Miracle-dz/UniFAR-FTUs huggingface dataset:
Progressive hippocampal and extrahippocampal atrophy in drug resistant epilepsy: review

Purpose of reviewThis article reviews recent experimental and clinical evidence for seizure-related progressive brain damage and discusses possible mechanisms of ongoing brain atrophy in epilepsy. Recent findingsExperimental data indicate that seizures induce brain plasticity that may result in either damage or protection. Brief seizures or status epilepticus may promote resistance to additional damage but also induce cumulative neuronal loss and increase susceptibility to network synchronization. Some experimental studies indicated that, following the initial damage caused by status epilepticus, further brief seizures may not produce significant continuing neuronal loss and hippocampal atrophy, whereas other studies showed the contrary. There is recent evidence that progressive damage and atrophy may occur after an acute insult but are not directly associated with recurrent seizures. Clinical research data continue to show discrepancies regarding whether ongoing seizures cause progressive atrophy. Some cross-sectional and longitudinal magnetic resonance imaging studies in patients with partial epilepsies have shown progressive hippocampal and extrahippocampal atrophy, the severity of which correlated with the duration of epilepsy, seizure frequency, or lifetime seizure number, whereas others have failed to show a clear association. SummaryExperimental data indicate that epileptogenesis in developing brain may not require significant neuronal loss, which is in keeping with clinical observations that progressive cognitive and behavioural impairment may occur in patients with no detectable brain atrophy. A better understanding of why, when and how progressive brain atrophy occurs will lead to better clinical management, earlier surgical intervention when necessary and, ultimately, prevention of epileptogenesis.
RNA crystallography.

The current state of three-dimensional structure analysis of RNA by x-ray crystallography is summarized. The methods of sample preparation, crystallization, data collection, and structure solution are discussed, followed by a review of the RNA structures that have been determined and of common structural features, and finally, an appraisal of future prospects for x-ray crystal structure analysis of RNA.
- 1THE STATE OF FRAMING RESEARCH : A CALL FOR NEW DIRECTIONS

1. The State of Framing Research in Political Communication . The concept of framing embodies a context-sensitive explanation for shifts in political beliefs and attitudes. Framing defines a dynamic, circumstantially-bound process of opinion formation in which the prevailing modes of presentation in elite rhetoric and news media coverage shape mass opinion (Iyengar 1991; Scheufele 1999). This definition stands in stark contrast to other models of opinion formation that explain attitudes on specific issues or events as a function of longstanding and stable political predispositions (Campell et al. 1960; Lazarsfeld, Berelson, and Gaudet 1948), of persuasive messaging (O'Keefe 2002), or of learning, information processing and other cognitive processes (Brossard, Lewenstein, and Bonney 2005; Delli Carpini and Keeter 1996). As a result, framing effects refer to behavioral or attitudinal outcomes that are not due to differences in what is being communicated, but rather to variations in how a given piece of information is being presented (or framed) in public discourse.
Aspect Ratio Effects of Multi-Walled Carbon Nanotubes on Electrical, Mechanical, and Thermal Properties of Polycarbonate/MWCNT Composites

Two multi-walled carbon nanotubes (MWCNTs) having relatively high aspect ratios of 313 and 474 with approximately the same diameter were melt mixed with polycarbonate (PC) in a twin-screw conical micro compounder. The effects of aspect ratio on the electrical, mechanical, and thermal properties of the PC/MWCNT composites were investigated. Electrical conductivities and storage moduli of the filled samples are found to be independent of the starting aspect ratio for these high aspect ratio tubes; although the conductivities and storage moduli are still significantly higher than values of composites made with nanotubes having more commercially common aspect ratios of ∼100. Transmission electron microscopy results suggest that melt-mixing reduces these longer nanotubes to the same length, but still approximately two times longer than the length of commercially common aspect ratio tubes after melt-mixing. Molecular weight measurements show that during melt-mixing the longer nanotubes significantly degrade the molecular weight of the polymer as compared to very similar nanotubes with aspect ratio ∼100. Because of the molecular weight reduction glass transition temperatures predictably show a large decrease with increasing nanotube concentration. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014, 52, 73–83
Cyclin D3-dependent control of the dNTP pool and HIV-1 replication in human macrophages

Cyclins control the activation of cyclin-dependent kinases (CDK), which in turn, control the cell cycle and cell division. Intracellular availability of deoxynucleotides (dNTP) plays a fundamental role in cell cycle progression. SAM domain and HD domain-containing protein 1 (SAMHD1) degrades nucleotide triphosphates and controls the size of the dNTP pool. SAMHD1 activity appears to be controlled by CDK. Here, we show that knockdown of cyclin D3 a partner of CDK6 and E2 a partner of CDK2 had a major impact in SAMHD1 phosphorylation and inactivation and led to decreased dNTP levels and inhibition of HIV-1 at the reverse transcription step in primary human macrophages. The effect of cyclin D3 RNA interference was lost after degradation of SAMHD1 by HIV-2 Vpx, demonstrating the specificity of the mechanism. Cyclin D3 inhibition correlated with decreased activation of CDK2. Our results confirm the fundamental role of the CDK6-cyclin D3 pair in controlling CDK2-dependent SAMHD1 phosphorylation and dNTP pool in primary macrophages.
Inferring single-cell gene expression mechanisms using stochastic simulation

MOTIVATION Stochastic promoter switching between transcriptionally active (ON) and inactive (OFF) states is a major source of noise in gene expression. It is often implicitly assumed that transitions between promoter states are memoryless, i.e. promoters spend an exponentially distributed time interval in each of the two states. However, increasing evidence suggests that promoter ON/OFF times can be non-exponential, hinting at more complex transcriptional regulatory architectures. Given the essential role of gene expression in all cellular functions, efficient computational techniques for characterizing promoter architectures are critically needed. RESULTS We have developed a novel model reduction for promoters with arbitrary numbers of ON and OFF states, allowing us to approximate complex promoter switching behavior with Weibull-distributed ON/OFF times. Using this model reduction, we created bursty Monte Carlo expectation-maximization with modified cross-entropy method ('bursty MCEM(2)'), an efficient parameter estimation and model selection technique for inferring the number and configuration of promoter states from single-cell gene expression data. Application of bursty MCEM(2) to data from the endogenous mouse glutaminase promoter reveals nearly deterministic promoter OFF times, consistent with a multi-step activation mechanism consisting of 10 or more inactive states. Our novel approach to modeling promoter fluctuations together with bursty MCEM(2) provides powerful tools for characterizing transcriptional bursting across genes under different environmental conditions. AVAILABILITY AND IMPLEMENTATION R source code implementing bursty MCEM(2) is available upon request. CONTACT absingh@udel.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Parahydrogen‐induced polarization in imaging: Subsecond 13C angiography

High nuclear spin polarization of 13C was reached in organic molecules. Enhancements of up to 104, compared to thermal polarization at 1.5 T, were achieved using the parahydrogen‐induced polarization technique in combination with a field cycling method. While parahydrogen has no net polarization, it has a high spin order, which is retained when hydrogen is incorporated into another molecule by a chemical reaction. By subjecting this molecule to a sudden change of the external magnetic field, the spin order is transferred into net polarization. A 13C angiogram of an animal was generated in less than a second. Magn Reson Med 46:1–5, 2001. © 2001 Wiley‐Liss, Inc.
MAPPINGS BETWEEN MAPS ASSOCATION OF DIFFERENT THEMATIC CONTENTS USING SITUATION THEORY

The notion of an object bearing information is central to the traditional situation semantics framework. Herein, this notion is extended to the realm of thematic maps as a vehicle for the formalization of their thematic content. Maps are the most acknowledged graphic representations of spatial phenomena. In the light of Situation Theory, we apply its evolution theory; Information Flow, to examine how information between different thematic maps can flow through channels that allow the generation of mappings. This approach views maps as distributed systems with regularities. These distributed systems can be further regarded as classifications in need for semantic interoperability. We therefore, explore the framework of Information Flow Theory, in order to provide a general framework for formalizing the thematic content of maps.
Exogenous NO administration and alpha-adrenergic vasoconstriction in human limbs.

Nitric oxide (NO) is capable of blunting alpha-adrenergic vasoconstriction in contracting skeletal muscles of experimental animals (functional sympatholysis). We therefore tested the hypothesis that exogenous NO administration can blunt alpha-adrenergic vasoconstriction in resting human limbs by measuring forearm blood flow (FBF; Doppler ultrasound) and blood pressure in eight healthy males during brachial artery infusions of three alpha-adrenergic constrictors (tyramine, which evokes endogenous norepinephrine release; phenylephrine, an alpha1-agonist; and clonidine, an alpha2-agonist). To simulate exercise hyperemia, the vasoconstriction caused by the alpha-agonists was compared during adenosine-mediated (>50% NO independent) and sodium nitroprusside-mediated (SNP; NO donor) vasodilation of the forearm. Both adenosine and SNP increased FBF from approximately 35-40 to approximately 200-250 ml/min. All three alpha-adrenergic constrictor drugs caused marked reductions in FBF and calculated forearm vascular conductance (P < 0.05). The relative reductions in forearm vascular conductance caused by the alpha-adrenergic constrictors during SNP infusion were similar (tyramine, -74 +/- 3 vs. -65 +/- 2%; clonidine, -44 +/- 6 vs. -44 +/- 6%; P > 0.05) or slightly greater (phenylephrine, -47 +/- 6 vs. -33 +/- 6%; P < 0.05) compared with the responses during adenosine. In conclusion, these results indicate that exogenous NO sufficient to raise blood flow to levels simulating those seen during exercise does not blunt alpha-adrenergic vasoconstriction in the resting human forearm.
Metabolic activity in external and internal awareness networks in severely brain-damaged patients.

OBJECTIVE An extrinsic cerebral network (encompassing lateral frontoparietal cortices) related to external/sensory awareness and an intrinsic midline network related to internal/self-awareness have been identified recently. This study measured brain metabolism in both networks in patients with severe brain damage. DESIGN Prospective [18F]-fluorodeoxyglucose-positron emission tomography and Coma Recovery Scale-Revised assessments in a university hospital setting. SUBJECTS Healthy volunteers and patients in vegetative state/unresponsive wakefulness syndrome (VS/UWS), minimally conscious state (MCS), emergence from MCS (EMCS), and locked-in syndrome (LIS). RESULTS A total of 70 patients were included in the study: 24 VS/UWS, 28 MCS, 10 EMCS, 8 LIS and 39 age-matched controls. VS/UWS showed metabolic dysfunction in extrinsic and intrinsic networks and thalami. MCS showed dysfunction mostly in intrinsic network and thalami. EMCS showed impairment in posterior cingulate/retrosplenial cortices. LIS showed dysfunction only in infratentorial regions. Coma Recovery Scale-Revised total scores correlated with metabolic activity in both extrinsic and part of the intrinsic network and thalami. CONCLUSION Progressive recovery of extrinsic and intrinsic awareness network activity was observed in severely brain-damaged patients, ranging from VS/UWS, MCS, EMCS to LIS. The predominance of intrinsic network impairment in MCS could reflect altered internal/self-awareness in these patients, which is difficult to quantify at the bedside.
Mitochondrial functionality in reproduction: from gonads and gametes to embryos and embryonic stem cells.

BACKGROUND Mitochondria are multitasking organelles involved in ATP synthesis, reactive oxygen species (ROS) production, calcium signalling and apoptosis; and mitochondrial defects are known to cause physiological dysfunction, including infertility. The goal of this review was to identify and discuss common themes in mitochondrial function related to mammalian reproduction. METHODS The scientific literature was searched for studies reporting on the several aspects of mitochondrial activity in mammalian testis, sperm, oocytes, early embryos and embryonic stem cells. RESULTS ATP synthesis and ROS production are the most discussed aspects of mitochondrial function. Metabolic shifts from mitochondria-produced ATP to glycolysis occur at several stages, notably during gametogenesis and early embryo development, either reflecting developmental switches or substrate availability. The exact role of sperm mitochondria is especially controversial. Mitochondria-generated ROS function in signalling but are mostly described when produced under pathological conditions. Mitochondria-based calcium signalling is primarily important in embryo activation and embryonic stem cell differentiation. Besides pathologically triggered apoptosis, mitochondria participate in apoptotic events related to the regulation of spermatogonial cell number, as well as gamete, embryo and embryonic stem cell quality. Interestingly, data from knock-out (KO) mice is not always straightforward in terms of expected phenotypes. Finally, recent data suggests that mitochondrial activity can modulate embryonic stem cell pluripotency as well as differentiation into distinct cellular fates. CONCLUSIONS Mitochondria-based events regulate different aspects of reproductive function, but these are not uniform throughout the several systems reviewed. Low mitochondrial activity seems a feature of 'stemness', being described in spermatogonia, early embryo, inner cell mass cells and embryonic stem cells.
A 1000 frames/s Vision Chip Using Scalable Pixel-Neighborhood-Level Parallel Processing

This paper presents a novel vision chip architecture based on pixel-neighborhood-level parallel processing. In the architecture, an 8-b RISC processing core is embedded in an <inline-formula> <tex-math notation="LaTeX">$8\times 8$ </tex-math></inline-formula> array of digital pixel sensors on the same focal plane. These neighborhood processors (NPs) are tiled in a 2-D array to form the final imager resolution. Program execution is carried out in parallel across the array of pixel-neighborhood processing cores, allowing for direct scalability in terms of resolution, without reduction in processing speed or frame rate. To accomplish this, a compact, low-complexity NP architecture along with a general-purpose, 8-b instruction set has been designed and implemented. A prototype vision chip containing an <inline-formula> <tex-math notation="LaTeX">$8 \times 10$ </tex-math></inline-formula> array of NPs with a <inline-formula> <tex-math notation="LaTeX">$64 \times 80$ </tex-math></inline-formula> resolution has been designed and fabricated in a 0.13-<inline-formula> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> 1P8M CMOS fabrication process. The system is reprogrammable and can perform a wide range of image and video processing tasks. Several example algorithms are implemented and tested on the single-chip vision system to demonstrate the functionality of pixel-neighborhood-level parallelism, including 1000-frames/s object tracking.
High data-rate millimetre-wave modulator modelling and design

In this paper a linear and nonlinear model for microwave modulator has been realized and discussed. The model is thought to be applied to modern high data rate digital communications. The model is specialized to the widely used direct conversion quadrature modulator architecture. The EVM, Image and LO rejection performances are modelled and estimated for QAM modulation schemes. Design charts have been extracted to help the design of the building blocks of the modulator. To validate the model a 45GHz – 65GHz MMIC vector modulator, based on a doubly balanced star mixer, has been designed using 0.2 commercial PHEMT process.
The impacts of physical layer parameters on the connectivity of ad-hoc networks

We study the effects of physical layer parameters on the connectivity of fading ad-hoc networks. Relying on a symbol error rate connectivity metric for such networks, we assume a pair of nodes are connected if their bi-directional measure of connectivity satisfies a given threshold. We investigate the effects of three parameters on the connectivity phenomenon. First and assuming the nodes are distributed over a fixed finite area, we study the effects of the changes in nodes' density. Next, we measure the connectivity effects of the interference coefficients, i.e., the portion of power an interfering node contributes to other links. Finally, we experiment with the threshold of link quality for connectedness. For each parameter, we also provide an intuitive explanation of the phenomena observed in our experiments. Our simulation results show that (1) depending on the value of interference coefficient, an increase in node density may increase or decrease, and (2) increasing the interference coefficients and thresholds of link quality will decrease the connectivity of fading ad-hoc networks.
Detecting Hazardous Events from Sequential Data with Multilayer Architectures

Multivariate time series data play an important role in many domains, including real-time monitoring systems. In this paper, we focus on multilayer neural architectures that are capable of learning high level representations from raw data. This includes our previous solution based on Recurrent Neural Networks with Long Short-Term Memory (LSTM) cells. We build upon this work and present improved methods that aim to achieve higher prediction quality and better generalization to other similar tasks. We apply new deep neural architectures, minimize feature engineering and explore different ways of model selection. In particular, our focus on architectures includes networks with attention mechanism and convolutional networks. We tackle overfitting challenges in a presence of concept drift.
Exploring the sensitivity to representation of an evolutionary algorithm for the design of shapes

Evolutionary algorithms have been used in many ways for design tasks and other creative endeavors. The choice of representation in these evolutionary algorithms influences the way in which the operators used by a given evolutionary algorithm need to be implemented. In this paper, I explore the way in which it also influences the performance of the algorithm, both from the point of view of the reliability and speed of the algorithms as well as from the point of view of the designs generated by them.
An Approach to Fractal image compression based on iterations

: The conception of digital image coding techniques is of great interest in various areas concerned with the storage or transmission of images. Fractal-based. Image coding or fractal image coding is a new method of image compression. In this method, similarities between different scales of the image are used for compression. Intuitively, fractals are sets that reveal details at every scale. These sets are in contrast to regular sets like lines, curves and planes that are typically studied in Euclidean geometry and become smooth when sufficiently magnified. In the early implementations of the theory, these similarities were found by human interaction and hence, the images were encoded by interactive computer programs. This resulted in codes for images that were extremely compact in size, but the decoded images had very low quality. In this paper, we propose an independent and novel approach to image coding, based on a fractal theory of iterated transformations.
Comparison of Different Types of Visemes using a Constraint-based Coarticulation Model

A common approach to producing visual speech is to interpolate the parameters describing a sequence of mouth shapes, known as visemes, where visemes are the visual counterpart of phonemes. A single viseme typically represents a group of phonemes that are visually similar. Often these visemes are based on the static poses used in producing a phoneme. In this paper we investigate alternative representations for visemes, produced using motion-captured data, in conjunction with a constraint-based approach for visual speech production. We show that using visemes which incorporate more contextual information produces better results that using static pose visemes.
Gene function prediction from synthetic lethality networks via ranking on demand

MOTIVATION Synthetic lethal interactions represent pairs of genes whose individual mutations are not lethal, while the double mutation of both genes does incur lethality. Several studies have shown a correlation between functional similarity of genes and their distances in networks based on synthetic lethal interactions. However, there is a lack of algorithms for predicting gene function from synthetic lethality interaction networks. RESULTS In this article, we present a novel technique called kernelROD for gene function prediction from synthetic lethal interaction networks based on kernel machines. We apply our novel algorithm to Gene Ontology functional annotation prediction in yeast. Our experiments show that our method leads to improved gene function prediction compared with state-of-the-art competitors and that combining genetic and congruence networks leads to a further improvement in prediction accuracy.
Modulating Human Auditory Processing by Transcranial Electrical Stimulation

Transcranial electrical stimulation (tES) has become a valuable research tool for the investigation of neurophysiological processes underlying human action and cognition. In recent years, striking evidence for the neuromodulatory effects of transcranial direct current stimulation, transcranial alternating current stimulation, and transcranial random noise stimulation has emerged. While the wealth of knowledge has been gained about tES in the motor domain and, to a lesser extent, about its ability to modulate human cognition, surprisingly little is known about its impact on perceptual processing, particularly in the auditory domain. Moreover, while only a few studies systematically investigated the impact of auditory tES, it has already been applied in a large number of clinical trials, leading to a remarkable imbalance between basic and clinical research on auditory tES. Here, we review the state of the art of tES application in the auditory domain focussing on the impact of neuromodulation on acoustic perception and its potential for clinical application in the treatment of auditory related disorders.