Firalink: A bioinformatics pipeline for long non-coding RNA data analysis.

Summary: The Firalink bioinformatics pipeline has been developed to analyse long non-coding RNA (lncRNA) data generated by targeted sequencing. This pipeline has been first implemented for use with the FIMICS panel containing 2906 lncRNAs useful for investigations in cardiovascular disease. It has been subsequently tested and validated using a panel of lncRNAs targeting brain disease.

Early cognitive comorbidities before disease onset: A common symptom towards prevention of related brain diseases?

Brain diseases are very heterogeneous; however they also display multiple common risk factors and comorbidities. With a paucity of disease-modifying therapies, prevention became a health priority. Towards prevention, one strategy is to focus on similar symptoms of brain diseases occurring before disease onset.

Unconventional short-range structural fluctuations in cuprate superconductors.

The interplay between structural and electronic degrees of freedom in complex materials is the subject of extensive debate in physics and materials science. Particularly interesting questions pertain to the nature and extent of pre-transitional short-range order in diverse systems ranging from shape-memory alloys to unconventional superconductors, and how this microstructure affects macroscopic properties. Here we use neutron and X-ray diffuse scattering to uncover universal structural fluctuations in LaSrCuO and TlBaCuO, two cuprate superconductors with distinct point disorder effects and with optimal superconducting transition temperatures that differ by more than a factor of two.

A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans.

Transposable elements (TEs) have been proposed to play an important role in driving the expansion of gene regulatory networks during mammalian evolution, notably by contributing to the evolution and function of long non-coding RNAs (lncRNAs). XACT is a primate-specific TE-derived lncRNA that coats active X chromosomes in pluripotent cells and may contribute to species-specific regulation of X-chromosome inactivation. Here we explore how different families of TEs have contributed to shaping the XACT locus and coupling its expression to pluripotency.

Potential causes of cognitive alterations in temporal lobe epilepsy.

Spatial and non-spatial memories are key processes whereby we process our environment on a daily basis, coding space, time and items to form unique memories. Both types of memory involve distributed and complex temporal lobe (TL) networks. In this review, we will discuss potential causes of spatial and non-spatial memory deficits, taking the example of temporal lobe epilepsy (TLE), a widespread neurological disorder characterized by cognitive comorbidities, in both animal models and TLE patients.

Update on temporal lobe-dependent information processing, in health and disease.

The past decade has been characterized by a lot of remodeling in the field of learning and memory. Both of them, often associated with neuronal oscillations, an emergent property of brain networks, are governed by temporal lobe (TL) functional connectivity. An impairment of oscillatory mechanisms indeed often leads to TL-dependent cognitive deficits.

Recording Quality of Mechanically Decoupled Floating Versus Skull-Fixed Silicon-Based Neural Probes.

Throughout the past decade, silicon-based neural probes have become a driving force in neural engineering. Such probes comprise sophisticated, integrated CMOS electronics which provide a large number of recording sites along slender probe shanks. Using such neural probes in a chronic setting often requires them to be mechanically anchored with respect to the skull.

Neurofeedback Training of Gamma Oscillations in Monkey Primary Visual Cortex.

In humans, neurofeedback (NFB) training has been used extensively and successfully to manipulate brain activity. Feedback signals were derived from EEG, fMRI, MEG, and intracranial recordings and modifications were obtained of the BOLD signal, of the power of oscillatory activity in distinct frequency bands and of single unit activity. The purpose of the present study was to examine whether neuronal activity could also be controlled by NFB in early sensory cortices whose activity is thought to be influenced mainly by sensory input rather than volitional control.

Crossover from Collective to Incoherent Spin Excitations in Superconducting Cuprates Probed by Detuned Resonant Inelastic X-Ray Scattering.

Spin excitations in the overdoped high temperature superconductors Tl_{2}Ba_{2}CuO_{6+δ} and (Bi,Pb)_{2}(Sr,La)_{2}CuO_{6+δ} were investigated by resonant inelastic x-ray scattering (RIXS) as functions of doping and detuning of the incoming photon energy above the Cu-L_{3} absorption peak. The RIXS spectra at optimal doping are dominated by a paramagnon feature with peak energy independent of photon energy, similar to prior results on underdoped cuprates. Beyond optimal doping, the RIXS data indicate a sharp crossover to a regime with a strong contribution from incoherent particle-hole excitations whose maximum shows a fluorescencelike shift upon detuning.

Response to Comment on "Broken translational and rotational symmetry via charge stripe order in underdoped YBa2Cu3O6+y".

Fine questions our interpretation of unidirectional stripes over a bidirectional checkerboard and illustrates his criticism by simulating a momentum space structure consistent with our data and corresponding to a checkerboard-looking real space density. Here, we use a local rotational-symmetry analysis to demonstrate that the simulated image is actually composed of locally unidirectional modulations of the charge density, consistent with our original conclusions.

Nematic Resonance in the Raman Response of Iron-Based Superconductors.

In a fully gapped superconductor the electronic Raman response has a pair-breaking peak at twice the superconducting gap Δ, if the Bogoliubov excitations are uncorrelated. Motivated by the iron based superconductors, we study how this peak is modified if the superconducting phase hosts a nematic-structural quantum critical point. We show that, upon approaching this point by tuning, e.

Symmetry of charge order in cuprates.

Charge-ordered ground states permeate the phenomenology of 3d-based transition metal oxides, and more generally represent a distinctive hallmark of strongly correlated states of matter. The recent discovery of charge order in various cuprate families has fuelled new interest into the role played by this incipient broken symmetry within the complex phase diagram of high-T(c) superconductors. Here, we use resonant X-ray scattering to resolve the main characteristics of the charge-modulated state in two cuprate families: Bi2Sr(2-x)La(x)CuO(6+δ) (Bi2201) and YBa2Cu3O(6+y) (YBCO).

Superconductivity. Broken translational and rotational symmetry via charge stripe order in underdoped YBa₂Cu₃O(6+y).

After the discovery of stripelike order in lanthanum-based copper oxide superconductors, charge-ordering instabilities were observed in all cuprate families. However, it has proven difficult to distinguish between unidirectional (stripes) and bidirectional (checkerboard) charge order in yttrium- and bismuth-based materials. We used resonant x-ray scattering to measure the two-dimensional structure factor in the superconductor YBa2Cu3O(6+y) in reciprocal space.

Observation of incipient charge nematicity in Ba(Fe(1-x)Co(x))2As2.

Using electronic Raman spectroscopy, we report direct measurements of charge nematic fluctuations in the tetragonal phase of strain-free Ba(Fe(1-x)Co(x))2As2 single crystals. The strong enhancement of the Raman response at low temperatures unveils an underlying charge nematic state that extends to superconducting compositions and which has hitherto remained unnoticed. Comparison between the extracted charge nematic susceptibility and the elastic modulus allows us to disentangle the charge contribution to the nematic instability, and to show that charge nematic fluctuations are weakly coupled to the lattice.

Changes in interictal spike features precede the onset of temporal lobe epilepsy.

Objective: One cornerstone event during epileptogenesis is the occurrence of the first spontaneous seizure (SZ1). It is therefore important to identify biomarkers of the network alterations leading to SZ1. In experimental models of temporal lobe epilepsy (TLE), interictal-like activity (ILA) precedes SZ1 by several days.

Pitfalls of high-pass filtering for detecting epileptic oscillations: a technical note on "false" ripples.

Objectives: To analyze interictal High frequency oscillations (HFOs) as observed in the medial temporal lobe of epileptic patients and animals (ripples, 80-200Hz and fast ripples, 250-600Hz). To show that the identification of interictal HFOs raises some methodological issues, as the filtering of sharp transients (e.g.

Early deficits in spatial memory and theta rhythm in experimental temporal lobe epilepsy.

Patients with temporal lobe epilepsy (TLE), the most common form of epilepsy in adults, often display cognitive deficits. The time course and underlying mechanisms of cognitive decline remain unknown during epileptogenesis (the process leading to epilepsy). Using the rat pilocarpine model of TLE, we performed a longitudinal study to assess spatial and nonspatial cognitive performance during epileptogenesis.

h channel-dependent deficit of theta oscillation resonance and phase shift in temporal lobe epilepsy.

I(h) tunes hippocampal CA1 pyramidal cell dendrites to optimally respond to theta inputs (4-12 Hz), and provides a negative time delay to theta inputs. Decreased I(h) activity, as seen in experimental temporal lobe epilepsy (TLE), could significantly alter the response of dendrites to theta inputs. Here we report a progressive erosion of theta resonance and phase lead in pyramidal cell dendrites during epileptogenesis in a rat model of TLE.

Treatment-induced prevention of learning deficits in newborn mice with brain lesions.

Perinatal brain injuries often result in irreversible learning disabilities, which manifest in early childhood. The molecular and cellular mechanisms of these injuries and potential pharmacological treatments are emerging, chiefly from studies in newborn rodents. In newborn mice, experimentally induced lesions can be dramatically reduced by appropriate neuroprotective treatments.

Olfactory classical conditioning in newborn mice.

Determining the behavioural phenotype of genetically altered mice is a valuable approach for elucidating the function of genes and their role in cognitive disorders. Methods for phenotyping newborn mice are scarce and generally confined to sensorimotor reflexes. Here, we describe a simple method for assessing associative abilities in newborn mice.