A symmetric multivariate leakage correction for MEG connectomes

AbstractAmbiguities in the source reconstruction of magnetoencephalographic (MEG) measurements can cause spurious correlations between estimated source time-courses. In this paper, we propose a symmetric orthogonalisation method to correct for these artificial correlations between a set of multiple regions of interest (ROIs). This process enables the straightforward application of network modelling methods, including partial correlation or multivariate autoregressive modelling, to infer connectomes, or functional networks, from the corrected ROIs. Here, we apply the correction to simulated MEG recordings of simple networks and to a resting-state dataset collected from eight subjects, before computing the partial correlations between power envelopes of the corrected ROItime-courses. We show accurate reconstruction of our simulated networks, and in the analysis of real MEGresting-state connectivity, we find dense bilateral connections within the motor and visual networks, together with longer-range direct fronto-parietal connections

Two spatially distinct posterior alpha sources fulfill different functional roles in attention

Directing attention helps extracting relevant information and suppressing distracters. Alpha brain oscillations (8-12Hz) are crucial for this process, with power decreases facilitating processing of important information and power increases inhibiting brain regions processing irrelevant information. Evidence for this phenomenon arises from visual attention studies (Worden et al., 2000b), however, the effect also exists in other modalities, including the somatosensory system (Haegens et al., 2011) and inter-sensory attention tasks (Foxe and Snyder, 2011). We investigated in human participants (10 females, 10 males) the role of alpha oscillations in focused (0/100%) vs. divided (40/60%) attention, both across modalities (visual/somatosensory; Experiment 1) and within the same modality (visual domain: across hemifields; Experiment 2) while recording EEG over 128 scalp electrodes. In Experiment 1 participants divided their attention between visual and somatosensory modality to determine the temporal/spatial frequency of a target stimulus (vibrotactile stimulus/Gabor grating). In Experiment 2, participants divided attention between two visual hemifields to identify the orientation of a Gabor grating. In both experiments, pre-stimulus alpha power in visual areas decreased linearly with increasing attention to visual stimuli. In contrast, pre-stimulus alpha power in parietal areas was lower when attention was divided between modalities/hemifields, compared to focused attention. These results suggest there are two alpha sources, where one reflects the ‘visual spotlight of attention’ and the other reflects attentional effort. To our knowledge, this is the first study to show that attention recruits two spatially distinct alpha sources in occipital and parietal brain regions, acting simultaneously but serving different functions in attention

Predicting haemodynamic networks using electrophysiology: The role of non-linear and cross-frequency interactions

Understanding the electrophysiological basis of resting state networks (RSNs) in the human brain is a critical step towards elucidating how inter-areal connectivity supports healthy brain function. In recent years, the relationship between RSNs (typically measured using haemodynamic signals) and electrophysiology has been explored using functional Magnetic Resonance Imaging (fMRI) and magnetoencephalography (MEG). Significant progress has been made, with similar spatial structure observable in both modalities. However, there is a pressing need to understand this relationship beyond simple visual similarity of RSN patterns. Here, we introduce a mathematical model to predict fMRI-based RSNs using MEG. Our unique model, based upon a multivariate Taylor series, incorporates both phase and amplitude based MEG connectivity metrics, as well as linear and non-linear interactions within and between neural oscillations measured in multiple frequency bands. We show that including non-linear interactions, multiple frequency bands and cross-frequency terms significantly improves fMRI network prediction. This shows that fMRI connectivity is not only the result of direct electrophysiological connections, but is also driven by the overlap of connectivity profiles between separate regions. Our results indicate that a complete understanding of the electrophysiological basis of RSNs goes beyond simple frequency-specific analysis, and further exploration of non-linear and cross-frequency interactions will shed new light on distributed network connectivity, and its perturbation in pathology

Replication, Pathogenesis and Transmission of Pandemic (H1N1) 2009 Virus in Non-Immune Pigs

The declaration of the human influenza A pandemic (H1N1) 2009 (H1N1/09) raised important questions, including origin and host range [1,2]. Two of the three pandemics in the last century resulted in the spread of virus to pigs (H1N1, 1918; H3N2, 1968) with subsequent independent establishment and evolution within swine worldwide [3]. A key public and veterinary health consideration in the context of the evolving pandemic is whether the H1N1/09 virus could become established in pig populations [4]. We performed an infection and transmission study in pigs with A/California/07/09. In combination, clinical, pathological, modified influenza A matrix gene real time RT-PCR and viral genomic analyses have shown that infection results in the induction of clinical signs, viral pathogenesis restricted to the respiratory tract, infection dynamics consistent with endemic strains of influenza A in pigs, virus transmissibility between pigs and virus-host adaptation events. Our results demonstrate that extant H1N1/09 is fully capable of becoming established in global pig populations. We also show the roles of viral receptor specificity in both transmission and tissue tropism. Remarkably, following direct inoculation of pigs with virus quasispecies differing by amino acid substitutions in the haemagglutinin receptor-binding site, only virus with aspartic acid at position 225 (225D) was detected in nasal secretions of contact infected pigs. In contrast, in lower respiratory tract samples from directly inoculated pigs, with clearly demonstrable pulmonary pathology, there was apparent selection of a virus variant with glycine (225G). These findings provide potential clues to the existence and biological significance of viral receptor-binding variants with 225D and 225G during the 1918 pandemic [5]

Optimal Inverse Design of Magnetic Field Profiles in a Magnetically Shielded Cylinder

Magnetic shields that use both active and passive components to enable the generation of a tailored low-field environment are required for many applications in science, engineering, and medical imaging. Until now, accurate field nulling, or field generation, has only been possible over a small fraction of the overall volume of the shield. This is due to the interaction between the active field-generating components and the surrounding high-permeability passive shielding material. In this paper, we formulate the interaction between an arbitrary static current flow on a cylinder and an exterior closed high-permeability cylinder. We modify the Green’s function for the magnetic vector potential and match boundary conditions on the shield’s interior surface to calculate the total magnetic field generated by the system. We cast this formulation into an inverse optimization problem to design active–passive magnetic field shaping systems that accurately generate any physical static magnetic field in the interior of a closed cylindrical passive shield. We illustrate this method by designing hybrid systems that generate a range of magnetic field profiles to high accuracy over large interior volumes, and simulate them in real-world shields whose passive components have finite permeability, thickness, and axial entry holes. Our optimization procedure can be adapted to design active–passive magnetic field shaping systems that accurately generate any physical user-specified static magnetic field in the interior of a closed cylindrical shield of any length, enabling the development and miniaturization of systems that require accurate magnetic shielding and control

Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (mSNV) analysis during an influenza A/H5N8 outbreak

As high-throughput sequencing technologies are becoming more widely adopted for analysing pathogens in disease outbreaks there needs to be assurance that the different sequencing technologies and approaches to data analysis will yield reliable and comparable results. Conversely, understanding where agreement cannot be achieved provides insight into the limitations of these approaches and also allows efforts to be focused on areas of the process that need improvement. This manuscript describes the next-generation sequencing of three closely related viruses, each analysed using different sequencing strategies, sequencing instruments and data processing pipelines. In order to determine the comparability of consensus sequences and minority (sub-consensus) single nucleotide variant (mSNV) identification, the biological samples, the sequence data from 3 sequencing platforms and the *.bam quality-trimmed alignment files of raw data of 3 influenza A/H5N8 viruses were shared. This analysis demonstrated that variation in the final result could be attributed to all stages in the process, but the most critical were the well-known homopolymer errors introduced by 454 sequencing, and the alignment processes in the different data processing pipelines which affected the consistency of mSNV detection. However, homopolymer errors aside, there was generally a good agreement between consensus sequences that were obtained for all combinations of sequencing platforms and data processing pipelines. Nevertheless, minority variant analysis will need a different level of careful standardization and awareness about the possible limitations, as shown in this study

A determination of the pairing interaction in the high Tc cuprate superconductor Tl2Ba2CaCu2O8 (Tl2212)

We have measured the near-normal reflectance of Tl2Ba2CaCu2O8 (Tl2212) for energies from 0.1 to 4.0 eV at room temperature and used a Kramers-Kronig analysis to find the complex, frequency dependent dielectric function, from which the optical conductivity was determined. Using Thermal-Difference-Reflectance (TDR) Spectroscopy the reflectance of the sample in the normal state just above the superconducting transition, and in the superconducting state were then obtained. From these data we determined the ratio of the superconducting- to normal-state optical conductivities. Mattis and Bardeen had calculated this function within the BCS theory, where the gap is a fixed energy-independent quantity. Taking into account the retarded nature of the electron-phonon coupling results in a complex, energy dependent gap causing deviations from the Mattis-Bardeen plot at energies where the phonon coupling function is large. We find a typical deviation near the phonon energies in Tl2212, and in addition, at 1.2 and 1.7eV. The phonon, and these electronic terms can each be described by a coupling constant. None of which by itself gives rise to a high transition temperature, but the combination does. Using Resonant Inelastic X-Ray Scattering (RIXS) we find that the d-to-d excitations of the cuprate ion in Tl2212 fall at the same energies as the dips in the Mattis-Bardeen plot. We conclude that the high superconducting transition temperature of the cuprates is due to the sum of the phonon interaction, and interactions with the Cu-ion d-shell.Comment: Preprint submitted to Physica C. Paper presented at M2S-HTSC-VIII, Dresden, Germany, July 9-14,200

Contributions of external nutrient loading and internal cycling to cyanobacterial bloom dynamics in Lake Taihu, China: Implications for nutrient management

Harmful cyanobacterial blooms (CyanoHABs) are linked to increasing anthropogenic nitrogen (N) and phosphorus (P) inputs. However, CyanoHABs in many large lakes continue despite extensive abatement efforts, mostly focused on external P loading. Internal nutrient cycling can modify nutrient availability and limitation; thus, understanding the relative importance of external vs. internal nutrient loading is essential for developing effective mitigation strategies for CyanoHABs. We estimated long-term nutrient budgets for Lake Taihu, China, from mass balance models using extensive monitoring of input and output nutrient data from 2005 to 2018 to quantify contributions from internal nutrient loading. The nutrient mass balance showed that 9% and 63% of annual external N and P inputs, respectively, were retained in the lake. Denitrification removed 54% of external N loading and can thus help explain rapid decreases in lake N concentrations and summer N limitation. Water column (Formula presented.) regeneration can help sustain CyanoHABs over the short term and contributed 38–58% of potential (Formula presented.) demand for summer-fall, Microcystis-dominated blooms. Internal P release contributed 23–90% of CyanoHABs P demand, although Taihu was a net P sink on an annual scale. Our results show that internal nutrient cycling helps sustain CyanoHABs in Taihu, despite reductions in external nutrient inputs. Furthermore, N is leaving the lake faster than P, thereby creating persistent N limitation. Therefore, parallel reductions in external N loading, along with P, will be most effective in reducing CyanoHABs and accelerate the recovery process in this and other large, shallow lakes