117 results match your criteria covariance inferred

Structural Covariance of Cortical Gyrification at Illness Onset in Treatment Resistance: A Longitudinal Study of First-Episode Psychoses.

Schizophr Bull 2021 Apr 14. Epub 2021 Apr 14.

Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.

Treatment resistance (TR) in patients with first-episode psychosis (FEP) is a major cause of disability and functional impairment, yet mechanisms underlying this severe disorder are poorly understood. As one view is that TR has neurodevelopmental roots, we investigated whether its emergence relates to disruptions in synchronized cortical maturation quantified using gyrification-based connectomes. Seventy patients with FEP evaluated at their first presentation to psychiatric services were followed up using clinical records for 4 years; of these, 17 (24. Read More

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Two-Stage Bayesian Optimization for Scalable Inference in State-Space Models.

IEEE Trans Neural Netw Learn Syst 2021 Apr 5;PP. Epub 2021 Apr 5.

State-space models (SSMs) are a rich class of dynamical models with a wide range of applications in economics, healthcare, computational biology, robotics, and more. Proper analysis, control, learning, and decision-making in dynamical systems modeled by SSMs depend on the accuracy of the inferred/learned model. Most of the existing inference techniques for SSMs are capable of dealing with very small systems, unable to be applied to most of the large-scale practical problems. Read More

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Tense-aspect-mood marking, language-family size and the evolution of predication.

David Gil

Philos Trans R Soc Lond B Biol Sci 2021 May 22;376(1824):20200194. Epub 2021 Mar 22.

Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.

This paper proposes a Complexity Covariance Hypothesis, whereby linguistic complexity covaries with cultural and socio-political complexity, and argues for an Evolutionary Inference Principle, in accordance with which, in domains where linguistic complexity correlates positively with cultural/socio-political complexity, simpler linguistic structures are evolutionarily prior to their more complex counterparts. Applying this methodology in a case study, the covariance of linguistic and cultural/socio-political complexity is examined by means of a cross-linguistic survey of tense-aspect-mood (TAM) marking in a worldwide sample of 868 languages. A novel empirical finding emerges: all else being equal, languages from small language families tend to have optional TAM marking, while languages from large language families are more likely to exhibit obligatory TAM marking. Read More

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Seasonal dependence of false-positives in detection of anomalous pCO using the covariance method with dissolved oxygen in monitoring offshore CO storage sites.

Mar Pollut Bull 2021 May 6;166:112238. Epub 2021 Mar 6.

Geological Carbon dioxide Storage Technology Research Association, Kizugawa 619-0292, Japan; CO(2) Storage Research Group, Research Institute of Innovative Technology for the Earth, Kizugawa 619-0292, Japan. Electronic address:

To elucidate the dependence of frequency of false-positives on the season for the covariance threshold based on partial pressure of CO (pCO) and the percentage dissolved oxygen saturation (DO%) for monitoring offshore CO storage, the deviation of observed pCO from a linear regression of pCO on DO% was investigated. The analyzed data were continuously observed for nearly 1 year in a semi-enclosed bay. Observed pCO tended to be higher than the linear regression in summer and fall, when false-positives would be more frequent. Read More

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Metabolic and Hemodynamic Resting-State Connectivity of the Human Brain: A High-Temporal Resolution Simultaneous BOLD-fMRI and FDG-fPET Multimodality Study.

Cereb Cortex 2021 May;31(6):2855-2867

Monash Biomedical Imaging, Melbourne, Vic, 3800 Australia.

Simultaneous [18F]-fluorodeoxyglucose positron emission tomography functional magnetic resonance imaging (FDG-PET/fMRI) provides the capacity to image 2 sources of energetic dynamics in the brain-glucose metabolism and the hemodynamic response. fMRI connectivity has been enormously useful for characterizing interactions between distributed brain networks in humans. Metabolic connectivity based on static FDG-PET has been proposed as a biomarker for neurological disease, but FDG-sPET cannot be used to estimate subject-level measures of "connectivity," only across-subject "covariance. Read More

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Bayesian inference assessment of protein secondary structure analysis using circular dichroism data - how much structural information is contained in protein circular dichroism spectra?

Anal Methods 2021 01;13(3):359-368

Department of Statistics, University of Warwick, Coventry, UK.

Circular dichroism spectroscopy is an important tool for determining the structural characteristics of biomolecules, particularly the secondary structure of proteins. In this paper we propose a Bayesian model that estimates the covariance structure within a measured spectrum and quantifies the uncertainty associated with the inferred secondary structures and characteristic spectra associated with each secondary structure type. Furthermore, we used tools from Bayesian model selection to determine the best secondary structure classification scheme and illustrate a technique for comparing whether or not two or more measured protein spectra share the same secondary structure. Read More

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January 2021

Importance of self-connections for brain connectivity and spectral connectomics.

Biol Cybern 2020 12 26;114(6):643-651. Epub 2020 Nov 26.

School of Physics, The University of Sydney, Sydney, NSW, 2006, Australia.

Spectral analysis and neural field theory are used to investigate the role of local connections in brain connectivity matrices (CMs) that quantify connectivity between pairs of discretized brain regions. This work investigates how the common procedure of omitting such self-connections (i.e. Read More

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December 2020

Crossed Cerebellar Diaschisis in Patients With Symptomatic Unilateral Anterior Circulation Stroke Is Associated With Hemodynamic Impairment in the Ipsilateral MCA Territory.

J Magn Reson Imaging 2021 04 28;53(4):1190-1197. Epub 2020 Oct 28.

Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland.

Background: In patients with steno-occlusive disease, recent findings suggest that hemodynamic alterations may also be associated with crossed cerebellar diaschisis (CCD) rather than a functional disruption alone.

Purpose: To use a quantitative multiparametric hemodynamic MRI to gain a better understanding of hemodynamic changes related to CCD in patients with unilateral anterior circulation stroke.

Study Type: Prospective cohort study. Read More

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Effects of home-based telerehabilitation in patients with stroke: A randomized controlled trial.

Neurology 2020 10 30;95(17):e2318-e2330. Epub 2020 Sep 30.

From the Departments of Neurology (J.C.) and Department of Gastroenterology and Hepatology (D.S.), Zhongshan Hospital, Fudan University, Shanghai; Department of Gastroenterology and Hepatology (D.S.), Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen; Departments of Neurology (J.C., S.Z., Y.S., C.R.), Rehabilitation (F.Q., Y.Z.), and Radiology (J.L.), Shanghai Fifth People's Hospital, Fudan University; and Department of Neurology (C.R.), Shanghai East Hospital, Tongji University, China.

Objective: To determine the effects of a 12-week home-based motor training telerehabilitation program in patients with subcortical stroke by combining motor function assessments and multimodality MRI analysis methods.

Methods: Fifty-two patients with stroke and hemiplegia were randomly assigned to either a home-based motor training telerehabilitation (TR) group or a conventional rehabilitation (CR) group for 12 weeks. The Fugl-Meyer assessment (FMA) for upper and lower extremities and the modified Barthel Index were used as primary outcomes. Read More

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October 2020

Estimating canopy gross primary production by combining phloem stable isotopes with canopy and mesophyll conductances.

Plant Cell Environ 2020 09 24;43(9):2124-2142. Epub 2020 Jul 24.

Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden.

Gross primary production (GPP) is a key component of the forest carbon cycle. However, our knowledge of GPP at the stand scale remains uncertain, because estimates derived from eddy covariance (EC) rely on semi-empirical modelling and the assumptions of the EC technique are sometimes not fully met. We propose using the sap flux/isotope method as an alternative way to estimate canopy GPP, termed GPP , at the stand scale and at daily resolution. Read More

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September 2020

Characterizing the heterogeneous metabolic progression in idiopathic REM sleep behavior disorder.

Neuroimage Clin 2020 26;27:102294. Epub 2020 May 26.

Department of Nuclear Medicine, University of Bern, Switzerland; Dept. Informatics, Technische Universität München, Munich, Germany.

Objective: Idiopathic rapid eye movement (REM) sleep behavior disorder (iRBD) is a prodromal stage of synucleinopathies such as Parkinson's disease (PD). Positron emission tomography (PET) with F-FDG reveals metabolic perturbations, which are scored by spatial covariance analysis. However, the resultant pattern scores do not capture the spatially heterogeneous trajectories of metabolic changes between individual brain regions. Read More

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Cognitive impairment in remitted late-life depression is not associated with Alzheimer's disease-related CSF biomarkers.

J Affect Disord 2020 07 1;272:409-416. Epub 2020 May 1.

Laboratorio de Neurociencias LIM27, Departamento e Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brasil.

Background: Cognitive impairment is a common feature of late-life depression (LLD). Early studies using Alzheimer's disease (AD) biomarkers inferred a biological link between AD pathology and LLD, but recent findings have challenged this association. The aim of this investigation was to determine a panel of AD-related cerebrospinal fluid (CSF) biomarkers in a cross-section of elders with mild cognitive impairment (MCI) with and without LLD. Read More

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Time Window Determination for Inference of Time-Varying Dynamics: Application to Cardiorespiratory Interaction.

Front Physiol 2020 28;11:341. Epub 2020 Apr 28.

Faculty of Medicine, Ss. Cyril and Methodius University, Skopje, Macedonia.

Interacting dynamical systems abound in nature, with examples ranging from biology and population dynamics, through physics and chemistry, to communications and climate. Often their states, parameters and functions are time-varying, because such systems interact with other systems and the environment, exchanging information and matter. A common problem when analysing time-series data from dynamical systems is how to determine the length of the time window for the analysis. Read More

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Pharmacokinetic interaction of brivaracetam on other antiepileptic drugs in adults with focal seizures: Pooled analysis of data from randomized clinical trials.

Epilepsy Res 2019 12 14;158:106218. Epub 2019 Oct 14.

UCB Pharma, Braine-l'Alleud, Belgium. Electronic address:

Objective: To assess the effect of brivaracetam (BRV) on steady-state plasma concentrations of commonly prescribed antiepileptic drugs (AEDs).

Methods: Data were pooled from five randomized, double-blind, placebo-controlled efficacy studies (NCT00175929, NCT00175825, NCT00490035, NCT00464269, and NCT01261325) in which adults with refractory epilepsy, and receiving stable doses of 1-2 AEDs, initiated adjunctive treatment with BRV (or placebo) for up to 12 weeks, following a 4-8 week baseline period. Concentrations of carbamazepine, carbamazepine epoxide, clobazam, clonazepam, lacosamide, lamotrigine, levetiracetam, oxcarbazepine (MHD), phenobarbital, phenytoin, pregabalin, topiramate, valproic acid and zonisamide, were measured during baseline and during BRV or placebo evaluation periods. Read More

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December 2019

School-based psychoeducation and storytelling: Associations with long-term mental health in adolescent survivors of the Wenchuan earthquake.

Epidemiol Psychiatr Sci 2019 Oct 23;29:e65. Epub 2019 Oct 23.

Hyogo Institute for Traumatic Stress, Kobe, Japan.

Aims: We explored the factors promoting long-term mental health among adolescent survivors of the 2008 Wenchuan earthquake in China. We examined the associations of their long-term mental health with disaster-related storytelling and school-based psychoeducation, and of school-based psychoeducation with disaster-related storytelling.

Methods: A secondary school-based cross-sectional survey was conducted 6 years after the disaster. Read More

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October 2019

Sperm morphology and count vary with fine-scale changes in local density in a wild lizard population.

Oecologia 2019 Nov 17;191(3):555-564. Epub 2019 Oct 17.

Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA.

Given that sperm production can be costly, theory predicts that males should optimally adjust the quantity and/or quality of their sperm in response to their social environment to maximize their paternity success. Although experiments demonstrate that males can alter their ejaculates in response to manipulations of the social environment and studies show that ejaculate traits covary with social environment across populations, it is unknown whether individual variation in sperm traits corresponds to natural variation found within wild populations. Using an island population of brown anole lizards (Anolis sagrei), we tested the prediction that sperm traits (sperm count, sperm morphology, sperm velocity) respond to natural variation in the risk of sperm competition, as inferred from the local density and operational sex ratio (OSR) of conspecifics. Read More

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November 2019

Bayesian, Likelihood-Free Modelling of Phenotypic Plasticity and Variability in Individuals and Populations.

Front Genet 2019 20;10:727. Epub 2019 Sep 20.

Agriculture, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.

There is a paradigm shift from the traditional focus on the "average" individual towards the definition and analysis of trait variation within individual life-history and among individuals in populations. This is a result of increasing availability of individual phenotypic data. The shift allows the use of genetic and environment-driven variations to assess robustness to challenge, gain greater understanding of organismal biological processes, or deliver individual-targeted treatments or genetic selection. Read More

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September 2019

Alternative SNP weighting for single-step genomic best linear unbiased predictor evaluation of stature in US Holsteins in the presence of selected sequence variants.

J Dairy Sci 2019 Nov 5;102(11):10012-10019. Epub 2019 Sep 5.

Department of Animal and Dairy Science, University of Georgia, Athens 30602.

Causal variants inferred from sequence data analysis are expected to increase accuracy of genomic selection. In this work we evaluated the gain in reliability of genomic predictions, for stature in US Holsteins, when adding selected sequence variants to a pre-existent SNP chip. Two prediction methods were tested: de-regressed proofs assuming heterogeneous (genomic BLUP; GBLUP) residual variances and by single-step GBLUP (ssGBLUP) using actual phenotypes. Read More

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November 2019

Trend analysis of surface ozone at suburban Guangzhou, China.

Sci Total Environ 2019 Dec 13;695:133880. Epub 2019 Aug 13.

Institute of Tropical and Marine Meteorology, China Meteorological Administration, Guangzhou, China.

The long-term variations of ozone are the combined results of climate change and air quality management. As Guangzhou is under the influence of both subtropical monsoon climate and rapid economic development, the ozone trend in recent years is uncertain. This paper presents the trend analysis of maximum daily average 8 h (MDA8) ozone and daily meteorological observations in Guangzhou from 2008 to 2018, using the Kolmogorov-Zurbenko (KZ) filter method. Read More

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December 2019

Use and abuse of correlation analyses in microbial ecology.

ISME J 2019 11 28;13(11):2647-2655. Epub 2019 Jun 28.

Institute for Systems Biology, Seattle, WA, USA.

Correlation analyses are often included in bioinformatic pipelines as methods for inferring taxon-taxon interactions. In this perspective, we highlight the pitfalls of inferring interactions from covariance and suggest methods, study design considerations, and additional data types for improving high-throughput interaction inferences. We conclude that correlation, even when augmented by other data types, almost never provides reliable information on direct biotic interactions in real-world ecosystems. Read More

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November 2019

Ozone flux and ozone deposition in a mountain spruce forest are modulated by sky conditions.

Sci Total Environ 2019 Jul 1;672:296-304. Epub 2019 Apr 1.

Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a, 603 00 Brno, Czech Republic. Electronic address:

In order to understand the main driving factors of ozone (O) deposition we tested the hypothesis that sky conditions (cloudy, partly cloudy, and clear sky) modulate O flux in forest ecosystems via stomatal regulation. The hypothesis is based on the fact that complex microclimate conditions under cloudy sky usually stimulate stomatal conductance. O fluxes were inferred from a concentration gradient in a mountainous Norway spruce forest in the Czech Republic (Central Europe) for years 2012-2016 and measured directly by eddy-covariance during the summer of 2017. Read More

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Ridge estimation of network models from time-course omics data.

Biom J 2019 03 22;61(2):391-405. Epub 2018 Aug 22.

Department of Epidemiology and Biostatistics, Amsterdam School of Public Health, VU University Medical Center, MB, Amsterdam, The Netherlands.

Time-course omics experiments enable the reconstruction of the dynamics of the cellular regulatory network. Here, we describe the means for this reconstruction and the downstream exploitation of the inferred network. It is assumed that one of the various vector-autoregressive models (VAR) models presented here serves as a reasonably accurate description of the time-course omics data. Read More

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Understanding the potential bias of variance components estimators when using genomic models.

Genet Sel Evol 2018 08 6;50(1):41. Epub 2018 Aug 6.

Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, Postboks 50, 8830, Tjele, Denmark.

Background: Genomic models that link phenotypes to dense genotype information are increasingly being used for infering variance parameters in genetics studies. The variance parameters of these models can be inferred using restricted maximum likelihood, which produces consistent, asymptotically normal estimates of variance components under the true model. These properties are not guaranteed to hold when the covariance structure of the data specified by the genomic model differs substantially from the covariance structure specified by the true model, and in this case, the likelihood of the model is said to be misspecified. Read More

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Estimating dynamic brain functional networks using multi-subject fMRI data.

Neuroimage 2018 12 24;183:635-649. Epub 2018 Jul 24.

Department of Biostatistics, Emory University, 1518 Clifton Road NE, Atlanta, GA 30322, USA.

A common assumption in the study of brain functional connectivity is that the brain network is stationary. However it is increasingly recognized that the brain organization is prone to variations across the scanning session, fueling the need for dynamic connectivity approaches. One of the main challenges in developing such approaches is that the frequency and change points for the brain organization are unknown, with these changes potentially occurring frequently during the scanning session. Read More

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December 2018

Observations of Local Positive Low Cloud Feedback Patterns and Their Role in Internal Variability and Climate Sensitivity.

Geophys Res Lett 2018 May 9;45(9):4438-4445. Epub 2018 May 9.

Earth Sciences Division NASA Goddard Space Flight Center Greenbelt MD USA.

Modeling studies have shown that cloud feedbacks are sensitive to the spatial pattern of sea surface temperature (SST) anomalies, while cloud feedbacks themselves strongly influence the magnitude of SST anomalies. Observational counterparts to such patterned interactions are still needed. Here we show that distinct large-scale patterns of SST and low-cloud cover (LCC) emerge naturally from objective analyses of observations and demonstrate their close coupling in a positive local SST-LCC feedback loop that may be important for both internal variability and climate change. Read More

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Accounting for the measurement error of spectroscopically inferred soil carbon data for improved precision of spatial predictions.

Sci Total Environ 2018 Aug 16;631-632:377-389. Epub 2018 Mar 16.

Sydney Institute of Agriculture, The University of Sydney, New South Wales, Australia.

Spatial modelling of environmental data commonly only considers spatial variability as the single source of uncertainty. In reality however, the measurement errors should also be accounted for. In recent years, infrared spectroscopy has been shown to offer low cost, yet invaluable information needed for digital soil mapping at meaningful spatial scales for land management. Read More

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Seasonal, interannual and decadal drivers of tree and grass productivity in an Australian tropical savanna.

Glob Chang Biol 2018 06 28;24(6):2530-2544. Epub 2018 Feb 28.

School of Earth, Atmosphere and Environment, Monash University, Clayton, Vic., Australia.

Tree-grass savannas are a widespread biome and are highly valued for their ecosystem services. There is a need to understand the long-term dynamics and meteorological drivers of both tree and grass productivity separately in order to successfully manage savannas in the future. This study investigated the interannual variability (IAV) of tree and grass gross primary productivity (GPP) by combining a long-term (15 year) eddy covariance flux record and model estimates of tree and grass GPP inferred from satellite remote sensing. Read More

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Urban flux measurements reveal a large pool of oxygenated volatile organic compound emissions.

Proc Natl Acad Sci U S A 2018 02 22;115(6):1186-1191. Epub 2018 Jan 22.

Institute of Ecology, University of Innsbruck, 6020 Innsbruck, Austria.

Atmospheric chemistry is fueled by a large annual influx of nonmethane volatile organic compounds (NMVOC). These compounds influence ozone formation, lead to secondary organic aerosol production, and play a significant role for the oxidizing capacity of the atmosphere. The anthropogenic NMVOC budget is considerably uncertain due to the diversity of urban emission sources. Read More

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February 2018

Trait-specific processes of convergence and conservatism shape ecomorphological evolution in ground-dwelling squirrels.

Evolution 2018 03 2;72(3):473-489. Epub 2018 Feb 2.

Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131.

Our understanding of mechanisms operating over deep timescales to shape phenotypic diversity often hinges on linking variation in one or few trait(s) to specific evolutionary processes. When distinct processes are capable of similar phenotypic signatures, however, identifying these drivers is difficult. We explored ecomorphological evolution across a radiation of ground-dwelling squirrels whose history includes convergence and constraint, two processes that can yield similar signatures of standing phenotypic diversity. Read More

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The dimensionality of individual niche variation.

Ecology 2018 03 23;99(3):536-549. Epub 2018 Jan 23.

Instituto de Biociências, Universidade Estadual Paulista (UNESP), Av. 24-A, 1515, Rio Claro, 15807, Brazil.

The inherently multidimensional nature of the niche has not yet been integrated into the investigation of individual niche specialization within populations. We propose a framework for modeling the between- and within-individual components of the population niche as a set of variance-covariance matrices, which can be visualized with ellipses or ellipsoids. These niche components can be inferred using multiple response mixed models, and can incorporate diverse types of data, including diet composition, stable isotopes, spatial location, and other continuous measures of niche dimensions. Read More

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