain significance (VUSs) that underwent splicing functional analyses. The capability of algorithms to differentiate VUSs away from the immediate splice site as being 'pathogenic' or 'benign' is likely to have substantial impact on diagnostic testing. Read More

View Article and Full-Text PDF
October 2021

Electronic and optical properties of bulk and surface of CsPbBr inorganic halide perovskite a first principles DFT 1/2 approach.

Sci Rep 2021 Oct 18;11(1):20622. Epub 2021 Oct 18.

Physical Sciences Research Center (PSRC), Department of Physics, Pachhunga University College, Mizoram University, Aizawl, India.

This work aims to test the effectiveness of newly developed DFT-1/2 functional in calculating the electronic and optical properties of inorganic lead halide perovskites CsPbBr. Herein, from DFT-1/2 we have obtained the direct band gap of 2.36 eV and 3. Read More

View Article and Full-Text PDF
October 2021

Marantodes pumilum: Systematic computational approach to identify their therapeutic potential and effectiveness.

J Ethnopharmacol 2021 Oct 15:114751. Epub 2021 Oct 15.

Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; Tasik Chini Research Centre, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. Electronic address:

Ethnopharmacological Relevance: Marantodes pumilum (MP) herbs, locally known as Kacip Fatimah, are widely used traditionally to improve women's health. The herb is frequently used for gynecological issues such as menstrual problems, facilitating and quickening delivery, post-partum medication, treats flatulence and dysentery, and. MP extracts are thought to aid in the firming and toning of abdominal muscles, tighten breasts and vaginal muscles, and anti-dysmenorrhea. Read More

View Article and Full-Text PDF
October 2021

Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions.

PLoS Comput Biol 2021 Oct 18;17(10):e1009321. Epub 2021 Oct 18.

Société Française de Bioinformatique Executive Board, Paris, France.

In 2020, the world faced the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic that drastically altered people's lives. Since then, many countries have been forced to suspend public gatherings, leading to many conference cancellations, postponements, or reorganizations. Switching from a face-to-face to a remote conference became inevitable and the ultimate solution to sustain scientific exchanges at the national and the international levels. Read More

View Article and Full-Text PDF
October 2021

Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities.

PLoS Comput Biol 2021 Oct 18;17(10):e1008952. Epub 2021 Oct 18.

Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.

Biochemical systems consist of numerous elementary reactions governed by the law of mass action. However, experimentally characterizing all the elementary reactions is nearly impossible. Thus, over a century, their deterministic models that typically contain rapid reversible bindings have been simplified with non-elementary reaction functions (e. Read More

View Article and Full-Text PDF
October 2021

Few-shot learning for deformable image registration in 4DCT images.

Br J Radiol 2021 Oct 18:20210819. Epub 2021 Oct 18.

School of Software Engineering, South China University of Technology, Guangzhou, Guangdong, China.

Objectives: To develop a rapid and accurate 4D deformable image registration (DIR) approach for online adaptive radiotherapy.

Methods: We propose a deep learning (DL)-based few-shot registration network (FR-Net) to generate deformation vector fields from each respiratory phase to an implicit reference image, thereby mitigating the bias introduced by the selection of reference images. The proposed FR-Net is pretrained with limited unlabeled 4D data and further optimized by maximizing the intensity similarity of one specific four-dimensional computed tomography (4DCT) scan. Read More

View Article and Full-Text PDF
October 2021

A heuristic algorithm for medical staff's scheduling problems with multiskills and vacation control.

Sci Prog 2021 Sep;104(3_suppl):368504211050301

Department of Industrial Management, 63370National Formosa University, Yunlin 632.

Introduction: The main issue related to the duty schedule is to allocate medical staff to each medical department by considering personnel skills and personal vocation preferences. However, how to effectively use staff's multiskill characteristics and how to execute vocation control have not been well investigated.

Objectives: This article aims to develop duty scheduling and vacation permission decisions to minimize the sum of customers' waiting costs, the overtime cost of medical staff, the cost of failing to meet medical staff' vacation requirements, and the cost of mutual support between departments. Read More

View Article and Full-Text PDF
September 2021

Insight into the Mechanism and Regioselectivity of Pd(OAc)-Catalyzed C-O Bond Activation via a β-O Elimination Approach: A Computational Study.

J Phys Chem A 2021 Oct 18. Epub 2021 Oct 18.

College of Chemistry, Key Lab of Green Chemistry and Technology in the Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China.

The density functional theory investigations were carried out to elucidate the mechanism and the origin of regioselectivity for the Pd(OAc)-catalyzed carbon-oxygen bond activation in the reaction between 4-phenoxy--(quinolin-8-yl) butanamide and -methylindole. The reaction proceeded through four main stages in succession: C-H activation, β-O elimination, nucleo-palladation of the new C-C bond formation, and proto-depalladation steps. A total of six pathways were considered since there were two possible forms of C-O bond breaking in the β-O elimination step and six reaction channels of nucleophilic attack in the crucial nucleo-palladation step. Read More

View Article and Full-Text PDF
October 2021

Multitask CapsNet: An Imbalanced Data Deep Learning Method for Predicting Toxicants.

ACS Omega 2021 Oct 29;6(40):26545-26555. Epub 2021 Sep 29.

Key Laboratory of Medical Electrophysiology, Ministry of Education of China, Medical Key Laboratory for Drug Discovery and Druggability Evaluation of Sichuan Province, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Luzhou 646000, China.

Drug development has a high failure rate, with safety properties constituting a considerable challenge. To reduce risk, in silico tools, including various machine learning methods, have been applied for toxicity prediction. However, these approaches often confront a serious problem: the training data sets are usually biased (imbalanced positive and negative samples), which would result in model training difficulty and unsatisfactory prediction accuracy. Read More

View Article and Full-Text PDF
October 2021

Search for RNA aptamers against non-structural protein of SARS-CoV-2: Design using molecular dynamics approach.

Beni Suef Univ J Basic Appl Sci 2021 12;10(1):64. Epub 2021 Oct 12.

Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, India.

Background: Recent outbreak of deadly Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) urges the scientist to identify the potential vaccine or drug to control the disease. SARS-CoV-2 with its single stranded RNA genome (length ~ 30 kb) is enveloped with active spike proteins. The genome is non-segmental with 5'-cap and 3'-poly tail and acts as a mRNA for the synthesis of replicase polyproteins. Read More

View Article and Full-Text PDF
October 2021

Coronary Computed Tomography Angiography Assessment of High-Risk Plaques in Predicting Acute Coronary Syndrome.

Front Cardiovasc Med 2021 1;8:743538. Epub 2021 Oct 1.

Department of Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.

Coronary computed tomography angiography (CCTA) is a comprehensive, non-invasive and cost-effective imaging assessment approach, which can provide the ability to identify the characteristics and morphology of high-risk atherosclerotic plaques associated with acute coronary syndrome (ACS). The development of CCTA and latest advances in emerging technologies, such as computational fluid dynamics (CFD), have made it possible not only to identify the morphological characteristics of high-risk plaques non-invasively, but also to assess the hemodynamic parameters, the environment surrounding coronaries and so on, which may help to predict the risk of ACS. In this review, we present how CCTA was used to characterize the composition and morphology of high-risk plaques prone to ACS and the current role of CCTA, including emerging CCTA technologies, advanced analysis, and characterization techniques in prognosticating the occurrence of ACS. Read More

View Article and Full-Text PDF
October 2021