8,966 results match your criteria bayesian inference

Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction.

Bioinformatics 2021 May 12. Epub 2021 May 12.

Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea.

Motivation: Characterizing drug-protein interactions is crucial to the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict drug-protein interactions without human trial and error. However, because data labeling requires significant resources, the available protein data size is relatively small, which consequently decreases model performance. Read More

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(Urticaceae), a new species from limestone karst in Guangxi, China.

PeerJ 2021 19;9:e11148. Epub 2021 Apr 19.

Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China.

L.F. Fu, A. Read More

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Phylogeography and genetic diversity of the widespread katydid (Thunberg, 1815) across China.

Ecol Evol 2021 May 8;11(9):4276-4294. Epub 2021 Mar 8.

College of Life Science Institute of Life Science and Green Development Hebei University Baoding China.

Habitat fragmentation can lower migration rates and genetic connectivity among remaining populations of native species. is one of the most widespread katydids in China, but little is known about its genetic structure and phylogeographic distribution. We combined the five-prime region of cytochrome c oxidase subunit I (COI-5P), 11 newly developed microsatellite loci coupled with an ecological niche model (ENM) to examine the genetic diversity and population structure of in China and beyond to Laos and Singapore. Read More

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Correlation analysis to investigate unconscious mental processes: A critical appraisal and mini-tutorial.

Cognition 2021 May 8;212:104667. Epub 2021 May 8.

University College London, United Kingdom.

As a method to investigate the scope of unconscious mental processes, researchers frequently obtain concurrent measures of task performance and stimulus awareness across participants. Even though both measures might be significantly greater than zero, the correlation between them might not, encouraging the inference that an unconscious process drives task performance. We highlight the pitfalls of this null-correlation approach and provide a mini-tutorial on ways to avoid them. Read More

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Morphological and Molecular Data Reveal Two New Species of Viannaia (Nematoda: Viannaiidae), Parasitizing Opossums (Mammalia: Didelphidae) in Mexico.

J Parasitol 2021 May;107(3):388-403

Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Ciudad Universitaria, C. P. 04510, Mexico City, Mexico.

Two new species of Viannaia from the intestine of the North American opossums, Didelphis virginiana (Virginia opossum), and Philander opossum (gray four-eyed opossum), are described based on morphological and molecular data, through an integrative taxonomic approach. Maximum likelihood and Bayesian inference analyses for each dataset and the concatenated dataset were performed using a mitochondrial cytochrome c oxidase subunit 1 (COI) gene, and the nuclear ribosomal internal transcribed spacer region (ITS1-5.8S-ITS2). Read More

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First Report of Causing Anthracnose of Guava () in Mexico.

Plant Dis 2021 May 10. Epub 2021 May 10.

Centro de Investigación en Alimentación y Desarrollo, Coordinación Culiacán, Carretera El Dorado Km 5.5, Campo el Diez, Culiacán, Sinaloa, Mexico, 80110;

Guava ( L.) is a small tree belonging to the Myrtaceae family and it is distributed worldwide in the tropical and subtropical areas. During the summer of 2019, symptoms of fruit anthracnose were observed on approx. Read More

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The complete mitochondrial genome of the freshwater crab Türkay and Dai 1997 (Decapoda: Brachyura: Potamoidea).

Mitochondrial DNA B Resour 2021 Apr 26;6(4):1554-1556. Epub 2021 Apr 26.

School of Basic Medical Sciences, Research lab of Freshwater Crustacean Decapoda & Paragonimus, Nanchang University, Nanchang, PR China.

We report the complete mitochondrial genome of for the first time, which is found to be 17,612 base pairs in length, and contains 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA), and 1 non-coding AT-rich region known as the D-loop. In addition, the mitogenome has 17 intergenic regions ranging from 1 to 1512 bp in length. The mitochondrial genome of is the first mitochondrial genome under the genus , providing DNA data for species identification, enriching the species diversity of Brachyura. Read More

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Short-term and long-term survival of patients with gastric cancer.

Gastroenterol Hepatol Bed Bench 2021 ;14(2):115-122

Department of Biostatistics and Epidemiology, Kerman University of Medical Sciences, Kerman, Islamic Republic of Iran.

Aim: The aim of this study was to apply the Bayesian mixture cure rate frailty model to determine the factors that influence short-term and long-term survival of patients with gastric cancer.

Background: Determining the risk factors of gastric cancer is currently considered very important, because the disease has become one of the most dangerous types of mortal cancers. Therefore, it is possible to determine the effective risk factors of short-term and long-term survival in patients through utilizing this model. Read More

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January 2021

Evaluating the monophyly of series (Cactaceae).

PhytoKeys 2021 28;177:25-42. Epub 2021 Apr 28.

Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico.

(Cactaceae) taxonomy has been historically problematic due to the morphological variability and sympatry of the species. This has led to several proposals for infrageneric classification, including subgeneric, section and series categories. Mammillaria ser. Read More

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A Bayesian inference approach to quantify average pathogen loads in farmyard manure and slurry using open-source Irish datasets.

Sci Total Environ 2021 Apr 30;786:147474. Epub 2021 Apr 30.

University College Dublin, School of Biosystems and Food Engineering, Belfield, Dublin 4, Ireland. Electronic address:

Farm-to-fork quantitative microbial risk assessments (QMRA) typically start with a preliminary estimate of initial concentration (C) of microorganism loading at farm level, consisting of an initial estimate of prevalence (P) and the resulting pathogen levels in animal faeces. An average estimation of the initial concentration of pathogens can be achieved by combining P estimates in animal populations and the levels of pathogens in colonised animals' faeces and resulting cumulative levels in herd farmyard manure and slurry (FYM&S). In the present study, 14 years of data were collated and assessed using a Bayesian inference loop to assess the likely P of pathogens. Read More

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A new regression model for overdispersed binomial data accounting for outliers and an excess of zeros.

Stat Med 2021 May 7. Epub 2021 May 7.

Department of Economics, Management and Statistics, University of Milano-Bicocca, Milan, Italy.

Binary outcomes are extremely common in biomedical research. Despite its popularity, binomial regression often fails to model this kind of data accurately due to the overdispersion problem. Many alternatives can be found in the literature, the beta-binomial (BB) regression model being one of the most popular. Read More

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Recombination patterns in coronaviruses.

bioRxiv 2021 Apr 28. Epub 2021 Apr 28.

As shown during the SARS-CoV-2 pandemic, phylogenetic and phylodynamic methods are essential tools to study the spread and evolution of pathogens. One of the central assumptions of these methods is that the shared history of pathogens isolated from different hosts can be described by a branching phylogenetic tree. Recombination breaks this assumption. Read More

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The mitochondrial genome of (Diptera: Dolichopodidae).

Mitochondrial DNA B Resour 2021 Apr 15;6(4):1419-1420. Epub 2021 Apr 15.

Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.

The long-legged fly belongs to the subfamily Diaphorinae of Dolichopodidae. The mitogenome of was sequenced, the first representative complete mitogenome from this subfamily. This mitogenome is 15,385 bp in size, includes 13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs. Read More

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Fossils improve phylogenetic analyses of morphological characters.

Proc Biol Sci 2021 May 5;288(1950):20210044. Epub 2021 May 5.

Department of Earth Sciences, University of Oxford, Oxford, UK.

Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. Read More

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Optimal attentional allocation in the presence of capacity constraints in uncued and cued visual search.

J Vis 2021 May;21(5)

Department of Brain and Cognitive Sciences, University of Rochester, Rochester, NY, USA.

The vision sciences literature contains a large diversity of experimental and theoretical approaches to the study of visual attention. We argue that this diversity arises, at least in part, from the field's inability to unify differing theoretical perspectives. In particular, the field has been hindered by a lack of a principled formal framework for simultaneously thinking about both optimal attentional processing and capacity-limited attentional processing, where capacity is limited in a general, task-independent manner. Read More

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Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel.

J Chem Phys 2021 Apr;154(16):165102

Department of Chemistry, Columbia University, New York, New York 10027, USA.

As the first potassium channel with an x-ray structure determined, and given its homology to eukaryotic channels, the pH-gated prokaryotic channel KcsA has been extensively studied. Nevertheless, questions related, in particular, to the allosteric coupling between its gates remain open. The many currently available x-ray crystallography structures appear to correspond to various stages of activation and inactivation, offering insights into the molecular basis of these mechanisms. Read More

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A new elastic characterization method for anisotropic bilayer specimens via Bayesian resonant ultrasound spectroscopy.

Ultrasonics 2021 Apr 24;115:106455. Epub 2021 Apr 24.

Materials Department, University of California, Santa Barbara, CA 93106, USA.

A novel nondestructive method for complete elastic characterization of substrate-coating bilayer specimens with distinct anisotropic layers via resonant ultrasound spectroscopy (RUS) and Bayesian inversion is developed here. Bayesian formulations of the RUS inversion problem-of quantifying elastic properties given a measured list of resonance frequencies recorded from a single, typically small, precisely fabricated, macroscopically homogeneous, linear-elastic specimen-are a recent development. Here we report the first Bayesian formulation of the bilayer problem, and through a series of practical examples, demonstrate novel parameter estimation capabilities of our open-source CmdStan-RUS code. Read More

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Error rates in SARS-CoV-2 testing examined with Bayes' theorem.

P M Bentley

Heliyon 2021 Apr 28;7(4):e06905. Epub 2021 Apr 28.

European Spallation Source ESS ERIC, Box 176, SE-221 00 Lund, Sweden.

The SARS-CoV-2 pandemic has created a demand for large scale testing, as part of the effort to understand and control transmission. It is important to quantify the error rates of test equipment under field conditions, which might differ significantly from those obtained in the laboratory. A literature review on SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR) is used to construct a test confusion matrix. Read More

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Complete chloroplast genomes of Achnatherum inebrians and comparative analyses with related species from Poaceae.

FEBS Open Bio 2021 May 1. Epub 2021 May 1.

State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China.

This article reports the complete chloroplast genome of Achnatherum inebrians, a poisonous herb that is widely distributed in the rangelands of Northern China. The genome is 137 714 bp in total and consists of a large single-copy (81 758 bp) region and small single-copy (12 682 bp) region separated by a pair of inverted repeats (21 637 bp). The genome contains 130 genes, including 84 protein-coding genes, 38 tRNA genes and 8 ribosomal RNA genes, and the guanine + cytosine content is 36. Read More

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Non-linear fitting with joint spatial regularization in arterial spin labeling.

Med Image Anal 2021 Apr 20;71:102067. Epub 2021 Apr 20.

Institute of Medical Engineering, Graz University of Technology, Stremayrgasse 16/III, Graz 8010, Austria; BioTechMed-Graz, Mozartgasse 12/II, Graz 8010, Austria. Electronic address:

Multi-Delay single-shot arterial spin labeling (ASL) imaging provides accurate cerebral blood flow (CBF) and, in addition, arterial transit time (ATT) maps but the inherent low SNR can be challenging. Especially standard fitting using non-linear least squares often fails in regions with poor SNR, resulting in noisy estimates of the quantitative maps. State-of-the-art fitting techniques improve the SNR by incorporating prior knowledge in the estimation process which typically leads to spatial blurring. Read More

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Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus.

Comput Biol Chem 2021 Apr 24;92:107496. Epub 2021 Apr 24.

Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India; Department of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam, 781001, India. Electronic address:

Exobasidium vexans, a basidiomycete pathogen, is the causal organism of blister blight disease in tea. The molecular identification of the pathogen remains a challenge due to the limited availability of genomic data in sequence repositories and cryptic speciation within its genus Exobasidium. In this study, the nuclear internal transcribed spacer rDNA region (ITS) based DNA barcode was developed for E. Read More

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Response-based outcome predictions and confidence regulate feedback processing and learning.

Elife 2021 Apr 30;10. Epub 2021 Apr 30.

University of Oxford, Oxford, United Kingdom.

Influential theories emphasize the importance of predictions in learning: we learn from feedback to the extent that it is surprising, and thus conveys new information. Here we explore the hypothesis that surprise depends not only on comparing current events to past experience, but also on online evaluation of performance via internal monitoring. Specifically, we propose that people leverage insights from response-based performance monitoring - outcome predictions and confidence - to control learning from feedback. Read More

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Generative Models for Active Vision.

Front Neurorobot 2021 13;15:651432. Epub 2021 Apr 13.

Wellcome Centre for Human Neuroimaging, Queen Square Institute of Neurology, London, United Kingdom.

The active visual system comprises the visual cortices, cerebral attention networks, and oculomotor system. While fascinating in its own right, it is also an important model for sensorimotor networks in general. A prominent approach to studying this system is active inference-which assumes the brain makes use of an internal (generative) model to predict proprioceptive and visual input. Read More

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Bayesian inference of gene expression states from single-cell RNA-seq data.

Nat Biotechnol 2021 Apr 29. Epub 2021 Apr 29.

Biozentrum, University of Basel, Basel, Switzerland.

Despite substantial progress in single-cell RNA-seq (scRNA-seq) data analysis methods, there is still little agreement on how to best normalize such data. Starting from the basic requirements that inferred expression states should correct for both biological and measurement sampling noise and that changes in expression should be measured in terms of fold changes, we here derive a Bayesian normalization procedure called Sanity (SAmpling-Noise-corrected Inference of Transcription activitY) from first principles. Sanity estimates expression values and associated error bars directly from raw unique molecular identifier (UMI) counts without any tunable parameters. Read More

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Taxonomy and Phylogeny of the Wood-Inhabiting Fungal Genus with Descriptions of Three New Species from East Asia.

J Fungi (Basel) 2021 Apr 16;7(4). Epub 2021 Apr 16.

Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.

Three new wood-inhabiting fungi, , and spp. nov., are proposed based on a combination of morphological features and molecular evidence. Read More

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The Use of Translational Modelling and Simulation to Develop Immunomodulatory Therapy as an Adjunct to Antibiotic Treatment in the Context of Pneumonia.

Pharmaceutics 2021 Apr 22;13(5). Epub 2021 Apr 22.

Department of Clinical Pharmacy & Biochemistry, Institute of Pharmacy, Freie Universitaet Berlin, 12169 Berlin, Germany.

The treatment of respiratory tract infections is threatened by the emergence of bacterial resistance. Immunomodulatory drugs, which enhance airway innate immune defenses, may improve therapeutic outcome. In this concept paper, we aim to highlight the utility of pharmacometrics and Bayesian inference in the development of immunomodulatory therapeutic agents as an adjunct to antibiotics in the context of pneumonia. Read More

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Neural Dynamics under Active Inference: Plausibility and Efficiency of Information Processing.

Entropy (Basel) 2021 Apr 12;23(4). Epub 2021 Apr 12.

Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, London WC1N 3BG, UK.

Active inference is a normative framework for explaining behaviour under the free energy principle-a theory of self-organisation originating in neuroscience. It specifies neuronal dynamics for state-estimation in terms of a descent on (variational) free energy-a measure of the fit between an internal (generative) model and sensory observations. The free energy gradient is a prediction error-plausibly encoded in the average membrane potentials of neuronal populations. Read More

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"Exact" and Approximate Methods for Bayesian Inference: Stochastic Volatility Case Study.

Entropy (Basel) 2021 Apr 15;23(4). Epub 2021 Apr 15.

Institute for Computing and Information Sciences, Radboud University Nijmegen, Toernooiveld 212, 6525 EC Nijmegen, The Netherlands.

We conduct a case study in which we empirically illustrate the performance of different classes of Bayesian inference methods to estimate stochastic volatility models. In particular, we consider how different particle filtering methods affect the variance of the estimated likelihood. We review and compare particle Markov Chain Monte Carlo (MCMC), RMHMC, fixed-form variational Bayes, and integrated nested Laplace approximation to estimate the posterior distribution of the parameters. Read More

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Characterization of Two Complete Mitochondrial Genomes of (Hemiptera: Cicadellidae: Cicadellinae) and the Phylogenetic Implications.

Insects 2021 Apr 11;12(4). Epub 2021 Apr 11.

Institute of Entomology, Guizhou University, Guiyang 550025, China.

The complete mitochondrial genomes of and were sequenced. The results showed that the mitogenomes of these two species are 15,621 and 15,895 bp in length, with A+T contents of 78.6% and 78. Read More

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Analysing Normative Influences on the Prevalence of Female Genital Mutilation/Cutting among 0-14 Years Old Girls in Senegal: A Spatial Bayesian Hierarchical Regression Approach.

Int J Environ Res Public Health 2021 Apr 6;18(7). Epub 2021 Apr 6.

Population Council, Avenue 5, 3rd Floor, Rose Avenue, Nairobi, Kenya.

Background: Female genital mutilation/cutting (FGM/C) is a harmful traditional practice affecting the health and rights of women and girls. This has raised global attention on the implementation of strategies to eliminate the practice in conformity with the Sustainable Development Goals (SDGs). A recent study on the trends of FGM/C among Senegalese women (aged 15-49) which examined how individual- and community-level factors affected the practice, found significant regional variations in the practice. Read More

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