Symmetry breaking organizes the brain's resting state manifold.

Spontaneously fluctuating brain activity patterns that emerge at rest have been linked to the brain's health and cognition. Despite detailed descriptions of the spatio-temporal brain patterns, our understanding of their generative mechanism is still incomplete. Using a combination of computational modeling and dynamical systems analysis we provide a mechanistic description of the formation of a resting state manifold via the network connectivity.

The virtual aging brain: Causal inference supports interhemispheric dedifferentiation in healthy aging.

The mechanisms of cognitive decline and its variability during healthy aging are not fully understood, but have been associated with reorganization of white matter tracts and functional brain networks. Here, we built a brain network modeling framework to infer the causal link between structural connectivity and functional architecture and the consequent cognitive decline in aging. By applying in-silico interhemispheric degradation of structural connectivity, we reproduced the process of functional dedifferentiation during aging.

RateML: A Code Generation Tool for Brain Network Models.

Whole brain network models are now an established tool in scientific and clinical research, however their use in a larger workflow still adds significant informatics complexity. We propose a tool, RateML, that enables users to generate such models from a succinct declarative description, in which the mathematics of the model are described without specifying how their simulation should be implemented. RateML builds on NeuroML's Low Entropy Model Specification (LEMS), an XML based language for specifying models of dynamical systems, allowing descriptions of neural mass and discretized neural field models, as implemented by the Virtual Brain (TVB) simulator: the end user describes their model's mathematics once and generates and runs code for different languages, targeting both CPUs for fast single simulations and GPUs for parallel ensemble simulations.

Integrating psychosocial variables and societal diversity in epidemic models for predicting COVID-19 transmission dynamics.

During the current COVID-19 pandemic, governments must make decisions based on a variety of information including estimations of infection spread, health care capacity, economic and psychosocial considerations. The disparate validity of current short-term forecasts of these factors is a major challenge to governments. By causally linking an established epidemiological spread model with dynamically evolving psychosocial variables, using Bayesian inference we estimate the strength and direction of these interactions for German and Danish data of disease spread, human mobility, and psychosocial factors based on the serial cross-sectional COVID-19 Snapshot Monitoring (COSMO; N = 16,981).

One-Enzyme RTX-PCR for the Detection of RNA Viruses from Multiple Virus Genera and Crop Plants.

Reverse transcription PCR (RT-PCR) is a popular method for detecting RNA viruses in plants. RT-PCR is usually performed in a classical two-step procedure: in the first step, cDNA is synthesized by reverse transcriptase (RT), followed by PCR amplification by a thermostable polymerase in a separate tube in the second step. However, one-step kits containing multiple enzymes optimized for RT and PCR amplification in a single tube can also be used.

Brain simulation as a cloud service: The Virtual Brain on EBRAINS.

The Virtual Brain (TVB) is now available as open-source services on the cloud research platform EBRAINS (ebrains.eu). It offers software for constructing, simulating and analysing brain network models including the TVB simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional brain networks; combined simulation of large-scale brain networks with small-scale spiking networks; automatic conversion of user-specified model equations into fast simulation code; simulation-ready brain models of patients and healthy volunteers; Bayesian parameter optimization in epilepsy patient models; data and software for mouse brain simulation; and extensive educational material.

High-resolution virtual brain modeling personalizes deep brain stimulation for treatment-resistant depression: Spatiotemporal response characteristics following stimulation of neural fiber pathways.

Over the past 15 years, deep brain stimulation (DBS) has been actively investigated as a groundbreaking therapy for patients with treatment-resistant depression (TRD); nevertheless, outcomes have varied from patient to patient, with an average response rate of ∼50%. The engagement of specific fiber tracts at the stimulation site has been hypothesized to be an important factor in determining outcomes, however, the resulting individual network effects at the whole-brain scale remain largely unknown. Here we provide a computational framework that can explore each individual's brain response characteristics elicited by selective stimulation of fiber tracts.

Neuronal Cascades Shape Whole-Brain Functional Dynamics at Rest.

At rest, mammalian brains display remarkable spatiotemporal complexity, evolving through recurrent functional connectivity () states on a slow timescale of the order of tens of seconds. While the phenomenology of the resting state dynamics is valuable in distinguishing healthy and pathologic brains, little is known about its underlying mechanisms. Here, we identify neuronal cascades as a potential mechanism.

Connectivity Between Brain Networks Dynamically Reflects Cognitive Status of Parkinson's Disease: A Longitudinal Study.

Background: Cognitive impairment in Parkinson's disease (PD) is associated with altered connectivity of the resting state networks (RSNs). Longitudinal studies in well cognitively characterized PD subgroups are missing.

Objectives: To assess changes of the whole-brain connectivity and between-network connectivity (BNC) of large-scale functional networks related to cognition in well characterized PD patients using a longitudinal study design and various analytical methods.

Spatial constraints on the diffusion of religious innovations: The case of early Christianity in the Roman Empire.

Christianity emerged as a small and marginal movement in the first century Palestine and throughout the following three centuries it became highly visible in the whole Mediterranean. Little is known about the mechanisms of spreading innovative ideas in past societies. Here we investigate how well the spread of Christianity can be explained as a diffusive process constrained by physical travel in the Roman Empire.

Robustness of Representative Signals Relative to Data Loss Using Atlas-Based Parcellations.

Parcellation-based approaches are an important part of functional magnetic resonance imaging data analysis. They are a necessary processing step for sorting data in structurally or functionally homogenous regions. Real functional magnetic resonance imaging datasets usually do not cover the atlas template completely; they are often spatially constrained due to the physical limitations of MR sequence settings, the inter-individual variability in brain shape, etc.

Large-scale cortico-subcortical functional networks in focal epilepsies: The role of the basal ganglia.

Objectives: The aim was to describe the contribution of basal ganglia (BG) thalamo-cortical circuitry to the whole-brain functional connectivity in focal epilepsies.

Methods: Interictal resting-state fMRI recordings were acquired in 46 persons with focal epilepsies. Of these 46, 22 had temporal lobe epilepsy: 9 left temporal (LTLE), 13 right temporal (RTLE); 15 had frontal lobe epilepsy (FLE); and 9 had parietal/occipital lobe epilepsy (POLE).

Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte?

Algae with secondary plastids of a red algal origin, such as ochrophytes (photosynthetic stramenopiles), are diverse and ecologically important, yet their evolutionary history remains controversial. We sequenced plastid genomes of two ochrophytes, Ochromonas sp. CCMP1393 (Chrysophyceae) and Trachydiscus minutus (Eustigmatophyceae).

Growth and stress response in Arabidopsis thaliana, Nicotiana benthamiana, Glycine max, Solanum tuberosum and Brassica napus cultivated under polychromatic LEDs.

Background: The use of light emitting diodes (LEDs) brings several key advantages over existing illumination technologies for indoor plant cultivation. Among these are that LEDs have predicted lifetimes from 50-100.000 hours without significant drops in efficiency and energy consumption is much lower compared to traditional fluorescent tubes.

Genome Sequence of Rhodococcus erythropolis Strain CCM2595, a Phenol Derivative-Degrading Bacterium.

We announce the completion of the genome sequence of a phenol derivative-degrading bacterium, Rhodococcus erythropolis strain CCM2595. This bacterium is interesting in the context of bioremediation for its capability to degrade phenol, catechol, resorcinol, hydroxybenzoate, hydroquinone, p-chlorophenol, p-nitrophenol, pyrimidines, and sterols.

The mitochondrion-like organelle of Trimastix pyriformis contains the complete glycine cleavage system.

All eukaryotic organisms contain mitochondria or organelles that evolved from the same endosymbiotic event like classical mitochondria. Organisms inhabiting low oxygen environments often contain mitochondrial derivates known as hydrogenosomes, mitosomes or neutrally as mitochondrion-like organelles. The detailed investigation has shown unexpected evolutionary plasticity in the biochemistry and protein composition of these organelles in various protists.

The plastid genome of Eutreptiella provides a window into the process of secondary endosymbiosis of plastid in euglenids.

Euglenids are a group of protists that comprises species with diverse feeding modes. One distinct and diversified clade of euglenids is photoautotrophic, and its members bear green secondary plastids. In this paper we present the plastid genome of the euglenid Eutreptiella, which we assembled from 454 sequencing of Eutreptiella gDNA.

Sound-speed image reconstruction in sparse-aperture 3-D ultrasound transmission tomography.

The paper is focused on sound-speed image reconstruction in 3-D ultrasound transmission tomography. Along with ultrasound reflectivity and the attenuation coefficient, sound speed is an important parameter which is related to the type and pathological state of the imaged tissue. This is important in the intended application, breast cancer diagnosis.

Purification and characterization of hydroquinone dioxygenase from Sphingomonas sp. strain TTNP3.

Hydroquinone-1,2-dioxygenase, an enzyme involved in the degradation of alkylphenols in Sphingomonas sp. strain TTNP3 was purified to apparent homogeneity. The extradiol dioxygenase catalyzed the ring fission of hydroquinone to 4-hydroxymuconic semialdehyde and the degradation of chlorinated and several alkylated hydroquinones.

An unexpected gene cluster for downstream degradation of alkylphenols in Sphingomonas sp. strain TTNP3.

In silico analysis of nucleotide sequences flanking the recently found hydroquinone dioxygenase in Sphingomonas sp. strain TTNP3 revealed a gene cluster that encodes a hydroquinone catabolic pathway. In addition to the two open-reading frames encoding the recently characterized hydroquinone dioxygenase, the cluster consisted of six open-reading frames.