Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets.

De novo assembly of transcriptomes from species without reference genome remains a common problem in functional genomics. While methods and algorithms for transcriptome assembly are continually being developed and published, the quality of de novo assemblies using short reads depends on the complexity of the transcriptome and is limited by several types of errors. One problem to overcome is the research gap regarding the best method to use in each study to obtain high-quality de novo assembly.

Robust and memory-less median estimation for real-time spike detection.

We propose a novel 1-D median estimator specifically designed for the online detection of threshold-crossing signals, such as spikes in extracellular neural recordings. Compared to state-of-the-art algorithms, our method reduces estimator variance by up to eight times for a given buffer length. Likewise, for a given estimator variance, it requires a buffer length that is up to eight times smaller.

The Phosphatase CSW Controls Life Span by Insulin Signaling and Metabolism Throughout Adult Life in .

Noonan syndrome and related disorders are caused by mutations in genes encoding for proteins of the RAS-ERK1/2 signaling pathway, which affect development by enhanced ERK1/2 activity. However, the mutations' effects throughout adult life are unclear. In this study, we identify that the protein most commonly affected in Noonan syndrome, the phosphatase SHP2, known in as (CSW), controls life span, triglyceride levels, and metabolism without affecting ERK signaling pathway.

Repeating or spacing learning sessions are strategies for memory improvement with shared molecular and neuronal components.

Intellectual disability is a common feature in genetic disorders with enhanced RAS-ERK1/2 signaling, including neurofibromatosis type 1 (NF1) and Noonan syndrome (NS). Additional training trials and additional spacing between trials, respectively, restores memory deficits in animal models of NF1 and NS. However, the relationship between the underlying mechanisms in these strategies remain obscure.

Seizure localization using pre ictal phase-amplitude coupling in intracranial electroencephalography.

Understanding changes in brain rhythms provides useful information to predict the onset of a seizure and to localize its onset zone in epileptic patients. Brain rhythms dynamics in general, and phase-amplitude coupling in particular, are known to be drastically altered during epileptic seizures. However, the neural processes that take place before a seizure are not well understood.

Ultrasound Axicon: Systematic Approach to Optimize Focusing Resolution through Human Skull Bone.

The use of axicon lenses is useful in many high-resolution-focused ultrasound applications, such as mapping, detection, and have recently been extended to ultrasonic brain therapies. However, in order to achieve high spatial resolution with an axicon lens, it is necessary to adjust the separation, called stand-off (δ), between a conventional transducer and the lens attached to it. Comprehensive ultrasound simulations, using the open-source k-Wave toolbox, were performed for an axicon lens attached to a piezo-disc type transducer with a radius of 14 mm, and a frequency of about 0.

Consistent Gradient of Performance and Decoding of Stimulus Type and Valence From Local and Network Activity.

The individual differences approach focuses on the variation of behavioral and neural signatures across subjects. In this context, we searched for intracranial neural markers of performance in three individuals with distinct behavioral patterns (efficient, borderline, and inefficient) in a dual-valence task assessing facial and lexical emotion recognition. First, we performed a preliminary study to replicate well-established evoked responses in relevant brain regions.

High mutual cooperation rates in rats learning reciprocal altruism: The role of payoff matrix.

Cooperation is one of the most studied paradigms for the understanding of social interactions. Reciprocal altruism -a special type of cooperation that is taught by means of the iterated prisoner dilemma game (iPD)- has been shown to emerge in different species with different success rates. When playing iPD against a reciprocal opponent, the larger theoretical long-term reward is delivered when both players cooperate mutually.

Putative dopamine neurons in the ventral tegmental area enhance information coding in the prefrontal cortex.

It has been proposed that neuronal populations in the prefrontal cortex (PFC) robustly encode task-relevant information through an interplay with the ventral tegmental area (VTA). Yet, the precise computation underlying such functional interaction remains elusive. Here, we conducted simultaneous recordings of single-unit activity in PFC and VTA of rats performing a GO/NoGO task.

A spherical treadmill system to train head-fixed adult rats.

Background: While spherical treadmills are widely used in mouse models, there are only a few experimental setups suitable for adult rats, and none of them include head-fixation.

New Method: We introduce a novel spherical treadmill apparatus for head-fixed rats that allows a wide repertory of natural responses. The rat is secured to a frame and placed on a freely rotating sphere.

Efficient enhancement of information in the prefrontal cortex during the presence of reward predicting stimuli.

The prefrontal cortex (PFC) is a key brain structure for decision making, behavioural flexibility and working memory. Neurons in PFC encode relevant stimuli through changes in their firing rate, although the metabolic cost of spiking activity puts strong constrains to neural codes based on firing rate modulation. Thus, how PFC neural populations code relevant information in an efficient way is not clearly understood.

Spontaneous Fluctuations in Visual Cortical Responses Influence Population Coding Accuracy.

Information processing in the cerebral cortex depends not only on the nature of incoming stimuli, but also on the state of neuronal networks at the time of stimulation. That is, the same stimulus will be processed differently depending on the neuronal context in which it is received. A major factor that could influence neuronal context is the background, or ongoing neuronal activity before stimulation.

Development of a multilocus sequence typing scheme for the study of Anaplasma marginale population structure over space and time.

Bovine Anaplasmosis caused by Anaplasma marginale is a worldwide disease prevalent in tropical and subtropical regions where Rhipicephalus microplus is considered the most significant biological vector. Molecular markers previously applied for A. marginale typing are efficient for isolate discrimination but they are not a suitable tool for studying population structure and dynamics.

Dopamine modulation of GABAergic function enables network stability and input selectivity for sustaining working memory in a computational model of the prefrontal cortex.

Dopamine modulation of GABAergic transmission in the prefrontal cortex (PFC) is thought to be critical for sustaining cognitive processes such as working memory and decision-making. Here, we developed a neurocomputational model of the PFC that includes physiological features of the facilitatory action of dopamine on fast-spiking interneurons to assess how a GABAergic dysregulation impacts on the prefrontal network stability and working memory. We found that a particular non-linear relationship between dopamine transmission and GABA function is required to enable input selectivity in the PFC for the formation and retention of working memory.

State-dependent changes of connectivity patterns and functional brain network topology in autism spectrum disorder.

Anatomical and functional brain studies have converged to the hypothesis that autism spectrum disorders (ASD) are associated with atypical connectivity. Using a modified resting-state paradigm to drive subjects' attention, we provide evidence of a very marked interaction between ASD brain functional connectivity and cognitive state. We show that functional connectivity changes in opposite ways in ASD and typicals as attention shifts from external world towards one's body generated information.

A computational theory for the learning of equivalence relations.

Equivalence relations (ERs) are logical entities that emerge concurrently with the development of language capabilities. In this work we propose a computational model that learns to build ERs by learning simple conditional rules. The model includes visual areas, dopaminergic, and noradrenergic structures as well as prefrontal and motor areas, each of them modeled as a group of continuous valued units that simulate clusters of real neurons.

A big-world network in ASD: dynamical connectivity analysis reflects a deficit in long-range connections and an excess of short-range connections.

Over the last years, increasing evidence has fuelled the hypothesis that Autism Spectrum Disorder (ASD) is a condition of altered brain functional connectivity. The great majority of these empirical studies relies on functional magnetic resonance imaging (fMRI) which has a relatively poor temporal resolution. Only a handful of studies has examined networks emerging from dynamic coherence at the millisecond resolution and there are no investigations of coherence at the lowest frequencies in the power spectrum-which has recently been shown to reflect long-range cortico-cortical connections.

Plasticity in the rat prefrontal cortex: linking gene expression and an operant learning with a computational theory.

The plasticity in the medial Prefrontal Cortex (mPFC) of rodents or lateral prefrontal cortex in non human primates (lPFC), plays a key role neural circuits involved in learning and memory. Several genes, like brain-derived neurotrophic factor (BDNF), cAMP response element binding (CREB), Synapsin I, Calcium/calmodulin-dependent protein kinase II (CamKII), activity-regulated cytoskeleton-associated protein (Arc), c-jun and c-fos have been related to plasticity processes. We analysed differential expression of related plasticity genes and immediate early genes in the mPFC of rats during learning an operant conditioning task.

Differential representation of sunflower ESTs in enriched organ-specific cDNA libraries in a small scale sequencing project.

Background: Subtractive hybridization methods are valuable tools for identifying differentially regulated genes in a given tissue avoiding redundant sequencing of clones representing the same expressed genes, maximizing detection of low abundant transcripts and thus, affecting the efficiency and cost effectiveness of small scale cDNA sequencing projects aimed to the specific identification of useful genes for breeding purposes. The objective of this work is to evaluate alternative strategies to high-throughput sequencing projects for the identification of novel genes differentially expressed in sunflower as a source of organ-specific genetic markers that can be functionally associated to important traits.

Results: Differential organ-specific ESTs were generated from leaf, stem, root and flower bud at two developmental stages (R1 and R4).