Miracle-dz/UniFAR-FTUs huggingface dataset:
Neurofilaments Form a Highly Stable Stationary Cytoskeleton after Reaching a Critical Level in Axons

The ultrastructural view of the axonal cytoskeleton as an extensively cross-linked network of neurofilaments (NFs) and other cytoskeletal polymers contrasts with the dynamic view suggested by axonal transport studies on cytoskeletal elements. Here we reconcile these perspectives by showing that neurons form a large NF network along axons which is unequivocally stationary, metabolically stable, and maintained by NFs and nonfilamentous subunit assemblies undergoing slow transport by intermittent rapid movements and pauses. In mouse primary cortical neurons transfected with EGFP-NFL, formation of this stationary NF network requires a critical level of NFs, which explains its absence in NF-poor developing neurons studied previously. Most NFs at proximal axon regions were in a stationary structure coexisting with a smaller pool of moving EGFP-NFL assemblies that were mainly nonfilamentous. Distally along the same axon, EGFP-labeled NFL was much less abundant, and we detected only short filaments moving bidirectionally by slow transport (rapid movements and pauses) as previously described. In living mice, >25% of radiolabeled newly synthesized NFs remained in optic axons after slowly transported NFs had exited. Retained NF remained fixed over several months in a nonuniform distribution and exhibited exceptionally slow turnover (t1/2 >2.5 months), implying that, at steady state, >90% of NFs in mature optic axons comprise the stationary cytoskeleton and <10% are undergoing slow transport. These findings reconcile in vitro and in vivo axonal transport observations, showing that slowly transported NFs or subunit oligomers are precursors to a highly stable stationary cytoskeletal network that supports mature axons.
Discovering Frequent Graph Patterns Using Disjoint Paths

Whereas data mining in structured data focuses on frequent data values, in semistructured and graph data mining, the issue is frequent labels and common specific topologies. The structure of the data is just as important as its content. We study the problem of discovering typical patterns of graph data, a task made difficult because of the complexity of required subtasks, especially subgraph isomorphism. In this paper, we propose a new apriori-based algorithm for mining graph data, where the basic building blocks are relatively large, disjoint paths. The algorithm is proven to be sound and complete. Empirical evidence shows practical advantages of our approach for certain categories of graphs
Conserved E2F mediated metastasis in mouse models of breast cancer and HER2 positive patients

To improve breast cancer patient outcome work must be done to understand and block tumor metastasis. This study leverages bioinformatics techniques and traditional genetic screens to create a novel method of discovering potential contributors of tumor progression with a focus on tumor metastasis. A database of 1172 of expression data from a variety of mouse models of breast cancer was assembled and queried using previously defined oncogenic activity signatures. This analysis revealed high activity of the E2F family of transcription factors in the MMTV-Neu mouse model. A genetic cross of MMTV-Neu mice into an E2F1 null, E2F2 null, or E2F3 heterozygous background revealed significant changes in tumor progression specifically reductions in tumor latency and metastasis with E2F1 or E2F2 loss. These findings were found to be conserved in human HER2 positive patients. Patients with high E2F1 activity were shown to have worse outcomes such as relapse free survival and distant metastasis free survival. This study shows conserved mechanisms of tumor progression in human breast cancer subtypes and analogous mouse models and underlies the importance of increased research into the characterization of and comparisons between mouse and human tumors to identify which mouse models resemble each subtype of human breast cancer.
Active disturbances rejection control of a quadruped robot leg

This paper is focused on the control of a biologically-inspired quadruped robot leg. After a brief introduction of mechanical construction, the leg's dynamic equations in operational space are built and active disturbances rejection controllers are designed for three degrees of freedom (DOF). The extended Jacobian matrix method is used to optimize redundant DOF. The core of this work is the comparison of performance between Active Disturbances Rejection Control (ADRC) and conventional PD control, and the robustness of ADRC in disturbance or model uncertainty conditions. Simulation results suggest that ADRC can solve the contradiction between rapid responses and overshoot well and improve the end positioning accuracy by an order of magnitude. Its behavior worsens little when model offsets or disturbed by measuring noise.
A coherent hybrid SRAM and STT-RAM L1 cache architecture for shared memory multicores

STT-RAM is an emerging NVRAM technology that promises high density, low energy and a comparable access speed to conventional SRAM. This paper proposes a hybrid L1 cache architecture that incorporates both SRAM and STT-RAM. The key novelty of the proposal is the exploition of the MESI cache coherence protocol to perform dynamic block reallocation between different cache partitions. Compared to the pure SRAM-based design, our hybrid scheme achieves 38% of energy saving with a mere 0.8% IPC degradation while extending the lifespan of STT-RAM partition at the same time.
A New Method to Compute the Word Relevance in News Corpus

In this paper we propose a new method to compute the relevance of term in news corpus. According to the characteristics of news corpus , we first propose that the news corpus should be divided into different channels, second we make use of the feature of news document , we divide the co-occurrence of terms into two cases, on the one hand the co-occurrence in the title of the news, On the other hand the co-occurrence in the news text, we use different methods to compute the co-occurrence. In the end, we introduce the web corpus Wikipedia to overcome some shortcomings of the news corpus
Neural Modelling of Congenitally Abnormal Visual Pathways

Albinism and achiasma are congenital conditions severely affecting the normal routing of input through the visual pathways. However, these conditions do not have the profound deleterious effects on perception that would be expected from their impact on visual pathway structure. Evidence in human experiments suggests that in both conditions, these aberrant inputs are mapped onto the primary visual cortex (V1) in superimposed visual hemifield representations. This leads to the hypothesis that intracortical interactions drive the development of hemifield dominance-driven feature preference maps, to make these representations available to be perceived relatively normally. However, current experimental protocols limit the possibility of directly observing this putative arrangement. In this thesis, computational modelling based on input-driven visual development was used to observe the likely map organization of V1 in these conditions, using a two-eyed ocular dominance model of GCAL, a selforganizing map-based model of the primary visual cortex. When the misrouting of inputs was simulated in the model, the resulting receptive fields and orientation map organization supported the theory that V1 rearranges into an interdigitating pattern dominated by hemifield dominance columns.
A comparison of motor adaptations to robotically facilitated upper extremity task practice demonstrated by children with cerebral palsy and adults with stroke

Nine children with cerebral palsy and nine adults with stroke were trained using 5 different upper extremity simulations using the NJIT-RAVR system for approximately nine to twelve hours over a three week period. Both groups made improvements in clinical measurements of upper extremity function and reaching kinematics. Patterns and magnitudes of improvement differ between the two groups. Responses to training required adjustment of the robotic system to accommodate the rehabilitation needs of children with cerebral palsy.
Study of nanosecond pulse switches for low voltage generator for diagnosis of power transformers

Influence of the switchboard type on parameters of an output impulse of the generator according to Vvedensky's scheme is analyzed. The technique of the switchboard choice is offered when using generator for diagnostics of a mechanical condition of power transformers windings. Switchboards were investigated: the mercury relay, the mechanical slider switch, the push-button switch, gas sealed-contact and vacuum sealedcontact, discharger. The technique of switchboards comparison consisted in comparison among them the impulses registered on coordinated loading at the exit of the created cable generator. Comparison of the initial and restored signals was carried out at different quantity of harmonicas. The technique for comparison of amplitudes ranges in the form of the power spectral density is offered. Research was carried out in the environment of MathCAD by means of Fourier's discrete transformation. The results of the study are given in the table.
Diffusion tensor regularization with constraints preservation

The paper deals with the problem of regularizing noisy fields of diffusion tensors, considered as symmetric and semi-positive definite n /spl times/ n matrices (such as for instance 2D structure tensors or DT-MRI medical images). We first propose a simple anisotropic, PDE-based scheme that acts directly on the matrix coefficients and preserves the semi-positive constraint thanks to a specific reprojection step. The limitations of this algorithm lead us to introduce a more effective approach based on constrained spectral regularizations acting on the tensor orientations (eigenvectors) and diffusivities (eigenvalues), while explicitly taking the tensor constraints into account. The regularization of the orientation part uses orthogonal matrix diffusion PDE's and local vector alignment procedures. For the interesting 3D case, a special implementation scheme designed to numerically fit the tensor constraints is also proposed. Experimental results on synthetic and real DT-MRI data sets finally illustrates the proposed tensor regularization framework.
IMAD: in-execution malware analysis and detection

The sophistication of computer malware is becoming a serious threat to the information technology infrastructure, which is the backbone of modern e-commerce systems. We, therefore, advocate the need for developing sophisticated, efficient, and accurate malware classification techniques that can detect a malware on the first day of its launch -- commonly known as "zero-day malware detection". To this end, we present a new technique, IMAD, that can not only identify zero-day malware without any apriori knowledge but can also detect a malicious process while it is executing (in-execution detection). The capability of in-execution malware detection empowers an operating system to immediately kill it before it can cause any significant damage. IMAD is a realtime, dynamic, efficient, in-execution zero-day malware detection scheme, which analyzes the system call sequence of a process to classify it as malicious or benign. We use Genetic Algorithm to optimize system parameters of our scheme. The evolutionary algorithm is evaluated on real world synthetic data extracted from a Linux system. The results of our experiments show that IMAD achieves more than 90% accuracy in classifying in-execution processes as benign or malicious. Moreover, our scheme can classify approximately 50% of malicious processes within first 20% of their system calls.
Harmonic Phase Flow for Tissue Motion Estimation in Tagged MR Sequences

In this work, we present a fully automated method for tissue deformation estimation in tagged magnetic resonance images (TMRI). The method consists of two main stages: in the first one, we use Gabor filter banks, tuned independently for each left ventricle level, that allows to obtain optimally filtered complex images the phase of which is a property that remains constant along the cardiac cycle. This fact can be thought as the brightness constancy condition required by classical optical flow (OF) methods. Pairs of these filtered sequences, together to a variational formulation are used in a second step with obtain dense continuous deformation map that we call Harmonic Phase Flow. This method has been used to determine reference values of ventricular torsion (VT) in a set of 8 healthy volunteers. The results encourage the use of VT as a useful parameter for ventricular function assessment in clinical routine.
Pre-orders for reasoning about stability

Pre-orders between processes, like simulation, have played a central role in the verification and analysis of discrete-state systems. Logical characterization of such pre-orders have allowed one to verify the correctness of a system by analyzing an abstraction of the system. In this paper, we investigate whether this approach can be feasibly applied to reason about stability properties of a system. Stability is an important property of systems that have a continuous component in their state space; it stipulates that when a system is started somewhere close to its ideal starting state, its behavior is close to its ideal, desired behavior. In [Cuijpers 07], it was shown that stability with respect to equilibrium states is not preserved by bisimulation and hence additional continuity constraints were imposed on the bisimulation relation to ensure preservation of Lyapunov stability. We first show that stability of trajectories is not invariant even under the notion of bisimulation with continuity conditions introduced in [Cuijpers 07]. We then present the notion of uniformly continuous simulations --- namely, simulation with some additional uniform continuity conditions on the relation --- that can be used to reason about stability of trajectories. Finally, we show that uniformly continuous simulations are widely prevalent, by recasting many classical results on proving stability of dynamical and hybrid systems as establishing the existence of a simple, obviously stable system that simulates the desired system through uniformly continuous simulations.
Statistical Approach to Ordinal Classification with Monotonicity Constraints

In the ordinal classification with monotonicity constraints, it is assumed that the class label of an object does not decrease when evaluations of this object on considered attributes increase. In this paper, we formulate the problem of ordinal classification with monotonicity constraints from statistical point of view, by imposing constraints both on the probability distribution and on the loss function. We propose a procedure for “monotonizing” the data by relabeling objects, based on minimization of the empirical risk in the class of all monotone functions. The procedure is then used as a preprocessing tool, improving the accuracy of the classifiers. We verify these claims in a computational experiment.
Program complexity measure for software development management

The program complexity measure currently seems to be the most capable measure for both quantitative and objective control of the software project. Five program complexity measures (step count, McCabe's V(G), Halstead's E, Weighted Statement Count and Process V(G)) were assessed from such a viewpoint. This empirical study was done with the data collected through a practical software project. All of these measures have highly significant correlations with the management data. Application of complexity measures to software development management is discussed and a method for the detection of anomalous modules in a program is proposed.
Nitrogen Fixation in Denitrified Marine Waters

Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria), whereas nitrogen losses occur in oxygen-depleted intermediate waters and sediments (mostly via denitrifying and anammox bacteria). Here we report on rates of nitrogen fixation obtained during two oceanographic cruises in 2005 and 2007 in the eastern tropical South Pacific (ETSP), a region characterized by the presence of coastal upwelling and a major permanent oxygen minimum zone (OMZ). Our results show significant rates of nitrogen fixation in the water column; however, integrated rates from the surface down to 120 m varied by ∼30 fold between cruises (7.5±4.6 versus 190±82.3 µmol m−2 d−1). Moreover, rates were measured down to 400 m depth in 2007, indicating that the contribution to the integrated rates of the subsurface oxygen-deficient layer was ∼5 times higher (574±294 µmol m−2 d−1) than the oxic euphotic layer (48±68 µmol m−2 d−1). Concurrent molecular measurements detected the dinitrogenase reductase gene nifH in surface and subsurface waters. Phylogenetic analysis of the nifH sequences showed the presence of a diverse diazotrophic community at the time of the highest measured nitrogen fixation rates. Our results thus demonstrate the occurrence of nitrogen fixation in nutrient-rich coastal upwelling systems and, importantly, within the underlying OMZ. They also suggest that nitrogen fixation is a widespread process that can sporadically provide a supplementary source of fixed nitrogen in these regions.
An Assessment of Pharmacokinetics and Antioxidant Activity of Free Silymarin Flavonolignans in Healthy Volunteers: A Dose Escalation Study

Milk thistle (Silybum marianum) extracts, one of the most widely used dietary supplements, contain a mixture of six major flavonolignans (silybin A, silybin B, isosilybin A, isosilybin B, silychristin, and silydianin) and other components. However, the pharmacokinetics of the free individual flavonolignans have been only partially investigated in humans. Furthermore, antioxidant effects of the extract, which may underlie the basis of many therapeutic effects, have not been thoroughly assessed. The present study evaluated the pharmacokinetics of the six major flavonolignans in healthy volunteers receiving single doses of either one (175 mg), two (350 mg), or three (525 mg) milk thistle capsule(s) on three separate study visits. Additionally, the steady-state pharmacokinetic parameters were determined after the subjects were administered one capsule three times daily for 28 consecutive days. Our results demonstrated that all six flavonolignans were rapidly absorbed and eliminated. In order of abundance, the exposure to free flavonolignans was greatest for silybin A followed by silybin B, isosilybin B, isosilybin A, silychristin, and silydianin. The systemic exposure to these compounds appeared linear and dose proportional. The disposition of flavonolignans was stereoselective, as evidenced by the apparent clearance of silybin B, which was significantly greater than silybin A, whereas the apparent clearance of isosilybin B was significantly lower than isosilybin A. The concentrations of urinary 8-epi-prostaglandin F2α, a commonly used biomarker of oxidative status in humans, were considerably decreased in study subjects after a 28-day exposure to the extract (1.3 ± 0.9 versus 0.8 ± 0.9 ng/mg creatinine) but failed to reach statistical significance (P = 0.076).
NADH/NADPH oxidase p22 phox gene polymorphism is associated with improved coronary endothelial vasodilator function.

AIMS The NADH/NADPH oxidase system plays a central role in vascular superoxide anion production, which appears to cause coronary endothelial dysfunction. Recently, it has been suggested that the C242T polymorphism of the NADH/NADPH oxidase p22 phox gene can reduce susceptibility to coronary artery disease. We therefore tested whether this polymorphism is associated with an altered endothelium-dependent vasodilator capacity of human coronary arteries in vivo. METHODS AND RESULTS The vasodilator function of epicardial arteries in 93 patients was assessed by endothelium-mediated, flow-dependent dilation and nitroglycerin, which is endothelium-independent. NADH/NADPH oxidase p22 phox polymorphism was determined by restriction fragment length polymorphism. Carriers of the CC genotype of the C242T p22 phox polymorphism (n = 44) revealed a significantly blunted endothelium-dependent dilator response (11 +/- 9.2% luminal area change vs 17 +/- 10%;P = 0.007), which was, by multivariate analysis, independent of other risk factors or atherosclerosis itself. There was only a trend towards decreased endothelium-independent dilation in patients bearing the p22 phox CC genotype (P = 0.07). CONCLUSIONS The C242T polymorphism of the p22 phox gene is an important independent determinant of coronary endothelial vasodilator function. These results provide the first clinical evidence for the functional significance of a polymorphism of a gene related to superoxide anion production in the vascular wall.
A semiparametric single-factor model of the term structure

We propose a semiparametric single-factor diffusion model for the term structure of interest rate. The This model is highly flexible and encompasses most parametric single-factor models proposed in the literature. We fit the semiparametric model to a proxy of the Eurodollar short term interst rate and compare it with the most flexible parametric model found in the literature: First directly, by testing the fully parametric model against the semiparametric one. Secondly, we look at how much the bond prices predicted by the competing models differ; this yields an alternative measure of the performance of the models. The fitted semiparametric model picks up nonlinearities which the fully parameteric model cannot capture. This leads to a rejection of the parametric model in favour of the semiparametric model in the direct comparison of the two fitted models. Moreover, the calculated bond prices implied by the two competing models are shown to be significantly different.
A Note on the Power of Money-Output Causality Tests

This study suggests that some empirical findings against money-output causality can be the consequence of ignoring autoregressive conditional heteroskedastic (ARCH) errors. Monte Carlo results confirm that ARCH effects drastically reduce the power of the standard causality test. The maximum likelihood approach allowing for ARCH effects, on the other hand, provides a good power performance. Using different specifications and sample period, Friedman and Kuttner (1993) and Thomas (1994) report limited evidence of money causing output. We detect significant ARCH effects in the models considered by these studies. Once ARCH effects are explicitly accounted for, we find that the monetary effect is significant though its magnitude is quite small. Copyright 2001 by Blackwell Publishing Ltd
Accurate and Resource-Aware Classification Based on Measurement Data

In this paper, we face the problem of designing accurate decision-making modules in measurement systems that need to be implemented on resource-constrained platforms. We propose a methodology based on multiobjective optimization and genetic algorithms (GAs) for the analysis of support vector machine (SVM) solutions in the classification error-complexity space. Specific criteria for the choice of optimal SVM classifiers and experimental results on both real and synthetic data will also be discussed.